title: CNCC_H3K27ac_R2

data_processing:
Align to genome using bowtie 2.3.1
Generate bam format and normalize with samtools(1.3.1) Sort and Index bam with samtools. Merged bams from alignment for 2 Replicates of 2N and 4N respectively to prepare for ChromImpute
Convert to tagAlign format for size estimation of combined and single replicates
Estimate fragment size using phantompeakqualtools (v.1.14) for combined and single replicates
Generated p value-based signal tracks relative to appropriate input controls based on estimated library fragment size using MACS2 (2.1.1.20160309).
Genome_build: hg19
Supplementary_files_format_and_content: p-value signals provided as bigWigs.

source_name: Cranial Neural Crest Cells

growth_protocol: Dissociated (using 40um filter) H9 ESCs were plated at 30,000 cells per cm^2 in NCC media with 10 ul Rock Inhibitor and 10 uL of 3mM stock CHIR99021. NCC Media:48.5 mL DMEM/F12 (Gibco#10565-018) 500uL 50U/mL penicillin, 500 uL 50U/mL streptomycin, 1mL B27. Media was changed daily, the rock inhibitor added on the day following plating and not after. Differentiation is complete by day 5.

extract_protocol:
Cotney and Noonan, CSHL Protocols 2015.
ChIP-seq libraries were prepared using the SMARTer® ThruPLEX® DNA-seq 48S Kit, Cat No. R400427, Takara Bio USA.

value: H9 ES-derived Cranial Neural Crest Cells

tag: antibody


title: PMN-MDSC-11

status: Public on Jun 26 2023

type: SRA

city: Shanghai

first: Zhigang

last: Lu

address: 130 Dongan Road, Shanghai

department: IBS

country: China

institute: Fudan University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9

molecule: total RNA

organism: Mus musculus

source_name: neutrophils

extract_protocol:
PMN-MDSCs were solated and 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

tag: cell type

value: neutrophils

tag: strain

tag: age

value: 8 weeks

tag: genotype

value: CD300ld KO


title: CNCC_H3K27me3_R2

city: Farmington

first: Tara

middle: N.

last: Yankee

state: Connecticut

address: 400 Farmington Ave

country: USA

institute: UConn Health

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: col2_066

city: Lausanne

first: Tomas

last: Kay

state: Vaud

address: Biophore building

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were mapped using STAR (to the reference genome and annotation), using default parameter settings
Reads were counted using FeatureCounts, using default parameter settings
Supplementary files format and content: csv file: unnormalised counts matrix

organism: Camponotus fellah

source_name: Brain

extract_protocol:
RNA was extracted using Tri reagent, following manufacturers protocol
RNA libraraies were prepared using the KAPA Stranded mRNASeq Library Preparation Kit, following manufacturers protocol

tag: tissue

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse

value: forage ratio:0


title: SHAM9

city: Aarhus

first: Marta

last: Diaz-delCastillo

address: Palle Juul-Jensens Boulevard 99

department: Department of Forensic Medicine

country: Denmark

institute: University of Aarhus

description: DRG tissue, SHAM

data_processing:
Salmon (version 1.5.2) was used to quantify transcript expression, using as reference the mouse cDNA set (coding and non-coding transcripts) corresponding to GRCm39. The salmon index was built using the corresponding GRCm39 genome as decoy sequence. Both the cDNA set and genome were obtained from Ensembl, release 104 (57, 58).
Gene-level expression estimates were further obtained using the tximport R package and differential expression analysis was performed using the Wald test from DESeq2 R package, to test for differences in expression between the MM and SHAM groups.
Only genes with counts different from 0 in at least 3 samples and with more than 10 reads estimatd in at least one of the samples were retained for further analysis
Assembly: GRCm39
Supplementary files format and content: Salmon output quantification files, with number of reads and estimated TPM per transcript
Supplementary files format and content: Text file with gene-level counts normalized using DESeq2 for all samples

source_name: DRG

extract_protocol:
Tissue was homogenized in a bead miller and total RNA was extracted with a Qiagen RNAse microkit
Prepared samples underwent DNBSEQ transcriptome sequencing by BGI Denmark

treatment_protocol: Mice were intrafemorally inoculated with 5TGM1-GFP myeloma cells or vehicle and Ipsilateral whole DRG lumbar L2, L3 and L4 were extracted and snap frozen on post-surgical day 24

value: DRG

tag: strain

tag: age

value: 5-7 weeks

tag: Sex

value: male

tag: treatment

value: SHAM


title: CNCC_H3K9me3_R2

tag: cell type

tag: antibody


title: col2_065

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest


title: col2_074

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: PMN-MDSC-1

tag: strain

tag: age

tag: genotype

value: WT


title: SHAM7

description: DRG tissue, SHAM

tag: Sex

tag: treatment


title: U2OS_ChIPseq_Dyskerin_flavopiridol_rep2

city: Solna

first: Federico

last: Agostini

state: Stockholm

address: Tomtebodavägen 23a

country: Sweden

institute: Science for Life Laboratories

data_processing:
Sequencing quality checks were performed on all experiments using FastQC (v0.11.9). X
Adapter sequences were removed using TrimGalore (v0.6.4_dev) and reads shorter than 20 nt were discarded.
Reads were aligned to the human reference genome (GRCh38/hg38) using bwa-mem (v0.7.17-r1188) with default options.
Reads that failed to align and those with MAPQ ≤ 30 were filtered out, and PCR duplicates were discarded using the Picard MarkDuplicates (v2.18.11) module.
Genome coverage tracks in bigWig format were generated using the bamCoverage module from deeptools (v3.2.1) with --binSize 50 --normalizeUsing CPM options.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, genomic coverage CPM-normalized

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
6 to 10 million cells were crosslinked for 5 minutes at room temperature with 16% methanol-free formaldehyde (Thermo Fisher Scientific) used at a final concentration of 1%. After quenching the reaction with 125 mM glycine final concentration, cells were washed twice in ice-cold PBS and collected by scraping. Pellets were resuspended in buffer A (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40 substitute) and incubated on ice for 10 minutes. After centrifugation (5000 rpm for 5 minutes at 4°C), the supernatants containing the cytoplasm were removed and the nuclei-containing pellets were washed in buffer A without detergent. Pellets were then resuspended in shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS) and sonicated with a ME220 focused-ultrasonicator (Covaris). After clarification by centrifugation (13000 rpm for 10 minutes at 4°C), the supernatant was adjusted in composition to RIPA buffer and transferred to a new tube to be used for immunoprecipitation. Equal amounts of chromatin (as measured by DNA concentration) were incubated rotating overnight at 4°C with pre-conjugated beads (20 μl of Dynabeads and 3 μg antibody, dyskerin (Abnova, H00001736-m04) or RNAPII (MBL, MAB0601)) in RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 200 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS). Immunoprecipitates were washed once with each of the following: RIPA buffer, RIPA buffer high salt (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LCiCl, 0.5% NP-40 substitute, 0.5% sodium deoxycholate), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The beads were then resuspended in TE buffer with 0.5% SDS supplemented with proteinase K (New England Biolabs) and RNase A (Thermo Fisher Scientific) and incubated with shaking at 65°C for 4 hours. The DNA was recovered by phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation using standard procedures, and resuspended in TE buffer.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: 250nM flavopiridol for 2 hours prior to cell harvest, added directly to culture medium.

tag: cell line

tag: cell type

value: Human bone osteosarcoma

value: Flavopiridol

tag: chip antibody

value: dyskerin (Abnova, H00001736-m04)


title: CNCC_H3K36me3_R2

tag: antibody


title: Tnrc6a_Ago2KO_2_input

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

description: Experiment 2

data_processing:
Base calling and quality scoring is performed using RTA software (v3.4.4), demultiplexing with  bcl2fastq2 v2.20.
Alignment was performed as follows: Samples were aligned against the GRCm38 mouse genome assembly from GENCODE (Frankish et al., 2021), primary assembly from release M24).(Rosenbloom et al., 2015) Alignments were performed using STAR version 2.7.3a with settings --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1(Gaidatzis et al., 2015). These settings follow ENCODE guidelines and report a single randomly selected alignment for reads that map to the genome no more than 20 times(Langmead et al., 2009) Gene annotations were also obtained from GENCODE release M24, transforming the gtf file into a Bioconductor TxDb object using the makeTxDbFromGFF function from the GenomicFeatures package (version 1.44.0, (Lawrence et al., 2013). Gene-level read counts were obtained by summing the counts from the union of all exons per gene, using the qCount function from the QuasR package (version 1.32.0, (Gaidatzis et al., 2015)) with the created TxDb and parameters orientation = “opposite”.
Assembly: mm10
Supplementary files format and content: csv: First column contains ENSEMBL transcript ID, second column contains ENSEMBL gene ID,  third column contains ENTREZ gene ID, fourth column contains gene symbol (Ensembl identifiers), fifth column contains gene nams (EMSENBL), sixth column contains summed width of exons per gene (quasr package),  columns named 'raw.count' contain raw counts of reads overlapping each gene for each sample, columns named 'rpkm' contain rpkm read counts overlapping each gene for each sample.

source_name: mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)

value: mouse embryonic stem cells

value: Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-


title: col2_064

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: SHAM6

description: DRG tissue, SHAM

tag: strain

tag: age


title: CNCC_H3K4me3_R2


title: TB2

extract_protocol:
PMN-MDSCs or neutrophils were solated  and 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

tag: group

value: tumor bearing


title: SHAM5

description: DRG tissue, SHAM

tag: Sex

tag: treatment


title: TB1

tag: cell type


title: col2_062

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: TF2

value: tumor free


title: CNCC_H3K4me2_R2

value: H9 ES-derived Cranial Neural Crest Cells

tag: antibody


title: CNCC_H3K4me1_R2


title: col2_061

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning forage

tag: grooming forage


title: TF1

value: neutrophils

tag: strain

tag: age

value: 8 weeks

tag: group


title: PMN-MDSC-6

tag: cell type

tag: genotype


title: SHAM8

description: DRG tissue, SHAM

tag: Sex

tag: treatment


title: SHAM3

description: DRG tissue, SHAM


title: SHAM2

description: DRG tissue, SHAM


title: CNCC_Input_R2


title: col2_059

value: Brain

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: maturity

tag: nurse


title: SHAM1

description: DRG tissue, SHAM

tag: tissue


title: CNCC_H3K27me3_R1

tag: antibody


title: LB

city: Montreal

first: Thulaj

last: Meharwade

state: QC

address: 110 Pine Ave W,

department: Division of Systems Biology

country: Canada

institute: Montreal Clinical Research Institute

data_processing:
Single-cell matrices were generated using Cellranger (v.4.0.0)
Assembly: mm10
Supplementary files format and content: tsv and mtx, scRNAseq matrices

molecule: polyA RNA

source_name: Embryonic stem cells

growth_protocol: ES cells were grown on gelatin (LB) or fibronectin (LBPXRS) cultures with a seeding density of 2-5*10^5 cells in 1well of 6well dish in N2B27 medium.

