title: Patient ID: 41, sample ID: 70


title: Patient ID: 36, sample ID: 65

status: Public on Nov 23 2021

type: RNA

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

country: Sweden

institute: Umeå University

hyb_protocol: Clariom D Human Arrays were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip TM Expression Wash, Stain and Scan Manual (PN 702731, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA) the arrays were then washed and stained using the GeneChip TM Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip TM Scanner 3000 7G.

data_processing: The dataset was Robust Multichip Average (RMA) normalized. Briefly, the raw intensity values were background corrected, log2 transformed and then quantile normalized.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: crista

label_protocol: 100 ng of RNA was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip TM WT PLUS Reagent Kit manual Target Preparation for GeneChip TM Whole Transcript (WT) Expression Arrays User Guide (P/N 703174, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA).

extract_protocol: Allprep RNA/DNA/Protein isolation protocol (Qiagen, Hilden, Germany)

tag: disease state

value: prostate cancer

tag: tissue

value: metastasis tissue sample

tag: tissue source

value: crista

tag: treatment group

value: Castration resistant

tag: patient id


title: Patient ID: 34, sample ID: 62


title: FED-H3K4me3_F1_ChIP-seq

type: SRA

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

country: USA

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mm9 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Genome_build: mm9
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K9bhb, H4K12bhb and H3K27ac enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

molecule: genomic DNA

organism: Mus musculus

source_name: Small Intestine

growth_protocol: Male and female mice (strains: Lgr5EGFP-IRES-CreERT2/+ Strain name: B6.129P2-Lgr5tm1(cre/ERT2)Cle/J, JAX, 008875) and C57BL/6J (JAX, 000664)) were purchased, bred in house, and maintained at 72°F +/- 2 °F on a 12h light/dark cycle. Six- to twelve-week-old aged matched males and females were randomly assigned to either fed or fasted groups. Fed animals were provided ad libitium access to food (PicoLab 5053, #0007688) and water for 24h, fasted animals were completely food deprived for 24h with ad libitium access to water. Experimental mice were singly housed on aspen bedding for the duration of experiments

extract_protocol:
Chromatin immunoprecipitations were performed using a previously published protocol with modifications for SI crypts. Briefly, whole isolated crypts from 4 animals were pooled per treatment per replicate and cross linked for 10 min at 37°C with 1% formaldehyde in supplemented media and quenched with 0.125M glycine for 5 min at 37°C. Crypts were washed with PBS with 1× protease inhibitor cocktail (Sigma-Aldrich) and stored at -80°C. Pellets were thawed and then lysed for 30 min on ice with I-ChIP buffer (12mM Tris–HCl pH 8.0, 6mM EDTA pH 8.0, 0.1x PBS, 0.5% SDS) plus cOmplete mini protease inhibitors. Sonication conditions were optimized for SI crypt cells using a Bioruptor (Diagnode) to achieve shear length of 250-500bp. 10% total chromatin was reserved as an input control. Chromatin was diluted 5 fold and immunoprecipitation was performed overnight by incubation of the sonicated cell lysate with 30ul of protein G magnetic dynabeads (Invitrogen) previously coupled to target antibody for a minimum of 1h at 4°C. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and reverse cross linking was performed in 50ul direct elution buffer (10mM Tris–HCl, pH 8.0, 5mM EDTA, pH 8.0, 300mM NaCl and 0.5% SDS) with Proteinase K and RNaseA at 65°C overnight. Eluted DNA was cleaned up with solid-phase reversible immobilization (SPRI) beads (Beckman-Coulter).
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol:
Crypt isolation followed previously published protocols with minor modifications [Guo, 2009 #5169;Tinkum, 2015 #4005]. Briefly fed or fasted mice were euthanized by CO2, the whole SI was collected, flushed with PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) to remove feces, and the mesentery was removed. The SI sample was cut longitudinally then cut transversely into 4 equal pieces. Each sample was placed on ice in PBS (Ca2+- and Mg2+-free, 100nM TSA) while the remaining samples were collected. After collection of all samples, SI were incubated in PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) for 10 min then transferred to HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA). Crypts were released through a series of vortex washes at 1,600rpm in HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) at 4°C. Supernatants from all vortex washes were filtered through 70-μm mesh and pooled into 50ml conical tubes to remove villus material and tissue fragments. Isolated crypts were pelleted at 1000rpm at 4°C. After this step, whole crypts were utilized for flow cytometry (detailed below), spheroid cell line establishment [de la Cruz Bonilla, 2018 #5161] and treatment (detailed below), or ChIP-seq (detailed below). For ChIP-seq, crypts were first suspended in ADMEM/F12 (D6421, Sigma) supplemented with 10 U/mL penicillin, 10μg/mL streptomycin, 2mM L-glutamine, 10mM HEPES, 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem), 10µM Y-27632 dihydrochloride (Sigma), 0.5mM N-acetylcysteine amide (Sigma), and 100nM TSA.
Whole crypt isolates were suspended in Matrigel™ and plated in a 24-well tissue culture dish (30 μl per well) as described [de la Cruz Bonilla, 2018 #5161]. Cultures were grown in 50% L-WRN conditioned media supplemented with 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem) and 10µM Y-27632 dihydrochloride (Sigma) added to each culture well. Media was changed every second day and spheroids were subcultured every third day. For experimental treatments of spheroid cultures, 50% L-WRN conditioned media was supplemented with either 5 or 10mM (R)-(–)-3-Hydroxybutyric acid (298360, Sigma) with 10µM TGF-β RI Kinase Inhibitor VI and 10µM Y-27632 dihydrochloride added to each treatment culture well. Standard media changes occurred for untreated control culture wells. All treatments were 24h prior to spheroid isolation from Matrigel™ for ChIP-qPCR or immunoblotting analyses.

value: crypt

tag: genotype

value: wildtype

tag: Sex

value: pooled male and female

tag: chip-antibody

value: H3K4me3 Abcam ab8580


title: Patient ID: 38, sample ID: 67


title: FED-H3K79me2_F4_ChIP-seq

value: H3K79me2 Abcam ab3594


title: FED-H3K79me2_F1_ChIP-seq


title: FED-H3K9me3_F1_ChIP-seq

value: H3K9me3 Abcam ab8898


title: Patient ID: 35, sample ID: 63


title: Patient ID: 43, sample ID: 73


title: FED-H3K9me3_F4_ChIP-seq


title: FED-H3K27ac_F1_ChIP-seq

value: H3K27ac Abcam ab4729


title: Patient ID: 42, sample ID: 72


title: FED-H3K4me1_F4_ChIP-seq

value: H3K4me1 Abcam ab8895


title: Patient ID: 36, sample ID: 64


title: Patient ID: 32, sample ID: 59

source_name: spine

value: spine


title: Patient ID: 32, sample ID: 58


title: FED-H3K4me1_F1_ChIP-seq


title: FASTED-H3K27ac_S2_ChIP-seq


title: Patient ID: 32, sample ID: 60


title: FED-H4K12bhb_F4_ChIP-seq


title: Patient ID: 31, sample ID: 55

value: Short-term castrated


title: Patient ID: 31, sample ID: 57


title: FED-H4K12bhb_F1_ChIP-seq


title: Patient ID: 30, sample ID: 53


title: Patient ID: 31, sample ID: 56


title: FED-H3K9bhb_F4_ChIP-seq

value: H3K9bhb PTM-biolabs PTM-1250


title: FED-H3K27ac_F4_ChIP-seq


title: FED-H3K9bhb_F1_ChIP-seq


title: Patient ID: 30, sample ID: 52


title: 9B04Jmjd5_15C_LTSO180412_R1

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

library_source: transcriptomic

data_processing:
For ChIP-seq, fastq reads were aligned to C. elegans and drosophila reference genomes (downloaded from wormbase, PRJNA13758, and UCSC, dm6, respectively) using bowtie with default parameters, discarding multimapping reads. PCR duplicates were removed using samblaster. Reads aligning to both PRJNA13758 and dm6 genomes were removed. Peaks were called with MACS2 with a p-value threshold of 1e-5 and were further annotated with ChIPseeker. To eliminate differences in library size and to perform a calibrated quantification of ChIP-seq signal, we calculated a normalization factor based on the reads aligning to the spike-in genome as described in (Orlando et al 2014).
For the RNA-seq of whole worm analyses, reads were aligned to C.elegans reference genome, ce10, using STAR with default parameters and removing multimapping reads. PCR duplicates were removed with samblaster and gene quantification was performed using featureCounts with default parameters. Differential expression analyses were performed with the R package DESeq2. P-values and log2 fold changes were further corrected with ihw and apeglm R packages, respectively, with default parameters. Finally, genes with an adjusted p-value < 0.01 and absolute log2FC >= 1 were considered differentially expressed
Genome_build: ce10
Supplementary_files_format_and_content: MACS2 narrowPeak and DESeq2 differtial expression analysis (tsv); raw counts

organism: Caenorhabditis elegans

growth_protocol: N2 and jmjd-5(zr1234) young adult worms ) were collected at the indicated temperature and generations, washed 3 times in M9 and flash-frozen in liquid nitrogen.

extract_protocol: Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) and Multiplex Oligos for Illumina (NEB E7335S, E7500S). Quality and size of the libraries were checked by Bioanalyzer (Agilent 2100 Bioanalyzer).

tag: developmental stage

value: Germline

tag: temperature of growth


title: 9B04Jmjd5_15C_LTSO180412_R2


title: Patient ID: 33, sample ID: 61


title: 8A04Jmjd5_15C_LTSO180412_R1


title: 53H03N2_25C_F3_LTSO180412_R2

source_name: N2 (wild type)

value: N2 (wild type)


title: Mac2_parietal

city: San Francisco

first: Alex

middle: A

last: Pollen

state: CA

address: 35 Medical Center Way

department: Neurology

institute: UCSF

data_processing:
kallisto quantification RheMac10
cellbender ambient RNA removal
normalization, +1 log transform and scaling applied to h5ad X
Genome_build: RheMac10
Supplementary_files_format_and_content: MacaqueDevInhibitoryNeurons.h5ad contains normalized, log1p, and scaled data along with PCA and UMAP projections, obs.csv contains cell metadata, var.csv contains gene metadata, X.csv is the raw cells by genes kallisto + cellbender matrix

molecule: polyA RNA

organism: Macaca mulatta

source_name: primary brain tissue

extract_protocol:
whole cells, dissociated using papain
10X chromium 3’ RNAseq V2/3

value: brain

tag: region

value: Parietal


title: Mac2_somatosensory

value: Somato


title: Patient ID: 29, sample ID: 51

value: prostate cancer

value: metastasis tissue sample

value: Hormone-naïve


title: 53H03N2_25C_F3_LTSO180412_R1


title: Mac2_CGE

value: CGE


title: Patient ID: 27, sample ID: 47

value: Castration resistant


title: Patient ID: 31, sample ID: 54


title: 8A04Jmjd5_15C_LTSO180412_R2


title: Patient ID: 27, sample ID: 48


title: Patient ID: 28, sample ID: 49


title: Patient ID: 26, sample ID: 46


title: Patient ID: 26, sample ID: 44


title: 52G03N2_25C_F3_LTSO180412_R1


title: Patient ID: 26, sample ID: 43


title: 52G03N2_25C_F3_LTSO180412_R2


title: LSR_375

first: Jonathan

middle: Thomas

last: Lei

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
paired-end cram file (contains both paired end reads)
Paired-end reads were provided to ChimeraScan v0.4.5
Aligned reads by TopHat2 were provided to INTEGRATE v0.1
ChimeraScan results were filtered by removing records with types marked as read through, overlapping converging, overlapping diverging, adjacent converging, and adjacent diverging
Genome_build: hg19
Supplementary_files_format_and_content: Fusion transcript output results from ChimeraScan and INTEGRATE

source_name: Breast

extract_protocol:
Poly A mRNA was isolated from frozen metastatic biopsies from patients with ER+ breast cancer
Illumina TruSeq sample prep kit was used for library preparation

value: Breast

tag: disease

value: estrogen receptor positive (ER+) breast cancer

tag: disease stage

value: late-stage relapse (LSR)

tag: sample type

value: Metastatic (stage IV)


