title: Bone Marrow Erythroid Cells 3

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

description: We performed mRNA profiling for 579 target genes, for 14 housekeeping genes, for 8 negative and 6 positive spike-in controls

hyb_protocol: 50ng of total RNA was hybridized with NanoString Immunology V2 panel according to the manufacturer's protocols.

data_processing: We performed QC on the raw data, performed background thresholding using the (mean of negative controls + 2 SD) + mean of POS_E controls, normalized gene expression using 15 housekeeping genes.

source_name: Bone Marrow Erythroid Cells

extract_protocol: We obtained adult bone marrow mononucler cells (MNCs) using Ficoll-paque density gradient, then labeled the MNCs with anti-CD71-biotin-magnetic bead antibody and sorted the cells using a magnetic separator.

value: 24 years

value: Adult Human Bone Marrow

value: Bone Marrow Erythroid Cells


title: MB131_naive1

status: Public on Aug 01 2023

type: SRA

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

library_source: transcriptomic

data_processing:
The adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR.
The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated.
The filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2
Assembly: dm6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include statistical results and fold enrichment comparing to naive samples

molecule: total RNA

organism: Drosophila melanogaster

source_name: mushroom body

growth_protocol: Flies were raised under a 12 h:12 h, light:dark cycle, at 25℃ and 60% humidity.

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis or RNA extraction for RNA-seq.
The library for nuclear RNA-seq was prepared by Oligo d(T)25 Magnetic Beads (New England Biolabs inc. Ipswich, MA, USA), and NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs inc. Ipswich, MA, USA), according to the manufacturer’s instructions.

treatment_protocol: Flies were subjected to optogenetic activation by expressing CsChrimson with red-light illumination.

tag: strain

tag: tissue

value: mushroom body

tag: treatment

value: naive


title: human TFEB-flag overexpressing_Fast #2

status: Public on Jul 31 2023

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of human TFEB-flag overexpressing, Fast biological rep2

data_processing: Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq. Sequence reads were trimmed BBDuk (sourceforge.net/projects/bbmap/) to remove adapter sequences and low-quality end bases (Q < 20). Alignment was performed with STAR 2.6.0a(1) on the Hg38 reference provided by UCSC Genome Browser (2). Alignment to mm10, and rn6 reference genome assembly (1), and counting by gene (3) using Ensembl assembly (release 93). Gene expression levels were determined with HTseq-count 0.9.1(3). Differential expression analyses were performed using edgeR (4) a statistical package based on generalized linear models, suitable for multifactorial experiments. The threshold for statistical significance chosen was False Discovery Rate (FDR)<0,05.

organism: Rattus norvegicus

source_name: INS-1E cells

growth_protocol: Cells were grown in 10cm dishes using RPMI 1640; 10%FBS; 10mM Hepes; 1mM PyrNa; 2mM Glutamine; 0,05 mM beta-mercaptoethanol, PenStrep.

extract_protocol:
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). For RNA-seq analysis, library preparation was performed with a total of 100ng of RNA from each sample using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen) according to manufacturer's instructions. Amplified fragmented cDNA of 300bp in size was sequenced in single-end mode by NovaSeq 6000 (Illumina) with a read length of 100bp
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

treatment_protocol: Cells were plated on 12-well plates and treated with full medium (GC) or Minimum Essential Medium (Fast) for 16h (overnight)

tag: rat insulinoma derived cell line

tag: gender

value: not provided


title: Bone Marrow Erythroid Cells 4

type: RNA

organism: Homo sapiens

tag: age

value: 23 years

value: female

tag: cell type


title: 03_3W-GSH-4_rep1

city: Kibichuo

first: Kenji

last: Henmi

state: Okayama

address: 7549-1 Yoshikawa

country: Japan

institute: Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences

hyb_protocol: Each 12.5 µg of labelled aRNA was hybridized for 16 h to Affymetrix GeneChip Arabidopsis ATH1 Genome Array, containing 22,810 probe sets. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The raw data were analyzed with Affymetrix GeneChip Command Console (AGCC) Software and Affymetrix Expression Console. The normalization between chips was performed using GeneSpring software.

label: biotin

organism: Arabidopsis thaliana

source_name: aerial parts of GSH-fed Col-0 plants 3 weeks after sowing

label_protocol: Biotinylated aRNA were prepared from 100 ng of total RNA by 3’ IVT Express kit (Affymetrix Inc.).

growth_protocol: Wild-type Arabidopsis (ecotype Columbia-0) plants were grown three plants in square plastic pots (6.5 x 6.5 x 5 cm) filled with 10 g of vermiculite at the bottom, 30 g of Kureha soil in the middle, and 5 g of vermiculite on the top layer. They were cultivated in an air-conditioned room for 16 h in the light period and 8 h in the dark at 22 °C.

extract_protocol: Total RNA extraction from leaves or aerial parts including meristem was performed using an RNeasy Plant Mini Kit (Qiagen Inc.).

