title: D425 cells, DMSO, 72 hours, replicate 3, RNAseq

description: processed_file: PLX240095_assay_data.csv: DMSO_3_D425

data_processing:
FASTQ files were processed using the nf-core RNA-seq pipeline (v3.7).
Adapter sequences were removed with Cutadapt.
Reads were aligned with STAR to GRCh38 and quantified to gene counts using RSEM.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

growth_protocol: D425 and D458 cell lines were cultured in DMEM supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (GIBCO), 1 × penicillin/streptomycin solution (Cellgro), and with 1 × L-glutamine (Cellgro).

extract_protocol:
Cells were collected in Qiazol and RNA extraction was performed using Rneasy Plus Mini Kit (Qiagen)
RNA purity, quantity and integrity was determined with NanoDrop (ThermoFisher Scientific) and TapeStation 4200 (Agilent) analysis prior to RNA-seq library preparation.  The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries.  Paired-end sequencing reads of 150bp was generated on NovaSeq 6000 (Illumina) sequencer at a target depth of 80 million paired-end reads per sample.  Raw sequencing reads were de-multiplexed using bcl2fastq.

treatment_protocol: Cells were treated with either 200 nM TG02, established IC50 value of atuveciclib, or DMSO control. TG02-treated cells were collected at 24 hours, while atuveciclib-treated cells were collected at 72 hours.

value: Myc-amplified medulloblastoma

value: DMSO

value: 72 hours


title: Spleen, 5mg-kg LPS, m7, d0.5

status: Public on Nov 14 2024

type: SRA

city: Chicago

first: Denis

last: Cipurko

state: IL

address: 900 E 57th St

department: Biological Sciences Division

country: USA

institute: University of Chicago

description:
SP_d0.5_7
Spleen_cpm_counts.txt

library_source: transcriptomic

data_processing:
Sequencing read files were processed to generate UMI (unique molecular identifier) count matrices using the python toolkit from the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/). In brief, reads were aligned to the mouse mm10 transcriptome with RapMap (https://github.com/COMBINE-lab/RapMap). Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/), Qualimap, MultiQC (https://github.com/ewels/MultiQC). Samples were demultiplexed using barcodes stored in Read 1 (first 6 bases) and raw UMI count matrices were computed using UMIs stored in Read 1 (bases 7 to 16) (https://github.com/vals/umis). Differential expression (DE) analysis was done using custom scripts in R (http://www.R-project.org). Raw count matrices were filtered to keep genes with at least 20 counts per million (cpm) or 5 UMIs in 2 samples and normalized across samples using the calcNormFactor function in edgeR (https://github.com/StoreyLab/edge).
Assembly: mm10
Supplementary files format and content: All count matrices are in tsv format. The first seven columns contain sample metadata (Organ, Treatment, Mouse ID, Mouse genotype, etc.). The remaining columns consist of normalized cpm counts. Matrices include all replicates for the organ.

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies). For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293).
Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

tag: tissue

value: Spleen

tag: mouse id

tag: time point

value: 12 hours

tag: genotype

tag: treatment

value: 5mg-kg LPS


title: Seeds, Col-0, 26d+ after pollination, Batch A, rep1

city: Wageningen

first: Mariana

middle: Aline

last: Silva Artur

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

data_processing:
Mapping was done with hisat2 v2.1.0 (command: hisat2 -p 12 --rna-strandness R -t --dta-cufflinks -x TAIR11 -U $f -S $name.sam)
Sorting of alignments (command: samtools sort -@ 12 -o $name.bam $name.sam)
Transcript quantification was done with stringtie v1.3.2 (command: stringtie -e -B -p 12 -G Araport11_GFF3_genes_transposons.201606.gtf -o ballgown/$name/$name.gtf $name.bam)
Raw counts were extracted using the script prepDE.py, available at StringTie GitHub repository (https://github.com/gpertea/stringtie/blob/master/prepDE.py).
Assembly: TAIR10 genome,Araport11gene annotation
Supplementary files format and content: comma-delimited text file with raw counts for every sample

organism: Arabidopsis thaliana

source_name: Seed

growth_protocol: Plants were grown on 4 x 4 cm Rockwool blocks in a growth chamber at 20°C/18°C (day/night) under a 16-h photoperiod of artificial light (150 μmol m-2 s-1) and 70% relative humidity. Plants were watered three times per week with standard nutrient solution Hyponex (He et al. 2014).

extract_protocol:
Total RNA was extracted using a hot borate method modified from Wan and Wilkins (1994). The homogenized seeds were mixed with an extraction buffer (0.2 M Na borate decahydrate (Borax), 30 mM EGTA, 1% SDS, 1% Na deoxy-cholate (Na-DOC)) containing 1.6 mg DTT and 48 mg PVP40 which had been heated to 80ºC. One mg proteinase K was added to this suspension and incubated for 15 min at 42ºC. After adding 64 μL of 2 M KCl the samples were incubated on ice for 30 min and subsequently centrifuged for 20 min at 12,000 g. 270 μL of ice-cold 8 M LiCl was added to the supernatant in a final concentration of 2 M and the tubes were incubated overnight on ice. After centrifugation for 20 min at 12,000 g at 4ºC, the pellets were washed with 750 μL ice-cold 2 M LiCl. The samples were centrifuged for 10 min at 10,000 g at 4ºC and the pellets were re-suspended in 100 μL DEPC treated water. The samples were cleaned with phenol chloroform and treated with DNAse (RQ1 DNase, Promega).
RNA was processed for RNA-seq using mRNA enrichment polyA capture (Illumina). The RNA-seq library was prepared for sequencing with strand-specific cDNA synthesis using random hexamer priming.

treatment_protocol: Several flowers were tagged in every plant of all genotypes just before anthesis to allow follow up on days after pollination (DAP). For each round of experiments plants were grown together and seeds were harvested from 12 DAP to 26 DAP in 2 days intervals. For each sample four biological replicates were used, and each biological replicate consisted of 4 to 6 siliques. Fresh siliques were immediately dissected, and the seeds were carefully removed. The samples for RNA extraction were frozen in liquid nitrogen and stored at -80°C. For extraction, three replicates of a pool of seeds from 4 siliques for each treatment were homogenized. The experiment was repeated 3 times, we refer to the different experiments as rounds 1 to 3. Round 1 consisted of pre-tests, and only RNA-Seq data of experimental rounds 2 and 3 is shared, as batch A and batch B, respectively.

value: Seed

tag: accession

value: wild-type

tag: genetic modification

tag: maturation stage

value: dry-stage

tag: batch

value: A

tag: experimental round

tag: replicate


title: Spleen, 5mg-kg LPS, m6, d0.5

description:
SP_d0.5_6
Spleen_cpm_counts.txt


title: F1.KPN.SIP.b1

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

institute: Amsterdam UMC

description:
F1.KPN.SIP.b1
RKA205ASIP

data_processing:
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
After log2 transformation and quantile normalization, data were visualized using PCA plots to assess the quality of data after alignment and possible batch effects.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

molecule: total RNA

source_name: Small Intestine

growth_protocol: Intestinal organoids were maintained in Advanced DMEM/F12 (ADF) media supplemented with penicillin (100ug/ml), 5ml 200 mM Glutamax, 5ml 10mM Hepes, B27 supplement (Invitrogen) and N2 supplement (Invitrogen). In addition to ADF we also use 50ng/ml recombinant Mouse EGF (Tebu-BIO), mouse Noggin-FC supernatant (~100ng/ml) and R-Spondin-FC supernatant(~ 500ng/ml). Cultures were maintained at 37 degrees celsius and checked monthly for mycoplasma contamination.

extract_protocol:
RNA was isolated using Bioke Nucleospin RNA isolation kit (Bioke) according to the manufacturer’s protocol. DNA degradation was performed using Bioke RNase-Free DNase. We assessed the quality of our RNA samples using Agelent 2100 Bioanalyzer (Agilent Technologies) and only high quality RNA samples were selected based on RIN value.
The organoid RNAseq libraries were prepared using KAPA mRNA HyperPrep (Roche) following the manufacturer’s protocol. They were barcoded, quantified using the Qubit DNA HS kit from Thermofisher and Tapestation 4200 from Agilent, pooled and multiplex sequencing was performed on the Illumina Novaseq6000 platform.

value: Small Intestine

tag: cell type

value: In Vitro organoids

value: KPN


title: D425 cells, DMSO, 72 hours, replicate 1, RNAseq

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: processed_file: PLX240095_assay_data.csv: DMSO_1_D425

