title: ChIP on H3K9K14ac and with no estradiol treatment of MCF-7 cells [H3K9K14ac_minusE2_Fan85]


title: Celiac disease [6735-5]

status: Public on Mar 24 2021

type: RNA

city: Halle

first: Edith

last: Willscher

state: Deutschland

address: Ernst-Grube-Straße 40

department: Internal Medicine IV

country: Germany

institute: Martin Luther University of Halle-Wittenberg

hyb_protocol: From each probe 750 ng of cRNA were hybridised to Human HT-12 v4 Expression BeadChips

scan_protocol: scanned on the Illumina HiScan instrument

data_processing: Raw probe data was quantile normalized and background corrected by Illumina GenomeStudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Gut

label_protocol: 250ng RNA per sample were ethanol precipitated with GlycoBlue (Invitrogen) as carrier and dissolved at a concentration of 100-150 ng/µl prior to probe synthesis using the TargetAmp™- Nano Labeling Kit for Illumina Expression BeadChip.

extract_protocol: Fresh tissue samples were snap frozen and stored in liquid nitrogen until preparation. Frozen biopsies were disrupted and homogenized by TissueLyzer from Quiagen (Hilden, Germany). Total RNA was isolated using AllPrep® DNA/RNA Micro kit (QIAGEN, Hilden, Germany) and stored at -70°C.  Before microarray analysis RNA integrity and concentration was examined on an Agilent 2100 Bioanalyzer

tag: disease

value: Celiac disease

tag: marsh stage

tag: age


title: Control [7507-1]

value: Control


title: Klf2KD_rep1_RNA-seq

type: SRA

city: Daejeon

first: Lin

last: Seo

address: Basic Science Bld Rm414, 291 Daehak-ro, Yuseong-gu, KAIST

department: Department of Biological Sciences

country: South Korea

institute: KAIST

library_source: transcriptomic

data_processing:
Reads were aligned to mm39 using HISAT2
Genome_build: mm39
Supplementary_files_format_and_content: Bigwig files were generated using deeptools2 bamCoverage

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: E14Tg2a cells were cultured in 0.1% gelatin coated dishes with KnockOut DMEM (Gibco) with 15% FBS, NEAA, L-glutamine, 2-mercaptoethanol, and 1,000 U/ml LIF.

extract_protocol:
RNA samples were lyesed with total RNA extraction kit.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: From HEK 293T cells, shControl, shKlf2 and shSnd1 lentiviruses were harvested. Lentiviral particles (MOI 10) with hexadimethrine bromide were infected in E14TG2a and selected with 2 ug/ml puromycin.

tag: background strain

tag: genotype

value: Wild-type

tag: treatment

tag: cell types


title: ESC_Ctrl_BRD4_TC0_2

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_BRD4_T0.n.bw

library_source: genomic

data_processing:
Read alignment was performed using BWA with default parameters. Low mapping quality read (MAPQ 10) and duplicated reads were removed using samtools. The DAC Blacklisted Regions were also omitted from the bam file using bedtools. Peaks were called using epic with the following parameters: --fragment-size 200 --gaps-allowed 5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: mouse ES cells

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments 11932748. ESCs were cultured in a custom-made N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium, without L-arginine and L-lysine (C.C.Pro GmbH, Oberdorla). The media was supplemented with L-arginine, L-lysine, 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1µM PD0325901, 3µM CT-99021 (custom-made by ABCR), 100µM 2-mercaptoethanol, 150µM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), as well as with 0.5x N2 supplement (made in house; or from Thermo Fisher Scientific).

extract_protocol:
Cells were cross-linked for 10 min at room temperature with 1% formaldehyde solution with gentle agitation and quenched with 0.125 M glycine. Cross-linked cells were washed once with PBS, added swelling buffer (10 mM Tris-HCl pH8.0, 1.5 mM MgCl2, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. After centrifugation, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) containing proteinase inhibitor cocktail (Roche), and then were sonicated by using a BioRuptor sonicator (Diagenode). After centrifugation, solubilized chromatin was recovered and incubated with 5 µg of antibody bound to protein A/G magnetic beads (Pierce). After overnight incubation at 4ºC, the magnetic beads were washed with RIPA buffer twice, RIPA high salt buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) and TE buffer. The bound materials were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) overnight at 65ºC and treated with RNaseA for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA was purified with a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared by using the NEBNext Ultra II DNA prep kit (NEB E7645) following the manufacturer's instruction and sequenced on a Next-Seq 500 Sequencer (Illumina).

treatment_protocol: A-485 (10uM) or JQ1 (0.5mM) were treated for 60 min if not indicated. For control samples, 0.1% DMSO was added.

tag: cell type

value: ES cells

tag: cell line

value: DMSO for 60 min

tag: chip antibody


title: ESC_Ctrl_BRD4_TC0_1


title: ChIP on H3K9K14ac and with estradiol treatment of MCF-7 cells (40min) [H3K9K14ac_plusE2_Fan136]

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

country: USA

institute: HHMI/UCSD

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) was used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align ChIP-seq and ChIRC-seq samples to hg38 genome and we have kept 1 copy/read per genome position.
Peak finding: we have called the ChIP-seq and ChiRC-seq peaks by using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/). For the CHIP-seq analysis, we have used the default settings in HOMER.
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

growth_protocol: MCF-7 cells were cultured in DMEM, 10% FBS and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
ChIP was performed as previously described, with minor modifications. Briefly, approximately 5 x 10^7 cells were crosslinked with 1% formaldehyde at room temperature for 15 min and quenched with 0.125M glycine for 5 min. Cells were then harvested and incubated with nuclei preparation buffer (50 mM Tris pH 7.5, 150 mM NaCl , 5 mM EDTA, 0.5% NP-40, 1% TX-100), with protease inhibitor (Sigma, Cat#P2714-1BTL) included, for 10 min. After centrifugation, the pellet was suspended in sonication buffer (10 mM Tris, pH8.0, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine, with protease inhibitor included) for sonication. After sonication, 1/10 volume of 10% Triton X-100 was added to sonicated lysate. The supernatant, after centrifugation, was then incubated with 5μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Protein G magnetic beads (Invitrogen, Cat#10004D). Immuno-complexes were washed with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate, with protease inhibitor included) for at least 5 times and TE buffer containing 50 mM Nacl once. After de-crosslinking, DNA was then purified by QIAquick Spin columns (Qiagen).
For Bio-ChIP, 5x10^7 MCF-7 cells stably expressing BirA and biotin acceptor peptide (BAP)-HP1α (4A) or BAP- HP1α (4E) were crosslinked with 1% formaldehyde at room temperature for 15 min, and then incubated with 0.125M glycine for 5 min. To isolate nuclei, cells were incubated with nuclei preparation buffer (50 mM Tris pH 7.5, 150 mM NaCl , 5 mM EDTA, 0.5% NP-40, 1% TX-100), with protease inhibitor (Sigma, Cat#P2714-1BTL) included, for 10 min. The obtained nuclei were suspended in immunoprecipitation buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and 1% Triton X-100, with protease inhibitor included) for sonication. The sonicated chromatin in immunoprecipitation buffer was then incubated with 50 ul of pre-blocked Pierce™ Streptavidin Magnetic Beads (Thermo Fisher, Cat#88816) overnight at 4°C on a rotating wheel. Beads were extensively washed with SDS buffer (10 mM Tris, pH 8, 1 mM EDTA, 2% SDS, protease inhibitor included) twice, high salt buffer (50 mM HEPES pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 500 mM NaCl) twice, DOC buffer (250 mM LiCl, 0.5%, NP-40, 0.5% deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) once and TE buffer containing 50 mM Nacl once. Beads were then treated with RNase A (Thermo Fisher Scientific, Cat# AM2270) and Proteinase K (Thermo Fisher Scientific, Cat# AM2548) before de-crosslinking overnight at 65°C. DNA was finally purified by QIAquick Spin columns (Qiagen, Cat#28106).
The library construction protocol followed the manufacturer’s instructions.

treatment_protocol: For estrogen stimulation, these cells were cultured in phenol-red free DMEM with 5% charcoal stripped FBS for at least 3 days and then treated with 100nM 17β-estradiol (E2) for 40 minutes. Control samples were treated with ethanol.


title: Control_rep2_RNA-seq

value: shControl


title: ChIP on H3K9K14ac and with no estradiol treatment of MCF-7 cells [H3K9K14ac_minusE2_Fan135]


title: Celiac disease [2994-8]


title: Celiac disease [4193-X]


title: ChIP on H3K56ac and with estradiol treatment of MCF-7 cells (40min) [H3K56ac_plusE2_Fan60]


title: ESC_A485_H3K27me3_1

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_H3K27me3.n.bw

value: 10uM A-485 for 60 min


title: ESC_A485_H3K27me3_2


title: Celiac disease [8280-3]


title: ChIP on H3K56ac and with estradiol treatment of MCF-7 cells (40min) [H3K56ac_plusE2_Fan88]


title: Control_rep1_RNA-seq


title: Control [3449-4]


title: ChIP on H3K56ac and with no estradiol treatment of MCF-7 cells [H3K56ac_minusE2_Fan87]


title: 5903-S17_Untrained_Female

city: Durham

first: Cagla

last: Eroglu

state: NC

address: 333A Nanaline building, Durham, NC 27710

department: Cell Biology

institute: Duke University

data_processing:
Trimmomatic(v0.38) was used to trim sequencing adapters
Reads were aligned to the mouse genome (mm10) via Bowtie2 (v2.3.5.1)
Reads were counted using featureCounts in the Subread package (v1.6.3)
Differential gene expression was done using edgeR (v3.30.3)
Genome_build: mm10
Supplementary_files_format_and_content: fastq sequencing files
Supplementary_files_format_and_content: tab delimited file of differential expression results including FPKMs