treatment_protocol: From the first week to the fifth week after sowing, a 25 ml of 1 mM oxidized glutathione (GSSG), 2 mM reduced glutathione (GSH) and 3 mM NH3NO4 aqueous solution per pot were applied by subirrigation once a week. Plants grown by water were used as control. The aerial parts including the shoot apical were harvested 3 weeks after sowing, and the second and third leaf blades from the top of the fully expanded leaves were harvested 4 and 5 weeks after sowing.

tag: ecotype

value: Columbia

value: aerial parts including the shoot apical

tag: developmental stage

value: 3 weeks after sowing

value: GSH


title: Bone Marrow Erythroid Cells 2

value: 26 years


title: normal cornea-rep4 [SP4_IP]

city: qingdao

first: HUIJIN

last: WANG

state: shandong province

address: yanerdao road

country: China

institute: Qingdao Eye Hospital of  Shandong First Medical University

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 4 out of 8 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: normal cornea_IP

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: cornea in both keratoconus patients (Trial group)  and non-keratoconus patients (Control group) was surgically obtained and preserved in −80℃liquid nitrogen tanks.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: subject status

value: non-keratoconus patient

tag: sample type

value: IP with anti-N6-methyadenosine (m6A) antibody


title: human TFEB-flag overexpressing_Fast #4

description: Transcriptome profile of human TFEB-flag overexpressing, Fast biological rep4


title: 04_3W-NH4NO3-4_rep1

source_name: aerial parts of NH4NO3-fed Col-0 plants 3 weeks after sowing


title: human TFEB-flag overexpressing_Fast #3

description: Transcriptome profile of human TFEB-flag overexpressing, Fast biological rep3


title: human TFEB-flag overexpressing_Fast #1

description: Transcriptome profile of human TFEB-flag overexpressing, Fast biological rep1


title: Control_for hTFEBflag_Fast #4

description: Transcriptome profile of wild type , Fast biological rep4


title: 01_3W-Control-4_rep1

source_name: aerial parts of Col-0 plants under control condition 3 weeks after sowing

value: None (Control)


title: 02_3W-GSSG-4_rep1

source_name: aerial parts of GSSG-fed Col-0 plants 3 weeks after sowing

value: GSSG


title: normal cornea-rep2 [SP2_IP]


title: Control_for hTFEBflag_Fast #2

description: Transcriptome profile of wild type , Fast biological rep2


title: human TFEB-flag overexpressing_GC #4

description: Transcriptome profile of human TFEB-flag overexpressing, GC biological rep4


title: normal cornea-rep3 [SP3_IP]

value: male


title: human TFEB-flag overexpressing_GC #3

description: Transcriptome profile of human TFEB-flag overexpressing, GC biological rep3


title: normal cornea-rep1 [SP1_IP]


title: RRMM19_T2

city: Heidelberg

first: Alexandra

middle: M

last: Poos

address: Im Neuenheimer Feld 410

country: Germany

institute: University Hospital Heidelberg

description: 10X Genomics

library_source: other

data_processing:
CellRanger ATAC version 1.2
Assembly: hg38
Supplementary files format and content: For each sample the fragments.tsv.gz, raw_peak_bc_matrix.h5 and singlecell.csv have been uploaded.

molecule: other

source_name: bone marrow

extract_protocol:
Viably frozenCD138+-enriched or CD138+-depleted (RRMM7) BMMCswere thawed at 37 ºC, resuspended in RPMI with 10% FBS and washed once in ice-cold PBS with cells being collected by centrifugation at 500 g for 5 min.
Library was performed according to the manufactur's instructions (scATAC-seq, v1.0 protocol, 10X Genomics)

value: bone marrow

value: CD138-positive fraction

value: post


title: Control_for hTFEBflag_GC #3

description: Transcriptome profile of wild type , GC biological rep3


title: Control_for hTFEBflag_Fast #1

description: Transcriptome profile of wild type , Fast biological rep1


title: Control_for hTFEBflag_GC #2

description: Transcriptome profile of wild type , GC biological rep2


title: human TFEB-flag overexpressing_GC #1

description: Transcriptome profile of human TFEB-flag overexpressing, GC biological rep1


title: Control_for hTFEBflag_Fast #3

description: Transcriptome profile of wild type , Fast biological rep3


title: Control_for hTFEBflag_GC #1

description: Transcriptome profile of wild type , GC biological rep1


title: Control_for hTFEBflag_GC #4

description: Transcriptome profile of wild type , GC biological rep4


title: human TFEB-flag overexpressing_GC #2

description: Transcriptome profile of human TFEB-flag overexpressing, GC biological rep2


title: Bone Marrow Erythroid Cells 1

description: We performed mRNA profiling for 579 target genes, for 14 housekeeping genes, for 8 negative and 6 positive spike-in controls

value: 25 years

value: Adult Human Bone Marrow

value: Bone Marrow Erythroid Cells


title: unstim_4

status: Public on Jul 28 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Quality control on raw sequence data was performed with FastQC (version 0.10.0; Babraham Institute, Cambridge, United Kingdom)
RNA-seq reads were aligned with STAR-aligner 2.7.8a using the genome build GENCODE Mus musculus GRCm39 Release M26
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GRCm39 build, GENCODE Release M26

organism: Mus musculus

source_name: brain

growth_protocol: Cerebellar cells from postnatal day 0-4 (P0-P4) mouse pups (C57BL/6) were dissociated and plated on poly-L-lysine-coated, 12-well plates (90,000 cells per well). Cells were maintained in Neurobasal Plus medium supplemented with B27 Plus (#A3653401, Thermo Fisher Scientific) and 2 mM GlutaMaxTM (#35050061, Thermo Fisher Scientific).

