title: nutrient starvation replicate 2

description:
rRNA depletion
PBS rep2
directional RNA-Seq


title: plate_060s_I5_S37_L006

status: Public on Mar 31 2022

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain single cell 233

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the mouse reference genome Gencode M26 genome with STAR software.
Genome_build: Gencode M26
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
We used transgenic mouse reporter line (SM22-Cre;Rosa26-stop-tdTomato). We chosed to focus our efforts to adult mice brain cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: brain

tag: age

value: adult mice

tag: notch3 genotype

value: KO

tag: celltype

value: Macrophages


title: Control 7-weeks Lean Zucker Brain 11

city: Niskayuna

first: John

last: Graf

state: New York

address: One Research Circle

country: USA

institute: GE Global Research

data_processing:
Fastq files of the paired end reads were merged into two files for each sample, one for R1 and one for R2 using Unix commands.
Base quality control was checked using Fast QC v0.10.1 from Babraham Bioinformatics.
Sequencing reads were mapped to the annotated rat genome version, Rattus norvegicus Rnor 6.0.91, using STAR_2.5.3a aligner.
Transcript abundance estimates were generated from the sorted BAM files using RSEM.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rsem_genes_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every gene and every sample
Supplementary_files_format_and_content: rsem_isoforms_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every transcript and every sample

organism: Rattus norvegicus

source_name: Lean Zucker

extract_protocol:
Tissue were rapidly collected at the terminal time point and and treated with RNAlater tissue storage reagent. RNA extraction from tissues, assessment of RNA quality and RNA sequencing were performed at the Roswell Park Cancer Institute, Genomics Shared Resource, Buffalo, New York.
Sequencing RNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions for the RNA from all tissues except the pancreas and adipose. For these samples, TruSeq Stranded Total RNA Sample Preparation Kit was used.

treatment_protocol: The porta hepatis was targeted for ultrasound stimulation using a 1.1 MHz single-element focused ultrasound system comprised of a signal generator (Model 33120A, Agilent Technologies Inc., Santa Clara, CA), a RF power amplifier (Model 350L, Electronics & Innovation Ltd., Rochester, NY) and a 1.1 MHz focused single-element ultrasound transducer (Model H102, Sonic Concepts Inc., Bothell, WA). The transducer was acoustically coupled to the animal through a 6-cm tall plastic standoff cone filled with degassed water. Prior to treatments, all rats were anesthetized at 2-4% isoflurane at 1 L/min O2. The Target porta hepatis was localized using a custom ultrasound imaging device (Vivid E9; GE Healthcare). Animals either received 3 minutes of ultrasonic stimulus (1.1 MHz, 200mV per pulse, 150 burst cycles, 500 µs burst period) or Sham stimulus where no energy was applied.

tag: model

value: Lean Zucker

value: Brain

tag: gender

value: Male

tag: treatment

value: Control 7-weeks


title: Control 7-weeks Lean Zucker Blood 11

value: Blood


title: plate_060s_I22_S173_L006

description: Brain single cell 232


title: Old-2-DistCol_scRNA-seq

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: Single cell RNA sequencing

data_processing:
The fastq files are mapped against mm10.e87 genome following by counting the UMI and removing duplicates for single cells using 'cellranger count' (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count ) with default parameters.
Genome_build: mm10.e87
Supplementary_files_format_and_content: The processed data is the expression matrix (raw counts) with genes in row (first column is the gene names) and cells in columns (firs row is the cell index)

source_name: Distal Colon

growth_protocol: 5 Young (1x 8week, 3x 12week and 1x 20week) and 6 old (2x 90week, 1x 92week ,3x 108week) female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility

extract_protocol:
Crypts from cecum, proximal and distal colon were isolated as described previously(Asad A Ahmad et al., 2014). After centrifugation, the crypts were re-suspended in 3ml of Single-Cell Isolation Solution (TrypLE supplemented with: 1mg/ml DNaseI, 5mM MgCl2, 80μM Y27) and incubated at 37°C for 20min, vortexing for 5 seconds after first 10min. Reaction was quenched by addition of 27ml ice-cold PBS and cells were centrifuged at 1000g for 5minutes at 4°C. Cell pellet was re-suspended in FACS staining medium (FSM - PBS supplemented with 2% Fetal Bovine Serum, 80μM Y27, 3mM EDTA) and treated with CD326 (EpCAM) (G8.8), PE-Cyanine7 coupled rat monoclonal antibody and a TotalSeq Hashtag antibody for 30min on ice in the dark. The cells were then centrifuged at 450g for 5min at 4°C and re-suspended in 500μl fresh FSM. An input of 10000 EpCAM positive FACS sorted single cells per compartment was added to each 10X Chromium Controller channel.
The 10X Single Cell 3’ v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction.

value: Distal Colon


title: Exponential phase replicate 2

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

description:
rRNA depletion
Exp rep2
directional RNA-Seq

data_processing:
Adapter sequence was trimmed using trim_galore.
The trimmed reads were mapped to the TB genome using bowtie2.
The number of read pairs mapped to each gene were counted using featureCount.
The differential expression was analyzed using DESeq2.
Assembly: Mycobacterium tuberculosis H37Rv assembly ASM19595v2.
Supplementary files format and content: *.deseq.gene.txt: Tab-delimited DESeq2 results.

organism: Mycobacterium tuberculosis H37Rv

source_name: Exponential phase

growth_protocol: M. tuberculosis was grown shaking at 37°C in Middlebrook 7H9 supplemented with 10% (v/v) OADC enrichment (5% (w/v) bovine albumin fraction V, 2% (w/v) dextrose, 0.003% (w/v) catalase, 0.85% (w/v) sodium chloride in water), 0.2% (v/v) glycerol and 0.05% (v/v) tyloxapol unless otherwise described in treatment protocol.

extract_protocol:
Cultures were spun down, resuspended in TRIzol, lyzed and the supernatants were transferred to Zymo-Spin IICR Columns and processed according to the manufacturer’s Direct-zolTM RNA Miniprep protocol.
RNA libraries were prepared for sequencing using NEB bacteria rRNA depletion kit and Ultra II directional RNAseq kit.

treatment_protocol: For nutrient limitation, actively growing cells were spun down, washed twice in PBS and resuspended in PBS supplemented with 0.05% tyloxapol. The cultures were incubated shaking at 37°C for 14 days. Stationary phase cultures of M. tuberculosis were obtained by incubating M. tuberculosis cultures shaking at 37°C for four weeks. Microaerophilic cultures of M. tuberculosis cultures were obtained by growing the cultures at 37°C in a glove box containing 1% oxygen and 5% CO2 for 14 days. Actively growing M. tuberculosis cultures in media acidified to pH 5.8 were grown shaking at 37°C for 14 days.

tag: genotype

value: wild type

tag: growth phase

value: Exponential

tag: condition

value: standard growth medium


title: Exponential phase replicate 1

description:
rRNA depletion
Exp rep1
directional RNA-Seq


title: pFUS 7-weeks Obese ZDF Muscle 10

source_name: Obese ZDF

value: Obese ZDF

value: Muscle

value: pFUS 7-weeks


title: plate_060s_I18_S141_L006

description: Brain single cell 229


title: Old-6-ProxCol_scRNA-seq

description: Single cell RNA sequencing

source_name: Proximal Colon

value: Proximal Colon


title: Old-1-DistCol_scRNA-seq

description: Single cell RNA sequencing


title: pFUS 7-weeks Obese ZDF Pancreas 10

value: Pancreas


title: Platelet purified by classical method

type: RNA

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

description: Gene expression data from platelet purified by classical method

hyb_protocol: Following fragmentation and terminal labeling, 5.5 μg of ds cDNA were hybridized for 16 hrs at 45°C and 60 rpm on Clariom D Human chips, as per the manufacturer’s protocol (Affymetrix, Santa Clara, CA, USA # 902922). The arrays were stained by using GeneChip Fluidics Station 450.

scan_protocol: Chips were scanned with Affymetrix GeneChip™ scanner 3000

data_processing: Data were generated with Affymetrix Expression Console v 1.4.1

label: biotin

organism: Homo sapiens

source_name: human blood

label_protocol: Biotinylated ds cDNA was prepared according to the WT PICO kit from 1 ng of total RNA

growth_protocol: Blood samples were collected in sodium citrate tubes and centrifuged at 200 g for 20 minutes in order to obtain platelet rich plasma (PRP). Platelets were then pelleted by PRP centrifugation at 1,000g for 10 minutes in the presence of 2mM Ethylenediaminetetraacetic acid (EDTA).

extract_protocol: RNeasy Mini Kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: After cell pelleting, platelets were either directly used for transcriptome analysis by microarray, or treated with magnetic microbeads to eliminate contaminating leukocytes and erythrocytes before transcriptome analysis.

tag: cell

value: platelet


title: plate_060s_I2_S13_L006

description: Brain single cell 230

value: brain

value: adult mice

value: KO


title: Tumor sample of Monkey RM9 (RNAseq)

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FASTQC toolkit was performed for quality control of FASTQ files
The fastp tool was performed to trim adapters and low-quality reads
Cleaned reads of total RNA sequencing were aligned to the reference genome using the STAR RNA sequencing aligner.
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Macaca mulatta

source_name: COLON

extract_protocol:
Macro-dissection was performed to decrease the admixture of adjacent normal tissue and to enrich the percentage of tumor material for subsequent RNA extraction. De-paraffinization of FFPE tumor and adjacent normal specimens was performed using QIAGEN de-paraffinization solution (QIAGEN, Valencia, CA). DNA and RNA from 19 tumor and adjacent normal samples was extracted using the AllPrep DNA/RNA FFPE Kit (QIAGEN) following the manufacturer’s protocol. In the case of the unavailability of FFPE samples, genomic DNA and RNA were extracted from fresh frozen tumor (n=2) and normal (n=3) samples using the ZR-Duet DNA/RNA MiniPrep extraction kit (ZYMO RESEARCH, Irvine, CA). Quantification was performed with a NanoDrop One™ spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Qubit™ Fluorometer 2.0 (Qubit, San Francisco, CA) using dsDNA and RNA assay kits. RNA integrity was analyzed using the Tape Station RNA assay kit (Agilent Technologies, Santa Clara, CA).
Truseq stranded total RNA library preparation kit (Illumina®, San Diego, CA) was used to prepare libraries of 21 tumors and 20 matched normal RNA samples

value: Tumor

tag: msi status

value: MSI-H

tag: sample id

value: Female

tag: mlh1 c.1029 (c>g) germline mutation status

value: Heterozygous


title: Old-4-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: Platelet purified by microbead method

description: Gene expression data from platelet purified by microbead method


title: plate_060s_I20_S157_L006

description: Brain single cell 231

value: Macrophages


title: pFUS 7-weeks Obese ZDF Liver 10

value: Liver

value: Male


title: pFUS 7-weeks Obese ZDF Brain 10

value: Brain


title: pFUS 7-weeks Obese ZDF Kidney 10

value: Obese ZDF

value: Kidney


title: Old-3-DistCol_scRNA-seq

description: Single cell RNA sequencing

value: Distal Colon


title: plate_060s_I17_S133_L006

description: Brain single cell 228


title: Normal sample of Monkey RM17 (RNAseq)