extract_protocol:
Single cell suspensions were prepared in calcium and magnesium-free 1X PBS containing 0.04% weight/volume BSA non-acetylated(400ug/ml), were loaded on a Next GEM Chip A (PN-1000009) together with Chromium Single Cell 3’ Gel Bead Kit v2 (PN 120235) and single cells were captured on a 10X Genomics Chromium controller with a recovery target of 5000 cells per sample.
cDNAs were generated following the 10X Genomics protocol. cDNAs were generated following the 10X Genomics protocol. cDNAs were size selected using Ampure XP beads from Beckman Coulter (A63881), and their quality was checked with a Bioanalyzer High Sensitivity DNA Kit from Agilent (5067-4626). One quarter of the total cDNA was used to generate libraries using Chromium Single Cell 3’ Library Kit v2 (PN-120234) and barcoded using the Chromium Multiplex Kit, 96 rxns (PN-120262) following the 10X protocol. Libraries were size selected using Ampure XP beads and their size distribution were assessed with the Bioanalyzer High Sensitivity DNA Kit (average size of 470 bp). Libraries were sequenced on Illumina Novaseq S Prime flowcell with a depth of 57,000-94,000 PE28-91 reads per cell.
scRNAseq, paired-end sequencing on NovaSeq 6000

treatment_protocol: Cells were treated either with LIF and BMP4(LB) or LIF, BMP4, PD0325901, Xav939, Resorcyclic lactone and SB431542(LBPXRS) for 72 hours.

value: Embryonic stem cells

tag: strain

value: treated with LB for 72 hours


title: MM9

description: DRG tissue, MM

value: DRG

tag: age

value: 5-7 weeks

value: MM


title: col2_027

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

value: forage ratio:0


title: col2_063

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare


title: col2_026

tag: guarding

tag: grooming nest

tag: queenattending


title: MM8

description: DRG tissue, MM

tag: tissue

tag: Sex

value: male

tag: treatment


title: SHAM4

description: DRG tissue, SHAM

tag: strain

tag: age

value: SHAM


title: CNCC_H3K36me3_R1

tag: cell type

tag: antibody


title: col2_025

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: maturity

tag: nurse


title: TCR_S.Mod_IMIN

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
The Cell Ranger package (10x Genomics) was used to perform single-cell data processing and to read alignments and feature-barcode matrices generation.
Samples were aligned mm10-2020-A and GRCm38-alts-ensembl-5.0.0 as references.
Assembly: mm10-2020-A, GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: feature, barcode, matrix

source_name: Lung

extract_protocol:
Lungs were harvested and single cells were obtained using a Lung Dissociation Kit (Miltenyi Biotec) following the manufacturer’s instructions. Lung cells were separated from debris using Percoll (GE Healthcare Life Sciences) density gradient centrifugation and were treated with ammonium-chloride-potassium lysis buffer to eliminate red blood cells. Cell suspensions were pooled from four lungs/group, and blocked with anti-CD16/CD32 (clone 2.4G2). Cells were stained with PE anti-mouse CD45.2 (eBioscience) antibody and 7-AAD (BioLegend) at 4°C for 30 min. After washing with DPBS containing 1% FBS, CD45.2+7-AAD- live lung immune cells were isolated using a BD FACSAria II (BD Biosciences).
Sorted cells were counted and resuspended to perform library preparation using Chromium Next GEM Single Cell 5' v2 (Dual Index) kits (10x Genomics) and Chromium Next GEM Single Cell VDJ library v2 kits (10x Genomics) according to the manufacturer’s protocol. Libraries were sequenced using a HiSeq X ten (Illumina) platform for 10,000 cells.

value: BALB/c

value: Lung

value: CD45.2+7-AAD- immune cells

tag: genotype

value: Wild type


title: TCR_S.Mod_IN


title: MM7

description: DRG tissue, MM


title: col2_024

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

value: forage ratio:NA


title: col2_060

tag: tissue

tag: grooming nest

tag: queenattending


title: TCR_S.WT_IMIM

tag: strain

tag: cell type

tag: treatment


title: CNCC_H3K4me3_R1

value: H9 ES-derived Cranial Neural Crest Cells

tag: antibody


title: MM6

description: DRG tissue, MM

tag: age

tag: Sex


title: CNCC_H3K27ac_R1


title: S.Mod_IMIN

tag: genotype


title: MM5

description: DRG tissue, MM


title: CNCC_H3K4me2_R1


title: CNCC_H3K4me1_R1


title: col2_023

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: maturity

tag: nurse


title: LBPXRS

value: treated with LBPXRS for 72 hours


title: S.Mod_IN

tag: tissue


title: col2_022

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: CNCC_H3K9me3_R1

tag: cell type

tag: antibody


title: MM4

description: DRG tissue, MM

tag: strain

tag: age

tag: Sex

tag: treatment


title: MM3

description: DRG tissue, MM


title: CNCC_Input_R1


title: S.WT_IMIM

tag: genotype


title: CNCC_R3_RNA-seq

data_processing:
Fastq's quality control checked with fastqc(0.11.7) and RseQC(4.0.0). Visualized with multiqc(1.11).
Aligned fastqs using rail-rna(0.2.4b)
Generated raw scaled counts tables from rail-rna output using recount2(leekgroup) pipeline.
bigWig files generated from rail-rna
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq signal provided as bigWigs. The combined counts table for all samples (including craniofacial) provided as a .tsv file.

extract_protocol:
miRNeasy RNA extraction kit with on-column DNAse treatment (Qiagen protocol)
TruSeq Stranded mRNA kit (Illumina)


title: Tmem216-KO_rep3

city: Qingdao

first: ying

middle: ying

last: wang

address: 72 Binhai RD

institute: Shandong university

data_processing:
Illumina Casava 1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sicklewith default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: Embryo

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.


title: col2_020

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: queenattending

tag: maturity


title: MM2

description: DRG tissue, MM

tag: tissue


title: RNCM_1uMAngII_n1

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

institute: McGill University

description: RNCMs Day 5 post-isolation

data_processing:
Fastq files were trimmed with TrimGalore.
Quality control was performed with FastQC.
Reads were aligned to Ensembl rat genome Rnor_6.0.94 or human Homo_sapiens.GRCh38.104 using STAR.
Transcripts were assembled using StringTie.
Differential expression analysis was performed using DEseq2.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: neonatal primay cells

extract_protocol:
Qiagen RNeasy Mini Kit.
NEB rRNA-depleted (HMR) stranded library preparation

value: neonatal primay cells

tag: cell line

value: Isolated rat neonatal cardiomyocytes

value: Wildtype

value: 1 uM Angiotensin II


title: Tmem216-KO_rep2


title: CNCC_R2_RNA-seq


title: Tmem216-KO_rep1


title: col2_019

value: Brain

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: nurse


title: col2_017

tag: colony


title: CNCC_R1_RNA-seq

tag: cell type


title: WT_rep3

tag: strain

tag: age

tag: genotype

value: wild type


title: col2_016

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: queenattending


title: WT_rep1


title: col2_021

tag: tissue

tag: trophallaxis nest

tag: broodcare

tag: maturity


title: col2_015

tag: guarding

tag: grooming nest

tag: trophallaxis forage

tag: cleaning forage


title: SUM159_JQ1

city: Brookline

first: Kornelia

last: Polyak

state: Massachusetts

address: 450 Brookline St

institute: Dana-Farber Cancer Institute

library_source: genomic single cell

data_processing:
Single-cell ATAC-seq data generated by 10x genomics are preprocessed using the Cell Ranger (https://www.10xgenomics.com/).
Assembly: hg19
Supplementary files format and content: h5 files were generated by the Cell Ranger

growth_protocol: SUM149, SUM159, SUM149R, SUM159R cells were grown in SUM Medium

extract_protocol: 10x Genomics Single Cell ATAC

treatment_protocol: SUM149, SUM159, SUM149R, SUM159R cells were incubated for 12 hr with JQ1 or DMSO treatment.

tag: cell line

tag: treatment


title: SUM159R_DMSO

value: DMSO


title: SUM159R_JQ1


title: SUM159_DMSO


title: col2_012

tag: colony

tag: grooming forage

tag: nurse


title: 2-3H_PQ-mut_input_rep1

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
Bowtie2 version 2.4.4 was used to align ChIP-seq reads to the Drosophila melanogaster genome (version dm6) with the following non-default parameters: -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Aligned reads were filtered to include only reads with a mapping quality score > 30. Reads mapping to unplaced scaffolds or the mitochondrial genome were discarded.
. Peak calling was performed using MACS2 version 2.2 with parameters -g dm --call-summits. Only peaks that were detected in all replicates were considered in downstream analysis.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins. Z-score normalized signal was multiplied by a scaling factor derived from the percentage of reads aligning to the spike-in genome.
Assembly: dm6
Supplementary files format and content: Replicates were merged into a single bigWig file. BigWig files contain z-score normalized read depth that scaled according to the percentage of spike-in reads.
Supplementary files format and content: narrowPeak files containing only peaks that were detected in both replicates.

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: All stocks were grown on molasses food at 25ºC.

extract_protocol:
ChIP was performed as described previously (Blythe and Wieschaus 2015) on hand selected 2-3 hr AEL embryos from: sfGFP-GAF/+ and sfGFP-GAFSDPQ/sfGFP-GAFSDPQ females. Briefly, 200-400 embryos were collected, dechorionated in 50% bleach for 3 min, fixed for 15 min in 4% formaldehyde and then lysed in 1 mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl). The fixed chromatin was then sonicated for 20 s 11 times at 20% output and full duty cycle (Branson Sonifier 250). Chromatin was incubated with 6 μg of anti-GFP antibody (Abcam #ab290) overnight at 4°C , and then bound to 50 μl of Protein A magnetic beads (Dynabeads Protein A, Thermo Scientific). The purified chromatin was then washed, eluted, and treated with 90 μg of RNaseA (37°C, for 30 min) and 100 μg of Proteinase K (65°C, overnight). The DNA was purified using phenol/chloroform extraction and concentrated by ethanol precipitation. Each sample was resuspended in 25 μl of water.
Sequencing libraries were made using the NEB Next Ultra II library kit. Libraries were sequenced on the Illumina NextSeq 500 using 75bp single-end reads at the Northwestern Sequencing Core (NUCore).

value: embryo

tag: genotype

value: sfGFP-GAFS-delta-PQ/sfGFP-GAFS-delta-PQ

tag: developmental stage

value: 2-3 hour embryo

tag: chip antibody

value: input


title: MM1

description: DRG tissue, MM

value: DRG

tag: strain

tag: age

value: 5-7 weeks

tag: Sex

value: male

value: MM


title: col2_009

tag: tissue

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: queenattending

value: forage ratio:0


title: 2-3H_control_input_rep2

value: sfGFP-GAF/+


title: 2-3H_PQ-mut_input_rep2


title: col2_008

tag: colony

tag: guarding

tag: grooming nest

tag: trophallaxis forage

tag: cleaning forage

tag: maturity


title: Hnf4g.IEC.rep#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
CUT&Tag
IEC_Hnf4g.merged.CPM.bigwig

data_processing:
Low quality reads were discared using Trimmomatic (v0.36)
Reads were mapped to the mouse reference genome (mm10) with bowtie2 (v2.29) using parameters --local --very-sensitive -no-mixed --no-discordant -I 10 -X 700
Bam files were generated and multimapping reads removed by samtools (v1.3.1), and duplicate reads were removed by picard (v2.8.0)
Bigwig files were generated using deeptools (v3.0.2) with counts-per-million normalization
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Small intestine

extract_protocol:
Cells were washed in wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), bound to concavalin A beads (Bangs Laboratories), permeabilized in wash buffer plus 0.05% digitonin, and incubated overnight with 1:50 primary rabbit anti-Hnf4g (Proteintech) at 4°C in wash buffer plus 0.05% digitonin, 2mM EDTA and 0.1% BSA. The next day, some samples were lightly fixed with 0.1% paraformaldehyde at room temperature for 2 minutes before proceeding. (We and others have observed improved CUT&Tag signal-to-noise ratio for some TFs with light fixation, but it did not seem to make a difference here) Samples were incubated with secondary guinea pig anti-rabbit (Rockland) at 1:100 for 1 hour at room temperature in wash buffer plus 0.05% digitonin. Samples were washed and incubated with pA-Tn5 (Addgene #124601, gift from Steve Henikoff, purified in-house) at 1:200 for 1 hour at room temperature in 300mM NaCl wash buffer plus 0.01% digitonin. Samples were washed twice then tagmented for 1 hour at 37°C in 300mM NaCl wash buffer plus 0.01% digitonin and 10mM MgCl.
Tagmentation was halted with EDTA, sodium dodecyl sulfate and proteinase K for 1 hour at 55°C. Tagmented DNA was phenol-chloroform extracted and amplified by PCR with NEBNext 2X Master Mix (NEB) using the following program: 72°C for 2min, 98°C for 30s, 16 cycles of 98°C for 10s and 63°C for 10s, 72°C for 1min, hold. Amplified libraries were quantified by Qubit (Thermo) and Tapestation (Agilent).

