title: Bulge cells, control mice 2, PD20

city: Ithaca

first: Kefei

middle: Nina

last: Li

state: NY

address: 153 VETERANS PL E408

department: Molecular Biology and Genetics

institute: Cornell University - Ithaca, NY

description:
BulgeCT2
3065D_rawCounts.txt

data_processing:
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
preprocessing: reads will be trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC. Parameters: -j 1 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC --length 50 --fastqc
subtract unwanted reads: unwanted reads will be removed with STAR v 2.7.0e. Parameters:--outReadsUnmapped Fastx
mapping: reads will be mapped to the reference genome/transcriptome Ensembl GRCm38 using STAR v2.7.0e.
Parameters: --outSAMstrandField intronMotif , --outFilterIntronMotifs RemoveNoncanonical, --outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts
gene expression analysis: SARTools and DESeq2 v1.26.0 will be used to generate normalized counts and statistical analysis of differential gene expression.
Parameters: fitType parametric, cooksCutoff TRUE, independentFiltering TRUE, alpha 0.05, pAdjustMethod BH, typeTrans VST, locfunc median
Assembly: mm10/mouse
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skin

extract_protocol:
RNA was harvested using TRIzol (Thermo Fisher) according to the manufacture's protocol.
The libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) using 100ng input total RNA, and polyA enrichment per NEB protocol.

treatment_protocol: Cdh5CreERT2; Alk1 flox/flox mice and littermate control mice were induced with 100ug/g of body weight of tamoxifen at PD17 via intraperitoneal injection and samples were collected on PD20

value: skin

value: bulge cells

value: control

tag: strain background

value: Tamoxifen IP injection, PD17


title: WT_unt_3_L8

status: Public on Feb 28 2023

type: SRA

city: Dunedin

first: Kiel

last: Hards

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: Mycobacterium smegmatis wild-type, Untreated, Lane 8, Replicate 3

library_source: transcriptomic

data_processing:
Reads were demultiplexed  and quality control performed using FastQC v0.11.5
Adapter reads were removed using Trimmomatic version 0.39 and trimmed to a quality score > 0.28
Reads were mapped to the reference genome using the Rsubread (version 2.2.6) subjunc aligner with a maximum fragment length of 600
Feature counts were genereated using the Rsubread (version 2.2.6) featureCounts function with a maximum fragment length of 600 and allowing multiple overlap
Differential expresison was calculated using DESeq 2 1.28.1, using a two-factor experimental design (i.e. strain*treatment)
Genome_build: NC_008596
Supplementary_files_format_and_content: Tab delimited Matrix table with raw gene counts for every gene and every sample and lane

molecule: total RNA

organism: Mycolicibacterium smegmatis

source_name: Bacterial cells

growth_protocol: Three 1 L flasks with 200 ml HdeB were inoculated with three biological replicates of M. smegmatis overnight cultures to an OD of 0.005 and grown at 37°C with 200 rpm until an OD of 0.5 was reached. Each biological replicate was then split, and 2x 50 ml of culture was transferred into two sterile 250 ml flasks.

extract_protocol:
Total RNA was extracted using TRIZOL® reagent (Invitrogen) according to the manufacturer's instructions. Cell lysis was achieved by three cycles of bead-beating in a Mini-Beadbeater (Biospec) at 5,000 rpm for 30 sec. DNA was removed from the RNA preparation by treatment with 2 U RNase-free DNase using the TURBO DNA-free kit (Ambion), according to the manufacturer's instructions. RNA concentrations were determined using a NanoDrop® ND-1000 spectrophotometer and the quality of RNA checked on a 1.2% agarose gel.
Library preparation and sequencing of the M. smegmatis transcriptome was carried out by the Otago Genomics and Bioinformatics Facility (OGBF) in conjunction with New Zealand Genomics Limited (NZGL). Prepared RNA was checked for quality on a Bioanalyzer (Agilent), followed by ribosomal RNA depletion with the Bacterial Ribo-zero RNA Removal Kit (Illumina). Quantification of nucleic acids was performed using a Qubit fluorometer® (Thermo Fisher Scientific). Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina), before being sequenced across two lanes on an Illumina HiSeq with paired-end read lengths of 125 base pairs and using the v4 chemistry.

treatment_protocol: One flask was treated with 50 nM final concentration TB47, and the other was treated with the same amount of DMSO as a control.

tag: strain

tag: treatment

value: Untreated

tag: replicate

tag: cell type

value: Bacterial cells


title: IP_WT-3 [H3K4me3]

city: shanghai

first: li

last: peng

country: China

institute: PSC

library_source: genomic

data_processing:
Cleaned the paired-end reads by Trimmomatic.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Mapped reads with low mapping quality (MAPQ < 30) or multiple positions on the genome were identified and removed by SAMtools (version 1.3).
Enriched peaks were identified by MACS (version 1.4) with default parameters.
The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional 1.5kb up- and down-stream of the TSS and TES was performed by deepTools6 (version 2.4.1).
The statistical test of the overlap between two gene lists was performed by GeneOverlap7 package.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 5-day-old seedlings

growth_protocol: Seedlings grown in half-strength MS media.

extract_protocol:
Nuclei were extracted from 5-day-old WT seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore).
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

tag: tissue

value: Total seedlings

tag: genotype

value: WT

tag: ecotype

tag: age

value: 5 days

tag: chip antibody

value: anti-H3K4me3 (Millipore, 05-745 R)


title: IP_WT-2 [H3K4me3]


title: R1-LiD-M-LK

city: STANFORD

first: Katja

last: Pekrun

state: CA

address: 269 Campus Drive

department: Pediatrics & Genetics

country: USA

institute: Stanford School of Medicine

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the hg38 or mm10 build of the human and mouse genome respectively, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: hg38 for human cells, mm10 for mouse cells
Supplementary files format and content: Bedgraph
Library strategy: Cut & Tag

organism: Mus musculus

source_name: Hepa 1-6

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x anti-anti. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, cells were collected 48 hours after rAAV transduction by trypsinization and washed with PBS. Nuclei were extracted with NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 5e5 nuclei per sample were used for the Tn5 library preparation.
Total gDNA was extracted using a QIAamp DNA Mini kit (Qiagen) including RNAse treatment. The protocol for Illumina DNA prep was followed as per manufacturer’s instructions with 100ng of DNA as input, 30min tagmentation and 8 cycles of PCR. The same indexed primers as for Cut&Tag were used for PCR amplification.
Illumina DNA prep kit. Sequencing was performed with Illumina NovaSeq 6000, 150 cycles total per lane (2 lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Cells were transduced with rAAV packaged using different capsids. The rAAV vector expressed the firefly luciferase under control of a CAG promoter.

tag: cell line

value: Hepa 1-6

value: Hepatoma


title: IP_WT-1 [H3K4me3]


title: Input_WT-2 [H3K4me3]


title: Input_WT-3 [H3K4me3]


title: Input_WT-1 [H3K4me3]


title: IP_WT-3 [H3K27me3]

value: anti-H3K27me3 (Millipore, 07-449)


title: IP_WT-2 [H3K27me3]


title: IP_WT-1 [H3K27me3]


title: Input_WT-2 [H3K27me3]


title: Rep2_IAA_Smc3

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie allowing 3 mismatches. DRIP-seq reads were trimmed with 14bp from the beginning and 16bp from the end.  Trimmed DRIP-seq reads were aligned to the hg19 genome assembly using Bowtie allowing 3 mismatches and a maximum insert size of 1000.
Data were filtered for PCR duplicates using SAMTOOLS
peaks were called using MISHA (v 3.5.6) with a ChIP percentile threshold (0.995).
Genome_build: hg19

organism: Homo sapiens

growth_protocol: Human RAD21-mAC cells were cultured in standard conditions of10% FCS and P/S.

extract_protocol:
Chromatin was extracted from cells, sonicated, pre-cleared and this lysate was used for ChIP libarry prep.  For DRIP-seq, chromatin was extracted from cells and treated with RNaseI and proteinase K. Nucleic acids were isolated, sonicated, pre-cleared and RNA:DNA hybrids were IP'd with s9.6 antibody. Purified eluate was converted to dsDNA and this lysate was used for DRIP library prep ahead of sequencing.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit with 6-8 cycles of PCR. DRIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: RAD21-mAC cells were treated with ethanol or IAA for 4hrs before chromatin was collected (see methods for confluence and concentrations).

value: HCT116 cells

value: auxin (IAA) treated_depletion


title: Input_WT-1 [H3K27me3]


title: Bulge cells, Cdh5CreERT2-driven Alk1 knockout mice 2, PD20

description:
BulgeKO2
3065D_rawCounts.txt

value: Alk1 endothelial knockout


title: Bulge cells, control mice 1, PD20

description:
BulgeCT1
3065D_rawCounts.txt


title: Bulge cells, Cdh5CreERT2-driven Alk1 knockout mice 1, PD20

description:
BulgeKO1
3065D_rawCounts.txt


title: P7.5 mouse bone, sorted,  rep1 [Zs-P]

city: Beijing

first: Xiao

last: Yang

address: 38# LifeScience Park, Changping District, Beijing 102206, China

institute: Beijing Institute of Lifeomics

description: 11x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hindlimb bones from postnatal day 7.5 mice.

extract_protocol:
The femur and tibia of P7.5 Col10a1-Cre;ROSA-ZsGreen mice were dissected and cleaned by brief digestion and brushing in 0.2% collagenase type I for 30 min. To exclude cell interference from the secondary ossification center and other sites of the growth plate, we only collected the proximal part of the femur and distal part of the tibia, with half of the growth plate cartilage excised. To help release the embedded cells, cortical bone, trabecular bone, and hypertrophic cartilage were stripped and sliced into pieces using a syringe needle under a stereoscope. The samples were then digested in 0.2% collagenase type I and 0.1% collagenase type II for 2–3 h at 37 °C under gentle agitation. The liberated cells were pipetted, filtered, neutralized, and centrifuged every 20 min. Dead cells were removed using a kit. The collected cells were prepared to establish two types of single-cell transcriptomes. The first was the unsorted scRNA-seq data, which were constitutive from skeletal cells of the whole bone with hematopoietic and endothelial cells briefly depleted by CD31/CD45/Ter119-coated magnetic beads. The other was composed of ZsGreen-positive cells sorted by FACS Aria III. Single cells were encapsulated in emulsion droplets using a chromium controller (10× Genomics).
The scRNA-seq libraries were prepared using Chromium Single Cell 3ʹ Reagent Kits v3 (10× Genomics), according to the manufacturer’s protocol. The scRNA-seq libraries were evaluated and quantified using an Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 and Qubit HS. The libraries were sequenced on a NovaSeq platform (Illumina) to generate 150 bp paired-end reads, according to the manufacturer’s instructions.

value: FACS-sorted hypertrophic chondrocytes and their progeny from Col10a1-Cre;ROSA-ZsGreen mice.

value: Col10a1-Cre;ROSA-ZsGreen mice in C57BL/6 background

value: postnatal day 7.5


title: P7.5 mouse bone, unsorted,  rep4 [C80Zs-4]

description: 10x Genomics

value: Unsorted bone cells and some remaining hematopoietic cells from Col10a1-Cre;ROSA-ZsGreen mice.

value: Hindlimb bones from postnatal day 7.5 mice.


title: P7.5 mouse bone, unsorted,  rep2 [C80Zs-2]

description: 10x Genomics

value: Unsorted bone cells and endothelial cells isolated from Col10a1-Cre;ROSA-ZsGreen mice, and some remaining hematopoietic cells.