organism: Homo sapiens

source_name: Myc-amplified medulloblastoma

tag: cell line

tag: timepoint


title: Seeds, Col-0, 24d after pollination, Batch A, rep2


title: Seeds, Col-0, 24d after pollination, Batch A, rep1


title: Spleen, 5mg-kg LPS, m5, d0.5

description:
SP_d0.5_5
Spleen_cpm_counts.txt


title: D425 cells, Atuveciclib, 72 hours, replicate 3, RNAseq

description: processed_file: PLX240095_assay_data.csv: Atuv_3_D425

value: Atuveciclib


title: F1.AP.CO.b1

description:
F1.AP.CO.b1
RCB241ACO

source_name: Colon

value: Colon

value: AP


title: Spleen, CTRL, m4, d0.5

description:
SP_d0.5_4
Spleen_cpm_counts.txt

value: PBS


title: D425 cells, Atuveciclib, 72 hours, replicate 2, RNAseq

description: processed_file: PLX240095_assay_data.csv: Atuv_2_D425

value: Myc-amplified medulloblastoma


title: F1.AP.SIP.a1

description:
F1.AP.SIP.a1
RCB231BSIP


title: Seeds, Col-0, 22d after pollination, Batch A, rep3


title: Spleen, 5mg-kg LPS, m8, d0.5

description:
SP_d0.5_8
Spleen_cpm_counts.txt


title: Seeds, Col-0, 22d after pollination, Batch A, rep2


title: Spleen, CTRL, m3, d0.5

description:
SP_d0.5_3
Spleen_cpm_counts.txt


title: F1.AP.CO.a1

description:
F1.AP.CO.a1
RCB231BCO


title: D425 cells, Atuveciclib, 72 hours, replicate 1, RNAseq

description: processed_file: PLX240095_assay_data.csv: Atuv_1_D425


title: Spleen, CTRL, m2, d0.5

description:
SP_d0.5_2
Spleen_cpm_counts.txt


title: D425 cells, DMSO, 72 hours, replicate 2, RNAseq

description: processed_file: PLX240095_assay_data.csv: DMSO_2_D425

value: DMSO


title: D458 cells, DMSO, 72 hours, replicate 2, RNAseq

description: processed_file: PLX249015_assay_data.csv: DMSO_2_D458

value: 72 hours


title: Seeds, Col-0, 22d after pollination, Batch A, rep1


title: Seeds, Col-0, 20d after pollination, Batch A, rep3


title: Spleen, CTRL, m1, d0.5

description:
SP_d0.5_1
Spleen_cpm_counts.txt

value: Spleen


title: F1.AKP.SIP.a1

description:
F1.AKP.SIP.a1
RCB164ASIP

value: AKP


title: D458 cells, DMSO, 72 hours, replicate 1, RNAseq

description: processed_file: PLX249015_assay_data.csv: DMSO_1_D458


title: Seeds, Col-0, 20d after pollination, Batch A, rep2


title: D458 cells, DMSO, 72 hours, replicate 3, RNAseq

description: processed_file: PLX249015_assay_data.csv: DMSO_3_D458


title: Liver, TNFKO + 5mg-kg LPS, m12, d0.5

description:
LI_d0.5_12
Liver_cpm_counts.txt

source_name: Liver

value: Liver

value: 12 hours

value: 5mg-kg LPS


title: F1.AKP.CO.a1

description:
F1.AKP.CO.a1
RCB164ACO


title: D458 cells, Atuveciclib, 72 hours, replicate 3, RNAseq

description: processed_file: PLX249015_assay_data.csv: Atuv_3_D458


title: F1.AP.SIP.b1

description:
F1.AP.SIP.b1
RCB241ASIP


title: D458 cells, Atuveciclib, 72 hours, replicate 2, RNAseq

description: processed_file: PLX249015_assay_data.csv: Atuv_2_D458


title: F1.AP2.SIP.b1

description:
F1.AP2.SIP.b1
RCB162DSIP


title: Seeds, Col-0, 20d after pollination, Batch A, rep1

value: Seed

value: wild-type


title: Liver, TNFKO + 5mg-kg LPS, m10, d0.5

description:
LI_d0.5_10
Liver_cpm_counts.txt


title: Seeds, Col-0, 18d after pollination, Batch A, rep3

value: A


title: F1.AP2.CO.b1

description:
F1.AP2.CO.b1
RCB162DCO

value: In Vitro organoids


title: Liver, TNFKO + 5mg-kg LPS, m9, d0.5

description:
LI_d0.5_9
Liver_cpm_counts.txt


title: Liver, TNFKO + 5mg-kg LPS, m11, d0.5

description:
LI_d0.5_11
Liver_cpm_counts.txt


title: D458 cells, Atuveciclib, 72 hours, replicate 1, RNAseq

description: processed_file: PLX249015_assay_data.csv: Atuv_1_D458


title: F1.AKP.SIP.b1

description:
F1.AKP.SIP.b1
RCB221ESIP

value: Small Intestine


title: Seeds, Col-0, 18d after pollination, Batch A, rep2


title: Liver, 5mg-kg LPS, m8, d0.5

description:
LI_d0.5_8
Liver_cpm_counts.txt


title: F1.AP2.SIP.a1

description:
F1.AP2.SIP.a1
RCB161BSIP


title: Seeds, Col-0, 18d after pollination, Batch A, rep1


title: F1.AP2.CO.a1

description:
F1.AP2.CO.a1
RCB161BCO


title: Liver, 5mg-kg LPS, m7, d0.5

description:
LI_d0.5_7
Liver_cpm_counts.txt


title: PASMC_PAH_siACLY_3

city: Quebec city

first: Francois

last: Potus

address: 2725 Ch Ste-Foy

country: Canada

institute: IUCPQ-Laval university

data_processing:
Sequenced reads were mapped to the human genome assembly (GRCh38) with STAR v2.6.1a
The quantification of the transcriptome-mapped reads was perfomred using FeatureCounts
The raw counts generated from rsem were normalized using DESEQ2
Assembly: hg38
Supplementary files format and content: CSV files including raw or normalized counts for each sample

source_name: Pulmonary artery smooth muscle cell

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen), according to the manufacturer’s instructions. RNA quality was checked, and RNA was quantified using a NanoDrop spectrophotometer.
RNA libraries were prepared using the TruSeq® Stranded mRNA Library

value: Pulmonary artery smooth muscle cell

value: Pulmonary artery hypertension, ACLY knockdown

value: siACLY


title: Seeds, Col-0, 16d after pollination, Batch A, rep3


title: Liver, 5mg-kg LPS, m6, d0.5

description:
LI_d0.5_6
Liver_cpm_counts.txt


title: PASMC_PAH_siSCR_2

value: Pulmonary artery hypertension, scrambled control

value: siSCR


title: Seeds, Col-0, 16d after pollination, Batch A, rep2


title: Cochlea, cisplatin, 4hour, rep 2

city: Winnipeg

first: Britt

last: Drögemöller

state: Manitoba

address: 309C-745 Bannatyne Avenue

department: Biochemistry and Medical Genetics

institute: University of Manitoba

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the the 10X Genomics Cell Ranger software v7.2.0. We used “cellranger count” to align the reads, assign them to cells, and for quantification. More details can be found at https://www.10xgenomics.com/support/software/cell-ranger/latest
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 and raw_feature_bc_matrix.h5 from 10x Genomics “cellranger count”

molecule: nuclear RNA

source_name: cochlea

extract_protocol:
Nuclei were isolated using 10X Genomics' Chromium Nuclei Isolation Kit.
snRNA-seq was conducted using 10X Genomics' Single Cell GEX & Fixed RNA Profiling Kit.

value: cochlea

tag: strain

value: CBA/CaJ

tag: developmental stage

value: cisplatin treatment


title: Cochlea, cisplatin, 4hour, rep 1

description: 10X Genomics


title: PASMC_PAH_siACLY_2


title: Seeds, Col-0, 16d after pollination, Batch A, rep1


title: Liver, CTRL, m4, d0.5

description:
LI_d0.5_4
Liver_cpm_counts.txt

value: PBS


title: Cochlea, control, 4hour, rep 2

description: 10X Genomics

value: saline control


title: PASMC_PAH_siSCR_1


title: Cochlea, control, 4hour, rep 1

description: 10X Genomics


title: Liver, CTRL, m3, d0.5

description:
LI_d0.5_3
Liver_cpm_counts.txt

value: Liver

value: 12 hours


title: Seeds, Col-0, 14d after pollination, Batch A, rep2

value: Seed


title: PASMC_PAH_siACLY_1


title: Seeds, Col-0, 14d after pollination, Batch A, rep3

value: wild-type


title: PASMC_PAH_siSCR_3


title: Liver, CTRL, m1, d0.5

description:
LI_d0.5_1
Liver_cpm_counts.txt


title: Liver, CTRL, m2, d0.5

description:
LI_d0.5_2
Liver_cpm_counts.txt


title: KO2_1

city: Hangzhou

first: Lixiao

last: Zhou

address: Yuhangtang road

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
The raw paired end reads were trimmedand quality controlled byfastp with default parameters.
Assembly: Clean reads were separately aligned to reference genome GRCm39 witGRCm39.h orientation mode using HISAT2 software.The mapped reads of each sample were assembled by StringTie in are ference-based approach.
Supplementary files format and content: text file
Library strategy: CUT&TAG

molecule: genomic DNA

source_name: brain

extract_protocol:
Cells were vollected and 1 ml of 1 XHB buffer was added into the tissue sample, grinding and filtering, filtrate centrifuged at 4℃ 500×g for 5 min, supernatant was discarded, density gradient centrifugation for 10 min, nucleus suspension was obtained and counted with LUNA-FL. CUT&Tag library was performed as the protocol provided by the kit. Briefly, the cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation. DNA sequence is tagmented,  with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPure.
The RNA-seq transcriptome library of wild-type NSPCs or Mina53-KO NSPCs was prepared following Illumina®Stranded mRNA Prep,Ligation(SanDiego, CA) using1μgof totalRNA. mRNAwas isolated according to poly A selectionmethodby oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300bp on2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase(NEB) for 15 PCR cycles.

value: brain

value: NSPCs

value: non


title: KO2_2


title: CASMC_CAD_siACLY_4

source_name: Coronary artery smooth muscle cell

value: Coronary artery smooth muscle cell

value: Coronary artery disease, ACLY knockdown


title: IRF2BP2

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Trim_galore was first applied to the raw fastq files with default parameters.
Data was mapped to the hg38 genome using bowtie2 allowing for a maximum of 1 mismatch in alignment.
Using samtools, unmapped reads were dropped and converted to a bam file. This was sorted, duplicate reads removed, reads that were not uniquely mapped removed, and the file was indexed
Bigwig file was generated using bamCoverage from deeptools with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Adipose

extract_protocol:
Sonicated input sample (10% of total chromatin) was saved and subjected to crosslink reversing and column purification. Sonicated chromatin samples were incubated overnight at 4°C with IRF2BP2 antibody in 1 ml ChIP buffer (50 mM HEPES pH 7.8, 140 mM NaCl, 1% Triton X-100, 0.1% Na-Deoxycholate and Complete protease inhibitor). IP was washed and then eluted by incubation at 65°C overnight in 50 μl ChIP elution buffer (50 mM Tris pH 7.5, 10 mM EDTA, 1% SDS) with 10 mM DTT. Beads were pelleted and the supernatant was transferred to a new tube. DNA was subsequently isolated by columns (NucleoSpin, Takara).
For ChIP-seq, ∼10 ng of ChIP DNA was prepared for sequencing according to the amplification protocol from Illumina.  ChIP-Seq libraries were prepared from formaldehyde-crosslinked hMSCs, using approximately 2–8 million cells per condition, depending on the abundance of the factor of interest.

treatment_protocol: Cells were treated with the differentiation cocktail of insulin, dexamethasone, and IBMX for 24 h prior to chromatin collection.