treatment_protocol: mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, and flow sorting mTECs into DMEM/10%FCS. IECs were prepared by dissociating small intestinal epithelium for 1h at 4C in PBS/20mM EDTA, trypsinizing cells for 1 minute at 37C, staining with antibodies against EpCAM and CD45 and isolating live EpCAM+CD45- IECs by flow cytometry.

value: Small intestine

tag: strain

tag: genotype

value: WT

tag: cell type

value: IEC

tag: antibody


title: Hnf4g.IEC.rep#1

description:
CUT&Tag
IEC_Hnf4g.merged.CPM.bigwig

tag: tissue


title: WT_rep2

tag: age


title: col2_006

tag: bodylength

tag: headwidth

tag: age (months)

tag: grooming forage

tag: nurse


title: 2-3H_control_input_rep1

tag: developmental stage

tag: chip antibody


title: 2-3H_PQ-mut_IP_rep2

value: anti-GFP (abcam #ab290)


title: Hnf4g.mTEC.rep#4

description:
CUT&Tag
MEC_Hnf4g_all.merged.CPM.bigwig

source_name: Thymus

value: Thymus

value: mTEC


title: col2_014

value: Brain

tag: colony

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending


title: col2_005

tag: trophallaxis forage

tag: cleaning forage

tag: maturity


title: hLESC ex vivo culture, treated with 5nm LY2090314, biological replicate 3

type: RNA

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

description: Gene expression data from ex vivo culture of hLESCs treated with GSK-3 inhibitor LY2090314

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Clariom S Human (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix)

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

label: biotin

source_name: hLESC ex vivo culture

label_protocol: 150 ng of total RNA was subjected to the GeneChip WT PLUS Reagent Kit (WT PLUS Kit), following the manufacturer’s protocol for whole-genome gene expression analysis (Affymetrix)

growth_protocol: hLESCs proliferated and expanded from the limbal biopsies in complex medium (COM) on six-well plates for nine days.

extract_protocol: Total RNA was isolated using Qiagen RNeasy Micro Kit  (Qiagen, Hilden, Germany) according to manufacturer’s protocol.

treatment_protocol: The complex medium (COM) was removed and replaced by COM containing 5 nM LY2090314, when applicable. In addition, LY2090314 was dissolved in DMSO, so DMSO reciprocal to the DMSO concentration in cultures treated with 10 nM LY2090314 was added to individual wells as controls. DMSO dilution of 10 nM LY2090314 concentration in COM medium was 1:10000.

tag: cell type

value: hLESCs

tag: treatment

value: treated with 5nm LY2090314


title: hLESC ex vivo culture, control, biological replicate 5

description: Gene expression data from ex vivo culture of hLESCs untreated control

value: untreated control


title: hLESC ex vivo culture, treated with 5nm LY2090314, biological replicate 6


title: hLESC ex vivo culture, treated with 5nm LY2090314, biological replicate 4


title: hLESC ex vivo culture, control, biological replicate 6


title: hLESC ex vivo culture, treated with 5nm LY2090314, biological replicate 5


title: 2-3H_PQ-mut_IP_rep1

tag: tissue

value: embryo

tag: genotype

value: sfGFP-GAFS-delta-PQ/sfGFP-GAFS-delta-PQ

value: 2-3 hour embryo


title: col2_004

tag: bodylength

tag: headwidth

tag: age (months)

tag: grooming forage

tag: nurse


title: 2-3H_control_IP_rep2

tag: developmental stage

tag: chip antibody


title: hLESC ex vivo culture, control, biological replicate 3


title: col2_002

tag: colony

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding


title: Hnf4g.mTEC.rep#2

description:
CUT&Tag
MEC_Hnf4g_all.merged.CPM.bigwig

tag: strain

tag: antibody


title: Hnf4g.mTEC.rep#1

description:
CUT&Tag
MEC_Hnf4g_all.merged.CPM.bigwig

tag: cell type


title: col2_001

tag: tissue

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: maturity


title: hLESC ex vivo culture, treated with 5nm LY2090314, biological replicate 2

tag: treatment


title: hLESC ex vivo culture, control, biological replicate 4


title: 2-3H_control_IP_rep1

tag: genotype

tag: developmental stage


title: hLESC ex vivo culture, control, biological replicate 2


title: Hnf4g.mTEC.rep#3

description:
CUT&Tag
MEC_Hnf4g_all.merged.CPM.bigwig


title: hLESC ex vivo culture, control, biological replicate 1


title: 7- hMφ 312 Control

status: Public on Jun 25 2023

city: Madrid

first: Lisardo

last: Bosca

state: Madrid

address: Arturo Duperier 4

department: Metabolism and cellular Signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang etal,2014) for removing the low-quality reads and trimming the Illumina adapter.
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and Log2 Fold Change values for differential expression of case vs control

source_name: Macrophages

growth_protocol: Monocyte-derived human macrophages were isolated from buffy coats by a ficoll gradient, cells were seeded 1h in DMEM without FBS and then cell media was replaced by DMEM+10%FBS for a week, then differentiated macrophages were treated with TRB or LUR 100nM for 6h in RPMI+2%FBS or vehicle (controls RPMI+2%FBS);

extract_protocol:
Total RNA was extracted using  TRI Reagent TM Solution (Invitrogen) protocol.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: hMφ+ veh; hMφ+ TRB 100nM 6h; hMφ+ LUR 100nM 6h

value: Monocyte-derived macrophages

value: Vehicle


title: 14- hMφ 335 +LUR 100nM 6h

value: LUR 100nM 6h


title: 16- hMφ 337 +LUR 100nM 6h


title: 3- hMφ 310 Control


title: 4- hMφ 310 +TRB 100nM 6h

value: TRB 100nM 6h


title: 10- hMφ 313 +TRB 100nM 6h


title: 20- hMφ 345 +LUR 100nM 6h


title: 19- hMφ 345 Control


title: 11- hMφ 334 Control


title: 18- hMφ 344 +LUR 100nM 6h


title: 5- hMφ 311 Control


title: 13- hMφ 335 Control


title: A125_48_3

city: Kunming

first: Jiangliu

last: Yang

address: No. 2, Cuihu North Road, Wuhua District, Kunming

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The wild-type and ΔAosnf1 mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C for 5 days.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280≥1.8, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: Fungal hyphae

value: Fungal hyphae cells

tag: time

value: deltaAorlmA mutant strain

value: Nematode extract induces trap production


title: A125_48_2


title: 1- hMφ 306 Control


title: 2- hMφ 306 +TRB 100nM 6h


title: 9- hMφ 313 Control


title: 15- hMφ 337 Control


title: 12- hMφ 334 +LUR 100nM 6h


title: 17- hMφ 344 Control


title: A125_48_1


title: A125_0_3


title: hLESC ex vivo culture, treated with 5nm LY2090314, biological replicate 1


title: A125_0_2


title: AO_48_3

value: wild type


title: AO_48_2


title: A125_0_1


title: 8-  hMφ 312 +TRB 100nM 6h


title: AO_0_3


title: AO_48_1


title: AO_0_2


title: AO_0_1


title: lncRNA profile of N HCC case1982

city: Guangzhou

first: Rui

last: Xu

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-Sen University Cancer Center

hyb_protocol: Labeled RNAs from paired HCC and noncancerous liver were then mixed and hybridized to the array with a 2x hybridization solution (ﬁnal concentration: 5x Denhart’s solution, 0.5% SDS, and 5x SSC) in a Hybridization Chamber (Corning Inc.) at 46℃ for 12 to 16 hours.

scan_protocol: microarray was scanned with a LuxScan 10 K Microarray Scanner (CapitalBio Inc.) at PMT 800 to 950. Scanned images were gridded using the GenPix Pro 6.0 software (Axon Instruments).

data_processing: Microarray raw data preprocessing included local background subtraction, averaging of intensities of duplicated probes, quantile normalization across multiple arrays, log2 transformation of expression levels. Only the lncRNAs with expression in more than 15% of samples were subjected to further statistical analysis.

source_name: Hepatocellular Carcinoma

label_protocol: 2μg of total RNA was used with 1mmol/L of Cy5-dUTP or Cy3-dUTP (Perkin Elmer) in a reverse transcription system (Promega) for a total reaction volume of 20μL.

growth_protocol: All tissue samples were incubated immediately in RNA Later (Ambion, Inc.) after surgical resection for overnight at 4°C and then transfer to –80°C for long-term storage.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

