title: 205332910124_R07C01 Case

description: Case

source_name: nasal epithelium, 680602


title: 205332910173_R08C01 Control

status: Public on Dec 23 2023

type: genomic

city: Baltimore

first: Rasika

middle: M

last: Mathias

state: MD

address: 5501 Bayview Cir

department: Allergy and Clinical Immunology

country: USA

institute: Johns Hopkins University

description: Control

hyb_protocol: bisulphite conversion was performed using the EZ DNA Methylation kit (Zymo Research)

scan_protocol: DNA methylation quantification was performed using Illumina Infinium protocol

data_processing:
minfi R-package
Final_methylation_matrix_processed.txt (Average Beta)
Final_methylation_signals.txt (Unmethylated and methylated signal intensities)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: nasal epithelium, 918819

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from nasal airway epithelial cells

tag: tissue

value: nasal epithelium

tag: site

value: Denver

tag: age

tag: Sex

value: Male

tag: plate number

tag: ancestry pc1

tag: ancestry pc2

tag: asthma

value: Control


title: 205332910021_R08C01 Case

description: Case

source_name: nasal epithelium, 760228

value: Female

value: Case


title: 205332910138_R02C01 Control

description: Control

source_name: nasal epithelium, 656722


title: Eomes-GFP+ CD4 T cells (replicat 1) [CnR]

type: SRA

city: Toulouse

first: Anne

middle: S

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

library_source: genomic

data_processing:
Adapter trimming and quality controls were performed using Trimgalore v0.6.5. and FastQC v0.11.7.
Reads were aligned to the mm10 reference genome by using Bowtie2 v2.2.9. with the splicing alignment feature switched off.
Assembly: mm10 reference genome
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

organism: Mus musculus

source_name: CD4 T cells

growth_protocol: Naive CD4+ T cells were isolated from spleen and lymph nodes by negative selection using the « Naive CD4 T Cell Isolation Kit » according to the manufacturer’s instructions (Miltenyi Biotec, Cat: 130-104-453). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 50 μM β-mercaptoethanol in 96 well plates at a seeding concentration of 2x105 cells per well. Polyclonal naïve CD4+ T cells were stimulated with 2 ug/mL anti-CD3 antibody (Biolegend) and 1 ug/mL anti-CD28 (BD Biosciences) under non-polarizing conditions.

extract_protocol:
CUT&RUN was performed as previously described (Krzywinska et al., 2022) with some modifications. Briefly, 50,000 cells were harvested and processed with the CUT&RUN (Cleavage Under Targets & Release Using Nuclease) Assay Kit (86652; Cell Signaling Technology) following the supplier’s instructions. Eomes monoclonal antibody (Dan11mag, Thermofisher, 14-4875-82) was used at 2 µg. DNA was purified using the QIAGEN MinElute kit (QIAGEN) and its quality was assessed on a 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries have been prepared according to Active Motif's protocol with some adjustments, using the Next Gen DNA Library Kit (Active Motif, Carlsbad, USA), assuming a starting input of 100 pg of dsDNA. Briefly, DNA first underwent a 2-phases reparation. Then, Illumina compatible adaptors were ligated, allowing the barcoding of the samples with single indices, and the addition of molecular identifiers (MIDs) composed of 9-bases random sequence. These MIDs will enable to distinguish PCR duplicates from fragmentation duplicates, and the removal of true PCR duplicates from the subsequent sequencing analysis. The libraries were then amplified using 15 cycles of PCR, and an additional 2-sides purification step was finally performed, allowing to obtain 250-1000 pb fragments.

tag: cell type

value: CD4 T cells

tag: genotype

value: Eomes-Ires-GFP


title: Eomes-KO CD4 T cells (replicat 1) [CnR]


title: 205332910118_R01C01 Case

description: Case

source_name: nasal epithelium, 971303


title: 205332910161_R05C01 Case

description: Case

source_name: nasal epithelium, 757465


title: 205332910146_R01C01 Control

description: Control

source_name: nasal epithelium, 574555


title: Eomes-GFP+ CD4 T cells (replicat 2) [CnR]


title: B6xBXD65 cross, 14 mo, 5XFAD/Ntg

city: Bar Harbor

first: Maria

middle: A

last: Telpoukhovskaia

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina base call files for all libraries were demultiplexed and converted to FASTQ files using Illumina bcl2fastq 2.20.0.422. A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 3.0.0, GRCm38.93 including introns for pre-mRNA mapping) using 10X Genomics CellRanger count version 3.1.0 for all samples.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: frontal cortex

extract_protocol:
Nuclei were isolated from snap-frozen frontal cortex (anterior to the anterior forceps of the corpus callosum) samples from one hemisphere using Nuclei Isolation Kit: Nuclei EZ Prep (Sigma-Aldrich Cat. No. NUC-101). Briefly, 50 µl of EZ Lysis Buffer and RNase inhibitor (1000 units/mL; Protector RNase Inhibitor, MilliporeSigma Cat. No. 03335399001, 2000 U, 40 U/µL) were added to 1.5 mL DNA LoBind tubes (Eppendorf Cat. No. 022431021) containing brain tissue. Tissue was ground with Bel-Art Disposable Pestle (Sigma Aldrich Cat. No. BAF199230000). The tissue was washed off from the pestle with 25 µl of Lysis Buffer, and the tube was placed on ice for 5 minutes. The sample was centrifuged at 500xg for 5 minutes at 4 °C. Supernatant was removed and the pellet was resuspended in 50 µL of Lysis Buffer using a wide bore tip. The sample was placed on ice for 5 minutes, after which 50 µl of PBS containing 0.04% BSA (from LAMPIRE Biological Laboratories Cell Culture Grade 35% BSA Liquid (Fisher Scientific Cat. No. 50-414-159) and RNase inhibitor (40 units/mL) were added. The sample was centrifuged for 5 minutes at 4 °C at 500xg. Thereafter, the sample was resuspended in 100 µl of PBS containing 0.04 % BSA and RNase inhibitor and pushed through a pre-wet 40 µm filter (PluriStrainer Mini 40 µm Cell Strainer (Pluri Select Cat. No. 43-10040-60)). The sample was centrifuged for 5 minutes at 4 °C at 500xg, and resuspended in 100 µl of PBS containing 0.04% BSA and RNase inhibitor, then pushed through a pre-wet 5 µm filter (PluriStrainer Mini 5 µm Cell Strainer (Pluri Select Cat. No. 43-10005-60)). After a final centrifugation step at 500xg for 5 minutes at 4 °C, the sample was resuspended in 1000 µL of PBS containing 0.04% BSA and RNase inhibitor and immediately processed as follows.
Nuclei quality was assessed via brightfield imaging and counted via Trypan Blue and a Countess II automated cell counter (ThermoFisher), and up to 12,000 nuclei were loaded onto one lane of a 10X Chromium Controller. Single nuclei capture, barcoding and library preparation were performed using the 10X Chromium platform version 3 chemistry and according to the manufacturer’s protocol (#CG00052). cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and pooled at 33.33% of an Illumina NovaSeq 6000 S2 flow cell lane, targeting 6,000 barcoded nuclei with an average sequencing depth of 100,000 reads per nuclei.
snRNA-seq

value: frontal cortex

value: female

tag: strain

value: 14 months


title: B6xBXD33 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics

value: Ntg


title: B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mm cross, 14 mo, B6-5XFAD

description: 10x Genomics


title: 205332910085_R01C01 Case

description: Case

source_name: nasal epithelium, 427020


title: B6xBXD161 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910124_R06C01 Case

description: Case

source_name: nasal epithelium, 330031


title: B6xBXD161 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics

value: 6 months


title: click response-treated c57b6l mice,repeated1

city: Shanghai

first: fei

last: sun

state: Shanghai

address: Laboratory of Biotechnology, School of Life Science, Baoshan Campus, Shanghai University, Dachang Town, Baoshan District, Shanghai

country: China

institute: Shanghai University

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequences reads were mapped to mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchworl
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: muscle

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1 µg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

value: muscle

tag: agent

value: click

value: WT


title: 205332910144_R08C01 NA

source_name: nasal epithelium, 861237


title: B6xBXD53 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6xBXD53 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: 205310780026_R06C01 Case

description: Case

source_name: nasal epithelium, 225875


title: 205332910090_R01C01 Case

description: Case

source_name: nasal epithelium, 167158


title: 205332910184_R04C01 Case

description: Case

source_name: nasal epithelium, 222032


title: 205310780003_R05C01 Case

description: Case

source_name: nasal epithelium, 282160


title: B6xBXD65 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: 205332910082_R02C01 Case

description: Case

source_name: nasal epithelium, 747625


title: B6xBXD66 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xD2Gpnmb cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mm cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD99 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910171_R03C01 Case

description: Case

source_name: nasal epithelium, 232787


title: 205332910085_R02C01 Control

description: Control

source_name: nasal epithelium, 397600


title: 205332910109_R05C01 Case

description: Case

source_name: nasal epithelium, 100837


title: 205310780043_R04C01 Case

description: Case

source_name: nasal epithelium, 161192


title: B6xBXD99 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD50 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910082_R03C01 Control

description: Control

source_name: nasal epithelium, 114480


title: 205332910115_R08C01 NA

source_name: nasal epithelium, 632087


title: 205310780049_R04C01 Case

description: Case

source_name: nasal epithelium, 577298


title: B6xBXD39 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics

source_name: frontal cortex


title: B6xBXD50 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD28 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mm cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD39 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910017_R01C01 Case

description: Case

source_name: nasal epithelium, 335973


title: 205332910087_R01C01 Case

description: Case

source_name: nasal epithelium, 376479


title: B6xBXD33 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6xBXD28 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: 205332910039_R03C01 Case