value: Adipose

value: adipocyte precursor cells


title: Seeds, Col-0, 12d after pollination, Batch A, rep3

value: A


title: Seeds, Col-0, 12d after pollination, Batch A, rep2


title: Liver, 5mg-kg LPS, m5, d0.5

description:
LI_d0.5_5
Liver_cpm_counts.txt

value: 5mg-kg LPS


title: WT2_1

value: WT


title: CASMC_CAD_siSCR_3

value: Coronary artery disease, scrambled control

value: siSCR


title: Seeds, Col-0, 12d after pollination, Batch A, rep1


title: CASMC_CAD_siACLY_3

value: siACLY


title: HepG2 cells, FXRDE5, 48 hours, replicate 3

city: Clermont-Ferrand

first: David

middle: H

last: VOLLE

address: 28 place Henri Dunant

country: France

institute: INSERM

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: hg38
Supplementary files format and content: raw, normalized, normalized and divided by median of transcripts length in kb

growth_protocol: Human HepG2 (hepatocellular carcinoma) cells were cultured in 10 cm plates in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
For RNA sequencing, human HepG2 hepatocarcinoma cell total RNA was extracted using Nucleospin RNA isolation kit (Macherey-Nagel SAS)
RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Not applicable

value: Liver

value: Hepatocyte

value: overexpression of FXRDE5


title: KO_3

data_processing:
The raw paired end reads were trimmedand quality controlled byfastp with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.The mapped reads of each sample were assembled by StringTie in are ference-based approach.
Assembly: GRCm39
Supplementary files format and content: text file

extract_protocol:
Total RNA was extracted from the wild-type NSPCs or Mina53-KO NSPCs using TRIzol Reagent (Takara) according the manufacturer’s instructions. Then RNA quality was determined by 5300Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0,>1μg) was used to construct sequencing library.
The RNA-seq transcriptome library of wild-type NSPCs or Mina53-KO NSPCs was prepared following Illumina®Stranded mRNA Prep,Ligation(SanDiego, CA) using1μgof totalRNA. mRNAwas isolated according to poly A selectionmethodby oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300bp on2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase(NEB) for 15 PCR cycles.


title: CASMC_CAD_siSCR_2


title: HepG2 cells, FXRDE5, 48 hours, replicate 2


title: HFD mice treated with control siRNA and gavaged with KHK inhibitor, rep4

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
We aligned the adapter-trimmed reads to the genome using STAR aligner with the two-pass option and estimated expression using RSEM.
Assembly: mm39
Supplementary files format and content: TSV of gene counts

source_name: liver

growth_protocol: RNA was isolated from the liver of our experimetnal mice

extract_protocol:
mRNA was purified using RNeasy Mini Kit columns
cDNA was made using High Capacity cDNA Reverse Transcription Kit

treatment_protocol: The mice were treated either with KHK siRNA or KHK inhibitor

value: liver

value: C57Bl6 mice

value: KHK inhbitor


title: KO_2

value: brain

value: NSPCs

value: non


title: HFD mice treated with control siRNA and gavaged with KHK inhibitor, rep3


title: KO_1


title: HepG2 cells, FXRDE5, 48 hours, replicate 1


title: HepG2 cells, FXR1a, 48 hours, replicate 3

value: overexpression of FXRa1


title: CASMC_CAD_siSCR_1

value: Coronary artery smooth muscle cell


title: CASMC_CAD_siACLY_2

value: Coronary artery disease, ACLY knockdown


title: CASMC_CAD_siSCR_4


title: Seeds, Col-0, 14d after pollination, Batch A, rep1

value: Seed

value: wild-type

value: A


title: WT_3

value: WT


title: HFD mice treated with control siRNA and gavaged with KHK inhibitor, rep2


title: HepG2 cells, FXR1a, 48 hours, replicate 2


title: WT_2


title: CASMC_CAD_siACLY_1

value: siACLY


title: WT2_2


title: HepG2 cells, FXR1a, 48 hours, replicate 1

value: Liver


title: Severely degeneration, replicate 3, scRNA-seq

city: Jining

first: Shu

last: Jia

state: Shandong

address: No. 133, Hehua Road, Taibai Lake New District, Jining City

department: Clinical Research Team for Spinal Cord Disorders

institute: Affiliated Hospital of Jining Medical University

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.10.0 with default parameters. Uniquely mapped reads were then assigned to exons with FeatureCounts (v2.0.1).
Successfully assigned reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Nucleus pulposus

extract_protocol:
The nucleus pulposus tissues were dissociated into single cell suspension with a Singleron PythoNTM Automated Tissue Dissociator and sCelLiveTM Tissue Dissociation Mix. Cell viability was determined by trypan blue staining and evaluated by microscopy. Samples with >80% cell viability were continued for subsequent experiments.
Single-cell suspensions were loaded onto microfluidic chips to obtain a single cell per  microwell. ScRNA-seq libraries were constructed by GEXSCOPE Single-Cell Sequencing Kit and Singleron Matrix Automated single-cell processing system. Individual libraries were diluted to 4 ng/µL and pooled for sequencing on Illumina novaseq 6000 with 150 bp paired end reads.

value: Nucleus pulposus

value: Nucleus pulposus cells

value: Wild


title: HFD mice treated with KHK siRNA and gavaged with methylcellulose control, rep4

value: liver

value: C57Bl6 mice

value: KHK siRNA


title: HepG2 cells, control, 48hours, replicate 2

value: Hepatocyte


title: WT_1

value: brain

value: NSPCs

value: non


title: HFD mice treated with control siRNA and gavaged with KHK inhibitor, rep1

value: KHK inhbitor


title: Severely degeneration, replicate 2, scRNA-seq


title: HFD mice treated with KHK siRNA and gavaged with methylcellulose control, rep3


title: HepG2 cells, control, 48hours, replicate 1


title: Severely degeneration, replicate 1, scRNA-seq


title: draining lymph node Treg of control mouse 3

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

data_processing:
The sequences which passed QC were mappted to mm10 using Hisat2.
Htseq was used to obtain gene expression counts.
DESeq2 was used to normalize gene counts and differentially expressed gene detection.
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for every sample.
Supplementary files format and content: Diffentially expressed gene analysis between synovial Tregs and draining lymph node Tregs of arthritis mice.

source_name: lymph node

extract_protocol:
Total RNA was extracted using Trizol reagent.
The libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Collagen-induced arthritis was induced as previously described (PMID: 35659346). Paws and draining lymph nodes were digested and Treg cells were sorted based on Foxp3-reporter YFP expression using a cell sorter.

value: lymph node

value: regulatory T cell

value: no treatment


title: HepG2 cells, FXRDE5, 24 hours, replicate 3

value: overexpression of FXRDE5


title: draining lymph node Treg of control mouse 2

value: WT


title: HFD mice treated with KHK siRNA and gavaged with methylcellulose control, rep1


title: Mildly degeneration, replicate 3, scRNA-seq


title: HepG2 cells, FXRDE5, 24 hours, replicate 2

value: Liver


title: draining lymph node Treg of control mouse 1


title: HFD mice treated with control siRNA and gavaged with methylcellulose control, rep4

value: HFD control


title: Mildly degeneration, replicate 2, scRNA-seq

value: Nucleus pulposus

value: Nucleus pulposus cells


title: HepG2 cells, FXRDE5, 24 hours, replicate 1


title: draining lymph node Treg of arthritis mouse  2

value: collagen-induced arthritis


title: draining lymph node Treg of arthritis mouse  3


title: HFD mice treated with control siRNA and gavaged with methylcellulose control, rep3

value: liver

value: C57Bl6 mice


title: Mildly degeneration, replicate 1, scRNA-seq

value: Wild


title: HepG2 cells, FXR1a, 24 hours, replicate 3

value: Hepatocyte

value: overexpression of FXRa1


title: DLD1 cultured in lipoprotein defecient serum treated with 3 uM Ivermectin for 24 h replicate 3

city: Adelbert Rd

first: Matthew

last: Atala Pleshinger

state: Ohio

institute: Case Western Reserve University

data_processing:
Alligned using Kallisto and TPMs were quantified. edgeR was used for differential gene expression
Assembly: hg38

source_name: Colorectal

extract_protocol:
Qiagen Rneasy mini kit, 4 ug of total RNA
Submitted to Azenta Life Sciences for library contruction

value: Colorectal

value: colorectal adenocarcinoma


title: HepG2 cells, FXR1a, 24 hours, replicate 2


title: draining lymph node Treg of arthritis mouse  1

value: lymph node


title: HFD mice treated with control siRNA and gavaged with methylcellulose control, rep1


title: synovial Treg of arthritis mouse 3

source_name: synovium

value: synovium

value: regulatory T cell


title: HFD mice treated with control siRNA and gavaged with methylcellulose control, rep2


title: HepG2 cells, FXR1a, 24 hours, replicate 1


title: synovial Treg of arthritis mouse 2


title: HepG2 cells, control, 24hours, replicate 2


title: DLD1 cultured in lipoprotein defecient serum treated with 3 uM Ivermectin for 24 h replicate 1


title: DLD1 cultured in lipoprotein defecient serum treated with 3 uM Fenretinide for 24 h replicate 3


title: chow mice treated with control siRNA and gavaged with methylcellulose control, rep3

value: Chow control


title: HFD mice treated with KHK siRNA and gavaged with methylcellulose control, rep2

value: KHK siRNA


title: chow mice treated with control siRNA and gavaged with methylcellulose control, rep4


title: DLD1 cultured in lipoprotein defecient serum treated with 3 uM Fenretinide for 24 h replicate 2

value: WT


title: chow mice treated with control siRNA and gavaged with methylcellulose control, rep2


title: pineal glands, puberty

city: Hefei

first: Bochao

last: Zhang

state: Anhui Province

address: No. 130 West Changjiang Road, Shushan District

institute: Anhui Agricultural University

data_processing:
The library was sequenced on Illumina Novaseq platform. Image analysis and base calling were performed with Illumina CASAVA pipeline, and finally generated 150bp paired-end reads.
First of all, we used FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through fastp (fastp 0.20.0). The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. Finally, we used FastQC to perform basic statistics on the quality of the clean data reads.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail).
Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng, Hao Wu, 2014; Hao Wu, 2015; Yongseok Park Hao Wu,2016) , The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
Assembly: ARS1.2
Supplementary files format and content: mC_level_Identification_stat.txt

organism: Capra hircus

source_name: pineal glands

extract_protocol:
Genomic DNA degradation and contamination was validated by agarose gels. DNA purity was checked using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: pineal glands

tag: Sex

value: Female

value: puberty

value: untreated


title: testis, 1700052I22Rik_KO_3

city: Beijing

first: Mengzhen

last: Li

address: 5 DONG DAN SAN TIAO

institute: Peking Union Medical College

data_processing:
libraryquantification was performed using the Qubit high sensitivity assay, while quality 354 control was conducted using Agilent 2100 bioanalyzer or Fragment Analyzer 5300; 355 the final library has an average size of ~350 bp. The libraries were sequenced on an 356 Illumina NovaSeq platform to generate 150-bp paired-end reads. Sequence reads were 357 mapped to the mouse genome (version mm10) using the HISAT2 (v2.0.0).
Assembly: the mouse genome (version mm10)
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: testis

extract_protocol:
RNA was harvest with TriZOl.
Sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep 352 Kit for Illumina by following the manufacturer’s recommendations.