title: LSR_347


title: Patient ID: 26, sample ID: 45

value: spine


title: LSR_337


title: LSR_385


title: LSR_349


title: LSR_360


title: LSR_316


title: 51E02N2_25C_F3_LTSO180412_R2


title: Patient ID: 26, sample ID: 42

value: Short-term castrated


title: 45D02N2_25C_F3_LTSO180412_R2


title: 51E02N2_25C_F3_LTSO180412_R1


title: LSR_307


title: LSR_301


title: LSR_294


title: LSR_281


title: 45D02N2_25C_F3_LTSO180412_R1


title: LSR_273


title: LSR_277


title: 2A01N2_15C_LTSO180412_R2


title: 42C02N2_25C_F3_LTSO180412_R2


title: LSR_276


title: Patient ID: 26, sample ID: 41


title: LSR_223


title: LSR_218


title: LSR_242


title: Patient ID: 24, sample ID: 37


title: Patient ID: 23, sample ID: 35


title: Patient ID: 25, sample ID: 40


title: Patient ID: 24, sample ID: 36


title: LSR_222


title: LSR_243


title: 42C02N2_25C_F3_LTSO180412_R1


title: LSR_217


title: 18E04Jmjd5_15C_LTSO180412_R2


title: LSR_230


title: LSR_211


title: 16D04Jmjd5_15C_LTSO180412_R2


title: Patient ID: 28, sample ID: 50


title: Patient ID: 23, sample ID: 34


title: 18E04Jmjd5_15C_LTSO180412_R1


title: 2A01N2_15C_LTSO180412_R1


title: Patient ID: 24, sample ID: 38


title: S11G2T2435

city: Seoul

first: PI EN

last: CHANG

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

department: Department of Orthodontics

country: South Korea

institute: Yonsei University College of Dentistry

data_processing:
Base calling was performed by bcl2fastq 2.0
The read length Hiseq2500 platform 100PE was used to put fastqc files.
Total Bases of sequencing statistics in raw data divided by Total Reads (=101): Progress with Hiseq2500 platform 100PE
Genome_build: 100PE
Supplementary_files_format_and_content: FPKM Excel file

source_name: adult premolar periodontal ligment

extract_protocol:
PDL cells were washed with cold PBS after gentle scrapping from the extracted premolar. Total RNA was extracted from PDL cells using TRIzol Reagent. The RNA was stored at −70 °C and measured at an optical density of 260 nm. The mixtures of total RNA were incubated with Oligo dT. Real-time PCR was performed for the selected upregulated and downregulated genes to verify RNA-seq results.
The library was constructed, sequenced using an Illumina HiSeq2500 sequencer, and the data obtained through RNA-seq.

value: adult tooth PDL

tag: treatment

value: no occlusal contact

tag: age


title: Patient ID: 22, sample ID: 32


title: Patient ID: 23, sample ID: 33


title: Patient ID: 21, sample ID: 31


title: S11G1T1445

value: normal occlusal contact


title: Patient ID: 21, sample ID: 30


title: LSR_192


title: LSR_338


title: G1S72434


title: G1S8T34


title: G2S71444


title: S10G2T45


title: 14E01N2_15C_LTSO180412_R1

value: N2 (wild type)

value: Germline


title: S10G1T350


title: 13D01N2_15C_LTSO180412_R2


title: Patient ID: 24, sample ID: 39


title: Patient ID: 21, sample ID: 29


title: G1S6T2534_TN1811R1452


title: 16D04Jmjd5_15C_LTSO180412_R1


title: G2S6T1544_TN1811R1453


title: 14E01N2_15C_LTSO180412_R2


title: Kim-24_Kim-34


title: 12C01N2_15C_LTSO180412_R2


title: 13D01N2_15C_LTSO180412_R1


title: 12C01N2_15C_LTSO180412_R1


title: G2S8T44


title: Kim-14_Kim-44


title: Patient ID: 20, sample ID: 28


title: 2018.05.24_14--2018.05.24_44


title: 2018.05.29_34


title: 2018.05.29_44


title: 2018.05.24_24--2018.05.24_34


title: Patient ID: 20, sample ID: 27


title: Patient ID: 19, sample ID: 26


title: 10C04Jmjd5_15C_LTSO180412_R2


title: Patient ID: 18, sample ID: 25


title: 11B01N2_15C_LTSO180412_R2


title: 10C04Jmjd5_15C_LTSO180412_R1


title: Patient ID: 18, sample ID: 24


title: TM-4

extract_protocol:
Young adults grown at 25°C at F3 generation were collected and washed in M9 to remove residual bacteria, flash-frozen in liquid nitrogen and stored at -80°C before RNA extraction. RNA was isolated from 4 independent cultures for each strain using TRIzol reagent and RNase-Free DNase Set. Sequencing libraries was constructed using TruSeq RNA Library Prep Kit v2.
Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) and Multiplex Oligos for Illumina (NEB E7335S, E7500S). Quality and size of the libraries were checked by Bioanalyzer (Agilent 2100 Bioanalyzer).

value: Young adults


title: normotrophic scar_01_RNA-Seq

city: Gangnam-gu

first: Seok-Hyung

last: Kim

state: Seoul

address: 81, Irwon-ro

department: Department of Pathology

institute: Samsung Medical Center

data_processing:
Adaptor sequence were trimmed out and sequence under 50bp after trimming, or reads with low base qualites were removed with Cutadapt using illumina adaptor sequence.
Processed reads are aligned to human genome (Gencode V22) with STAR 2-pass alignment mode.
Aligned reads were quantified in gene level via HTSeq-count with intersection-nonempty mode.
Differential expression analysis processed with Ensemble approache of Limma-voom, edgeR, DESeq2.
Genome_build: Gencode V22
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: FFPE cell block

extract_protocol:
Consecutive 10 μm sections were generated from each of the FFPE cell blocks using a standard microtome blade. Deparaffinization of FFPE samples was performed using xylene at room temperature for 30 min followed by two washes with 100% ethanol. Then lesion of each slide was manually dissected. The manual isolation of RNA was performed using RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to manufacturers’ instructions.
For library preparation, the Illumina TruSeq RNA Access Library Prep Kit (Cat. No. 20020189, Illumina, San Diego, CA, USA) was used with 40 ng of FFPE RNA. The libraries were prepared according to the manufacturer’s protocol with the following change for the FFPE samples.

value: skin


title: normotrophic scar_03_RNA-Seq


title: Patient ID: 17, sample ID: 22

value: prostate cancer

value: metastasis tissue sample


title: normotrophic scar_02_RNA-Seq


title: 2018.4.17_14


title: 11B01N2_15C_LTSO180412_R1


title: 2018.4.17_44


title: Patient ID: 18, sample ID: 23


title: 2018.4.17_34


title: keloid_04_RNA-Seq


title: 2018.4.17_24


title: keloid_02_RNA-Seq


title: 2018.06.11_14--2018.06.11_44


title: 2018.06.11_24--2018.06.11_34


title: TM-2


title: TM-3


title: HypertrophicScar_05_RNA-Seq


title: keloid_03_RNA-Seq


title: Patient ID: 15, sample ID: 20


title: Patient ID: 15, sample ID: 19


title: QM-4


title: keloid_01_RNA-Seq


title: Patient ID: 14, sample ID: 18


title: HypertrophicScar_03_RNA-Seq


title: monocytes_LPS+iJAK2_3

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL) and with TG101348 (500nM) during all the culture
counts_table.txt
vst_table.txt
ML_iJAK2_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to hg38 genome with hisat2 2.1.0 (standard options)
Aligned reads with not proper pair and secondary alignments were filtered out with samtools (samtools view -h -f 0x2 $file | samtools view -h -b -f 0x100 -U $file".filter.bam" > discarded.bam)
Reads were asigned to genes using featureCounts v1.6.4 with options -s 2 -B -C -p
Differential expressed genes and VST values for representation were obtained from counts matrix with the R package DESeq2 (version 1.26.0). Ashr was used in the lfcShrink function.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with variance stabilizing transformation values for every gene and every sample

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide and TG101348, donor 3

growth_protocol: Monocytes were isolated from buffy coats by CD14 positive selection (MACS) and cultured 4 days in Roswell Park Memorial Institute (RPMI) Medium 1640 + GlutaMAX™ containing 10% human pooled serum, 100 units/mL penicillin, and 100 mg/mL streptomycin.

extract_protocol:
Total RNA was isolated utilising Maxwell® RSC simplyRNA Cells Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the first day of culture, monocytes were cultured in the presence/absence of LPS (10 ng/mL) and TG101348 (500nM). After 24 hours, monocytes were washed and left to rest for 3 days in RPMI supplemented with human pooled serum (10%), in the presence/absence of TG101348 (500nM).

tag: cell type

value: Monocytes

tag: individual

value: Donor 3


title: HypertrophicScar_01_RNA-Seq

tag: tissue


title: monocytes_LPS+iJAK2_1

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL) and with TG101348 (500nM) during all the culture
counts_table.txt
vst_table.txt
ML_iJAK2_1

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide and TG101348, donor 1

value: Donor 1


title: Patient ID: 13, sample ID: 17

tag: disease state

tag: tissue source

value: Hormone-naïve


title: HypertrophicScar_04_RNA-Seq


title: monocytes_LPS+iJAK2_2

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL) and with TG101348 (500nM) during all the culture
counts_table.txt
vst_table.txt
ML_iJAK2_2

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide and TG101348, donor 2

value: Donor 2


title: QM-3


title: TM-1


title: monocytes_LPS_2

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL)
counts_table.txt
vst_table.txt
ML_2

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide, donor 2

value: LPS


title: HypertrophicScar_02_RNA-Seq


title: monocytes_LPS_1

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL)
counts_table.txt
vst_table.txt
ML_1

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide, donor 1


title: Patient ID: 16, sample ID: 21

value: spine

tag: treatment group

tag: patient id


title: Patient ID: 13, sample ID: 16


title: QM-1

tag: genotype


title: monocytes_LPS_3

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL)
counts_table.txt
vst_table.txt
ML_3

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide, donor 3


title: monocytes_CTL_2

description:
4-days cultured (RPMI 10% human serum)  CD14+ cells  from PBMCs without treatment
counts_table.txt
vst_table.txt
MN_2

source_name: 4-days cultured CD14+ cells without treatment from PBMCs, donor 2

value: control


title: monocytes_noncultured_2

description:
Non-cultured CD14+ cells from PBMCs
counts_table.txt
vst_table.txt
MO_2

source_name: Non-cultured CD14+ cells from PBMCs, donor 2

value: noncultured


title: QM-2


title: N2-2


title: N2-4


title: Patient ID: 13, sample ID: 15


title: N2-3


title: N2-1


title: jmjd1-2-4


title: monocytes_CTL_1

description:
4-days cultured (RPMI 10% human serum)  CD14+ cells  from PBMCs without treatment
counts_table.txt
vst_table.txt
MN_1

source_name: 4-days cultured CD14+ cells without treatment from PBMCs, donor 1


title: monocytes_noncultured_3

description:
Non-cultured CD14+ cells from PBMCs
counts_table.txt
vst_table.txt
MO_3

source_name: Non-cultured CD14+ cells from PBMCs, donor 3


title: monocytes_noncultured_1

description:
Non-cultured CD14+ cells from PBMCs
counts_table.txt
vst_table.txt
MO_1

source_name: Non-cultured CD14+ cells from PBMCs, donor 1


title: Patient ID: 12, sample ID: 14

source_name: spine

value: Castration resistant


title: jmjd1-2-2


title: FASTED-Input-Hmgcs2-IKO_R2_ChIP-seq

source_name: Small Intestine

growth_protocol: Male and female mice (strains: Lgr5EGFP-IRES-CreERT2/+ Strain name: B6.129P2-Lgr5tm1(cre/ERT2)Cle/J, JAX, 008875) and C57BL/6J (JAX, 000664)) were purchased, bred in house, and maintained at 72°F +/- 2 °F on a 12h light/dark cycle. Six- to twelve-week-old aged matched males and females were randomly assigned to either fed or fasted groups. Fed animals were provided ad libitium access to food (PicoLab 5053, #0007688) and water for 24h, fasted animals were completely food deprived for 24h with ad libitium access to water. Experimental mice were singly housed on aspen bedding for the duration of experiments. Intestinal-specific Hmgcs2 knockout was achieved as previously described in Cheng et al., 2019 (https://doi.org/10.1016/j.cell.2019.07.048) . Briefly, adult Hmgcs2loxp/loxp;Villin-CreERT2 mice received tamoxifen injections (10 mg/ml, 250ul per 25 g of body weight) every other day, for up to ten days for a total of five doses. Two weeks after the last tamoxifen injection, mice were assigned to ad libitum and fasting groups for 24hrs.