description: Case

source_name: nasal epithelium, 177746


title: 205332910123_R01C01 Case

description: Case

source_name: nasal epithelium, 453307


title: 205332910172_R06C01 NA

source_name: nasal epithelium, 695124


title: B6xBXD113 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910102_R08C01 Control

description: Control

source_name: nasal epithelium, 385813


title: 205332910157_R05C01 Case

description: Case

source_name: nasal epithelium, 348240


title: B6xBXD83 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: 205332910088_R07C01 Control

description: Control

source_name: nasal epithelium, 573327


title: 205332910120_R01C01 Case

description: Case

source_name: nasal epithelium, 634324


title: 205310780034_R02C01 Case

description: Case

source_name: nasal epithelium, 688913


title: B6xBXD124 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD33 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD53 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910047_R03C01 Case

description: Case

source_name: nasal epithelium, 407037


title: B6xBXD39 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: 205310780054_R04C01 Case

description: Case

source_name: nasal epithelium, 198289


title: 205332910155_R08C01 NA

source_name: nasal epithelium, 705879


title: B6xD2Gpnmb cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD53 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD113 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910078_R08C01 Case

description: Case

source_name: nasal epithelium, 778968


title: 205310780034_R05C01 Case

description: Case

source_name: nasal epithelium, 208550


title: B6xBXD65 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6xBXD99 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910181_R04C01 Case

description: Case

source_name: nasal epithelium, 479870


title: B6xBXD66 cross, 14 mo, _Ntg/Ntg

description: 10x Genomics

source_name: frontal cortex


title: B6xBXD66 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: Basilic vein 2 (piece 2)

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: 10X Genomics

data_processing:
FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2).
The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger human reference package (version 2020-A), from GRCh38 Ensembl build 98/GENCODE v32 gene annotations.
Assembly: GRCh38 Ensembl build 98
Supplementary files format and content: tab-seperated value and matrix files

source_name: Basilic vein

extract_protocol:
Veins approximately 2 cm in length were cut longitudinally with a sterile scalpel and then into 1-2 mm square sections. Samples were enzymatically digested for 90 minutes at 37°C with shaking using a combination of collagenase type II, soybean trypsin inhibitor, elastase, Dispase, DNAse I, collagenase type XI, hyaluronidase type I, and HEPES in HBSS with Ca2+ and Mg2+. After 90 minutes, an equal volume of Accumax was added to the dissociation mix and incubated for an additional 5 minutes. Single cells were filtered through a 40 μM strainer, washed with HBSS twice, and incubated with red blood cell lysis buffer for 5-10 min. Cells were washed once again with HBSS and resuspended in 0.1% BSA in PBS for counting and RNA sequencing.
Samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells or 5,000 for sample BV3. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and subsequently run on a thermocycler (Eppendorf). Sequencing libraries were evaluated for quality on the Agilent Tape Station (Agilent Technologies, Palo Alto, CA) and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and qPCR before sequencing on the Illumina NovaSeq 6000.

value: Basilic vein

tag: age (years)

tag: race/ethnicity

value: Hispanic


title: B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mm cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: Basilic vein 3

description: 10X Genomics

value: White


title: Basilic vein 2 (piece 1)

description: 10X Genomics


title: Basilic vein 1

description: 10X Genomics

value: Male


title: B6xBXD83 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD124 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD33 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: 205332910056_R01C01 Case

description: Case

source_name: nasal epithelium, 350325

value: nasal epithelium

value: Denver


title: B6xBXD83 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6xBXD99 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics


title: Cephalic vein 1

description: 10X Genomics

source_name: Cephalic vein

value: Cephalic vein

value: Female

value: Black


title: B6xD2Gpnmb cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics

value: frontal cortex


title: B6xBXD66 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics

value: female


title: B6xBXD83 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics

value: 14 months


title: B6xBXD50 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics

value: Ntg


title: B6xBXD124 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6xBXD65 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD161 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: Eomes-KO CD4 T cells (replicat 2) [ATAC]

data_processing:
Basecalls were performed using bcl2fastq for Nextseq output
Adapter trimming and quality controls were performed using Trimgalore v0.6.5. and FastQC v0.11.7.
Reads were aligned to the mm10 reference genome by using Bowtie2 v2.2.9. with the splicing alignment feature switched off.
The chromatin-accessible peaks were called using Macs2 callpeaks v2.2.7.1 (q-value <0,01).
FeatureCount (package R subread v 2.10.1) was used to count the number of reads map to each peak
Assembly: mm10 reference genome
Supplementary files format and content: bigwig, bed file of merge peaks
Supplementary files format and content: comma-delimited text file incuding raw count of each sample

source_name: CD4 T cells

extract_protocol:
ATAC-seq was performed as previously described (Adoue et al., 2019) with minor modifications. Briefly, 50 000 cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase at 37°C for 30 min. DNA was purified using the QIAGEN MinElute kit (QIAGEN).
The libraries were prepared using Tagment DNA Enzyme and Buffer kits (Illumina), NEBNext High-Fidelity 2X PCR Master Mix (NEB, catalog # M0541S) with custom sequencing primers (Ackermann et al., 2016; Buenrostro et al., 2016, 2013; Tsompana and Buck, 2014). The libraries were purified twice using AMPure XP beads (Beckman) following a double-sided protocol to remove primer dimers and large fragments. Libraries quality was assessed using the NGS High Sensitivity Kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA).

value: CD4 T cells


title: hiPSC-derived glutamatergic neurons, GapmerB CAn-5uM, ASGM-119

city: Basel

first: Marco

last: Terrigno

address: Grenzacherstrasse 124

department: Neuroscience

country: Switzerland

institute: F. Hoffmann-La Roche AG

data_processing:
NovaSeq Control Software 1.7.5
Basecalling was performed using Real-Time Analysis (RTA)v3.4.4 and fastq generated with bcl2fastq2.20 v2.20.0.422
The Trimmomatic package (v. 0.32) was used for adapter trimming, and reads were aligned to the human reference genome (GRCh38) with STAR (v. 2.7.6a)
The BAM files generated by STAR (two-pass alignment) were analyzed for differential splicing using the ASpli R package (Bioconductor release 3.17) with default parameters.
Assembly: GRCh38
Supplementary files format and content: Alternative splicing analysis of glutamatergic neurons  after treatment with TDP43 antisense gapmers and (CA)n oligonucleotides. Tab-delimited text file includes normalized reads counts.

source_name: iCell Glutaneurons

extract_protocol:
RNA isolation was performed using RNeasy Mini Kit (Qiagen) following manufacture’s instruction.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Gold rRNA Removal Kit
Coding and non-coding RNA-Seq

tag: cell line

value: iCell Glutaneurons

value: neurons

value: wt

tag: treatment

value: GapmerB CAn 5uM


title: hiPSC-derived glutamatergic neurons, untreated_3

data_processing:
NovaSeq Control Software 1.7.5
Basecalling was performed using Real-Time Analysis (RTA)v3.4.4 and fastq generated with bcl2fastq2.20 v2.20.0.422
The Trimmomatic package (v. 0.32) was used for adapter trimming, and reads were aligned to the human reference genome (GRCh38) with STAR (v. 2.7.6a)
RSEM (V1.3.3) with default parameters was used for estimating gene expression levels and export raw gene counts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw and normalized gene counts.

value: untreated


title: hiPSC-derived glutamatergic neurons, CAn-5uM_3

value: CAn 5uM


title: hiPSC-derived glutamatergic neurons, CAn-5uM_1


title: hiPSC-derived glutamatergic neurons, CAn-5uM_2


title: hiPSC-derived glutamatergic neurons, GapmerB CAn-5uM, ASGM-118


title: Eomes-KO CD4 T cells (replicat 1) [ATAC]


title: B6xBXD113 cross, 6 mo, _ Ntg/Ntg

description: 10x Genomics

value: 6 months


title: Eomes-GFP+ CD4 T cells (replicat 3) [ATAC]

value: Eomes-Ires-GFP


title: hiPSC-derived glutamatergic neurons, GapmerA CAn-5uM, ASGM-117

value: GapmerA CAn 5uM


title: Eomes-GFP+ CD4 T cells (replicat 2) [ATAC]


title: hiPSC-derived glutamatergic neurons, GapmerA CAn-5uM, ASGM-116


title: Eomes-GFP+ CD4 T cells (replicat 1) [ATAC]


title: hiPSC-derived glutamatergic neurons, GapmerA CAn-5uM, ASGM-115


title: hiPSC-derived glutamatergic neurons, untreated_1


title: hiPSC-derived glutamatergic neurons, GapmerB CAn-5uM, ASGM-120


title: B6xBXD113 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: B6xBXD124 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics


title: B6xBXD28 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics


title: hiPSC-derived glutamatergic neurons, untreated_2


title: hiPSC-derived glutamatergic neurons, GapmerB CAn-1uM, ASGM-114

value: GapmerB CAn 1uM


title: healthy_donor6

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
For the RNA-seq data, we used the TopHat2 to align the reads to the UCSC hg19 reference genome and the gene annotation format file (GTF file) from GENCODE (Release 19, GRCh37) was fed to the TopHat2 for defining transcript coordinates. Gene-level expression abundance and the results of differential gene expression analysis were obtained from the Cufflinks package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated from cryopreserved samples using the All Prep DNA/RNA Mini Kit (Qiagen Company, Cat. 80204). RNA concentration and purity were measured with Qubit 2.0 Fluorometer (Life Technologies) and Bioanalyzer 2100 (Agilent Technologies).
Libraries were prepared according to the protocol of the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB Company, Cat. E7420L). Briefly, poly-A mRNA was isolated from the total RNAs using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), and were then fragmented, reversely transcribed, and adapter-appended. Library quality was assessed by Bioanalyzer 2100 (Agilent Technologies).