source_name: ACC bulk RNAseq

extract_protocol:
ACC was microdissected within 1h after the last day of training and flash-frozen in liquid nitrogen. Total RNA was extracted in Trizol.
RNA-sequencing libraries were made from ≥500ng of purified mouse ACC RNA using the Kapa Stranded mRNA-seq kit

tag: strain

value: WT

tag: tissue

value: Anterior Cingulate Cortex

tag: Sex

value: Female

tag: treatment group

value: Untrained


title: 5903-S16_Untrained_Male

value: Male


title: ESC_Ctrl_H3K27me3_1

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_H3K27me3.n.bw


title: ChIP on H3K4me3 and with estradiol treatment of MCF-7 cells (40min) [H3K4me3_plusE2_Fan153]


title: ChIP on H3K56ac and with no estradiol treatment of MCF-7 cells [H3K56ac_minusE2_Fan59]


title: 5903-S13_Trained_Male

value: Trained


title: Control [0582-9]


title: body skin

city: Vienna

first: Julia

last: Lachner

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Initial analysis was performed using the 10xGenomics software cellranger version 3.0.2
For further analysis of the filtered feature barcode matrix, the “R” based package Seurat Version 3 from Satija Lab was used. In order to reduce unwanted background signal, cells were filtered according to their feature counts, lower than 1500 and higher than 200, and mitochondrial content, below 5%. Additionally, the data was normalized by a scale factor of 10000, and 3000 variable features determined. After scaling the data, a principal component analysis (PCA) was performed. Within 15 significantly detected principal components, neighboring cells were identified and clusters calculated based on the Louvain algorithm at a resolution of 0.2. Finally relations between cells based on their gene expression were depicted in a Uniform Manifold Approximation and Projection (UMAP).
Genome_build: ggal5, ensembl 91 annotations plus custom annotations described in this paper
Supplementary_files_format_and_content: Tab-separated plain text file and matrix data file

molecule: polyA RNA

organism: Gallus gallus

source_name: body skin

extract_protocol:
One day old chicks (strain Lohmann) were obtained from Schropper GmbH, Gloggnitz, Austria. Skin was excised from the leg of sacrificed animals and incubated in thermolysin (0.5 mg/ml) (Sigma-Aldrich, #T7902) at 37°C for 45 minutes. The lower dermis was removed using forceps and the remaining tissue, including the epidermis and parts of the upper dermis, was processed further according to protocols established for human skin (Vorstandlechner et al. 2020; Kalinina et al. 2020). For the isolation of cells, the tissue was split into two fractions that were incubated either in buffer-enzyme mix of the Whole Skin Dissociation Kit human (MACS Milteny Biotech, #130-101-540) for 2.5 h at 37°C or with 0.05% trypsin/EDTA (Thermo Fisher Scientific, #25300) and DNase 1 (10 µg/ml) (Roche Diagnostics, #10104159001) at 37°C for 15 minutes. Afterwards the samples were combined and processed according to the manufactor’s protocol (Whole Skin Dissociation Kit human, MACS Milteny Biotech, #130-101-540). In brief, the epidermis-enzyme mix was diluted in 0.5 ml medium and dissociated with the gentleMACS Dissociator. The ground tissue was filtered through 100-micron (Falcon, #352360) and 40-micron (Falcon, # 352340) meshes. Subsequently, cells were stained with DAPI and viable cells were purified by fluorescence-activated cell sorting at the Core Facility Flow Cytometry, Medical University of Vienna. Sequencing libraries of viable cells were prepared using Cell Ranger (10x Genomics) version 3.0.2 at the Center for Molecular Medicine, Vienna, Austria.
10x Genomics Chromium Single Cell 3' Reagent Kit v2

value: skin


title: Celiac disease [0951-4]


title: Control [3341-3]


title: 5903-S12_Trained_Male


title: Control [7871-5]


title: ChIP on H3K4me3 and with estradiol treatment of MCF-7 cells (40min) [H3K4me3_plusE2_Fan98]


title: ESC_A485_p300_1

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_p300.n.bw


title: Celiac disease [8221-0]


title: Celiac disease [0062-4]


title: ChIP on H3K4me3 and with no estradiol treatment of MCF-7 cells [H3K4me3_minusE2_Fan152]


title: 5903-S10_Untrained_Male


title: ESC_Ctrl_p300_2

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_p300.n.bw


title: ESC_Ctrl_p300_1


title: ESC_Ctrl_H3K27me3_2


title: ChIP on H3K4me3 and with no estradiol treatment of MCF-7 cells [H3K4me3_minusE2_Fan97]


title: 5903-S14_Trained_Male


title: ChIP on H3K36me3 and with estradiol treatment of MCF-7 cells (40min) [H3K36me3_plusE2_Fan134]


title: ESC_A485_p300_2


title: ChIP on H3K36me3 and with estradiol treatment of MCF-7 cells (40min) [H3K36me3_plusE2_Fan58]


title: ESC_A485_Pol2S5_2

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_Pol2S5.n.bw

value: Pol2 phosphoSer5 (Abcam, ab5131)


title: 5903-S5_Untrained_Female


title: ESC_A485_Pol2S5_1


title: 5903-S3_Trained_Female


title: Control [2005-0]


title: Celiac disease [2141-9]


title: ChIP on H3K36me3 and with no estradiol treatment of MCF-7 cells [H3K36me3_minusE2_Fan57]


title: Celiac disease [1419-0]


title: 5903-S2_Trained_Female


title: Control [6391-X]


title: Control [0417-6]


title: ESC_A485_Pol2S2_2

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_Pol2S2.n.bw

value: Pol2Ser2 (Abcam, ab5095)


title: 5903-S6_Untrained_Female


title: 5903-S1_Trained_Female


title: Celiac disease [0353-0]


title: Celiac disease [4161-6]


title: ChIP on H3K27me3 and with estradiol treatment of MCF-7 cells (40min) [H3K27me3_plusE2_Fan100]


title: iKras_p53_Tumor_B

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: Michigan

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

data_processing:
Samples OT_Tumor_1, Control_Scaff_B and iKras_p53_Scaff were run on HiSeq 4000. All other samples were run on the NovaSeq 6000 (Illumina). All samples were run using paired end 50 cycle reads to a depth of 100,000 reads.
The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 2.2.0, 3.0.0, or 3.1.0 with default settings was used, with an initial expected cell count of 10,000.
Genome_build: Mouse samples were aligned to the mouse genome mm10-3.0.0 using Cell Ranger. Human samples were aligned to the human genome hg19-3.0.0.
Supplementary_files_format_and_content: Zipped GZ archive file containing barcodes.tsv, genes.tsv/features.tsv, and matrix.mtx files, and .h5 files for reading into R using the Seurat Pipeline.

source_name: iKras p53 tumor

growth_protocol: 7940b cells were grown in DMEM supplemented with 10% FBS and 1% Pen-Strep. Mouse tumors were harvested after three weeks. Biomaterial scaffolds were harvested three weeks after tumor cell implantation.

extract_protocol:
Samples were mechanically and enzymatically (Collagenase P; 1mg/mL in DMEM) digested under constant agitation. Single cell suspension was obtained by filtering through a 40 µm mesh. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.).
Single-cell cDNA libraries were prepared and sequenced using the 10x Genomics Platform at the University of Michigan Advanced Genomics Core.

treatment_protocol: iKras* and iKras* p53*mice were administered doxycycline chow (BioServ, F3949) to induce expression of KrasG12D for 72 hours, followed by two days of 8 intraperitoneal injections of caerulein (Sigma, 75 ?g/kg) to induce pancreatitis. Doxycycline chow was continuously administered until experiment endpoint.

tag: doxycycline treatment duration

value: 14 weeks

tag: condition

value: PDA


title: ESC_A485_Pol2_2

description:
Cells were treated with 10uM A-485 for 60 min.
processed data file: ChIP.ESC_A485_Pol2.n.bw

value: Pol2 (Abcam, ab817)


title: ChIP on H3K36me3 and with no estradiol treatment of MCF-7 cells [H3K36me3_minusE2_Fan133]


title: ESC_A485_Pol2_1


title: iKras_p53_Tumor_A


title: ESC_A485_Pol2S2_1


title: Control_Panc_B

source_name: Healthy pancreas

value: Healthy control

value: p48Cre; R26rtTa/rtTa


title: ChIP on H3K27me3 and with no estradiol treatment of MCF-7 cells [H3K27me3_minusE2_Fan99]


title: Control_Panc_A

value: 3 weeks


title: ChIP on H3K27me3  and with no estradiol treatment of MCF-7 cells [H3K27me3_ctrlaso_minusE2_Fan25]


title: ESC_Ctrl_Pol2S5_2

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_Pol2S5.n.bw

value: ES cells

value: DMSO for 60 min


title: ChIP on H3K27me3 and with estradiol treatment of MCF-7 cells (40min) [H3K27me3_ctrlaso_plusE2_Fan26]


title: ChIP on H3K122ac and with estradiol treatment of MCF-7 cells (40min) [H3K122ac_plusE2_Fan62]


title: ChIP on H3K122ac and with no estradiol treatment of MCF-7 cells [H3K122ac_minusE2_Fan61]


title: Control [9412-6]

value: Control


title: ESC_Ctrl_Pol2S2_1

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_Pol2S2.n.bw

value: Pol2 phosphoSer2 (Abcam, ab5095)


title: ESC_Ctrl_Pol2S5_1


title: Control [8549-0]


title: ESC_Ctrl_Pol2S2_2


title: Celiac disease [5279-0]

value: Celiac disease


title: Control [4346-2]


title: Control [1605-0]


title: Celiac disease [8173-X]


title: Control [2694-2]


title: ChIP on G9a (EHMT2) and with estradiol treatment of MCF-7 cells (40min) [G9a_plusE2_Fan92]