value: Normal

value: MSI-L

value: Wild type


title: pFUS 7-weeks Obese ZDF Blood 10

value: Blood

value: pFUS 7-weeks


title: Old-3-ProxCol_scRNA-seq

description: Single cell RNA sequencing

value: Proximal Colon


title: plate_060s_I15_S117_L006

description: Brain single cell 227

value: brain

value: adult mice

value: KO


title: Normal sample of Monkey RM8 (RNAseq)

value: MSI-H


title: pFUS 7-weeks Obese ZDF Pancreas 9

value: Pancreas


title: Tumor sample of Monkey RM17 (RNAseq)

value: Tumor

value: Female


title: plate_060s_I14_S109_L006

description: Brain single cell 226

value: Microglia


title: Tumor sample of Monkey RM8 (RNAseq)

value: Male


title: pFUS 7-weeks Obese ZDF Muscle 9

value: Obese ZDF

value: Muscle


title: plate_060s_I13_S101_L006

description: Brain single cell 225


title: Old-1-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: Old-5-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: plate_060s_I12_S93_L006

description: Brain single cell 224

value: Macrophages


title: Old-6-Cecum_scRNA-seq

description: Single cell RNA sequencing

source_name: Cecum

value: Cecum


title: plate_060s_I1_S5_L006

description: Brain single cell 223


title: plate_060s_H9_S260_L006

description: Brain single cell 222


title: Normal sample of Monkey RM2 (RNAseq)

value: Normal

value: MSS

value: Wild type


title: pFUS 7-weeks Obese ZDF Blood 9

value: Blood

value: pFUS 7-weeks


title: pFUS 7-weeks Obese ZDF Kidney 9

value: Kidney


title: Tumor sample of Monkey RM6 (RNAseq)


title: Normal sample of Monkey RM6 (RNAseq)


title: Old-5-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: Old-4-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: pFUS 7-weeks Obese ZDF Brain 9

value: Brain


title: Old-2-ProxCol_scRNA-seq

description: Single cell RNA sequencing

value: Proximal Colon


title: pFUS 7-weeks Obese ZDF Liver 9

value: Liver


title: Old-3-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: Old-2-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: Tumor sample of Monkey RM2 (RNAseq)

value: Tumor


title: plate_060s_H6_S236_L006

description: Brain single cell 220

value: brain

value: adult mice

value: KO


title: plate_060s_H8_S252_L006

description: Brain single cell 221


title: Normal sample of Monkey RM1 (RNAseq)

value: MSI-L

value: Female


title: Old-1-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: pFUS 7-weeks Obese ZDF Pancreas 8

value: Obese ZDF

value: Pancreas

value: Male


title: Tumor sample of Monkey RM1 (RNAseq)


title: pFUS 7-weeks Obese ZDF Kidney 8


title: plate_060s_H4_S220_L006

description: Brain single cell 219

value: Microglia


title: plate_060s_H24_S380_L006

description: Brain single cell 218

value: Macrophages


title: Young-5-DistCol_scRNA-seq

description: Single cell RNA sequencing

value: Distal Colon


title: Normal sample of Monkey RM4 (RNAseq)

value: Normal

value: Wild type


title: plate_060s_H22_S364_L006

description: Brain single cell 217


title: pFUS 7-weeks Obese ZDF Brain 8

value: Brain

value: pFUS 7-weeks


title: Tumor sample of Monkey RM4 (RNAseq)


title: Young-4-DistCol_scRNA-seq

description: Single cell RNA sequencing


title: pFUS 7-weeks Obese ZDF Liver 8

value: Liver


title: Young-3-DistCol_scRNA-seq

description: Single cell RNA sequencing


title: Normal sample of Monkey RM14 (RNAseq)

value: MSI-H


title: Young-1-DistCol_scRNA-seq

description: Single cell RNA sequencing


title: plate_060s_H18_S332_L006

description: Brain single cell 215

value: brain


title: pFUS 7-weeks Obese ZDF Pancreas 7


title: pFUS 7-weeks Obese ZDF Kidney 7

value: Kidney


title: Tumor sample of Monkey RM16 (RNAseq)

value: Tumor


title: plate_060s_H13_S292_L006

description: Brain single cell 213

value: adult mice

value: KO


title: pFUS 7-weeks Obese ZDF Blood 8

value: Obese ZDF

value: Blood


title: Normal sample of Monkey RM13 (RNAseq)

value: Female


title: plate_060s_H19_S340_L006

description: Brain single cell 216


title: plate_060s_H17_S324_L006

description: Brain single cell 214


title: pFUS 7-weeks Obese ZDF Brain 7

value: Male


title: Normal sample of Monkey RM16 (RNAseq)


title: pFUS 7-weeks Obese ZDF Blood 7


title: Young-4-ProxCol_scRNA-seq

description: Single cell RNA sequencing

value: Proximal Colon


title: plate_060s_H10_S268_L006

description: Brain single cell 210

value: Macrophages


title: Tumor sample of Monkey RM13 (RNAseq)


title: Normal sample of Monkey RM18 (RNAseq)

value: Normal


title: Tumor sample of Monkey RM14 (RNAseq)

value: Wild type


title: pFUS 7-weeks Obese ZDF Pancreas 6

value: Pancreas


title: Young-5-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: plate_060s_H11_S276_L006

description: Brain single cell 211


title: plate_060s_H12_S284_L006

description: Brain single cell 212


title: pFUS 7-weeks Obese ZDF Liver 7

value: pFUS 7-weeks


title: Young-3-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: plate_060s_H1_S196_L006

description: Brain single cell 209


title: Young-2-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: pFUS 7-weeks Obese ZDF Muscle 6

value: Muscle


title: pFUS 7-weeks Obese ZDF Kidney 6


title: Young-2-DistCol_scRNA-seq

description: Single cell RNA sequencing

value: Distal Colon


title: Young-1-ProxCol_scRNA-seq

description: Single cell RNA sequencing


title: Tumor sample of Monkey RM18 (RNAseq)

value: MSI-H


title: plate_060s_G2_S12_L006

description: Brain single cell 205

value: brain


title: pFUS 7-weeks Obese ZDF Liver 6

value: Liver


title: Young-1-Cecum_scRNA-seq

description: Single cell RNA sequencing

value: Cecum


title: Control 7-weeks Obese ZDF Pancreas 5

value: Control 7-weeks


title: plate_060s_G3_S20_L006

description: Brain single cell 208

value: adult mice

value: KO


title: Young-5-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: plate_060s_G15_S116_L006

description: Brain single cell 203

value: Microglia


title: Young-4-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: Tumor sample of Monkey RM10 (RRBS)

library_source: genomic

data_processing:
FASTQC toolkit was performed for quality control of FASTQ files
TrimGalore was performed to trim adapters and low-quality reads
Diversity trimming and filtering were completed with NuGEN’s diversity trimming scripts
Processed fastq files were aligned to the reference genome (Mmul_10) with bismark bisulfite mapper.
The methylation information was extracted with bismark methylation extractor script.
Genome_build: Mmul_10
Supplementary_files_format_and_content: bedGraph file with the estimated methylation rate

molecule: genomic DNA

extract_protocol:
Macro-dissection was performed to decrease the admixture of adjacent normal tissue and to enrich the percentage of tumor material for subsequent RNA extraction. De-paraffinization of FFPE tumor and adjacent normal specimens was performed using QIAGEN de-paraffinization solution (QIAGEN, Valencia, CA). DNA and RNA from 19 tumor and adjacent normal samples was extracted using the AllPrep DNA/RNA FFPE Kit (QIAGEN) following the manufacturer’s protocol. In the case of the unavailability of FFPE samples, genomic DNA and RNA were extracted from fresh frozen tumor (n=2) and normal (n=3) samples using the ZR-Duet DNA/RNA MiniPrep extraction kit (ZYMO RESEARCH, Irvine, CA). Quantification was performed with a NanoDrop One™ spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Qubit™ Fluorometer 2.0 (Qubit, San Francisco, CA) using dsDNA and RNA assay kits. RNA integrity was analyzed using the Tape Station RNA assay kit (Agilent Technologies, Santa Clara, CA).
DNA libraries of RRBS were constructed from FFPE tissue samples of 14 tumors/adjacent normal tissue pairs using the Ovation RRBS Methyl-Seq System at The Epigenomics Profiling Core (EpiCore) of MDACC. In preparation, DNA was digested with a restriction enzyme and selected for size based on established protocols used in the EpiCore. Post-adapter ligation ensured enrichment for CpG islands, and DNA was bisulfite-treated, amplified with universal primers, and qualified libraries were then sequenced on Novaseq6000™ and MiSeq sequencers at the UTMDACC ATG

value: Tumor

value: Female


title: Normal sample of Monkey RM10 (RRBS)


title: plate_060s_G13_S100_L006

description: Brain single cell 202

value: Macrophages


title: plate_060s_G22_S172_L006

description: Brain single cell 206


title: Normal sample of Monkey RM25 (RRBS)

value: Normal


title: Young-3-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: Tumor sample of Monkey RM38 (RRBS)

value: Male

value: Heterozygous


title: Tumor sample of Monkey RM25 (RRBS)

value: Wild type


title: Young-2-Cecum_scRNA-seq

description: Single cell RNA sequencing


title: pFUS 7-weeks Obese ZDF Blood 6

value: Obese ZDF

value: Blood

value: pFUS 7-weeks


title: plate_060s_G17_S132_L006

description: Brain single cell 204

value: brain


title: Normal sample of Monkey RM38 (RRBS)

value: MSI-H


title: plate_060s_G23_S180_L006

description: Brain single cell 207


title: pFUS 7-weeks Obese ZDF Brain 6

value: Brain


title: Normal sample of Monkey RM17 (RRBS)

value: MSI-L


title: siA-3_TCDD

city: GALVESTON

first: Kamil

last: Khanipov

address: 301 University Blvd

institute: University of Texas Medical Branch

data_processing:
The sequenced reads were trimmed and filtered based on adapter content and quality by a modified-Mott trimming algorithm (CLC Genomics Workbench 21, Qiagen). Filtered sequencing reads were locally aligned against the Homo sapiens (hg38) reference genome with annotated genes and transcripts (83). The resulting gene counts were normalized, and differential expression analysis on the complete list of genes and transcripts was used to evaluate the level and significance of mRNA expression changes (84). All genes with a fold change ≥1.5 were included in the pathway analysis using Ingenuity Pathway Analysis to highlight molecular function, biological process, and cellular component.
Genome_build: hg38
Supplementary_files_format_and_content: Differential gene expression as processed by CLC Genomics Workbench

source_name: Karpas 299 cell line

growth_protocol: Karpas 299 cells were propagated in RPMI-1640 medium (Corning, 15-041-CV) complete with 10% FBS (Atlanta Biologicals, S11550) and 2 mM GlutaMAX (Gibco, 35050-061) at 37 °C, 5% CO2. Hepa-1c1c7 cells were cultured in MEM Alpha (1X) + 2 mM GlutaMAX (Gibco, 32561-037) with 10% FBS at 37 °C, 5% CO2. Stable BpRc1 cells, an Arnt-null variant of Hepa-1c1c7 cells, were cultured in DMEM (Corning, 15-018-CV) with 10% FBS, 2 mM GlutaMAX, and 2 mg/mL puromycin (Invivogen, ant-pr) at 37 °C, 5% CO2. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) (Cerilliant, ED-901-C), a high affinity AhR ligand, was used to activate the AhR pathway in samples that include TCDD in the label. TCDD was added to a final concentration of 10 nM and incubated for 2 hours, followed by total RNA collection.