value: mononucleated cells

tag: patient id

value: healthy donor6

tag: disease

value: healthy donor


title: healthy_donor7

value: healthy donor7


title: healthy_donor5

value: healthy donor5


title: hiPSC-derived glutamatergic neurons, GapmerB CAn-1uM, ASGM-113


title: B6xBXD161 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics

tag: tissue

value: frontal cortex

value: female


title: B6xBXD28 cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics

tag: age


title: healthy_donor2

value: healthy donor2


title: healthy_donor3

value: healthy donor3


title: B6xBXD50 cross, 14 mo, _ 5XFAD/Ntg

description: 10x Genomics

tag: Sex

value: 14 months


title: healthy_donor1

value: healthy donor1


title: hiPSC-derived glutamatergic neurons, GapmerA CAn-1uM, ASGM-111

value: iCell Glutaneurons

value: neurons

value: wt

value: GapmerA CAn 1uM


title: hiPSC-derived glutamatergic neurons, GapmerA CAn-1uM, ASGM-110


title: patient20150816_CMR

source_name: Bone marrow

tag: time point

value: complete molecular remission (CMR)

value: acute leukemia


title: hiPSC-derived glutamatergic neurons, GapmerA CAn-1uM, ASGM-109


title: Brain_DOX-RT_1 [C3-14]

type: RNA

city: St Paul

first: Davis

last: Seelig

state: MN

address: 1352 Boyd Ave.

department: Department of Veterinary Clinical Sciences

institute: University of Minnesota

description: 100ng of RNA was used for NanoString nCounter Glial Profiling Panel

hyb_protocol: A total of 100 nanograms of RNA from each sample was used to evaluate gene expression by the nCounter® Glial Cell Profiling Panel from NanoString (NanoString Technologies, Seattle, WA, USA) following manufactures protocol (MAN-10023-11 nCounter XT Assay User Manual).

scan_protocol: A total of 100 nanograms of RNA from each sample was used to evaluate gene expression by the nCounter® Glial Cell Profiling Panel from NanoString (NanoString Technologies, Seattle, WA, USA) following manufactures protocol (MAN-C0035-07, nCounter Analysis System Manual).

data_processing: The nSolver™ Analysis Software version 4.0 (NanoString Technologies, Seattle, WA, USA) quality control parameters were used to assess quality of imaging, binding density, positive control linearity and positive control limit of detection. The nSolver™ Analysis Software Advanced Analysis Module (version 2.0.134) was used to analyze gene expression data, including gene normalization, and differential expression volcano plots with p-values from linear regression.The Advanced Analysis Module was used to normalize raw gene data for each sample to the geometric mean of the endogenous housekeeping genes using the geNorm algorithm. The normalized gene expression data was analyzed using Prism 9.5.1 (GraphPad Software, San Diego, CA,USA). One-way analysis of variance (ANOVA) with the Tukey post-hoc test was used to evaluate differences between groups.

label: not provided

source_name: Brain

label_protocol: not provided

extract_protocol: RNA was extracted using the PureLink FFPE total RNA isolation kit (Invitrogen, Carlsbad, CA) according to manufactures instructions.

treatment_protocol: SKH1 mice were treated introperitoneal with doxrorubicin (DOX), hindlimb radation (RT) or both (DOX-RT)   .  Brains were collected and processed in to parafin blocks from 6 mice per group including control group (no treatment).. The mouse brains were split into two paraffin blocks and a total of 20, 10µm sections were collected for RNA extraction.

value: Brain

value: Female

value: both doxrorubicin and hindlimb radation (DOX-RT)


title: HaCat_NUP153i

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description:
HaCat_002
Gene expression three days after siRNA transfection.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded.  After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: HaCat, NUP153 knocked down cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2µg RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin/streptomycin (P/S)

extract_protocol: Total RNAs were extracted with NucleoSpin RNA (MACHERY-NAGEL) according to the manufacturer's instructions.

value: HaCa

value: Cancer cell line

tag: genotype/variation

value: NUP153 knocked down


title: patient20150816_CHR

value: mononucleated cells

value: complete hematological remission (CHR)


title: B6xBXD39 cross, 14 mo, _ Ntg/Ntg

description: 10x Genomics

value: frontal cortex

value: female

value: Ntg


title: hiPSC-derived glutamatergic neurons, GapmerB, ASGM-102

value: iCell Glutaneurons

value: GapmerB


title: Brain_RT_6 [C3-10]

value: hindlimb radation (RT)


title: patient20150816_primary_PB

value: primary diagnosis (Primary)


title: patient20150816_primary_BM


title: healthy_donor4

value: healthy donor4

value: healthy donor


title: hiPSC-derived glutamatergic neurons, GapmerB, ASGM-101

value: neurons

value: wt


title: Brain_RT_5 [C3-9]

value: Brain

value: Female


title: hiPSC-derived glutamatergic neurons, GapmerB CAn-1uM, ASGM-112

value: GapmerB CAn 1uM


title: Pax7_H3K27ac_rep2_sample

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description:
multicov_Izumi_0114_Pax73T3_ChIP_TSS_pm2p5kb__bowtie2__20200930__CountMatrix.csv
Izumi_0114_Pax73T3_ChIP_TSS_pm2p5kb__bowtie2__20200930__normcount_H3K27ac_sample_genename.csv

data_processing:
For RNA-seq, extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were trimmed using Cutadapt (M. Martin, 2011)  (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  -a GATCGTCGGACT. The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1).  Note that UMIs were not used and mitochondrial chromosome genes are excluded in the analysis.
For ChIL-seq analysis, raw sequencing data were trimmed using Cutadapt (version 2.6) wapper, Trim Galore! (version 0.6.6).
Bowtie2 (B. Langmead et al., 2012) (version 2.3.5.1) was used to map the raw sequence reads (fastq) to the mouse mm10 reference genome. Note that the uniquely mapped reads were retained.
The software BEDtools (A. R. Quinlan et al., 2010) (version 2.29.2) with “multicov” option was used to count reads of ChIP-seq within 2.5kb±TSS regions of the first exons.
For RNA-seq and ChIP-seq,Downstream analysis was conducted by DESeq2 software (M. I. Love et al., 2014) (1.28.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: ChIP-seq signal tracks (bigWig) were created using  the software deepTools (Ramírez et al., 2016) (version 3.3.0) with the options: bamCoverage --binSize 100 --smoothLength 1000 --normalizeUsing CPM.
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix and normalized count matrix.

source_name: Pax7 stably expressed 3T3-L1 adipocyte, day 0 (d0) after differentiation

growth_protocol: The control or Pax7 stably expressed 3T3-L1 adipocytes were cultured with 10% FBS DMEM medium on 35mm dish until the cells reached to confluent. They were kept for two days with the confluency. The media was changed to 3T3-L1 adipocyte differentiation medium for three days and to adipocyte maintenance medium for nine days.

extract_protocol:
Total RNA was obtained from the 3T3-L1 cells using NucleoSpin RNA XS (Takara) .
For CEL-Seq2, sequencing was performed using HiSeq PE Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2 (50 Cycles) on Illumina HiSeq 1500 sequencers with the following cycles: 15 cycles for read 1 and 45 cycles for read 2. for ChIP-seq. For ChIP-Seq2, the libraries were sequenced on Illumina HiSeq 1500 sequencers using the Hiseq SR Cluster Kit v4-cBot and Hiseq SBS Kit v4 (50cycles), and on Illumina NovaSeq 6000 sequencers using NovaSeq 6000 SP Reagent Kit (100 Cycles).
The cells were harvested at d0, d6 and d12, then extracted RNA was utilized for RNAseq by CEL-Seq2. The 3T3-L1 cells at d0 were used for the ChIP-seq analysis.

treatment_protocol: Day 0 (d0) is set when the media was replaced to the adipocyte differentiation media. The cells were harvested at d0, d6 and d12.

value: 3T3-L1 adipocyte

value: Pax7 stably expressed

tag: time

value: day 0 (d0) after differentiation

tag: chip antibody

value: mouse anti-H3K27ac CMA309 [PMID 18227620]


title: patient20130227_relapse

tag: cell type

value: mononucleated cells

value: relapse

value: acute leukemia


title: hiPSC-derived glutamatergic neurons, GapmerA, ASGM-99

value: iCell Glutaneurons

tag: genotype

value: GapmerA


title: Brain_DOX-RT_1 [C2-14]

tag: strain

value: both doxrorubicin and hindlimb radation (DOX-RT)


title: B6xD2Gpnmb cross, 6 mo, _ 5XFAD/Ntg

description: 10x Genomics

value: frontal cortex

value: female

value: 6 months


title: HaCat_CTLi

description:
HaCat_001
Gene expression three days after siRNA transfection.