value: G9a (EHMT2)


title: 43

city: Chicago

first: Leon

middle: Maing

last: Tai

state: IL

address: 808 S.Wood Street, MC512, Room 578

department: Anatomy and Cell Biology

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to custom reference consisting of mm10 genome and hg38 human APOE Gene (ENST00000485628.2, ENST00000425718.1, ENST00000434152.5, ENST00000252486.8, ENST00000446996.5) using STAR (Dobin et al., 2013). . ENSEMBL genes were quantified using FeatureCounts (Liao, Smyth, & Shi, 2014).
Genome_build: mm10 and hg38 (human ApoE ENST00000485628.2, ENST00000425718.1, ENST00000434152.5, ENST00000252486.8, ENST00000446996.5)
Supplementary_files_format_and_content: Table of raw counts per gene – tabular text file

source_name: Isolated brain endothelial cells

growth_protocol: Primary cortical mouse brain endothelial cells were isolated from mixed male and female human APOE3- and APOE4-targeted replacement mice (Taconic, 1548 and 1549, respectively) that express the human APOE gene isoforms under the endogenous mouse APOE promoter. Briefly, cerebral cortices were dissected from 21-28-day-old mice; the hippocampus, striatum, midbrain and cerebellum were discarded, and meninges were removed. Tissue was diced in cold DMEM, centrifuged at 1,000 × g for 5 min at 4 °C, then resuspended in papain (20 U/ml)/DNase (2,000 U/ml; Worthington Biochemical, LK003178, LK003170) in DMEM and lightly triturated through a 19G needle. Brain homogenate was incubated for exactly 15 min at 37 °C, then further triturated with a 21G needle, being careful not to over-triturate. Brain homogenates were mixed with 2 ml of 25% BSA in HBSS without calcium and magnesium per cortex, vortexed briefly and centrifuged at 4,000 × g for 5 min at 4 °C to separate out the myelin. The supernatant was collected, vortexed again, and centrifuged a second time at 4,000 × g for 5 min at 4 °C. Pellets from both centrifugations were resuspended in a complete growth media of EBM-2 (Lonza, CC-3156) containing EGMTM-2 MV Microvascular Endothelial SingleQuotsTM (Lonza, CC-4147) and supplemented with 5.5 U/ml heparin (Sigma, H3149). Resuspended cell pellets from both centrifugations were combined and passed through a 100 µm cell strainer and pelleted at 1,000 × g for 5 min at 4 °C. Resuspended cells were plated at 1 cortex per well of a 12-well plate, on a growth matrix of fibronectin (Sigma, F0895), collagen (Sigma, C8919) and laminin (Sigma, L2020), and placed at 37 °C with 5% CO2. Four to 6 hours after plating, red blood cells and debris were gently washed away with F12. F12 was replaced with heparin-supplemented complete growth media and incubated overnight at 37 °C. The following morning, cells were washed once more and then incubated in 8 µg/ml puromycin (Sigma, P8833) in complete growth media for 48 h to negatively select for brain endothelial cells. After puromycin was removed, brain endothelial cells were washed with HBSS with calcium and magnesium, and cells were grown to confluence in complete growth media. Media was then replaced, cells incubated for 48 hrs and then RNA isolation performed.

extract_protocol:
Brain endothelial cells were cultured as biological replicates in 12-well plates (i.e. 1 brain per well) and grown to confluence. Total RNA was extracted using miRNeasy Mini Kit (Qiagen, 217004) and used for sequencing library construction. RNA samples were quantified using NanoDrop™ One Spectrophotometer (Thermo Scientific) and analyzed for integrity using 4200 TapeStation (Agilent). Levels of remaining DNA were checked using Qubit fluorometer (Invitrogen). DNA amounts did not exceed 10% of the total amount of NA
Sequencing libraries for Illumina sequencing were prepared using 100ng of total RNA per sample. Library prep was carried with the Universal Plus mRNA-Seq kit (NuGen, 0520-A01), as written in the product manual (NuGen, M01485 v5). In brief, RNA underwent poly-A selection, enzymatic fragmentation, and generation of double-stranded cDNA using a mixture of oligo (dT) and random priming. The cDNA underwent end repair, ligation of dual-index adaptors, strand selection, and 17 cycles of PCR amplification. The number of cycles was determined by qPCR on a small aliquot of the un-amplified libraries. All intermediate purification steps, and final library purification was carried out using Agencourt AMPure XP Beads (Beckman Coulter A63881). Final amplified libraries were measured with the Qubit 1X dsDNA HS Assay Kit (Invitrogen, Q33231), and fragment size distribution was confirmed using the D5000 ScreenTape assay (Agilent, 5067-5588, 5067-5589).  Concentration of the final library pool was confirmed by qPCR, and subjected to test sequencing in order to check sequencing efficiencies and adjust accordingly proportions of individual libraries. The pool was purified with the Agencourt AMPure XP Beads (Beckman Coulter A63881), quantified by qPCR using KAPA Library Quantification Kit and run on a NovaSeq6000 SP flow cell, 2x50 nt, two lanes of , at the University of Illinois Roy J. Carver Biotechnology Center High-Throughput Sequencing and Genotyping Unit.

treatment_protocol: Cells were not treated

value: F


title: 40


title: ChIP on G9a (EHMT2) and with estradiol treatment of MCF-7 cells (40min) [G9a_plusE2_Fan84]


title: 39


title: ChIP on G9a (EHMT2) and with no estradiol treatment of MCF-7 cells [G9a_minusE2_Fan91]


title: ESC_Ctrl_Pol2_1

description:
Cells were treated with DMSO for 60 min.
processed data file: ChIP.ESC_Ctrl_Pol2.n.bw


title: 41


title: ESC_Ctrl_Pol2_2


title: 37

value: M


title: Bio-ChIP on CBX5 (mutant 4E) and with no estradiol treatment of MCF-7 cells [CBX5_4E_bioChIP_minusE2_FanC218]

value: HP1A (CBX5)


title: 38


title: ChIP on G9a (EHMT2) and with no estradiol treatment of MCF-7 cells [G9a_minusE2_Fan83]


title: bone tissue cells-S3

city: Changsha

first: Xiang

last: Qiu

state: Hunan

address: 172 Tongzipo Road, Yuelu District

department: School of Basic Medical Science

country: China

institute: Central South University

data_processing:
The FASTQ files were mapped to the human transcriptome (GRCh38/hg38) using Cell Ranger 3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). To create Cell Ranger-compatible reference genomes, the references were rebuilt according to instructions from 10x Genomics (https://www.10xgenomics.com), which performs alignment, filtering, barcode counting and UMI counting. Finally, the digital gene expression matrix was generated. For quality control (QC), we used the R (version 3.6.1, https://www.r-project.org/) and Seurat R package (version 3.1, https://satijalab.org/seurat/) to calculate the distribution of genes detected per cell and remove the cells in the top or the bottom 2% quantile. We also excluded cells in which more than 10% of the transcripts were attributed to mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone tissue cells

extract_protocol:
Bone tissue cells were extracted from the femoral head specimens based on widely used dissociation protocols with a few adjustments. First, femoral heads were washed three times with αMEM (Cat: SH30265.01, HyClone, USA) and dissected into small pieces of approximately 1-2 mm in diameter. Bone pieces (10 g wet weight) were placed into a 50 ml conical tube with 20 ml of 2 mg/ml collagenase type II (Cat: A004174-0001, Sangon Biotech, China) dissolved in αMEM with 100 U/ml Penicillin and 100μg/ml Streptomycin (Cat: 15140-122, Gibco, USA) and digested with gentle agitation for 25 minutes at 37 °C. After that, the collagenase solution was aseptically removed and bone pieces were rinsed in 10 ml PBS for 3 times. Briefly, after five rounds of digestion, we combined the collagenase solutions from the last two rounds of digestion and filtered the solution through a 40 μm filter. Finally, we incubated the collected cells with red blood cell (RBC) lysis buffer (Cat: R1010, Solarbio, China) for 5 minutes and then washed it twice with PBS.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ethnicity

value: Chinese subject of Han ethnicity

value: femoral head

tag: gender

value: male


title: bone tissue cells-S4


title: bone tissue cells-S2

value: female


title: Bio-ChIP on CBX5 (mutant 4A) and with no estradiol treatment of MCF-7 cells [CBX5_4A_bioChIP_minusE2_FanC216]


title: bone tissue cells-S1


title: Celiac disease [0927-8]

tag: disease

tag: marsh stage


title: Celiac disease [1131-5]

tag: age


title: 35

tag: genotype


title: 36


title: 33


title: Control [9770-0]


title: Celiac disease [7149-2]


title: Control [6704-3]


title: Peadiatric glioblastoma cell G34R KO rep3

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

country: United Kingdom

institute: University of Edinburgh

description:
Cell line
GBM002_normalised_counts.txt

data_processing:
Paired end RNA sequencing reads were trimmed with Cutadapt (version 1.14) with default parameters and aligned to hg38 genome using Kallisto (version 0.43.1).
Read counts were summarised via the package Tximport (version 1.8.0) and subsequent normalisation was completed via DESeq2 (version 1.27.32) as regularised-logarithm transformation (rlog).
Genome_build: hg38
Supplementary_files_format_and_content: Three sets of tab-delimited files for pHGG, NSCs, and engineered NSCs containing raw counts, and normalised counts as calculated by DESeq2 (rlog and FPM).
Supplementary_files_format_and_content: DESeq2 fpm
Supplementary_files_format_and_content: DESeq2 normalised counts rlog
Supplementary_files_format_and_content: raw counts

source_name: pHGG

growth_protocol: Cultures were maintained in DMEM/HAMS-F12 serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Sigma, 1 µg/ml) and growth factors EGF and bFGF (Peprotech, 10 ng/ml)

extract_protocol:
total RNA was extracted with Qiagen Rneasy plus mini kit
Libraries were generated with 200ng of RNA input using the KAPA mRNA HyperPrep kit and KAPA SeqCap adapters. Fragmentation was carried out at 94°C for 6 minutes and libraries amplified for 12 cycles
Pooled libraries were diluted and processed for sequencing using the Illumina HiSeq 2500 platform.