value: crypt

tag: Sex

value: male


title: jmjd1-2-1

tag: developmental stage


title: jmjd1-2-3

tag: temperature of growth


title: J5DD-jmjd1-2-3

source_name: jmjd-5 (zr1234);jmjd-1.2 (zr1010) double mutant


title: J5DD-jmjd1-2-4

value: jmjd-5 (zr1234);jmjd-1.2 (zr1010) double mutant


title: x323_5_13

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Fastp (version 0.19.4) was used to collect QC metrics of the raw reads.
RNA sequences were aligned and sorted by coordinates to the NCBI human genome build 38 (GRCh38.p12) with version 94 of gene annotations, using the STAR aligner (STAR_2.6.1a_08-27)
The removal of alignment duplicates was done with Sambamba (version 0.6.8)
Quantification of genes was performed using featureCounts (v1.6.3). File matrix was demultiplexed in per sample files with the file extension .count
DESeq2 (v 1.20.0) was used to normalize feature counts and to test find the differentially expressed genes
The HGNC symbols were extracted and added to the DESeq2 results data frame using biomaRt (version 2.36.1) using the "hsapiens_gene_ensembl" dataset and the "Ensembl Release 94 (October 2018)" mart
Genome_build: GRCh38.p12 release 94
Supplementary_files_format_and_content: Count files (from the demultiplexed featureCount matrix file)  containing raw reads mapped to genes for each sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Cell culture

growth_protocol: Stably-transduced cell cultures were maintained in RPMI containing 1 ug/ml puromycin and 10% FBS

extract_protocol:
Cells were lysed in RLT Plus lysis buffer and total RNA was extracted using the RNeasy Plus Mini kit (Qiagen) according to manufacturer's protocol. High RNA quality was verified using the Bioanalyzer RNA 6000 Nano assay (Agilent).
Libraries were prepared from 500 nanograms of total RNA per sample using standard Illumina protocols

treatment_protocol: Cells were lentivirally transduced with the indicated shRNA clones or the empty pLKO.1 shRNA expression vector

tag: cell line

value: KatoII

tag: culture conditions

value: suspension

tag: lentiviral shrna clone


title: x322_5_22


title: pLKO_6_19


title: x323_5_22


title: pLKO_5_22


title: x323_6_19


title: pLKO_5_13


title: FED-Input-Hmgcs2-IKO_R2_ChIP-seq


title: FASTED-H3K9bhb-Hmgcs2-IKO_R2_ChIP-seq

tag: chip-antibody

value: H3K9bhb PTM-biolabs PTM-1250


title: S3_hcc

city: Los Angeles

first: Marcus

last: Alvarez

address: 695 Charles E Young Dr South, Gonda 6335

department: Human Genetics

institute: UCLA

data_processing:
Template switch oligo, primer, and polyA sequences of at least 20 bp in length were trimmed from the fastq files.
Reads were aligned to the hg38 genome using STARsolo from STAR v2.7.3a.
Empty and contaminated droplets were removed using DIEM. Doublets were removed by clustering and manual identification of doublet clusters.
Clustering was performed using Seurat with SCTransform and CCA integration.
Genome_build: hg38
Supplementary_files_format_and_content: Text files in matrix market format

source_name: Liver

extract_protocol:
Frozen biposies were homgogenized in lysis buffer, filtered and washed, suspended, and processed with a 10X Chromium using the Single Cell 3' v3 library prep.
10X Single Cell 3' v3

value: Tumor

tag: condition

value: NASH

value: Female


title: S2_hcc


title: S3_ant

value: Adjacent non-tumor


title: J5DD-jmjd1-2-2

value: Young adults


title: FED-H3K9bhb-Hmgcs2-IKO_R2_ChIP-seq


title: Patient ID: 10, sample ID: 10

value: prostate cancer

value: metastasis tissue sample

value: Hormone-naïve


title: Patient ID: 12, sample ID: 13

value: spine


title: Patient ID: 8, sample ID: 8


title: Patient ID: 12, sample ID: 12


title: J5DD-4


title: J5DD-jmjd1-2-1


title: J5DD-2


title: S2_ant


title: GC086119

city: Leuven

first: Kathrin

middle: Ingrid

last: Liszt

address: O&N1 Herestraat 49 – bus 701

country: Belgium

institute: KU Leuven

data_processing:
Quality control of raw reads was analyzed with FastQC v0.11.7 (63) and adapters were filtered with ea-utils fastq-mcf v1.05.
Splice-aware alignment was conducted with STAR v2 (65) against the human reference genome hg19 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded.
Resulting BAM alignment files were processed with Samtools v1.5.
Quantification of reads per gene was calculated with HT-seq Count v2.7.14.  Count-based differential expression analysis was performed with R-based  Bioconductor package DESeq2.
Reported P-values were adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate.
Genome_build: hg19

source_name: intestinal crypt cells

growth_protocol: A piece of mucosal layer was dissected from the fresh jejunal tissue, minced and digested with collagenase XI (0.35 mg/ml) in DMEM at 37°C. Crypt suspensions were centrifuged, resuspended in DMEM (supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin, 1% L-glutamine, and 10µM Y-27632), and filtered (100 µM). Crypts were seeded on Matrigel (1.4% (v/v)) coated 12-well plates  incubated for 24h at 37°C to form a monolayer.

extract_protocol:
RNA was isolated from cells (Relia PrepTM kit, Promega) and frozen at -80 °C
Sequence libraries were prepared with Lexogen QuantSeq 3' mRNA-Seq Library prep kit (Lexogen) and quality and size range was assessed using a Bioanalyzer with the DNA 1000 kit (Agilent Technologies.
RNA seq. Libraries (2 nM) were sequenced using an Illumina HiSeq4000 platform (single-end reads of 50bp length with a minimum of 1x106 reads per sample).

treatment_protocol: Jejunal primary crypts were stimulated with DMEM (control) or bitter agonists 1 mM DB or 30 µM aloin in DMEM for 4h at 37°C.

tag: weight

value: lean

value: TAS2R43+ (positive)

tag: 4h treatment

value: 30 µM Aloin

tag: patient


title: Patient ID: 11, sample ID: 11

tag: tissue


title: GC086120


title: Patient ID: 5, sample ID: 5

tag: disease state


title: GC086118


title: J5DD-3


title: S1_hcc

value: NAFLD


title: J5DD-1


title: Patient ID: 9, sample ID: 9

tag: tissue source

value: Short-term castrated


title: Patient ID: 4, sample ID: 4

tag: treatment group


title: GC086116


title: Patient ID: 3, sample ID: 3

tag: patient id


title: Patient ID: 2, sample ID: 2


title: Patient ID: 6, sample ID: 6


title: GC086115

value: 1 mM Denatonium Benzoate


title: Patient ID: 1, sample ID: 1


title: N2-input-F3-25C

source_name: N2 (wild type)

extract_protocol:
Frozen drops were grinded to powder using cold mortar and pestle, and the powder is then incubated with 1% formaldehyde (diluted in M9) for a final volume of 15 ml each tube and gently rocked for 10´ at room temperature.  Crosslinking is stopped adding 0.125 mM Glycine. Crosslinked lysate was centrifuged 3 times (4000 G, 3´) and washed in PBS containing inhibitors of proteases. The lysate was resuspended with 10ml of ice cold SDS-buffer. After centrifugation (2000 G, 10´) supernatant was removed and the pellet resuspended with IP buffer. Chromatin was sonicated using Diagenode bioruptor sonicator. Centrifugation (20000 G 30´) was performed and supernatant collected. Chromatin was de-crosslinked for 3h at 65C. Pre-cleared chromatin was incubated ON at 4C with 3ug of antibody.
Libraries for sequencing were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) and Multiplex Oligos for Illumina (NEB E7335S, E7500S). Quality and size of the libraries were checked by Bioanalyzer (Agilent 2100 Bioanalyzer).

tag: genotype

value: N2 (wild type)

tag: antibody

value: input


title: monocytes_CTL_3

description:
4-days cultured (RPMI 10% human serum)  CD14+ cells  from PBMCs without treatment
counts_table.txt
vst_table.txt
MN_3

source_name: 4-days cultured CD14+ cells without treatment from PBMCs, donor 3

tag: cell type

value: Monocytes

tag: treatment

value: control

tag: individual

value: Donor 3


title: n2_snrp_sz305_rs023

city: Santa Cruz

first: Alan

middle: M

last: Zahler

address: Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

data_processing:
The sequencing center delivered variable length reads. The maximum read length was 75bp (for both read1 and read2), with most (over 98%) reads longer than 70bp.
All reads were trimmed at the 3' end to 70bp using cutadapt. Read-pairs were discarded if either read1 or read2 was shorter than 70bp.
Trimmed reads were mapped with Bowtie2 to the RepeatMasker library of C.elegans repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining trimmed reads were mapped to the indicated genome assembly using STAR.
Potential PCR duplicates were removed with samtools rmdup.
Splice junctions were extracted from the bam files by examining the CIGAR string, resulting in a non-redundant set of introns spanned by these splice junctions.
Alternative splicing events of types A5,A3 were identified from the splice junctions found in all sequencing libraries.
A5 events: A custom script was employed to identify junctions that define alternative 5' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
A3 events: A custom script was employed to identify junctions that define alternative 3' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
Alternative splicing events of types SE, RI, MS, MX, AF, AL were extracted from the ce10 EnsemblArchive65 transcript annotation using junctionCounts:infer_pairwise_events (github ajw2329/junctionCounts)
The program junctionCounts (github ajw2329/junctionCounts) was used to determine PSI (percent spliced in) for all events in all samples. The option "suppress_eij_use" was used for the A5,A3 events
The junctionCounts PSI estimates for a sample were merged into a gtf with the scores for the 2 alternative transcripts of an event representing (1000 times) its PSI (and 1-PSI) values. If junctionCounts reported a non-zero span of the PSI estimate, these scores were reduced by a factor of (1-spanPSI).
Genome_build: Oct. 2010 (WS220/ce10)
Supplementary_files_format_and_content: The ensArch65 gtf file for a sample contains the 2 alternative transcripts for each event of type SE, RI, MS, MX, AF, AL derived from the ce10 EnsembleArchive65 annotation. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. This score is modified by a factor of (1-spanPSI) if there is a non-zero span in the estimate of PSI.
Supplementary_files_format_and_content: The libIntrons gtf file for a sample contains the 2 alternative transcripts for each event of type A3, A5 derived from the introns found in all sample sequencing libraries. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. For these event types the span in the estimate of PSI is always zero.

growth_protocol: Indicated strains were grown at 20C on NGM agar plates fed OP50 E. coli

extract_protocol:
Worms were lysed in Trizol and total RNA recovered according to manufacturers protocol.
mRNA libraries for high throughput sequencing were prepared from polyA selected mRNAs using the NuGen Universal mRNA kit. Paired directional 75nt reads, 9 libraries per lane, were obtained from an Illumina NovaSeq 6000 operated by RealSeq Biosciences of Santa Cruz, CA.