source_name: HaCat, negative control cells

value: HaCa

value: Cancer cell line

value: negative control


title: Pax7_d12_rep1

description:
CEL0428raw_Izumi_Pax73T3_countmatrix_genename.csv
CEL0428raw_Izumi_Pax73T3_normalizedcount_genename.csv

source_name: Pax7 stably expressed 3T3-L1 adipocyte, day 12 (d12) after differentiation

value: day 12 (d12) after differentiation


title: Brain_DOX-RT_1 [C3-13]

value: Brain

value: Female


title: Pax7_d12_rep2

value: 3T3-L1 adipocyte

value: Pax7 stably expressed


title: patient20130227_CMR2

value: mononucleated cells

value: complete molecular remission (CMR2)


title: Pax7_H3K27ac_rep2_input

description: multicov_Izumi_0114_Pax73T3_ChIP_TSS_pm2p5kb__bowtie2__20200930__CountMatrix.csv

value: day 0 (d0) after differentiation


title: Pax7_d6_rep2

source_name: Pax7 stably expressed 3T3-L1 adipocyte, day 6 (d6) after differentiation

value: day 6 (d6) after differentiation


title: patient20130227_CMR4

value: complete molecular remission (CMR4)

value: acute leukemia


title: Pax7_d6_rep1


title: patient20130227_CMR1

value: complete molecular remission (CMR1)


title: Brain_RT_4 [C2-10]

value: hindlimb radation (RT)


title: hiPSC-derived glutamatergic neurons, GapmerA, ASGM-98

value: iCell Glutaneurons

value: neurons

value: wt

value: GapmerA


title: Brain_RT_3 [C2-9]


title: hiPSC-derived glutamatergic neurons, GapmerA, ASGM-97


title: hiPSC-derived glutamatergic neurons, untreated, ASGM-96

value: control


title: Brain_DOX-RT_1 [C1-14]

value: Brain

value: both doxrorubicin and hindlimb radation (DOX-RT)


title: patient20130227_CHR

value: complete hematological remission (CHR)


title: Brain_RT_2 [C1-10]

value: Female


title: patient20130227_CCR

value: mononucleated cells

value: complete cytogenetic remission (CCR)


title: Pax7_d0_rep2

value: 3T3-L1 adipocyte

value: Pax7 stably expressed

value: day 0 (d0) after differentiation


title: Control_d12_rep2

source_name: Control 3T3-L1 adipocyte, day 12 (d12) after differentiation

value: Control

value: day 12 (d12) after differentiation


title: Control_d12_rep1


title: hiPSC-derived glutamatergic neurons, GapmerB, ASGM-100

value: GapmerB


title: Brain_RT_1 [C1-9]

value: hindlimb radation (RT)


title: Brain_DOX-RT_1 [C1-13]


title: Pax7_d0_rep1


title: hiPSC-derived glutamatergic neurons, untreated, ASGM-95

value: iCell Glutaneurons

value: neurons


title: Brain_DOX-RT_1 [C2-13]


title: patient20130227_PHR

value: partial hematological remission (PHR)

value: acute leukemia


title: Control_d0_rep2

source_name: Control 3T3-L1 adipocyte, day 0 (d0) after differentiation


title: hiPSC-derived glutamatergic neurons, untreated, ASGM-94

value: wt

value: control


title: Brain_Control_6 [C3-2]

value: Brain


title: Control_d0_rep1


title: HepG2 cells, FFA treatment, 48 hours, 3

first: Fulin

last: Nian

address: 2800 Gongwei Road, Pudong, Shanghai, China

institute: Department of Digestive, Shanghai Pudong Hospital, Fudan University Pudong Medical Center

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO6, KEGG7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Liver

value: hepatocellular carcinoma cells

value: WT

value: Free fatty acid (FFA)


title: patient20130227_NR

value: mononucleated cells

value: no remission (NR)


title: HepG2 cells, FFA+TMAO treatment, 48 hours, 3

value: Free fatty acid (FFA)+TMAO


title: patient20130227_primary

value: primary diagnosis (Primary)


title: Eomes-KO CD4 T cells_T24 (replicat 4) [RNAseq]

data_processing:
After trimming of adaptor sequences and removal of low-quality bases (-q value, < 15),
high-quality reads were aligned to the mouse reference genome mm10 (Genome Reference Consortium) using TopHat version 2.0.5 (Trapnell et al. 2009)
Count of the reads mapping to each gene was performed using FeatureCount (package R subread v 2.10.1).
Differential gene expression analysis was performed with DESeq2 using the SARTools R package.
Assembly: mm10 reference genome
Supplementary files format and content: tab-delimited text file includes raw count for each sample

growth_protocol: Naive CD4+ T cells were isolated from spleen and lymph nodes by negative selection using the « Naive CD4 T Cell Isolation Kit » according to the manufacturer’s instructions (Miltenyi Biotec, Cat: 130-104-453). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 50 μM β-mercaptoethanol in 96 well plates at a seeding concentration of 2x105 cells per well. Polyclonal naïve CD4+ T cells were stimulated with 2 ug/mL anti-CD3 antibody (Biolegend) and 1 ug/mL anti-CD28 (BD Biosciences) under non-polarizing conditions. After 0, 12 or 24hrs of stimulation, viable CD4+ T cells (in triplicates for T0 or T12 or quadruplicate for T24, pool of 2 mice per genotype) were flow-sorted.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) and its quality was assessed on a 2100 Bioanalyzer (Agilent Technologies).
High-quality RNA (i.e., RNA of integrity number > 7) was subsequently used for Libraries preparation with TruSeq Stranded mRNA kit protocol according supplier recommendations (Illumina).

value: CD4 T cells


title: HepG2 cells, FFA+TMAO treatment, 48 hours, 1


title: Brain_DOX_6 [C3-6]

value: Female

value: doxrorubicin (DOX)


title: HepG2 cells, FFA+TMAO treatment, 48 hours, 2


title: Brain_DOX_5 [C3-5]


title: Pax7_H3K27me3_rep2_sample

description:
multicov_Izumi_0114_Pax73T3_ChIP_TSS_pm2p5kb__bowtie2__20200930__CountMatrix.csv
Izumi_0114_Pax73T3_ChIP_TSS_pm2p5kb__bowtie2__20200930__normcount_H3K27me3_sample_genename.csv

value: 3T3-L1 adipocyte

value: Pax7 stably expressed

value: day 0 (d0) after differentiation

value: mouse anti-H3K27me3 CMA323  [PMID 21576221]


title: Eomes-KO CD4 T cells_T24 (replicat 1) [RNAseq]


title: Eomes-KO CD4 T cells_T24 (replicat 3) [RNAseq]


title: Eomes-KO CD4 T cells_T24 (replicat 2) [RNAseq]


title: Pax7_H3K27me3_rep2_input


title: HepG2 cells, FFA treatment, 48 hours, 1


title: Brain_DOX_4 [C2-6]


title: Brain_Control_5 [C3-1]

value: control


title: betaSEC31AKD-3

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were pseudoaligned to human transcriptome (Ensembl version 104) using kallisto.
Transcript counts were collapsed into gene counts using tximport.
Assembly: GRCh38/Ensembl 104
Supplementary files format and content: CSV files include gene counts for each Sample

source_name: Islet

extract_protocol:
Total RNA was harvested using RNAeasy Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

value: Islet

value: beta

tag: bmi

tag: ethnicity

value: Caucasian


title: Eomes-WT CD4 T cells_T24 (replicat 3) [RNAseq]


title: HepG2 cells, FFA treatment, 48 hours, 2

value: Liver

value: hepatocellular carcinoma cells

value: WT


title: Eomes-WT CD4 T cells_T24 (replicat 2) [RNAseq]


title: Brain_Control_4 [C2-2]

value: Brain


title: Control_d6_rep2

source_name: Control 3T3-L1 adipocyte, day 6 (d6) after differentiation

value: Control

value: day 6 (d6) after differentiation


title: Brain_Control_3 [C2-1]


title: Control_d6_rep1


title: Brain_DOX_3 [C2-5]


title: alphaSEC31AKD-5

value: alpha


title: Eomes-WT CD4 T cells_T24 (replicat 1) [RNAseq]

value: CD4 T cells


title: Pax7_H3K27me3_rep1_sample


title: control alpha-4

value: Female


title: control beta-3


title: Eomes-KO CD4 T cells_T12 (replicat 3) [RNAseq]


title: Eomes-WT CD4 T cells_T24 (replicat 4) [RNAseq]


title: betaSEC31AKD-2

value: Male


title: Pax7_H3K27ac_rep1_input

value: 3T3-L1 adipocyte

value: Pax7 stably expressed


title: Pax7_H3K27me3_rep1_input

value: day 0 (d0) after differentiation


title: Control_H3K27me3_rep2_sample

value: mouse anti-H3K27me3 CMA323  [PMID 21576221]


title: Pax7_H3K27ac_rep1_sample

value: mouse anti-H3K27ac CMA309 [PMID 18227620]


title: alphaSEC31AKD-3

value: Islet

value: Black or African American


title: Eomes-KO CD4 T cells_T12 (replicat 2) [RNAseq]


title: Brain_DOX_2 [C1-6]

value: doxrorubicin (DOX)


title: alphaSEC31AKD-4

value: Caucasian


title: Eomes-KO CD4 T cells_T12 (replicat 1) [RNAseq]


title: Control_H3K27ac_rep2_sample


title: Eomes-WT CD4 T cells_T12 (replicat 3) [RNAseq]


title: Control_H3K27me3_rep2_input


title: Brain_Control_1 [C1-1]

value: control


title: Brain_Control_2 [C1-2]

value: Brain


title: NS_4

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse cortex

growth_protocol: Multisensory stimulation was performed as in Martorell et al. 2018 (PMID: 30879788).  Briefly, mice were moved from the vivarium and held in a quiet room. Following one hour of habituation to the room, individual mice were placed in separate chambers. The chamber was illuminated by a light-emitting diode programmed to 40 Hz (12.5 ms light on, 12.5 ms light off, 60 W). Speakers (AYL, AC-48073) were placed above the chambers and programmed to present a 10 kHz tone that was 1 ms in duration and delivered at 60 decibels tones at 8 Hz or tones at 40 Hz. The LED and speakers were programmed via a microcontroller (Teensy) such that the sensory input was delivered simultaneously (that is, stimulus pulses of each modality were aligned to the onset of each pulse). Following one hour of stimulation, and one hour of rest, mice were sacrificed and cortex was prepared for single nucleus purification.

extract_protocol: Libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v.3.1 (Dual Index) according to the manufacturer’s protocol (10X Genomics).