value: Peadiatric glioblastoma cell line

value: pHGG

tag: embryo

tag: disease state

value: Cancer


title: Celiac disease [7104-3]


title: Peadiatric glioblastoma cell G34R KO rep2

description:
Cell line
GBM002_normalised_counts.txt


title: PRO-seq  with estradiol treatment of MCF-7 cells (40min) and with shCTRL

description: nascent RNA

data_processing:
Library strategy: PRO-seq
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) was used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align PRO-seq samples to hg38 genome, and we have kept 1 copy/read per genome position.
Read counting: we have used the HOMER scripts analyzeRNA.pl and analyzeRepeats.pl in order to estimate the raw counts per gene in POL2-seq and PRO-seq data, and to compute the Pausing Ratio. The aligned reads were counted over the RefSeq gene bodies (after excluding a TSS 400bp-proximal region downstream of TSS).
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Precision Run-on sequencing (PRO-seq) experiments were  performed as previously described . Briefly, MCF-7 cells, for nuclei isolation, were incubated with swelling buffer (10 mM Tris-Cl pH7.5, 2 mM MgCl2, 3 mM CaCl2) for 5min on ice and then incubated with lysis buffer (swelling buffer with 0.5% NP-40 and 10% glycerol) for 5 min on ice, before being re-suspended in 100μl of freezing buffer (50 mM Tris-Cl pH8.0, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA). For Run-on assay, an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 20 units of SuperaseIn, 1% sarkosyl, 500 μM ATP, GTP, bio-UTP and bio-CTP) was added into each sample before incubation at 30°C for 5 min. The nuclear run-on RNA was then extracted with TRIzol LS reagent (Invitogen) and subjected to hydrolysis, buffer exchange and purification by streptavidin beads (Thermo Fisher). Purified RNA was treated with PNK before being used for cDNA synthesis by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® Kit (NEB). Obtained cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) for deep sequencing.
The library construction protocol followed the manufacturer’s instructions.


title: Peadiatric glioblastoma cell G34R KO rep1

description:
Cell line
GBM002_normalised_counts.txt


title: PRO-seq  with no estradiol treatment of MCF-7 cells and with shKAP1

description: nascent RNA


title: 31


title: PRO-seq  with no estradiol treatment of MCF-7 cells and with shCTRL new

description: nascent RNA


title: PRO-seq  with no estradiol treatment of MCF-7 cells and with shHP1a_shHP1b new

description: nascent RNA


title: PRO-seq  with estradiol treatment of MCF-7 cells (40min) and with shKAP1

description: nascent RNA


title: Peadiatric glioblastoma cell G34R rep2

description:
Cell line
GBM002_normalised_counts.txt


title: 28


title: 30


title: Celiac disease [0047-7_1]


title: Peadiatric glioblastoma cell G34R rep3

description:
Cell line
GBM002_normalised_counts.txt


title: 27


title: Control [8663-6]


title: 26


title: Celiac disease [8929-2]


title: PRO-seq  with no estradiol treatment of MCF-7 cells and with shCTRL rep2

description: nascent RNA


title: Neural stem cell Neocortex  WT G34 rep1 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_G43RW_normalised_counts.txt

source_name: Neocortex

value: Neural stem cell line

value: Neocortex

value: GCGR-NS13 - 13.5 pcw

value: Normal


title: 25


title: Peadiatric glioblastoma cell G34R rep1

description:
Cell line
GBM002_normalised_counts.txt


title: Neural stem cell Engineered Neocortex  PP5 WT G34 rep2 GCGR-NS13 - 13.5 pcw


title: adipocyte WT rep3 (RNA-Seq)

city: Seoul

first: Yoon Jeong

last: Park

address: San 56-1, Sillim-Dong, Gwanak-Gu

institute: Seoul National University

description:
Adipocyte_FPKM_value.xlsx
AD6

data_processing:
For WGBS data, sequenced reads were trimmed with adaptor sequences and performed quality control using TrimGalore v0.5.0. Then, the trimmed reads were mapped to the mouse genome (GRCm38) using Bismark v0.22.1. Cytosines that were mapped less than five reads were discarded for downstream analyses. Methylation levels of individual CpGs were determined using Bismark Methylation Extractor.
For RNA-seq data, Sequenced reads of  adipocytes were trimmed with adaptor sequences and performed quality control by using trim galore. The trimmed reads were mapped to the mouse genome (GRCm38) using Rsubread v2.0.1. Raw read counts per genes were measured using featurecounts program in Rsubread with the builid-in mouse genome annotation (GRCm38).
Genome_build: mm10
Supplementary_files_format_and_content: wig files include CpG methylation values for each sample
Supplementary_files_format_and_content: Excel file include FPKM values for every genes and every adipocyte WT replicates.

source_name: adipocytes

extract_protocol:
Briefly, primary adipocytes were lysed for 1 h in lysis buffer at 37°C and digested with 10 g/mL proteinase K for 3 h at 50°C. After cell lysis, DNA and RNA was isolated by phenol-chloroform extraction and using trizol, respectively.
For WGBS library construction, 100ng of genomic DNA was treated with the EZ DNA Methylation-Gold kit (Zymo Research, Orange, CA, USA) for bisulfite conversion. Then, the sequencing libraries were prepared according to the manufacturer’s instructions of TruSeq DNA Methylation Library Preparation Kits (Illumina, #EGMK91396). Briefly, bisulfite-converted DNA is random-primed using a polymerase to synthesize DNA containing a specific sequence tag. The 3’ ends of the newly synthesized DNA strands are tagged with a second specific sequence. The di-tagged DNA molecules are amplified using FailSafe PCR Enzyme (Epicentre, #FSE51100) and TruSeq Index PCR Primer. The final purified product is quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 2100 Bioanalyzer (Agilent). Finally, sequencing was performed using the HiSeqX platform (Illumina). In case of RNA-seq,   RNA libraries were prepared for sequencing using standard Illumina protocols.

value: epididymal adipose tissue

tag: cell type

value: adipocytes

value: 17wks old

value: wild type


title: PRO-seq  with no estradiol treatment of MCF-7 cells and with shHP1a_shHP1b rep2

description: nascent RNA

tag: cell line


title: ChIRC on NEAT1 and with estradiol treatment of MCF-7 cells (40min)

data_processing:
Library strategy: ChIRC-seq
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) was used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
Read alignment: Bowtie2 (Langmead et al., Nature Methods 2012) was employed to align ChIP-seq and ChIRC-seq samples to hg38 genome and we have kept 1 copy/read per genome position.
Peak finding: we have called the ChIP-seq and ChIRC-seq peaks by using HOMER findPeaks subroutine (Heinz et al., 2010, http://homer.ucsd.edu/homer/). For the ChIRC-seq analysis, we have used the input samples in order to estimate the background, and the default settings were adjusted to order to capture the biology of ncRNA binding to the genome.
Generation of bedgraph files: we have used the HOMER scripts makeUCSCfile and makeMultiWigHub.pl in order to generate bedgraph files for visualization in the UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

extract_protocol:
All the experiments were performed in RNase-free environment and every buffer used in the experiment was supplemented with SUPERase• In™ RNase Inhibitor (Thermo Fisher Scientific, Cat#AM2696). Briefly, 5x10^7 cells stably expressing biotin acceptor peptide (BAP)-dCas13a, BirA and corresponding gRNA were crosslinked with 1% formaldehyde at room temperature for 15 min before being quenched with 0.125M glycine for 5 min. Cells were first incubated in Lysis buffer 1 (10 mM Tris pH 8, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, protease inhibitor included) for 10 min on ice and then were incubated in Lysis buffer 2 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA and 200 mM NaCl, protease inhibitor included) for 5 min on ice for nuclei isolation. After centrifugation, the pellet was suspended in immunoprecipitation buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and 1% Triton X-100, with protease inhibitor included) for sonication. The supernatant, after centrifugation, was then incubated with 50 ul of pre-blocked Pierce™ Streptavidin Magnetic Beads (Thermo Fisher, Cat#88816) at 4°C overnight. Beads were then washed with SDS buffer (10 mM Tris, pH 8, 1 mM EDTA, 2% SDS, protease inhibitor included) twice, high salt buffer (50 mM HEPES pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 500 mM NaCl) twice, DOC buffer (250 mM LiCl, 0.5%, NP-40, 0.5% deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) once and TE buffer containing 50 mM Nacl once. After RNase A, Proteinase K treatment and de-crosslinking, DNA was then purified by QIAquick Spin columns (Qiagen)
For ChIRC-seq, the extracted DNA was ligated to specific adaptors followed by deep sequencing with the Illumina's HiSeq 2500 system according to the manufacturer's instructions.

tag: complex


title: adipocyte WT rep2 (RNA-Seq)

description:
Adipocyte_FPKM_value.xlsx
AD5

tag: strain


title: ChIRC on NEAT1 and with no estradiol treatment of MCF-7 cells


title: adipocyte WT rep1 (RNA-Seq)

description:
Adipocyte_FPKM_value.xlsx
AD1

tag: tissue


title: ChIRC on scrambleRNA and with estradiol treatment of MCF-7 cells (40min)


title: Neural stem cell Engineered Neocortex  PP5 WT G34 rep1 GCGR-NS13 - 13.5 pcw


title: 32

tag: Sex

value: F


title: MDAMB231 cells with BRCA1P1-KO rep2

first: Yoo-Jeong

last: Han

address: 900E. 57th street

department: Medicine

institute: University of Chicago

description:
200641620037_E
3 replicates
YH5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Breast cancer cell lines