value: Matched noncancerous tissue

tag: survival status after 5 years

value: dead


title: lncRNA profile of N HCC case1828

value: alive


title: lncRNA profile of N HCC case1685


title: lncRNA profile of N HCC case1714


title: lncRNA profile of N HCC case1718


title: lncRNA profile of N HCC case1925


title: lncRNA profile of N HCC case1953


title: lncRNA profile of N HCC case1729


title: lncRNA profile of N HCC case1713


title: lncRNA profile of N HCC case1795


title: lncRNA profile of N HCC case1683


title: lncRNA profile of N HCC case1927


title: lncRNA profile of N HCC case1778


title: lncRNA profile of N HCC case1790


title: lncRNA profile of N HCC case1751


title: lncRNA profile of N HCC case1676


title: lncRNA profile of N HCC case1823


title: lncRNA profile of N HCC case1768


title: lncRNA profile of N HCC case1764


title: lncRNA profile of N HCC case1686


title: lncRNA profile of N HCC case1923


title: lncRNA profile of N HCC case1693


title: lncRNA profile of N HCC case1699


title: lncRNA profile of N HCC case1894


title: lncRNA profile of N HCC case1753


title: lncRNA profile of N HCC case1776


title: lncRNA profile of N HCC case1903


title: lncRNA profile of N HCC case1671


title: lncRNA profile of N HCC case1670


title: lncRNA profile of N HCC case1681


title: lncRNA profile of N HCC case1669


title: lncRNA profile of N HCC case1643


title: lncRNA profile of N HCC case1650


title: lncRNA profile of N HCC case1626


title: lncRNA profile of N HCC case1658


title: lncRNA profile of N HCC case1549


title: lncRNA profile of N HCC case1661


title: lncRNA profile of N HCC case1589


title: lncRNA profile of N HCC case1558


title: lncRNA profile of N HCC case1619


title: lncRNA profile of N HCC case1606


title: lncRNA profile of N HCC case1592


title: lncRNA profile of N HCC case1545


title: lncRNA profile of N HCC case1615


title: lncRNA profile of N HCC case1538


title: lncRNA profile of N HCC case1593


title: lncRNA profile of N HCC case1629


title: lncRNA profile of N HCC case1603


title: lncRNA profile of N HCC case1577


title: lncRNA profile of N HCC case1587


title: lncRNA profile of N HCC case1617


title: lncRNA profile of N HCC case1532


title: lncRNA profile of N HCC case1636


title: lncRNA profile of N HCC case1641


title: lncRNA profile of N HCC case1536


title: lncRNA profile of N HCC case1529


title: lncRNA profile of N HCC case1522


title: lncRNA profile of N HCC case1519


title: lncRNA profile of N HCC case1564


title: lncRNA profile of N HCC case1493


title: lncRNA profile of N HCC case1388


title: lncRNA profile of N HCC case1485


title: lncRNA profile of N HCC case1409


title: lncRNA profile of N HCC case1401


title: lncRNA profile of N HCC case1340


title: lncRNA profile of N HCC case1382


title: lncRNA profile of N HCC case1455


title: lncRNA profile of N HCC case1073


title: lncRNA profile of N HCC case1081


title: lncRNA profile of N HCC case1279


title: lncRNA profile of N HCC case1075


title: lncRNA profile of N HCC case1078


title: lncRNA profile of N HCC case1237


title: lncRNA profile of N HCC case900


title: lncRNA profile of N HCC case957


title: lncRNA profile of N HCC case924


title: lncRNA profile of N HCC case939


title: lncRNA profile of N HCC case901


title: lncRNA profile of N HCC case916


title: lncRNA profile of N HCC case1223


title: lncRNA profile of N HCC case1071


title: lncRNA profile of N HCC case915


title: lncRNA profile of N HCC case1072


title: lncRNA profile of N HCC case883


title: lncRNA profile of N HCC case896


title: lncRNA profile of N HCC case884


title: lncRNA profile of N HCC case1079


title: lncRNA profile of N HCC case1225


title: lncRNA profile of N HCC case880


title: lncRNA profile of N HCC case879


title: lncRNA profile of N HCC case788


title: lncRNA profile of N HCC case822


title: lncRNA profile of N HCC case792


title: lncRNA profile of N HCC case876


title: lncRNA profile of N HCC case847


title: lncRNA profile of N HCC case778


title: lncRNA profile of N HCC case783


title: lncRNA profile of N HCC case784


title: lncRNA profile of N HCC case742


title: lncRNA profile of N HCC case738


title: lncRNA profile of N HCC case729


title: lncRNA profile of N HCC case737


title: lncRNA profile of N HCC case744


title: lncRNA profile of N HCC case785


title: lncRNA profile of N HCC case732


title: lncRNA profile of N HCC case746


title: lncRNA profile of N HCC case704


title: lncRNA profile of N HCC case734


title: lncRNA profile of N HCC case707


title: lncRNA profile of N HCC case690


title: lncRNA profile of N HCC case736


title: lncRNA profile of N HCC case720


title: lncRNA profile of N HCC case767


title: lncRNA profile of N HCC case662


title: lncRNA profile of N HCC case693


title: lncRNA profile of N HCC case739


title: lncRNA profile of N HCC case731


title: lncRNA profile of N HCC case108


title: lncRNA profile of N HCC case112


title: lncRNA profile of N HCC case111


title: lncRNA profile of N HCC case115


title: lncRNA profile of N HCC case113


title: lncRNA profile of N HCC case109


title: lncRNA profile of N HCC case106


title: lncRNA profile of N HCC case116


title: lncRNA profile of N HCC case107


title: lncRNA profile of N HCC case101


title: lncRNA profile of N HCC case91


title: lncRNA profile of N HCC case97


title: lncRNA profile of N HCC case93


title: lncRNA profile of N HCC case102


title: lncRNA profile of N HCC case95


title: lncRNA profile of N HCC case90


title: lncRNA profile of N HCC case87


title: lncRNA profile of N HCC case86


title: lncRNA profile of N HCC case89


title: lncRNA profile of N HCC case103


title: lncRNA profile of N HCC case83


title: lncRNA profile of N HCC case84


title: lncRNA profile of N HCC case79


title: lncRNA profile of N HCC case81


title: lncRNA profile of N HCC case82


title: lncRNA profile of N HCC case85


title: lncRNA profile of N HCC case99


title: lncRNA profile of N HCC case78


title: lncRNA profile of N HCC case76


title: lncRNA profile of N HCC case71


title: lncRNA profile of N HCC case67


title: lncRNA profile of N HCC case69


title: lncRNA profile of N HCC case65


title: lncRNA profile of N HCC case68


title: lncRNA profile of N HCC case63


title: lncRNA profile of N HCC case62


title: lncRNA profile of N HCC case58


title: HCC_tumor_sample_S296_Pt146

type: genomic

city: Barcelona

first: Roser

last: Pinyol

address: C/Rosselló

institute: IDIBAPS

hyb_protocol: Following Illumina HumanOmniExpressExome-8v1_A kit-associated protocol.

data_processing:
Genomic DNA extracted from the samples was genotyped using HumanOmniExpressExome-8v1_A (Illumina).
Genotype: AA,AB,BB,or empty (no call)

label: C-Bio and A-DNP

source_name: Hepatocellular carcinoma tumor tissue

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed with the ChargeSwitch gDNA Mini Tissue Kits (Invitrogen, CS11204)

tag: disease state

value: Hepatocellular Carcinoma

value: Liver tumor


title: HCC_tumor_sample_S293_Pt148

scan_protocol: Following Illumina HumanOmniExpressExome-8v1_A kit-associated protocol.


title: HCC_tumor_sample_S299_Pt149

label_protocol: Following Illumina HumanOmniExpressExome-8v1_A kit-associated protocol.