extract_protocol:
Cerebellar neurons were harvested and lysed in 300 μl RLT buffer of the RNeasy Micro Kit (#74004, Qiagen) and total RNA was extracted according to the manufacturers’ protocol.
Library preparation for RNA-seq was performed with the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, Calif).

treatment_protocol: At DIV14, primary neuronal cells were stimulated with 30 ng/ml or 100 ng/ml of Recombinant Murine IL-12p70 (#210-12, Peprotech) for 18 hours.

value: brain

value: neurons

tag: genotype

value: C57BL/6 wt

value: untreated


title: IL-12_30_4

value: 30 ng/ml Recombinant Murine IL-12p70


title: IL-12_30_3


title: unstim_5


title: IL-12_30_5


title: unstim_3


title: unstim_2


title: unstim_1


title: IL-12_30_1


title: IL-12_30_2


title: IL-12_100_5

value: 100 ng/ml Recombinant Murine IL-12p70


title: IL-12_100_2


title: EFZ1008571AR

city: New York

first: Assaf

last: Magen

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

country: USA

institute: Human Immune Monitoring Center

data_processing:
The bulk TCR FASTQ files were processed using Immune Profiler v1.0 and then the data was combined using ImmuneArch.
Supplementary files format and content: CSV file containing VDJ clone information
Library strategy: TCR-seq

source_name: liver tumor resection

extract_protocol:
Takara Bio SMARTer Human TCR profiling kit
Libraries for TCR-seq were prepared from 100 ng of total RNA using the SMARTer Human TCR a/b Profiling Kit v.2 (Takara Bio). Eighteen cycles were used for each of the two seminested PCR ampli- fication steps. Sequencing was performed on an Illumina NovaSeq by multiplexed paired-read run with 2 × 251 cycles.
Qiagen RNA & DNA all-prep with clear up

treatment_protocol: Pre-treatment tumor biopsies and post-treatment tumor resections were analyzed used bulk TCR sequencing across patients.

value: liver tumor resection

tag: patient id

value: Cemiplimab


title: EFZ1010693AR

source_name: liver tumor biopsy

value: liver tumor biopsy


title: IL-12_100_1


title: IL-12_100_4


title: EFZ966185AR


title: EFZ916391AR


title: EFZ774822AR


title: EFZ836046AR


title: EFZ798740AR


title: EFZ825769AR


title: EFZ771080AR


title: EFZ775068AR


title: EFZ762238AR


title: EFZ761334AR


title: EFZ1027710AR


title: 114079R


title: 103614R


title: IL-12_100_3


title: 114396R


title: 105267R


title: 113622R


title: EFZ722477AR


title: 113068R


title: EFZ1008544AR


title: HCI-005 Decitabine 1

status: Public on Jul 24 2023

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

library_source: genomic

data_processing:
Sequencing reads from WGBS data were aligned to the human genome using version 1.2 of an internally developed pipeline Meth10X. It is publicly available and can be downloaded fromhttps://github.com/luuloi/Meth10X(Nair et al., 2018). The pipeline backbone is built based on workflow control Bpipe (Sadedin SP at el. 2012) version 0.9.9.2 which mainly help to make automation, parallelism, restarting jobs and integration with cluster resource managers easier following the pipeline structure ofP3BSseq (Luu PL, et al., 2017). Meth10X takes raw bisulphite reads in fastq files as inputs and produces a html report of all necessary metrics of bisulphite quality control and a tsv file of DNA methylation of 28 million CpG as rows and samples as columns. Briefly, adaptor sequences were removed using in-house bash script in paired end mode following prep kit guide. Bwa-meth verion 0.20 (https://github.com/brentp/bwa-meth) was then used to align reads to hg38 using bwa version 0.7.13 (https://github.com/lh3/bwa). The generated bam files are merged and marked duplication by Picard tools 2.3.0 (http://broadinstitute.github.io/picard). The merged bam files are checked with Qualimap 2.2.1 (Konstantin Okonechnikov at el. 2015) for quality as well as all metrics of WGBS. MethylDackel (https://github.com/dpryan79/MethylDackel) and Biscuit (https://github.com/zwdzwd/biscuit) are used to call DNA methylation and SNP. Samtools version 1.2 (Li H.et al. 2009) is used to manipulate bam files and all the plots are done with ggplot2 in R (H. Wickham. 2009).
Assembly: hg38
Supplementary files format and content: BigWig file containing counts of methylated (C) and coverage (cov, methylated Cs + unmethylated Ts) at each CpG site assayed.

molecule: genomic DNA

source_name: HCI005 Decitabine tumour

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.