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

growth_protocol: RPMI+10% FBS

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: BRCA1P1 gene was deleted  from the human genome using CRISPR-Cas 9 method

value: BRCA1P1 knockout


title: Neural stem cell Engineered Neocortex  PP5 G34R rep2 GCGR-NS13 - 13.5 pcw


title: MDAMB231 cells with wild type rep1

description:
200641620037_H
3 replicates
YH8

value: control


title: ChIRC on scrambleRNA and with no estradiol treatment of MCF-7 cells


title: MDAMB231 cells with BRCA1P1 ASO rep3

description:
9977363097_L
3 replicates
FO-12

treatment_protocol: Cells were transfected with 10nM ASO using Dharmafect

value: BRCA1P1 knockdown


title: MDAMB231 cells with BRCA1P1-KO rep1

description:
200641620037_A
3 replicates
YH1


title: MDAMB231 cells with wild type rep2

description:
200641620037_L
3 replicates
YH12


title: Tumor_Scaff

source_name: Biomaterial scaffold

value: pancreatic cancer (PDA)

tag: genotype/variation

value: KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre (7940b)

value: Biomaterial scaffold


title: Neural stem cell Engineered Neocortex  G34R rep2 GCGR-NS13 - 13.5 pcw


title: ChIRC on 7SK and with no estradiol treatment of MCF-7 cells and shKAP1


title: MDAMB231 cells with negative control ASO rep3

description:
9977363097_I
3 replicates
FO-9


title: MDAMB231 cells with BRCA1P1 ASO rep1

description:
9977363097_J
3 replicates
FO-10


title: Neural stem cell Engineered Posterior Brainstem  PP5 WT G34 rep2 GCGR-NS13 - 13.5 pcw

source_name: Posterior Brainstem

value: Posterior Brainstem


title: Control_Scaff

value: Healthy control


title: ChIRC on 7SK and with no estradiol treatment of MCF-7 cells and shHP1a and shHP1b


title: ChIRC on 7SK and with no estradiol treatment of MCF-7 cells and shCTRL


title: Neural stem cell Engineered Neocortex  G34R rep1 GCGR-NS13 - 13.5 pcw

value: Neural stem cell line


title: MDAMB231 cells with BRCA1P1 ASO rep2

description:
9977363097_K
3 replicates
FO-11


title: MDAMB231 cells with negative control ASO rep1

description:
9977363097_G
3 replicates
FO-7


title: ChIRC on 7SK and with no estradiol treatment of MCF-7 cells FanC213


title: Neural stem cell Engineered Neocortex  PP5 G34R rep1 GCGR-NS13 - 13.5 pcw

value: Neocortex


title: MDAMB231 cells with negative control ASO rep2

description:
9977363097_H
3 replicates
FO-8


title: T47D cells with BRCA1P1 ASO rep2

description:
9977363097_E
3 replicates
FO-5


title: Neural stem cell Engineered Posterior Brainstem  PP5 G34R rep2 GCGR-NS13 - 13.5 pcw

value: GCGR-NS13 - 13.5 pcw


title: ChIRC on 7SK and with estradiol treatment of MCF-7 cells (40min)


title: Neural stem cell Engineered Posterior Brainstem  PP5 WT G34 rep1 GCGR-NS13 - 13.5 pcw

value: Normal


title: HMED-DD-pbabe-HER2-3

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

institute: Medical University of South Carolina

description:
Breast
processed data file: HER2_vs_Control_allGenes.txt

data_processing:
Quality check of the Fastq files using FastQC v0.11.5.
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11.
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out via Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). This is an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_vs_Control_allGenes.txt: Tab-delimited text files include the DESEQ2 output for the E76A vs. Control; HER2 vs. Control; and H1047R vs. Control comparisons. Column headers are: Name (HGNC Symbol), Description, Fold Change, Log Fold Change, p-Value, p-Adj, Average Log2 Expression, then raw counts for HMEC_DD_pBABE_1, HMEC_DD_pBABE_2, HMEC_DD_pBABE_3, HMEC_DD_H1047R_1, HMEC_DD_H1047R_2, HMEC_DD_H1047R_3; OR HMEC_DD_ SHP2_E76A_1, HMEC_DD_ SHP2_E76A_2, HMEC_DD_ SHP2_E76A_3; OR HMED_DD_pbabe_HER2_1, HMED_DD_pbabe_HER2_2, HMED_DD_pbabe_HER2_3, Gene ID, Alias Columns to the right of the Description column represent DEseq2 output. Columns contain raw count data for the three Control and three E76A or H1047R or HER2 treatment RNAseq libraries. Symbols represent the HUGO Gene symbols for Homo sapiens.

source_name: Human mammary epithelial cell line (HMEC)

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Retroviruses of human HER2, PI3KCA(H1047R), HMEC-DD-SHP2(E76A), or control pBABE produced by 293 phoenix cells were used for infection of HMEC cells in media containing polybrene (8 μg/ml). After infection, cells were selected with puromycin and cultured in HMEC medium.

value: HMEC

value: Mammary epithelial cells


title: ChIRC on 7SK and with no estradiol treatment of MCF-7 cells Fan154


title: Neural stem cell Engineered Posterior Brainstem  PP5 G34R rep1 GCGR-NS13 - 13.5 pcw


title: OT_Tumor_2

source_name: Orthotopic pancreas tumor

value: mouse orthotopic pancreatic tumors


title: Neural stem cell Striatum rep2 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Striatum

value: Striatum

value: GCGR-NS15 - 15.0 pcw


title: PRO-seq  with no estradiol treatment of MCF-7 cells and with shCTRL

description: nascent RNA


title: HMED-DD-pbabe-HER2-2


title: Neural stem cell Striatum rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt


title: Neural stem cell Spinalcord rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Spinalcord

value: Spinalcord


title: HMED-DD-pbabe-HER2-1


title: HMEC-DD-SHP2-E76A-3

description:
Breast
processed data file: E76A_vs_Control_allGenes.txt


title: T47D cells with negative control ASO rep3

description:
9977363097_C
3 replicates
FO-3

value: control


title: T47D cells with negative control ASO rep1

description:
9977363097_A
3 replicates
FO-1


title: HMEC-DD-SHP2-E76A-2


title: HMEC-DD-SHP2-E76A-1


title: Neural stem cell Anterior Brainstem rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Anterior Brainstem

value: Anterior Brainstem


title: Neural stem cell Diencephalon rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Diencephalon

value: Diencephalon


title: HMEC-DD-H1047R-3

description:
Breast
processed data file: H1047R_vs_Control_allGenes.txt


title: Neural stem cell Neocortex  rep2 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt


title: HMEC-DD-H1047R-2


title: T47D cells with negative control ASO rep2

description:
9977363097_B
3 replicates
FO-2


title: T47D cells with BRCA1P1 ASO rep1

description:
9977363097_D
3 replicates
FO-4

value: BRCA1P1 knockdown


title: NT, biological rep3

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported into the Affymetrix Expression Console™ Software and CHP files were generated.

source_name: Hippocampus of non-transgenic control mouse

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 5 months of age.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturers’ instructions.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 40 ml of saline via the left ventricle. Hippocampi were isolated and preserved at –80°C until RNA preparation.

value: Hippocampus

value: non-transgenic wild type

value: 5 months of age

value: male


title: Neural stem cell Posterior Brainstem  rep2 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Neural stem cell line

value: Posterior Brainstem


title: HMEC-DD-H1047R-1


title: Neural stem cell Neocortex  rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Neocortex

value: Normal


title: T47D cells with BRCA1P1 ASO rep3

description:
9977363097_F
3 replicates
FO-6


title: NT, biological rep1


title: Neural stem cell Posterior Brainstem  rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt


title: NT, biological rep2


title: HMEC-DD-pBABE-3

description:
Breast
processed data file: E76A_vs_Control_allGenes.txt
processed data file: H1047R_vs_Control_allGenes.txt
processed data file: HER2_vs_Control_allGenes.txt

value: HMEC

value: Mammary epithelial cells

value: pBABE (vector control)


title: Neural stem cell Anterior Brainstem rep2 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: GCGR-NS15 - 15.0 pcw


title: S_3

city: Chengdu

first: Liming

last: Chang

state: Sichuan

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

institute: Chengdu Institute of 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;The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
Genome_build: de novo
Supplementary_files_format_and_content: fasta file includes the sequences of all unigenes across samples

organism: Rana omeimontis

source_name: Liver

extract_protocol:
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then, PCR was performed with a Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 2500 platform by NovoGene (Beijing), and paired-end reads were generated.

value: Liver

tag: Stage

value: Before ontogenetic fat accumulation

tag: collection sites

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 706 m) in Sichuan Province, China.


title: Neural stem cell Cerebellum rep1 GCGR-NS15 - 15.0 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Cerebellum

value: Cerebellum


title: HMEC-DD-pBABE-2


title: HMEC-DD-pBABE-1


title: S_2

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 705 m) in Sichuan Province, China.


title: S_1

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 704 m) in Sichuan Province, China.


title: F26_120_3

city: Taian

first: shan

last: feng

address: Daizong Avenue

department: Forestry College

institute: Shandong Agricultural University

description: Walnut trees (Juglans regia L.) of the anthracnose-resistant clone B26 was grown at the Forestry Experimental Station of Shandong Agricultural University, Tai’an, Shandong Province, China (N36°10′ 19.2″, E117°09′ 1.3″).Colletotrichum gloeosporioides m9 isolates (GenBank ID: GU597332) used in this study were maintained by our group.