tag: tissue

value: testis


title: chow mice treated with control siRNA and gavaged with methylcellulose control, rep1

value: liver

value: C57Bl6 mice


title: pineal glands, prepuberty

value: prepuberty


title: testis, 1700052I22Rik_KO_2


title: DLD1 cultured in lipoprotein defecient serum replicate 3

value: cultured in lipoprotein defecient serum


title: puberty-3

description:
gene_fpkm.txt
gene_count.txt

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Females

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Females


title: DLD1 cultured in lipoprotein defecient serum treated with 3 uM Ivermectin for 24 h replicate 2

value: Colorectal

value: colorectal adenocarcinoma


title: DLD1 cultured in lipoprotein defecient serum replicate 2


title: puberty-2

description:
gene_fpkm.txt
gene_count.txt


title: testis, 1700052I22Rik_KO_1


title: DLD1 cultured in lipoprotein defecient serum replicate 1


title: puberty-1

description:
gene_fpkm.txt
gene_count.txt


title: DLD1 cultured in 10% FBS replicate 3

value: cultured in 10% FBS


title: DLD1 cultured in 10% FBS replicate 2


title: HepG2 cells, control, 24hours, replicate 1

value: Liver

value: Hepatocyte


title: testis, WT_1


title: prepuberty-3

description:
gene_fpkm.txt
gene_count.txt


title: synovial Treg of arthritis mouse 1

value: synovium

value: regulatory T cell

value: collagen-induced arthritis


title: DLD1 cultured in 10% FBS replicate 1

value: WT


title: GIC52, Input, ChIP

status: Public on Nov 13 2024

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

data_processing:
TrimGalorev0.6.5 was used to remove low-quality and adapter sequences (Phred score < 20 removed)
Alignment to the Ensembl GRCh38 human reference genome was performed via Bowtie v2.3.4
Santools v1.10 was used to convert SAM files to BAM files, and then to remove unmapped reads, secondary alignments, and keep mapped reads with a score > 10
Deeptools algorithm; bamCoverage was used to generate bigwig files for each sample from bam files
Deeptools algorithm; bamCompare was used to generate bigwig files for each sample relative to Input samples (vsInput.bw)
Assembly: Human ensembl GRCh38 release 87
Supplementary files format and content: bigwig

source_name: Primary Glioblastoma Inititating Cells

growth_protocol: GIC cells were cultured on laminin-coated plates in NeuroCult NS-A proliferation kit media (Stem Cell Technologies) supplemented with 1% penicillin/streptomycin solution heparin (2µg/ml), mEGF (20ng/ml) and hFGF (10ng/ml) and iNSC were cultured in geltrex-coated plates in Neurobasal 0.5X, Advanced™ DMEM⁄F-12 0.5X, supplemented with 1% penicillin/streptomycin solution and neural induction supplement (Gibco)

extract_protocol:
Cells were fixed with formaldehyde-based fixing solution and lysed with provided lysis solution supplemented with protease inhibitors. Nuclei pellets were lysed, and chromatin sonicated with Bioruptor Plus sonication device (Diagenode) to obtain DNA fragments within the recommended 200–1200-bp range. In total, 25µg of sheared chromatin was then incubated with 4µg of antibody against H3K4me3 (Diagenode, C15410003-50) H3K36me3 (abcam, ab9050), H3K27ac (abcam, ab4729) or H3K27me3 (Diagenode C15410195) overnight at 4 °C with rotation. Following incubation with Protein G agarose beads, bound chromatin was washed, eluted and purified following the manufacturer’s protocols. Validation by qPCR-ChIP on target genes was done before proceeding to sequencing.
ChIPed DNA was end-repaired, A-tailed and adapter-ligated before size selection and amplification. The obtained libraries were QC’ed and multiplexed before 75-bp paired-end sequencing on HiSeq4000 (Illumina).

treatment_protocol: GIC were isolated from fresh tumour tissue following the published protocol (Pollard et al., 2009) and fibroblast from a small strips of dura mater. Fibroblasts were then reprogrammed into EPSCs, which were induced into iNSC following manufactured protocol (Gibco, #A1647801).

value: Primary Glioblastoma Inititating Cells


title: GIC50, Input, ChIP


title: GIC61, Input, ChIP


title: prepuberty-2

description:
gene_fpkm.txt
gene_count.txt

value: untreated


title: STm, 1P, ChIP

city: Suwon

first: Eunsuk

last: Kim

address: 206 World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University

data_processing:
Raw FASTQ files were aligned to the S. Typhimurium 14028 reference genome (Accession No: CP001362.1, CP001363.1) using Burrows–Wheeler Aligner (Version 0.7.17) of global alignment mode.
The aligned reads were sorted using SAMtools (version 1.11) and duplicates were removed using Picard Tools (Version 2.21.1)
Peak calling was conducted using MACS2 (Version 2.2.7.1), with the significance cut-off q-value <=0.05
Assembly: Accession No: CP001362.1, CP001363.1
Supplementary files format and content: narrowPeak

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: cell culture

growth_protocol: Cultured in LB broth up to mid-log phase at 37°C

extract_protocol:
At the mid-log growth phase, chromatin cross-linking was performed using 1% formaldehyde for 20 min and quenched with 125 mM glycine. Cell disruption and DNA shearing was conducted using a sonicator.
The whole-genome library was prepared using the TruSeq ChIP Library Preparation Kit according to the manufacturer’s guidelines. The size and quality of the libraries were assessed using the TapeStation system with high-sensitivity D5000 screen tape.

tag: serovar

value: Typhimurium

value: cell culture


title: DLD1 cultured in lipoprotein defecient serum treated with 3 uM Fenretinide for 24 h replicate 1


title: GIC54, Input, ChIP


title: GIC31, Input, ChIP


title: egfp-3_Ribo

city: 杭州市

first: li

last: yucong

state: 浙江省

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

library_source: other

data_processing:
aligned to the S. mediterranea reference transcriptome smed_2010614
Assembly: S. mediterranea reference transcriptome (smed_20140614)
Supplementary files format and content: txt file with counts of each sample
Library strategy: Ribo-seq

molecule: other

organism: Schmidtea mediterranea

source_name: head, trunk, tail

extract_protocol: The RPF library was constructed by End Repair, linker ligation, Reverse Transcription, Circularize the cDNA ,and PCR amplification. RNA-seq libraries were constructed with a VAHTS Total RNA-seq (H/M/R) Library Prep Kit.

value: head, trunk, tail

value: egfp knockdown

value: RNAi


title: egfp-2_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC61, Input, ChIP

source_name: iPSC-derived induced Neural Stem Cells

value: iPSC-derived induced Neural Stem Cells


title: GIC30, Input, ChIP


title: GIC26, Input, ChIP


title: egfp-2x-3_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: egfp_2x knockdown


title: GIC19, Input, ChIP


title: GIC18, Input, ChIP


title: egfp-2x-2_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: RYBP.rat.CM

city: Guangzhou

first: Chao

last: Wei

address: No.74 Zhongshan Rd.2

institute: Sun Yat-Sen University

data_processing:
The Fastq data underwent quality checking using trim_galore
subsequent alignment of paired-end reads to the Rnor_6.0 reference genome
Assembly: Rnor_6.0
Supplementary files format and content: NO
Supplementary files format and content: NO

organism: Rattus norvegicus

source_name: heart

growth_protocol: cardiomyocytes were cultured in ESC medium containing DMEM (Hyclone), 10% (v/v) fetal bovine serum (FBS, Hyclone) in 37 C, 5% CO2 incubator.

extract_protocol: ChIP-seq was performed according the manufacture's protocol

treatment_protocol: cardiomyocytes were isolated from newborn rat heart

value: heart

value: NO

value: cardiomyocyte

value: control


title: Input.rat.CM


title: testis, WT_3

value: testis


title: testis, WT_2


title: GIC17, Input, ChIP


title: egfp-1_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: fbl-2_3_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: fbl-2 knockdown


title: iNSC31, Input, ChIP


title: iNSC54, Input, ChIP


title: egfp-2x-1_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC30, Input, ChIP


title: fbl-2_1_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC19, Input, ChIP


title: iNSC50, Input, ChIP


title: fbl-1_3_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: fbl-1 knockdown


title: iNSC52, Input, ChIP


title: prepuberty-1

description:
gene_fpkm.txt
gene_count.txt

value: Females


title: fbl-2_2_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC26, Input, ChIP


title: fbl-1_2_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: fbl-1_1_Ribo

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC17, Input, ChIP


title: iNSC61, H3K4me3, ChIP


title: iNSC18, Input, ChIP


title: iNSC52, H3K4me3, ChIP


title: egfp-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

data_processing:
aligned to the S. mediterranea reference transcriptome smed_2010614
Assembly: S. mediterranea reference transcriptome (smed_20140614)
Supplementary files format and content: txt file with counts of each sample


title: iNSC31, H3K4me3, ChIP


title: iNSC54, H3K4me3, ChIP


title: fbl-2_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC26, H3K4me3, ChIP


title: iNSC50, H3K4me3, ChIP


title: egfp-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: egfp-2x-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC18, H3K4me3, ChIP


title: iNSC17, H3K4me3, ChIP


title: egfp-2x-2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC30, H3K4me3, ChIP


title: iNSC19, H3K4me3, ChIP


title: fbl-2_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: fbl-1_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: WFBL2_3.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

data_processing:
fastaq RNA-seq data adapter trimming by fastap
Assembly: 18s28sribosome.fa
Supplementary files format and content: processed files include raw counts for each sample after  adapter trimming by fastap
Library strategy: RiboMeth-Seq

extract_protocol:
RNA was harvested using TRIGene Reagent(Genstar Cat#ZP118-101S). 3 μg of total RNA was used for the construction of sequencing libraries.
NEBNext Small RNA Library kit for library preparation


title: egfp-2x-1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC61, H3K36me3, ChIP


title: fbl-1_2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: fbl-2_1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC54, H3K36me3, ChIP


title: iNSC52, H3K36me3, ChIP


title: WFBL2_2.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: WFBL2_1.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: egfp-3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: W4xGFP_3.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC30, H3K36me3, ChIP


title: iNSC50, H3K36me3, ChIP


title: iNSC31, H3K36me3, ChIP


title: iNSC26, H3K36me3, ChIP


title: W4xGFP_2.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: W4xGFP_1.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC18, H3K36me3, ChIP


title: WFBL1_3.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: WFBL1_2.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC61, H3K27ac, ChIP


title: WFBL1_1.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC54, H3K27ac, ChIP


title: iNSC52, H3K27ac, ChIP


title: W2xGFP_2.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: iNSC50, H3K27ac, ChIP


title: iNSC31, H3K27ac, ChIP


title: iNSC30, H3K27ac, ChIP


title: W2xGFP_1.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: W2xGFP_3.fq.gz