extract_protocol:
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for WGBS experiments. Using a cryostat (Leica, #CM3050-S), 15x 30 µm sections were cut from each tumour at  -20 ̊C and these samples were subjected to DNA extraction.
Library preparation and indexing were carried out as described in the CEGX TruMethyl WG user guide v2 wih minor improvements as described in Nair et al., 2018.

treatment_protocol: Mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).

value: Breast cancer PDX model HCI005

value: Decitabine

tag: replicate


title: HCI-005 Vehicle 2

source_name: HCI005 Vehicle tumour

value: Vehicle


title: HCI-005 Decitabine 2


title: Gar15-13 Vehicle 1

source_name: Gar15-13 Vehicle tumour

value: Breast cancer PDX model Gar15-13


title: Gar15-13 Decitabine 1

source_name: Gar15-13 Decitabine tumour


title: EFZ1008495AR


title: HCI-005 Vehicle 1


title: Gar15-13 Decitabine 2


title: Gar15-13 Vehicle 2


title: NFAT5 KO

status: Public on Jul 23 2023

city: Epalinges

first: Grégory

last: Verdeil

state: Vaud

address: Chemin des Boveresses 155

department: Department of Oncology

institute: University of Lausanne

data_processing:
Read alignment, barcode counting and generation of count matrices for peaks were performed with the Cell Ranger ATAC pipeline (v1.2.0, https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
The files with the set of ATAC-seq fragments were imported into R and processed using the GenomicRanges (v1.44.0) R package. After converting fragment sets into GenomicRanges objects, genome wide read coverage was computed using the coverage() function, and averaged across genomic partitions of sizes 5bp or 10bp using the binnedAverage() function. Finally, BigWig read coverage track files were created using the export() function from the rtracklayer R package (v. 1.52.1).
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig read coverage track files, averaged genome wide read coverage

source_name: B16-gp33 tumors

growth_protocol: B16-gp33 were cultured in complete DMEM GlutaMAXTM-I with 100μg/ml G418 (Calbiochem). Primary T cells were cultured in complete RPMI 1640 GlutaMAXTM-I.

extract_protocol:
Nuclei were extracted following 10x protocol using the low input numbers suggestions.
Libraries were prepared following the 10x protocol.

treatment_protocol: Tumors were collected and processed with gentleMACS™ Dissociator followed by CD45 positive enrichment following Miltenyi Biotec protocol. Samples were then pooled by genotype and sorted for transferred P14 CD8 T cells.

value: B16-gp33 tumors

tag: cell line

value: P14 T cells

value: CD8 T cells

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ    NFAT5 fl/fl CD4-Cre+/-

value: T cell transfer on day 7


title: SL389313

status: Public on Jun 26 2023

city: Huntsville

first: Belle

middle: Aine

last: Moyers

state: AL

address: 601 Genome Way

institute: HudsonAlpha

data_processing:
Files were processed according to established ENCODE TF-ChIP-seq analysis pipeline.  Details are available at https://www.encodeproject.org/chip-seq/transcription_factor/
Assembly: hg38
Supplementary files format and content: ENCODE narrowPeak format. Contains the location of each ChIP-seq peak and various other metrics, detailed at http://genome.ucsc.edu/FAQ/FAQformat.html#format12

extract_protocol:
Crosslinking: 1% formaldehyde, 10 minutes, room temperature. See Meadows et al. (2020) "Epitope tagging ChIP-seq of DNA binding proteins using CETCh-seq".  For input FASTQs, no antibody pulldown was performed.
ChIP-seq libraries were prepared using the ENCODE standardized protocol. 5-50 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Libraries were validated and quantified using KAPA library quantification kit.