treatment_protocol: The protocol for the isolation of was adapted from a previous study (Mathys et al., 2019, PMID: 31042697). All procedures were carried out on ice. Following 1 hour of gamma stimulation or control and one hour of rest, cortices were dissected and snap frozen in liquid nitrogen and stored at −80 °C. Then, 3 mouse cortices were pooled per sample (4 samples per condition) and homogenized in 1 ml homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, 0.1% IGEPAL CA-630, 1 mM β-mercaptoethanol, and 0.4 U µl-1 recombinant RNase inhibitor (Clontech) using a Wheaton Dounce tissue grinder (15 strokes with the tight pestle). The homogenized tissue was filtered through a 40-μm cell strainer, mixed with an equal volume of working solution (50% OptiPrep density gradient medium (Sigma-Aldrich), 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, and 1 mM β-mercaptoethanol) and loaded on top of an OptiPrep density gradient (29% OptiPrep solution (29% OptiPrep density gradient medium,134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, 1 mM β-mercaptoethanol, 0.04% IGEPAL CA-630, and 0.17 U µl-1 recombinant RNase inhibitor) on top of  35% OptiPrep solution (35% OptiPrep density gradient medium, 96 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, 1 mM β-mercaptoethanol, 0.03% IGEPAL CA-630, and 0.12 U µl-1 recombinant RNase inhibitor). The nuclei were separated by ultracentrifugation using an SW32 rotor (5 min, 10,000xG, 4°C). Nuclei were collected from the 29%/35% interphase, washed with PBS containing 0.04% BSA, centrifuged at 300g for 3 min (4 °C) and washed with 1 ml of PBS containing 1% BSA. The nuclei were counted and diluted to a concentration of 1,000 nuclei per microliter in PBS containing 1% BSA.

value: mouse cortex

value: No stimulation


title: NS_3

description: 10x Genomics


title: Brain_DOX_1 [C1-5]


title: Eomes-WT CD4 T cells_T12 (replicat 2) [RNAseq]


title: ST_4

description: 10x Genomics

value: Stimulation


title: Control_H3K27ac_rep2_input

value: Control


title: Eomes-KO CD4 T cells_T0 (replicat 3) [RNAseq]

value: CD4 T cells


title: control beta-2

value: beta

value: WT

value: Male


title: Eomes-WT CD4 T cells_T12 (replicat 1) [RNAseq]


title: alphaSEC31AKD-2

value: alpha


title: NS_2

description: 10x Genomics


title: Eomes-KO CD4 T cells_T0 (replicat 2) [RNAseq]


title: Control_H3K27me3_rep1_sample

value: 3T3-L1 adipocyte

value: day 0 (d0) after differentiation

value: mouse anti-H3K27me3 CMA323  [PMID 21576221]


title: ST_3

description: 10x Genomics


title: control alpha-2

value: Islet


title: Control_H3K27ac_rep1_sample

value: mouse anti-H3K27ac CMA309 [PMID 18227620]


title: betaSEC31AKD-1

value: Hispanic/Latino


title: control alpha-3

value: Female

value: Black or African American


title: NS_1

description: 10x Genomics

value: mouse cortex


title: control alpha-1


title: Control_H3K27me3_rep1_input


title: Eomes-WT CD4 T cells_T0 (replicat 1) [RNAseq]


title: Eomes-KO CD4 T cells_T0 (replicat 1) [RNAseq]


title: Control_H3K27ac_rep1_input


title: ST_2

description: 10x Genomics


title: control beta-1


title: Y4_liver_240_Input

status: Public on Dec 22 2023

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Illumina sequencing reads (~31 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned to the GRCm38/mm10 genome assembly using bowtie/2-2.4.2 with parameters “--end-to-end --no-mixed --no-discordant --very-sensitive -I 10 -X 700”.
SAM output files were then filtered to keep reads with a minimum mapping quality of 10 using samtools/1.9. sambamba/0.7.1 was used to keep uniquely mapping reads with parameters “-F "[XS] == null and not unmapped and not duplicate"”. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis using bedtools/2.30.0.
The bamCoverage function in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. Input reads were subtracted from 5hmC samples using bigWigCompare function.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using the bamCoverage function in deepTools/3.5/0; Scores represent the coverage on the genome location.
Library strategy: hMeDIP-Seq

source_name: liver

extract_protocol:
Genomic DNA was isolated from ~25 mg of frozen tissue using the Quick-DNA Miniprep Pus Kit (Zymo Research) following the manufacturer's protocol with an overnight proteinase K digestion. The amount and quality of extracted DNA was assessed by NanoDrop One (Thermo Fisher). The hMeDIP assay was performed using the MagMeDIP-seq Package (Diagenode, C02010040) with an antibody against 5hmC (Diagenode, C15200200-50). 1.2 µg of genomic DNA was sonicated into ~200 bp fragments using the S220 focused ultrasonicator (Covaris). To maximize IP yield, we processed the samples in duplicates and then pool before performing IPure purification. Prior to immunoprecipitation, samples were spiked with hydroxymethylated (Diagenode, C02040018) and unmethylated DNA controls.
Immunoprecipitated and 10% input DNA was used to prepare libraries according to the MagMeDIP-seq Package protocol except libraries were dual indexed using the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (New England Biolabs) followed by PCR amplification. The quantity and quality of individual libraries were verified on a BioAnalyzer DNA 1000 (Agilent) then pooled into equimolar amounts. The quantity of the pooled library was assessed using the NEBNext Library Quant Kit (New England Biolabs) and Qubit HS DNA kit (Thermo Fisher).

treatment_protocol: Old as treated group

value: liver

tag: antibody

value: male

value: 15 weeks

value: 240h post-70% partial hepatectomy


title: alphaSEC31AKD-1


title: O4_liver_240_Input

value: 81 weeks


title: O2_liver_240_Input

value: female

value: 95 weeks


title: ST_1

description: 10x Genomics

value: Stimulation


title: NASH-T goat

city: Yangling

first: Yue

last: Wang

address: No.22_Xinong Road

department: College of Animal science and Technology

institute: Northwest A&F University

description: 10x Genomics

data_processing:
Reads were processed using the Cell Ranger 7.0.0 pipeline with default and recommended parameters.
Assembly: ARS1
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Capra hircus

extract_protocol:
Liver tissue were transported in In sterile culture dish with 10 ml 1× DPBS solution (Solarbio, cat. no. D1040) on ice to remove the residual MACS Tissue Storage Solution (Miltenyi Biotec, cat. no. 130-100-008), then minced on ice. We used dissociation enzyme 0.25% Trypsin (Hyclone, cat. no. SH30042.01) and 10 ug/mL Recombinant DNase I (RNase-free) (TaKaRa, cat. no. 2270B) dissolved in DPBS with 5% Fetal Bovine Serum (FBS, Thermo Fisher Scientific, cat. no. SV30087.02) to digest the tissues. XX tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1× Red Blood Cell Lysis buffer (Thermo Fisher Scientific, cat. no. 00-4333-57) . Dissociated cells were washed with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar Fluorescence Cell Analyzer (Aber Instruments).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were generated. The sequencing and bioinformatics analysis were performed by Majorbio Co., Ltd (Shanghai, China).

tag: collection date

tag: geo loc_name

value: Feeding HRDS diet


title: Con group

description: 10x Genomics

tag: treatment

value: Feeding LRDS diet


title: NASH goat

description: 10x Genomics


title: Eomes-WT CD4 T cells_T0 (replicat 3) [RNAseq]

source_name: CD4 T cells

value: CD4 T cells


title: O1_liver_240_Input

value: 86 weeks


title: ENKL-J1, mRNA-derived cDNA

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

institute: Juntendo University

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw data were demultiplexed, aligned to human reference genome (GRCh38-2020-A) and EBV reference genome (ASM240226v1), and quantified using Cell Ranger (v7.0.0, 10X Genomics). Downstream analyses used the Seurat R package (version 4.1.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-Separated Values files and matrix files

source_name: Extranodal natural killer (NK)/T-cell lymphoma, nasal type (ENKL)

extract_protocol:
Approximately 0.12 x 106 cells, viability >80%, were used.
sample was suspended in 50 μl of ice - chilled phosphate-buffered saline + 0.04% bovine serum albumin (Thermo Fisher Scientific) and processed to yield scRNA-seq libraries using 10X Chromium Next Gem Single Cell 3’ Reagent Kits v 3.1 (Dual Index) (10x Genomics, Pleasanton, CA) following standard manufacturer protocols. A Bio-Rad T100 thermal cycler (Bio-Rad, Hercules, CA) was used for PCR. After library quality was assessed using Bioanalyzer 2100 (Agilent, Tokyo, Japan), samples were sequenced (Macrogen, Seoul, South Korea) on the HiseqX (Illumina, San Diego, CA) platform at a depth of 2,000,000 pair reads/sample.

value: Cultured ENKL cells


title: Y4_liver_240_5hmC


title: Y2_liver_240_Input

value: 11 weeks


title: Y1_liver_240_5hmC

value: 12 weeks


title: Y2_liver_240_5hmC


title: Y1_liver_240_Input


title: O3_liver_240_5hmC

value: 79 weeks


title: Y3_liver_240_5hmC


title: Eomes-WT CD4 T cells_T0 (replicat 2) [RNAseq]


title: O4_liver_240_5hmC


title: Y3_liver_240_Input


title: O2_liver_240_5hmC


title: O1_liver_240_5hmC


title: Control #114

type: protein

city: Bethesda

first: Avindra

last: Nath

address: 10 Center Drive

institute: NIH/NINDS

description:
Fatigue-125
Control

hyb_protocol: Hypbridization was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).

scan_protocol: Scanning was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).