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Human aortic smooth muscle cells,OE-p-414aa,48hour,rep3

city: haikou

first: shaoguang

last: sun

state: hainan

address: No. 3 Xueyuan Road

institute: hainan medical university

description: FPKM_ p-414aa-rep3

data_processing:
Rawdata(or Rawr eads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality(low quality, the number of lines with a string quality value  less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information can not be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference  genome with orientation mode using HISAT2 software to obtain mapped reads.
Feature Counts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Ensembl
Supplementary files format and content: The xls file includes the raw counts for each sample.
Supplementary files format and content: The xls file include FPKM values for each Sample

source_name: aorta

growth_protocol: Human aortic smooth muscle cells (HASMCs) (ScienCell) were cultured in Smooth Muscle Cell Medium (ScienCell) with additions of 2% fetal bovine serum (FBS, ScienCell), 1% Smooth Muscle Cell Growth Supplement (ScienCell), and 1% penicillin/streptomycin solution (ScienCell),at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNAwas extracted from the HASMCs using TRIzol® Reagent according the manufacturer’s instructions (Magen).
Paired-end libraries were prepared using a Abclonal mRNA-seq Lib Prep Kit (ABclonal) following the manufacturer’s instructions.

treatment_protocol: HASMCs were transfected with either the pcDNA3.1-EGFP plasmid or the pcDNA3.1(+) plasmid overexpressing p-414aa using GP-transfect-Mate (GenePharma). The cells were then cultured for 48 hours.

value: aorta

value: HASMC

value: Human aortic smooth muscle cells

value: WT

value: overexpression of p-414aa protein


title: iNSC26, H3K27ac, ChIP


title: HeLa, RAP80, ChIP, 20h

first: jie

last: Wang

state: Beijing

address: 5 Summer Palace Road, Haidian District, Beijing

institute: school of Life science

data_processing:
Adapters and low quality reads were trimmed from raw fastq reads using fastp v0.23.2.
Clean reads were aligned to the human genome hg38 using Bowtie2 v2.5.3.
Then mapped bam files were first sorted and then duplicates were removed using picard（GATK V4.0.0）
Peaks were called using MACS2 v2.2.9.1 and bigwig files were generated using bedGraphToBigWig v2.9.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: HeLa

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

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cells were infected with HSV-1 for 3h and 20h.

value: HeLa

value: Cervical cancer epithelial cells

tag: infection

value: anti-RAP80 (ab70822, Abcam)

tag: time


title: hESC(RUES2)-Cardiomyocyte-TDI  bio_rep2

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

description:
m5C_loci.xlsx
DESeq2_DEGs.xlsx
HTseqCount_raw.txt

data_processing:
The raw fastq file were merge into one R1 and one R2 file by Concatenate datasets tool on Galaxy web platform.
Use Trim Galore! tool remove reads with Q score less than 20 and the adaptor seqeunces. With the followed arguments: for read 1 ‘-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’ and read 2 ‘-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT’
The trimmed and quality reads were aligned to human reference genome GRCh38 (Release-100 from Ensembl website) with gene transfer format (GTF) by meRanGh align, and with arguments of maximum mismatch ratio set at 0.1 (‘-mmr 0.1’).
The SAM files were then proceed to meRanCall with arguments ‘-rl 150 -md 5 -ei 0.1 -cr 99 -fdr 0.05 -mcov 10 -mr 0.05’ to identifiy  m5C sites
The gene annotaion of m5C sites were retrieved by meRanAnnotate with arguments of ‘-f 'gene' -g Homo_sapiens.GRCh38.100.gff3‘
Assembly: hg38
Supplementary files format and content: excel file with m5C sites commonly present in preplicates
Supplementary files format and content: excel file with differential gene expression data between groups
Supplementary files format and content: tab-delimited txt files of HTseq-count reads counts of each sample

source_name: embryonic tissue

growth_protocol: All hPSCs include hiPSCs and hESC were cultured on Matrigel matrix (Corning; 354230) pre-coated cell culture dish in Stemflex medium (Thermo; A3349401). Addition of ROCK inhibitor Y27632 (10uM; Cayman; 10005583) allows cells to attach.

extract_protocol:
Total RNA was purifed with Direct-zol RNA MiniPrep kit (Zymo) and treated with DNAse I followed manufactorers instruction. Purify the poly(A) RNA sample by Dynabeads mRNA DIRECT purification kit (Thermo) with twice purification process, followed by bisulfite conversion reaction with three cycles of 70℃ 10minutes and 64℃ 45 minutes by EZ RNA methylation kit (Zymo).
The bisulfite treated mRNA samples librarires were generated with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: The hPSCs were differentiated followed the well-established 14 days protocol by Burridge et al (2014). On day 0, the RPMI-1640 medium contains B27 minus insulin supplement (Thermo; 1895201) and Wnt activator Chir99021 (5 µM; Stemcell Technology; 72054). On Day 2, medium was changed to RPMI-1640 supplemented with B27 minus insulin. On day 3, addition of Wnt inhibitor IWR-1 (5 µM; Sigma; I0161) to the medium. On day 7, addition of insulin (B27 supplement; Thermo; 17504044) to induce cardiomyocyte formation. The medium was changed every 2 days untill the completion of the 14 days protocol.

value: embryonic tissue

value: human embryonic stem cells derived cardiomyocyte

tag: genotype

value: wild-type

tag: treatment

value: TDI treatment


title: Human aortic smooth muscle cells,OE-p-414aa,48hour,rep2

description: FPKM_ p-414aa-rep2


title: iNSC19, H3K27ac, ChIP

value: iPSC-derived induced Neural Stem Cells


title: iNSC19, H3K36me3, ChIP


title: hESC(RUES2)-Cardiomyocyte-TDI  bio_rep1


title: normal tissue from patient 65

type: genomic

city: Nanchang

first: Leyan

state: Jiangxi

address: Donghu District

institute: The First Affiliated Hospital of Nanchang University

hyb_protocol: Hybridize the resuspended DNA sample with the prepared chip and place it in a hybridization oven overnight. In the process of hybridization, the fragmented DNA undergoes denaturation and anneals to 50 site-specific bases, and these 50 specific bases are connected to one of the 935,000 beads on the chip, one type of bead corresponds to the detection of one site.

scan_protocol: Put the processed chip into a scanner, use laser to excite the fluorescent group of the single-base extension product on the chip, and the scanner obtains the fluorescence emitted by the fluorescent group and generates a high-resolution picture. The data thus obtained is directly imported into GenomeStudio software for analysis, so as to obtain the methylation data of each sample.

data_processing: Idat files were imported and then preprocessed with ChAMP(version 2.29.1) package in R to get raw data. Next, the raw data was  normalized with BMIQ method.

source_name: adjacent normal tissue

label_protocol: The samples that passed the quality inspection were subjected to sulfite conversion. Under the treatment of bisulfite, unmethylated cytosine (C) was converted to uracil (U); methylated cytosine was not affected.

extract_protocol: DNA was extracted by QIAamp DNA Mini Kit following the manufacturer's instructions.

value: adjacent normal tissue


title: normal tissue from patient 126


title: Human aortic smooth muscle cells,OE-p-414aa,48hour,rep1

description: FPKM_ p-414aa-rep1


title: hESC(RUES2)-Cardiomyocyte-lac  bio_rep3

value: Glucose-Depleted and Lactate-Supplemented Conditions


title: tumor tissue from patient 65

source_name: gastric cancer tissue

value: gastric cancer tissue


title: iNSC17, H3K27ac, ChIP


title: iNSC17, H3K36me3, ChIP


title: HeLa, RAP80, ChIP, 3h


title: hESC(RUES2)-Cardiomyocyte-lac  bio_rep1


title: Human aortic smooth muscle cells,control(p-EGFP),48hour,rep3

description: FPKM_ p-EGFP-rep3

value: transfected with the control empty vector plasmid(pcDNA3.1-EGFP)


title: hAFSC-iPSC-Cardiomyocyte-TDI bio_rep3

source_name: Amniotic fluid stem cell

value: Amniotic fluid stem cell

value: AFSC-iPSC

value: Amniotic fluid stem cell-induced pluripotent stem cell


title: Human aortic smooth muscle cells,control(p-EGFP),48hour,rep2

description: FPKM_ p-EGFP-rep2

value: aorta

value: HASMC

value: Human aortic smooth muscle cells

value: WT


title: hAFSC-iPSC-Cardiomyocyte-TDI bio_rep2


title: iNSC18, H3K27ac, ChIP


title: iNSC50, H3K27me3, ChIP


title: iNSC61, H3K27me3, ChIP


title: hAFSC-iPSC-Cardiomyocyte-TDI bio_rep1


title: hAFSC-iPSC-Cardiomyocyte-lac bio_rep3


title: Tumor draining Lymh Nodes 2x4Gy 24h

first: Nektarios

last: Kostopoulos

address: 3400 Civic Center Blvd.

data_processing:
Trimmomatic v.0.36
STAR aligner v.2.5.2b
Subread package v.1.5.2
DESeq2
GeneSCF v.1.1-p2
Assembly: Mus musculus GRCm38 ERCC
Supplementary files format and content: The DESeq2 analysis results files

source_name: lymph node

growth_protocol: BALB/c mice were bearing two A20 tumors, right and left flank. Tumors were being monitored every two days.

extract_protocol:
Tumors were harvested and treated with collagenase IV fro 30 minutes in 37C. Tumors were then smashed and passed through a 70um filter. Tumor cells were spun down and resuspended in TRIzol reagent. RNA extraction was done by the manufacture's guidance.
A polyA approach was used with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina in addition to ERCC RNA Spike-In Control Mixes at a 1:1000 ratio following manufacture instructions.

treatment_protocol: When tumors reached approximately 300mm3, only the right flank tumors were irradiated with either 8Gyx1 fraction or 4Gyx2 fractions and 24h or 7 days later, both right (irradiated) and left (non-irradiated) tumors were collected for RNA seq.