extract_protocol:
Total RNA was extracted using QIAshredder (Qiagen, 79656) and RNeasy Kits (Qiagen, 74104)
TruSeq

treatment_protocol: 1 × 107 Karpas 299 or Peer cells were transfected with 4 uM of target siRNA duplexes using a Bio-Rad Gene Pulser Xcell electroporator set on infinite resistance, 300 V for Karpas 299 cells or 250 V for Peer cells, and 950 microfarads. Cells were suspended in RPMI-1640 medium containing 20% FBS and 2 mM GlutaMAX. Sixteen hours post-transfection, dead cells were removed by centrifugation at 400 × g for 20 min with Ficoll-Paque PLUS (GE Healthcare, 17-1440-02). The live cell layer was then transferred to RPMI-1640 medium complete with 10% FBS and 2 mM GlutaMAX at 0.5 × 106 cells/mL for 24 hours. The siRNA (MilliporeSigma) target sequences are as follows: siA-1 5’-UGC CAG GUC GGA UGA UGA GCA-3′, siA-3 5’-CGG UUU GCC AGG GAA AAU C-3’, siA-1/3 5’-GAC UCG UAC UUC CCA GUU U-3’ and 5’-CUU UGC UCC UGA GAC UGG A-3’, and AhR (MilliporeSigma, SASI_Hs01_00140202). The target sequence for siControl is a scrambled siA-1/3 sequence (31).

tag: cell type

value: T cell-derived anaplastic large cell lymphoma

value: ARNT isoform 3 siRNA + TCDD


title: siA-1_TCDD

value: ARNT isoform 1 siRNA + TCDD


title: Control 7-weeks Obese ZDF Muscle 5

value: Muscle

value: Control 7-weeks


title: siA-3_DMSO_rep2

value: ARNT isoform 3 siRNA + DMSO


title: Control 7-weeks Obese ZDF Kidney 5

value: Kidney


title: Tumor sample of Monkey RM17 (RRBS)

value: Tumor

value: Female


title: Normal sample of Monkey RM37 (RRBS)

value: Normal

value: Wild type


title: plate_060s_F6_S235_L006

description: Brain single cell 198

value: adult mice

value: KO

value: Microglia


title: siA-1/3_TCDD

value: ARNT isoform 1 and 3 siRNA + TCDD


title: Tumor sample of Monkey RM37 (RRBS)

value: MSI-H


title: siA-3_DMSO_rep1


title: siA-1/3_DMSO_rep2

value: ARNT isoform 1 and 3 siRNA + DMSO


title: Control 7-weeks Obese ZDF Blood 5

value: Obese ZDF

value: Blood

value: Male


title: plate_060s_G1_S4_L006

description: Brain single cell 201

value: brain

value: Macrophages


title: plate_060s_F9_S259_L006

description: Brain single cell 200


title: siA-1_DMSO_rep2

value: T cell-derived anaplastic large cell lymphoma

value: ARNT isoform 1 siRNA + DMSO


title: Control 7-weeks Obese ZDF Liver 5

value: Liver

value: Control 7-weeks


title: siA-1/3_DMSO_rep1


title: Normal sample of Monkey RM31 (RRBS)

value: Normal

value: Female

value: Heterozygous


title: Control 7-weeks Obese ZDF Brain 5

value: Brain


title: Control 7-weeks Obese ZDF Muscle 4

value: Muscle


title: Tumor sample of Monkey RM30 (RRBS)

value: Tumor

value: Wild type


title: plate_060s_F5_S227_L006

description: Brain single cell 197

value: adult mice

value: KO


title: Control 7-weeks Obese ZDF Pancreas 4

value: Obese ZDF

value: Pancreas


title: Control 7-weeks Obese ZDF Kidney 4

value: Kidney

value: Male


title: siA-1_DMSO_rep1

value: T cell-derived anaplastic large cell lymphoma


title: Tumor sample of Monkey RM31 (RRBS)

value: MSI-H


title: plate_060s_F21_S355_L006

description: Brain single cell 193

value: brain

value: Macrophages


title: siControl_DMSO_rep2

value: control (scramble) siRNA + DMSO


title: plate_060s_F7_S243_L006

description: Brain single cell 199


title: plate_060s_F20_S347_L006

description: Brain single cell 192

value: Microglia


title: Control 7-weeks Obese ZDF Brain 4

value: Control 7-weeks


title: Normal sample of Monkey RM30 (RRBS)

value: Normal

value: Female


title: siControl_DMSO_rep1


title: plate_060s_F23_S371_L006

description: Brain single cell 195


title: Normal sample of Monkey RM18 (RRBS)


title: plate_060s_F22_S363_L006

description: Brain single cell 194


title: plate_060s_F17_S323_L006

description: Brain single cell 191


title: siControl_TCDD

value: control (scramble) siRNA + TCDD


title: Tumor sample of Monkey RM18 (RRBS)

value: Tumor

value: Wild type


title: Control 7-weeks Obese ZDF Kidney 3


title: Control 7-weeks Obese ZDF Liver 4

value: Liver


title: Normal sample of Monkey RM40 (RRBS)


title: Normal sample of Monkey RM1 (RRBS)

value: MSI-L


title: Control 7-weeks Obese ZDF Brain 3

value: Obese ZDF

value: Brain


title: Control 7-weeks Obese ZDF Blood 4

value: Blood

value: Male


title: plate_060s_F14_S299_L006

description: Brain single cell 189

value: adult mice

value: KO


title: plate_060s_F4_S219_L006

description: Brain single cell 196

value: brain

value: Macrophages


title: Tumor sample of Monkey RM40 (RRBS)

value: MSI-H


title: Control 7-weeks Obese ZDF Pancreas 3

value: Pancreas

value: Control 7-weeks


title: plate_060s_F11_S275_L006

description: Brain single cell 187


title: plate_060s_F16_S315_L006

description: Brain single cell 190


title: Control 7-weeks Obese ZDF Liver 3


title: Control 7-weeks Obese ZDF Pancreas 2


title: Tumor sample of Monkey RM1 (RRBS)

value: Female


title: Control 7-weeks Obese ZDF Brain 2


title: plate_060s_F13_S291_L006

description: Brain single cell 188

value: Microglia


title: plate_060s_F10_S267_L006

description: Brain single cell 186


title: Normal sample of Monkey RM2 (RRBS)

value: Normal

value: MSS


title: Tumor sample of Monkey RM26 (RRBS)

value: Tumor

value: Wild type


title: plate_060s_E5_S35_L006

description: Brain single cell 182


title: plate_060s_E6_S43_L006

description: Brain single cell 183


title: Control 7-weeks Obese ZDF Liver 2

value: Obese ZDF

value: Liver


title: Control 7-weeks Obese ZDF Muscle 1

value: Muscle


title: LGC1

city: Yangzhou

first: LiLing

last: Li

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区

country: China

institute: Yangzhou University

description: control

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Assembly: hg19
Supplementary files format and content: Number of raw junction read

organism: Capra hircus

source_name: fetal fibroblast cells

extract_protocol:
RNA samples were prepared from the cells using Trizol (TANGEN, Beijing, China) according to the manufacturer’s protocol and the optical density (OD260/280) value was determined by using a NanoDrop ND-2000 instrument (Thermo Fisher Scientific, Waltham, MA, United States) to measure the RNA concentration.
Use the commercial service provided by Cloud-Seq Biotech (Shanghai, China). In brief, the ribosomal RNA (rRNA) was depleted by treating the total RNA with a Ribo-Zero rRNA Removal kit (Illumina, San Diego, CA, United States). The purified RNA samples were used to generate the RNA library using the TruSeq Stranded Total RNA Library Prep kit (Illumina, San Diego, CA, United States) according to the manufacturer’s protocol. The quantification of the constructed libraries as well as their quality was measured using BioAnalyzer 2100 system. Finally, 10-pM libraries were denatured into single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ, clustered, and 150 cycles of sequencing were performed on the Illumina HiSeq sequencer according to the manufacturer’s instructions

value: fetal fibroblast cells

value: 50 day

value: control


title: LGC2

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区

description: control


title: Tumor sample of Monkey RM2 (RRBS)


title: LGT3

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区

description: The cells were exposed to continuous treatment with GO-AgNPs (0 and 0.5 μg/mL) for 10 weeks in 10% FBS-DMEM/F-12. During the treatment period, the cells were passaged every 2-3 d.

value: GO-AgNPs


title: plate_060s_F1_S195_L006

description: Brain single cell 185

value: brain

value: adult mice

value: KO


title: LGT2

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区


title: Control 7-weeks Obese ZDF Blood 2

value: Blood

value: Male

value: Control 7-weeks


title: plate_060s_E9_S67_L006

description: Brain single cell 184

value: Macrophages


title: plate_060s_E23_S179_L006

description: Brain single cell 180


title: Normal sample of Monkey RM26 (RRBS)

value: Normal

value: MSS


title: plate_060s_E24_S187_L006

description: Brain single cell 181

value: Microglia


title: Control 7-weeks Obese ZDF Liver 1

value: Obese ZDF


title: LGC3

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区

description: control


title: plate_060s_E19_S147_L006

description: Brain single cell 179


title: LGT1

address: 中国江苏省扬州市双桥街道扬州大学文汇路校区


title: Control 7-weeks Obese ZDF Pancreas 1

value: Pancreas


title: Control 7-weeks Obese ZDF Kidney 1

value: Kidney


title: Control 7-weeks Obese ZDF Kidney 2


title: RNA-seq_Lens fiber cells_rep3

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Road

institute: Florida Atlantic University

data_processing:
Cutadapt  was used to remove adaptor-contaminated reads, low quality bases and undetermined bases
Reads were mapped to galgal6 genome (ensemble version 96) using Bowtie2  and HISAT2
The mapped reads were assembled using StringTie
Comprehensive transcriptomes were generated using gffcompare and StringTie
The R package edgeR  was used to estimate the expression levels of all transcripts and to identify differentially expressed genes (log2 fold change FPKM > 0.4 or <-0.4) with parametric F-test comparing nested linear models (p < 0.05)
Genome_build: galgal6
Supplementary_files_format_and_content: FibervEpi_RNAseq.txt file: 4,582 genes were found to be differentially expressed between lens epithelial cells relative to lens fiber cells

organism: Gallus gallus

source_name: Lens Fiber cells

extract_protocol:
Total RNA was isolated from biological triplicates of microdissected chick lens epithelial and fiber cells using TRIZOL® reagent (Invitrogen, prod no: 15593018) according to the manufacturer’s instructions.
Libraries were prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol.