title: P7.5 mouse bone, unsorted,  rep3 [C80Zs-3]

description: 10x Genomics


title: Liver nonparenchymal cells-poly(I:C) 7h+LPS 12h

city: Changsha

first: Xuejing

last: Sun

state: Hunan

address: Ton-zi po road

department: Department of Cardiology

institute: Third Xinagya Hospital

data_processing:
Sequencing data were processed into transcript count tables using the Cell Ranger Single Cell Software Suite version 2.2.0 by 10× Genomics (http://www.10xgenomics.com/).
Base calls from the MGISEQ-2000 were pre-processed into demultiplexed, processed reads.
The quality of the raw sequencing data were as_x0002_sessed with FastQC v0.11.7.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

source_name: liver nonparenchymal cells

extract_protocol:
Briefly, after anesthetization, mice were perfused through the portal vein with buffer solution lacking Ca2+ and Mg2+ and then perfused with 0.05% type IV collagenase at 37℃. The liver was then excised, minced and filtered through a 70 µm filter. Nonparenchymal cells were stored temporarily in Dulbecco's Modified Eagle Medium with 10% fetal bovine serum (FBS), 15 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 100 U/ml penicillin, and streptomycin after digestion. Parenchymal cells were separated by centrifugation at 50 × g for 2 min twice. Cell viability was typical > 90% by trypan blue exclusion.
Libraries generated using the 10× Genomics Chromium system require a conversion step using the MGIEasy Universal Library Conversion kit (App-A) (Part Number: 1000004155) before sequencing can be performed on the MGISEQ-2000 instrument.

treatment_protocol: A murine model of endotoxemia has been developed. Male mice were injected intraperitoneally (i.p.) with poly(I:C) and LPS solubilized in 0.9% sterile sodium chloride by sonication and vortexing. These mice were primed with poly(I:C) and then challenged 7 hour later with LPS. After fasting overnight, the mice were randomly divided into the following groups as designed: the control group received saline ; the poly(I:C) group received poly(I:C) only; the lps 3 hour group were primed with poly(I:C) for 7 hour and later received LPS for 3 hour; the lps 12 hour group were primed with poly(I:C) for 7 hour and later received LPS for 12 hour. All mice were randomly assigned to the treatment groups by random number via invoking computer. Blinding procedures were used to prevent researcher bias. No animals were excluded from the study.

value: Isolated liver nonparenchymal cells

value: liver

tag: Sex

value: Male

value: Mice were primed with poly(I:C) for 7 hours and later received LPS for 12 hours


title: Input_WT-3 [H3K27me3]

value: Total seedlings

value: WT

value: 5 days


title: Liver nonparenchymal cells-control

value: Mice were injected with saline


title: RFe_BiPS2-R2 [RRBS]

status: Public on Feb 27 2023

city: New York

first: Thomas

last: Zwaka

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine

data_processing:
75 bp single-end sequencing reads (SE75) were generated by Illumina sequencing (using NextSeq 500) to a depth of at least 27 million reads (total of 54 million reads), with at least 2.9 million covered CpGs.
Assembly: GenBank assembly accession GCA_004115265.2, assembled and annotated by the Vertebrate Genomes Project (https://vertebrategenomesproject.org)
bedGraph file with methylation at CpG sites

organism: Rhinolophus ferrumequinum

source_name: BPS Replicate 2: Methylation data of wildtype bat induced pluripotent stem cells

extract_protocol:
Active Motif RRBS Service, Cat# 25069
Qiagen EpiTect Fast DNA Bisulfite Kit
Ovation RRBS Methyl-Seq System (Tecan)
75 bp single-end sequencing reads (SE75)
The libraries were sequenced to at least 27 million reads, with at least 2.9 million covered CpGs.

value: reprogrammed embryonic fibroblasts

value: wildtype


title: RFe_BiPS2-R1 [RRBS]

source_name: BPS Replicate 1: Methylation data of wildtype bat induced pluripotent stem cells


title: RFe_BEF-R2 [RRBS]

source_name: BEF Replicate 2: Methylation data of wildtype bat fibroblasts

value: embyronic fibroblasts


title: RFe_BiPS2_H3K27me3

description: BiPS: H3K27me3 methylation status of wildtpype bat induced pluripotent stem cells

data_processing:
75-nt single-end (SE75) sequence reads were generated by Illumina sequencing (using NextSeq 500) to a depth of at least 36 million reads per sample
Assembly: GenBank assembly accession GCA_004115265.2, assembled and annotated by the Vertebrate Genomes Project (https://vertebrategenomesproject.org)
bigWig files containing average number of fragments in 32-nt bins
txt files describing intervals

source_name: reprogrammed embryonic fibroblasts

extract_protocol:
Active Motif HistoPath ChIP-seq service, Cat# 25001
Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantification with Clariostar (BMG Labtech).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara).

tag: antibody

value: H3K427e3 antibody, Active Motif:39155


title: RFe_BEF_H3K27me3

description: BEF: H3K27me3 methylation status of wildtpype bat embryonic fibroblasts

source_name: embyronic fibroblasts


title: NASH liver tissue

city: Shanghai

first: Huiyi

address: No. 1800, Yuntai Rd

department: Department of Gastroenterology

institute: Shanghai East Hospital

description: 10x Genomics

data_processing:
Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (v1.8), which included filtering by read quality, annotating reads, annotating molecules, determining putative cells and generating a single-cell expression matrix. Among all the output files, the matrix of UMI counts for each gene per cell was used for downstream analysis. Genome Reference Consortium Mouse Build 38 (GRCm38) was used as a reference for the BD pipeline.
Assembly: GRCm38

source_name: liver

extract_protocol: Liver tissues were cut into about 1-2mm3 pieces and digested in SoloTM Tumor Dissociation Kit (Sinotech Genomics Co. Ltd., Shanghai, China, JZ-SC-58201) at 37°C for 30-60min. Then we stopped enzymatic digestion with excess RPMI-1640 medium, and filtered cell with 40 μm Cell strainer. Single cell solution were kept on ice before loading to BD Rhapsody cartridge for single cell transcriptome capturation. Samples from NASH and control groups were pooled separately for scRNAseq analysis.

value: nonparenchymal cells

tag: group

value: NASH


title: control liver tissue

description: 10x Genomics

value: control


title: RFe_BiPS2_H3K4me3

description: BiPS: H3K4me3 methylation status of wildtpype bat induced pluripotent stem cells

value: H3K4me3 antibody, Active Motif:39159


title: GT1-7 1

type: RNA

city: Milan

first: Anna

last: Cariboni

address: Via Balzaretti 9

department: Disfeb

country: Italy

institute: Università degli Studi di Milano

description: Gene expression data from GT1-7 cells

hyb_protocol: Hybridisation was performed for 17 hr at 45°C on Rat Gene 1.0 ST Array. Chips were washed and stained following Affymetrix protocol.

scan_protocol: Scanning and image acquisition were performed according to Affymetriz standard protocols.

data_processing: Data were processed using the third part AMDA software (Pelizzola, M. et al. AMDA: an R package for the automated microarray data analysis. BMC Bioinformatics 7, 335 (2006). doi: 10.1186/1471-2105-7-335)

label: biotin

source_name: Immortalized mature GnRH neurons

label_protocol: The RNA was converted using the WT Expression kit (Ambion), fragmented and labelled using the WT Terminal Labelling kit (Affymetrix)

extract_protocol: Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy Micro kit clean-up procedure. Bioanalyzer has been run to verify RNA integrity (RNA 6000 Nano kit). RNA with RIN>7 were used

tag: generation


title: P7.5 mouse bone, unsorted,  rep1 [C80Zs-1]

description: 10x Genomics

value: Unsorted bone cells and endothelial cells isolated from Col10a1-Cre;ROSA-ZsGreen mice, and some remaining hematopoietic cells.

value: Hindlimb bones from postnatal day 7.5 mice.

value: Col10a1-Cre;ROSA-ZsGreen mice in C57BL/6 background

value: postnatal day 7.5


title: RFe_BEF_H3K4me3

description: BEF: H3K4me3 methylation status of wildtpype bat embryonic fibroblasts


title: E20_GFP+

description: Gene expression data from GFP+ cells of E20 embryos

organism: Rattus norvegicus

source_name: Rat E20 embryo head, sorted GFP positive cells

label_protocol: The RNA was amplified using the Ovation Pico WTA System V2 kit (Nugen), converted using the WT-Ovation Exon Module (Nugen), fragmented and labelled using the Encore Biotin Module (Nugen)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Bioanalyzer has been run to verify RNA integrity (RNA 6000 Pico kit). RNA with RIN>7 were used.

treatment_protocol: FACS analysis was performed on dissociated cells from 8-10 embryos. FACS was performed by the Wolfson Scientific Support Services (UCL, London, UK) by using a MoFlo Sorter (Dako, Copenhagen, Denmark); a non- green embryo was used as a control for fluorescence. Cells were excited by using a 488-nm Argon laser and detected by using a 530/40 (FL1) bandpass filter. A cell purity of 95–98.5% was obtained for each sort.

value: Wistar

value: whole head


title: E17_GFP+

description: Gene expression data from GFP+ cells of E17 embryos

source_name: Rat E17 embryo head, sorted GFP positive cells


title: E14_GFP+

description: Gene expression data from GFP+ cells of E14 embryos

source_name: Rat E14 embryo head, sorted GFP positive cells


title: Liver nonparenchymal cells-poly(I:C) 7h+LPS 3h

value: Isolated liver nonparenchymal cells

value: liver

value: Male

value: Mice were primed with poly(I:C) for 7 hours and later received LPS for 3 hours


title: E20_GFP-

description: Gene expression data from GFP- cells of E20 embryos

source_name: Rat E20 embryo head, unsorted cells


title: E17_GFP-

description: Gene expression data from GFP- cells of E17 embryos

source_name: Rat E17 embryo head, unsorted cells


title: E14_GFP-

description: Gene expression data from GFP- cells of E14 embryos

source_name: Rat E14 embryo head, unsorted cells


title: RFe_BiPS2-R1

data_processing:
42 bp paired-end sequencing reads (PE42) were generated by Illumina sequencing (using NextSeq 500) to a depth of at least 83 million total reads
The reads were mapped using the BWA (v0.7.12)algorithm, reads with no more than 2 mismatches and which mapped uniquely to the genome were used in subsequent analysis. Duplicate PCR reads removed.
The genome was divided into 32 bp bins and the number of fragments in each bin was determined and stored in bigWig files using bigToBigWig (v4).
Assembly: GenBank assembly accession GCA_004115265.2, assembled and annotated by the Vertebrate Genomes Project (https://vertebrategenomesproject.org)
xlsx file with merged regions
BigWig file containing number of fragments in 32bp bins

source_name: BiPS2 Replicate 1: Open chromatin data of wildtype bat induced pluripotent stem cells

extract_protocol:
Active Motif ATAC-seq service, Cat# 25079
Illumina Nextera Library Prep Kit using Tn5 tagmentation

value: reprogrammed embryonic fibroblasts

value: wildtype


title: RFe_BEF-R2

source_name: BEF Replicate 2: Open chromatin data of wildtype bat fibroblasts

value: embyronic fibroblasts


title: RFe_BEF-R1 [RRBS]

source_name: BEF Replicate 1: Methylation data of wildtype bat fibroblasts


title: RFe_BiPS2-R2

source_name: BiPS2 Replicate 2: Open chromatin data of wildtype bat induced pluripotent stem cells


title: RFe_BEF-R1

source_name: BEF Replicate 1: Open chromatin data of wildtype bat fibroblasts


title: HSC, 7-day cultured

city: Boston

first: Xiaolong

last: Zhang

state: Massachusetts

address: 200 Longwood Ave, 142 Warren Alpert Building

institute: Boston Children's Hospital

description: Gene expression data from HSCs cultured for 7 day.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse Gene ST 1.0 arrays.