tag: sample id

tag: group

value: GroupK

value: lymph node

value: lymph node cell suspension

value: BALB/c

value: Female

value: 2x4Gy RT

value: 24h post RT


title: Tumor draining Lymh Nodes 1x8Gy 24h

value: GroupJ

value: 8Gy RT


title: iNSC30, H3K27me3, ChIP

value: iPSC-derived induced Neural Stem Cells


title: hESC(RUES2)-Cardiomyocyte-TDI  bio_rep3

value: embryonic tissue

value: human embryonic stem cells derived cardiomyocyte

value: wild-type

value: TDI treatment


title: Human aortic smooth muscle cells,control(p-EGFP),48hour,rep1

description: FPKM_ p-EGFP-rep1

value: aorta

value: HASMC

value: transfected with the control empty vector plasmid(pcDNA3.1-EGFP)


title: iNSC54, H3K27me3, ChIP


title: tumor tissue from patient 126

value: gastric cancer tissue


title: tumor tissue from patient 81


title: B2_P1_Day_10_Bridge_Bots

city: Medford

first: Michael

last: Levin

address: 200 Boston Ave

department: Biology

institute: Tufts University

data_processing:
kallisto
Reads were trimmed for adapter, filtered by sequencing Phred quality (>= Q15)
aligned to the human transcriptome (Ensembl version 110) using kallisto
Assembly: human transcriptome (Emsembl version 110)
Supplementary files format and content: processed data is an RDS format file of gene counts

source_name: airway epithelium

growth_protocol: All progenitor NHBE cells were maintained in Bronchial Epithelial Growth Medium from Lonza (CC-3170) and all bots were maintained in a 50/50 mix of Bronchial Epithelial Basal Medium (CC-3171 Lonza) and DMEM with Bronchial Epithelial Growth Medium SingleQuots Supplements (CC-4175) minus Triiodothyronine and Retinoic acid (Retinoic acid was added every 2 days fresh). All conditions were incubated at 5% CO2 and 37C.

extract_protocol:
All RNA was extracted using the TRIzol following the TRIzol Reagent User Guide provided by Thermo Fisher Scientific
Illumina Stranded mRNA

treatment_protocol:
All progenitor NHBE cells were maintained and passaged as normal, no special treatment
All bots were grown from seeded NHBE cells in Matrigel for 14 days before being dissolved from the matrix. Their RNA was collected at the mentioned timepoints, 0, 10 days post-dissolution

value: airway epithelium

value: normal bronchial epithelial cells

value: WT

value: 10 day aggregates post-Matrigel


title: D1_P2_ALI_Culture_Replicate_2

value: air-liquid-interface cell culture


title: tumor tissue from patient 142


title: iNSC52, H3K27me3, ChIP


title: D2_P2_ALI_Culture_Replicate_3


title: hAFSC-iPSC-Cardiomyocyte-lac bio_rep1

value: Amniotic fluid stem cell

value: AFSC-iPSC

value: Amniotic fluid stem cell-induced pluripotent stem cell

value: Glucose-Depleted and Lactate-Supplemented Conditions


title: A2_P4_Day_10_Bots_Replicate_2

value: 10 day collection post-Matrigel


title: iNSC31, H3K27me3, ChIP

value: iPSC-derived induced Neural Stem Cells


title: hiPSCs(1103)-Cardiomyocyte-TDI bio_rep3

source_name: Peripheral blood mononuclear cell

value: Peripheral blood mononuclear cell

value: human induced pluripotent stem cell derived cardiomyocyte

value: wild-type


title: B7_P2_ALI_Culture_Replicate_1


title: normal tissue from patient 81

value: adjacent normal tissue


title: hESC(RUES2)-Cardiomyocyte-lac  bio_rep2

value: embryonic tissue

value: human embryonic stem cells derived cardiomyocyte


title: iNSC18, H3K27me3, ChIP


title: hAFSC-iPSC-Cardiomyocyte-lac bio_rep2


title: iNSC26, H3K27me3, ChIP


title: 2x4 7d NIR 210

source_name: non-irradiated tumor

value: GroupI

value: non-irradiated tumor

value: Tumor cell suspension

value: BALB/c

value: Female

value: 2x4Gy RT

value: 7d post RT


title: normal tissue from patient 142


title: 2x4 7d IR 209

source_name: irradiated tumor

value: GroupH

value: irradiated tumor


title: A1_P2_Day_10_Bots_Replicate_2

value: airway epithelium

value: normal bronchial epithelial cells

value: WT

value: 10 day collection post-Matrigel


title: A6_P2_Day_10_Bots_Replicate_1


title: iNSC17, H3K27me3, ChIP

value: iPSC-derived induced Neural Stem Cells


title: GIC61, H3K4me3, ChIP

value: Primary Glioblastoma Inititating Cells


title: hiPSCs(1103)-Cardiomyocyte-lac bio_rep3

value: Peripheral blood mononuclear cell

value: human induced pluripotent stem cell derived cardiomyocyte

value: wild-type

value: Glucose-Depleted and Lactate-Supplemented Conditions


title: iNSC19, H3K27me3, ChIP


title: C8_P4_Day_0_Bots_Replicate_3

value: immediate collection post-Matrigel


title: 2x4 7d NIR 209

value: GroupI

value: non-irradiated tumor

value: Tumor cell suspension

value: BALB/c


title: GIC54, H3K4me3, ChIP


title: 2x4 24h NIR 207

value: GroupG

value: Female

value: 2x4Gy RT

value: 24h post RT


title: A7_P4_Day_10_Bots_Replicate_1

value: airway epithelium

value: normal bronchial epithelial cells

value: WT


title: hiPSCs(1103)-Cardiomyocyte-lac bio_rep2


title: C7_P4_Day_0_Bots_Replicate_2


title: B3_P3_Day_10_Bridge_Bots

value: 10 day aggregates post-Matrigel


title: hiPSCs(1103)-Cardiomyocyte-TDI bio_rep2

value: Peripheral blood mononuclear cell

value: TDI treatment


title: 2x4 24h NIR 206


title: GIC52, H3K4me3, ChIP

value: Primary Glioblastoma Inititating Cells


title: 2x4 24h IR 208

value: GroupF

value: irradiated tumor


title: hiPSCs(1103)-Cardiomyocyte-TDI bio_rep1

value: human induced pluripotent stem cell derived cardiomyocyte

value: wild-type


title: GIC31, H3K4me3, ChIP


title: C5_P2_Day_0_Bots_Replicate_2

value: immediate collection post-Matrigel


title: 2x4 24h NIR 208

value: non-irradiated tumor

value: Tumor cell suspension

value: BALB/c


title: 2x4 7d IR 210

value: GroupH

value: Female

value: 2x4Gy RT

value: 7d post RT


title: C4_P4_Progenitor_Cells_Replicate_2

value: airway epithelium

value: normal bronchial epithelial cells

value: WT

value: progenitor


title: 1x8 7d NIR 215

value: GroupE

value: 8Gy RT


title: GIC26, H3K4me3, ChIP

value: Primary Glioblastoma Inititating Cells


title: hiPSCs(1103)-Cardiomyocyte-lac bio_rep1

value: Peripheral blood mononuclear cell

value: human induced pluripotent stem cell derived cardiomyocyte

value: Glucose-Depleted and Lactate-Supplemented Conditions


title: GIC19, H3K4me3, ChIP


title: A5_P4_Day_0_Bots_Replicate_1

value: immediate collection post-Matrigel


title: WT-2

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

data_processing:
For RNA-seq data analysis, the raw paired-end reads were checked using the FastaQC Package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). By using Cutadapt, adaptor sequences, low-quality sequence reads, and the short reads (<25 bp) were removed from the data sets. These clean reads were mapped to the reference genome of A. flavus by Hisat2 tools (version 2.0.4) . For ChIP-seq, the clean reads were mapped to the reference genome of A. flavus by Burrows-Wheeler Alignment tool (BWA, version 0.7.15) [41]. MACS2 (v2.1.1) was used for peak calling. Bedtools (v2.25.0) was used for peak annotation and peak distribution analysis. Differential binding peaks were identified using python script with Fisher’s test (q value <0.05). Homer (v4.10) was used for motif analysis. Genes less than 2000 bp away were associated to the corresponding peak.
Supplementary files format and content: tab-delimited text files include SNTB_HA_vs_WT.peak_annotation
Supplementary files format and content: tab-delimited text files include gene fpkm for each sample

organism: Aspergillus flavus

source_name: mycelia

growth_protocol: For RNA-seq, the conidia (104/ml) for each strain were inoculated in 100 mL PDB shaking at 180 rpm under 29°C for 72 h. ChIP-seq analysis was carried out on the WT and sntB-HA strains. The conidia (104/ml) for each strain were inoculated in 100 mL PDB shaking at 180 rpm under 29°C for 72h, and subjected to ChIP -seq

extract_protocol:
For RNA-seq, total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al. For ChiP-seq, the mycelium were cross-linked with 1% formaldehyde for 10 min at room temperature, after which 0.125 mol/L glycine was added, and the mixture was rested for 5 min to terminate the cross-linking reaction. Nuclei were collected by centrifuging the samples at 2,000 g for 5 min at 4 °C after being treated with lysis buffer (ECOTOP, ES-8523-500). To fragment chromatin DNA, nuclei were treated with nucleus lysis buffer and sonicated. For the lysis-sonicated chromatin, 10% was stored as “Input”, 90% was used in IP reactions with specific anti-HA magnetic beads (Beyotime, P2121, China). The Input DNA and IP DNA were extracted using the phenol-chloroform method.
For ChiP-seq, high-throughput DNA sequencing libraries were prepared using a NEXTFLEX® ChIP Seq Kit (NOVA-514120, Bioo Scientific). The library products corresponding to 200-500 bp were enriched, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina, USA) using the PE150 model.

value: mycelia


title: GIC50, H3K4me3, ChIP

source_name: Primary Glioblastoma Inititating Cells


title: GIC18, H3K4me3, ChIP


title: KOsnt2-3

value: snt2 gene knock-out strain


title: A3_P4_Progenitor_Cells_Replicate_1


title: WT-1


title: fbl-1_3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: head, trunk, tail

value: fbl-1 knockdown

value: RNAi


title: C6_P2_Day_0_Bots_Replicate_3


title: GIC17, H3K4me3, ChIP


title: 2x4 24h IR 207

city: Philadelphia

institute: University of Pennsylvania

value: GroupF

value: irradiated tumor

value: Tumor cell suspension

value: BALB/c

value: Female

value: 2x4Gy RT

value: 24h post RT


title: 1x8 7d IR 214

value: GroupD

value: 8Gy RT

value: 7d post RT


title: A4_P2_Day_0_Bots_Replicate_1

value: airway epithelium

value: normal bronchial epithelial cells

value: WT


title: GIC61, H3K36me3, ChIP

value: Primary Glioblastoma Inititating Cells


title: KOsnt2-2

value: mycelia

value: snt2 gene knock-out strain


title: GIC30, H3K4me3, ChIP


title: A2_P3_Progenitor_Cells_Replicate_1

value: progenitor


title: 2x4 24h IR 206

value: GroupF


title: 1x8 24h NIR 212

value: GroupC

value: non-irradiated tumor


title: GIC54, H3K36me3, ChIP


title: C1_P2_Progenitor_Cells_Replicate_2


title: Lung, Infected, timecourse (mixed samplse)

city: Livermore

first: Dina

last: Weilhammer

state: California

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

description:
10x Genomics
D0_Noninfected, Lung
D5_Infected, Lung
D9_Infected, Lung
D14_Infected, Lung

data_processing:
Data processing, including demultiplexing, alignment, barcode assignment, and gene expression quantification, was performed using the Cell Ranger software pipeline version 7.2.0 and the mm10 2020-A reference transcriptome from 10x Genomics (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mm10
Supplementary files format and content: The processed data files for each experimental group are the standard 10x Cell Ranger output files, including a gene list (features.tsv), cell barcodes (barcodes.tsv), and gene/barcode matrices (matrix.mtx).