title: HCC_adjacent_sample_S295_Pt150

source_name: Hepatocellular carcinoma adjacent tissue

value: Liver adjacent


title: lncRNA profile of N HCC case64


title: HCC_tumor_sample_S297_Pt147


title: HCC_adjacent_sample_S294_Pt149


title: lncRNA profile of N HCC case57


title: HCC_tumor_sample_S300_Pt150


title: HCC_adjacent_sample_S292_Pt147


title: lncRNA profile of N HCC case75


title: lncRNA profile of N HCC case52


title: lncRNA profile of N HCC case51


title: lncRNA profile of N HCC case50


title: lncRNA profile of N HCC case1618


title: lncRNA profile of N HCC case48


title: HCC_tumor_sample_S289_Pt145


title: lncRNA profile of N HCC case47


title: lncRNA profile of N HCC case54


title: lncRNA profile of N HCC case49


title: lncRNA profile of N HCC case117


title: HCC_adjacent_sample_S298_Pt148


title: lncRNA profile of N HCC case45


title: lncRNA profile of N HCC case44


title: HCC_tumor_sample_S287_Pt144


title: HCC_tumor_sample_S286_Pt143


title: HCC_tumor_sample_S285_Pt143


title: lncRNA profile of N HCC case43


title: HCC_adjacent_sample_S291_Pt146


title: HCC_tumor_sample_S283_Pt142


title: HCC_adjacent_sample_S282_Pt141


title: lncRNA profile of N HCC case36


title: lncRNA profile of N HCC case46


title: HCC_adjacent_sample_S288_Pt144


title: HCC_adjacent_sample_S280_Pt140


title: lncRNA profile of N HCC case39


title: lncRNA profile of N HCC case28


title: HCC_tumor_sample_S279_Pt140


title: lncRNA profile of N HCC case30


title: HCC_adjacent_sample_S278_Pt139


title: lncRNA profile of N HCC case34


title: lncRNA profile of N HCC case27


title: HCC_tumor_sample_S277_Pt139


title: lncRNA profile of N HCC case26


title: HCC_tumor_sample_S276_Pt138


title: lncRNA profile of N HCC case25


title: HCC_adjacent_sample_S275_Pt138


title: lncRNA profile of N HCC case24


title: HCC_adjacent_sample_S284_Pt142


title: HCC_tumor_sample_S281_Pt141


title: HCC_tumor_sample_S274_Pt137


title: HCC_adjacent_sample_S273_Pt137


title: lncRNA profile of N HCC case23


title: HCC_adjacent_sample_S272_Pt136


title: HCC_adjacent_sample_S270_Pt135


title: HCC_tumor_sample_S271_Pt136


title: HCC_tumor_sample_S269_Pt135


title: lncRNA profile of N HCC case17


title: lncRNA profile of N HCC case18


title: lncRNA profile of N HCC case13


title: lncRNA profile of N HCC case14


title: HCC_tumor_sample_S267_Pt134


title: HCC_tumor_sample_S263_Pt132


title: HCC_tumor_sample_S265_Pt133


title: HCC_adjacent_sample_S266_Pt133


title: lncRNA profile of N HCC case10


title: lncRNA profile of N HCC case21


title: HCC_tumor_sample_S261_Pt131


title: lncRNA profile of N HCC case6


title: lncRNA profile of N HCC case22


title: lncRNA profile of N HCC case16


title: HCC_adjacent_sample_S268_Pt134


title: HCC_adjacent_sample_S260_Pt130


title: lncRNA profile of N HCC case11


title: lncRNA profile of N HCC case7


title: lncRNA profile of N HCC case19


title: lncRNA profile of N HCC case12


title: lncRNA profile of N HCC case9


title: HCC_tumor_sample_S259_Pt130


title: HCC_adjacent_sample_S264_Pt132


title: lncRNA profile of N HCC case2


title: HCC_adjacent_sample_S258_Pt129


title: lncRNA profile of N HCC case3


title: lncRNA profile of N HCC case5


title: HCC_adjacent_sample_S262_Pt131


title: lncRNA profile of T HCC case1982

value: Tumor tissue


title: HCC_tumor_sample_S255_Pt128


title: lncRNA profile of N HCC case1


title: HCC_adjacent_sample_S256_Pt128


title: lncRNA profile of T HCC case1953


title: HCC_adjacent_sample_S254_Pt127


title: HCC_tumor_sample_S253_Pt127


title: HCC_adjacent_sample_S252_Pt126


title: HCC_tumor_sample_S251_Pt126


title: HCC_adjacent_sample_S250_Pt125


title: HCC_tumor_sample_S257_Pt129


title: lncRNA profile of T HCC case1923


title: lncRNA profile of T HCC case1925


title: HCC_tumor_sample_S247_Pt124


title: HCC_adjacent_sample_S246_Pt123


title: lncRNA profile of N HCC case4


title: lncRNA profile of T HCC case1823


title: lncRNA profile of T HCC case1828


title: lncRNA profile of T HCC case1894


title: lncRNA profile of T HCC case1903


title: HCC_tumor_sample_S245_Pt123


title: HCC_tumor_sample_S244_Pt122


title: lncRNA profile of T HCC case1795


title: lncRNA profile of T HCC case1790


title: lncRNA profile of T HCC case1776


title: lncRNA profile of T HCC case1778


title: HCC_adjacent_sample_S243_Pt122


title: lncRNA profile of T HCC case1927


title: lncRNA profile of T HCC case1768


title: HCC_adjacent_sample_S241_Pt121


title: HCC_tumor_sample_S240_Pt120


title: lncRNA profile of T HCC case1753


title: HCC_tumor_sample_S242_Pt121


title: lncRNA profile of T HCC case1751


title: HCC_tumor_sample_S249_Pt125


title: HCC_adjacent_sample_S239_Pt120


title: HCC_tumor_sample_S238_Pt119


title: lncRNA profile of T HCC case1729


title: lncRNA profile of T HCC case1718


title: HCC_adjacent_sample_S235_Pt118


title: HCC_tumor_sample_S236_Pt118


title: HCC_adjacent_sample_S237_Pt119


title: lncRNA profile of T HCC case1714


title: HCC_tumor_sample_S234_Pt117


title: lncRNA profile of T HCC case1713


title: lncRNA profile of T HCC case1699


title: HCC_adjacent_sample_S233_Pt117


title: HCC_adjacent_sample_S248_Pt124


title: HCC_adjacent_sample_S232_Pt116


title: HCC_adjacent_sample_S230_Pt115


title: HCC_tumor_sample_S229_Pt115


title: lncRNA profile of T HCC case1764


title: HCC_adjacent_sample_S228_Pt114


title: HCC_tumor_sample_S227_Pt114


title: lncRNA profile of T HCC case1693


title: lncRNA profile of T HCC case1686


title: lncRNA profile of T HCC case1681


title: HCC_tumor_sample_S223_Pt112


title: lncRNA profile of T HCC case1683


title: lncRNA profile of T HCC case1670


title: HCC_tumor_sample_S225_Pt113


title: HCC_adjacent_sample_S224_Pt112


title: lncRNA profile of T HCC case1661


title: lncRNA profile of T HCC case1676


title: lncRNA profile of T HCC case1669


title: HCC_adjacent_sample_S222_Pt111


title: lncRNA profile of T HCC case1685


title: HCC_tumor_sample_S221_Pt111


title: HCC_adjacent_sample_S220_Pt110


title: lncRNA profile of T HCC case1641


title: lncRNA profile of T HCC case1636


title: lncRNA profile of T HCC case1671


title: HCC_adjacent_sample_S218_Pt109


title: HCC_tumor_sample_S219_Pt110


title: lncRNA profile of T HCC case1643


title: lncRNA profile of T HCC case1650


title: lncRNA profile of T HCC case1626


title: lncRNA profile of T HCC case1658


title: lncRNA profile of N HCC case40


title: lncRNA profile of T HCC case1619


title: HCC_adjacent_sample_S214_Pt107


title: HCC_tumor_sample_S217_Pt109


title: HCC_adjacent_sample_S216_Pt108


title: HCC_tumor_sample_S215_Pt108


title: HCC_tumor_sample_S290_Pt145


title: lncRNA profile of T HCC case1618


title: lncRNA profile of T HCC case1629


title: HCC_tumor_sample_S211_Pt106


title: HCC_adjacent_sample_S210_Pt105


title: HCC_tumor_sample_S209_Pt105


title: HCC_tumor_sample_S231_Pt116


title: lncRNA profile of T HCC case1603


title: lncRNA profile of T HCC case1606


title: lncRNA profile of T HCC case1592


title: HCC_adjacent_sample_S208_Pt104


title: lncRNA profile of T HCC case1589


title: lncRNA profile of T HCC case1593


title: lncRNA profile of T HCC case1615


title: HCC_adjacent_sample_S206_Pt103


title: lncRNA profile of T HCC case1587


title: HCC_tumor_sample_S205_Pt103


title: HCC_tumor_sample_S207_Pt104


title: HCC_adjacent_sample_S204_Pt102


title: HCC_tumor_sample_S203_Pt102


title: HCC_tumor_sample_S213_Pt107


title: lncRNA profile of T HCC case1617


title: lncRNA profile of T HCC case1577


title: HCC_adjacent_sample_S212_Pt106


title: lncRNA profile of T HCC case1549


title: lncRNA profile of T HCC case1564


title: lncRNA profile of T HCC case1558


title: HCC_adjacent_sample_S202_Pt101


title: HCC_tumor_sample_S201_Pt101


title: HCC_tumor_sample_S200_Pt100


title: lncRNA profile of T HCC case1536


title: lncRNA profile of T HCC case1545


title: HCC_adjacent_sample_S199_Pt100


title: lncRNA profile of T HCC case1538


title: HCC_adjacent_sample_S198_Pt99


title: HCC_tumor_sample_S197_Pt99


title: HCC_tumor_sample_S195_Pt98


title: HCC_tumor_sample_S191_Pt96


title: HCC_tumor_sample_S193_Pt97


title: HCC_adjacent_sample_S194_Pt97


title: HCC_adjacent_sample_S192_Pt96


title: HCC_adjacent_sample_S196_Pt98


title: HCC_tumor_sample_S189_Pt95


title: lncRNA profile of T HCC case1529


title: lncRNA profile of T HCC case1519


title: lncRNA profile of T HCC case1493


title: lncRNA profile of T HCC case1522


title: lncRNA profile of T HCC case1532


title: lncRNA profile of T HCC case1401


title: lncRNA profile of T HCC case1382


title: lncRNA profile of T HCC case1409


title: lncRNA profile of T HCC case1485


title: lncRNA profile of T HCC case1455


title: HCC_adjacent_sample_S186_Pt93


title: lncRNA profile of T HCC case1388


title: HCC_tumor_sample_S187_Pt94


title: lncRNA profile of T HCC case1340


title: HCC_tumor_sample_S185_Pt93


title: lncRNA profile of T HCC case1081


title: lncRNA profile of T HCC case1223


title: lncRNA profile of T HCC case1237


title: lncRNA profile of T HCC case1225


title: HCC_adjacent_sample_S190_Pt95


title: HCC_adjacent_sample_S184_Pt92


title: HCC_adjacent_sample_S182_Pt91


title: HCC_tumor_sample_S183_Pt92


title: lncRNA profile of T HCC case1279


title: lncRNA profile of T HCC case1078


title: lncRNA profile of T HCC case1079


title: lncRNA profile of T HCC case1075


title: HCC_adjacent_sample_S188_Pt94


title: HCC_adjacent_sample_S180_Pt90


title: HCC_tumor_sample_S179_Pt90


title: HCC_tumor_sample_S181_Pt91


title: HCC_tumor_sample_S177_Pt89


title: HCC_adjacent_sample_S176_Pt88


title: HCC_tumor_sample_S175_Pt88


title: lncRNA profile of T HCC case1072


title: lncRNA profile of T HCC case1073


title: HCC_tumor_sample_S173_Pt87


title: HCC_adjacent_sample_S174_Pt87


title: lncRNA profile of T HCC case957


title: lncRNA profile of T HCC case1071


title: lncRNA profile of T HCC case939


title: lncRNA profile of T HCC case924


title: HCC_tumor_sample_S171_Pt86


title: lncRNA profile of T HCC case916


title: HCC_tumor_sample_S170_Pt85


title: HCC_adjacent_sample_S178_Pt89


title: lncRNA profile of T HCC case915


title: HCC_adjacent_sample_S169_Pt85


title: lncRNA profile of T HCC case901


title: lncRNA profile of T HCC case896


title: HCC_adjacent_sample_S167_Pt84


title: HCC_tumor_sample_S168_Pt84


title: HCC_adjacent_sample_S166_Pt83


title: lncRNA profile of T HCC case884


title: lncRNA profile of T HCC case847


title: HCC_adjacent_sample_S172_Pt86


title: HCC_adjacent_sample_S164_Pt82


title: lncRNA profile of T HCC case879


title: lncRNA profile of T HCC case876


title: HCC_tumor_sample_S163_Pt82


title: lncRNA profile of T HCC case900


title: HCC_adjacent_sample_S162_Pt81


title: lncRNA profile of T HCC case880


title: HCC_adjacent_sample_S160_Pt80


title: lncRNA profile of T HCC case883


title: lncRNA profile of T HCC case792


title: HCC_tumor_sample_S159_Pt80


title: lncRNA profile of T HCC case785


title: lncRNA profile of T HCC case822


title: lncRNA profile of T HCC case784


title: HCC_adjacent_sample_S226_Pt113


title: HCC_adjacent_sample_S158_Pt79


title: lncRNA profile of T HCC case788


title: lncRNA profile of T HCC case783


title: HCC_tumor_sample_S157_Pt79


title: lncRNA profile of T HCC case778


title: HCC_tumor_sample_S165_Pt83


title: HCC_adjacent_sample_S156_Pt78


title: lncRNA profile of T HCC case767


title: lncRNA profile of T HCC case746


title: HCC_tumor_sample_S161_Pt81


title: HCC_tumor_sample_S153_Pt77


title: HCC_adjacent_sample_S154_Pt77


title: lncRNA profile of T HCC case742


title: HCC_adjacent_sample_S152_Pt76


title: lncRNA profile of T HCC case744


title: lncRNA profile of T HCC case739


title: HCC_tumor_sample_S151_Pt76


title: HCC_adjacent_sample_S150_Pt75


title: HCC_tumor_sample_S149_Pt75


title: lncRNA profile of T HCC case738


title: HCC_tumor_sample_S147_Pt74


title: HCC_adjacent_sample_S146_Pt73