scan_protocol: Microarrays were scanned on an Affymetrix GeneChip scanner

data_processing: Data were extracted by the Affymetrix Expression Console. Microarray data were pre-processed using the Microarray Suite Software 5.0.

source_name: HSC from naive C57BL/6 mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HSCs were maintained in DMEM supplemented with 10% FBS in a 37°C, 5% CO2 humid incubator for 1, 7, or 14 days.

extract_protocol: The RNA of cells was purified by phenol chloroform extraction and isopropanol precipitation in the presence of glycoblue carrier

value: 6-10 weeks


title: HSC, 14-day cultured

description: Gene expression data from HSCs cultured for 14 day.


title: Setaria viridis Root Nuclei_2

first: Bruno

last: Guillotin

address: 12 Waverly Place, Floor 6

department: Biology

institute: NYU-Biology-CGSB

description:
10x Genomics 3' RNA seq V3
Maize_Sorghum_Setaria_Cells_Nuclei_Seurat_Obj.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_raw_counts.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_Norm_counts.RData

data_processing:
Cell Ranger 5.0.1 (10x Genomics) to generate gene-cell matrices. Gene reads were aligned to the Arabidopsis TAIR10.38, Maize B73 v4, Sorghum bicolor v3 and Setaria viridis v2 reference genomes.
Replicates (see Supplementary Table 1) were integrated and cells mapped using the Seurat package v4.0 66 as follows: first, genes with counts in fewer than three cells were excluded from the analysis and their counts were removed. Second, low-quality cells were removed using threshold variable depending on the library quality (see supplementary Table 1). Clustering of cells or nuclei separately were done by log-normalized raw counts and the 2000 most variable genes were identified for each replicate using the “vst” method in Seurat. Next, we used the FindIntegrationAnchors function to identify anchors between the three datasets, using 20 dimensions. A new profile with an integrated expression matrix containing cells from all replicates was produced with the IntegrateData function. For dimensionality reduction, the integrated expression matrix was scaled (linear transformed) using the ScaleData function, and Principal Component analysis (PCA) performed. The top 30 principal components were selected. Cells or nuclei were clustered using a K-nearest neighbor (KNN) graph, which is based on the Euclidean distance in PCA space. The FindNeighbors and FindClusters function with a resolution of 0.5. was applied. Next, non-linear dimensional reduction was performed using the UMAP algorithm with the top 30 PCs.
For the co-clustering of cells and nuclei, either dataset were treated similarly, all replicates were integrated at once using the seurat 'SCT' approach. First raw reads were normalized using the SCTransform function, then SelectIntegrationFeatures was used to identify anchors between the datasets, using 3000 features.
For multiple species clustering, all orthologous genes names from were replaced by their corresponding maize ID in sorghum and setaria raw features.tsv.gz files (Gene conversion in Supplementary Table 1). Anchors are combined using PrepSCTIntegration and selected using FindIntegrationAnchors. For clustering of maize, sorghum and setaria together, all species were considered equally using the FindIntegrationAnchors function. Finally, a Principal Component analysis (PCA) is performed using the first 100 principal components and a non-linear dimensional reduction was performed using the UMAP algorithm with the top 100 PCs.
Supplementary files format and content: Processed data include, R Seurat Objects of integrated datasets, expression matrices normalized and raw count extracted from the Seurat objects, and a metadata containing the cell identities, genes or UMI per cell.

organism: Setaria viridis

source_name: root meristem

growth_protocol: Arabidopsis seeds were imbibed for 48h at 4°C before being surface sterilized and placed on a nylon mesh (110um) and agar plates-1/2 × Murashige and Skoog salts (Sigma M5524), 0.5% sucrose, 0.8% Agar (Sigma A1296). Plant were transferred vertically in growth chambers set to 23°C and a 16 h light/8 h dark cycle (400 μmol m−2 s−1). Root tips were collected 7 days after transfer, cut with a feather scalpel at 150um from the tip and directly transferred to either the protoplast solution at room temperature or the nuclei lysis buffer at 4°C. Maize, Sorghum seeds were sterilized using bleach (1.5% active chloride) and 0.001% tween 20 for 20mins then 4% chloramine T for 20mins. Setaria seed germination was induced by incubation in 4% liquid smoke (Colgin, Authentic Natural Hickory) at 29°C for 24h.Then setaria seeds were sterilized using bleach (1.5% active chloride) and 0.001% tween 20 for 20mins. All seeds were placed between two layers of brown paper (Anchor Paper&Cie., 38# regular), rolled and covered with aluminum foil to prevent roots from exposure to direct light. Rolls were placed in a bucket of tap water at 28/24°C at 16 h light/8 h dark cycle (250 μmol m−2 s−1) for 7 days (15days for Setaria) before harvesting the root tips. Primary and seminal root tips were cut using a fine scalpel at 0.5 cm form the tip for Maize and Sorghum, 0.2cm from the tip for Setaria and transferred either to the pre-incubation solution for single cell or to the nuclei lysis buffer.

extract_protocol:
Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts, or in lysis buffer for nuclei extraction. Protoplasts or nuclei were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' kit
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2 and V3 protocol

value: Nuclei

value: root meristem

value: 10 days old


title: Setaria viridis Root Cell_3

value: Protoplast


title: Setaria viridis Root Nuclei_1


title: Setaria viridis Root Cell_2


title: Setaria viridis Root Cell_1

description:
10x Genomics 3' RNA seq V2
Maize_Sorghum_Setaria_Cells_Nuclei_Seurat_Obj.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_raw_counts.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_Norm_counts.RData


title: HSC, one-day cultured, biological rep1

description: Gene expression data from HSCs cultured for 1 day.


title: HSC, one-day cultured, biological rep2


title: LSEC, biological rep3

description: Gene expression data from freshly isolated LSECs.

source_name: LSECs from naive C57BL/6 mouse


title: IR2MX3

city: Uppsala

first: Mareike

last: Koppik

address: Norbyvägen 18D

department: Department of Ecology and Genetics

country: Sweden

institute: Uppsala University

data_processing:
reads (no quality trimming) were mapped to the Callosobruchus maculatus transcriptome with TopHat2 v2.1.0 with inner-mate-distance set to 100bp (-r 100), library type set to firststrand (--library-type fr-firststrand) and coverage based search for junctions disabled (--no-coverage-search), all other settings were kept at their default state
mapped reads were counted using HTSeq-0.11.2 with strandedness set to reverse (-s reverse) and id attribute set to locus_tag (-i locus_tag), all other parameters were kept at their default state
Genome_build: GCA_900659725.1_ASM90065972v1
Supplementary_files_format_and_content: separate text files for each sample and lane (2 lanes) containing absolute counts for each gene (LOCUS tag) obtained from HTSeq

molecule: polyA RNA

organism: Callosobruchus maculatus

source_name: partial reproductive tract

extract_protocol:
total RNA was isolated from pooled partial male reproductive tracts with Qiagen RNeasy Mini Kit including on-column DNA digestion with Qiagen RNase free DNase Set
libraries were constructed using Illumina TruSeq stranded mRNA library preparation kit with polyA selection

tag: irradiation treatment

value: irradiated

tag: experimental day

tag: social environment

value: mixed

tag: line

value: partial reproductive tract


title: IR2VG3

value: virgin


title: IR2VG1


title: IR2MM3

value: male-male


title: IR2MX1


title: LSEC, biological rep1


title: t-ADSCs_2

first: Shuang

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.8.4)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: fat

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

extract_protocol:
RNA was harvested using  using TRIzol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded  mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: fat

value: primary cell

value: mesenchymal stem cells

value: WT

tag: treatment

value: TNF-α-Activated


title: t-ADSCs_3


title: LSEC, biological rep2

value: liver


title: Kupffer cells, biological rep2

description: Gene expression data from freshly isolated Kupffer cells.

source_name: Kupffer cells from naive C57BL/6 mouse


title: Kupffer cells, biological rep1


title: Kupffer cells, biological rep3


title: t-ADSCs_1


title: IR2MA1

value: mated


title: hepatocytes, biological rep3

description: Gene expression data from freshly isolated hepatocytes.

source_name: hepatocytes from naive C57BL/6 mouse

value: 6-10 weeks


title: ADSCs_3


title: IR2MA3


title: IR2MM1


title: hepatocytes, biological rep1


title: hepatocytes, biological rep2


title: IR1VG3

value: day 1


title: ADSCs_2


title: ADSCs_1


title: VSMC, replicate 3, scRNA-seq

city: Milwaukee

first: Jing

last: Huang

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

data_processing:
Single cell feature counts were generated by cellranger count (Cell Ranger v6.0.0, 10x Genomics) with  human reference GRCh38 dataset.
Remove-background from CellBender v0.2.1 with FPR=0.01
Cells with fewer than 200 or more than 5,000 detected genes were filtered out with Seurat R package v4.1.1
Assembly: hg38
Supplementary files format and content: Comma-separated values file with count data

source_name: Human iPSC line 039B

growth_protocol: Cells were treated with N2B27 medium plus 8 μM CHIR99021 and 25 ng/ml BMP4 for 3 days to generate mesoderm cells.

extract_protocol:
Total RNA was extracted from iPSC-derived ECs or VSMCs with TRIzol reagent.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

treatment_protocol:
ECs were further induced with StemPro-34 SFM medium supplemented with 200ng/ml VEGF and 2 μM forskolin for 2 days and purified with CD144 magnetic beads.
For VSMC induction, mesoderm cells were treated with N2B27 medium supplemented with 10 ng/ml PDGF-BB and 2 ng/ml Activin A for 2 days.  Contractile VSMCs were then induced with N2B27 supplemented with 2 ng/ml Activin A and 2 μg/ml Heparin for 5 days.

value: Human iPSC line 039B

value: Vascular smooth muscle cells


title: IR1MX1


title: IR1MX3


title: CALDOX24 - 2

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

description:
CALDOX24 - 2
Total RNA isolated from cells in culture

hyb_protocol: Following fragmentation and labeling, ss-cDNA were hybridized for 16 hr at 45°C to Affymetrix Hu 133 probe array A.