treatment_protocol: Worms were harvested from the plates by washing them off with M9 media

value: whole worm

tag: developmental state

value: mixed stage


title: n2_snrp_sz305_rs022


title: S1_ant

value: Adjacent non-tumor

tag: Sex

value: Female


title: GC086114


title: Patient ID: 7, sample ID: 7

value: prostate cancer

value: metastasis tissue sample

value: Hormone-naïve


title: GC086111

value: lean

value: TAS2R43+ (positive)


title: N2-input-20C

tag: developmental stage

value: Young adults

tag: temperature of growth


title: GC086108

tag: weight

value: DMEM (control)


title: GC086113

tag: 4h treatment

value: 1 mM Denatonium Benzoate


title: N2-H3K36me3-F3-25C-2

value: N2 (wild type)

value: H3K36me3 active motif (61902)


title: N2-H3K36me3-F3-25C-1


title: GC086107

tag: patient


title: n2_prp8_sz304_rs018

tag: tissue

value: PRP-8(D1549N) mutation


title: n2_prp8_sz304_rs019


title: GC086106


title: GC086103

value: obese

value: TAS2R43- (negative)

value: 30 µM Aloin

value: N


title: GC086109


title: N2-H3K36me2-F3-25C-1

value: H3K36me2  abcam (ab9049)


title: n2_prp8_sz304_rs017

value: whole worm

value: mixed stage


title: GC086097

value: L


title: GC086101


title: GC086102

value: M


title: GC086098


title: n2_snrp_sz305_rs021


title: n2_prp8_sz299_rs016

value: PRP-8(R540K) mutation


title: GC086100

value: K


title: n2_prp8_sz299_rs015


title: GC086099

value: 2 mM Denatonium Benzoate


title: N2-H3K36me2-20C-2

value: Young adults


title: GC086096

value: 1 mM Denatonium Benzoate


title: n2_prp8_sz299_rs014


title: x322_5_13

tag: cell line

value: KatoII

tag: culture conditions

value: suspension

tag: lentiviral shrna clone


title: GC086095

value: J


title: N2-H3K36me2-20C-1

value: N2 (wild type)


title: GC086093

value: obese

value: TAS2R43- (negative)

value: DMEM (control)


title: GC086094

value: I


title: N2-H3K27me3-F3-25C-1

value: H3K27me3  MABI0323


title: N2-H3K36me2-F3-25C-2

value: H3K36me2  abcam (ab9049)


title: GC086092


title: GC086091

value: L


title: n2_ctrl_sz181_rs012

value: whole worm

value: mixed stage

value: control


title: n2_ctrl_sz181_rs011


title: N2-H3K27me3-20C-2


title: E100somato

source_name: primary brain tissue

value: brain

tag: region

value: Somato


title: E100septumANDnucleusAccumbens

value: Septum+NAc


title: n2_ctrl_sz181_rs013

tag: genotype


title: GC086088


title: N2-H3K27me3-F3-25C-2

tag: antibody

value: Young adults


title: GC086086

value: TAS2R43+ (positive)

value: 30 µM Aloin

value: F


title: GC086087

value: obese

value: G


title: N2-H3K27me3-20C-1

value: N2 (wild type)


title: J5DD-input-20C

value: input


title: E100parietal

value: Parietal


title: GC086084

value: D


title: J5DD-H3K36me3-F3-25C-2

value: H3K36me3 active motif (61902)


title: GC086083

value: C


title: E100insula

value: Insula


title: GC086082

value: B


title: E100hypothalamusANDPoA

value: brain

value: POH+POA


title: J5DD-input-F3-25C


title: GC086090

value: TAS2R43- (negative)

value: DMEM (control)

value: K


title: J5DD-H3K36me2-F3-25C-2

value: H3K36me2  abcam (ab9049)

value: Young adults


title: GC086079

value: obese

value: TAS2R43+ (positive)

value: 1 mM Denatonium Benzoate

value: F


title: GC086080

value: G


title: GC086077

value: D


title: E100hippo

value: Hippocampus


title: GC086078

value: E


title: GC086076


title: GC086085

value: 30 µM Aloin


title: J5DD-H3K36me2-F3-25C-1


title: GC086073


title: E100cingulate

value: Cingulate


title: GC086072


title: J5DD-H3K36me2-20C-1


title: GC086075

value: A


title: E100motor

value: brain

value: Motor


title: E100V1


title: GC086074

value: DMEM (control)

value: H


title: GC086071


title: GC086081


title: J5DD-H3K36me2-20C-2

value: H3K36me2  abcam (ab9049)


title: GC086070


title: E90-2019_Somatosensory

value: Somato


title: GC086069

value: obese

value: C


title: J5DD-H3K27me3-F3-25C-1

value: H3K27me3  MABI0323

value: Young adults


title: GC086068

value: TAS2R43+ (positive)

value: B


title: J5DD-H3K36me3-F3-25C-1

value: H3K36me3 active motif (61902)


title: x322_6_19

value: KatoII

value: suspension


title: E90-2019_PFC

value: PFC


title: GC086067

value: A


title: J5DD-H3K27me3-20C-2


title: E90-2019_Motor_2

value: brain


title: J5DD-H3K27me3-20C-1


title: ddm1-2_16C_SmartSeq2_S7_11F

first: magdalena

middle: ewelina

last: potok

address: 4045 Terasaki Life Sciences Building

department: MCDB

data_processing:
Reads were aligned to TAIR10 with chloroplast and mitochondria excluded using hisat2 with default settings. Samtools view was used to filter uniquely mapped proper pairs with the following parameters: -b -q 60 -f 2. Duplicates reads were removed using Picard tools MarkDuplicates.jar (https://broadinstitute.github.io/picard/). Counts for each gene were generated using htseq-count using Araport 11 genes and TEs annotations. FPKM values and differential gene expression were analyzed using Cuffdiff with default settings. CummeRbound package was used to generate a boxplot of FPKM across sample replicates, a dendogram of Jensen-Shannon distance between sample replicates and the multi-dimensional scaling (MDS) plot for sample replicates for all genes. Poor quality libraries were filtered out, 2-4 replicates per ploidy/sample were retinaed and used in analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text file includes counts for each gene generated by htseq-count.

organism: Arabidopsis thaliana

source_name: cotyledons

extract_protocol:
Fresh nuclei  isolated from two-week-old cotyledons  grown on 1%MS under long day conditions were isolated as follows.  Roughly 50 cotyledons were finely chopped with razor into 50 ul Partec nuclei extraction buffer (Sysmex America, 05-5002), and stained with 400 ul Partec nuclei staining buffer. Samples were filtered once through a 35um nylon mesh (Falcon, 352235) and subjected to fluorescent activated nuclei sorting. Nuclei were sorted from 2C, 4C, 8C and 16C peaks based on DAPI fluorescence. 50 nuclei from each peak were sorted into individual wells of a 96 well plate. Three to four replicates per ploidy/genotype were collected. Negative controls, with no nuclei sorted into a well, were included in every plate and carried through library preparation and sequencing.
Libraries were prepared according to Smart-seq V2 protocol at reduced volume and with few modifications as described previously (Picard, C,L et al, bioRxive, 2020).

tag: dapi fluorescence peak

value: two-week-old

value: cotyledons

tag: cell compartment

value: nuclei


title: ddm1-2_16C_SmartSeq2_S7_11G


title: ddm1-2_8C_SmartSeq2_S7_11C


title: ddm1-2_8C_SmartSeq2_S7_11D


title: E90-2019_putamen_AND_Septum

value: Septum+Putamen


title: E90-2019_Motor_1

value: Motor


title: ddm1-2_4C_SmartSeq2_S7_10G


title: E80temporal

value: Temporal


title: ddm1-2_2C_SmartSeq2_S7_10C


title: ddm1-2_4C_SmartSeq2_S7_10H


title: J5DD-H3K27me3-F3-25C-2


title: ddm1-2_2C_SmartSeq2_S7_10D


title: ddm1-2_4C_SmartSeq2_S7_10F


title: E90-2019_MGE_AND_CGE_AND_LGE

value: MGE+CGE+LGE


title: E80putamenANDclaustrumANDbasalGanglia

value: Striatum+Claustrum


title: E80motor


title: ddm1-2_2C_SmartSeq2_S7_10B


title: E80insula

value: Insula


title: atxr5/6 (W)_16C_SmartSeq2_S6_12G

value: atxr5/6 (W)


title: atxr5/6 (W)_16C_SmartSeq2_S6_11H


title: atxr5/6 (W)_16C_SmartSeq2_S6_11G


title: E80hippo

value: Hippocampus


title: atxr5/6 (W)_8C_SmartSeq2_S6_12E


title: E80V1


title: ddm1-2_8C_SmartSeq2_S7_11B


title: atxr5/6 (W)_8C_SmartSeq2_S6_11E


title: atxr5/6 (W)_4C_SmartSeq2_S6_12D


title: atxr5/6 (W)_4C_SmartSeq2_S6_12C


title: E80MGE

value: xLGE


title: atxr5/6 (W)_8C_SmartSeq2_S6_12F


title: atxr5/6 (W)_8C_SmartSeq2_S6_11F


title: atxr5/6 (W)_4C_SmartSeq2_S6_11C


title: atxr5/6 (W)_4C_SmartSeq2_S6_11D


title: E80CGE-LGE

value: CGE+LGE


title: E80-2019_V1


title: E80-2019_Parietal

value: Parietal


title: E80-2019_PFC

value: PFC


title: WT_16C_SmartSeq2_S6_9H

value: WT


title: WT_16C_SmartSeq2_S6_10H


title: atxr5/6 (W)_2C_SmartSeq2_S6_11B


title: E80-2019_Motor_2

value: brain


title: atxr5/6 (W)_2C_SmartSeq2_S6_11A

value: two-week-old


title: WT_16C_SmartSeq2_S6_10G

value: cotyledons


title: WT_8C_SmartSeq2_S6_10E

value: nuclei


title: WT_8C_SmartSeq2_S6_10F


title: WT_8C_SmartSeq2_S6_9E


title: WT_8C_SmartSeq2_S6_9F


title: WT_4C_SmartSeq2_S6_10C


title: WT_4C_SmartSeq2_S6_10D


title: E80-2019_Temporal


title: sid_4010_dis_HC_age_15_gender_M

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

institute: Linköping University

hyb_protocol: Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression v2 8x60K microarray kit, according to the manufacturer’s instruction (Agilent Technologies).

scan_protocol: Standard Agilent protocol.

data_processing: All gene expression microarrays were processed using the LIMMA [R] package: background correction and between array normalization. Technical replicates were averaged. All probes not higher expressed than 1.2 times the background signal were removed. In the publication, all probes representative of the same Entrez Gene ID were averaged.

source_name: CD4+ T cells

label_protocol: The cRNA was prepared using a Low Input QuickAmp Labeling Kit.

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Micro kit (Qiagen, Hilden, Germany; cat. no. 80284) according to the manufacturer’s instructions.

tag: cell type

value: CD4+ T cells

tag: primary diagnosis

value: Male

tag: age


title: E80-2019_Motor_1

value: Motor


title: WT_4C_SmartSeq2_S6_9D

tag: developmental stage


title: WT_2C_SmartSeq2_S6_10B


title: E80-2019_LGE_AND_CGE


title: WT_2C_SmartSeq2_S6_9B


title: sid_4011_dis_HC_age_12_gender_M

tag: Sex


title: sid_4009_dis_HC_age_13_gender_F

value: Female


title: sef1-1 atxr5/6 (W)_R4_MP22Pool2-8-4_S-3425-4_S11

data_processing:
Reads were aligned using Tophat by allowing up to two mismatches and mapping only to one location. Chromosome mitochondria and chloroplast were exluded from alignments.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina).

value: sef1-1 atxr5/6


title: WT_2C_SmartSeq2_S6_9A


title: WT_2C_SmartSeq2_S6_10A


title: sid_4006_dis_HC_age_10_gender_M


title: sef1-1 atxr5/6 (W)_R2_MP22Pool2-8-2_S-3425-2_S1


title: sid_4002_dis_HC_age_9_gender_M


title: sef1-1 atxr5/6 (W)_R1_MP22Pool2-8-1_S-3425-1_S3


title: E65-2019B_Somatosensory

value: Somato


title: E80-2019_Hippocampus


title: E65-2019B_PFC


title: atxr5/6 (W)_R3_MP22Pool1-2-3_S-4627-3_S12


title: sid_4005_dis_HC_age_13_gender_F


title: atxr5/6 (W)_R4_MP22Pool1-2-4_S-4627-4_S18


title: atxr5/6 (W)_R2_MP22Pool1-2-2_S-4627-2_S10


title: WT_R4_MP22Pool1-1-4_S-4623-4_S13


title: sid_4000_dis_HC_age_17_gender_M


title: atxr5/6 (W)_R1_MP22Pool1-2-1_S-4627-1_S17


title: WT_R2_MP22Pool1-1-2_S-4623-2_S9


title: WT_R3_MP22Pool1-1-3_S-4623-3_S16


title: E65-2019B_MGE

value: MGE


title: WT_R1_MP22Pool1-1-1_S-4623-1_S11


title: ChIPseq_input_atxr5/6 (W)_Floral buds

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie using default settings and allowing only uniquely mapping reads.
Duplicated reads were removed using Samtools.
Normalized read coverage tracks and data metaplots were generated using deepTools.
Genome_build: TAIR10
Supplementary_files_format_and_content: bw

source_name: Floral buds

growth_protocol: About 2g of 4-week-old rosette leaves or 1 g of 4-week old floral buds grown on soil were collected and frozen in -80 °C.