value: Lens Fiber cells

tag: developmental stage

value: Embryonic day 13

value: White leghorn


title: Control 7-weeks Obese ZDF Brain 1

value: Brain


title: RNA-seq_Lens fiber cells_rep2

tag: strain


title: Control 7-weeks Obese ZDF Blood 3

tag: tissue


title: RNA-seq_Lens fiber cells_rep1


title: Control 7-weeks Obese ZDF Blood 1


title: plate_060s_E13_S99_L006

description: Brain single cell 176

value: brain

tag: age


title: plate_060s_E16_S123_L006

description: Brain single cell 177

value: adult mice

tag: notch3 genotype


title: pFUS 7-weeks DIO-stz Kidney 8

source_name: DIO-stz

value: DIO-stz

value: pFUS 7-weeks


title: pFUS 7-weeks DIO-stz Brain 10

value: Male


title: plate_060s_E11_S83_L006

description: Brain single cell 175

value: KO

tag: celltype


title: RNA-seq_Lens epithelial cells_rep2

source_name: Lens epithelial cells

value: Lens epithelial cells


title: plate_060s_E1_S3_L006

description: Brain single cell 174

value: Macrophages


title: RNA-seq_Lens epithelial cells_rep3


title: pFUS 7-weeks DIO-stz Brain 8

tag: model


title: pFUS 7-weeks DIO-stz Kidney 7

tag: gender


title: pFUS 7-weeks DIO-stz Muscle 7

value: Muscle

tag: treatment


title: plate_060s_C4_S26_L006

description: Brain single cell 172


title: stem-pooled RNA-seq

city: St Paul

first: Shaun J

middle: J

last: Curtin

email: shaun.curtin@usda.gov, curti242@umn.edu

state: MN

address: 1991 Upper Buford Circle, 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: USDA-ARS-PSRU

data_processing:
Raw fastq reads were quality-filtered with Trimmomatic (BOLGER et al. 2014) and quality-checked with Fastqc(2010) before and after filtering.
Filtered reads were mapped to the medsa.XinJiangDaYe.gnm1assembly (CHEN et al. 2020) that had been modified to include the genomic clone sequence of MsPho2-B4, using Star (DOBIN et al. 2012).
The generated bam files and featureCounts (LIAO et al. 2014) were used to count uniquely aligned read pairs.
Raw feature counts were then TMM-normalized using edgeR package in R

organism: Medicago sativa

source_name: stem

growth_protocol: RegenSY27x alfalfa plants were grown at 22oC and 18oC day/night temperatures with a photoperiod of 16 hours and three replicates of 8-week-old leaf, stem, flower, seedpod, root and nodule tissue harvested.

extract_protocol:
The RNA was extracted from these plants using a Qiagen RNeasy Plant Mini kit according to the manufacturer's instructions, pooled and used to construct libraries
For the RNA-seq, the libraries were validated using a High Sensitivity Chip on the Agilent 2100 Bioanalyzer. The samples were barcoded, multiplexed and sequenced in an Illumina HiSeq 2000 machine using paired-end reads with 150 cycles. The cDNA library preparation and sequencing reactions were conducted in the Biomedical Genomics Center, University of Minnesota.

value: stem

value: 20 week days old plant

tag: genotype


title: seedpod-pooled RNA-seq

source_name: seedpod

value: seedpod


title: plate_060s_E18_S139_L006

description: Brain single cell 178


title: plate_060s_C22_S170_L006

description: Brain single cell 170


title: roots-pooled RNA-seq

source_name: roots

value: roots


title: Control 7-weeks DIO-stz Intestine 3

value: Intestine

value: Female

value: Control 7-weeks


title: nodules-pooled RNA-seq

source_name: nodules

value: nodules


title: plate_060s_C23_S178_L006

description: Brain single cell 171

source_name: Brain

value: brain


title: Control 7-weeks DIO-stz Liver 6

value: Liver


title: plate_060s_C7_S50_L006

description: Brain single cell 173

value: adult mice


title: RNA-seq_Lens epithelial cells_rep1

value: Embryonic day 13

value: White leghorn


title: plate_060s_C18_S138_L006

description: Brain single cell 168

value: KO

value: Microglia


title: plate_060s_C21_S162_L006

description: Brain single cell 169


title: pFUS 7-weeks DIO Diet Resistant Brain 2

source_name: DIO Diet Resistant

value: DIO Diet Resistant

value: Brain

value: pFUS 7-weeks


title: pFUS 7-weeks Lean Zucker Intestine 19

source_name: Lean Zucker

value: Lean Zucker

value: Male


title: flower-bud-pooled RNA-seq

source_name: flower

value: flower

value: 20 week days old plant


title: pFUS 7-weeks Lean Zucker Intestine 18

value: Intestine


title: leaf-pooled RNA-seq

source_name: leaf

value: leaf


title: plate_060s_C13_S98_L006

description: Brain single cell 165

value: Macrophages


title: plate_060s_C16_S122_L006

description: Brain single cell 167

value: brain


title: Control 7-weeks Lean Zucker Intestine 15

value: Control 7-weeks


title: pFUS 7-weeks Lean Zucker Intestine 16


title: plate_060s_C15_S114_L006

description: Brain single cell 166

value: adult mice


title: plate_060s_B8_S249_L006

description: Brain single cell 163


title: Control 7-weeks Lean Zucker Intestine 13


title: plate_060s_C11_S82_L006

description: Brain single cell 164


title: HMRS38

city: okayama

first: Shotaro

last: Namba

state: okayama

address: 3-1-1 tsusimanaka

department: Graduate school of environment and life science

country: Japan

institute: Okayama University

data_processing:
Read quality was checked for each sample using FastP(0.20.0)
Alignment was done using Hisat2 (2.2.0) and The data was then formatted by Samtools(1.11).
The expression levels were quantified using String tie.
EdgeR (3.28.1) was used to determine the number of reads with sample-to-sample correction by Spikein.
Genome_build: 1/1/2082
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in liquid culture at 30 ˚C with shaking until OD1.0どじょうけん ばいようされた

extract_protocol:
After RNA extraction by hot phenol method, RNA was purified using Qiagen's RNeasy mini
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: biological replicate

value: MOXop


title: plate_060s_B7_S241_L006

description: Brain single cell 162


title: HMRS36

value: GFPop


title: HMRS35


title: HMRS39


title: Control 7-weeks Lean Zucker Intestine 14


title: HMRS37


title: plate_060s_B6_S233_L006

description: Brain single cell 161

value: KO


title: Control 7-weeks Lean Zucker Intestine 12


title: Control 7-weeks Lean Zucker Intestine 11


title: pFUS 7-weeks Obese ZDF Muscle 8

source_name: Obese ZDF

value: Obese ZDF

value: Muscle


title: plate_060s_B23_S369_L006

description: Brain single cell 158

value: Microglia


title: plate_060s_B24_S377_L006

description: Brain single cell 159


title: HMRS32

value: Vector


title: HMRS31


title: HMRS34


title: pFUS 7-weeks Obese ZDF Intestine 10

value: pFUS 7-weeks


title: pFUS 7-weeks Obese ZDF Intestine 9

value: Male


title: plate_060s_B21_S353_L006

description: Brain single cell 157


title: pFUS 7-weeks Obese ZDF Intestine 7


title: plate_060s_B19_S337_L006

description: Brain single cell 156


title: plate_060s_B14_S297_L006

description: Brain single cell 154


title: plate_060s_B16_S313_L006

description: Brain single cell 155


title: pFUS 7-weeks Obese ZDF Intestine 8


title: C4-2B_Olaparib_rep2

city: Boston

first: Li

last: Jia

state: Massachusetts

address: 20 Shattuck Street, Thorn 1529

department: Surgery

institute: Brigham and Women's Hospital

data_processing:
Raw RNA-seq reads are aligned to version hg19 of human genome by using STAR 2.5.2b
Bam files were sorted using samtool.
Gene counts are quantified by using HT-seq with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Count Matrix Files

source_name: prostate cancer cells

extract_protocol:
Cells were harvested then RNA was extracted using Rneasy mini kit.
Library preparations were conducted by GENEWIZ.

tag: cell line

value: Olaparib


title: LNCaP_Olaparib_rep1

value: LNCaP


title: C4-2B_DMSO_rep2

value: DMSO


title: plate_060s_B1_S193_L006

description: Brain single cell 153


title: pFUS 7-weeks Obese ZDF Muscle 7


title: pFUS 7-weeks Obese ZDF Intestine 6

value: Intestine


title: C4-2B_Olaparib_rep1


title: Control 7-weeks Obese ZDF Intestine 5


title: LNCaP_Olaparib_rep2


title: plate_060s_B3_S209_L006

description: Brain single cell 160


title: Control 7-weeks Obese ZDF Intestine 4


title: HMRS33


title: plate_060s_A5_S33_L006

description: Brain single cell 151

value: Macrophages


title: LNCaP_DMSO_rep1


title: Control 7-weeks Obese ZDF Muscle 3


title: plate_060s_A9_S65_L006

description: Brain single cell 152

value: brain


title: HepG2_siPT_1-3

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
Sequenced reads were mapped to the mouse reference genome sequences (hg19) using TopHat v2.1.1.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
mRNA was extracted from HepG2 with the RNeasy Plus Mini kit (Qiagen). Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: PtenTraf3 knockdown


title: LNCaP_DMSO_rep2


title: Control 7-weeks Obese ZDF Intestine 3

value: Control 7-weeks


title: plate_060s_A3_S17_L006

description: Brain single cell 150

value: adult mice


title: HepG2_siPT_1-2


title: C4-2B_DMSO_rep1


title: plate_060s_A22_S169_L006

description: Brain single cell 149

value: KO


title: Control 7-weeks Obese ZDF Intestine 2

value: Obese ZDF


title: Control 7-weeks Obese ZDF Intestine 1


title: HepG2_siNC-2

value: Wild type


title: plate_060s_A18_S137_L006

description: Brain single cell 148

value: Microglia


title: HepG2_siNC-3


title: plate_060s_A16_S121_L006

description: Brain single cell 146


title: Control 7-weeks Obese ZDF Muscle 2

value: Muscle


title: plate_060s_A13_S97_L006

description: Brain single cell 144


title: RNAseq_mH2A1.1 KD_Rep2

city: TOULOUSE

first: Ludmila

middle: Alexandra

last: Recoules

address: 69 avenue Marianne Grunberg-Manago, 31062 Toulouse Cedex 9, Toulouse

institute: CNRS

data_processing:
Reads qualities were estimated with FastQC (Illumina 1.0.0)
Sequenced reads were aligned to the human hg38 genome using STAR (2.5.1) algorithm with defaults parameters.
Aligned reads were filtered by quality upper to 10
For RNA-seq, Unstranded normalized Bedgraph files were obtained with STAR using Output Wiggle parameters (Options bedgraph, unstranded, RPM), as well as using Bamcompare in DeepTools utilities (3.1.3) (Options : normalization using RPKM, operation subsract, binsize 50 bp and smoothLenght 150 bp). Reads quantification on gene was performed with htseq-count.  FPKM for all genes were calculated. Differential expression analysis was perfomed with DESeq2 package with cutoff |FC| > 1.5 and padj < 0.1.
Genome_build: hg38

source_name: Triple negative breast cancer cells

growth_protocol: MDA-MB231 cells were maintained and amplified in DMEM media supplemented with gentamycin (50µg/ml), fetal bovine serum (10%) and sodium pyruvate (100 mM).

extract_protocol: For RNA-seq, RNA were extracted with RNAeasy midi kit (Quiagen). Library preparation and sequencing was done with the kit TruSeq Stranded total RNA according to mmanufacturer's institutions. Sequencing was done with HiSeq3000-HWI-J00115 according to the manufacturer's protocol.

treatment_protocol: For RNA-seq data, cells were transfected with siRNA against mH2A1.1 during 3 days (with INTERFERINE, 11 nM). For WT condition, cells were transfected without any siRNA.