data_processing:
FASTQC (v 0.11.5) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). was used to assess the quality of raw sequence data and Trimmomatic was used to filter low-quality reads
The previously published genome database the J. regia genome sequence (https://www.ncbi.nlm.nih.gov/genome/?term=Juglans%20regia) was used as reference genome to map the high-quality reads by using HISAT (version 0.11.5) with default parameters
Stringtie (v 1.3.1) was used to assemble the aligned reads for all sample into transcripts
StringTie-Merge to combine the StringTie assembly results of each sample and the gene expression (FPKM) was calculated using StringTie's own script prepDE.py
The differently expressed genes (DEGs) were identified by using DESeq2 (version 1.22.1)
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Juglans%20regia

organism: Juglans regia

source_name: The anthracnose-resistant F26 fruits samples at 120 hour during infection proces

growth_protocol: Walnut trees (Juglans regia L.) of the anthracnose-resistant clone B26 and the clone 4-23 were grown at the Forestry Experimental Station of Shandong Agricultural University, Tai’an, Shandong Province, China (N36°10′ 19.2″, E117°09′ 1.3″). The fruits of 4-23 clone (i.e., F423 fruits) and B26 clone (i.e., F26 fruits) were used as experimental materials. Colletotrichum gloeosporioides m9 isolates (GenBank ID: GU597322) used in this study were maintained by our group.

extract_protocol:
Total RNA was extracted from F423 and F26 samples with the Thermo Gene JET Plant RNA Purification Mini Kit (Thermo Fisher Scientific Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi of F26 and F423  fruit bracts

value: Juglans regia clone B26

value: fruit sample


title: Neural stem cell Striatum rep1 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Striatum

value: GCGR-NS13 - 13.5 pcw


title: F26_72_3

source_name: The anthracnose-resistant F26 fruits samples at 72 hour during infection proces


title: L_3

value: After ontogenetic fat accumulation

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 703 m) in Sichuan Province, China.


title: Neural stem cell Neocortex  rep2 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Neural stem cell line

value: Neocortex

value: Normal


title: L_2

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 702 m) in Sichuan Province, China.


title: F26_48_3

source_name: The anthracnose-resistant F26 fruits samples at 48 hour during infection proces


title: L_1

value: Anzihe Natural Reserve (103.459885° E, 30.744614° N, 701 m) in Sichuan Province, China.


title: F26_24_3

source_name: The anthracnose-resistant F26 fruits samples at 24 hour during infection proces


title: F26_0_3

source_name: The anthracnose-resistant F26 fruits samples at 0 hour during infection proces


title: ADH/WT, biological rep3

source_name: Hippocampus of ADH/WT mouse

growth_protocol: Each mouse was maintained in specific pathogen-free (SPF) condition and sacrificed at 5 months of age.

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturer's instructions.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 40 ml of saline via the left ventricle. Hippocampi were isolated and preserved at -80°C until RNA preparation.

value: Hippocampus

tag: strain/background

value: Homozygous APPSwe and tauP301L transgenes with a homozygous Psen1M146V mutation

value: 5 months

value: male


title: ADH/TO-DKH, biological rep3

source_name: Hippocampus of ADH/TO-DKH mouse

value: Homozygous APPSwe and tauP301L transgenes with a homozygous Psen1M146V mutation and Mth1/Ogg1-double deficiency


title: Treg_SPF_4

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using STAR (version 2.5.3a) with parameters --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1.
Duplicates were removed using picard MarkDuplicates (https://broadinstitute.github.io/picard/).
Peaks were called on de-duplicated bam-files using macs2 callpeak with the parameters --broad -g mm -q 0.05 for each replicate.distribution around the TSS was computed using computeMatrix with the reference-point -a 3000 -b 3000 and plotted using plotHeatmap. The regions identified via macs2 were merged across all replicates into one set of regions, by combining peaks over-lapping with at least one base-pair and removing peaks that overlapped with blacklisted regions. Differential accessibility of raw ATAC-seq counts for each region/peak across all replicates of all samples were normalized across replicates with size factors computed with DESeq2 (version 1.22). Pairwise comparisons were performed with DESeq2 and differentially accessible regions (DARs) were called with an FDR adjusted p-value of less than 0.05 and a fold change (FC) of at least 2. Genomic features were identified via getAnnotation from ChIPpeakANNO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of all significantly differentially accesssible regions with foldchange > 2 and adjusted p-Value < 0.05

source_name: Adoptively transferred DO.11.10

growth_protocol: Single cell suspensions from spleen and LNs of Foxp3hCD2xRag2‑/‑xDO11.10 mice were generated. CD4+ T cells were enriched with CD4 (L3T4) MicroBeads and autoMACS separation (Miltenyi Biotec) after which CD4+ T cells were labelled with CPDviolet (Invitrogen) to track cell proliferation before being adoptively transferred. Approximately 3‑10x10^6 cells in 100µl PBS were injected i.v. per recipient mouse.

extract_protocol:
The following fluorochrom-conjugated antibodies were purchased from BD, Biolegend and eBioscience (human)-CD2 (RPA-2.10), CD4 (RM4-5), Ova‑TCR (KJ1.26), CD62L (MEL14). To prevent unspecific antibody binding, cell suspensions were incubated with 10µg/ml Chrom Pure rat IgG (Jackson ImmunoResearch Laboratories) and 10 µg/ml anti-mouse CD16/CD32 antibody (BioXcell). For surface staining cells were washed and then incubated with the corresponding antibodies dissolved in PBS containing 0.2% BSA for 15 min on ice. Cell sorting for RNA-seq and ATAC-seq analysis was performed at the cell sorting facility (Helmholtz Centre for Infection Research, Braunschweig, Germany) on FACSAria IIu (BD Bioscience) and FACS Aria-II SORP (BD Bioscience). Acquired data was analyzed utilizing FlowJo software (Tree Star).
Cells were washed once with PBS before DNA transposition was performed with the Nextera DNA Library Prep Kit (Illumina). Per sample, the following kit components (25 µl TD, 2.5 µl TDE1 and 22µl nuclease free water) were combined and placed at 37°C for 3 min before 0.5µl of 1% Digitonin (Promega) was added to the master mix (64). Samples were resuspended in the transposition reaction mix and incubated for 30 min at 37°C at 300rpm. After transposition DNA purification was carried out with the MinElute PCR Purification kit (Qiagen) according to manufacturer’s instructions. Transposed DNA fragments were pre-amplified by combining the following reagents per reaction (5μl transposed DNA, 10μl nuclease free water, 2.5μl 25 μM custom Nextera PCR primer 1, 2.5μl 25 μM custom Nextera PCR primer 2, 25μl NEBNext High-Fidelity 2x PCR Master Mix (New England BioLabs)) and running the following 6-cycle PCR program (1 cycle of 72°C for 5 min, 98°C for 30 sec; 5 cycles of 98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). The forward primer was identical for all samples 5′-AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG-3′ whereas the reverse primer contained a barcode (underlined) used for demultiplexing 5′-CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGT-3′ (65). The appropriate amount of further amplification cycles was determined by qPCR prior to the final sample amplification (45μl of previously PCR amplified DNA, 39.7μl nuclease free water, 2.25μl 25 μM customized Nextera PCR primer 1, 2.25μl 25 μM customized Nextera PCR Primer 2, 0.81μl 100x SYBR Green I, 45μl NEBNext High-Fidelity 2x PCR Master Mix) with the PCR program (1 cycle of 98°C for 30 sec; 8-10 cycles of 98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). PCR purification was again carried out using the MinElute PCR Purification kit. Finally, size selection was performed with SPRIselect beads (Beckmann-Coulter) according to manufacturers instructions. DNA quality, content and fragment size was assessed with Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements.
Sequencing of libraries was carried out at the sequencing facility on Illumina NOVASeq6000 using 50 bp paired-end reads and quality of sequenced libraries was verified with FastQC.

treatment_protocol: Starting one day after adoptive transfer of CD4+ T cells of Foxp3hCD2xRag2‑/‑xDO11.10 mice, 20 µg Ova323‑339 peptide was injected i.v. on two consecutive days to study de novo Treg induction. Two days after the last dose of Ova immunization, recipient mice were sacrificed and cells were isolated from indicated endogenous LNs.

value: Treg

tag: condition

tag: treatment


title: ADH/WT, biological rep2


title: Neural stem cell Striatum rep2 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt


title: Treg_SPF_3


title: ADH/TO-DKH, biological rep1


title: ADH/TO-DKH, biological rep2


title: F423_120_3

description: Walnut trees (Juglans regia L.) of the clone 4-23 was grown at the Forestry Experimental Station of Shandong Agricultural University, Tai’an, Shandong Province, China (N36°10′ 19.2″, E117°09′ 1.3″). Colletotrichum gloeosporioides m9 isolates (GenBank ID: GU597322) used in this study were maintained by our group.

source_name: the anthracnose-susceptible F423 fruits samples at 120 hour during infection proces

value: Juglans regia clone 4-23


title: Treg_SPF_2


title: ADH/WT, biological rep1


title: Neural stem cell Striatum rep2 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: GCGR-NS19 - 19.3 pcw


title: Neural stem cell Posterior Brainstem  rep1 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Posterior Brainstem

value: Posterior Brainstem


title: Neural stem cell Posterior Brainstem  rep2 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: GCGR-NS13 - 13.5 pcw


title: F423_72_3

source_name: the anthracnose-susceptible F423 fruits samples at 72 hour during infection proces

value: fruit sample


title: Treg_SPF_1


title: Neural stem cell Neocortex rep1 GCGR-NS13 - 13.5 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Neocortex


title: Neural stem cell Spinalcord rep2 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Spinalcord

value: Spinalcord


title: F423_48_3

source_name: the anthracnose-susceptible F423 fruits samples at 48 hour during infection proces


title: BT549 cells, scrambled

city: Chang Sha

first: zhuoxian

last: rong

state: Hu Nan

address: Xiangya road 87th

institute: central south universty

data_processing:
using Illumina Novaseq platform
Index of the reference genome was built using Hisat2 v2.0.5
Genome_build: hg18
Supplementary_files_format_and_content: FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent. Sequencing was completed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer


title: Neural stem cell Spinalcord rep1 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Neural stem cell line


title: Wt

city: Tokyo

first: Katsuyoshi

last: Kumagai

institute: Tokyo Medical University

description: total RNA from the cervix of 6-month-old female mice was used as a sample.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Cervix of 6-month-old female mice of C57BL/6N genetic background