data_processing: Data processing was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).  In brief, systematic effects on the data introduced during the hybridization step were corrected followed by median normalization (i.e., hybNorm.plateScale.medNorm).

molecule: protein

source_name: CSF

label_protocol: Labeling was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).

extract_protocol: Serum samples were assayed at three dilutions (40%, 1%, and 0.005%) with each sample dilution added to a corresponding subset of the 1,305 SOMAmer detection reagents binned according to manufacturer’s predicted target abundance in serum. Cerebrospinal fluid was run at a single 15% concentration dilution with protease inhibitors and polyanionic competitor reagent added.

value: Male

tag: group

value: Control


title: Control #116

description:
Fatigue-128
Control

value: Female


title: Patient #309

description:
Fatigue-119
Patient

value: Patient


title: Control #105

description:
Fatigue-105
Control


title: Patient #304

description:
Fatigue-111
Patient


title: Patient #313

description:
Fatigue-129
Patient


title: Control #121

description:
Fatigue-141
Control


title: Patient #305

description:
Fatigue-114
Patient


title: Patient #303

description:
Fatigue-109
Patient


title: Control #119

description:
Fatigue-135
Control


title: Control #101

description:
Fatigue-101
Control


title: Patient #323

description:
Fatigue-144
Patient


title: Control #115

description:
Fatigue-127
Control


title: Control #102

description:
Fatigue-102
Control


title: Patient #306

description:
Fatigue-115
Patient


title: Patient #302

description:
Fatigue-108
Patient


title: Control #107

description:
Fatigue-110
Control


title: Control #117

description:
Fatigue-132
Control


title: Control #103

description:
Fatigue-103
Control


title: Control #111

description:
Fatigue-121
Control


title: Control #104

description:
Fatigue-104
Control


title: Patient #315

description:
Fatigue-131
Patient


title: Patient #319

description:
Fatigue-138
Patient


title: Patient #307

description:
Fatigue-117
Patient


title: Patient #320

description:
Fatigue-139
Patient


title: Control #120

description:
Fatigue-136
Control


title: O3_liver_240_Input

tag: tissue

value: liver

value: 240h post-70% partial hepatectomy


title: Control #108

description:
Fatigue-112
Control

tag: age


title: patient #322

description:
Fatigue-142
Patient

tag: Sex


title: Patient #310

description:
Fatigue-120
Patient


title: Patient #311

description:
Fatigue-123
Patient


title: 22Rv1, Input DNA

city: Rochester

first: LIGUO

last: WANG

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
The image data were processed using the Illumina Standard Pipeline. Base-calling and data filtering were carried out by the Mayo Clinic sequence core using the Cassava 1.7 pipeline.
The raw sequences were then mapped to the reference genome (hg38) using BWA (v1.10) with default parameters. Subsequently, the BAM files were sorted and indexed using samtools (v1.10).
Raw sequences were mapped to reference genome (hg38) using BWA (v1.10) with default parameters. BAM files were sorted and indexed using samtools (v1.10).
For peak calling, MASC2 (v2.0.10) was employed with the following options: -f BAMPE --SPMR --bdg. ChIP-seq signal was normalized to per millioin reads. To facilitate downstream analysis, the bedGraph files were converted into bigWig files using UCSC's wigToBigWig tool.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak (except for input samples)

growth_protocol: Human prostate cancer cell line 22Rv1were grown in RPMI supplemented with 10% FBS and 1x Steptomycin-penicillin

extract_protocol:
Cells were cross-linked incubating with 1% formaldehyde solution 10min at room temperature followed by glycine addition to stop crosslinking. Chromatin was obtained by lysing cross-linked cells with Lysis Buffer 1 (LB1) (50mM Hepes-KOH, 140mM NaCl, 1mMEDTA, 10% Glycerol, 0.5%NP-40/Igepal, 0.25% Triton X-100) then LB2 (10mM Tris-HCl pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Each lysis buffer was followed by gentle rocking on ice for 10min prior to centrifugation at 4C. Cell pellets were resuspended in LB3 (10mM Tris-HCl pH 8, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine sodium salt) and sonicated using a Bioruptor Pico sonication device (Diagenode). Sonicated chromatin samples were incubated overnight at 4C with MITF (Active Motif) antibody-conjugated protein A magnetic beads (Dynabeads, Thermo Fisher) in Blocking Buffer (0.5% BSA in 1x PBS). DNA-protein-antibody beads were then washed, and eluted chromatin decross-linked by incubating beads at 65C overnight in Elution Buffer (1% SDS, 0.1M NaHCO3) followed by RNAse A (Thermo Scientific) andProteinase K(New England BioLabs) treatments. DNA was immunoprecipitated by phenol:chloroform:isoamyl alcohol (P:C:IA) and analyzed by qPCR using specific primers
Paired end libraries were prepared using Chip-derived DNA according to the manufacturer’s instructions for the NEBNext Ultra II library prep kit (New England BioLabs).  The concentration and size distribution of the completed libraries was determined using an Advanced Analytical Fragment Analyzer (Agilent Technologies Inc.) and Qubit fluorometry (Thermo Fisher Scientific Inc).
Libraries were sequenced at (6samples/P2 Flow cell) following Illumina’s standard protocol using the Illumina NextSeq™ 2000 and P2 flow cell. The flow cells were sequenced as 50 X 2 paired end reads using NextSeq 1000/2000 Control Software Suite v1.4.1 and RTA3.

tag: cell line

value: human prostate carcinoma epithelial cell


title: 22Rv1, MIFT ChIP, replicate 2

value: MITF (Active Motif)


title: 22Rv1, MIFT ChIP, replicate 1


title: Control #112

description:
Fatigue-122
Control


title: Control #109

description:
Fatigue-113
Control


title: Patient #308

description:
Fatigue-118
Patient


title: Patient #318

description:
Fatigue-137
Patient


title: Patient #321

description:
Fatigue-140
Patient


title: Control #122

description:
Fatigue-143
Control


title: Patient #301

description:
Fatigue-107
Patient


title: Control #106

description:
Fatigue-106
Control


title: NDC, iPSC, N2, Rep2, Untr

city: Philadelphia

first: Daniel

last: Xu

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
MASTER_neurons_and_iPSCs_counts.txt
DX22-N2-iPSC-2

data_processing:
FASTQ files were aligned using STAR 2.7.1a using hg38 Gencode reference genome
Read counts of genes were quantified by STAR using --quantMode GeneCounts parameter.
Normalized read counts were generated using DESeq2. And batch corrected reads are further generated by limma.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read count values for each sample, with separate sequencing runs for unique samples combined

source_name: iPSC

extract_protocol:
Thermo TRIzol Reagent manual for RNA seperation; ZYMO RNA Clean & Concentrator™-5  RNA Clean-up protocol
Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L); NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760L) Instruction Manual

value: iPSC

value: NDC

tag: donor

tag: batch

value: Batch 1

value: Untr

tag: replicate


title: APPdup, iPSC, A1, Rep2, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX25-A1-iPSC-2

tag: cell type

value: APPdup


title: APPdup, iPSC, A2, Rep5, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX5-A2-iPSC-5

tag: genotype


title: NDC, iPSC, N1, Rep6, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX20-N1-iPSC-6


title: APPdup, iPSC, A2, Rep1, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX1-A2-iPSC-1


title: Control #110

description:
Fatigue-116
Control


title: DJB-2

first: Qingnan

last: Zhao

address: 650 XinSongjiang Rd

institute: Shanghai Jiao Tong University School of medicine affiliated Shanghai General Hospital

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: C57BL/6 mice

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: C57 BL/6 mice were fed with high-fat diet starting from 6 weeks of age. After 12 weeks of HFD, mice achieved typical diabetic phenotypes and were randomized into 2 groups undergoing either DJB or sham procedure. The DJB group was performed with the 5-cm biliopancreatic limb and 4-cm Roux limb under anesthesia (Buprenorphine, 0.15mg/kg, i.p.), and the sham group underwent the same abdominal incision and transections of the intestine but was resutured in situ without any change.

value: abdominal adipose tissues

value: DJB surgery


title: Patient #316

description:
Fatigue-134
Patient


title: NDC, iPSC, N1, Rep2, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX16-N1-iPSC-2


title: NDC, iPSC, N1, Rep1, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX15-N1-iPSC-1


title: NDC, neuron, N1, Rep5, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_P300_2

source_name: neuron

value: neuron

value: Batch 2


title: Sham-3

value: Sham surgery


title: Control #113

description:
Fatigue-124
Control

value: Male

value: Control


title: Patient #312

description:
Fatigue-126
Patient

value: Female

value: Patient


title: NDC, neuron, N2, Rep5, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_CTRL_3

value: CTRL


title: NDC, neuron, N2, Rep3, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_CTRL_1


title: APPdup, iPSC, A2, Rep2, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX2-A2-iPSC-2


title: APPdup, iPSC, A2, Rep3, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX3-A2-iPSC-3


title: DJB-3


title: NDC, neuron, N2, Rep4, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_CTRL_2


title: APPdup, iPSC, A2, Rep4, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX4-A2-iPSC-4


title: APPdup, iPSC, A1, Rep3, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX26-A1-iPSC-3


title: DJB-1


title: NDC, iPSC, N2, Rep3, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX23-N2-iPSC-3


title: APPdup, iPSC, A1, Rep1, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX24-A1-iPSC-1


title: NDC, iPSC, N2, Rep1, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX21-N2-iPSC-1


title: NDC, neuron, N2, Rep4, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_P300_1


title: NDC, neuron, N1, Rep5, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_CTRL_3


title: NDC, iPSC, N1, Rep5, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX19-N1-iPSC-5


title: NDC, neuron, N1, Rep4, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_CTRL_2


title: NDC, iPSC, N1, Rep3, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX17-N1-iPSC-3