value: Epithelial cells

value: mammary gland/breast; derived from metastatic site:pleural effusion

tag: genotype/variation

value: mH2A1.1 knockdown


title: plate_060s_A15_S113_L006

description: Brain single cell 145


title: plate_060s_A12_S89_L006

description: Brain single cell 143


title: RNAseq_WT_Rep2

value: wild type


title: plate_059s_K5_S38_L005

description: Brain single cell 142

value: WT


title: plate_059s_K23_S182_L005

description: Brain single cell 141


title: RNAseq_WT_Rep1


title: plate_060s_A17_S129_L006

description: Brain single cell 147


title: Input

data_processing:
Reads qualities were estimated with FastQC (Illumina 1.0.0)
Sequenced reads were aligned to the human hg38 genome using STAR (2.5.1) algorithm with defaults parameters.
Aligned reads were filtered by quality upper to 10
Bigwig files for ChIP-seq were obtained with Bamcompare in DeepTools utilities (3.1.3) (Options : normalization using RPGC, operation subsract, binsize 50 bp and smoothLenght 150 bp). Peaks were determined with NormR package (Option enrichR(), fdr = 0.05, binsize =3000 bp)
Genome_build: hg38

extract_protocol: For ChIP-seq, cells were cross-linked with PAF.  Chromatin was sheared using a Bioruptor (Diagenode)  (30 cycles, 30 sec ON/ 30 sec OFF).  Proteins were immunoprecipited with antibodies. After RNA and protein degradation, DNA was extracted with a phenol-chloroform extraction. Sequencing was done HiSeq3000-HWI-J00115 according to the manufacturer’s protocol.

treatment_protocol: No treatment for ChIP-seq data.


title: ChIP-seq_mH2A1

data_processing:
Reads qualities were estimated with FastQC (Illumina 1.0.0)
Sequenced reads were aligned to the human hg38 genome using STAR (2.5.1) algorithm with defaults parameters.
Aligned reads were filtered by quality upper to 10.
Bigwig files for ChIP-seq were obtained with Bamcompare in DeepTools utilities (3.1.3) (Options : normalization using RPGC, operation subsract, binsize 50 bp and smoothLenght 150 bp). Peaks were determined with NormR package (Option enrichR(), fdr = 0.05, binsize =3000 bp)
Genome_build: hg38

tag: chipseq antibodies

value: Ab37264 (Abcam) (Ab αmH2A1)


title: plate_059s_K16_S126_L005

description: Brain single cell 139

data_processing:
The sequencing reads were first aligned to the mouse reference genome Gencode M26 genome with STAR software.
Genome_build: Gencode M26
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample


title: ChIP-seq_mH2A1.1

value: Custom polyclonal antibody (Ab αmH2A1.1)


title: plate_059s_K18_S142_L005

description: Brain single cell 140

value: brain


title: plate_059s_K15_S118_L005

description: Brain single cell 138

value: Macrophages


title: plate_059s_K12_S94_L005

description: Brain single cell 137


title: plate_059s_J8_S253_L005

description: Brain single cell 136


title: RNAseq_mH2A1.1 KD_Rep1


title: plate_059s_J6_S237_L005

description: Brain single cell 135


title: CD4+CD25+YFP+ Tregs, WTaKG3

city: shang hai

first: Qi

last: Liu

address: 280 S. Chongqing Road

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X ten platform and 125 bp/150 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of four conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: isolated CD4+CD25+YFP+ Treg cells from Foxp3YFP-creTKT+/+  mouse treated with DMαKG by flow cytometry

growth_protocol: All mice were maintained in the animal facility of Shanghai Jiao Tong University School of Medicine under specific pathogen-free conditions

extract_protocol:
Total RNA was isolated from Tregs by Trizol, then used for RNA sequencing analysis by the Illumina HiSeq X Ten platform
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We supplied DMαKG or vehicle into the drinking water from female pregnancy to offspring adulthood.

value: spleen and lymph node

value: post natal 7-week-old

value: DMαKG


title: CD4+CD25+YFP+ Tregs, KOaKG3

institute: Shanghai Jiao Tong University School of Medicine

source_name: isolated CD4+CD25+YFP+ Treg cells from Foxp3YFP-creTKTfl/fl mouse treated with DMαKG  by flow cytometry

value: Treg specific TKT knockout


title: CD4+CD25+YFP+ Tregs, KOaKG2


title: CD4+CD25+YFP+ Tregs, KOaKG1


title: plate_059s_J4_S221_L005

description: Brain single cell 134

extract_protocol:
We used transgenic mouse reporter line (SM22-Cre;Rosa26-stop-tdTomato). We chosed to focus our efforts to adult mice brain cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: adult mice


title: CD4+CD25+YFP+ Tregs, WTaKG2


title: plate_059s_J3_S213_L005

description: Brain single cell 133


title: plate_059s_J23_S373_L005

description: Brain single cell 132


title: CD4+CD25+YFP+ Tregs, WTaKG1


title: plate_059s_J20_S349_L005

description: Brain single cell 131


title: CD4+CD25+YFP+ Tregs, KO3

source_name: isolated CD4+CD25+YFP+ Treg cells from Foxp3YFP-creTKTfl/fl mouse treated with vehicle  by flow cytometry

value: vehicle


title: D14_LG_m_rep1

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

description: Gene expression after 14 days in low glucose

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.).

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array.Array probes that have Flag A in samples were filtered out.

source_name: Dental pulp cells, D14, LG, minus-inducers, replicate1

label_protocol: RNA labeling were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: RNA was extracted using TRIzolTM reagent (Invitrogen, Thermo Fisher scientific, Waltham, MA,USA) according to the manufacturer's instructions. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Human dental pulp cells were cultures under 5.5mM glucose DMEM (Low glucose) and 25mM DMEM (High glucose) supplimented with 10%FBS under odontogenic inducing conditions for 1 and 14 days before RNA was collected.

value: Dental pulp cells


title: D14_HG_p_rep_2

description: Gene expression after 14 days in high glucose supplimented with odontogenic inducers

source_name: Dental pulp cells, D14, HG, plus-inducers, replicate2


title: D14_LG_p_rep_1

description: Gene expression after 14 days in low glucose supplimented with odontogenic inducers

source_name: Dental pulp cells, D14, LG, plus-inducers, replicate1


title: CD4+CD25+YFP+ Tregs, KO2


title: D1_HG_p_rep_2

description: Gene expression after 1 day in high glucose supplimented with odontogenic inducers

source_name: Dental pulp cells, D1, HG, plus-inducers, replicate2


title: D14_HG_p_rep_1

source_name: Dental pulp cells, D14, HG, plus-inducers, replicate1


title: plate_059s_J19_S341_L005

description: Brain single cell 130

value: Microglia


title: D1_LG_p_rep_2

description: Gene expression after 1 day in low glucose supplimented with odontogenic inducers

source_name: Dental pulp cells, D1, LG, plus-inducers, replicate2


title: D14_LG_p_rep_2

source_name: Dental pulp cells, D14, LG, plus-inducers, replicate2


title: D1_HG_p_rep_1

source_name: Dental pulp cells, D1, HG, plus-inducers, replicate1


title: D1_LG_p_rep_1

source_name: Dental pulp cells, D1, LG, plus-inducers, replicate1


title: D1_LG_m_rep_2

description: Gene expression after 1 day in low glucose

source_name: Dental pulp cells, D1, LG, minus-inducers, replicate2


title: CD4+CD25+YFP+ Tregs, KO4


title: D14_LG_m_rep2

source_name: Dental pulp cells, D14, LG, minus-inducers, replicate2


title: D1_LG_m_rep_1

source_name: Dental pulp cells, D1, LG, minus-inducers, replicate1


title: plate_059s_I7_S53_L005

description: Brain single cell 128

source_name: Brain


title: plate_059s_J15_S309_L005

description: Brain single cell 129


title: CD4+CD25+YFP+ Tregs, WT3

source_name: isolated CD4+CD25+YFP+ Treg cells from Foxp3YFP-creTKT+/+  mouse treated with vehicle by flow cytometry


title: plate_059s_I3_S21_L005

description: Brain single cell 126


title: CD4+CD25+YFP+ Tregs, WT2


title: plate_059s_I23_S181_L005

description: Brain single cell 125


title: plate_059s_I6_S45_L005

description: Brain single cell 127


title: 20-A477-03 - C2C12 siSATB2 rep1

city: Ottawa

first: Lynn

last: Megeney

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
HiC data were analyzed with Juicer v1.6
Paired-end reads were aligned to mm10 using bwa mem;
KR normalized .hic matrices were generated using Juicer v1.6.
Genome_build: mm10
Supplementary_files_format_and_content: identified TADs and Loops in bed format

source_name: proliferating C2C12 cells

growth_protocol: Cells of the immortalized mouse cell line, C2C12, were grown on non-collagen coated cell culture plates in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (growth medium).

extract_protocol:
Arima HiC
After the Arima-HiC protocol, Illumina-compatible sequencing libraries were prepared by first shearing purified Arima-HiC proximally ligated DNA and then size-selecting DNA fragments from ~200-600 bp using SPRI beads. The size-selected fragments were then enriched for biotin and converted into Illumina-compatible sequencing libraries using the KAPA Hyper Prep kit (P/N: KK8504). After adapter ligation, DNA was PCR amplified and purified using SPRI beads. The purified DNA underwent standard quality control (qPCR and Bioanalyzer) and was sequenced on the HiSeq X following the manufacturer's protocols.

treatment_protocol: siRNA duplexes were used to suppress Satb2 gene expression in C2C12 cells. C2C12 cells were transfected at 25% confluence with 10 nM siRNA (siSatb2 or siControl) and the Lipofectamine RNAiMAX reagent, as directed by the manufacturer’s protocol (Invitrogen). After an overnight incubation, fresh media was added onto the cells and the cells were re-transfected. This continued until the cells reached 100% confluence, after which differentiation media was added to the cells. Media change and re-transfection occurred every 24 h throughout the indicated time course.

value: Proliferating


title: 20-A477-04 - C2C12 siSATB2 rep2


title: plate_059s_I21_S165_L005

city: Uppsala

first: L.

last: He

institute: Uppsala University

description: Brain single cell 124


title: plate_059s_I18_S141_L005

description: Brain single cell 122


title: 20-A477-01 - C2C12 siControl rep1

value: siControl


title: plate_059s_I19_S149_L005

description: Brain single cell 123


title: cKO2-Treg cells (RNA-seq)