title: HCC_tumor_sample_S145_Pt73


title: HCC_tumor_sample_S155_Pt78


title: HCC_adjacent_sample_S144_Pt72


title: lncRNA profile of T HCC case732


title: lncRNA profile of T HCC case736


title: HCC_tumor_sample_S143_Pt72


title: lncRNA profile of T HCC case734


title: lncRNA profile of T HCC case729


title: HCC_adjacent_sample_S142_Pt71


title: lncRNA profile of T HCC case731


title: lncRNA profile of T HCC case707


title: lncRNA profile of T HCC case693


title: HCC_tumor_sample_S141_Pt71


title: HCC_adjacent_sample_S140_Pt70


title: HCC_tumor_sample_S137_Pt69


title: HCC_tumor_sample_S139_Pt70


title: HCC_adjacent_sample_S138_Pt69


title: HCC_tumor_sample_S136_Pt68


title: lncRNA profile of T HCC case704


title: HCC_adjacent_sample_S148_Pt74


title: lncRNA profile of T HCC case737


title: HCC_adjacent_sample_S135_Pt68


title: HCC_adjacent_sample_S134_Pt67


title: lncRNA profile of T HCC case113


title: lncRNA profile of T HCC case720


title: HCC_tumor_sample_S133_Pt67


title: lncRNA profile of T HCC case117


title: lncRNA profile of T HCC case116


title: HCC_adjacent_sample_S132_Pt66


title: HCC_adjacent_sample_S130_Pt65


title: HCC_tumor_sample_S131_Pt66


title: HCC_tumor_sample_S129_Pt65


title: lncRNA profile of T HCC case690


title: HCC_adjacent_sample_S128_Pt64


title: lncRNA profile of T HCC case103


title: HCC_tumor_sample_S127_Pt64


title: HCC_adjacent_sample_S126_Pt63


title: lncRNA profile of T HCC case101


title: lncRNA profile of T HCC case102


title: lncRNA profile of T HCC case115


title: lncRNA profile of T HCC case662


title: lncRNA profile of T HCC case107


title: lncRNA profile of T HCC case108


title: HCC_adjacent_sample_S122_Pt61


title: lncRNA profile of T HCC case109


title: lncRNA profile of T HCC case112


title: HCC_tumor_sample_S121_Pt61


title: HCC_tumor_sample_S123_Pt62


title: HCC_tumor_sample_S125_Pt63


title: HCC_adjacent_sample_S120_Pt60


title: lncRNA profile of T HCC case106


title: HCC_tumor_sample_S119_Pt60


title: HCC_tumor_sample_S117_Pt59


title: HCC_adjacent_sample_S118_Pt59


title: HCC_adjacent_sample_S124_Pt62


title: lncRNA profile of T HCC case99


title: lncRNA profile of T HCC case95


title: lncRNA profile of T HCC case89


title: lncRNA profile of T HCC case93


title: HCC_tumor_sample_S115_Pt58


title: lncRNA profile of T HCC case111


title: lncRNA profile of T HCC case97


title: lncRNA profile of T HCC case85


title: HCC_adjacent_sample_S114_Pt57


title: HCC_adjacent_sample_S112_Pt56


title: lncRNA profile of T HCC case90


title: HCC_tumor_sample_S111_Pt56


title: lncRNA profile of T HCC case87


title: HCC_adjacent_sample_S110_Pt55


title: lncRNA profile of T HCC case86


title: lncRNA profile of T HCC case91


title: HCC_tumor_sample_S109_Pt55


title: lncRNA profile of T HCC case83


title: lncRNA profile of T HCC case82


title: lncRNA profile of T HCC case84


title: lncRNA profile of T HCC case81


title: lncRNA profile of T HCC case75


title: lncRNA profile of T HCC case78


title: lncRNA profile of T HCC case79


title: HCC_adjacent_sample_S108_Pt54


title: HCC_adjacent_sample_S116_Pt58


title: lncRNA profile of T HCC case76


title: HCC_tumor_sample_S107_Pt54


title: HCC_tumor_sample_S105_Pt53


title: lncRNA profile of T HCC case71


title: HCC_tumor_sample_S113_Pt57


title: HCC_adjacent_sample_S106_Pt53


title: HCC_adjacent_sample_S104_Pt52


title: lncRNA profile of T HCC case68


title: HCC_tumor_sample_S103_Pt52


title: LuCaP173_1_BG15_20uM_BU

city: Cleveland

first: Hyunmin

last: Kim

state: OH

address: 10900 Euclid Ave.

department: genetics and genome sciences

institute: Case western reserve university

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: TPM files are provided in txt format at the gene-level

source_name: prostate cancer patient derived xenograft

growth_protocol: Cell lines were grown in DMEM (LNCaP-XIP, LAMP), RPMI-1640 (LNCaP, 22Rv1) or Haim's F-12K medium (PC3) supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from cell lines using the RNeasy mini kit (Qiagen catalogue # 74136) with QiaShredder (Qiagen catalogue # 79654). For CUT&RUN, DNA was extracted using the Epicypher CUTANA CUT&RUN kit (catalogue # 14-1048). For HiChIP, the Dovetail MNase HiChIP kit (Catalogue # 21007) was used.  Briefly, cells were fixed with DSG and 37% formaldehyde, treated with MNase, and immunoprecipitated with anti-H3K27ac, anti-AR, or anti-CTCF antibody, and washed with noted salt concentration buffers.  On-bead bridge incorporation and religation was performed, followed by reversal of crosslinks and proteinase K treatment and DNA purification.
Dual-Index Illumina barcodes were introduced during library preparation (Dovetails catalogue # 25010).

treatment_protocol: For all cell line sequencing studies, cells were grown in complete medium overnight then underwent treatment as described above. Collection was performed in complete media with centrifugation and taken directly into assay steps.

tag: treatment time

value: 3days, 20uM


title: lncRNA profile of T HCC case69


title: PC3_DMSO

source_name: Prostate cancer cell line

value: Prostate cancer cell line

value: DMSO


title: lncRNA profile of T HCC case67


title: HCC_tumor_sample_S101_Pt51


title: HCC_adjacent_sample_S100_Pt50


title: LuCaP173_1_Ctl_BU

value: prostate cancer patient derived xenograft

value: Vehicle


title: LuCaP167_DMSO_rep2_ARIA


title: HCC_adjacent_sample_S096_Pt48


title: HCC_adjacent_sample_S094_Pt47


title: LuCaP167_DMSO_rep1_ARIA


title: lncRNA profile of T HCC case64


title: lncRNA profile of T HCC case65


title: 22RV1_BG15n


title: 22RV1_DMSO


title: lncRNA profile of T HCC case58


title: lncRNA profile of T HCC case62


title: HCC_adjacent_sample_S092_Pt46


title: HCC_tumor_sample_S093_Pt47


title: lncRNA profile of T HCC case63


title: HCC_tumor_sample_S091_Pt46


title: LNCaP-XIP_DMSOhi_2d


title: HCC_adjacent_sample_S102_Pt51


title: HCC_adjacent_sample_S090_Pt45


title: LNCaP-XIP_DMSOhi_1d


title: HCC_tumor_sample_S089_Pt45


title: HCC_adjacent_sample_S088_Pt44


title: HCC_tumor_sample_S099_Pt50


title: HCC_tumor_sample_S097_Pt49


title: HCC_adjacent_sample_S098_Pt49


title: lncRNA profile of T HCC case57


title: HCC_adjacent_sample_S086_Pt43


title: lncRNA profile of T HCC case54


title: HCC_tumor_sample_S085_Pt43


title: HCC_tumor_sample_S087_Pt44


title: lncRNA profile of T HCC case52


title: HCC_tumor_sample_S095_Pt48


title: HCC_adjacent_sample_S084_Pt42


title: LNCaP-XIP_BG15n_30uM_1d


title: LNCaP-XIP_BG15n_20uM_2d


title: HCC_tumor_sample_S083_Pt42


title: HCC_adjacent_sample_S082_Pt41


title: LNCaP-XIP_BG15n_20uM_1d


title: HCC_adjacent_sample_S080_Pt40


title: HCC_tumor_sample_S081_Pt41


title: LNCaP-XIP_BG15n_10uM_2d


title: HCC_tumor_sample_S079_Pt40


title: HCC_adjacent_sample_S078_Pt39


title: HCC_tumor_sample_S077_Pt39


title: LNCaP-XIP_BG15n_10uM_1d


title: HCC_adjacent_sample_S076_Pt38


title: LNCaP-XIP_BG15n_30uM_2d


title: lncRNA profile of T HCC case48


title: lncRNA profile of T HCC case51


title: lncRNA profile of T HCC case49


title: HCC_tumor_sample_S075_Pt38


title: LNCaP_XIP_DMSO


title: lncRNA profile of T HCC case50


title: lncRNA profile of T HCC case46


title: lncRNA profile of T HCC case47


title: HCC_adjacent_sample_S070_Pt35


title: HCC_tumor_sample_S073_Pt37


title: HCC_adjacent_sample_S074_Pt37


title: HCC_adjacent_sample_S072_Pt36


title: HCC_tumor_sample_S069_Pt35


title: LNCaP_XIP_BG15a


title: LAMP_R1881_K27ac

tag: ip target


title: HCC_adjacent_sample_S068_Pt34


title: HCC_tumor_sample_S065_Pt33


title: HCC_adjacent_sample_S064_Pt32


title: lncRNA profile of T HCC case43


title: lncRNA profile of T HCC case44


title: LAMP_DMSO_K27ac


title: LAMP_ENZA_K27ac

value: Enzalutamide


title: lncRNA profile of T HCC case45


title: HCC_tumor_sample_S071_Pt36


title: lncRNA profile of T HCC case40


title: lncRNA profile of T HCC case39


title: 22Rv1_BG15n_NCOR1

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: TPM files are provided in txt format at the gene-level
Library strategy: CUT&RUN


title: LAMP_BG15n_K27ac


title: SiHa cells,  KD HSPA9, Day0, replicate3

city: shenzhen

first: Keyi

last: Ao

address: Xinan

institute: shenzhen hospital of Southern medical school

data_processing:
The image data of the sequencing fragments were converted into sequence data (reads) by CASAVA base recognition, and the file was fastq Format, which mainly contains the sequence information of the sequencing fragment and its corresponding sequencing quality information
The index of the reference genome was constructed using HISAT2 v2.0.5, and the paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.5
StringTie (Mihaela Pertea.et al. 2015) was used for novel gene prediction
FeatureCounts were used to calculate the readings mapped to each gene. FPKM was then calculated for each gene based on its length and the readings mapped to that gene were calculated
DESeq2 R software (1.16.1) was used for differential expression analysis between the two comparison combinations
Assembly: ENSEMBL
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: Cervical cancer Epithelial tissue

growth_protocol: SiHa, KD HSPA9 SiHa and H8 cells were incubated in RPMI 1640 media (Gibco, US) in a humid atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using TransZolMUp Plus RNA Kit (TransGen). 1ug of total RNA was used for the construction of sequencing libranes
RNA libraries for RNA-seq were prepared using Illumina NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: no treatment

value: Cervical cancer Epithelial tissue

value: SiHa

value: cervical cancer cells

value: HSPA9 knockdown

value: no treatment

tag: source gender

value: female


title: SiHa cells,  KD HSPA9, Day0, replicate2

tag: cell type


title: HCC_adjacent_sample_S062_Pt31

tag: tissue


title: 22Rv1_DMSO_NCOR1


title: lncRNA profile of T HCC case36

value: dead


title: H8 cells, shControl, Day0, replicate3

value: cervical immortalized cervical cells

value: WT


title: HCC_tumor_sample_S067_Pt34

value: Hepatocellular Carcinoma

value: Liver tumor


title: LNCaP_XIP_BG15n


title: lncRNA profile of T HCC case30

value: Tumor tissue


title: HCC_adjacent_sample_S066_Pt33

value: Liver adjacent


title: 22Rv1_BG15n_SMRT

value: Prostate cancer cell line

value: SMRT


title: HCC_tumor_sample_S061_Pt31


title: lncRNA profile of T HCC case28

value: alive


title: H8 cells, shControl, Day0, replicate2


title: lncRNA profile of T HCC case34


title: HCC_adjacent_sample_S060_Pt30


title: HCC_tumor_sample_S059_Pt30


title: LNCaP_BG15n_NCOR1


title: H8 cells, shControl, Day0, replicate1


title: HCC_tumor_sample_S063_Pt32


title: lncRNA profile of T HCC case27


title: LNCaP_DMSO_NCOR1

value: DMSO


title: SiHa cells, shControl, Day0, replicate3

value: Cervical cancer Epithelial tissue


title: SiHa cells, shControl, Day0, replicate2

value: SiHa


title: HCC_adjacent_sample_S058_Pt29


title: HCC_tumor_sample_S057_Pt29


title: HCC_adjacent_sample_S056_Pt28


title: SiHa cells, shControl, Day0, replicate1

value: cervical cancer cells


title: LNCaP_DMSO_SMRT


title: LNCaP_BG15n_SMRT


title: LNCaP-XIP_BG-15n_AR

value: AR


title: HCC_tumor_sample_S055_Pt28


title: 22Rv1_DMSO_SMRT


title: DIP_coculture_rep3

city: Changsha

first: Siyi

last: Wanggou

state: Hunan

address: Xiangya Road, No.87

department: Departmeng of Neurosurgery

institute: Xiangya Hospital, Central South University

data_processing:
The Illumina sequencer’s base call files (BCls) were demultiplexed into FASTQ files using cellranger mkfastq.
The FASTQ files were aligned to GRCh38 (hg38) human genome reference and GRCm38 (mm10) mouse genome reference to generate transcript matrices by cellranger count and hisat2.
Assembly: hg38

source_name: GBM cell (G411)-neuron coculture model

growth_protocol: Mice were maintained in specific pathogen-free conditions in the animal facility with 12:12 h light/dark cycles.