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

data_processing: The raw CEL files were normalized using RMA background correction with quantile normalization, log2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes were considered significant if p-value with

label: Biotin

source_name: CAL51 cells resistant to 0.4 micro molar doxorubicin treated for 24 h with 4 micro molar doxorubicin - biological sample 2

label_protocol: Biotin labelled cRNA for hybridisation was prepared by in vitro transcription using the BioArray HighYield RNA Transcript Labelling kit (Enzo Life Sciences) according to manufacturer’s recommendations.

growth_protocol: CAL51 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 1 g/L glucose, 10% foetal calf serum and 4 mM glutamine. CALDOX cells were generated by long time incubation in the presence of 0.4 μM doxorubicin and were routinely maintained in DMEM with 0.4 M doxorubicin

extract_protocol: Qiagen Rneasy total RNA extraction

treatment_protocol: CAL51 cells were grown in 75 cm2 flasks and treated with 0.4 μM doxorubicin for 24 and 48 h when they reached 50% confluency. CALDOX cells were grown for three passages drug-free and then treated with 4 μM doxorubicin for 24 h in 75 cm2 flasks when they reached 50% confluency.

tag: tumor

value: breast cancer

value: CALDOX


title: CALDOX24 - 1

description:
CALDOX24 - 1
Total RNA isolated from cells in culture

source_name: CAL51 cells resistant to 0.4 micro molar doxorubicin treated for 24 h with 4 micro molar doxorubicin - biological sample 1


title: IR1MM3

description: after initial RNA extraction this sample underwent an additional clean-up with Qiagen Rneasy Mini Kit

value: irradiated


title: VSMC, replicate 2, scRNA-seq

tag: cell type


title: CALDOX24 - 3

description:
CALDOX24 - 3
Total RNA isolated from cells in culture

source_name: CAL51 cells resistant to 0.4 micro molar doxorubicin treated for 24 h with 4 micro molar doxorubicin - biological sample 3


title: H69 MIX biological rep1

city: Shreveport

first: Ana-Maria

last: Dragoi

state: Louisiana

address: 1501 Kings Hwy, Molecular and Cellular Physiology Room 4-208

institute: LSU-Health Shreveport

description: Gene expression data from H69 and CCD8 cells.

hyb_protocol: Approximately 250 nanograms of fragmented, biotin-labeled sense-strand ss-cDNA were hybridized to Affymetrix GeneChip Clariom D Human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Transcriptome Analysis Console (TAC) verison 4.0.
Summarization method: Gene level- SST-RMA. Gene fold value < -2 or > 2.

source_name: H69 mix condition

label_protocol: Biotin labeling was performed according to the standard GeneChip® Whole Transcript (WT) Sense Target Labeling Assay.

growth_protocol: H69 and CCD8 cells were grown in RPMI in a tissue culture incubator.

extract_protocol: Total RNA extraction was performed using the QIAGEN RNeasy kit according to the manufacturer's instructions.

treatment_protocol: H69 and CCD8 were cultured for 72h under three conditions: control, indirect contact (INS), and direct contact (MIX)

value: lung human cell line


title: H69 MIX biological rep2


title: CALDOX - 3

description:
CALDOX - 3
Total RNA isolated from cells in culture

source_name: CAL51 cells resistant to 0.4 micro molar doxorubicin - biological sample 3


title: H69 INS biological rep3

source_name: H69 insert condition


title: H69 MIX biological rep3


title: H69 INS biological rep1


title: H69 INS biological rep2


title: H69 CT biological rep2

source_name: H69 control condition


title: EC, replicate 3, scRNA-seq

value: Endothelial cells


title: IR1MM1

value: male-male

tag: tissue

value: partial reproductive tract


title: VSMC, replicate 1, scRNA-seq


title: IR1VG1

value: virgin


title: R1-LiD-M-DJ

source_name: Hepa 1-6

extract_protocol:
Briefly, cells were collected 48 hours after rAAV transduction by trypsinization and washed with PBS. Nuclei were extracted with NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 5e5 nuclei per sample were used for the Tn5 library preparation.
Total gDNA was extracted using a QIAamp DNA Mini kit (Qiagen) including RNAse treatment. The protocol for Illumina DNA prep was followed as per manufacturer’s instructions with 100ng of DNA as input, 30min tagmentation and 8 cycles of PCR. The same indexed primers as for Cut&Tag were used for PCR amplification.
Illumina DNA prep kit. Sequencing was performed with Illumina NovaSeq 6000, 150 cycles total per lane (2 lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

value: Hepa 1-6

value: Hepatoma


title: EC, replicate 2, scRNA-seq


title: CAL48 - 3

description:
CAL48 - 3
Total RNA isolated from cells in culture

source_name: CAL51 48 h with 0.4 micro molar doxorubicin - biological sample 3


title: IR1MA3


title: CAL48 - 2

description:
CAL48 - 2
Total RNA isolated from cells in culture

source_name: CAL51 48 h with 0.4 micro molar doxorubicin - biological sample 2


title: EC, replicate 1, scRNA-seq


title: CALDOX - 2

description:
CALDOX - 2
Total RNA isolated from cells in culture

source_name: CAL51 cells resistant to 0.4 micro molar doxorubicin - biological sample 2


title: CCD8 MIX biological rep3

source_name: CCD8 mix condition


title: CT2VG3

source_name: partial reproductive tract

value: non-irradiated control


title: H69 CT biological rep3


title: CCD8 MIX biological rep2


title: CAL48 - 1

description:
CAL48 - 1
Total RNA isolated from cells in culture

source_name: CAL51 48 h with 0.4 micro molar doxorubicin - biological sample 1


title: H69 CT biological rep1


title: VSMC, replicate 3, bulk RNA-seq

data_processing:
Trim Galore v0.6.6 for trimming the adapter and low-quality raw reads
Reads were then aligned to the human reference genome GRCh38-2020-Awith STAR tools
Reads per gene were counted by htseq-count of htseq v0.13.5
Assembly: hg38
Supplementary files format and content: Tab-separated values files with count data

extract_protocol:
Total RNA was extracted from iPSC-derived ECs or VSMCs with TRIzol reagent
NEBNext Ultra II RNA Library Prep kit following its Section I protocol.


title: CCD8 MIX biological rep1


title: CALDOX - 1

description:
CALDOX - 1
Total RNA isolated from cells in culture

source_name: CAL51 cells resistant to 0.4 micro molar doxorubicin - biological sample 1


title: CAL24 - 3

description:
CAL24 - 3
Total RNA isolated from cells in culture

source_name: CAL51 24 h with 0.4 micro molar doxorubicin - biological sample 3


title: VSMC, replicate 1, bulk RNA-seq

source_name: Human iPSC line 039B


title: CT2MX3

value: mixed


title: CT2MX1


title: CT2VG1


title: IR1MA1

value: mated


title: VSMC, replicate 2, bulk RNA-seq


title: CT2MM3


title: EC, replicate 2, bulk RNA-seq


title: EC, replicate 3, bulk RNA-seq


title: CAL24 - 1

description:
CAL24 - 1
Total RNA isolated from cells in culture

source_name: CAL51 24 h with 0.4 micro molar doxorubicin - biological sample 1


title: CT2MM1


title: CT2MA3


title: NAS_2  FIB_0  STH_0 patient 91

city: Indianapolis

first: Nick

last: Powell

state: United States

address: 950 W. Walnut St.

institute: IUSM

data_processing:
Raw data QC was performed, including base composition quality, fragment size, mapping read count, 3’ bias, read count mapping breakdown, adapter/phiX content, heterologous organism contamination, and sex/ethnicity prediction concordance. Greater than 100 million reads were obtained per sample and reads were mapped to a reference human transcriptome. The ratio between the highest and lowest total mapped reads per sample was 4.2, indicating good read depth consistency across samples. Each sample (or library) was assessed in 4 or 5 replicates (assays). Data correlation of replicates from the same sample were checked. One replicate from all 434 assays was excluded due to low correlation. Replicates were aggregated into one measurement value per sample per gene. There were 93 unique patients in the final cohort with both phenotype information and RNA-seq data.
Assembly: reads were mapped to a human transcriptome, GRCh37
Supplementary files format and content: NAFLD_RNA_counts.csv contains comma separated values of aggregated read counts per gene per sample

source_name: Liver

extract_protocol:
BioChain Broad Range Total RNA isolation kit
Illumina HT Truseq Stranded kit

value: Liver

tag: nas

tag: fibrosis

tag: steatohep


title: NAS_4  FIB_2  STH_2 patient 93


title: NAS_4  FIB_4  STH_2 patient 92


title: CAL24 - 2

description:
CAL24 - 2
Total RNA isolated from cells in culture

source_name: CAL51 24 h with 0.4 micro molar doxorubicin - biological sample 2


title: EC, replicate 1, bulk RNA-seq


title: CAL - 1

description:
CAL - 1
Total RNA isolated from cells in culture

source_name: CAL51 naïve - biological sample 1


title: CCD8 INS biological rep2

source_name: CCD8 insert condition


title: CCD8 CT biological rep3

source_name: CCD8 control condition


title: CCD8 INS biological rep3


title: Hela cells si-control-U1-AMO-replicate-2

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

description:
mRNA 3'-seq was carried out to examine the polyadenylation site map
3'-seq analysis in Hela cells treated with negative control siRNA and U1 AMO (antisense morpholino oligonucleotide)

data_processing:
Sequencing analysis was carried out using our recently published pipeline QuantifyPoly(A) (Brief Bioinform . 2021 Nov 5;22(6):bbab268. doi: 10.1093/bib/bbab268.)
Assembly: hg38
Supplementary files format and content: bw

source_name: HeLa

growth_protocol: Hela cells were grown in DMEM supplemented 10% FBS

extract_protocol:
Total RNAs were extracted with Trizol Reagent (Thermo Fisher)
Negative control siRNA and U1 AMO was transfected into Hela cells, 3'-seq  was subsequently carried out to examine the polyadenylation site usage at the transcriptome level using a lexgen kit (Cat. 016.24)

treatment_protocol: control siRNA and U1 AMO were transfected into Hela cells

value: HeLa

value: tumor cell line

value: transfected with negative control siRNA and U1 AMO


title: CT2MA1


title: NAS_1  FIB_0  STH_0 patient 90


title: CCD8 CT biological rep2


title: CCD8 INS biological rep1


title: CCD8 CT biological rep1


title: CT1VG3

value: day 1


title: NAS_6  FIB_2  STH_2 patient 88


title: Hela cells si-control-U1-AMO-replicate-1


title: NAS_2  FIB_0  STH_0 patient 89


title: CT1VG1


title: CAL - 3

description:
CAL - 3
Total RNA isolated from cells in culture

source_name: CAL51 naïve - biological sample 3

value: breast cancer


title: NAS_2  FIB_2  STH_2 patient 86


title: CT1MX3


title: CT1MM3


title: CT1MX1


title: CAL - 2

description:
CAL - 2
Total RNA isolated from cells in culture

source_name: CAL51 naïve - biological sample 2


title: NAS_2  FIB_0  STH_0 patient 84


title: NAS_6  FIB_1  STH_2 patient 83


title: CT1MM1


title: NAS_5  FIB_3  STH_2 patient 87


title: NAS_3  FIB_0  STH_0 patient 82


title: CT1MA1


title: CT1MA3


title: NAS_5  FIB_3  STH_2 patient 81


title: NAS_1  FIB_0  STH_0 patient 80


title: NAS_4  FIB_2  STH_2 patient 85


title: 410.4 NETs_2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
bclconvert include in Illumina NextSeq2000
STAR-2.7.10a
subread-2.0.3 featureCounts
Assembly: mm10

source_name: breast

growth_protocol: 410.4 breast cancer cells were maintained in DMEM supplemented with 0.5% fetal calf serum (FCSII) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA library for RNAseq were prepared using  Illumina Stranded mRNA Prep following Manufacturer's protocols

treatment_protocol: 410.4 cells were treated with NETs conditioned media (NETs were isolated in 0.5% DMEM) or control media (DMEM 0.5%) for a period of 2-day (designated day 410.4 NETs)

value: breast

value: cancer cells

value: NETs


title: 410.4 NETs_3


title: 410.4 NETs_1


title: NAS_0  FIB_0  STH_0 patient 79


title: 410.4 Veh_3

value: control


title: LGG-172

type: genomic

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

institute: University of Gothenburg

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC beadchips using standard Illumina protocols.

scan_protocol: Standard Illumina protocol

data_processing: Raw methylation data were processed on the HumanMethylation450 BeadChip with the R package wateRmelon and normalized with dasen using the statistical software R.