title: SL399477


title: SL414436


title: SL414418


title: SL399478


title: SL421012


title: SL471745


title: SL436334


title: SL389312


title: SL373232


title: SL366273


title: SL373233


title: SL356948


title: SL373234


title: SL366274


title: SL348791


title: SL373295


title: SL339631


title: ZZZ3

tag: chip antibody

value: Monoclonal Anti-FLAG M2

tag: chip antibody_vendor

value: Sigma-Aldrich

tag: chip antibody_cat/lot/batch_#

tag: input sample

value: Used SL339631 as input


title: SL421013


title: SL348722


title: SL356949


title: ZNF879

value: Used SL414436 as input


title: ZSCAN25

value: Used SL373295 as input


title: ZUFSP

value: Used SL373234 as input


title: SL471699


title: ZNF850

value: Used SL399478 as input


title: ZNF85


title: ZNF816


title: ZNF790

value: Used SL421013 as input


title: ZNF746

value: Used SL373232 as input


title: ZNF827

value: Used SL414418 as input


title: ZNF783

value: Used SL356948 and SL356949 as input


title: ZNF747

value: Used SL356948 as input


title: ZNF74

value: Used SL389312 as input


title: ZNF865


title: WT

tag: tissue

value: B16-gp33 tumors

value: P14 T cells

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ NFAT5 fl/fl CD4-Cre-/-

tag: treatment


title: ZNF853


title: ZNF558


title: ZNF704

value: Used SL339631 and SL263546 as input


title: ZNF552

value: Monoclonal Anti-FLAG M2

value: Used SL366273 as input


title: ZNF701

value: Sigma-Aldrich

value: Used SL373233 as input


title: ZNF45


title: ZNF546


title: ZNF529


title: ZNF334

value: Used SL421012 as input


title: ZNF431

value: Used SL373234 as input


title: ZNF669


title: ZNF439


title: ZNF646


title: ZNF544

value: Used SL154817 as input


title: ZNF430

value: Used SL436334 as input


title: ZNF688


title: ZNF329

value: Used SL356949 as input


title: ZNF75D

value: Used SL348791 as input


title: ZNF528

value: Used SL339631 as input


title: ZNF251


title: ZNF222


title: ZNF275

value: Used SL348722 and SL263546 as input


title: ZNF235

value: Used SL348722 as input


title: ZNF559

value: Used SL366274 as input


title: ZNF571


title: ZNF18


title: ZNF160


title: ZNF140


title: ZMYM4

value: Used SL414418 as input


title: ZMYM2


title: ZFP91


title: ZNF280C

value: Used SL399477 as input


title: ZFHX3

value: Used SL421013 as input


title: ZNF284

value: Monoclonal Anti-FLAG M2


title: ZBTB47


title: TRIM24


title: SRY

value: Used SL356949 and SL373232 as input


title: ZGLP1

value: Sigma-Aldrich

value: Used SL373295 as input


title: ZFP90

value: Used SL154817 and SL263546 as input


title: SP110

value: Used SL339631 and SL366273 as input


title: SMAD7


title: STAT5A

value: Used SL348722 and SL339631 as input


title: THAP1


title: SIX5


title: NCOA1


title: RCOR3


title: SALL2

value: Used SL263546 as input


title: SCMH1

value: Used SL373234 as input


title: NR1H2

value: Used SL471699 as input


title: PAX8

value: Used SL339631 as input


title: NPAS2

value: Used SL154817 as input


title: SALL1

value: Used SL471745 as input


title: POU2F1


title: MZF1

value: Used SL389313 as input


title: REV3L


title: NFIB

value: Used SL436334 as input


title: MGA


title: ZIM2

value: Used SL356948 as input


title: MED12

value: Used SL348722 as input


title: L3MBTL4

value: Monoclonal Anti-FLAG M2

value: Used SL366274 as input


title: ZBTB22

value: Sigma-Aldrich


title: HMGN3

value: Used SL399478 as input


title: HSF4

value: Used SL373233 as input


title: HIC2


title: KLF15

value: Used SL263546 and SL348722 as input


title: MEIS1


title: HES6

value: Used SL414436 as input


title: KAT6A


title: HES4

value: Used SL421013 as input


title: LHX6


title: ZBTB12

value: Used SL414418 as input


title: HKR1

value: Used SL373295 as input


title: JRK

value: Used SL389312 as input


title: GPBP1L1

value: Used SL373234 as input


title: GLYR1


title: GLMP


title: FOXO4


title: FAM200B


title: EBF1

value: Used SL154817 as input


title: E4F1


title: FOXC1


title: DPF1


title: E2F8

value: Used SL471745 as input


title: CENPX


title: CENPBD1

value: Used SL356949 and SL373232 as input


title: BAZ2A


title: AFF1


title: SL154817


title: SL263546


title: ZSCAN12

value: Used SL263546 as input


title: TTF1


title: ZFAT


title: TSC22D2


title: PHTF1


title: PRDM4


title: PRMT5


title: TEAD2


title: PEG3


title: E2F7


title: NCOA2


title: PBX3


title: MLXIP


title: CSDA

value: Used SL348722 as input


title: MED13L

value: Monoclonal Anti-FLAG M2


title: MEIS2


title: ELK3


title: EP300


title: ELK4


title: CAMTA1


title: ZNF219


title: ZNF593


title: ZNF148


title: ZCCHC11


title: SLC30A9


title: Experiment_3_Pool_5_TCR_sequencing

status: Public on Jun 18 2023

city: Munich

first: Sebastian

last: Jarosch

state: Bavaria

address: Trogerstr. 30

department: institut für Medizinische Mikrobiologie, Immunologie und Hygiene

institute: TU Munich

description:
TCR sequences
scRNAseq

library_source: transcriptomic single cell

data_processing:
Patient 3: Cell Ranger (version 6.0.2; 10x Genomics) was used for demultiplexing and alignment using default parameters
Python software package SCANPY (version 1.8.0) was used for downstream analysis
Assembly: human reference genome GRCh38 (Ensembl 98)
Supplementary files format and content: Output of the Cell Ranger count Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized)
Supplementary files format and content: Output of the Cell Ranger VDJ Analysis Pipeline (json file for clonotype annotation)

source_name: gastrointestinal biopsy

extract_protocol:
Chromium Next GEM Single Cell 5' GEM, Library & Gel Bead Kit (10x genomics)
Chromium Next GEM Single Cell 5' Library Kit (10x genomics)   Chromium Single Cell V(D)J EnrichmentKit, Human T Cell (10x genomics)  Chromium Single Cell 5' Feature Barcode Library Kit (10x genomics)
Illumina paired-end sequencing

treatment_protocol: Single cell suspensions were generated from gastrointestinal biopsies via protease digestions and frozen in FCS containing 10% DMSO. On the day of the experiment, cells were thawed and CD45+ cells enriched for scRNA sequencing via flow sorting.