source_name: Lung

extract_protocol:
Lungs were removed and placed in PBS. The tissue was digested in a buffer containing DMEM/F12, DNase I, and collagenase I, then minced, incubated, and triturated to create a cell suspension. After two rounds of digestion and filtration, the cells were neutralized with DMEM/F12 + 10% FBS, pelleted, and red blood cells were lysed. The final cell suspension was counted using an automated cell counter before downstream analysis.
10x Genomics Chromium Single Cell Fixed RNA Profiling (Flex) Kit (cat# 100475), following the manufacturer's protocol

value: Lung

value: mixed sample (Day 0, Day 5, Day 9, Day 14)

value: Coccidioides posadasii Infection


title: KOsnt2-1


title: WT-3


title: GIC50, H3K36me3, ChIP


title: A1_P2_Progenitor_Cells_Replicate_1


title: VF_D14, Lung

description: 10x Genomics, Formalin Fixed & Paraffin Embedded (FFPE) Visium Spatial Gene Expression

data_processing:
Data processing, including demultiplexing, alignment, barcode assignment, and gene expression quantification, was performed using the Space Ranger software pipeline version 2.1.1, mm10 2020-A reference transcriptome, and Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A probe set from 10x Genomics (https://www.10xgenomics.com/support/software/space-ranger/latest).
Assembly: mm10
Supplementary files format and content: The dataset includes the Space Ranger generated files necessary for downstream analysis. It contains barcodes.tsv.gz with a list of spatial barcodes and features.tsv.gz with gene IDs. The gene expression count data is stored in matrix.mtx.gz. Tissue-related images are provided, including aligned_fiducials.jpg.gz for aligned fiducials, detected_tissue_image.jpg.gz for the tissue and spots, tissue_hires_image.png.gz for a high-resolution image, and tissue_lowres_image.png.gz for a low-resolution image. Additionally, scalefactors_json.json.gz contains scalefactors in JSON format, and tissue_positions_list.csv.gz lists spatial barcodes and coordinates specifying spots.
Library strategy: Spatial Transcriptomics

extract_protocol: Visium Spatial Gene Expression for FFPE

value: Day 14


title: S_3192_Lcorl KO

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

data_processing:
Quality control was performed using fastqc.
Reads were aligned to mm10 genome using STAR.
Read counts were generated using FeatureCounts.
Normalized counts were generated and the differential gene expression analysis was performed using DESeq2 using the apelgm fold change shrinkage model. Adjusted p value of <0.05 was used for identifying differentially expressed genes.
Assembly: mm10
Supplementary files format and content: csv file for differential expression results
Supplementary files format and content: csv file for normalized counts

source_name: Liver

growth_protocol: 3 week old mice at the time of weaning were sacrificed around 10 am. Livers were harvested and frozen using dry ice.

extract_protocol:
RNA extraction was performed using STAT60 and chloroform extraction. After addition of isopropanol, the samples were transferred to columns from Direct-zol RNA MiniPrep (Zymo Research). Protocol from the kit was followed including DNAse treatment.
TruSeq Standard Total RNA LT Sample Prep Kit

value: Liver

value: Female

tag: age

value: 3 weeks

value: Lcorl KO


title: 1x8 24h IR 211

value: GroupB

value: irradiated tumor

value: Tumor cell suspension

value: BALB/c

value: 8Gy RT

value: 24h post RT


title: 1x8 7d NIR 214

value: GroupE

value: 7d post RT


title: S_3190_WT

value: WT


title: CaSkiRB1_miR218

city: Chilpancingo

first: Gloria

last: Fernández Tilapa

state: Guerrero

address: Ciudad Universitaria Sur, Av. Lázaro Cárdenas S/N

country: Mexico

institute: Autonomous University of Guerrero

data_processing:
The quality of the raw reads was assessed using FastQC (v0.73)
The paired-end fastq files were mapped against the GRCh38 using STAR (v2.7.10b) with default parameters.
Uniquely mapped reads from bam files were used to assess gene counts using FeatureCounts (v2.0.3).
Gene counts were used to conduct differential gene expression analysis using EdgeR (v3.36.0).
Assembly: hg38
Supplementary files format and content: List of differentially expressed genes in tabular format

source_name: Cervix

growth_protocol: C-33A and CaSki cells were grown in DMEM high glucose supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) reagent according to the manufacturer's protocol.
mRNA was enriched from total RNA using oligo(dT) beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand of cDNA synthesis using dTTP. Subsequent steps of end repair, A-tailing, adapter ligation, size selection, amplification, and purification were performed to obtain double-stranded cDNA libraries. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Cervix

value: CaSki

value: Metastatic cervical squamous cell carcinoma (HPV-positive)


title: CaSkiRB2_miR218


title: 1x8 7d IR 215

value: GroupD


title: C3_P3_Progenitor_Cells_Replicate_3

value: airway epithelium

value: normal bronchial epithelial cells

value: progenitor


title: Control 203

source_name: tumor

value: GroupA

value: tumor

value: Female

value: No treatment


title: CaSkiRB3_miR23b

value: 100 nM hsa-miR-23b-3p


title: 1x8 24h NIR 213

value: GroupC

value: non-irradiated tumor

value: Tumor cell suspension

value: BALB/c

value: 8Gy RT


title: GIC31, H3K36me3, ChIP

data_processing:
TrimGalorev0.6.5 was used to remove low-quality and adapter sequences (Phred score < 20 removed)
Alignment to the Ensembl GRCh38 human reference genome was performed via Bowtie v2.3.4
Santools v1.10 was used to convert SAM files to BAM files, and then to remove unmapped reads, secondary alignments, and keep mapped reads with a score > 10
Deeptools algorithm; bamCoverage was used to generate bigwig files for each sample from bam files
Deeptools algorithm; bamCompare was used to generate bigwig files for each sample relative to Input samples (vsInput.bw)
Assembly: Human ensembl GRCh38 release 87
Supplementary files format and content: bigwig

value: Primary Glioblastoma Inititating Cells


title: 1x8 24h NIR 211

value: 24h post RT


title: GIC52, H3K36me3, ChIP


title: VF_WT, Lung

value: Lung

value: Day 0

value: Coccidioides posadasii Infection


title: S_3195_WT

value: Liver

value: 3 weeks

value: WT


title: 1x8 24h IR 213

value: GroupB

value: irradiated tumor


title: S_3165_Lcorl KO

value: Female

value: Lcorl KO


title: CaSkiRB3_miR124

value: Cervix

value: CaSki

value: Metastatic cervical squamous cell carcinoma (HPV-positive)


title: S_3194_Lcorl KO


title: C2_P3_Progenitor_Cells_Replicate_2

value: airway epithelium

value: normal bronchial epithelial cells

value: progenitor


title: CaSkiRB3_miR218


title: CaSkiRB2_miR124


title: GIC26, H3K36me3, ChIP

value: Primary Glioblastoma Inititating Cells


title: GIC30, H3K36me3, ChIP


title: GIC19, H3K36me3, ChIP


title: GIC54, H3K27ac, ChIP


title: Control 202

value: GroupA

value: tumor

value: Tumor cell suspension

value: BALB/c

value: No treatment


title: CaSkiRB2_miR23b

value: 100 nM hsa-miR-23b-3p


title: CaSkiRB1_miR124


title: GIC18, H3K36me3, ChIP


title: 1x8 24h IR 212

value: GroupB

value: 8Gy RT

value: 24h post RT


title: Control 201

value: Female


title: S_3168_Lcorl KO

value: Liver

value: 3 weeks

value: Lcorl KO


title: S_3155_WT

value: WT


title: CaSkiRB3_Sc

value: Cervix

value: CaSki

value: Metastatic cervical squamous cell carcinoma (HPV-positive)

value: 100 nM negative control n#1


title: H3L

type: RNA

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

hyb_protocol: According to NanoString nCounter® XT Assay user manual

data_processing:
The raw data was analysed by ROSALIND® (https://rosalind.bio/). The normalization, fold changes and p values for the data were calculated using the nCounter® Advanced Analysis protocol. In brief, the counts within a lane are divided by the geometric mean of the normalizer probes from the same lane. For normalization genes, housekeeping probes are selected based on the geNorm algorithm as implemented in the NormqPCR R library 29. Fold changes and p values are calculated using the fast method and Generalized Linear Model (GLM) as described in the nCounter® Advanced Analysis 2.0 User Manual. P value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Downstream analyses were done using R.
Data collection is performed using epifluorescence microscopy and CCD capture technology on an nCounter instrument to yield hundreds of thousands of target molecule counts. Digital images are processed within the nCounter instrument, and the Reporter Probe counts are tabulated in a comma separated value (CSV) format for convenient data analysis with NanoString’s free nSolver™ Analysis Software or the application of your choice.

label: biotin

source_name: B16F10 murine melanoma cell line

growth_protocol: The B16-F10 melanoma cells were obtained from the American Type Culture Collection (ATCC). The cells were cultured in complete Dulbecco's Modified Eagle's Medium (DMEM, high glucose) supplemented with 10% (v/v) Fetal Bovine Serum (FBS), and maintained at 37°C in a humidified incubator with 5% CO2. 120'000 tumor cells were implanted with a microsurgery in the mice ear pinnae in a mixture of thrombin and fibrinogen. Melanomas were left growing for 10 days prior to irradiation treatment.

extract_protocol: Exctraction was performed according to the protocols of the company Canopy Biosciences (a Bruker company) from whom we purchsed the Nanostring assay.

treatment_protocol: The following irradiations were delivered at the European Synchrotron Radiation Facility (France): MRT (400 Gy peak-dose, 6.2 Gy valley-dose, 50 µm beam width, 200 µm spacing) and uniform RT (6.2 Gy). The control group received no treatment (0 Gy).