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

tag: strain background

value: wild-type

value: female

value: cervix


title: Treg_GF_2


title: F423_0_3

source_name: the anthracnose-susceptible F423 fruits samples at 0 hour during infection proces


title: Treg_GF_3


title: BT549 cells, shSIK2

value: Wnt3a-SIK2 knockdown


title: Neural stem cell Anterior Brainstem rep2 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Anterior Brainstem

value: Anterior Brainstem

value: Normal


title: Treg_GF_1


title: Neural stem cell Neocortex  WT G34 rep2 GCGR-NS13 - 13.5 pcw

value: Neocortex


title: SCRTRAPLATEOSROOT3

city: Davis

first: Siobhan

last: Brady

address: 451 Health Sciences Dr

department: Genome Center and Plant Biology

institute: University of California Davis

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
SCRTRAPLATEOSROOT3
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1

data_processing:
Library strategy: TRAP-seq
Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to ITAG3.2 transcriptome (cDNA) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values.
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters.
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1".
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Rice TRAP-seq. Barcoded libraries were pooled together and sequenced on Illumina HiSeq 3000 at the UC Davis DNA Technologies Core to obtain 50-bp reads.
Rice TRAP-seq. R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
Rice TRAP-seq. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to IRGSP-1.0 transcriptome (CDS, https://rapdb.dna.affrc.go.jp/index.html) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values. Splice variants were summed to assess transcript values.
Genome_build: Tomato: SOLANUM LYCOPERSICUM: ITAG3.20 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/)
Genome_build: Rice: IRGSP-1.0 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples.
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows.
Supplementary_files_format_and_content: .csv files contain raw counts.

organism: Oryza sativa Japonica Group

source_name: 7 days-old seedling roots

growth_protocol:
growth protocol 1: Transgenic Solanum lycopersicum seeds from transgenic lines were surface sterilized in 50% (v/v) bleach solution for 20 min (S. lycopersicum) and then rinsed three times with sterile distilled water. Seven seeds were plated on 10 cm x 10 cm plates containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose and germination was scored daily after plating. Seedlings were grown for 3-5 days after germination in a growth chamber (16 h day / 8 h night;  at 22°C/22°C day/night; 60-65 ?Em-2s-1) and 1cm primary root tips were harvested and flash frozen into liquid nitrogen.
growth protocol 2: 1-month-old control plants: Transgenic Solanum lycopersicum seeds were germinated on 1xMS media with 1% sucrose and 200ug/ml Kanamycin. After 7d, seedlings were transplanted into pots with Turface Athletic Profile Field & Fairway clay substrate (Turface Athletics, 2017) that was pre-wetted with a nutrient water solution containing 4% nitrogen, 18% phosphoric acid, and 38% soluble potash. Plants were grown in a randomized design for 31 d in a Conviron Growth Chamber at 22°C, 70% RH, 16/8 h light/dark cycle, light intensity of 150-200 µmol/m2/s.
growth protocol 3: Field: Transgenic Solanum lycopersicum seeds were germinated on 1xMS plate (0-7d), screened for correct GFP pattern from root tip, transplanted on soil and grown in a growth chamber for one week (7-14d) ,  grown in a screenhouse for two weeks (14-28d), and finally transplanted into the field and grown for one month (29-60d)  with drip watering and weekly removal of flower buds.
growth protocol 4: Rice seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. Seedlings were grown on plates (10 cm x 10 cm) containing half-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 ?Em-2s-1). The whole root system was placed immediately into liquid nitrogen upon harvesting.

extract_protocol:
extract protocol 1: Translating Ribosome Affinity Purification (TRAP) was performed as previously described (Reynoso et al, 2019).
extract protocol 2: Nuclei were purified from frozen and pulverized tissue as previously described (Reynoso et al, 2019). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of  streptavidin-coated beads (NEB) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet  to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
extract protocol 3: For Rice: TRAP was performed as previously described (Reynoso et al, 2019)
library construction protocol 1: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.
library construction protocol 2: RNA-seq libraries  were prepared from poly(A)+ selected total and TRAP mRNA as described by Townsley et al. (2014) for random primer primed libraries.

tag: cultivar

value: Nipponbare

tag: line

tag: age

value: 7 days

value: Roots


title: Neural stem cell Anterior Brainstem rep1 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

tag: embryo

value: GCGR-NS19 - 19.3 pcw

tag: disease state


title: Neural stem cell Striatum rep1 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Striatum

tag: cell line

value: Striatum


title: Neural stem cell Diencephalon rep2 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Diencephalon

value: Diencephalon


title: Tnaive_1

source_name: Input Adoptively transferred DO.11.10

tag: cell type

value: Tnaive

value: NonInjected


title: CMZTRAPLATEOSROOT2B

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
CMZTRAPLATEOSROOT2B
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: blood-derived macrophages BRI-787

city: Boston

first: Soumya

last: Raychaudhuri

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Cellranger v3.1.0 was used to process the raw BCL files. First, raw BCL files were demultiplexed using cellranger mkfastq to generate FASTQ files.
These FASTQ files were aligned to the GRCh38 human reference genome.
Gene/antibody reads were quantified simultaneously using cellranger count.
Cell barcodes and UMIs were extracted for gene/hashtag antibodies for each run.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: macrophages

extract_protocol:
We isolated CD14+ monocytes from each sample using human CD14 microbeads (Miltenyi Biotec) and differentiated these cells into blood-derived macrophages for 1 day at 37° C in macrophage CSF (MCSF; 10 ng/ml) (PeproTech) and RPMI 1640 medium (Corning) supplemented with 10% defined fetal bovine serum (FBS) (HyClone), 1% Penicillin-Streptomycin (Thermo Fisher Scientific), and 1% L-glutamine (Thermo Fisher Scientific) in a 6-well plate at a concentration of 1.2 million cells/mL.
We harvested macrophages from each well and aliquoted one fifth of the cells, ~750,000 cells per condition, for staining in subsequent steps. We washed the cells in filtered labeling buffer (PBS with 1% BSA) and resuspended in 50 ul of labeling buffer with Human TruStain FcXTM (Biolegend Cat #422302, 5 ul per stain) for 10 min at 4° C. Next, we added 50 ul of labeling buffer with 1.6 ng/uL of a Total-seq hashtag (1, 2, 4, 5, 6, 7, 8, 9, or 12) per condition per donor for 25 minutes at 4° C. Next, we washed all samples in 2 mL, 1 mL, and 1 mL of labeling buffer, sequentially. We counted the remaining cells using a cellometer (Nexcelom Cellometer Auto 1000) and aliquoted the equivalent of 60,000 cells from each condition into one Eppendorf tube per donor. From here, we filtered through a 40um mesh and resuspended in PBS with 0.04% BSA to a concentration of 643.7 cells/ ul.

value: blood

value: macrophage


title: blood-derived macrophages BRI-789


title: Paediatric glioblastoma cell GBM002-Parental input DNA G34R rep2

data_processing:
ChIP-seq reads were quality and adapter trimmed with Cutadapt (version 1.14), before being aligned to the human hg38 genome with bowtie2 (version 2.3.5) using default parameters.
Resulting BAM files were sorted and indexed with samtools and reads were filtered from ENCODE blacklist regions with samtools view (version 1.9) and bedtools intersect (version 2.29.0).
PCR duplicates were filtered with picard tools MarkDuplicates (version 2.18.26).
Peaks were called on filtered input and control BAM files with MAC2 set to broadPeak (H3.3, H3K36me3, H3K27me3), and narrowPeak (H3K4me3). Narrow peaks were called using MACS2 (version 2.1.2) with the following command line parameters: macs2 callpeak -t Input.bam -c Control.bam -f BAMPE -g 2701495761 -s 50 --keep-dup all -B --SPMR --nomodel --shift 0 --extsize 146 -q 0.05. Broad peaks were called with the additional parameters --broad --broad-cutoff 0.1 instead of -q 0.05.
RPM normalised bedgraph files were generated via MACS2 following peak calling. Subtracted coverage files were generated using MACS2 bdgcmp between input and control BAMs - where negative values were set to 0.
BigWig coverage files were generated using bedGraphToBigWig (version 4) from MACS2 resulting bedgraphs.
Where merged samples are reported (_0), samtools merge was used on filtered BAMs across sample replicates before undergoing the same peak calling, bedgraph, and bigWig generation process.
Coverage of each histone mark over gene regions for boxplots were summarised using bedtools multicov on filtered and processed BAM files, and normalised to RPKM using gene length
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 Peakfiles
Supplementary_files_format_and_content: Bigwig files of histone marks
Supplementary_files_format_and_content: RPKM histone coverage over genes

source_name: pHGG

growth_protocol: Cultures were maintained in DMEM/HAMS-F12 serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Sigma, 1 µg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/protein-DNA complexes were isolated using antibodies.
Libraries were constructed using the NEBNext Ultra II DNA Library Kit and NEBNextdual index primer sets for Illumina (Cat. #E7645S and #E7600S) in accordance with the manufacturers instructions.