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X ten platform and 125 bp/150 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD4+CD25+YFP+ Treg cells

treatment_protocol: no treatment

value: post natal 7-week- old

value: Mus spleen and lymph node

value: isolated CD4+CD25+YFP+ Treg cells from Foxp3cre/+ TKTfl/fl female mouse by flow cytometery


title: plate_059s_H7_S244_L005

description: Brain single cell 120

value: WT


title: cKO3-Treg cells (RNA-seq)


title: CD4+CD25+YFP+ Tregs, WT4

value: wild type


title: plate_059s_I17_S133_L005

description: Brain single cell 121

value: brain


title: WT3-Treg cells (RNA-seq)

source_name: CD4+CD25+YFP+Treg cells

value: isolated CD4+CD25+YFP+ Treg cells from Foxp3cre/+ female mouse by flow cytometery


title: plate_059s_H23_S372_L005

description: Brain single cell 117

value: Macrophages


title: plate_059s_H5_S228_L005

description: Brain single cell 119


title: cKO1-Treg cells (RNA-seq)


title: plate_059s_H22_S364_L005

description: Brain single cell 116


title: WT1-Treg cells (RNA-seq)


title: WT2-Treg cells (RNA-seq)


title: plate_059s_H4_S220_L005

description: Brain single cell 118


title: S2-1

city: Harbin

first: Huimin

last: Lu

state: Heilongjiang

address: 157 Baojian Road

department: Nutrition and Food Hygiene

institute: Harbin Medical University

description: S vs C_DE_sig

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Genome_build: ensembl mm10
Supplementary_files_format_and_content: text files include FPKM values and rawreads for each Sample

source_name: β-TC6 cells

growth_protocol: β-TC6 cells were cultrured in Dulbecco’s modified Eagle’s medium, supplemented with 15% fetal bovine serum, 50  g/mL streptomycin, 50 IU/mL penicillin (Gibco/Life Technologies), and 1.5 g/L NaHCO3.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen) with rRNA depletion.
1μg total RNA with RIN value above 7 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®).

treatment_protocol: β-TC6 cells were treated with 400 μmol/L stearic or palmitic acid in the presence of 1.3% BSA for 24 h.

value: an insulin-secreting cell line derived from insulinoma in transgenic mice

value: treated with stearic acid for 24 hours


title: S1-1

description: S vs C_DE_sig


title: S3-1

description: S vs C_DE_sig


title: 20-A477-02 - C2C12 siControl rep2


title: plate_059s_H16_S316_L005

address: Dag Hammarskjölds Väg 20

description: Brain single cell 113


title: P3-1

description: P vs C_DE_sig

value: treated with palmitic acid for 24 hours


title: plate_059s_H13_S292_L005

description: Brain single cell 111

value: adult mice


title: plate_059s_H14_S300_L005

description: Brain single cell 112


title: P2-1

description: P vs C_DE_sig


title: plate_059s_H10_S268_L005

description: Brain single cell 109


title: C3-1

value: untreated


title: P1-1

description: P vs C_DE_sig


title: plate_059s_G9_S68_L005

description: Brain single cell 108


title: plate_059s_H11_S276_L005

description: Brain single cell 110


title: plate_059s_G8_S60_L005

description: Brain single cell 107


title: plate_059s_H17_S324_L005

description: Brain single cell 114


title: plate_059s_G19_S148_L005

description: Brain single cell 104


title: plate_059s_G23_S180_L005

description: Brain single cell 105


title: plate_059s_H2_S204_L005

description: Brain single cell 115


title: plate_059s_G5_S36_L005

description: Brain single cell 106


title: plate_059s_G16_S124_L005

description: Brain single cell 102


title: plate_059s_G14_S108_L005

description: Brain single cell 101


title: plate_059s_G12_S92_L005

description: Brain single cell 100


title: plate_059s_F6_S235_L005

description: Brain single cell 97


title: plate_059s_G10_S76_L005

description: Brain single cell 98


title: plate_059s_F5_S227_L005

description: Brain single cell 96


title: 58_HHSEC_HARD_12h_1

city: Rochester

first: Aditya

last: Bhagwate

address: 200 1st Street SW

institute: Mayo Clinic

description:
GeneCount_human.tsv
HHSEC_SOFT_12h_vs_HHSEC_HARD_12h.diff.xls

data_processing:
Reads aligned using Tophat v2.1.0
FeatureCounts used for calculating gene counts
edgeR used for differential expression
Assembly: GRCh38 (hg38) for human; mm10 for mouse
Supplementary files format and content: tsv format containing gene counts

source_name: Cell-Line

growth_protocol: Company derived human hepatic sinusoidal endothelial cells grown in Endothelial Cell Growth Media

extract_protocol:
RNA was extracted according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were plated on gels of stiffness 0.2kPa and 32 kPa

value: Hepatic Sinusoidal Endothelial Cells

value: Plated on Hard gel


title: plate_059s_F22_S363_L005

description: Brain single cell 94


title: 57_HHSEC_SOFT_12h_3

value: Plated on Soft get


title: 60_HHSEC_HARD_12h_3


title: plate_059s_F23_S371_L005

description: Brain single cell 95


title: C2-1


title: 59_HHSEC_HARD_12h_2


title: C1-1


title: 56_HHSEC_SOFT_12h_2


title: plate_059s_F21_S355_L005

description: Brain single cell 93

value: Microglia


title: 54_HHSEC_HARD_6h_3

description:
GeneCount_human.tsv
HHSEC_SOFT_6h_vs_HHSEC_HARD_6h.diff.xls


title: 55_HHSEC_SOFT_12h_1


title: 53_HHSEC_HARD_6h_2


title: 52_HHSEC_HARD_6h_1


title: 51_HHSEC_SOFT_6h_3


title: Adnp_SETDBsh2_UT_R1

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: ChIPseq

data_processing:
Reads were quality filtered according to the illumina pipeline
Single end reads were mapped to the mouse mm10 genome (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html) by exploiting the mapping steps of ShortStack (Johnson et al. 2016).Briefly, ShortStack exploits bowtie to identify all best-matched alignments for each read. It will compute a probability for each alignment to different loci in the genome. To do so the frequency of uniquely aligned reads mapping within the vicinity of multi-mapping reads is used to redistribute multi-mapping reads accordingly.
Mapped reads were filtered in order to remove randomly placed multi-mappers and unmapped reads using SAMtools standard procedure (version 1.9)(Li et al. 2009).
In order to identify high confidence genome wide site of enrichment per antibody we implemented three strategies accordingly to the type of signal distribution evaluated after visual inspection of bigwig tracks on IGV (Robinson et al. 2011):  (i) For narrow TFs-like peaks such as PU.1 and CTCFs we implemented MACS2 version 2.2.6 (Zhang et al. 2008) with parameters “--keep-dup 'all' --call-summits --nomodel --nolambda --extsize 300”. Each ChIP was compared to the input DNA from bone marrow-derived macrophages. A reference set of peaks per antibody was generated by selecting significant peaks in each samples/replicate (qvalue ≤ 10E-5 for CTCF and qvalue ≤ 10E-15 for PU.1) and being consistent between replicates (overlapping area of at least 50% between replicates).  (ii) For H2K27Ac we used peaks identified in ATAC-seq samples (see below) expanding the ATAC peaks by 1.5 kb on both sides.   (iii) For H3K9me3 we exploited SICER v1.1 (Zang et al. 2009) with parameters “mm10 1 250 300 0.80 1000 .01” against the input DNA from macrophages. To increase the signal-to-noise, given the lower and more dispersed signal of H3K9me3 in euchromatic active compartments, we combined the samples by conditions and selected significant blocks with an FDR ≤0.01.
Read counts per samples at the identified loci were retrieved using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013). Sample normalization was achieved by selecting invariant peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Differentially regulated peaks were selected using DESEq2 (R/Bioconductor package version 1.26.0; R version 3.6.2) (Love et al. 2014) after turning off the default normalization DESEq2 applies.
Genome_build: mm10
Supplementary_files_format_and_content: .bw are BigWig normalised files

source_name: mouse bone marrow derived macrophages

extract_protocol:
genomic DNA
ChIP-seq was carried out as previously described (Balestrieri et al. 2018). Briefly, 106 lentiviral-infected BMDM cells (H3K27ac, H3K9me3, PU.1) or 20 x 106 lentiviral-infected BMDM cells (CTCF) were fixed with 1% of formaldehyde (Merck cod. 252549) for 10 min at RT and lysed to prepare nuclear extracts.   40 x 106 lentiviral-infected BMDM cells (2% of formaldehyde fixation) were used for Adnp ChIP-seq. After chromatin shearing by sonication with a Branson Ultrasonics™ Sonifier™, lysates were incubated overnight at 4°C with protein G Dynabeads (Invitrogen, cod.10009D) previously coupled with 1 μg of anti-histone antibody or 10 μg of anti-TF antibody (all the antibodies are listed in the Suppl. Table 9). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Immunoprecipitated chromatin was eluted and cross-link reverted overnight at 65°C. DNA was purified with QIAquick PCR Purification Kit (QIAGEN) and then quantified with QuantiFluor (Promega). DNA libraries were prepared for NextSeq500 sequencing as described (Austenaa et al. 2021). The purified DNA libraries were quantified with the Quantifluor reagent (Cod.E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the High Sensitivity Assay HD5000 (Agilent cod.5067-5592). Library DNA were diluted to a working concentration of 4 nM and Single Reads (76bp) sequenced on an Illumina NextSeq500 platform.

treatment_protocol: LPS (10 ng/ml) treatment for 2h

value: BMDM

value: UNTREATED_SETDB1 knock down

tag: antibody


title: 50_HHSEC_SOFT_6h_2


title: Adnp_SETDBsh1_UT_R1

description: ChIPseq


title: plate_059s_F11_S275_L005

description: Brain single cell 90


title: plate_059s_F10_S267_L005

description: Brain single cell 89


title: Adnp_NTsh2_UT_R1

description: ChIPseq


title: 49_HHSEC_SOFT_6h_1


title: plate_059s_F1_S195_L005

description: Brain single cell 88


title: Adnp_NTsh1_UT_R1

description: ChIPseq


title: Promoter Capture HiC Run 2 mH2A1.1 KD

data_processing:
Library strategy: PCHi-C
For PCHi-C, Reads were aligned to the hg38 genome assembly using Bowtie, then paired, mapped to restriction fragment space and filtered for PCR duplicates and other Hi-C artefacts, essentially as HiCUP (Wingett et al., 2015).  ChiCMaxima_calling was done using the same default parameters and merging of replicate results as in Ben Zouari et al.,(2019) after processing the fastq files with custom scripts, essentially performing the same analysis as HiCUP (Wingett et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: ibed

source_name: Triple negative breast cancer cells

extract_protocol: PCHi-C was essentially performed as in (Schoenfelder et al., 2018), using nearly the same promoter library as (Mifsud et al., 2015)  (omitting probes from chromosomes 8, 9 and X).

treatment_protocol: Cells were transfected with siRNA against mH2A1.1 during 3 days (with INTERFERINE, 11 nM). For WT condition, cells were transfected without any siRNA.

value: mammary gland/breast; derived from metastatic site:pleural effusion

value: Epithelial cells


title: plate_059s_E7_S51_L005

description: Brain single cell 87

value: WT


title: plate_059s_F18_S331_L005

description: Brain single cell 92

value: brain


title: plate_059s_F16_S315_L005

description: Brain single cell 91


title: Promoter Capture HiC Run 1 WT

data_processing:
For PCHi-C, Reads were aligned to the hg38 genome assembly using Bowtie, then paired, mapped to restriction fragment space and filtered for PCR duplicates and other Hi-C artefacts, essentially as HiCUP (Wingett et al., 2015).  ChiCMaxima_calling was done using the same default parameters and merging of replicate results as in Ben Zouari et al.,(2019) after processing the fastq files with custom scripts, essentially performing the same analysis as HiCUP (Wingett et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: ibed


title: plate_059s_E24_S187_L005

description: Brain single cell 84


title: BSA1

city: Bunkyo-ku

first: Masanori

last: Itakura

state: Tokyo

address: 1-1-1 Yayoi

institute: The University of Tokyo

data_processing:
Trimmed reads are mapped to reference genome (mm10) with HISAT2.
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (DHA-BSA_vs_BSA) as requested using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: data2.xlsx: Matrix table with raw gene counts and normalized abundance measurements for every gene and every sample.