value: MRT_7 days

value: female


title: H21R

scan_protocol: According to NanoString nCounter® XT Assay user manual


title: CaSkiRB1_miR23b


title: CaSkiRB2_Sc


title: GIC61, H3K27ac, ChIP

extract_protocol:
Cells were fixed with formaldehyde-based fixing solution and lysed with provided lysis solution supplemented with protease inhibitors. Nuclei pellets were lysed, and chromatin sonicated with Bioruptor Plus sonication device (Diagenode) to obtain DNA fragments within the recommended 200–1200-bp range. In total, 25µg of sheared chromatin was then incubated with 4µg of antibody against H3K4me3 (Diagenode, C15410003-50) H3K36me3 (abcam, ab9050), H3K27ac (abcam, ab4729) or H3K27me3 (Diagenode C15410195) overnight at 4 °C with rotation. Following incubation with Protein G agarose beads, bound chromatin was washed, eluted and purified following the manufacturer’s protocols. Validation by qPCR-ChIP on target genes was done before proceeding to sequencing.
ChIPed DNA was end-repaired, A-tailed and adapter-ligated before size selection and amplification. The obtained libraries were QC’ed and multiplexed before 75-bp paired-end sequencing on HiSeq4000 (Illumina).

value: Primary Glioblastoma Inititating Cells


title: S_3169_Lcorl KO


title: CaSkiRB1_Sc


title: GIC17, H3K36me3, ChIP


title: GIC30, H3K27ac, ChIP


title: S_3151_WT


title: S_3104_WT


title: S_3101_Lcorl KO


title: GIC50, H3K27ac, ChIP


title: GIC31, H3K27ac, ChIP


title: C33ARB1_miR218

value: Cervical squamous cell carcinoma (HPV-negative)


title: GIC19, H3K27ac, ChIP


title: C33ARB3_miR218


title: GIC52, H3K27ac, ChIP


title: GIC26, H3K27ac, ChIP


title: C33ARB3_miR23b

value: 100 nM hsa-miR-23b-3p


title: C33ARB2_miR218


title: C33ARB2_miR23b


title: GIC17, H3K27ac, ChIP


title: GIC61, H3K27me3, ChIP


title: GIC18, H3K27ac, ChIP


title: C33ARB1_miR23b


title: C33ARB3_miR124


title: H15L

label_protocol: According to NanoString nCounter® XT Assay user manual

value: BB_7 days


title: G43L


title: G2R


title: G48R


title: G26R


title: G19L


title: GIC52, H3K27me3, ChIP


title: S_3174_WT


title: TC 012

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
GeoMx_NGS_Pipeline_ 2.0.0
Counts from barcodes corresponding to RNA probes were normalized with internal positive and negative controls and then normalized to ROI area.
The FastQ files generated by the Illumina sequencing were converted into digital count conversion (dcc) files, then loaded into the GeoMx DSP analysis suite as raw counts. The GeoMx DSP software captures the number of SYTO13 positive nuclei in each segment as well as the surface area of each segment, which were exported for data calibrations. From the software, the counts for oligonucleotides per segment were also exported into a package for quality control and data normalization protocols. Biological probe quality control was performed using default settings. A total of 112 AOIs were all carefully reviewed for segments with sequencing saturation of less than 45%, nuclei of fewer than 160, negative probe counts of less than 8, or a surface area of less than 12,000 squared microns. All 112 AOIs were included for further analysis following the NanoString user’s manual recommendations. Background correction and scaling were performed using geometric means and normalization was performed using Q3 averages of housekeeping genes. Genes with expression levels at or lower than the limit of quantification (LOQ) in at least 5% of segments were filtered out. A total of 1,223 genes passed quality control and were analyzed. Eight patients with four sporadic EOCC and four sporadic LOCC were processed. Per patient, a total of six ROIs with tumor invasive margin (TIM, three ROIs) and tumor center (TC, three ROIs), were selected, respectively.
Assembly: GRCh38.p13
Supplementary files format and content: Nanostring GeoMx normalized data, annotation, and probe data files as xlsx format
Library strategy: Spatial Transcriptomics

source_name: Melanoma liver metastasis

extract_protocol:
FFPE tissue sections of 5 µm thickness was prepared according to vendor's protocol with slight modifications. Sections baked at 60°C for 30 min, and incubated sequentially 3x 5 min in xylene, then 2x 5 min each in 100% EtOH, 95% EtOH, and H2O. Antigen retrieved by placing in EDTA at 100°C 20 min, followed by PBS 5 min. Slides then placed in staining jar of 1mg/mL Proteinase K at 37°C 15 min. This was followed by washing in 10% NBF 10 min, 2x washes in NBP stop buffer, and 1x PBS. RNA probe mix was added to tissue slides with a hybridization coverslip at 37°C overnight. Then, slides were washed 2x with SSC buffer and formamide at 37°C, then 2x with SSC buffer. Slides stained for morphology markers SYTO13, PanCK+, VIM, and FAP. Slides were loaded onto NanoString GeoMx DSP for imaging/barcode acquisition, following the manufacturer's protocol. Manual selection of 600-650 µm ROIs and AOIs were performed based on pathology defined areas and morphological markers.
Libraries constructed using NanoString NGS readout protocol. Dried aspirates in the collection plate were resuspended with 10 μL of nuclease-free water for 10 min, and 4 μL were transferred to a polymerase chain reaction (PCR) plate. Two μL of 5X PCR Master Mix (NanoString Technologies, Inc., Seattle, WA) and 4 μL of 17 a unique primer mix (NanoString) assigned by their position on the collection plate were added to each well. Contents were mixed by pipetting and the sealed PCR plate was transferred to a thermal cycler for an amplification for 18 cycles. PCR products were pooled in equal amounts. Pooled library was purified twice with a 1.2X magnetic beads-to-sample ratio with KAPA Pure Beads (Roche, Basel, Switzerland), each followed by two 80% ethanol washes, then eluted with Elution Buffer (Nanostring). The quality and quantity of the purified pooled library were assessed with High Sensitivity D1000 ScreenTape System (Agilent, Santa Clara, CA) and Qubit dsDNA High Sensitivity assay (Invitrogen, Waltham, MA), respectively. The library was denatured following Illumina’s recommendations and sequenced on NextSeq 550 (Illumina, San Diego, CA) with 27 paired-end cycles, achieving the minimum read depth (30 reads per μm2) or higher determined by the selected AOI’s sizes.
RNA (amplified oligo nucleotide probes)

value: Melanoma liver metastasis

tag: tissue type

value: MLiM

tag: segment tag

value: T HMB45 D

tag: scan id

tag: roi id


title: ANH 014

value: AN HepPar1


title: ANH 012


title: ANH 011


title: DNH 008

value: IN HepPar1


title: DNH 009


title: ANH 013


title: TC 013


title: C33ARB2_miR124

tag: cell line

tag: cell type


title: TM 007

value: T HMB45 P


title: GIC50, H3K27me3, ChIP


title: GIC54, H3K27me3, ChIP


title: TM 006


title: C33ARB3_Sc


title: GIC31, H3K27me3, ChIP


title: C33ARB1_Sc


title: DNH 007


title: TM 005


title: GIC26, H3K27me3, ChIP


title: GIC30, H3K27me3, ChIP


title: C33ARB2_Sc


title: BP_3

city: Chongqing

first: mingwang

last: zhang

address: No. 30 Gaotanyan Street, Shapingba District, Chongqing

department: Department of Dermatology

institute: Southwest Hospital, Army Medical University

data_processing:
The raw sequencing data were visually evaluated by FastQC and filtered by Trim_galore to obtain clean data. HISAT2 was used to map the clean reads to the reference genome, and the quality assessment of mRNA libraries was accomplished by Rseqc. StringTie software was used to analyze transcript abundance.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skin

extract_protocol:
Total RNA was extracted from skin tissue both BP patients and controls using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
The rRNA-depleted purification RNA library was constructed via VAHTS mRNA Capture Beads (Vazyme, China) and VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, China)

value: skin


title: BP_2


title: ANH 010


title: TC 011


title: GIC18, H3K27me3, ChIP

first: Silvia


title: GIC19, H3K27me3, ChIP


title: BP_1


title: GIC17, H3K27me3, ChIP


title: ANH 009


title: Ctr_3


title: G16264-2-T105

city: Belmont

first: Shu

last: Dan

address: 115 Mill St

department: Basic Neuroscience

institute: McLean Hospital, Harvard Medical School

data_processing:
The obtained RNAseq data were processed through the bulk RNA-seq pipeline in bcbio (v1.2.8, Chapman et al 2021).
Reads were aligned using STAR against transcriptome references of the human genome (build 94, Dobin et al. 2013) and quantified with Salmon (Patro et al. 2017).
N/A
N/A
N/A
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
Total RNA was extracted using the Norgen Total RNA Purification Kit (Cat. 17200, Norgen Biotek Corp, Thorold, ON, Canada) and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc., Waltham, MA).
RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina. The sequencing libraries were multiplexed and clustered on seven lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: blood

tag: mdd phenotype

value: Hyper

tag: visit

tag: condition

value: NS

tag: time point


title: ANH 008

tag: tissue


title: Ctr_2


title: G16264-2-T0


title: TC 010


title: ANH 007


title: Ctr_1


title: G16264-1-T105

value: S


title: ANH 006


title: Neuron derived from SB2-iPSC,Div35 [snRNA-seq]

city: Ota-ku

first: Taro

last: Sato

state: Tokyo

address: 2-1-1 Kitasenzoku

department: Prosthodontics

institute: Showa University School of Dentistry

data_processing:
The demultiplexing, barcode processing, gene counting and aggression were made using the Cell Ranger software v7.1.0 .
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: All neurons were cultured on dishes coated with poly-L-lysine (Sigma-Aldrich) and fibronectin (Corning, Corning, NY, USA) in 5% CO2 at a density of 2 ×106 cells/well in 6-well plates. The medium was changed to Neurobasal Plus Medium (Thermo Fisher Scientific) supplemented with 1 ×B-27 Plus supplement,0.5% penicillin/streptomycin, 20 ng/mL brain-derived neurotrophic factor (BDNF; BioLegend, San Diego, CA, USA), 20 ng/mL glial cell-derived neurotrophic factor (GDNF; Alomone Labs, Jerusalem BioPark, Israel), 0.2 mM ascorbic acid (Sigma-Aldrich), 0.5 mM dbcAMP (Nacalai Tesque), 1 ng/mL transforming growth factor-β (TGF-β; BioLegend), 10 μM DAPT (Sigma-Aldrich), and 3 μM CHIR99021. Half of the medium volume was replaced with fresh medium (including all supplements except CHIR99021) every three or four days.

extract_protocol:
Nuclei isolation was performed by referring to the protocol provided by 10x Genomics (Nuclei Isolation for Single Cell Multisome ATAC + Gene Expression Sequencing CG000365 RevC).
cDNA synthesis and gene expression libraries were performed according to the protocol provided by 10x Genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) CG000315 Rev E). The quality of cDNA and libraries was evaluated by electrophoresis.

value: neuron

tag: time


title: G16264-1-T0


title: ANH 005