extract_protocol:
Xenograft model: 2,000 G411 cells were orthotopically injected into 6- to 10-week-old female NSG mice. The mice were allowed to recover for 4 or 10 days. For peptide treatment, surgeries were performed at day 4 or day 10. Preassembled, peptide-loaded osmotic pumps were soaked in DPBS in 37℃ cell culture incubator overnight. The pump model and peptide concentration were specified in each individual experiment. Coculture model: 10,000 G411 cells were seeded into DIV 7 neuron cultures and co-cultured for 3 days. 50 µM of K59-78TAT or K90-114TAT were added into the cultures and incubated for 8 hours.
Xenograft model: 10 days after peptide treatment, 3 mice from K59-78TAT group and K90-114TAT group were anaesthetized and perfused with DPBS, the brains were isolated and kept in ice-cold DPBS. The tumors were then dissected under a fluorescent dissection scope to selectively collect GFP+ tumor tissues, and the tumors were dissociated with Papain dissociation system (Worthington #LK003150). Sample quality control, library prep, and sequencing were performed by The Center for Applied Genomics. Coculture model: Total RNA was extracted from the treated cells using RNeasy Mini Kit (QIAGEN). Sample quality control, library prep, and sequencing were performed by The Center for Applied Genomics.
One merged sample from 3 mice of K59-78TAT treated Xenograft model. One merged sample from 3 mice of K90-114TAT treated Xenograft mice model. Three biological replicates of K59-78TAT treated GBM cell-neuron coculture model. Three biological replicates of K90-114TAT treated GBM cell-neuron coculture model. Eight libraries in total.

treatment_protocol: Control peptide K59-78TAT treated Xenograft mice vs Designer peptide K90-114TAT treated Xenograft mice. Control peptide K59-78TAT treated GBM cell-neuron coculture model vs Designer peptide K90-114TAT treated GBM cell-neuron coculture model.

value: Glioblastoma cell

value: K90-114TAT treated

value: neuron coculture


title: lncRNA profile of T HCC case24


title: DIP_coculture_rep1


title: DIP_coculture_rep2


title: HCC_adjacent_sample_S054_Pt27


title: lncRNA profile of T HCC case23


title: HCC_tumor_sample_S053_Pt27


title: LNCaP-XIP_DMSO_AR


title: lncRNA profile of T HCC case21

value: dead


title: lncRNA profile of T HCC case22


title: lncRNA profile of T HCC case25


title: Ctrl_coculture_rep3

value: K59-78TAT treated


title: lncRNA profile of T HCC case26


title: HCC_adjacent_sample_S052_Pt26

value: Hepatocellular Carcinoma


title: lncRNA profile of T HCC case19


title: LNCaP-XIP_DMSO_H3K27ac


title: lncRNA profile of T HCC case18


title: HCC_tumor_sample_S051_Pt26

value: Liver tumor


title: lncRNA profile of T HCC case17

value: Tumor tissue


title: Ctrl_coculture_rep2


title: HCC_tumor_sample_S050_Pt25


title: LNCaP-XIP_BG-15n_H3K27ac


title: DIP_xenograft

description: DIP

library_source: transcriptomic single cell

source_name: Xenograft GBM tumor (G411)-bearing NSG mice

value: Glioblastoma tissue


title: HCC_adjacent_sample_S049_Pt25

value: Liver adjacent


title: lncRNA profile of T HCC case16


title: HCC_adjacent_sample_S048_Pt24


title: LNCaPXIP_BG15n_H3K27ac

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: TPM files are provided in txt format at the gene-level
Library strategy: HiChIP

value: Prostate cancer cell line


title: HCC_tumor_sample_S047_Pt24


title: LNCaPXIP_NT_med_AR

value: No Treatment


title: lncRNA profile of T HCC case14


title: lncRNA profile of T HCC case13

value: alive


title: LNCaPXIP_NT_low_AR


title: HCC_adjacent_sample_S046_Pt23


title: cDPC 2D_1

city: Seoul

first: Jin Yong

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

institute: Seoul National University College of Medicine

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose qualityscores are less than 20 and reads whose average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Filtered reads were mapped to the human reference genome (Ensembl release 72, Flicek P. et al., 2013) using the aligner Tophat (Trapnell C et al. 2012).
Genome_build: Ensembl release 72
Supplementary_files_format_and_content: text file with FPKM values.

source_name: cultured human dermal papilla cell

growth_protocol: hi-NCSCs were generated by FGF2, fibronectin, and N2 medium from hiPSCs, hi-DPPCs were generated in DMEM/F12 medium supplemented with FGF2 (10 ng/mL), 6-bromoindirubin-3'-oxime (BIO; 1 μM), and short-term addition of BMP4 (1 ng/mL), followed by passage and final expansion in DMEM/F12 medium supplemented with FGF2 (10 ng/mL). Then, expanded DPPCs were isolated and created into three-dimensional (3D) spheres. cDPC 2D were cultured in routine DMEM + 10% FBS media and cDPC 3D were generated from cDPC 2D isolated and created into three-dimensional (3D) spheres.

extract_protocol:
Total RNA was isolated from hi-NCSCs, hi-DPPCs, cultured DPCs and cultured DPC spheres using RNAiso Plus.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cultured human dermal papilla cell


title: cDPC 2D_2


title: lncRNA profile of T HCC case12


title: LNCaPXIP_DMSO_AR

value: DMSO


title: HCC_tumor_sample_S045_Pt23


title: cDPC 3D_2

source_name: cultured human dermal papilla cell sphere


title: lncRNA profile of T HCC case11


title: cDPC 3D_1

value: cultured human dermal papilla cell sphere


title: LNCaPXIP_BG15n_AR

value: AR


title: HCC_adjacent_sample_S044_Pt22


title: lncRNA profile of T HCC case10


title: LNCaPXIP_AR_dupin


title: hi-DPPC_2

source_name: hiPSC-derived dermal papilla precursor cell


title: PC3_BG15n


title: lncRNA profile of T HCC case7


title: HCC_tumor_sample_S043_Pt22


title: Ctrl_xenograft

description: Ctrl


title: HCC_adjacent_sample_S042_Pt21


title: lncRNA profile of T HCC case9


title: LuCaP170_1_BG15_20uM_BU

value: prostate cancer patient derived xenograft

value: 3days, 20uM


title: hi-DPPC_1

value: hiPSC-derived dermal papilla precursor cell


title: HCC_tumor_sample_S041_Pt21


title: hi-NCSC_2

source_name: hiPSC-derived neural crest stem cell

value: hiPSC-derived neural crest stem cell


title: HCC_adjacent_sample_S040_Pt20


title: LuCaP167_BG15n_rep2_ARIA


title: LuCaP167_BG15n_rep1_ARIA


title: lncRNA profile of T HCC case4


title: HCC_tumor_sample_S039_Pt20


title: LNCaP_DMSO


title: HCC_adjacent_sample_S038_Pt19


title: lncRNA profile of T HCC case5


title: lncRNA profile of T HCC case6

value: dead


title: HCC_tumor_sample_S037_Pt19

value: Hepatocellular Carcinoma


title: L2_2709

city: London

first: Kiyan

last: Shabestary

address: Exhibition Road

country: United Kingdom

institute: Imperial College London

data_processing: Reads were mapped to reference genome using HISAT2.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Rich media (YPD) for 4h from an overnight culture

extract_protocol:
RNA was extracted with a RNAprep Pure Plant Plus kit (Tiangen).
After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by a second strand cDNA synthesis.

treatment_protocol: Cells were washed twice in PBS and resuspended in nitrogen-limited media with proline (0.8 mM) as nitrogen source.

value: S. cerevisiae

tag: strain

value: pRPL28 GFP

value: 1 hour NLIM-PRO


title: L_2909


title: H_2909


title: LNCaP_BG15n


title: lncRNA profile of T HCC case1

value: Tumor tissue


title: LuCaP170_1_Ctl_BU

value: Vehicle


title: HCC_tumor_sample_S036_Pt18

value: Liver tumor


title: LNCaP_BG15a

value: Prostate cancer cell line


title: hi-NCSC_1


title: 509, wt, 16wk

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: kidney

extract_protocol:
Kidneys were decapsulated, minced, and then digested with Type 1 Collagenase and DNase to get the single cell suspension. TAL cells were separated from the single cell suspension using the Dynabead magnetic bead conjugation system. Then TAL total RNA was purified.
oligo-dT

value: TAL epithelium

value: kidney

tag: age

value: wt


title: 508, del, 16wk

value: del


title: L1_2709


title: LAmp122_DMSOhi_48h_RNA

value: DMSO


title: H2_2709


title: 507, del, 16wk


title: HCC_adjacent_sample_S035_Pt18

value: Liver adjacent


title: LAmp122_BG15n30uM_48h_RNA


title: HCC_tumor_sample_S034_Pt17


title: lncRNA profile of T HCC case3

value: alive


title: lncRNA profile of T HCC case2


title: L2_2609


title: 506, wt, 16wk


title: 22RV1_BG15a


title: L1_2609


title: HCC_tumor_sample_S032_Pt16


title: 504, del, 16wk


title: si_αKG

city: beijing

first: zhenxi

last: zhang

address: Dongdan Santiao No. 5

institute: PUMC

data_processing:
Reads from ChIP-seq data for polymerase II antibodies were aligned to the hg19 genome using bowtie2 (v2.3.5.1).
Peaks were called using MACS2(v2.2.6).
Different peaks were generated using bdgdiff.
Motifs were found to analyze the DNA sequence of poly II protein binding through motifmatchr(v 1.20.0).
Visualization was realized by IGV(v2.8.9).
Assembly: hg19
Supplementary files format and content: bigWig,
Supplementary files format and content: narrowPeak

source_name: cell line

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: For ChIP–seq analysis, briefly, reads from ChIP-seq data for polymerase II antibodies were aligned to the hg19 genome using bowtie2 (v2.3.5.1). Peaks were called using MACS2(v2.2.6) for polymerase II. Different peaks were generated using bdgdiff. The ChIP-seq pileup heatmaps were generated using plotHeatmap. GO/KEGG enrichment analysis was performed using the R package clusterProfiler(v4.0). Visualization was realized by IGV(v2.8.9). Motifs were found to analyze the DNA sequence of poly II protein binding through motifmatchr(v 1.20.0)[1].

value: cell line

value: SK-Hep1 cells

tag: chip antibody

value: anti-polymerase II ((Abcam, ab26721)


title: si_αKG_input


title: H2_2609

value: S. cerevisiae


title: HCC_adjacent_sample_S031_Pt16

value: Hepatocellular Carcinoma


title: H1_2609

value: pRPL28 GFP

value: 1 hour NLIM-PRO


title: si_2


title: 503, wt, 16wk


title: HCC_adjacent_sample_S030_Pt15


title: 502, del, 16wk


title: H1_2709


title: nc_2

value: nc


title: 501, del, 16wk


title: si_input_2


title: HCC_adjacent_sample_S028_Pt14


title: M3D_Heat_2_RNA_seq

first: Guopei

last: Zhang

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University

data_processing:
HISAT2
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each Sample

source_name: Hepatocellular carcinoma

extract_protocol:
RNA of the 2D, 3D, and animal models were extracted using Rneasy Mini Kit (74104, Qiagen, USA). The RNA samples were transported to Lianchuan Biotechnology Co., Ltd for libraries’ generation and sequencing.
Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform.