value: CD45+ T cells

value: gastrointestinal tract


title: Experiment_2_Pool_4_TCR_sequencing

description:
TCR sequences
scRNAseq


title: Experiment_3_Pool_9_TCR_sequencing

description:
TCR sequences
scRNAseq


title: Experiment_3_Pool_7_TCR_sequencing

description:
TCR sequences
scRNAseq


title: Experiment_3_Pool_7_gene expression

description:
total mRNA + HTO
scRNAseq


title: Experiment_3_Pool_6_TCR_sequencing

description:
TCR sequences
scRNAseq


title: Experiment_3_Pool_8_gene expression

description:
total mRNA + HTO + Surface
scRNAseq


title: Experiment_3_Pool_6_gene expression

description:
total mRNA + HTO + Surface
scRNAseq


title: Experiment_3_Pool_9_gene expression

description:
total mRNA + HTO
scRNAseq


title: Experiment_3_Pool_8_TCR_sequencing

description:
TCR sequences
scRNAseq


title: FOSL1

value: Sigma-Aldrich


title: Experiment_3_Pool_5_gene expression

description:
total mRNA + HTO
scRNAseq


title: Experiment_2_Pool_4_gene expression

description:
total mRNA + HTO + Surface
scRNAseq


title: HS20 Week 0

type: protein

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

institute: Liverpool Hospital

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS20W0

data_processing:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay. (Assarsson et al., 2014). All of the samples met the quality control (QC) for the Olink panels. Gene set enrichment (pathway) analysis was performed using Reactome (Croft et al., 2014), False discovery rate cutoff at 0.05 was used to identify significant enrichment.
IPC normalized

label: OLINK PEA

molecule: protein

source_name: Serum

extract_protocol: 5mL of serum was drawn from patients at baseline and after 4 weeks of therapy with Upadacitinib 15mg daily. Samples were centrifuged after collection, and serum was stored at -80 C.

tag: disease

value: Hidradenitis Suppurativa

tag: time point

value: Baseline


title: Experiment_2_Pool_3_TCR_sequencing

description:
TCR sequences
scRNAseq

tag: cell type


title: HS19 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS19W0


title: HS18 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS18W0


title: HS17 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS17W0


title: HS16 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS16W0


title: Experiment_2_Pool_3_gene expression

description:
total mRNA + HTO
scRNAseq


title: HS14 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS14W0


title: Experiment_2_Pool_2_gene expression

description:
total mRNA + HTO + Surface
scRNAseq


title: HS12 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS12W0


title: HS9 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS9W0


title: HS11 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS11W0


title: HS13 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS13W0


title: Experiment_2_Pool_2_TCR_sequencing

description:
TCR sequences
scRNAseq


title: Experiment_1_Pool_1_TCR_sequencing

description:
TCR sequences
scRNAseq


title: HS10 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS10W0


title: HS15 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS15W0


title: HS7 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS7W0


title: HS4 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS4W0


title: HS2 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS2W0


title: Experiment_1_Pool_1_gene expression

description:
total mRNA + HTO
scRNAseq


title: MK6974_2: K562 Sample 3

status: Public on Jun 14 2023

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were limited to the number denoted in the accompanying manuscript (Deronisha et al., 2023)
NextSeq: Technical read: Read 2 -UMI/Cell barcodes are positioned exactly as in (Klein et al., 2015) Biological read: read1 -transcript
NovaSeq:Technical read: Read1 - UMI/cell barcodes are positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - transcript
Assembly: Mouse: GRCm38.85; Human: GRCh38.p7
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows

source_name: K562 cell line

growth_protocol: primary cells, cell lines grown in standard conditions of C02 and DMEM

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index)

tag: prep

value: inDrop scRNA-seq

value: parental line

value: K562 cell line


title: HS5 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS5W0


title: 2242_EC: Gastric Corpus

source_name: stomach

value: WT

value: stomach


title: HS3 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS3W0


title: HS1 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS1W0


title: MK6974_1: K562 Sample 2


title: HS6 Week 0

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS6W0


title: 1291_AS_4_Coffey: cell viability enrichment

source_name: colon

value: colon


title: 1309_AS_1_Hughey: cell viability enrichment


title: 1309_AS_3_Hughey: cell viability enrichment


title: 1291_AS_1_Coffey: cell viability enrichment


title: 1291_AS_3_Coffey: cell viability enrichment


title: 5394-YX-2: Tipload S2 (CP but minced)


title: 6690-yx-2: All Cell AC S2


title: 6690-yx-3: All Cell AC S3


title: 6690-yx-1: All Cell AC S1


title: 4903-YX-6: S2 BHM normal (tip load)


title: 4903-YX-3: S2 Tip loading


title: 4903-YX-4: S3 standard tubing (CP on crypts)