extract_protocol:
Following tissue grining and in-vitro fixation, isolated nuclei were sonicate, cell lysates were cleared and  histone-DNA complexes were isolated with  antibody.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

value: Floral buds

tag: chip antibody

value: input

value: atxr5/6 (W)


title: E65-2019B_Motor_2


title: sef1-1 atxr5/6 (W)_R3_MP22Pool2-8-3_S-3425-3_S10


title: sid_3034_dis_HC_age_69_gender_M


title: E65-2019B_Temporal

value: Temporal


title: E65-2019B_LGE

value: LGE


title: sid_3036_dis_HC_age_60_gender_F


title: ChIPseq_input_sac3b-3 atxr5/6 (W)_leaves_R2

source_name: Rosette leaves

value: Rosette leaves

value: sac3b-3 atxr5/6 (W)


title: E65-2019B_Motor_1

value: brain


title: ChIPseq_input_mbd9-3 atxr5/6 (W)_leaves_R2

value: mbd9-3 atxr5/6 (W)


title: sid_4001_dis_HC_age_10_gender_F


title: ChIPseq_input_subl2-3 atxr5/6 (W)_leaves_R2

value: subl2-3 atxr5/6 (W)


title: monocytes_P3C_1

type: genomic

description:
4-days cultured CD14+ cells from PBMCs treated with Pam3Cys from day 0 to day 1 (10ug/mL)
MP1

hyb_protocol: BS-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Data were processed using R studio

label: Cy5 and Cy3

source_name: 4-days cultured CD14+ cells from PBMCs treated with Pam3Cys, donor 1

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted by the proteinase K protocol.

treatment_protocol: In the first day of culture, monocytes were cultured in the presence/absence of LPS (10 ng/mL) or P3C (10ug/mL). After 24 hours, monocytes were washed and left to rest for 3 days in RPMI supplemented with human pooled serum (10%)

value: Monocytes

tag: agent

tag: donor

value: Donor 1


title: monocytes_LPS_3

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL)
ML3

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide, donor 3

value: LPS

value: Donor 3


title: monocytes_P3C_2

description:
4-days cultured CD14+ cells from PBMCs treated with Pam3Cys from day 0 to day 1 (10ug/mL)
MP2

source_name: 4-days cultured CD14+ cells from PBMCs treated with Pam3Cys, donor 2

value: Donor 2


title: E65-2019B_Hippocampus_choroid

tag: tissue

value: Hippocampus


title: ChIPseq_input_atxr5/6 (W)_leaves_R2


title: ChIPseq_H3K27me1_atxr5/6 (W)_Floral buds


title: E65-2019A_Temporal


title: monocytes_noncultured_3

description:
Non-cultured CD14+ cells from PBMCs
M03

source_name: Non-cultured CD14+ cells from PBMCs, donor 3

value: noncultured


title: ChIPseq_H3K27me1_mbd9-3 atxr5/6 (W)_leaves_R2

value: H3K27me1 (Millipore Sigma 07-448)


title: ChIPseq_input_stubl2-3_leaves_R2

value: input


title: monocytes_LPS_2

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL)
ML2

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide, donor 2


title: ChIPseq_input_WT_leaves_R2

value: WT


title: ChIPseq_H3K27me1_sac3b-3 atxr5/6 (W)_leaves_R2


title: ChIPseq_H3K27me1_stubl2-3_leaves_R2


title: ChIPseq_input_WT_Floral buds

value: Floral buds


title: ChIPseq_H3K27me1_subl2-3 atxr5/6 (W)_leaves_R2


title: monocytes_P3C_3

description:
4-days cultured CD14+ cells from PBMCs treated with Pam3Cys from day 0 to day 1 (10ug/mL)
MP3

source_name: 4-days cultured CD14+ cells from PBMCs treated with Pam3Cys, donor 3


title: E65-2019A_PFC

value: PFC


title: E65-2019A_Parietal

value: Parietal


title: ChIPseq_H3K27me1_WT_Floral buds


title: E65-2019A_Motor_2

value: Motor


title: ChIPseq_H3K27me1_WT_leaves_R2

value: Rosette leaves


title: ChIPseq_H3K27me1_atxr5/6 (W)_leaves_R2

value: atxr5/6 (W)


title: sid_3031_dis_HC_age_67_gender_F

value: CD4+ T cells

value: Female


title: sid_3029_dis_HC_age_38_gender_F


title: sid_3035_dis_HC_age_63_gender_M

value: Male


title: E65-2019A_V1

value: brain


title: monocytes_CTL_1

description:
4-days cultured (RPMI 10% human serum)  CD14+ cells  from PBMCs without treatment
MN1

source_name: 4-days cultured CD14+ cells without treatment from PBMCs, donor 1

value: Monocytes

value: control

value: Donor 1


title: sid_3030_dis_HC_age_27_gender_F


title: sid_3033_dis_HC_age_61_gender_M


title: E65-2019A_Motor_1


title: E65-2019A_MGE

value: MGE


title: monocytes_CTL_3

description:
4-days cultured (RPMI 10% human serum)  CD14+ cells  from PBMCs without treatment
MN3

value: Donor 3


title: sid_3027_dis_HC_age_36_gender_F


title: monocytes_LPS_1

description:
4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide from day 0 to day 1 (10ng/mL)
ML1

source_name: 4-days cultured CD14+ cells from PBMCs treated with lipopolysaccharide, donor 1

value: LPS


title: monocytes_noncultured_1

description:
Non-cultured CD14+ cells from PBMCs
M01

source_name: Non-cultured CD14+ cells from PBMCs, donor 1

value: noncultured


title: E50hippo

value: Hippocampus


title: sid_3028_dis_HC_age_58_gender_F


title: monocytes_noncultured_2

description:
Non-cultured CD14+ cells from PBMCs
M02

source_name: Non-cultured CD14+ cells from PBMCs, donor 2

value: Donor 2


title: PHLC314

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

institute: University Health Network

description: DASL

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data were normalised using quantile normalisation and log2 transformation,background correction with the lumi package in R

label: biotin

source_name: Xenograft

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit/DASL Assay kit for Illumina arrays

growth_protocol: Human primary lung tumors grown in the subcutaneous pocket at the flank of NOD SCID mice to form xenograft tumors

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment was applied to the cells prior to extraction

value: patient-derived xenograft (PDX)

tag: histology

value: Pleom LUAD


title: sid_3025_dis_HC_age_39_gender_M


title: PHLC536

description: DASL

value: LUAD


title: sid_3023_dis_HC_age_23_gender_M


title: E50_temporal

extract_protocol:
whole cells, dissociated using papain
10X chromium 3’ RNAseq V2/3

value: Temporal


title: E65-2019A_Somatosensory

value: Somato


title: sid_3024_dis_HC_age_68_gender_M

value: CD4+ T cells


title: sid_3026_dis_HC_age_24_gender_M

value: Male


title: PHLC524

description: DASL


title: sid_3022_dis_HC_age_49_gender_M


title: PHLC325

description: DASL

value: LUSC


title: E50_septum

value: brain

value: Septum


title: sid_3021_dis_HC_age_46_gender_F

value: Female


title: sid_3020_dis_HC_age_47_gender_F


title: PHLC422

description: DASL


title: PHLC402

description: DASL


title: PHLC462

description: DASL


title: PHLC426

description: DASL


title: PHLC379

description: DASL


title: PHLC518

description: DASL


title: E50_PFC

value: PFC


title: PHLC417

description: DASL


title: sid_3019_dis_HC_age_67_gender_M


title: PHLC428

description: DASL


title: E50_parietal

value: Parietal


title: E50_motor

value: Motor


title: monocytes_CTL_2

description:
4-days cultured (RPMI 10% human serum)  CD14+ cells  from PBMCs without treatment
MN2

source_name: 4-days cultured CD14+ cells without treatment from PBMCs, donor 2

value: Monocytes

value: control


title: PHLC412

description: DASL


title: PHLC451

description: DASL


title: E50_MGE

source_name: primary brain tissue

value: MGE


title: PHLC410

description: DASL

value: patient-derived xenograft (PDX)


title: E40hippo

value: Hippocampus


title: PHLC377

description: DASL


title: sid_3016_dis_HC_age_55_gender_F


title: E50_V1


title: sid_3015_dis_HC_age_55_gender_F


title: sid_3012_dis_HC_age_63_gender_M

description: This Sample represents 2 technical replicates.


title: E50_CGE-LGE

value: CGE+LGE


title: PHLC328

description: DASL


title: sid_3011_dis_HC_age_41_gender_F


title: PHLC390

description: DASL

value: Pleom LUAD


title: PHLC111

description: DASL

value: LUAD


title: PHLC362

description: DASL


title: sid_3010_dis_HC_age_28_gender_M

value: CD4+ T cells


title: PHLC82

description: DASL


title: PHLC236

description: DASL


title: PHLC83

description: DASL


title: PHLC81

description: DASL


title: E40_V1


title: E40_Pre-optic

value: POA


title: E40_somato

value: Somato


title: sid_3009_dis_HC_age_30_gender_F


title: PHLC296

description: DASL

value: LUSC


title: sid_3006_dis_HC_age_48_gender_M

value: Male


title: sid_3008_dis_HC_age_58_gender_M


title: PHLC295

description: DASL


title: E40_PFC

value: brain


title: E40_MGE


title: E40_CGE-LGE


title: E65-2019A_Hippocampus_choroid


title: PHLC205

description: DASL


title: PHLC369

description: DASL


title: sid_3005_dis_HC_age_55_gender_M


title: PHLC255

description: DASL


title: Freeze_disome

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

description: Ribosome Profiling

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with bowtie2 v2.1.0
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Escherichia coli

source_name: E. coli culture

extract_protocol: MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification

tag: treatment

value: tigecycline, capreomycin

tag: strain


title: sid_3002_dis_HC_age_43_gender_M

source_name: CD4+ T cells


title: PHLC132

description: DASL


title: sid_3003_dis_HC_age_47_gender_M


title: PHLC268

description: DASL


title: PHLC62

description: DASL


title: PHLC229

description: DASL


title: PHLC151

description: DASL


title: Freeze_monosome

description: Ribosome Profiling


title: sid_3004_dis_HC_age_24_gender_F

value: Female


title: PHLC228

description: DASL


title: sid_162_dis_ECZ_age_49_gender_M_dis2_SAR_ASTHMA


title: PHLC256

description: DASL


title: PHLC299

description: DASL


title: CD8+ T-cells with IL-12 80%TCM  [Treatment3_3]

city: Kolkata

first: Debaleena

last: Bhowmik

address: 4 Raja S.C. Mullick Road

department: Cell Biology and Physiology

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR v2.7.7a with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM
Counts per Million (CPM) values were calculated using edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Splenocytes

extract_protocol:
Total RNA was extracted from the vehicle and bortezomib treated mice livers using TRIzol and purified according to manufacter's instructions.
A modified NEBNext RNA Ultra II directional protocol was used to prepare the libraries for total RNA.