value: Hepatocellular carcinoma

value: Hepatocellular Carcinoma Cell Line

tag: biological replicates

value: biological replicate_2

value: MHCC-97H in the 3D model-heat treatment


title: M3D_Heat_3_RNA_seq

value: biological replicate_3


title: HCC_adjacent_sample_S033_Pt17


title: 500, wt, 16wk

value: TAL epithelium

value: kidney

value: wt


title: M3D_Heat_1_RNA_seq

value: biological replicate_1


title: nc_input_2

value: cell line


title: 505, wt, 16wk


title: HCC_tumor_sample_S027_Pt14

value: Liver tumor


title: HCC_adjacent_sample_S026_Pt13

value: Liver adjacent


title: M3D_Ctrl_3_RNA_seq

value: MHCC-97H in the 3D model-treatment control


title: M3D_Ctrl_2_RNA_seq


title: APP-KI;C3aRKO, replicate 4, 9 months, bulk RNAseq

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
trimmed reads mapped to reference genome by TopHat2.
Read count caculated by featurecounts
DEGs identified by DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Takara SMARTer Total RNA Pico kitv3. The first 8 nt of Read 2 are UMIs followed by 3 nucleotides derived from the Pico v3 SMART UMI Adapter, both of which will need to be trimmed.

value: brain

value: 9 months old


title: sample_12

city: Calgary

first: Pinaki

last: Bose

state: AB

address: HMRB 354, 3330 Hospital Dr. NW

institute: University of Calgary

data_processing:
All raw FASTQ reads were aligned to Homo_sapiens : GRCh38 reference using the spaceranger count algorithim and quantified through the 10X Genomics space ranger spatial transcriptomics pipeline, with default and recommended parameters. Spaceranger outputs were combined and read depth normalized using the spaceranger aggr function, producing aggregated feature-barcode matrices used in downstream analysis.
Assembly: Homo_sapiens : GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from spaceranger pipeline, Spatial tissue position list CSV, high resolution tissue image as a PNG, scalefactors for tissue positions as a JSON
Library strategy: Spatial Transcriptomics

source_name: OSCC

extract_protocol:
Banked fresh-frozen OSCC samples were obtained from the in collaboration with the Ohlson Research Institute and the Department of Pathology and Laboratory Medicine. This study was reviewed and approved by the Health Research Ethics Board of Alberta – Cancer Committee (reference number: HREBA.CC-16-0644) A subset of samples were then chosen for downstream processing based on tissue quality. OSCC samples were permeabilized enzymatically according to the Visium Protocol CG000240. Samples were then processed using the Visium Spatial Gene Expression Reagent Kit according to the manufacturer’s instructions (10x Genomics, Pleasanton, CA, USA).
OSCC samples were permeabilized enzymatically according to the Visium Protocol CG000240. Samples were then processed using the Visium Spatial Gene Expression Reagent Kit according to the manufacturer’s instructions (10x Genomics, Pleasanton, CA, USA).

tag: Stage

value: Stage IVA

value: Oral squamous cell carcinoma (OSCC)

tag: library preparation

value: 10X Genomics Visium Spatial Gene Expression Slide & Reagent kit


title: sample_11

value: Stage II


title: HCC_tumor_sample_S025_Pt13

source_name: Hepatocellular carcinoma tumor tissue

value: Hepatocellular Carcinoma


title: HCC_tumor_sample_S029_Pt15


title: APP-KI;C3aRKO, replicate 5, 9 months, bulk RNAseq

tag: genotype


title: APP-KI;C3aRKO, replicate 3, 9 months, bulk RNAseq


title: M3D_Ctrl_1_RNA_seq

value: Hepatocellular carcinoma

value: Hepatocellular Carcinoma Cell Line

tag: treatment


title: APP-KI;C3aRKO, replicate 2, 9 months, bulk RNAseq


title: sample_10


title: HCC_tumor_sample_S023_Pt12


title: APP-KI;C3aRKO, replicate 1, 9 months, bulk RNAseq


title: sample_9


title: HCC_adjacent_sample_S022_Pt11

source_name: Hepatocellular carcinoma adjacent tissue


title: MAD_2_RNA_seq

tag: cell line

value: biological replicate_2

value: MHCC-97H in the animal model


title: MAD_3_RNA_seq

value: biological replicate_3


title: C3aRKO, replicate 3, 9 months, bulk RNAseq


title: sample_8


title: MAD_1_RNA_seq

value: biological replicate_1


title: HCC_tumor_sample_S021_Pt11


title: C3aRKO, replicate 2, 9 months, bulk RNAseq


title: SiHa cells,  KD HSPA9, Day0, replicate1

value: Cervical cancer Epithelial tissue

value: SiHa

value: cervical cancer cells

value: HSPA9 knockdown

value: no treatment

value: female


title: HCC_adjacent_sample_S020_Pt10

value: Liver adjacent


title: HCC_adjacent_sample_S024_Pt12


title: M3D_3_RNA_seq

value: MHCC-97H in the 3D model


title: sample_6

value: Oral squamous cell carcinoma (OSCC)

value: 10X Genomics Visium Spatial Gene Expression Slide & Reagent kit


title: HCC_tumor_sample_S019_Pt10

value: Hepatocellular Carcinoma

value: Liver tumor


title: C3aRKO, replicate 1, 9 months, bulk RNAseq

value: brain

value: 9 months old


title: HCC_adjacent_sample_S018_Pt9


title: APP-KI, replicate 6, 9 months, bulk RNAseq

value: APP-KI


title: APP-KI, replicate 5, 9 months, bulk RNAseq


title: sample_4

value: Stage IVA


title: M2D_3_RNA_seq

value: Hepatocellular carcinoma

value: Hepatocellular Carcinoma Cell Line

value: biological replicate_3

value: MHCC-97H in the 2D model


title: HCC_tumor_sample_S017_Pt9


title: sample_7


title: HCC_adjacent_sample_S016_Pt8


title: M2D_2_RNA_seq

value: biological replicate_2


title: sample_2


title: APP-KI,C3aR+, replicate 3, 9 months, bulk RNAseq


title: M2D_1_RNA_seq

value: biological replicate_1


title: HCC_tumor_sample_S015_Pt8


title: sample_1


title: sample_3

value: Stage I


title: M3D_2_RNA_seq


title: HCC_adjacent_sample_S014_Pt7

value: Liver adjacent


title: LNCaPXIP_DMSO_H3K27ac

value: Prostate cancer cell line

value: DMSO


title: sample_5

value: Stage II

value: Oral squamous cell carcinoma (OSCC)

value: 10X Genomics Visium Spatial Gene Expression Slide & Reagent kit


title: LNCaPXIP_BG15n_24hr_AR

value: AR


title: M3D_1_RNA_seq

value: MHCC-97H in the 3D model


title: HCC_tumor_sample_S013_Pt7

value: Hepatocellular Carcinoma

value: Liver tumor


title: APP-KI, C3aR+, replicate 1, 9 months, bulk RNAseq

value: brain

value: APP-KI

value: 9 months old


title: RAW_CC_PRX_4

city: Nagoya

first: Michiko

last: Itoh

state: Aichi

address: Furo-cho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
Low-quality reads and adapter sequences were trimmed using fastp software (doi: 10.1093/bioinformatics/bty560).
The reads were mapped to the mm10 reference genome using HISAT2 (doi: 10.1038/s41587-019-0201-4) followed by transcript assembly and quantification using StringTie (doi:10.1038/nbt.3122).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: RAW264 macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was purified using RNeasy MiniElute Cleanup Kit (QIAGEN, Hilden, Germany).
RNA-seq libraries were constructed by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB) and MGIEasy RNA Directional Library Prep Set (MGI), according to the manufacturer’s instruction.

treatment_protocol: Macrophages treated with cholesterol crystals (500 ug/ml) with or without β-cyclodextrin polyrotaxane (βCD-PRX, 1mM) for 24 hours.

value: macrophage

value: cholesterol crystals, betaCD-PRX


title: RAW_CC_PRX_3


title: LNCaPXIP_BG15n_6hr_AR


title: APP-KI, replicate 4, 9 months, bulk RNAseq


title: RAW_CC_PRX_2


title: WT, replicate 6, 9 months, bulk RNAseq

value: WT


title: HCC_adjacent_sample_S012_Pt6


title: RAW_CC_PRX_1


title: WT, replicate 5, 9 months, bulk RNAseq


title: LNCaPXIP_BG15n_1hr_AR


title: HCC_tumor_sample_S011_Pt6


title: APP-KI, C3aR+, replicate 2, 9 months, bulk RNAseq


title: Ctrl_coculture_rep1

value: Glioblastoma cell

value: K59-78TAT treated

value: neuron coculture


title: WT, replicate 4, 9 months, bulk RNAseq


title: RAW_CC_4

value: cholesterol crystals


title: WT, C3aR+, replicate 3, 9 months, bulk RNAseq


title: LNCaPXIP_DMSO_1hr_AR

value: Prostate cancer cell line

value: DMSO


title: HCC_adjacent_sample_S010_Pt5

value: Liver adjacent


title: SJSA-1 cells overexpressing RUNX2 shRNA rep5

first: Jianlin

last: Zhou

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.87 whole genome
Fragments per kilobase per million mapped fragments (FPKM) were calculated using a protocol from Trapnell, C. et al, Nature  biotechnology, 2010.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and normalized read count

source_name: SJSA-1 cell

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

value: human osteosarcoma cell

tag: knockdown

value: RUNX2 shRNA


title: SJSA-1 cells overexpressing RUNX2 shRNA rep6


title: RAW_CC_3


title: WT, C3aR+, replicate 2, 9 months, bulk RNAseq


title: LNCaPXIP_CTCF

source_name: Prostate cancer cell line

value: No Treatment

value: CTCF


title: WT, C3aR+, replicate 1, 9 months, bulk RNAseq

value: brain


title: SJSA-1 cells overexpressing RUNX2 shRNA rep4


title: RAW_CC_2


title: HCC_tumor_sample_S007_Pt4

value: Hepatocellular Carcinoma

value: Liver tumor


title: RAW_CC_1

value: macrophage


title: SJSA-1 cells overexpressing RUNX2 shRNA rep3


title: HCC_tumor_sample_S009_Pt5


title: 12month Ctrl

city: Chicago

last: Yi

state: IL

address: 303 E. Chicago Avenue

institute: Northwestern University

description: 10x Genomics

data_processing:
Raw reads were aligned to mouse genome build mm10 using cellrange-atac v2.0.0
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: Filtered_peak_bc_matrix from cellranger-atac output with cell barcode as column name and peak as row name.

source_name: Skin

extract_protocol:
Total backskin from mice of indicated age was dissociated with collagenase treatment followed by trypsinization, single cell suspesion was obtained to load onto 10x Genomics single cell ATACseq profiling platform.
scATAC libraries were constructed following 10x Genomics single cell ATAC v1 protocol.

value: Skin

value: 12 months

value: Wildtype

value: No


title: RAW_PRX_4

value: betaCD-PRX


title: HCC_adjacent_sample_S008_Pt4


title: RAW_PRX_3


title: SJSA-1 cells overexpressing RUNX2 shRNA rep2


title: HCC_tumor_sample_S005_Pt3


title: SJSA-1 cells overexpressing RUNX2 shRNA rep1