value: Paediatric glioblastoma cell

value: pHGG

value: Cancer

tag: chip antibody

tag: genotype


title: blood-derived macrophages BRI-785

tag: tissue


title: HXP6

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: heart tissue

extract_protocol:
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: heart tissue

tag: group

value: HXP Treatment


title: RSS1TRAPLATEOSROOT3

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
RSS1TRAPLATEOSROOT3
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: blood-derived macrophages BRI-783


title: F423_24_3

source_name: the anthracnose-susceptible F423 fruits samples at 24 hour during infection proces

tag: strain

value: Juglans regia clone 4-23

value: fruit sample


title: Paediatric glioblastoma cell GBM002-Parental input DNA G34R rep1


title: HXP5


title: CMZTRAPLATEOSROOT1B

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
CMZTRAPLATEOSROOT1B
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1

value: Nipponbare


title: Tnaive_2


title: CMZTRAPLATEOSROOT2A

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
CMZTRAPLATEOSROOT2A
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1

value: 7 days


title: SHRTRAPLATEOSROOT3

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
SHRTRAPLATEOSROOT3
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1

value: Roots


title: Paediatric glioblastoma cell GBM002-Parental H3K4me3 G34R rep2


title: Paediatric glioblastoma cell GBM002-Parental H3K4me3 G34R rep1


title: Neural stem cell Posterior Brainstem  rep2 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

source_name: Posterior Brainstem

extract_protocol:
total RNA was extracted with Qiagen Rneasy plus mini kit
Libraries were generated with 200ng of RNA input using the KAPA mRNA HyperPrep kit and KAPA SeqCap adapters. Fragmentation was carried out at 94°C for 6 minutes and libraries amplified for 12 cycles
Pooled libraries were diluted and processed for sequencing using the Illumina HiSeq 2500 platform.

value: Neural stem cell line

value: Posterior Brainstem

value: GCGR-NS19 - 19.3 pcw

value: Normal


title: HXP3


title: Neural stem cell Posterior Brainstem rep1 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt


title: HXP2


title: Tissue Spinalcord GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Spinalcord

value: GCGR-NS15 - 15.0 pcw


title: CMZTRAPLATEOSROOT1A

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
CMZTRAPLATEOSROOT1A
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: Paediatric glioblastoma cell GBM002-Parental H3K36me3 G34R rep1


title: Paediatric glioblastoma cell GBM002-Parental H3K27me3 G34R rep2


title: Neural stem cell Diencephalon rep1 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Diencephalon


title: HXP1


title: HXP4


title: Neural stem cell Cortex rep1 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Neocortex


title: RSS1TRAPLATEOSROOT2

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
RSS1TRAPLATEOSROOT2
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: MI6

value: MI


title: MI5


title: Tissue RHB GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Anterior Brainstem


title: Tissue CHB GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt


title: WAPL Tg

tag: genotype/variation

value: WAPL Tg

tag: Sex

value: female

value: cervix


title: SCRTRAPLATEOSROOT1

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
SCRTRAPLATEOSROOT1
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: MI4

value: heart tissue


title: Paediatric glioblastoma cell GBM002-Parental G34R G34R rep2

value: Paediatric glioblastoma cell

value: pHGG

value: Cancer


title: SHRTRAPLATEOSROOT2

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
SHRTRAPLATEOSROOT2
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1

value: Nipponbare

value: 7 days

value: Roots


title: Paediatric glioblastoma cell GBM002-Parental H3K36me3 G34R rep2


title: Neural stem cell Cortex rep2 GCGR-NS19 - 19.3 pcw

description:
Cell line
GCGR_NS_normalised_counts.txt

value: Neural stem cell line

value: GCGR-NS19 - 19.3 pcw

value: Normal


title: RSS1TRAPLATEOSROOT1

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
RSS1TRAPLATEOSROOT1
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: Tissue Midbrain GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Midbrain

value: Midbrain

value: GCGR-NS15 - 15.0 pcw


title: MI3

value: MI


title: Paediatric glioblastoma cell GBM002-Parental G34R G34R rep1


title: Paediatric glioblastoma cell GBM002-P2D3 v5-tag G34R KO rep2

value: G34R KO


title: X35STRAPLATEOSROOT3

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
X35STRAPLATEOSROOT3
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1

value: p35S:HF-FLAG-OsRPL18 (Zhao et al., 2016)


title: MI2


title: SHRTRAPLATEOSROOT1

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
SHRTRAPLATEOSROOT1
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: Paediatric glioblastoma cell GBM002-P2D3 v5-tag G34R KO rep1


title: Tissue Diencephalon GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Diencephalon


title: MI1


title: X35STRAPLATEOSROOT2

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
X35STRAPLATEOSROOT2
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: Tissue Striatum GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Striatum


title: SCRTRAPLATEOSROOT2

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
SCRTRAPLATEOSROOT2
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: Paediatric glioblastoma cell GBM002-P2D3 input DNA G34R KO rep2


title: Paediatric glioblastoma cell GBM002-P2D3 input DNA G34R KO rep1


title: control5

value: heart tissue

value: control


title: control6


title: X35STRAPLATEOSROOT1

description:
Oryza sativa japonica cv. Nipponbare
Random primed libraries
TRAP RNA
X35STRAPLATEOSROOT1
processed data file: Rice_ATLAS_raw_counts.csv
protocols used: growth protocol 4, extract protocol 3 and library construction protocol 1


title: Tissue Neocortex GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Neocortex

value: Neocortex


title: Paediatric glioblastoma cell GBM002-P2D3 H3K4me3 G34R KO rep2

value: Paediatric glioblastoma cell

value: pHGG

value: Cancer


title: Tissue Cerebellum GCGR-NS15 - 15.0 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

source_name: Cerebellum

value: Cerebellum


title: XYINTQ

description:
Solanum lycopersicum cv. M82
Random primed libraries
N05
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2

data_processing:
Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to ITAG3.2 transcriptome (cDNA) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values.
ATAC-seq raw reads were aligned to each species' corresponding genome using Bowtie2 with default parameters.
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<2.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1".
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
For accurate visualization, all filtered ATAC-seq bam files for a given tissue were scaled to the same number of reads and combined per condition to create a single merged bam file for a condition in a tissue type. The merged bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Filtered ATAC-seq bam files from genomic DNA samples were scaled to the total number of reads present in the merged bam files for a given tissue type. The scaled bam file was converted to a bigwig file using a bin size resolution of 1 base pair and the "--normalizeUsingRPKM" option.
Rice TRAP-seq. Barcoded libraries were pooled together and sequenced on Illumina HiSeq 3000 at the UC Davis DNA Technologies Core to obtain 50-bp reads.
Rice TRAP-seq. R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
Rice TRAP-seq. Sequences were pooled, and then trimmed and filtered using Trim Galore! (v0.4.5) with parameter -a GATCGGAAGAGCACA. Trimmed reads were pseudo-aligned to IRGSP-1.0 transcriptome (CDS, https://rapdb.dna.affrc.go.jp/index.html) using Kallisto (v0.43.1), with the parameters -b 100 --single -l 200 -s 30, to obtain count estimates and transcript per million (TPM) values. Splice variants were summed to assess transcript values.
Genome_build: Tomato: SOLANUM LYCOPERSICUM: ITAG3.20 (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/)
Genome_build: Rice: IRGSP-1.0 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary_files_format_and_content: .bed files contain Transposase Hypersensitive Site (THS) coordinates for individual samples or for each tissue type they are organized as (All) all the replicated THSs identified in that sample set in either control or submergence samples, (Up) THSs upregulated in submergence samples, and (Down) THSs downregulated in submergence samples.
Supplementary_files_format_and_content: .bw files contain aligned reads for individual samples, or combined samples for a specific condition of a given tissue, at a resolution of 1 bp bin sized windows.
Supplementary_files_format_and_content: .csv files contain raw counts.

organism: Solanum lycopersicum

source_name: 3-5 days-old seedling 1 cm roots tips

value: S18pro:WPP:GFP:BLRP / SlACT2pro:mBirA

value: 3-5 days

value: Roots tips


title: Tissue Anterior Brainstem GCGR-NS13 - 13.5 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

data_processing:
Paired end RNA sequencing reads were trimmed with Cutadapt (version 1.14) with default parameters and aligned to hg38 genome using Kallisto (version 0.43.1).
Read counts were summarised via the package Tximport (version 1.8.0) and subsequent normalisation was completed via DESeq2 (version 1.27.32) as regularised-logarithm transformation (rlog).
Genome_build: hg38
Supplementary_files_format_and_content: Three sets of tab-delimited files for pHGG, NSCs, and engineered NSCs containing raw counts, and normalised counts as calculated by DESeq2 (rlog and FPM).
Supplementary_files_format_and_content: DESeq2 fpm
Supplementary_files_format_and_content: DESeq2 normalised counts rlog
Supplementary_files_format_and_content: raw counts

value: Anterior Brainstem

value: GCGR-NS13 - 13.5 pcw

value: Normal


title: control4


title: control2


title: control3


title: Tissue Cerebellum GCGR-NS13 - 13.5 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt


title: Paediatric glioblastoma cell GBM002-P2D3 H3K36me3 G34R KO rep2

value: G34R KO


title: XYINTN

description:
Solanum lycopersicum cv. M82
Random primed libraries
K08
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: XYINTK

description:
Solanum lycopersicum cv. M82
Random primed libraries
I07
protocols used: growth protocol 1, extract protocol 2 and library construction protocol 2


title: Tissue Midbrain GCGR-NS13 - 13.5 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Midbrain


title: Paediatric glioblastoma cell GBM002-P2D3 H3K36me3 G34R KO rep1


title: control1


title: Tissue Diencephalon GCGR-NS13 - 13.5 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Diencephalon


title: Tissue Posterior GCGR-NS13 - 13.5 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Posterior Brainstem


title: Paediatric glioblastoma cell GBM002-P2D3 H3K27me3 G34R KO rep2


title: Tissue Striatum GCGR-NS13 - 13.5 pcw

description:
Tissue
GCGR_NS_normalised_counts.txt

value: Striatum