value: CD8+ T-cells


title: sid_3001_dis_HC_age_34_gender_M


title: PHLC242

description: DASL


title: PHLC274

description: DASL


title: PHLC267

description: DASL


title: PHLC272

description: DASL


title: PHLC271

description: DASL


title: CD8+ T-cells with IL-12 80%TCM  [Treatment3_1]


title: CD8+ T-cells with IL-12  [Treatment2_3]


title: sid_159_dis_ECZ_age_22_gender_M


title: sid_165_dis_ECZ_age_23_gender_F


title: PHLC164

description: DASL


title: PHLC220

description: DASL


title: CD8+ T-cells with IL-12 80%TCM  [Treatment3_2]


title: CD8+ T-cells with IL-12  [Treatment2_2]


title: CD8+ T-cells with IL-2 80%TCM  [Treatment1_3]

value: IL-2 80%TCM


title: PHLC215

description: DASL


title: PHLC243

description: DASL


title: sid_156_dis_ECZ_age_76_gender_M


title: PHLC106

description: DASL


title: CD8+ T-cells with IL-12  [Treatment2_1]


title: PHLC181

description: DASL


title: PHLC194

description: DASL


title: sid_150_dis_ECZ_age_49_gender_M_dis2_ASTHMA

value: ASTHMA


title: sid_CD9_dis_CROHN_age_76_gender_M


title: PHLC235

description: DASL


title: CD8+ T-cells with IL-2 80%TCM  [Treatment1_2]


title: sid_CD8_dis_CROHN_age_50_gender_F


title: PHLC153

description: DASL


title: sid_152_dis_ECZ_age_24_gender_F


title: PHLC273

description: DASL


title: PHLC239

description: DASL


title: sid_153_dis_ECZ_age_42_gender_F


title: CD8+ T-cells with IL-2 80%TCM  [Treatment1_1]


title: CD8+ T-cells with IL-2  [Control_3]


title: PHLC196

description: DASL


title: PHLC252

description: DASL


title: PHLC189

description: DASL


title: sid_CD7_dis_CROHN_age_48_gender_F


title: CD8+ T-cells with IL-2  [Control_2]


title: PHLC116

description: DASL


title: PHLC225

description: DASL


title: PHLC247

description: DASL


title: CD8+ T-cells with IL-2  [Control_1]


title: sid_CD6_dis_CROHN_age_53_gender_F


title: PHLC223

description: DASL


title: sid_CD5_dis_CROHN_age_65_gender_F


title: PHLC200

description: DASL


title: sid_CD3_dis_CROHN_age_45_gender_F


title: PHLC171

description: DASL


title: CAP8 BAY Release Rep3

city: Beijing

first: Zihan

last: Xu

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description: processed data file: CAP8BR.txt

data_processing:
Quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore with parameters ‘-q 30 --length 30 --stringency 5’.
The clean paired-end reads were aligned to the mm10 reference genome by Tophat with the parameter --no-novel-juncs. Gene expression levels and differentially expressed genes between samples were calculated with Cuffdiff and visualized with the R package cummeRbund.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each sample

source_name: CAP8 prostate cancer cell line

growth_protocol: Lncap/CAP2/CAP8/PC3 was cultured as ATCC described, Pb-Cre;pten loxp mice was maintained as described (Wang et al. 2003 cancer cell).

extract_protocol:
RNA was extracted using RNA extraction kit from Qiagen.
Tumor tissue or cell line library was constructed using kits from NEB(E7530),  CD8T cell and cancer cell library was constructed using smart-seq 2 protocol.

treatment_protocol: Cell lined was treated with vehicle or 5umol BAY1082439 for 48h then harvasted, castrated CP mice was treated with vehicle, BAY1082439 for 2 days, daily or intermittent for 4 weeks, intermittent 4 weeks then release 4 weeks or intermittent follow PD-1 therapy for 4 weeks, tumor tissue, tumor CD8T cell and cancer cell was harvasted

value: CAP8 prostate cancer cell line

value: BAY1082439 treatment 48hr withdraw 72h


title: PHLC198

description: DASL

value: patient-derived xenograft (PDX)

value: Pleom LUSC


title: CAP8 BAY Release Rep2

description: processed data file: CAP8BR.txt


title: PHLC122

description: DASL


title: PHLC204

description: DASL


title: PHLC156

description: DASL


title: sid_CD10_dis_CROHN_age_67_gender_F


title: CAP2 BAY Release Rep3

description: processed data file: CAP2BR.txt

source_name: CAP2 prostate cancer cell line

value: CAP2 prostate cancer cell line


title: PHLC277

description: DASL

value: LUAD


title: PHLC315

description: DASL


title: sid_CD2_dis_CROHN_age_31_gender_F

value: CD4+ T cells


title: sid_CD4_dis_CROHN_age_56_gender_F


title: PHLC251

description: DASL


title: sid_CD11_dis_CROHN_age_31_gender_F


title: CAP2 BAY Release Rep1

description: processed data file: CAP2BR.txt


title: PHLC309

description: DASL


title: PHLC237

description: DASL


title: CAP2 BAY Release Rep2

description: processed data file: CAP2BR.txt


title: PHLC192

description: DASL


title: PHLC169

description: DASL


title: PHLC188

description: DASL


title: PHLC344

description: DASL


title: sid_CLL3_dis_CLL_age_66_gender_M


title: sid_CLL4_dis_CLL_age_80_gender_F


title: sid_CD1_dis_CROHN_age_36_gender_M


title: PHLC282

description: DASL


title: sid_CLL2_dis_CLL_age_72_gender_M


title: Four cycles BAY release cancer cell Rep4

description: processed data file: CancerCell.txt

source_name: cancer cell isolated in prostate tumor

value: cancer cell isolated in prostate tumor

value: castration + BAY-I withdraw 4 weeks


title: sid_CLL1_dis_CLL_age_51_gender_M


title: PHLC334

description: DASL


title: PHLC286

description: DASL

value: LUSC


title: Four cycles BAY release cancer cell Rep6

description: processed data file: CancerCell.txt


title: PHLC321

description: DASL


title: PHLC356

description: DASL


title: sid_602_dis_CLL_age_74_gender_M

value: Male


title: PHLC137

description: DASL


title: PHLC339

description: DASL


title: sid_601_dis_CLL_age_67_gender_F


title: sid_603_dis_CLL_age_60_gender_M_dis2_ASTHMA_OB


title: PHLC322

description: DASL


title: PHLC353

description: DASL


title: Four cycles BAY release cancer cell Rep3

description: processed data file: CancerCell.txt


title: Trp-free Rif-treated wild-type, rep3

city: Omaha

first: Scot

middle: P

last: Ouellette

state: NE

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_pos_RIF_3

data_processing:
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Streptococcus pyogenes NZ131 by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Genome_build: http://bacteria.ensembl.org/Streptococcus_pyogenes_nz131_gca_000018125/Info/Index
Supplementary_files_format_and_content: Excel file showing abundance measurements

organism: Streptococcus pyogenes NZ131

source_name: Pure bacterial culture

growth_protocol: S. pyogenes strains were cultured for 1h in the presence or absence of tryptophan in the presence or absence of rifampicin (Rif).

extract_protocol:
For S. pyogenes, total RNA was collected, DNased, and processed to remove rRNA during the RNAseq library preparation step.
NuGen Universal Prokaryotic RNA-Seq AnyDeplete kit

tag: protocol

value: Trp-free DMEM

tag: genotype/variation

value: wild-type strain

value: +Rif


title: Trp-free Rif-treated wild-type, rep2

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_pos_RIF_2


title: Four cycles BAY release 4 weeks CD8T Rep5

description: processed data file: CD8T.txt

source_name: CD8T cell isolated in prostate tumor

value: CD8+T cell isolated in prostate tumor


title: PHLC134

description: DASL

value: Pleom LUAD


title: PHLC154

description: DASL


title: PHLC178

description: DASL


title: PHLC191

description: DASL


title: sid_600_dis_CLL_age_78_gender_F

value: Female


title: PHLC148

description: DASL


title: Four cycles BAY release 4 weeks CD8T Rep6

description: processed data file: CD8T.txt


title: Four cycles BAY release cancer cell Rep1

description: processed data file: CancerCell.txt


title: Four cycles BAY release 4 weeks CD8T Rep4

description: processed data file: CD8T.txt


title: PHLC119

description: DASL


title: Trp-free Rif-treated wild-type, rep1

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_pos_RIF_1


title: Four cycles BAY release cancer cell Rep2

description: processed data file: CancerCell.txt


title: Four cycles BAY release 4 weeks CD8T Rep3

description: processed data file: CD8T.txt


title: PHLC133

description: DASL


title: sid_5008_dis_BC_age_82_gender_F


title: Four cycles BAY release 4 weeks CD8T Rep2

description: processed data file: CD8T.txt


title: sid_5009_dis_BC_age_67_gender_F


title: PHLC211

description: DASL


title: sid_5010_dis_BC_age_67_gender_F


title: sid_5007_dis_BC_age_69_gender_F


title: Trp-free untreated wild-type, rep1

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_neg_RIF_1

value: -Rif


title: Trp-free untreated wild-type, rep3

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_neg_RIF_3


title: Four cycles BAY follow PD1 tissue Rep7

description: processed data file: FourCycleTissue.txt

source_name: prostate tumor tissue

value: prostate tumor tissue

value: castration + BAY-I follow PD-1


title: Four cycles BAY follow PD1 tissue Rep6


title: Rif-treated wild-type, rep3

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
PL_W_pos_RIF_3

value: Normal DMEM


title: Four cycles BAY release 4 weeks CD8T Rep1

description: processed data file: CD8T.txt


title: Trp-free untreated wild-type, rep2

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
M_W_neg_RIF_2


title: Four cycles BAY follow PD1 tissue Rep5


title: sid_5005_dis_BC_age_82_gender_F


title: Four cycles BAY follow PD1 tissue Rep4


title: Untreated wild-type, rep3

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
PL_W_neg_RIF_3


title: Four cycles BAY follow PD1 tissue Rep3


title: PHLC655

description: DASL

value: patient-derived xenograft (PDX)


title: PHLC139

description: DASL


title: sid_5002_dis_BC_age_81_gender_F


title: sid_5004_dis_BC_age_70_gender_F


title: PHLC77

description: DASL


title: PHLC12

description: DASL

value: LUAD


title: Rif-treated wild-type, rep1

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
PL_W_pos_RIF_1


title: PHLC86

description: DASL


title: med12 atxr5/6 (W)_R3_SxaQSEQsYB029L7_index_25

data_processing:
Reads were aligned using Tophat by allowing up to two mismatches and mapping only to one location. Chromosome mitochondria and chloroplast were exluded from alignments.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each genes generated by Cufflinks

source_name: rosette leaves

extract_protocol:
Total RNA was extracted from four-week-old rosette leaves grown on soil under long day conditions.  Three replicates from seperate plants were collected for each genotype. Each replicate conisted of 1 rosette leaf. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina).

value: four-week-old

value: rosette leaves

tag: genotype

value: med12 atxr5/6 (W)


title: Untreated wild-type, rep1

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
PL_W_neg_RIF_1


title: PHLC193

description: DASL

value: LUSC


title: PHLC149

description: DASL


title: sid_309_dis_ATHERO_age_77_gender_F

value: CD4+ T cells

value: ATHEROSCLEROSIS


title: Rif-treated wild-type, rep2

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
PL_W_pos_RIF_2

value: wild-type strain


title: Untreated wild-type, rep2

description:
rRNA depleted
Processed RNAseq data for GAS Rif.xlsx
PL_W_neg_RIF_2


title: B 3 days in culture

city: London

first: Sara

middle: Elgaard

last: Jager

address: Hodgkin Building, Guy's Campus

country: United Kingdom

institute: King's College London

data_processing:
The raw sequencing reads were processed using Cell Ranger version 3.0.2 and mapped to the reference genome mm10-3.0.0, Ensemble 93.
The resulting count matrices were analysed with Seurat v3 (Stuart et al., 2019) in R.
Cells with low quality (less than 200 detected genes and many mitochondiral genes) were filtered out.
Next the counts were normalized and natural log-transformed.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat objects as rds files

source_name: Dissociated dorsal root ganglia

extract_protocol:
The cells were detached with trypsin.
The cell suspensions were processed with the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics, PN 1000075) according to the manufacturer’s instructions.
scRNAseq 10x Genomics v3, the libraries were sequenced using DNBSEQ-G400.