label: Cy5 and Cy62

source_name: Lower-grade glioma_172

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA FFPE tissue Kit  (Qiagen) according to the manufacturer's instructions except lysis with Proteinase K was performed overnight.

treatment_protocol: Tissue specimen were formalin-fixed and paraffin-embedded.

tag: genotype

value: IDH mutant

tag: tissue brain tumor

value: Lower-grade glioma


title: NAS_3  FIB_0  STH_1 patient 78


title: NAS_6  FIB_1  STH_2 patient 77


title: NAS_5  FIB_3  STH_2 patient 74


title: 410.4 Veh_1

tag: cell line


title: NAS_2  FIB_1  STH_0 patient 76


title: 410.4 Veh_2


title: LGG-171

label: Cy5 and Cy61

source_name: Lower-grade glioma_171


title: LGG-168

label: Cy5 and Cy58

source_name: Lower-grade glioma_168


title: LGG-169

label: Cy5 and Cy59

source_name: Lower-grade glioma_169


title: NAS_2  FIB_0  STH_0 patient 75


title: LGG-170

label: Cy5 and Cy60

source_name: Lower-grade glioma_170


title: GDM1_ACTseqBS_H3K27ac

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

data_processing:
TrimGalore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was deployed together with Cutadapt v. 1.14 (https://cutadapt.readthedocs.io/en/stable/) using the non-default parameters “--paired”, “--nextera”, “--length_1 35”, and “--length_2 35” to perform adapter and quality trimming.
Bowtie2 v. 2.2.6 (PMID: 22388286) was used with the “--very-sensitive” flag and a maximum insertion length of 2500 bp to map trimmed reads against the GRCh37/hg19 reference genome.
Aligned reads belonging to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Discordant mappings and alignments with a Phred score below 20 were removed using SAMtools view.
The aligner and methylation caller Bismark (version 0.22.3) (PMID: 21493656) was used to obtain the methylation levels. The Bismark pipeline involves four steps. First, adapters were trimmed, and read quality was controlled by TrimGalore (version 0.6.7; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). Second, clean reads were aligned back to the human genome (GRCh37/hg19) by Bismark. Third, duplicated reads were removed by the deduplicate_bismark function. Fourth, methylation was called by the bismark_methylation_extractor function.
Methrix (version 1.2.06) (PMID: 33346800) was adopted to produce the collapsed BED files for the CpG sites with the called methylation levels (beta value) and supporting read coverage.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: ACT-seq-BS

growth_protocol: GDM-1 cells were grown in RPMI 1640 supplemented with 20% fetal bovine serum.

extract_protocol:
ACT-seq-BS was done by combining ACT-seq (PMID: 31431618) and tagmentation-based whole genome bisulfite sequencing (TWGBS; PMID: 29224141) as follows. For the transposome, a methylated load adapter (PMID: 29224141) was generated. Cell permeabilization of native cells and tagmentation reaction with pA-Tn5 transposome-antibody complex for "Antibody-guided chromatin tagmentation (ACT-seq)" according to Carter et al (PMID: 31431618). Tagmented DNA was purified with MinElute (Qiagen) columns (ACTseq) according to the provider's instruction. After oligonucleotide replacement/gap repair, the bead-purified DNA was bisulfite-converted according to PMID: 29224141.
Libraries were prepared according to Weichenhan et al. (PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.

value: leukemic

tag: chip antibody

value: K27ac (Abcam ab4729)


title: GDM1_ACTseqBS_H3K4me1

value: K4me1 (Abcam ab8895)


title: NAS_4  FIB_0  STH_0 patient 73


title: NAS_3  FIB_1  STH_2 patient 72


title: GDM1_ACTseq_MNX1_2

data_processing:
TrimGalore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was deployed together with Cutadapt v. 1.14 (https://cutadapt.readthedocs.io/en/stable/) using the non-default parameters “--paired”, “--nextera”, “--length_1 35”, and “--length_2 35” to perform adapter and quality trimming.
Bowtie2 v. 2.2.6 (PMID: 22388286) was used with the “--very-sensitive” flag and a maximum insertion length of 2500 bp to map trimmed reads against the GRCh37/hg19 reference genome.
Aligned reads belonging to the same lane-multiplexed library were combined using SAMtools merge v. 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Discordant mappings and alignments with a Phred score below 20 were removed using SAMtools view.
Trimmed reads were additionally aligned against the S. cerevisiae R64 reference genome followed by post-alignment filtering as described above. To derive a library-specific scaling factor, the multiplicative inverse of the number of filtered alignments against the yeast genome were calculated. Coverage tracks were generated using the bamCoverage functionality of Deeptools v. 3.1.1 (https://anaconda.org/bioconda/deeptools/files?version=3.1.1) with the non-default parameters “--ignoreForNormalization chrM chrY chrX” and “--effectiveGenomeSize 2652783500” as well as the “--scaleRatio” option to specify the spike-in-derived scaling factor.
Peak calling to identify common MNX1 peaks was performed with MACS v.2.2.6 (https://pypi.org/project/MACS2/) using a wrapper script callpeaks provided by Encode (https://www.encodeproject.org/chip-seq/histone/); for input subtraction, ACT-seq data from non-targeting IgG control was used.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: ACT-seq

extract_protocol:
Cell permeabilization of native cells and tagmentation reaction with pA-Tn5 transposome-antibody complex for "Antibody-guided chromatin tagmentation (ACT-seq)" according to Carter et al (PMID: 31431618). For normalization of sequence reads between biological replicates, ~4,000 permeabilized nuclei of yeast Saccharomyces cerevisiae, prepared according to (PMID: 25827087) and incubated with pA-Tn5ome-ab complex targeting yeast H2B, were spiked into each mix of cells and pA-Tn5ome-ab complex.  Tagmented DNA was purified with MinElute (Qiagen) columns (ACTseq) according to the provider's instruction.
Libraries were prepared according to Weichenhan et al. (PMID: 29224141). Briefly, tagmented DNA was amplified by PCR under real-time conditions using a universal Illumina forward and a barcoded reverse primer and the NEBNext High Fidelity 2x PCR Master-Mix (NEB), and amplfication was monitored by inspecting real time the amplification curves. DNA was HighPrep bead-purified, Qubit (Invitrogen) quantitated and sized by TapeStation (Agilent) profiling.

value: MNX1 (Invitrogen PA5-23407)


title: line 1, D115, organoid

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
scRNA libraries sequenced using the NovaSeq 6000 instrument (Illumina, San Diego, CA) generating 100-bp paired end reads. FASTQ files were generated from base calls with the bcl2fastq software (Illumina), and reads were mapped to the pre-built GRCh38 reference with Cell Ranger (version 6.0) (10X Genomics) using the ‘count’ function. Only cells passing the default Cell Ranger call were analyzed further. Only cells with between 500 and 7,000 unique genes (features) and with < 15% of reads mapping to mtDNA-encoded genes and <25% of reads mapping to ribosomal genes were included in the analysis.
Assembly: GRCh38
Supplementary files format and content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: retinal organoid

extract_protocol:
Approximately ten representative organoids were selected from culture. Organoids were allowed to settle by gravity in a 1.5 mL tube and medium was aspirated. Organoids were then dissociated with 20 units/mL of papain (Worthington Biochemical Corporation, Lakewood, NJ) with 60 units/mL DNase I (Worthington Biochemical Corporation) on a shaker at 37˚C for approximately 60 minutes. Following dissociation, cells were pelleted at 400 x g for 5 minutes, resuspended in dPBS -/- (Thermo Fisher Scientific) with 0.04% non-acetylated bovine serum albumin (New England Biolabs, Ipswich, MA), and processed immediately for encapsulation and barcoding using the Chromium Controller (10X Genomics, Pleasanton, CA). Cells were filtered through a 70 µm filter and further diluted to target 8,000 cells per run. Single cells were then partitioned and barcoded with the Chromium Controller instrument (10X Genomics) and Single Cell 3' Reagent (v3.1 chemistry) kit (10X Genomics) according to the manufacturer’s specifications with no modification (Rev C). Final libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and diluted to 3 ng/µL in buffer EB (Qiagen, Hilden, Germany). Library quality and concentration was confirmed using the Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, Santa Clara, CA) prior to sequencing.
Libraries were prepared using the Single Cell 3' Reagent (v3.1 chemistry) kit (10X Genomics) according to the manufacturer’s specifications with no modification (Rev C).

value: retinal organoid

tag: time


title: LGG-166

label: Cy5 and Cy56

source_name: Lower-grade glioma_166


title: GDM1_ACTseq_MNX1_1


title: NAS_2  FIB_0  STH_0 patient 71

value: Liver


title: GDM1_RNAseq

data_processing:
nf-core/rnaseq v3.9
Reads were trimmed using TrimGalore!.
Alignment was done using STAR.
Quantification was performed using Salmon.
Assembly: GRCh37/hg19
Supplementary files format and content: raw read counts and TPM

extract_protocol:
Qiagen RNeasy Plus Mini kit
TruSeq Stranded mRNA


title: GDM1_ACTseq_IgG2

value: IgG (Millipore PP64)


title: GDM1_ACTseq_H3K4me3

value: K4me3 (Diagenode C15410003)


title: GDM1_ACTseq_H3K4me1


title: NAS_0  FIB_0  STH_0 patient 70


title: LGG-151

label: Cy5 and Cy48

source_name: Lower-grade glioma_151


title: 4C_AHI1-ex20vp

description: 4C-seq using using as viewpoint the AHI1 exon 20 (chr6:135645039-135644600;hg19)

data_processing:
4C-fastq single read data was processed using the pipe4C platform as described (PMID: 31351925).
Reads were aligned using bowtie2, version 2.3.5.1. (PMID: 22388286) and samtools 1.5 (https://github.com/samtools/samtools/releases/tag/1.5).
Final processing was done under R3.6.2 using the pipe4C script with default parameters. Reads mapped to the 4C fragment end library were normalized according to the default normalizeFactor 1000000. 3′-ends of sequences were trimmed using a sliding window (size 21) as soon as 2 out of 5 nucleotides had a quality encoding less than the default Q-score. The quality cutoff and trimlength were 0, the minimum amount of reads was 1000. NonBlind and mapUnique were set to FALSE.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig (bw)
Library strategy: 4C-seq

extract_protocol:
Circular chromosome conformation capture (4C) was done essentially as described (PMID: 22961246) using two million cells and two rounds of restriction digestion with either BglII and NlaIII, or with NlaIII and Csp6I, depending on the viewpoint, each time followed by ligation.
First PCR 98°C for 30 sec, 10 cycles with 98°C for 15 sec, 61°C, 60°C or 54°C depending on the viewpoint for 20 sec with 0.5°C touch-down per cycle, 72°C for 2 min, then 30 or 25 cycles with 98°C for 15 sec, 56°C, 55°C or 49°C, depending on the viewpoint  for 20 sec, 72°C for 2 min, finally followed by 72°C for 1 min. Second PCR with 95°C, 3 min (initial melting) and 95°C, 20 sec, 62°C, 15 sec, 72°C, 40 sec (8 cycles).
4C sequencing libraries were generated in two PCR steps. In the first step, the  second ligation products, inverse primers and Q5 high fidelity enzyme were used. Libraries were generated in the second step with DNA from the first step essentially according to (PMID: 29224141) under real-time conditions.