source_name: Macrophages

extract_protocol:
Peritoneal macrophages were isolated, flash frozen on dry ice, and RNA was harvested using FastGene RNA Basic Kit (NIPPON Genetics). Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Peritoneal macrophages

value: BSA


title: plate_059s_E3_S19_L005

description: Brain single cell 85


title: AGEs1

value: AGEs


title: plate_059s_E22_S171_L005

description: Brain single cell 83

value: Macrophages


title: Hippocampus_nucleus_mTLE non-HS5 [Hip_nuc_E14-07]

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

description: mTLE non-HS

data_processing:
mRNAs:
For analyzing mRNAs, following trimming of low-quality bases and adapter sequences with FASTQ-MCF (version 0.0.13), processed reads were mapped to the hg19/GCh37 reference human genome (iGenomes) with TopHat2 (version 2.0.13) (Kim et al., 2013. Genome Biology). For the alignments of the total RNA-seq data, the ‘fr-secondstrand’ option was chosen. Mapped counts for each gene were summarised using the python script htseq-count (Anders et al., 2015. Bioinformatics).
For differential expression analysis, genes and transcripts count data was analysed for differential expression in R using the Bioconductor package EdgeR version 3.12.1 (Robinson et al., 2010. Bioinformatics) with the trimmed mean of M-values (TMM) normalisation method (Robinson and Oshlack., 2010. Genome Biology). Gene expression levels were corrected for batch and gender effects by including the series of sequencing rounds, sexes of controls and patients to a generalised linear model. Using the Benjamini-Hochberg false discovery rate (FDR) adjusted P-values for multiple testing were calculated and only genes with an FDR < 0.05 were considered significantly differentially expressed (DE). Visualisation of data was performed in R using the ggplot2 library (version 2.1.0).
circRNAs:
For analyzing circularRNAs (circRNA), sequencing data were preprocessed by removing adapter sequences and trimming away low quality bases (Phred score 20) with Trim Galore which uses the Cutadapt algorithm (Martin, 2011. EMBnet.journal). CircRNA detection was performed by mapping filtered reads to the human genome (hg19) with Bowtie (Langmead et al., 2009. Genome Biology), using find_circ (Memczak et al., 2013. Nature) to detect back-splice junction (BSJ) spanning reads from the reads that do not map linearly to the human genome. Only circRNAs with two or more supporting BSJ reads within single samples were kept. A second circRNA detection algorithm, CIRCexplorer (Zhang et al., 2014. Cell), was used to verify the detected circRNAs. CIRCexplorer was guided by Ensembl Release 71 gene annotations on human genome (hg19).
Differential expression analysis was done using DESeq2 (Love et al., 2014. Genome Biology) in R. Raw counts of BSJ read numbers detected by find_circ were used as input for DESeq2. Statistical metrics produced by DESeq2 including probability value (p-value, p) and Benjamini-Hochberg adjusted p-values are reported with the normalized BSJ expression values generated by DESeq2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: guide_*txt: ordered IDs; Abundance measurements or Significant genes

source_name: Hippocampus

extract_protocol:
Complete details can be found on manuscripts methods section. Briefly, subcellular fractionation was performed isolating pure cytosolic and nuclei cell compartments. Isolated cytoplasmic and nuclei samples were stored in Qiazol (Qiagen) at -80oC until RNA extraction was performed. Total RNA was extracted using miRNeasy kit (Qiagen), according to manufacturer’s protocol.
A total of 2 ug of RNA per sample in a 5 ul volume was rRNA-depleted using the Ribo-Zero Magnetic Kit (human/mouse/rat; Illumina) before library preparation. Stranded, paired-end sequencing libraries were prepared using the ScriptSeq v2 (Epicentre), after which samples were subjected to quality control on the 2100 Bioanalyzer (Agilent). Sequencing was performed as paired end 100 bp reads on an Illumina HiSeq 4000 sequencer at the Beijing Genomics Institute (BGI) (Hongkong, China).

tag: fraction

value: Nucleus

tag: sample type

value: mTLE non-HS

value: Hippocampus


title: Promoter Capture HiC Run 2 WT

tag: cell type


title: HIC_SETDB1sh1_UT

data_processing:
Reads were quality filtered according to the illumina pipeline
In-situ HiC pair end reads were analyzed using HiC-pro (Servant et al. 2015) version 3.0.0 with parameters “--very-sensitive -L 25 --score-min L,-0.6,-0.2 --end-to-end –reorder” for both local and global alignment.
Unique and valid pairs were kept and contact maps generated at 10, 20 and 40kb resolutions.
Individual contact matrixes have been normalized using the iterative correction normalization (ICE) method provided by HiC-pro and previously presented by Imakaev and colleagues (Imakaev et al. 2012).
Genome_build: mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline.

extract_protocol: 5x106 BMDM cells were detached from a 10 cm plate using Versene® (EDTA), 0.02% (Lonza  cod. BE17-711E), washed twice with ice-cold PBS and fixed with 1% of methanol-free formaldehyde (Thermofisher cod. 28906) at RT for 15 min. For efficient quenching of the formaldehyde, glycine (0.125M) was added to the single cell suspension for 5 min at RT. After two washes with PBS, cells were lysed in 500 μL of freshly prepared ice-cold lysis buffer supplemented with protease inhibitors (10 mM Tris-HCl pH8.0; 10 mM NaCl; 0.2% NP40; 1X Protease inhibitors (Roche cod.11873580001) and incubated on ice for 20 minutes. The integrity of the nuclei was checked under the microscope.  After centrifugation, nuclei were washed once with 1X NEBuffer2 (NEB cod. B7002S) and the pellet was resuspended with 200 μL of 1X NEBuffer2 containing 10 μL of 10% SDS (final concentration 0.5%) and incubated at 37°C for 60 min, shaking at 900 rpm. The nuclei membrane permeabilization was then quenched by adding 400 μL of 1X NEBuffer2 and then 120 μL of 10% Triton X-100. Nuclei were washed once and then gently resuspended in 300 μl of 1XNEBuffer2. To digest the chromatin, 400 U of MboI (NEB cod. BA0147M) were added and the incubation was left at 37°C overnight, 700 rpm. A second round of digestion was performed, adding 200 U of MboI for 120 min. MboI inactivation was performed at 65°C for 15 min.   To biotinylate the free chromatin ends, the following mix was added: 1.5 μL of 10 mM dCTP, 1.5 μL of 10mM dGTP; 1.5 μL of 10 mM dTTP; 37.5 μL of 0.4 mM Biotin-11-dATP; 1 μL of 50U/μL DNA Polymerase I Large (Klenow) fragment (NEB cod. M0210M), and incubated for 45 min at 37°C, 750 rpm. After enzyme inactivation at 65 °C and centrifugation at 3,000 rpm, free chromatin ends were ligated in a total volume of 1200 μl by adding T4 DNA Ligase buffer (NEB cod. B0202S) (1x final), 10% Triton (0.8% final), 120 μg BSA, 2000 U ligase (NEB cod.M0202S) at 16oC overnight. Following the incubation, nuclei were pelleted at 3,000 rpm for 5 min and resuspend in 200 μL of 1X NEBuffer2. RNA and Proteins were digested upon addition first of 5 μl RNAse A for 15 minutes at 37oC and then of 400 μg Proteinase K for 30 min at 55 °C. The chromatin was then reverse crosslinked at 65°C overnight. The next day, DNA was purified with Phenol/Chloroform/Isoamyl Alcohol and precipitated by adding 3M NaAc pH 5.2 and EtOH 100%. DNA was sheared on the Diagenode Bioruptor Pico and size controlled on a Tapestation (Agilent). DNA fragments were in the range of 200-300 bp. Ligated and biotinylated fragments were enriched through biotin pulldown using Magnetic Streptavidin T1 beads (Thermofisher cod.65601). End-repair, A-tailing and ligation of the adapters were performed on beads and streptavidin beads containing the biotinylated DNA fragments were used as template for the PCR amplification step, following the NEB Next Ultra protocol (NEB cod. E7370S). The HiC library was then purified with 1.8× Agencourt Ampure Xp beads and quality controlled on a Tapestation. The HiC library was sequenced on an Illumina NovaSeq Platform, 100 cycles, paired-end reads (2x51 bp).

value: SETDB1 sh1


title: Hippocampus_nucleus_mTLE non-HS4 [Hip_nuc_E13-12]

description: mTLE non-HS


title: Hippocampus_nucleus_mTLE non-HS3 [Hip_nuc_E05-33]

description: mTLE non-HS


title: AGEs2

tag: strain


title: BSA2


title: plate_059s_E16_S123_L005

description: Brain single cell 81

tag: tissue

value: adult mice


title: plate_059s_E13_S99_L005

description: Brain single cell 80

tag: age


title: plate_059s_E2_S11_L005

description: Brain single cell 82

tag: notch3 genotype


title: HIC_NTsh1_UT

value: NT sh1


title: Hippocampus_nucleus_mTLE non-HS2 [Hip_nuc_E05-35]

description: mTLE non-HS


title: Hippocmapus_nucleus_mTLE non-HS1 [Hip_nuc_E06-13]

description: mTLE non-HS


title: plate_059s_G17_S132_L005

description: Brain single cell 103

tag: celltype

value: Microglia


title: WT_rep3

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

institute: Karolinska institute

data_processing:
Reads mapping and gene expression quantification:Sequencing data were aligned and quantified by using the Cell Ranger Pipeline v6.0.2 (10x Genomics) with the default setting against the mm10 reference genome (v.2020-, downloaded from the 10X Genomics website).
Quality control and normalization: We used 3 parameters to assess the quality of our cells. First, cut-off based on the number of expressed genes (nGene) and the expression level of mitochondrial genes (percent.mito) were used to filter out the low-quality cells. In detail, cells with percent.mito less than 0.15 and 1500 < nGene < 6000 were retained. In addition, Cells with more than 5% of total reads mapped to Rn45s repeat are likely contaminated or dead cells, as such, those cells were further removed from our analysis. Following the selection of high-quality cells, we then further filtered based on genes. Genes were considered truly expressed if they contained one or more counts in at least five cells (assessed for each sample separately). Log-normalized counts were calculated using the deconvolution strategy implemented by the computeSumFactors function in scran package (v.1.14.6). We then performed rescaled normalization using the multiBatchNormfunction in the batchelor package (v.1.2.4) so that the size factors were comparable across samples. The log-normalized expression after rescaling was used in marker gene detection and differential gene expression analysis.
Data integration, dimensionality reduction and clustering: We integrated the filtered count matrices from the wildtype and knockout samples using the sctransform approach implemented in Seurat package on the 3000 anchor features. After integration, principal component analysis (PCA) was performed on the integrated data followed by embedding into low dimensional space with Uniform Manifold Approximation and Projection (UMAP) based on the top 30 dimensions. Formed clusters generated by FindClusters function from Seurat package were assigned to cell types by consulting the expression of known marker genes and automatic annotation from SingleR package (v1.4.1). To obtain the different types of endocrine cells present, cells from the endocrine cluster were further extracted and integrated based on 2000 anchor features and top 30 dimensions. In addition, scRNA-sequencing data of human pancreatic islets was integrated using the same parameters as above, with our dataset to further confirm the cell identities. Ortholog genes with the same gene symbols according to Ensemble annotation were used for the integration.
Genome_build: mm10
Supplementary_files_format_and_content: results from cellranger

source_name: Islet from WT mice at 12-14 weeks

growth_protocol: β-cell-specific 14-3-3ζ knockout mice on a C57/BL6 background and 14-3-3ζTAP transgenic mice on a CD1 background were housed on a 12-h light/dark cycle with free access to water and standard diet (15% fat by energy).