treatment_protocol: Dorsal root ganglia was dissected from 2 week old mice, digested with enzymes and cultured for 3 days.

value: primary cultured dorsal root ganglia cells

value: Swiss

value: Tissue was taken from 2 week old mice


title: A 3 days in culture


title: sid_311_dis_ATHERO_age_69_gender_M

value: Male


title: sid_310_dis_ATHERO_age_74_gender_F

value: Female


title: sid_5000_dis_BC_age_77_gender_F


title: med12 atxr5/6 (W)_R2_SxaQSEQsYB029L7_index_19


title: sid_308_dis_ATHERO_age_76_gender_M


title: Four cycles BAY follow PD1 tissue Rep2

value: prostate tumor tissue


title: atxr5/6 (W)_R3_SxaQSEQsYB029L7_index_10

value: atxr5/6 (W)


title: empty_1_SmartSeq2_S7_10E

organism: blank sample

source_name: Negative control with no nuclei

tag: dapi fluorescence peak


title: empty_3_SmartSeq2_S7_11E

tag: cell compartment


title: Four cycles BAY follow PD1 tissue Rep1

tag: cell type

value: castration + BAY-I follow PD-1


title: sid_305_dis_ATHERO_age_73_gender_M

tag: primary diagnosis


title: sid_306_dis_ATHERO_age_60_gender_M

tag: age


title: CAP8 BAY Release Rep1

description: processed data file: CAP8BR.txt

value: CAP8 prostate cancer cell line

value: BAY1082439 treatment 48hr withdraw 72h


title: atxr5/6 (W)_R1_SxaQSEQsYB029L7_index_15

tag: developmental stage

value: four-week-old


title: Sph_eLCM_3

city: Cambridge

first: Linda

last: Griffith

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

description: Sample 18

data_processing:
Sequenced reads were mapped to GRCh38.p13 using STAR v2.7 and quantified using RSEM 1.3.3
Raw gene counts were pooled and summarized using tximport
Transcript data was filtered to contain only protein-coding genes and >1cpm for every sample
For detailed code see: https://github.com/ajwang3/WangHydrogel-RNASeq
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for for every sample after filtering low-counts and nonprotein-coding genes

source_name: hepatocytes

extract_protocol:
Cells were lysed in Trizol, followed by purification using Direct-Zol Microprep (Zymo)
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit v2 (Takara)

tag: tissue preparation

value: primary cryopreserved

value: hepatocytes

tag: scaffold

value: Microwell spheroids

tag: media treatment

value: enhanced liver culture media


title: Four cycles BAY follow isotype tissue Rep5

value: castration + BAY-I withdraw 4 weeks


title: Sph_eLCM_2

description: Sample 17


title: Four cycles BAY follow isotype tissue Rep4


title: Sph_eLCM_1

description: Sample 16


title: Four cycles BAY follow isotype tissue Rep6


title: empty_2_SmartSeq2_S7_11A


title: Four cycles BAY follow isotype tissue Rep7


title: atxr5/6 (W)_R2_SxaQSEQsYB029L7_index_1

value: rosette leaves


title: WT_R1_SxaQSEQsYB029L8_index_23

value: WT


title: med12 atxr5/6 (W)_R1_SxaQSEQsYB029L7_index_13

value: med12 atxr5/6 (W)


title: Sph_HCM_3

description: Sample 15

value: hepatocyte culture media


title: sid_302_dis_ATHERO_age_53_gender_M

value: CD4+ T cells

value: ATHEROSCLEROSIS

tag: Sex

value: Male


title: sid_300_dis_ATHERO_age_49_gender_M_dis2_ATHERO


title: sac3b-3 atxr5/6 (W)_R3_SxaQSEQsYA109L6_index_22

source_name: floral buds

extract_protocol:
Total RNA was extracted from four-week-old floral buds grown on soil under long day conditions.  Three replicates from seperate plants were collected for each genotype. Each replicate conisted of 4 floral bud. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo).
1ug of total RNA was used to prepare libraries using the NeoPrep Library Prep System (Illumina).

tag: tissue

value: floral buds

value: sac3b-3 atxr5/6 (W)


title: WT_R2_SxaQSEQsYB029L7_index_6


title: Four cycles BAY follow isotype tissue Rep1

value: prostate tumor tissue


title: Four cycles BAY follow isotype tissue Rep3


title: Sph_HCM_2

description: Sample 14


title: sid_229_dis_ASTHMA_age_61_gender_F

value: ASTHMA

value: Female


title: sid_301_dis_ATHERO_age_80_gender_M


title: Four cycles BAY prostate CD8T Rep9

description: processed data file: CD8T.txt

value: CD8+T cell isolated in prostate tumor

value: castration + BAY-I


title: sac3b-3 atxr5/6 (W)_R2_SxaQSEQsYA109L6_index_21

value: four-week-old


title: Four cycles BAY follow isotype tissue Rep2


title: sid_304_dis_ATHERO_age_61_gender_M


title: PEG_eLCM_2

description: Sample 11

value: primary cryopreserved

value: hepatocytes

value: LiverChip PEG

value: enhanced liver culture media


title: Four cycles BAY prostate CD8T Rep7

description: processed data file: CD8T.txt


title: sid_226_dis_ASTHMA_age_31_gender_M


title: sid_228_dis_ASTHMA_age_41_gender_F


title: sac3b-3 atxr5/6 (W)_R1_SxaQSEQsYA109L6_index_20


title: Four cycles BAY prostate CD8T Rep8

description: processed data file: CD8T.txt


title: Sph_HCM_1

description: Sample 13

value: Microwell spheroids


title: PEG_eLCM_3

description: Sample 12


title: mbd9-3 atxr5/6 (W)_R3_SxaQSEQsYA109L6_index_15

value: mbd9-3 atxr5/6 (W)


title: Four cycles BAY prostate CD8T Rep6

description: processed data file: CD8T.txt


title: PEG_HCM_2

description: Sample 8

value: hepatocyte culture media


title: mbd9-3 atxr5/6 (W)_R2_SxaQSEQsYA109L6_index_14


title: Four cycles BAY prostate CD8T Rep3

description: processed data file: CD8T.txt


title: Four cycles BAY prostate CD8T Rep5

description: processed data file: CD8T.txt


title: mbd9-3 atxr5/6 (W)_R1_SxaQSEQsYA109L6_index_13


title: Four cycles BAY prostate CD8T Rep4

description: processed data file: CD8T.txt


title: stubl2-3 atxr5/6 (W)_R3_SxaQSEQsYA109L6_index_12

value: stubl2-3 atxr5/6 (W)


title: sid_225_dis_ASTHMA_age_74_gender_M_dis2_ATHERO

value: CD4+ T cells

value: ATHEROSCLEROSIS

value: Male


title: PEG_HCM_1

description: Sample 7


title: stubl2-3 atxr5/6 (W)_R2_SxaQSEQsYA109L6_index_11

value: floral buds


title: PS_eLCM_2

description: Sample 5

value: LiverChip polystyrene


title: PEG_eLCM_1

description: Sample 10


title: stubl2-3 atxr5/6 (W)_R1_SxaQSEQsYA109L6_index_10


title: Four cycles Vehicle prostate CD8T Rep6

description: processed data file: CD8T.txt

value: castration + vehicle


title: sid_222_dis_ASTHMA_age_51_gender_F

value: ASTHMA

value: Female


title: sid_224_dis_ASTHMA_age_61_gender_M


title: Four cycles BAY prostate CD8T Rep2

description: processed data file: CD8T.txt

value: CD8+T cell isolated in prostate tumor

value: castration + BAY-I


title: PS_eLCM_3

description: Sample 6

value: primary cryopreserved

value: hepatocytes


title: PEG_HCM_3

description: Sample 9

value: LiverChip PEG


title: sid_223_dis_ASTHMA_age_37_gender_M


title: atxr5/6 (W)_R3_SxaQSEQsYA109L6_index_6

value: four-week-old

value: atxr5/6 (W)


title: atxr5/6 (W)_R1_SxaQSEQsYA109L6_index_4


title: PS_HCM_3

description: Sample 3

value: hepatocyte culture media


title: Four cycles Vehicle prostate CD8T Rep5

description: processed data file: CD8T.txt


title: atxr5/6 (W)_R2_SxaQSEQsYA109L6_index_5


title: Four cycles BAY prostate CD8T Rep1

description: processed data file: CD8T.txt


title: PS_eLCM_1

description: Sample 4

value: enhanced liver culture media


title: PS_HCM_2

description: Sample 2


title: WT_R3_SxaQSEQsYA109L6_index_3

value: WT


title: sid_219_dis_ASTHMA_age_63_gender_M_dis2_ECZ

value: CD4+ T cells


title: sid_218_dis_ASTHMA_age_56_gender_M

value: Male


title: PHLC365

description: DASL

source_name: Xenograft

value: patient-derived xenograft (PDX)

tag: histology

value: LUSC


title: sid_221_dis_ASTHMA_age_20_gender_F


title: sid_1750_dis_BC_age_56

hyb_protocol: Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression v2 8x60K microarray kit, according to the manufacture’s instruction (Agilent Technologies).

data_processing: All gene expression microarrays were processed using the LIMMA [R] package: background correction and between array normalization. All probes not higher expressed than 1.2 times the background signal were removed. In the publication, all probes representative of the same Entrez Gene ID were averaged.

value: Breast cancer


title: Four cycles Vehicle prostate CD8T Rep3

description: processed data file: CD8T.txt

tag: treatment

value: castration + vehicle


title: arp6-1 atxr5/6 (W)_R4_SxaQSEQsYAP054L7_index_14

source_name: cotyledons

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo). RNA for stubl2-3 atxr5/6 (W) genotype was successfully extracted for only two out of four replicates.
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .

value: two-week-old

value: cotyledons

value: arp6-1 atxr5/6 (W)


title: Four cycles BAY release cancer cell Rep5

description: processed data file: CancerCell.txt

value: cancer cell isolated in prostate tumor

value: castration + BAY-I withdraw 4 weeks


title: sid_6011_dis_HC_age_53

value: Control

value: Female


title: Unstimulated_rep1

city: Chicago

first: Amy

last: Kenter

state: Illinois

address: 835 S Wolcott Ave

institute: University of Illinois at Chicago

data_processing:
Library strategy: 5C-seq
5C products were analyzed by Solexa paired-end deep sequencing.
A virtual genome of all potential 5C products was created using DNA sequence adjacent to Hind III restriction fragment sites.
Reads were aligned to the virtual genome using Novoalign (http://www.novocraft.com).
Each paired-end read was mapped independently and only paired-ends for which one end mapped to a 5C forward primer and the other to a 5C reverse primer were considered. Reads that mapped to more than one location were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Files are tab-delimited text tables. Comment header lines give sequence alignment statistics. Data lines have the following columns: (1) forward primer and genomic coordinates, (2) reverse primer and genomic coordinates, (3) number of reads, (4) value = 1 (unused)

source_name: Resting splenic B cells

growth_protocol: B cells were sorted for CD43-  B cells using anti-CD43 magnetic microbeads (MACS, Miltenyi) according to the manufacturer’s instructions.

extract_protocol: The 5C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. The cells are then lysed and chromatin is digested with the Hind III restriction enzyme. The digested fragments are ligated under dilute conditions to promote intra-molecular ligation. A genome-wide interaction library of ligation products corresponding to all possible chromatin interactions is produced by this method.