title: NAS_7  FIB_2  STH_2 patient 67

source_name: Liver


title: LGG-153

label: Cy5 and Cy49

source_name: Lower-grade glioma_153


title: GDM1_ACTseq_H3K27ac

value: K27ac (Abcam ab177178)


title: LGG-161

label: Cy5 and Cy54

source_name: Lower-grade glioma_161


title: LGG-167

label: Cy5 and Cy57

source_name: Lower-grade glioma_167


title: LGG-143

label: Cy5 and Cy43

source_name: Lower-grade glioma_143


title: LGG-160

label: Cy5 and Cy53

source_name: Lower-grade glioma_160


title: NAS_1  FIB_3  STH_2 patient 66


title: LGG-147

label: Cy5 and Cy45

source_name: Lower-grade glioma_147


title: LGG-155

label: Cy5 and Cy50

source_name: Lower-grade glioma_155


title: 4C_MYBvp

description: 4C-seq using using MYB as viewpoint (chr6:135511183-135511908;hg19)


title: NAS_7  FIB_2  STH_2 patient 65


title: LGG-158

label: Cy5 and Cy52

source_name: Lower-grade glioma_158


title: LGG-148

label: Cy5 and Cy46

source_name: Lower-grade glioma_148


title: LGG-162

label: Cy5 and Cy55

source_name: Lower-grade glioma_162


title: LGG-135

label: Cy5 and Cy39

source_name: Lower-grade glioma_135


title: LGG-150

label: Cy5 and Cy47

source_name: Lower-grade glioma_150


title: LGG-157

label: Cy5 and Cy51

source_name: Lower-grade glioma_157


title: NAS_4  FIB_4  STH_2 patient 64


title: NAS_3  FIB_1  STH_2 patient 63


title: EG-10-NeuralCrestSortedD22-1_S6

city: Lexington

first: Justin

last: Levens

state: KY

address: 2365 Harrodsburg Road

institute: Markey Cancer Center

description: sox10:dsRed 4

data_processing:
The 24 single-end raw sequencing files (.fastq) representing two conditions, three  replicates per condition, four lanes per replicate, were analyzed in Illumina’s BaseSpace   (https://basespace.illumina.com/). Data was analyzed using the tuxedo suite pipeline. Quality control (QC) of the raw sequence data was performed using FastQC (version 0.11.7)
The concatenated sequences were directly aligned to the Danio rerio GRCz11 reference  genome assembly (GRCz11.fa) using STAR (version 2.6), generating alignment files in  bam format. The alignment rate for each sample is above 90%.
For the Cuffdiff2 analysis, Cuffnorm was used to produce FPKM (Fragments Per Kilobase  Million) normalized counts. The counts were then filtered to include only genes with minimum expression of one FPKM in three or more samples and an average expression of at least one FPKM.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Danio rerio

source_name: sox10-positive cells Shoc2 KO rep1

extract_protocol:
mRNAs were isolated from from FACS purifyied sox10:dsRed positive cells of shoc2 CRISPR/Cas9 mutants and wild type larvae
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: devepopmental stage

value: 6 days post fertilization

value: 6 dpf embryo


title: SHEP MYCN-ER sgEAF1 FP-TT-Seq 4-OHT rep3

city: Chapel Hill

first: Donghai

last: Wang

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description:
spiked in TT-seq
Shep-MYCN-ER-sgEAF1-TT-4OHT-merge.bw

data_processing:
All RNA-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) by HISAT2 version 2.1.0, respectively. Raw read counts were normalized to RPM (Reads per Million) per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Read counts at indicated regions were calculated by HTSeq-count (version 0.12.3) and were provided to DEseq2 (version 1.32.0) for differential gene expression analysis. Human gene expression was normalized using Drosophila spiked-in genes. An FDR threshold of 0.05 and a log2 fold change cut off of 0.5 was used to identify differentially expressed genes.
TT-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) using HISAT2 version 2.1.0. The resulting reads were normalized to total reads aligned (Reads per Million) for each strand with deepTools (version 3.3.0). The read counts across each gene were counted with HT-seq (version 0.12.3), and DESeq2 were used for differentially gene expression analysis.
ChIP-seq raw reads were aligned to the human genome (hg38) with Bowtie (version 1.1.2) using default settings. Read coverage was performed with deepTools and were visualized on the UCSC genome browser. Peaks were called using MACS2 (version 2.1.2) using default parameters and an FDR cut off at 1e10-5 prior to annotation by ChIPseeker (version 1.28.3).
Assembly: hg38
Assembly: dm6
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: TT-seq

source_name: SHEP MYCN-ER

growth_protocol: SHEP MYCN-ER cells were cultured in RPMI-1640 (Hyclone, #SH30809.01) medium supplemented with 10% fetal bovine serum (FBS, Gibco, #10099-141) and 1% penicillin/streptomycin (Hyclone, #S110JV).

extract_protocol:
For TT-seq, total RNA extraction with Trizol reagent.
For RNA-seq, Total RNA was extracted from 50 million SHEP MYCN-ER cells spiked-in with 15% Drosophila S2 cells using Trizol reagent. mRNA was purified from 1 ug total RNA with the VAHTS mRNA capture beads, and fragmented to 200-500 bp size long in 2× ProtoScript II buffer. First- and second-strand DNA synthesis and adaptor ligation were conducteded using NEB Next Ultra RNA library prep kit for Illumina. The resulting strand-specific RNA-Seq libraries were subjected to 150 bp paired-end sequencing on a NovaSeq 6000.

treatment_protocol: A total of 1 × 107 SHEP MYCN-ER cells were treated with DMSO or 4-OHT (100 nM). For TT-seq, cells were then labeled with 400 μM 4-thiouridine at 37°C for 10 minutes before total RNA extraction with Trizol reagent. To assess elongation rates, cells were pre-treated with flavopiridol for 1 hour to pause Pol II near the transcription start sites (TSS) before 4sU labeling.The extracted total RNA was spiked-in with 4sU-labeled Drosophila S2 RNA.

value: SHEP MYCN-ER

tag: antibody


title: EG-09-NeuralCrestSortedWT-3_S5

description: sox10:dsRed 3

source_name: sox10-positive cells WT rep3

value: WT


title: LGG-141

label: Cy5 and Cy42

source_name: Lower-grade glioma_141


title: NAS_3  FIB_2  STH_2 patient 69

source_name: Liver


title: NAS_5  FIB_3  STH_2 patient 62


title: NAS_6  FIB_4  STH_2 patient 61


title: SHEP MYCN-ER sgEAF1 FP-TT-Seq 4-OHT rep2


title: SHEP MYCN-ER sgEAF1 FP-TT-Seq 4-OHT rep1


title: EG-08-NeuralCrestSortedWT-2_S4

description: sox10:dsRed 2

source_name: sox10-positive cells WT rep2


title: NAS_2  FIB_0  STH_0 patient 60


title: SHEP MYCN-ER sgEAF1 FP-TT-Seq DMSO rep3

description:
spiked in TT-seq
Shep-MYCN-ER-sgEAF1-TT-DMSO-merge.bw


title: NAS_2  FIB_0  STH_0 patient 68


title: LGG-146

label: Cy5 and Cy44

source_name: Lower-grade glioma_146


title: LGG-136

label: Cy5 and Cy40

source_name: Lower-grade glioma_136


title: LGG-133

label: Cy5 and Cy37

source_name: Lower-grade glioma_133


title: EG-07-NeuralCrestSortedWT-1_S3

description: sox10:dsRed 1

source_name: sox10-positive cells WT rep1


title: SHEP MYCN-ER sgEAF1 FP-TT-Seq DMSO rep2


title: NAS_5  FIB_3  STH_2 patient 59


title: NAS_1  FIB_3  STH_1 patient 58


title: P5A3_25

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

data_processing:
The bacterial sequencing reads were filtered for quality and aligned against the P. aeruginosa PAO1 genome (accession number NC_002516.2) using the BowTie2 read aligner.
DESeq2 was then used to obtain the list of differentially expressed genes.
Supplementary_files_format_and_content: tab delimited text file

organism: Pseudomonas aeruginosa

source_name: bacterial culture

growth_protocol: The overnight culture of P. aeruginosa PAO1 was diluted 1:100 in fresh LB medium and incubated aerobically for 3 h at 37°C. The culture was then diluted again 1:100 and grown in a total volume of 200 µl.

extract_protocol:
Two 200 µl cultures were pooled together and the total RNA was isolated from three samples using an RNeasy Mini Kit (Qiagen) following manufacturer’s guidelines.
The rRNA was removed using a Ribo-ZeroTM rRNA Removal kit for Bacteria (Epicentre). The first strand cDNA was constructed using the SuperScript II Reverse Transcriptase (Thermo Fisher Scientific), while the second strand was constructed using random hexamers (Thermo Fisher Scientific) and HiFi HotStart Readymix (Kapa Biosystems). The sequencing library was prepared using the Nextera XT (Illumina) tagmentation reaction with 1 ng of RNA serving as an input, following manufacturer’s instructions.

treatment_protocol: Bacterial cells were grown with or without the addition of 2.5 mM pillararene for 24 h with constant shaking.

tag: strain

value: Treatment with 2.5 mM pillararene


title: SHEP MYCN-ER sgEAF1 FP-TT-Seq DMSO rep1


title: LGG-128

label: Cy5 and Cy34

source_name: Lower-grade glioma_128


title: LGG-129

label: Cy5 and Cy35

source_name: Lower-grade glioma_129


title: NAS_1  FIB_0  STH_0 patient 57


title: P5A2_25


title: P5A1_25


title: SHEP MYCN-ER sgctrl FP-TT-Seq 4-OHT rep3

description:
spiked in TT-seq
Shep-MYCN-ER-sgctrl-TT-4OHT-merge.bw


title: SHEP MYCN-ER sgctrl FP-TT-Seq 4-OHT rep2


title: NAS_6  FIB_4  STH_2 patient 56


title: Ctrl3

value: Negative control (untreated sample)


title: SHEP MYCN-ER sgctrl FP-TT-Seq 4-OHT rep1


title: LGG-127

label: Cy5 and Cy33

source_name: Lower-grade glioma_127

value: IDH mutant


title: LGG-126

label: Cy5 and Cy32

source_name: Lower-grade glioma_126

value: Lower-grade glioma


title: LGG-134

label: Cy5 and Cy38

source_name: Lower-grade glioma_134


title: LGG-139

label: Cy5 and Cy41

source_name: Lower-grade glioma_139


title: LGG-124

label: Cy5 and Cy31

source_name: Lower-grade glioma_124


title: SHEP MYCN-ER sgctrl FP-TT-Seq DMSO rep3

description:
spiked in TT-seq
Shep-MYCN-ER-sgctrl-TT-DMSO-merge.bw

source_name: SHEP MYCN-ER

value: sgctrl/DMSO


title: Ctrl1


title: NAS_5  FIB_1  STH_2 patient 53


title: SHEP MYCN-ER sgctrl FP-TT-Seq DMSO rep2


title: SHEP MYCN-ER sgctrl FP-TT-Seq DMSO rep1


title: Zea mays Root Nuclei_4

city: New York

description:
10x Genomics 3' RNA seq V2
Maize_Sorghum_Setaria_Cells_Nuclei_Seurat_Obj.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_raw_counts.RData
Maize_Sorghum_Setaria_Cells_Nuclei_expression_matrix_Norm_counts.RData