title: Sham-2


title: NDC, neuron, N1, Rep4, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_P300_1


title: NDC, neuron, N2, Rep6, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_CBP_3

value: CBP


title: APPdup, neuron, A2, Rep3, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_P300_2


title: NDC, neuron, N2, Rep5, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_CBP_2


title: APPdup, neuron, A2, Rep4, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_CTRL_2


title: APPdup, neuron, A2, Rep5, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_CTRL_3


title: NDC, neuron, N2, Rep4, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_CBP_1


title: NDC, iPSC, N1, Rep4, Untr

description:
MASTER_neurons_and_iPSCs_counts.txt
DX18-N1-iPSC-4


title: NDC, neuron, N1, Rep5, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_CBP_2


title: NDC, neuron, N1, Rep4, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_CBP_1


title: NDC, neuron, N1, Rep6, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_P300_3


title: NDC, neuron, N2, Rep6, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_P300_3


title: APPdup, neuron, A2, Rep4, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_CBP_1


title: Sham-1


title: APPdup, neuron, A1, Rep5, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_P300_2


title: NDC, neuron, N1, Rep6, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_CBP_3


title: NDC, neuron, N2, Rep5, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2_P300_2


title: APPdup, neuron, A1, Rep4, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_P300_1


title: NDC, neuron, N1, Rep3, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1_CTRL_1


title: APPdup, neuron, A2, Rep2, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_P300_1


title: APPdup, neuron, A2, Rep4, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_P300_3


title: APPdup, neuron, A1, Rep6, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_CTRL_3


title: APPdup, neuron, A2, Rep3, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_CTRL_1


title: APPdup, neuron, A1, Rep4, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_CTRL_1


title: APPdup, neuron, A1, Rep5, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_CBP_2


title: APPdup, neuron, A1, Rep5, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_CTRL_2


title: NDC, neuron, N2, Rep3, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-CBP-Sample-51


title: NDC, neuron, N2, Rep1, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-P300-Sample-46


title: APPdup, neuron, A1, Rep4, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_CBP_1


title: APPdup, neuron, A1, Rep6, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_CBP_3


title: APPdup, neuron, A2, Rep5, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_CBP_2


title: NDC, neuron, N2, Rep2, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-CTRL-Sample-59


title: APPdup, neuron, A2, Rep6, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2_CBP_3


title: NDC, neuron, N2, Rep2, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-P300-Sample-47


title: NDC, neuron, N2, Rep3, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-P300-Sample-48


title: NDC, neuron, N1, Rep3, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-P300-Sample-33


title: NDC, neuron, N2, Rep2, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-CBP-Sample-50


title: NDC, neuron, N2, Rep1, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-CTRL-Sample-58


title: NDC, neuron, N1, Rep2, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-P300-Sample-32


title: APPdup, neuron, A2, Rep1, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2-P300-Sample-17


title: APPdup, neuron, A2, Rep1, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2-CTRL-Sample-28


title: NDC, neuron, N1, Rep1, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-CBP-Sample-34


title: NDC, neuron, N1, Rep1, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-P300-Sample-31


title: NDC, neuron, N1, Rep2, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-CTRL-Sample-44


title: APPdup, neuron, A1, Rep2, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-P300-Sample-2


title: NDC, neuron, N1, Rep2, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-CBP-Sample-35


title: NDC, neuron, N2, Rep1, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N2-CBP-Sample-49


title: APPdup, neuron, A2, Rep1, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2-CBP-Sample-19


title: APPdup, neuron, A1, Rep2, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-CTRL-Sample-14


title: APPdup, neuron, A1, Rep1, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-CTRL-Sample-13


title: NDC, neuron, N1, Rep1, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-CTRL-Sample-43


title: APPdup, neuron, A1, Rep6, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1_P300_3


title: APPdup, neuron, A1, Rep3, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-P300-Sample-3


title: APPdup, neuron, A1, Rep2, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-CBP-Sample-5


title: APPdup, neuron, A2, Rep2, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2-CBP-Sample-20


title: APPdup, neuron, A1, Rep1, P300 RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-P300-Sample-1


title: APPdup, neuron, A2, Rep2, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2-CTRL-Sample-29


title: APPdup, neuron, A1, Rep3, CTRL RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-CTRL-Sample-15


title: APPdup, neuron, A1, Rep1, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-CBP-Sample-4


title: APPdup, neuron, A1, Rep3, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A1-CBP-Sample-6


title: WT_CAC_Tomato_rep1

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

data_processing:
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq
All the above were performed through the Bioconductor package metaseqr
Assembly: mm10
Supplementary files format and content: txt (tab separated) files containing all the results from metaseqr analysis including expression per replicate, fold change compared to each other and p-values.

source_name: Colon tumors

growth_protocol: Col6a1-Cre;Rosa26-mTmG mice underwent the AOM/DSS protocol for the development of colitis-asssociated cancer

extract_protocol:
Total RNA was extracted using the Single Cell RNA Purification kit by Norgen Biotek, according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer from Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™V2 chips (ThermoFisher Scientific) on an Ion Proton™System, according to the manufacturer's instructions.

treatment_protocol: Colonic adenomas were digested using Collagenase IV, dispase, and DNAse for 1h at 37 C. The cell suspension was used for the isolation of linage negative (CD45-, EpCAM-, CD31-, Ter119-) GFP+ and Tomato+ fibroblasts.

value: Colon tumors

tag: strain

value: Fibroblasts

value: Col6a1-cre, Rosa26-mTmG

tag: disease model

value: AOM/DSS

tag: cell population


title: WT_CAC_Tomato_rep3


title: WT_CAC_Tomato_rep2


title: WT_CAC_GFP_rep3


title: APPdup, neuron, A2, Rep3, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
A2-CBP-Sample-21

value: Batch 1


title: 4th round of regeneration

city: Dresden

first: Fabian

last: Rost

address: Pfotenhauerstraße 108

country: Germany

institute: MPI-CBG

description: 10x Genomics

data_processing:
A reference based on GRCz10, Ensembl annotation e98 was created, by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0
fastq files were processed with `cellranger count` from 10X genomics version 3.0.0
Assembly: GRCz10
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format.

organism: Danio rerio

source_name: Fin

extract_protocol:
For each experiment about 8000 cells from zebrafish fin regenerates were flow-sorted into BSA-coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA-seq v2. In short, the droplets were directly subjected to reverse transcription, the emulsion was broken and cDNA was purified using silane beads. After amplification of cDNA with 12 cycles, it underwent a purification with 0.6 volume of SPRI select beads.
After quality check and quantification using the Fragment Analyzer (Agilent), 30 ng cDNA were used to prepare sc RNA-seq libraries - involving fragmentation, dA-Tailing, adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. After quantification, both libraries were sequenced on an Illumina Nextseq500 system in paired-end mode with 26 bp/57 bp (for read 1 and 2 respectively), thus generating ~60-90 mio. fragments for the transcriptome library on average.

treatment_protocol: Fin regenerates of quadruple transgenic fish [Tg(7xTCF-Xla.Sia:NLS-mCherry)ia5 x Tg(-2.7shha:GFP)t10 x Tg(Ola.Sp7:CreERT2-p2a-mCherry)tud8 x Tg(Hsa.RUNX2-Mmu.Fos:EGFP)zf259] were harvested at 3 dpa, cut into small pieces with a scalpel and transferred into 1 ml collagenase-dispase solution (1 mg/ml in PBS, Roche #10269638001) for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated, flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution (without CaCl2 and MgCl2, Gibco #12082739). After centrifugation (15 minutes, 1800 rpm, 4°C), the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet (1µl 10mM, Invitrogen #C34858) was added to the cell solution and incubated for 30 minutes. Calcein violet, GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence-activated cell sorting (BD LSR Fortessa) and processed for single-cell RNA sequencing analysis based on 10X Genomics (10X Chromium system, 10X library preparation according to the manufacturer's instructions).

value: Fin

value: siam+, shha+, osterix+, RUNX2+ fin regenerate cells

tag: treatment /stage

value: 3 days post amputation


title: 3rd round of regeneration

description: 10x Genomics

value: Tg(7xTCF-Xla.Sia:NLS-mCherry)ia5 x Tg(-2.7shha:GFP)t10 x Tg(Ola.Sp7:CreERT2-p2a-mCherry)tud8 x Tg(Hsa.RUNX2-Mmu.Fos:EGFP)zf259


title: WT_CAC_GFP_rep2


title: 2nd round of regeneration

description: 10x Genomics


title: WT_CAC_GFP_rep1


title: hESC, PE (pellet extract), Day0, rep1 [W6-1_RRL21035-V]

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatics (version 0.36).
Trimmed sequence reads were mapped to hg38 (GENCODE v28) human genome using Hisat2 (v2.0.5) with parameter “--rna-strandness RF”.
The gatk was used to remove PCR duplicates from aligned BAM files.
Raw counts at the gene level were calculated with featureCounts (version 1.6.2). Isoform-level expression was quantified as transcripts per million reads (TPM) with Salmon (version 1.3.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: H1 hESC

growth_protocol: Human ESC line H1 were maintained in mTeSR1 (StemCell Technologies, 85850) on matrigel (Corning, 354277)-coated plates. hESCs were fed with fresh hESC medium daily.