title: 4903-YX-1: S1F1 Tip loading


title: 4858-AS-3: S3 1% PFA fixed test


title: 4858-AS-2: S2 0.1X DSP fixed test


title: 4858-AS-1: S1 Un fixed test (CP on crypts)


title: 4812-YX-2: All Cell S2 100c:150 dil


title: 4706-AS-1: S1 F1 MACS enzyme on crypts


title: 4498-AS-4: CP (minced) S2 F1


title: 4812-YX-1: All Cell S1 200c:50 Dil


title: 4498-AS-3: MACS (minced) S1 F1


title: 4498-AS-2: Cold Protease S2 F1 (CP on crypts)


title: 1172_AS_3: cell viability enrichment


title: Saccharomyces cerevisiae-wild-type (Arp4-3Flag)-repeat2

status: Public on May 31 2023

city: Shanghai

first: Yue

last: Pan

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science, CAS

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Paired-end sequencing reads were trimmed for adaptor and low-quality reads by fastp (version: 0.21.0).
Then, trimmed reads was aligned to the reference genome (Saccharomyces genome database: https://www.yeastgenome.org) using subcommand mem of BWA (version: 0.7.15-r1140) with default parameters.
Bam file was sorted and de-duplicated using the samtools (version: 1.4).
We used MACS2 (Version: 2 2.1.1.20160309) to call Swc4 ChIP–seq peaks with the qvalue < 0.05
GTF (gene transfer format) file for Saccharomycescerevisiae was used to annotate the ChIP-seq peaks.
Assembly: S288C
Supplementary files format and content: bigWig, narrowPeak

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: The yeast cells inoculated in to 50 ml YPD medium were grown to mid-log phase (0D600 ~0.6).

extract_protocol:
The yeast cell lysates were clarified from sonicated nuclei and Arp4-DNA complexes were isolated with antibody.
Sequencing library was constructed by The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, cat#E7645).

value: yeast cells

value: Flag (ABclonal, cat#AE005)

value: wild-type with ARP4-3FLAG

value: mid-log phase yeast cells, cultured at 30°C


title: Aorta, Kdr-KO, scRNAseq

status: Public on Jun 12 2023

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

description: 10x Genomics

data_processing:
Each scRNA-seq data set was processed by CellRanger (v4.0.0) pipeline to perform the alignment against the modified mouse reference genome mm10, filter the alignment and count barcodes and UMIs
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aorta

extract_protocol:
Kdr-KO mice were treated with tamoxifen at 8 weeks old. Then 8 weeks later, aortas were harvested from the mice, perfused with cold PBS, and then finely minced and transferred to the digestion mix (HBSS, 1U/µl Collagenase type 1 (LS004197, Worthington)). Tissues were incubated with the digestion mix at 37℃ for 30 minutes. The cell suspension was filtered through a 70 µm cell strainer and then pelleted by centrifugation at 300g for 5 minutes. After washing cells with 500ml HBSS, cells were loaded onto the 10x Chromium controller the generate Gel Bead-in-Emulsions (GEMs), which were further processed into single cell 5’ gene expression libraries using Chromium Single Cell 5’ Library Kit (v1.1).
The cell suspense was loaded in 10x Chromium controller to generate GEMs, which were further processed into single cell 5ʹ gene expression libraries using Chromium Single Cell 5ʹ Library Kit (v1.1).

value: Aorta

value: Aortic cell

value: R26-DreER, Ki67-CrexER, R26-GFP, Kdr-rox

value: tamoxifen at 8 weeks old, and harvested after 8 weeks


title: Saccharomyces cerevisiae-wild-type (no tag)-repeat2

value: wild-type with no-tag


title: Saccharomyces cerevisiae-wild-type (no tag)-repeat1


title: Saccharomyces cerevisiae-wild-type (Arp4-3Flag)-repeat1


title: animal337_peptides1012_bigenic_female

first: Dieter

last: Edbauer

state: Select...

address: Feodor-Lynenstr. 17

institute: DZNE

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor (adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.  Software Information: SOAPnuke (Version v1.5.2); Parameters -l 15 -q 0.2 -n 0.05
Software of HISAT use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area.   Software Information: HISAT2 (Version: v2.0.4); Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8
Expression quantification: We used Bowtie2[1] to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM[2] to calculate the gene expression level of each sample.   Software Information: Bowtie2 (version: v2.2.5); Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200; Official Website: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml  RSEM: (version: v1.2.8); Parameters：-p 8 --forward-prob 0.5 --paired-end; Official Website: http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html  References: [1] Langmead, B. et al. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012);  [2] Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
Assembly: mm10
Supplementary files format and content: Comma-separated file including raw count values for all samples

source_name: cerebral cortex (whole tissue)

extract_protocol:
RNA from approximately 30 mg of each mouse neocortical tissue was harvested using Direct-zol RNA Microprep   (Zymo Research). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using BGI in house mRNA-Seq Library Prep Kit following manufacturer's protocols (sample QC, mRNA Isolation, mRNA Fragmentation, cDNA Synthesis, End Repair, Add A and Adaptor Ligation, PCR, Library QC, Circularization). Libraries were paired-end sequenced with a read length of 100 bp and an average depth of 20 million reads .