data_processing:
Cell Ranger 5.0.1 (10x Genomics) to generate gene-cell matrices. Gene reads were aligned to the Arabidopsis TAIR10.38, Maize B73 v4, Sorghum bicolor v3 and Setaria viridis v2 reference genomes.
Replicates (see Supplementary Table 1) were integrated and cells mapped using the Seurat package v4.0 66 as follows: first, genes with counts in fewer than three cells were excluded from the analysis and their counts were removed. Second, low-quality cells were removed using threshold variable depending on the library quality (see supplementary Table 1). Clustering of cells or nuclei separately were done by log-normalized raw counts and the 2000 most variable genes were identified for each replicate using the “vst” method in Seurat. Next, we used the FindIntegrationAnchors function to identify anchors between the three datasets, using 20 dimensions. A new profile with an integrated expression matrix containing cells from all replicates was produced with the IntegrateData function. For dimensionality reduction, the integrated expression matrix was scaled (linear transformed) using the ScaleData function, and Principal Component analysis (PCA) performed. The top 30 principal components were selected. Cells or nuclei were clustered using a K-nearest neighbor (KNN) graph, which is based on the Euclidean distance in PCA space. The FindNeighbors and FindClusters function with a resolution of 0.5. was applied. Next, non-linear dimensional reduction was performed using the UMAP algorithm with the top 30 PCs.
For the co-clustering of cells and nuclei, either dataset were treated similarly, all replicates were integrated at once using the seurat 'SCT' approach. First raw reads were normalized using the SCTransform function, then SelectIntegrationFeatures was used to identify anchors between the datasets, using 3000 features.
For multiple species clustering, all orthologous genes names from were replaced by their corresponding maize ID in sorghum and setaria raw features.tsv.gz files (Gene conversion in Supplementary Table 1). Anchors are combined using PrepSCTIntegration and selected using FindIntegrationAnchors. For clustering of maize, sorghum and setaria together, all species were considered equally using the FindIntegrationAnchors function. Finally, a Principal Component analysis (PCA) is performed using the first 100 principal components and a non-linear dimensional reduction was performed using the UMAP algorithm with the top 100 PCs.
Supplementary files format and content: Processed data include, R Seurat Objects of integrated datasets, expression matrices normalized and raw count extracted from the Seurat objects, and a metadata containing the cell identities, genes or UMI per cell.

organism: Zea mays

source_name: root meristem

extract_protocol:
Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts, or in lysis buffer for nuclei extraction. Protoplasts or nuclei were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' kit
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2 and V3 protocol

value: Nuclei

value: root meristem

tag: age

value: 10 days old


title: NAS_3  FIB_0  STH_0 patient 54


title: Ctrl2


title: EG-11-NeuralCrestSortedD22-2_S7

description: sox10:dsRed 5

source_name: sox10-positive cells Shoc2 KO rep2


title: NAS_4  FIB_1  STH_2 patient 52

source_name: Liver


title: LGG-119

label: Cy5 and Cy29

source_name: Lower-grade glioma_119


title: LGG-123

label: Cy5 and Cy30

source_name: Lower-grade glioma_123


title: NAS_4  FIB_1  STH_2 patient 51


title: NAS_5  FIB_2  STH_2 patient 55


title: NAS_0  FIB_2  STH_1 patient 50


title: Zea mays Root Nuclei_2


title: Zea mays Root Nuclei_3


title: NAS_7  FIB_1  STH_NA patient 49


title: LGG-116

label: Cy5 and Cy26

source_name: Lower-grade glioma_116


title: LGG-131

label: Cy5 and Cy36

source_name: Lower-grade glioma_131


title: CPX rep3

data_processing:
RNA-seq reads quality was evaluated using FastQC (version 0.11.9) and mapped to the human genome reference assembly (hg19) using STAR 2.4.1.7 Differential gene expression analysis was performed using DESeq2 (version 1.32.0). Differential alternative splicing (AS) events were quantified by using rMATS8 and JUM9 for five major types (SE, A5SS, A3SS, MXE, IR). AS events were considered as significant if |IncLevelDifference| or |ΔPSI |>0.1 and p-value < 0.05.
For RIP-Seq, the reads quality was evaluated using FastQC (version 0.11.9) and mapped to the human genome reference assembly (hg38) using STAR software (version 2.7.5c). The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Genes with Log2[fold change (FC)] > 1 and FDR < 0.05 found by DESeq were considered to be significant enrichment..
For scRNA-seq, we demultiplexed the sequencing reads into single cells according to unique barcode sequences and aligned them to the mm10 reference using Cell Ranger (version 6.0.2). We merged the single cell expression data from Dhx15fl/fl and Dhx15 KO thymocytes and eliminated potential doublets using Scanpy (version 1.7.1). We retained cells expressing more than 500 genes and containing less than 20% of transcripts mapping to mitochondrial genes, and filtered out uninformative genes which were detected in less than 3 cells. We further excluded the cells with gene counts or unique molecule identifier (UMI) counts detected outside the interval of mean value plus or minus two-fold standard deviation. We then normalized, scaled and log-transformed gene expression for each cell, and performed principal component analysis using the highly variable genes selected by dispersion-based methods in Scanpy. Uniform Manifold Approximation and Projection (UMAP) was used to visualize the distribution of cells in the projection of the significant principal components and cells were clustered using Leiden algorithm. Trajectory analysis were performed using Monocle 3. Cell cycle states (G1, S, G2/M) of cells were annotated by scoring gene sets with Scanpy.
Assembly: hg38
Assembly: mm10
Supplementary files format and content: csv and tsv

growth_protocol: T-ALL line CUTLL1 cells were grown in complete RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gemini), 1% penicillin/streptomycin (Hyclone), 1% non-essential amino acids (Gibco), 2mM L-glutamine (Sigma), 1 mM sodium pyruvate (Sigma), and 100 μM β-mercaptoethanol (Sigma).

extract_protocol:
For RNA-seq, total RNA was extracted using Trizol.
For RIP-seq, total RNA extraction with Trizol.
For scRNA-seq, total RNA was extracted using Trizol.
For RNA-seq, total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and subjected to quality control for RNA integrity by Agilent Bioanalyzer 2100 system (Agilent Technologies). Total RNA was further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN). Poly(A)+ RNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) and sequenced as 150 bp paired-end reads by Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation).
For RIP-seq, ten million CUTLL1 cells were lysed in RIP lysis buffer [20 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1 mM EDTA, 0.1% SDS, 100 U/ml RNasin Ribonuclease Inhibitors (Promega)]. The resulting cell lysates were incubated with 5 µg of DHX15 antibody (Abcam) or control IgG at 4°C overnight. Protein A/G magnetic beads (Thermo Fisher Scientific) were then added and incubated for 2 h at 4°C to conjugate the protein-antibody complexes. After washing with RIP buffer, beads were resuspended in 80 μl PBS, followed by DNase treatment (Thermo Fisher Scientific) and proteinase K (50 μg) (Thermo Fisher Scientific) digestion at 37 °C for 15 min.  Input and co-immunoprecipitated RNAs were isolated by TRIzol reagent (Thermo Fisher Scientific), and analyzed by qPCR or RNA-seq. NEBNext rRNA Depletion Kit v2 (New England BioLabs) was used to remove rRNA, and NEBNext Ultra II RNA Library Prep Kit (New England BioLabs) was then applied for library construction. RNAs were sequenced as 150 bp paired-end reads using Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation, China).
For scRNA-seq, single-cell suspensions of total thymocytes from 6-week-old Dhx15fl/fl or Dhx15 KO mice were prepared by filtering thymus tissues against a 40-μm cell strainer. Single cells were captured in droplet emulsions using a GemCode Single-Cell Instrument (10Genomics). scRNA-seq libraries were constructed according to the 10 Genomics protocol using Chromium Single-Cell 3′ Library and Gel Bead Kit V3.1 (10Genomics), and sequenced using Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation).

treatment_protocol: CUTLL1 cells were infected with lentiviruses expressing DHX15 shRNA or treated with ciclopirox (MedChemExpress, HY-B0450)  for indicated hours .

value: ciclopirox


title: DMSO rep3

value: DMSO


title: CPX rep1


title: CPX rep2


title: Zea mays Root Nuclei_1


title: NAS_6  FIB_2  STH_2 patient 48

value: Liver


title: s3917_cbl

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

data_processing:
nf-core-rnaseq-3.4 was used for the following steps of data processing: fastq quality control, adapter trimming, alignment to the reference genome (GRCm39, GCA_000001635.9) using STAR, quantification using salmon.
The resulting gene counts were transformed to Log2 counts per million (CPM). Lowly expressed genes were filtered out and libraries were normalized by trimmed mean of M-values. The Limma R package was used to calculate differential expression among genes. Log2 fold change values were calculated for Ethanol compared to Control, and genes with an adjusted (adj.) p ≤ 0.05 were considered statistically significant.
Assembly: GRCm39, GCA_000001635.9
Supplementary files format and content: comma-delimited text file including gene count data calculated using salmon.

source_name: Brain, Cerebellum

extract_protocol:
Tissue was homogenized using a B2X24B Bullet Blender and 0.5 mm glass beads as described by the manufacturer (Next Advance, Troy, NY).  RNA was isolated using the RNeasy Lipid Tissue Mini Kit with on-column DNase digestion using the RNase-free DNase Set (Qiagen, Valencia, CA, Cat #74804 and #79254).
RNA-seq libraries were prepared using Illumina TruSeq mRNA Library Prep Kit with TruSeq Unique Dual Indexed adapters (Illumina, San Diego, CA) and were quantified with Qubit 1X dsDNA High-Sensitivity NGS Gel Kit (Thermo Fisher Scientific). KAPA Library Quantification (Roche, Basel, Switzerland) was used for further library characterization and Agilent Fragment Analyzer with the High-sensitivity NGS Gel Kit (Agilent) was used for determining fragment size

value: Brain, Cerebellum

value: adult

value: Ethanol


title: s3918_cbl


title: LGG-118

label: Cy5 and Cy28

source_name: Lower-grade glioma_118


title: DMSO rep2


title: NAS_2  FIB_NA  STH_NA patient 47


title: s3813_cbl


title: NAS_6  FIB_1  STH_1 patient 46


title: s3812_cbl


title: LGG-115

label: Cy5 and Cy25

source_name: Lower-grade glioma_115


title: NAS_3  FIB_0  STH_0 patient 45


title: LGG-117

label: Cy5 and Cy27

source_name: Lower-grade glioma_117


title: NAS_4  FIB_0  STH_1 patient 44


title: s3810_cbl


title: s3925_cbl

value: Control


title: IP rep1

value: IP DHX15


title: IP rep2


title: EG-12-NeuralCrestSortedD22-3_S8

description: sox10:dsRed 6

source_name: sox10-positive cells Shoc2 KO rep3

value: 6 days post fertilization

value: 6 dpf embryo


title: s3924_cbl


title: DMSO rep1


title: NAS_7  FIB_3  STH_2 patient 43


title: LGG-114

label: Cy5 and Cy24

source_name: Lower-grade glioma_114


title: NAS_1  FIB_0  STH_0 patient 42


title: NAS_5  FIB_2  STH_2 patient 41


title: igG

value: igG


title: s3923_cbl


title: input

value: input


title: sh2 rep3


title: 4C_AHI1-E1vp

description: 4C-seq using using as viewpoint the enhancer candidate E1 in AHI1 (chr6:135748430-135748869;hg19)

value: leukemic


title: s3818_cbl


title: NAS_4  FIB_1  STH_2 patient 40


title: s3815_cbl


title: NAS_4  FIB_2  STH_2 patient 39


title: sh2 rep2


title: NAS_6  FIB_1  STH_2 patient 38


title: Yeti_3

city: San Francisco

first: Tien

last: Peng

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

data_processing:
FASTQC for  quality control, Cuadapt and Sickle for triming adaptors
reads were aligned and mapped using STAR
DESeq was use to call differential gene expression, in Rstudio
Assembly: UCSC Mouse (GRCm38/mm10)

source_name: Lung mesenchyme

extract_protocol: The RNA was extracted by QIAGEN RNeasy Mini Kits from the cultured cells, and the amount and quality of extracted RNA was measured by RNA 6000 Pico Kit (Agilent). The Bulk RNA-seq was done in GENEWIZ.