extract_protocol:
Isolated mouse islets were dispersed in trypsin (0.05%) for 5 minutes at 37⁰C. To image proliferative β-cells, dispersed islets were seeded in chamber slides (ThermoFisher Scientific) coated with poly-D-lysine hydrobromide (Sigma-Aldrich), and cells were cultured in RPMI1640 medium containing 11 mM glucose with 10% FBS for 72 h in the presence of 10μM of BVO2, 14-3-3i and harmine (Sigma-Aldrich). Media were changed every 24 h. After successive washes with PBS, cells were fixed with 4% paraformaldehyde, followed by co-immunostaining for insulin (ab63820;1:50 dilution; Abcam) and the proliferative markers Ki67, (ab15580; 1:300; Abcam).
Single-cell RNA-seq libraries were made with the 10x Genomics Chromium Next GEM Single Cell 3' Library Kit (v3.1) and sequenced using an Illumina NovaSeq6000 (100bp x2, 50k reads/cell). Approximately 9600 cells were loaded per sample with an anticipated recovery of 6000 cells.

treatment_protocol: β-cell-specific 14-3-3ζ knockout mice (β14-3-3ζKO) were generated by breeding Ins1-CreThor mice with mice harboring alleles with LoxP sites flanking exon 4 of Ywhaz.

value: Islet

value: 12-14 weeks

value: wild type


title: Promoter Capture HiC Run 1 mH2A1.1 KD

value: mammary gland/breast; derived from metastatic site:pleural effusion

value: Epithelial cells


title: Hippocampus_nucleus_control9 [Hip_nuc_S06-062]

description: Control

value: Postmortem controls


title: plate_059s_E6_S43_L005

description: Brain single cell 86

value: brain

value: WT


title: plate_059s_G11_S84_L005

description: Brain single cell 99


title: HIC_SETDB1sh2_UT

value: BMDM

value: SETDB1 sh2


title: WT_rep2


title: plate_059s_E1_S3_L005

description: Brain single cell 78


title: Hippocampus_nucleus_control3 [Hip_nuc_C05-93]

description: Control

value: Nucleus


title: HIC_NTsh2_UT

value: NT sh2


title: Hippocampus_nucleus_control8 [Hip_nuc_S09-007]

description: Control

value: Hippocampus


title: plate_059s_D5_S226_L005

description: Brain single cell 77

value: Macrophages


title: WT_rep1


title: KO_rep3

source_name: Islet from beta14-3-3 KO mice at 12-14 weeks

value: beta14-3-3 knock out


title: plate_059s_E12_S91_L005

description: Brain single cell 79

value: adult mice


title: Hippocampus_nucleus_control2 [Hip_nuc_C04-05]

description: Control


title: Hippocampus_cytoplasm_mTLE non-HS5 [Hip_cyt_E14-07]

description: mTLE non-HS

value: Cytoplasm

value: mTLE non-HS


title: plate_059s_D20_S346_L005

description: Brain single cell 74

value: Microglia


title: KO_rep2

value: Islet

value: 12-14 weeks


title: plate_059s_D19_S338_L005

description: Brain single cell 73


title: KO_rep1


title: plate_059s_D14_S298_L005

description: Brain single cell 72


title: plate_059s_D23_S370_L005

description: Brain single cell 75


title: Hippocampus_cytoplasm_mTLE non-HS4 [Hip_cyt_E13-12]

description: mTLE non-HS


title: Hippocampus_nucleus_control1 [Hip_nuc_C02-05]

description: Control


title: Typ2-S-3

city: Chicago

first: Harrison

middle: Shea

last: Greenbaum

state: Illinois

address: GCIS W325, 929 E. 57th Street

institute: Ben May Department for Cancer Research

description: BaF3 cell line with plasmid overexpression

data_processing:
The libraries were sequenced by a Novaseq 6000 in two runs to generate paired-end 100bp reads. For each sample, the raw FASTQ files from two flow cells were combined before downstream processing.
RNA-seq data were analyzed using a local Galaxy  20.05 instance. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3.
The reads were mapped to the mouse genome (GRCm38.p4 with GENCODE annotation) using RNA STAR  2.7.5b.
The resulting mapped reads from each sample were counted by featureCounts  1.6.4 for per gene read counts.
The raw counts were analyzed for differential expression between experimental conditions using DESeq2  1.22.1 .
Genome_build: Mouse (GRCm38.p4)
Supplementary_files_format_and_content: Comma delimited text file containing a matrix table with raw gene counts for every gene and every sample

source_name: CALR type 2 mutation starved rep 3

growth_protocol: BaF3 cells were maintained in 10% FBS RPMI media in 5% CO2.

extract_protocol:
Total RNA extraction by the Rneasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

treatment_protocol: Cells were washed three times with PBS followed by media replacement using growth media with or without IL3 addition. In unstarved conditions, cells were supplied with the cytokine IL3 at a 1:10,000 dilution for a final concentration of 2 ng/mL; in starved conditions, cells were depleted of the IL3 cytokine addition for twenty-four hours.

tag: overexpression

value: Thrombopoietin receptor and Type 2 mutant CALR

value: No IL3


title: Hippocampus_cytoplasm_mTLE non-HS3 [Hip_cyt_E05-33]

description: mTLE non-HS


title: plate_059s_C7_S50_L005

description: Brain single cell 71

value: brain


title: VF-S

source_name: JAK2 with V617F mutation starved

value: Thrombopoietin receptor and JAK2 with the V617F mutation


title: Hippocampus_cytoplasm_mTLE non-HS2 [Hip_cyt_E05-35]

description: mTLE non-HS


title: WT-S-3

source_name: CALR wild-type starved rep 3

value: Thrombopoietin receptor and wild-type CALR


title: plate_059s_C6_S42_L005

description: Brain single cell 70

value: WT


title: plate_059s_C3_S18_L005

description: Brain single cell 69


title: Hippocmapus_cytoplasm_mTLE non-HS1 [Hip_cyt_E06-13]

description: mTLE non-HS


title: plate_059s_D4_S218_L005

description: Brain single cell 76


title: Hippocampus_cytoplasm_control9 [Hip_cyt_S06-062]

description: Control

value: Postmortem controls


title: VF-U

source_name: JAK2 with V617F mutation unstarved

value: IL3 (2 ng/mL)


title: plate_059s_C24_S186_L005

description: Brain single cell 68

source_name: Brain


title: Typ2-US-3

source_name: CALR type 2 mutation unstarved rep 3


title: Hippocampus_cytoplasm_control8 [Hip_cyt_S09-007]

description: Control

value: Hippocampus


title: plate_059s_C22_S170_L005

description: Brain single cell 66

value: Macrophages


title: WT-US-3

source_name: CALR wild-type unstarved rep 3


title: Hippocampus_cytoplasm_control2 [Hip_cyt_C04-05]

description: Control


title: Typ1-US-3

source_name: CALR type 1 mutation unstarved rep 3

value: Thrombopoietin receptor and Type 1 mutant CALR


title: Hippocampus_cytoplasm_control3 [Hip_cyt_C05-93]

description: Control


title: Typ2-S-2

source_name: CALR type 2 mutation starved rep 2


title: Hippocampus_cytoplasm_control1 [Hip_cyt_C02-05]

description: Control


title: plate_059s_C19_S146_L005

description: Brain single cell 64

value: adult mice


title: plate_059s_C2_S10_L005

description: Brain single cell 65


title: WT-S-2

source_name: CALR wild-type starved rep 2


title: Typ1-S-3

source_name: CALR type 1 mutation starved rep 3


title: Typ2-S-1

source_name: CALR type 2 mutation starved rep 1


title: Cortex_nucleus_mTLE non-HS16_pre [Cx_nuc_E15-07-Pre]

description: mTLE non-HS

source_name: Cortex

value: Nucleus

value: Cortex


title: plate_059s_C17_S130_L005

description: Brain single cell 63

value: Microglia


title: plate_059s_B8_S249_L005

description: Brain single cell 61


title: Cortex_nucleus_mTLE non-HS16_post [Cx_nuc_E15-07-Post]

description: mTLE non-HS

value: mTLE non-HS


title: Typ1-S-1

source_name: CALR type 1 mutation starved rep 1


title: plate_059s_B24_S377_L005

description: Brain single cell 60


title: Cortex_nucleus_mTLE non-HS15_pre [Cx_nuc_E15-06-Pre]

description: mTLE non-HS


title: plate_059s_B2_S201_L005

description: Brain single cell 59


title: plate_059s_C23_S178_L005

description: Brain single cell 67


title: Typ2-US-2

source_name: CALR type 2 mutation unstarved rep 2


title: Typ1-US-2

source_name: CALR type 1 mutation unstarved rep 2


title: Cortex_nucleus_mTLE non-HS15_post [Cx_nuc_E15-06-Post]

description: mTLE non-HS


title: plate_059s_B15_S305_L005

description: Brain single cell 58


title: Typ1-S-2

source_name: CALR type 1 mutation starved rep 2


title: Cortex_nucleus_mTLE+HS14 [Cx_nuc_E11-17]

description: mTLE+HS

value: mTLE+HS


title: Cortex_nucleus_mTLE+HS13 [Cx_nuc_E07-28]

description: mTLE+HS


title: WT-US-2

source_name: CALR wild-type unstarved rep 2


title: Cortex_nucleus_mTLE+HS12 [Cx_nuc_E06-19]

description: mTLE+HS


title: plate_059s_B10_S265_L005

description: Brain single cell 57


title: Cortex_nucleus_mTLE non-HS17_pre [Cx_nuc_015-02-Pre]

description: mTLE non-HS


title: Typ1-US-1

source_name: CALR type 1 mutation unstarved rep 1


title: Cortex_nucleus_mTLE non-HS17_post [Cx_nuc_015-02-Post]

description: mTLE non-HS


title: Cortex_nucleus_mTLE+HS11 [Cx_nuc_E08-17]

description: mTLE+HS


title: plate_059s_C1_S2_L005

description: Brain single cell 62


title: plate_059s_A4_S25_L005

description: Brain single cell 55


title: plate_059s_A17_S129_L005

description: Brain single cell 53


title: WT-S-1

source_name: CALR wild-type starved rep 1


title: plate_059s_A21_S161_L005

description: Brain single cell 54


title: Cortex_nucleus_mTLE+HS10 [Cx_nuc_E06-21]

description: mTLE+HS


title: WT-US-1

source_name: CALR wild-type unstarved rep 1


title: plate_059s_A10_S73_L005

description: Brain single cell 51

source_name: Brain


title: Cortex_nucleus_mTLE+HS9 [Cx_nuc_E05-03]

description: mTLE+HS


title: Cortex_nucleus_mTLE non-HS8 [Cx_nuc_E11-18]

description: mTLE non-HS


title: plate_059s_A11_S81_L005

description: Brain single cell 52