extract_protocol:
definitive mesoderm cells differentiation protocol:
To initiate mesoderm differentiation, hESCs were plated onto matrigel-coated 6-well plates with 70% of cell confluence, and then these cells were cultured in IMDM medium (Gibco, 12440053) plus 10% FBS (Gibco, 10099141), 2 mM Glutamine (Gibco, 25030164), 50 μg/mL Ascorbic Acid (StemCell Technologies, 72132), 0.1 μM Monothioglycerol (Sigma, M6145), 10 ng/mL BMP4 (StemCell Technologies, 02524) for 1 day. And then cells were cultured 4 days in the above medium supplemented with bFGF (2.5 ng/mL, StemCell Technologies, 78003.1). Cells were fed with fresh medium daily.
subcellular isolation protocol:
Operations refer to Subcellular Protein Fractionation Kit’s (Thermo Fisher, 78840) instruction. We collected cells and added cytoplasmic extraction buffer in the tube. After incubating the tube at 4°C for 10 min and centrifuging at 500 × g for 5 min, we immediately transferred the supernatant (cytoplasmic extract). Then we added the membrane extraction buffer, incubated at 4℃ for 10 min and centrifuged at 3000 × g for 5 min, and transferred the supernatant (membrane extract). We further added the nuclear extraction buffer. After incubating at 4℃ for 30 min and centrifuging at 5000 × g for 5 min, we transferred the supernatant (soluble nuclear extract) fraction. Similarly, we added nuclear extraction buffer containing CaCl2 (5 mM) and micrococcal nuclease (300 units), incubated at room temperature for 15 min, centrifuged at 20,000 × g for 5 min, and transferred the supernatant (chromatin-bound nuclear extract) fraction. Finally, pellet extraction buffer was added in tube. After incubating at room temperature for 10 min and centrifuging at 20,000 × g for 5 min, we obtained the supernatant (i.e., the cytoskeletal extract). All of the buffers were supplemented with protease inhibitor and RNase inhibitor.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: H1 hESC

value: embryonic stem cells

value: WT

tag: time

value: Day 0


title: hESC, PE (pellet extract), Day0, rep2 [W6-2_RRL21036-V]


title: PM3

city: Seoul

first: Myungkyung

last: Noh

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

data_processing:
Reads were mapped using TopHat software to obtain the alignment file
assemble transcripts, estimate abundances, and detect the differential expression of genes/isoforms using Cufflinks
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RC values for each Sample

source_name: lung

extract_protocol:
RNA was isolated using an easy-BLUE total RNA extraction kit (Intron Biotechnology)
A library was constructed using a SENSE mRNA-Seq Library Prep Kit (Lexogen)

value: lung

value: PM, i.t.


title: PM2


title: hESC, SNE (soluble nuclear extract), Day0, rep2 [W4-2_RRL21032-V]


title: hESC, CBNE (chromatin-bound nuclear extract), Day0, rep1 [W5-1_RRL21033-V]


title: CT3

value: Veh (PBS), i.t.


title: NDC, neuron, N1, Rep3, CBP RNAi

description:
FINAL_OUTPUT_combined-counts_CORRECTED_N.txt
N1-CBP-Sample-36

value: neuron

value: NDC

value: CBP


title: hESC, SNE (soluble nuclear extract), Day0, rep1 [W4-1_RRL21031-V]


title: hESC, CBNE (chromatin-bound nuclear extract), Day0, rep2 [W5-2_RRL21034-V]


title: hESC, ME (membrane extract), Day0, rep2 [W3-2_RRL21030-V]


title: hESC, ME (membrane extract), Day0, rep1 [W3-1_RRL21029-V]


title: Day45, Rep3

city: Nottingham

first: Fei

last: Sang

address: QMC

country: United Kingdom

institute: Nottingham University

data_processing:
Base calling was done by Real-Time Analysis (RTA).
Raw PE reads were trimmed against adaptor sequences by fastp before being map to the genome using HISAT2 v2.0.5 with default settings
Uniquely and correctly mapped reads wre quatitated using featureCounts v1.5.0-p3.
Gene expression level was then normalised by Fragments Per Kilobase Per Million (FPKM).
Assembly: PRJNA808222

organism: Psophocarpus tetragonolobus

source_name: pod

growth_protocol: Each biologilca replicates were collected from different individual plants grown in the growth chamber at 26/20°C temperature with 12-hou adylength throughout

extract_protocol:
Total RNA was extracted using Rneasy Plant Mini Kit with DNase treatment, according to the manufacturer’s instructions
Library prep was performed with polyA non-stranded library for mRNA-seq and sequenced using standard Illumina protocols.

value: pod

value: Day 45 after anthesis


title: Day45, Rep2


title: hESC, CE (cytoplasmic extract), Day0, rep1 [W2-1_RRL21027-V]


title: hESC, CE (cytoplasmic extract), Day0, rep2 [W2-2_RRL21028-V]


title: CT1


title: hESC, INPUT, Day0, rep2 [W1-2_RRL21026-V]


title: Day45, Rep1


title: Day37, Rep3

value: Day 37 after anthesis


title: hESC, INPUT, Day0, rep1 [W1-1_RRL21025-V]


title: 1st round of regeneration

description: 10x Genomics

value: Fin


title: hESC, PE (pellet extract), Day5, rep2 [Q18-2_RRL21079-V]

value: mesoderm differentiation

value: Day 5


title: Day30, Rep3

value: Day 30 after anthesis


title: hESC, PE (pellet extract), Day5, rep1 [Q18-1_RRL21078-V]

value: H1 hESC


title: Day37, Rep1


title: Day37, Rep2


title: hESC, CBNE (chromatin-bound nuclear extract), Day5, rep1 [Q17-1_RRL21076-V]

value: embryonic stem cells


title: PM1

value: WT


title: Day30, Rep2


title: CT2


title: Day30, Rep1


title: Day15, Rep3

value: Day 15 after anthesis


title: hESC, SNE (soluble nuclear extract), Day5, rep2 [Q16-2_RRL21075-V]


title: Day15, Rep1


title: hESC, ME (membrane extract), Day5, rep2 [Q15-2_RRL21073-V]


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_322

description:
Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline
Illuminasoftware bcl2fastq v.2.17

data_processing:
Illuminasoftware bcl2fastq v.2.17
RNA sequences were subjected to quality control  through FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Adapters were removed using Trimmomatic: https://github.com/timflutre/trimmomatic
Alignment to the human genome (GRCh38) using STAR
Gene expression levels were quantified using FeaturesCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene expression levels for each sample

source_name: Blood

extract_protocol:
RNA was extracted from PBMC’s of participants using miRNeasy Micro Kit (QIAGEN).
Dual index libraries were constructed with at least one unique index per each patient library using the TruSeq Stranded Total RNA HT Kit (Illumina).

value: Blood

value: Male


title: Day15, Rep2


title: hESC, ME (membrane extract), Day5, rep1 [Q15-1_RRL21053-V]


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_316

value: Female


title: hESC, INPUT, Day5, rep2 [Q13-2_RRL21050-V]


title: hESC, CE (cytoplasmic extract), Day5, rep2 [Q14-2_RRL21052-V]


title: hESC, CE (cytoplasmic extract), Day5, rep1 [Q14-1_RRL21051-V]


title: hESC, CBNE (chromatin-bound nuclear extract), Day5, rep2 [Q17-2_RRL21077-V]


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_311


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_305


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_302


title: hESC, SNE (soluble nuclear extract), Day5, rep1 [Q16-1_RRL21074-V]


title: hESC, INPUT, Day5, rep1 [Q13-1_RRL21049-V]


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_310


title: hESC, CE (cytoplasmic extract), Day3, rep1 [D8-1_RRL21039-V]

value: Day 3


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_312


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_313


title: hESC, ME (membrane extract), Day3, rep1 [D9-1_RRL21041-V]


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_120

description:
Peripheral Blood Mononuclear Cells, HV, Baseline
Illuminasoftware bcl2fastq v.2.17


title: hESC, INPUT, Day3, rep2 [D7-2_RRL21038-V]


title: hESC, INPUT, Day3, rep1 [D7-1_RRL21037-V]


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_121


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_117


title: Peripheral Blood Mononuclear Cells, PI-ME/CFS, Baseline MECFS_319


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_113


title: hESC, PE (pellet extract), Day3, rep1 [D12-1_RRL21047-V]


title: hESC, CBNE (chromatin-bound nuclear extract), Day3, rep2 [D11-2_RRL21046-V]


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_115


title: hESC, CBNE (chromatin-bound nuclear extract), Day3, rep1 [D11-1_RRL21045-V]


title: hESC, SNE (soluble nuclear extract), Day3, rep2 [D10-2_RRL21044-V]


title: hESC, ME (membrane extract), Day3, rep2 [D9-2_RRL21042-V]


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_112


title: hESC, PE (pellet extract), Day3, rep2 [D12-2_RRL21048-V]


title: hESC, CE (cytoplasmic extract), Day3, rep2 [D8-2_RRL21040-V]


title: THP-1, LPS+TFF2, 3h

city: Shanghai

first: Guanxing

last: Zhai

address: 2901 Caolang Road, Shanghai

institute: Shanghai Public Health Clinical Center, Fudan University

data_processing:
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: hg38
Supplementary files format and content: Excel files include the FPKM values of for each sample.

growth_protocol: THP-1 cells were cultured in RPMI1640 supplemented with 10%FBS+1%P/S, seeded in a 24-well plate, 1E5/well.

extract_protocol:
Total RNA was extracted using the RNAzol reagent (Molecular Research Center, OH, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: THP-1 treatment was divided into the following groups: Mock (Blank), LPS, LPS+TIF, LPS+IFNα2, and LPS+TFF2. After treatment with the above protein at 100 μM for 2 h, LPS (10 ng/ml) was stimulated for 1, 3, 6, 12, and 24 h.

value: leukemia monocytic cell


title: THP-1, LPS+TFF2, 24h


title: THP-1, LPS+TFF2, 6h


title: THP-1, LPS+TFF2, 12h


title: THP-1, LPS+IFNα2, 12h


title: Peripheral Blood Mononuclear Cells, HV, Baseline MECFS_101