treatment_protocol: mice were Tamoxifen injected

value: Adult


title: sh1 rep3


title: Yeti_2


title: LGG-110

label: Cy5 and Cy21

source_name: Lower-grade glioma_110

value: IDH mutant

value: Lower-grade glioma


title: LGG-112

label: Cy5 and Cy23

source_name: Lower-grade glioma_112


title: LGG-109

label: Cy5 and Cy20

source_name: Lower-grade glioma_109


title: LGG-111

label: Cy5 and Cy22

source_name: Lower-grade glioma_111


title: sh1 rep2


title: NAS_4  FIB_3  STH_2 patient 37


title: LGG-106

label: Cy5 and Cy17

source_name: Lower-grade glioma_106


title: LGG-108

label: Cy5 and Cy19

source_name: Lower-grade glioma_108


title: LGG-105

label: Cy5 and Cy16

source_name: Lower-grade glioma_105


title: sh1 rep1


title: Yeti_1


title: LGG-107

label: Cy5 and Cy18

source_name: Lower-grade glioma_107


title: Yeti Control_3


title: NAS_0  FIB_0  STH_0 patient 35

source_name: Liver


title: NAS_6  FIB_1  STH_2 patient 36


title: ctrl rep3

value: shGFP


title: LGG-95

label: Cy5 and Cy12

source_name: Lower-grade glioma_95


title: NAS_5  FIB_2  STH_2 patient 34


title: ctrl rep2


title: sh2 rep1


title: Yeti Control_2


title: LGG-103

label: Cy5 and Cy15

source_name: Lower-grade glioma_103


title: LGG-101

label: Cy5 and Cy14

source_name: Lower-grade glioma_101


title: ctrl rep1


title: LGG-97

label: Cy5 and Cy13

source_name: Lower-grade glioma_97


title: NAS_4  FIB_0  STH_1 patient 33


title: LGG-93

label: Cy5 and Cy10

source_name: Lower-grade glioma_93


title: NAS_5  FIB_NA  STH_2 patient 32


title: Yeti Control_1


title: 10 days old P19 neuronal exosomal RNA sample #5

city: Manhattan

first: Meena

last: Kumari

state: KS

address: 231 Coles Hall

institute: Kansas State University

data_processing:
Each library was indexed to multiplex six samples for sequencing on the Illumina NextSeq platform using NextSeq mid output 150 cycles kit, PE 75bp, (Illumina, #FC-404-2001). The raw data was processed to generate FASTQ files. During this step, the 3’ adaptor sequences were trimmed and low quality reads were removed. Sequences from all samples were processed independently using the CLC Genomics Workbench (Qiagen®) to generate paired sequences that were concatenated. The default parameters in the Workbench were used to analyze the samples and derive the counts. The number of reads ranged between ~1.6 to ~4 million. The miRbase and ncRNA databases were used to annotate the samples. Differential gene expression was determined by using the empirical analysis of DGE tool of the Workbench which implements the 'Exact Test' for two-group comparison as incorporated in the edgeR Bioconductor package. The test uses the raw counts, and implicitly carries out normalization and transformation of these counts. It is based on the assumption that the count data follows a Negative Binomial distribution. Using the ENSEMBL ncRNA database, several ncRNAs were differentially expressed (FDR < 0.05) between UD-P19 exosomes and P19 neuronal exosomes.
The Fastq files were each sample were merged to get the total reads for each sample using CLC Genomics Workbench (Qiagen) with a custom workflow
The reads were aligned to Mus musculus ensembl v80 sequences without masking using default parameters
Reads were annotated using Mus musculus GRCm38.ncRNA
Differential Expression determined using CLC Genomics Workbench which uses default settings in edgeR Bioconductor package
Genome_build: Mus musculus ensembl v80
Supplementary_files_format_and_content: Tab delimited text. All annotated ncRNAs

source_name: 10 days old P19 neuronal exosomal RNA

growth_protocol: UD-P19 cells were cultured in 75 cm2 flasks in alpha-MEM supplemented with 10% fetal bovine serum (FBS). Cells were plated to reach ~ 50% confluency in 24h. Next day, cells were washed three times with PBS and maintained in 10 ml defined culture medium [alpha-MEM supplemented with N2 supplement]. Twenty four hours later, conditioned medium was collected and processed immediately to isolate exosomes. To isolate exosomes from conditioned medium of P19 neurons, UD-P19 cells cultured in alpha-MEM supplemented with 5% FBS were induced to differentiate into neurons by exposure to retinoic acid for 4 days with change of medium after two days (Anji and Kumari (2009) J Neurosci Res 87:1591-1601). P19 neurons were cultured in neurobasal media containing 0.5 mM glutamine, B27 and N2 supplements for 8 to 16 days in vitro in 75 cm2 flasks. Condition medium collected on day 8, day 10, and day 12 was used to isolate exosomes by ultracentrifugation method.

extract_protocol:
Conditioned medium (CM) collected from cultured cells was processed immediately for exosome isolation by differential centrifugation method. CM was initially centrifuged at 2,500 xg/10 min/4ºC in tabletop low speed centrifuge (Allegra, Beckman Coulter, Inc.). Pellet containing cells was discarded. Supernatants were recovered and centrifuged at 14,500 rpm/10 min/4ºC/SW 55Ti rotor (XL80K Beckman ultracentrifuge). Pellets were discarded and supernatants were centrifuged at 45,900 rpm/33 min/4ºC/ SW 55Ti rotor. Supernatants were discarded and pellets containing exosomes were recovered from all six tubes using ice-cold 1X phosphate buffered saline (PBS) by gentle pipetting. Exosomes recovered from all tubes were pooled and centrifuged again at 45,900 rpm/33 min/4ºC (wash step). Supernatant was discarded. Pellet containing washed exosomes was suspended in 100 µL DEPC water by gentle pipetting and processed immediately for isolation of RNA using miRCURY™ RNA isolation kit (Exiqon, Inc.; now Qiagen) according to the instructions of the Supplier. Purified RNA was eluted using 50 µl of DEPC water. Two µl aliquot was used to measure RNA concentration using NanoDrop™ 8000 spectrophotometer and analyzed on BioAnalyzer and by 5’-end-labeling with T4 polynucleotide kinase and analysis on denaturing gel.
RNA from exosomes of UD-P19 cells (three biological replicates) and P19 neurons (8, 10, and 12 days old) were processed to generate double stranded barcoded cDNA libraries using NEBNext® Multiplex Small RNA Library Prep Set (NEB) according to instructions of the supplier. All six cDNA libraries had a unique barcode. All barcoded cDNA libraries were purified using AMPure XP beads (Beckman Coulter) and quantitated on BioAnalyzer using Agilent DNA High Sensitivity chip. The libraries were pooled in equimolar amounts. The final cDNA library pool was quantified with KAPA Library Quantification kit for Illumina (KAPA Biosystems, #KK4824) using the BioRad CFX96 Real Time PCR system. Pooled libraries were sequenced at K-State Integrated Genomics Facility with NextSeq mid output 150 cycles kit, PE 75bp, (Illumina, #FC-404-2001) on Illumina NextSeq 500 platform according to manufacturer's recommendations to provide full to partial coverage of various RNA molecules in the samples.
No size fractionation

treatment_protocol: Cells were not exposed to any drug.

value: 10 days old P19 neuron

tag: sample type

value: Exosomal RNA


title: 12 days old P19 neuronal exosomal RNA sample #6

source_name: 12 days old P19 neuronal exosomal RNA

value: 12 days old P19 neuron


title: riboseq analysis in hela cells treated with u1 amo

data_processing:
sequenced were mapped to hg38 genome, clean reads were obtained by removing low quality reads, such as N rich reads, no adapter reads,
rRNA, tRNA reads were removed
Genome build: hg38
Library strategy: Ribo-Seq

source_name: Hela cell

extract_protocol: 1. cells were lysated 2. ribosome-associated RNAs were purified. 3. rRNAs were removed 4. Ribosome-protected RNAs were used for making small RNA libraries.

value: Hela cell

value: tumor cell line

tag: treatment

value: U1 AMO


title: riboseq analysis in hela cells treated with control amo

value: control AMO


title: LGG-94

label: Cy5 and Cy11

source_name: Lower-grade glioma_94


title: NAS_6  FIB_NA  STH_2 patient 31

data_processing:
Raw data QC was performed, including base composition quality, fragment size, mapping read count, 3’ bias, read count mapping breakdown, adapter/phiX content, heterologous organism contamination, and sex/ethnicity prediction concordance. Greater than 100 million reads were obtained per sample and reads were mapped to a reference human transcriptome. The ratio between the highest and lowest total mapped reads per sample was 4.2, indicating good read depth consistency across samples. Each sample (or library) was assessed in 4 or 5 replicates (assays). Data correlation of replicates from the same sample were checked. One replicate from all 434 assays was excluded due to low correlation. Replicates were aggregated into one measurement value per sample per gene. There were 93 unique patients in the final cohort with both phenotype information and RNA-seq data.
Assembly: reads were mapped to a human transcriptome, GRCh37
Supplementary files format and content: NAFLD_RNA_counts.csv contains comma separated values of aggregated read counts per gene per sample

extract_protocol:
BioChain Broad Range Total RNA isolation kit
Illumina HT Truseq Stranded kit

value: Liver


title: NAS_3  FIB_0  STH_1 patient 30


title: LGG-90

label: Cy5 and Cy7

source_name: Lower-grade glioma_90


title: mRNAseq analysis in hela cells treated with u1 amo

description: mRNA-seq analysis in U1 amo treated hela cells

data_processing:
sequenced were mapped to hg38 genome, clean reads were obtained by removing low quality reads, such as N rich reads, no adapter reads,
rRNA, tRNA reads were removed
Genome build: hg38

extract_protocol:
1. cells were lysated 2. polyA+ mRNAs were purified with oligodT beads. 3. polyA+ mRNAs were used for making transcriptome sequencing libraries.
RNAs were fragmented, dephorsphorylated, and further ligated to 5' and 3' adaptors. cDNAs were made by reverse transcription.PCR were used for making libraries for sequencing.


title: LGG-92

data_processing: Raw methylation data were processed on the HumanMethylation450 BeadChip with the R package wateRmelon and normalized with dasen using the statistical software R.

label: Cy5 and Cy9

source_name: Lower-grade glioma_92

extract_protocol: Genomic DNA was extracted using the QIAamp DNA FFPE tissue Kit  (Qiagen) according to the manufacturer's instructions except lysis with Proteinase K was performed overnight.


title: mRNAseq analysis in hela cells treated with control amo

description: mRNA-seq analysis in control hela cells


title: NAS_2  FIB_0  STH_0 patient 28


title: Undifferentiated  P19  cell exosomal RNA sample #3

source_name: Undifferentiated  P19  cell exosomal RNA

value: undifferentiated P19 cells


title: Undifferentiated  P19  cell exosomal RNA sample #1


title: 8 days old P19 neuronal exosomal RNA sample #4

source_name: 8 days old P19 neuronal exosomal RNA

value: 8 days old P19 neuron