tag: strain

value: splenic B cell

value: Unstimulated


title: Four cycles Vehicle prostate CD8T Rep4

description: processed data file: CD8T.txt

value: CD8+T cell isolated in prostate tumor


title: PS_HCM_1

description: Sample 1

value: primary cryopreserved

value: hepatocytes

value: LiverChip polystyrene

value: hepatocyte culture media


title: sid_6003_dis_HC_age_38

value: CD4+ T cells


title: splenic B cells, LPS+IL4_rep2 (5C-seq)

data_processing:
Library strategy: 5C-seq
5C products were analyzed by Solexa paired-end deep sequencing.
A virtual genome of all potential 5C products was created using DNA sequence adjacent to Hind III restriction fragment sites.
Reads were aligned to the virtual genome using Novoalign (http://www.novocraft.com).
Each paired-end read was mapped independently and only paired-ends for which one end mapped to a 5C forward primer and the other to a 5C reverse primer were considered. Reads that mapped to more than one location were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: Files are tab-delimited text tables. Comment header lines give sequence alignment statistics. Data lines have the following columns: (1) forward primer and genomic coordinates, (2) reverse primer and genomic coordinates, (3) number of reads, (4) value = 1 (unused)

source_name: Activated splenic B cells

growth_protocol: B cells were sorted for CD43-  B cells using anti-CD43 magnetic microbeads (MACS, Miltenyi) according to the manufacturer’s instructions. B cells were cultured at a density of 5-8 x 10^5 cells/ml in RPMI, glutamine (4 mM), penicillin (100 U/ml)-streptomycin (100 mg/ml), b-mercaptoenthanol (50 mM), supplemented with FCS (20% vol/vol) with the activators, LPS (50 mg/ml) and IL4 (10 ng/ml).

treatment_protocol: B cells were grown ex vivo in the  presence of LPS+IL4 for 40 hours.


title: sid_1786_dis_BC_age_73

source_name: CD4+ T cells

value: Breast cancer


title: WT_R1_SxaQSEQsYA109L6_index_1

value: four-week-old

value: floral buds

value: WT


title: Four cycles Vehicle prostate CD8T Rep2

description: processed data file: CD8T.txt

value: castration + vehicle


title: Unstimulated_rep2


title: sid_1756_dis_BC_age_72


title: Four cycles BAY spleen CD8T Rep7

description: processed data file: CD8T.txt

source_name: CD8T cell isolated in spleen

value: CD8+T cell isolated in spleen

value: castration + BAY-I


title: Four cycles BAY spleen CD8T Rep8

description: processed data file: CD8T.txt


title: Four cycles BAY spleen CD8T Rep6

description: processed data file: CD8T.txt


title: arp6-1 atxr5/6 (W)_R3_SxaQSEQsYAP054L7_index_13

value: two-week-old

value: cotyledons

value: arp6-1 atxr5/6 (W)


title: sid_1758_dis_BC_age_53

value: Female


title: sid_227_dis_ASTHMA_age_56_gender_F

value: ASTHMA


title: Input-epithelium

city: Bethesda

first: Yasuo

last: Yoshitomi

state: MD

address: 30 Convent Dr.

department: NIDCR

institute: NIH

data_processing:
36 nt 5’- single-end sequencing reads were obtained using an Illumina Genome Analyzer II.
ChIP-seq reads were aligned to the mouse mm9 genome assembly using the ELAND algorithm
Only reads that map uniquely, have no more than two mismatches and pass quality control Q filtering were used. The reads were extended in silico using Active Motif TM software at their 3´-ends to a length of 130 bp.
BAR files were obtained by dividing the genome into into 32-nt bins and determining the number of reads (density) in each bin.
BED files were obtained from MACS files. The MACS (version 1.3.7.1) with a cutoff of p value <10e-7, band width of 130, and model fold of 12 was used to identify peaks.
Xlsx files contain Sp6 ChIP peaks within 10,000 bases of a known gene MGSC (build 37)
BAR files were obtained dividing the genome into into 32-nt bins and determining the number of reads (density) in each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bar files and Bed files can be viewed in Integrated Genome Browser (IGB)
Xlsx files contain Sp6 ChIP peaks within 10,000 bases of a known gene MGSC (build 37)

source_name: dental epithelium

extract_protocol:
Dental epithelium and mesenchyme samples from 30 newborn C57BL/6 P1 molars was isolated. After crosslinking with PFA, and sonication, Sp6 antibody was used for DNA immunoprecipitation.
DNA sequencing libraries were prepared by Active Motif and sequenced using an Illumina Genome Analyzer 2.

value: dental epithelium

tag: chip antibody


title: Four cycles Vehicle prostate CD8T Rep1

description: processed data file: CD8T.txt

value: CD8+T cell isolated in prostate tumor


title: arp6-1 atxr5/6 (W)_R2_SxaQSEQsYAP054L7_index_12


title: Four cycles BAY spleen CD8T Rep5

description: processed data file: CD8T.txt


title: WT_R2_SxaQSEQsYA109L6_index_2


title: splenic B cells, LPS+IL4_rep1 (5C-seq)

value: splenic B cell


title: arp6-1 atxr5/6 (W)_R1_SxaQSEQsYAP054L7_index_11


title: sid_1752_dis_BC_age_41

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Micro kit (Qiagen, Hilden, Germany; cat. no. 80284) according to the manufacturer’s instructions.


title: Four cycles BAY spleen CD8T Rep4

description: processed data file: CD8T.txt


title: sid_1764_dis_BC_age_88


title: stubl2-3 ddm1-2_R3_SxaQSEQsYAP054L7_index_9

value: stubl2-3 ddm1-2


title: Sp6-epithelium

value: Sp6 antibody (in house)


title: stubl2-3 ddm1-2_R4_SxaQSEQsYAP054L7_index_10


title: sid_6010_dis_HC_age_60

value: CD4+ T cells

value: Control


title: Input-mesenchyme

source_name: dental mesenchyme

value: dental mesenchyme


title: Four cycles BAY spleen CD8T Rep1

description: processed data file: CD8T.txt


title: stubl2-3 ddm1-2_R2_SxaQSEQsYAP054L7_index_8


title: sid_6005_dis_HC_age_44


title: stubl2-3 ddm1-2_R1_SxaQSEQsYAP054L7_index_7


title: sid_1755_dis_BC_age_35

value: Breast cancer


title: Four cycles BAY spleen CD8T Rep2

description: processed data file: CD8T.txt


title: sid_1762_dis_BC_age_83


title: sid_1763_dis_BC_age_78


title: stubl2-3_R4_SxaQSEQsYAP054L7_index_4


title: stubl2-3_R3_SxaQSEQsYAP054L7_index_3


title: Four cycles Vehicle spleen CD8T Rep9

description: processed data file: CD8T.txt

value: castration + vehicle


title: sid_6007_dis_HC_age_51


title: 178-A031919

city: Basel

first: Jasmin

last: Haslbauer

address: Schönbeinstrasse 40

department: Institute of Medical Genetics and Pathology

country: Switzerland

institute: University of Basel

data_processing:
Alignment: four demultiplexed FASTQ files per well in the assay sequenced with the HTG EdgeSeq Parser (version 5.0.535.3181) see HTG EdgeSeq System User Manual (RUO).
Post sequencing quality control: POS% ≥ 28% as failure; Read depth ≤ 750,000 as failure; RSD ≤ 0.094 as failure .
Normalization: No pre-filtering is applied to the data prior to analysis. The DESeq2 (package version 1.14.1)model corrects for library size using the median ratio method from Anders and Huber (2010).
Dispersions are estimated with the Cox Reid-adjusted profile likelihood method developed by McCarthy et al. (2012).  Log2 fold change is estimated via Tikhonov/ridge regularization with a zero-centered normal prior distribution with variance calculated using the observed distribution of maximum likelihood coefficients (see DESeq2 documentation for details).
Supplementary_files_format_and_content: Excel file containing tables of raw, QC raw, log2 CPM (counts per million), and median normalized data.

source_name: COVID-19_lymph node

extract_protocol:
HTG uses an extraction free technology that involves resuspending crude sample in Lysis Buffer.  The sample is then treated with Proteinase K and stored or used.
HTG EdgeSeq library construction is defined in the HTG EdgeSeq System User Manual (RUO)

tag: group

value: lymph node


title: Sp6-mesenchyme


title: stubl2-3_R2_SxaQSEQsYAP054L7_index_2

tag: genotype


title: 178-A031916

source_name: Control_lymph node


title: Four cycles Vehicle spleen CD8T Rep6

description: processed data file: CD8T.txt

value: CD8+T cell isolated in spleen


title: 178-A031921


title: 178-A031917


title: Four cycles Vehicle spleen CD8T Rep8

description: processed data file: CD8T.txt


title: stubl2-3 atxr5/6 (W)_R1_SxaQSEQsYAP054L7_index_5

value: two-week-old

value: stubl2-3 atxr5/6 (W)


title: sid_1770_dis_BC_age_50


title: stubl2-3 atxr5/6 (W)_R2_SxaQSEQsYAP054L7_index_6

value: cotyledons


title: Four cycles Vehicle spleen CD8T Rep7

description: processed data file: CD8T.txt


title: Four cycles BAY spleen CD8T Rep3

description: processed data file: CD8T.txt

value: castration + BAY-I


title: 178-A031918


title: stubl2-3_R1_SxaQSEQsYAP054L7_index_1


title: 178-A031914


title: 178-A031915


title: sid_1751_dis_BC_age_67

value: Female


title: sid_1768_dis_BC_age_68


title: sid_6013_dis_HC_age_59


title: sid_1769_dis_BC_age_67


title: 178-A031912


title: Four cycles Vehicle spleen CD8T Rep5

description: processed data file: CD8T.txt


title: sid_1767_dis_BC_age_43


title: Four cycles Vehicle spleen CD8T Rep3

description: processed data file: CD8T.txt


title: Four cycles Vehicle spleen CD8T Rep2

description: processed data file: CD8T.txt


title: ddm1-2_R2_SxaQSEQsYAP054L7_index_23


title: 178-A031911


title: 178-A031909


title: atxr5/6 (W)_R4_SxaQSEQsYAP054L6_index_21

value: atxr5/6 (W)


title: ddm1-2_R1_SxaQSEQsYAP054L7_index_22


title: Four cycles BAY cancer cell Rep9

description: processed data file: CancerCell.txt

source_name: cancer cell isolated in prostate tumor

value: cancer cell isolated in prostate tumor


title: Four cycles Vehicle spleen CD8T Rep4

description: processed data file: CD8T.txt


title: atxr5/6 (W)_R3_SxaQSEQsYAP054L6_index_20


title: 178-A031908


title: ddm1-2_R3_SxaQSEQsYAP054L7_index_25


title: sid_6006_dis_HC_age_58


title: sid_1766_dis_BC_age_63


title: 178-A031910


title: ddm1-2_R4_SxaQSEQsYAP054L7_index_27


title: sid_6012_dis_HC_age_60


title: 178-A031906


title: atxr5/6 (W)_R2_SxaQSEQsYAP054L6_index_19


title: sid_6004_dis_HC_age_39


title: atxr5/6 (W)_R1_SxaQSEQsYAP054L6_index_18


title: sid_1765_dis_BC_age_55


title: Four cycles BAY cancer cell Rep8

description: processed data file: CancerCell.txt


title: WT_R3_SxaQSEQsYAP054L6_index_15

value: WT


title: Four cycles BAY cancer cell Rep4

description: processed data file: CancerCell.txt


title: Four cycles BAY cancer cell Rep3

description: processed data file: CancerCell.txt


title: 178-A031903


title: 178-A031907


title: sid_1760_dis_BC_age_70


title: WT_R1_SxaQSEQsYAP054L6_index_13


title: 178-A031902


title: WT_R4_SxaQSEQsYAP054L6_index_16


title: Four cycles BAY cancer cell Rep6

description: processed data file: CancerCell.txt


title: 178-A031905


title: Four cycles Vehicle spleen CD8T Rep1

description: processed data file: CD8T.txt


title: Four cycles BAY cancer cell Rep7

description: processed data file: CancerCell.txt


title: Four cycles BAY cancer cell Rep5

description: processed data file: CancerCell.txt


title: sid_6002_dis_HC_age_41


title: sid_1759_dis_BC_age_53


title: sid_6009_dis_HC_age_57


title: sid_1761_dis_BC_age_61


title: Four cycles BAY cancer cell Rep1

description: processed data file: CancerCell.txt


title: stubl2-3_R4_SxaQSEQsYA067L2_index_16

extract_protocol:
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .


title: 178-A031898


title: 178-A031901


title: WT_R2_SxaQSEQsYAP054L6_index_14


title: 178-A031904


title: sid_6008_dis_HC_age_52


title: stubl2-3_R3_SxaQSEQsYA067L2_index_15


title: Four cycles Vehicle cancer cell Rep5

description: processed data file: CancerCell.txt


title: sid_1754_dis_BC_age_50


title: 178-A031892