treatment_protocol:
Starting at 8 weeks of age, all mice were vaccinated five times before (monthly vaccinations) and once after transgene induction. The total dose of 40 µg peptide (or PBS for controls) was administered half intraperitoneally and half subcutaneously.
To induce transgene expression, doxycycline was removed from the chow at 25.5 weeks of age. All animals were sacrificed 3 weeks after transgene induction (at 28.5 weeks of age) using ketamine/xylazine and transcardially perfused with ice-cold phosphate-buffered saline according to local animal law. Brain tissue was snap-frozen using liquid nitrogen.

value: cerebral cortex (whole tissue)

tag: strain

value: mixed C57BL/6J x C3H/HeJ

tag: Sex

value: female

value: bigenic

value: combined peptides 10+12

tag: group


title: animal343_PBS_monogenic_female

tag: genotype

value: monogenic

value: PBS (control)

value: ctrl-PBS


title: 4903-YX-5: S1 BHM frozen (tip load)

value: inDrop scRNA-seq

value: WT

value: colon


title: animal328_peptide15_bigenic_female

value: peptide 15


title: animal346_peptide15_bigenic_male

value: male


title: animal301_peptides1012_bigenic_male


title: animal318_PBS_monogenic_female


title: animal313_peptides1012_bigenic_female


title: animal280_PBS_monogenic_female


title: animal284_peptide15_bigenic_male


title: animal266_peptides1012_bigenic_female


title: animal261_peptide15_bigenic_male


title: animal269_peptide15_bigenic_female


title: animal277_peptides1012_bigenic_female


title: 4498-AS-1: Colagenase + DNaseS1 F1


title: animal254_peptide15_bigenic_female


title: animal270_PBS_bigenic_female

value: TDP-PBS


title: animal243_peptide15_bigenic_male


title: animal233_PBS_bigenic_female


title: animal322_PBS_monogenic_male


title: animal251_PBS_bigenic_male


title: animal242_peptides1012_bigenic_male


title: animal232_PBS_monogenic_male


title: animal221_PBS_monogenic_female


title: animal184_peptide15_bigenic_male


title: animal200_peptides1012_bigenic_female


title: animal193_PBS_monogenic_female


title: animal217_PBS_bigenic_male


title: animal181_PBS_monogenic_female


title: animal146_PBS_monogenic_female


title: animal131_PBS_monogenic_male


title: animal137_PBS_monogenic_male


title: animal126_peptide15_bigenic_male


title: animal214_peptide15_bigenic_female


title: animal99_PBS_monogenic_female


title: animal91_PBS_bigenic_male


title: animal82_PBS_bigenic_female


title: animal54_peptide15_bigenic_female


title: animal71_PBS_monogenic_male


title: animal47_peptides1012_bigenic_female


title: animal51_peptides1012_bigenic_male


title: animal110_PBS_monogenic_male


title: animal196_PBS_bigenic_male


title: animal42_PBS_bigenic_female


title: animal41_PBS_monogenic_male


title: animal26_PBS_bigenic_male


title: animal59_peptide15_bigenic_male


title: NCC030, scRNA-seq

status: Public on May 30 2023

city: Singapore

first: Chun Chau Lawrence

last: Cheung

address: 20 College Road

department: Department of Anatomical Pathology

country: Singapore

institute: Singapore General Hospital

description: 10x Genomics

data_processing:
Paired-end sequencing at 2 × 150-bp was performed using the Illumina NovaSeq 6000 platform (Illumina, Inc., San Diego, CA, USA). The raw reads were aligned and quantified using the Cell Ranger (version 4.0.0, 10× Genomics) against the GRCh38 human reference genome (GenBank Assembly ID GCA_000001405.28). The gene expression data were cleaned up and processed using Seurat R package (v4.0.3) with the default parameters unless otherwise specified, as follows: (i) excluding cells with <200 unique genes (low-quality cells or empty droplets), >4,000 unique genes (doublets), or >35% mitochondrial genes (low-quality or dying cells), and subsequently (ii) normalization (SCTransform), (iii) projection to lower dimensional space (RunPCA and RunUMAP), (iv) cell clustering (FindNeighbors and FindClusters), and (v) mapping to references of 2,700 PBMC cells with cell-type annotation (FindTransferAnchors, MapQuery)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood mononuclear cells

extract_protocol:
PMBCs from 6 ICB-treated patients were extracted for single-cell RNA sequencing. Approximately 16,000 PBMCs were loaded onto the Chromium Controller (10x Genomics, San Francisco, CA, USA) for targeted recovery of 10,000 single cells. The cells were partitioned into nanoliter-scale Gel Bead-In Emulsions and individually barcoded.
The 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics, San Francisco, CA, USA) was used for reverse transcription, cDNA amplification, and library construction of gene expression libraries according to the manufacturer’s instructions. Library quality was assessed using BioAnalyzer 2100 with an Agilent High Sensitivity DNA Kit (Agilent Technologies, Inc., Santa Clara, CA, USA).

tag: disease state

value: ICB-treated HCC patients

value: peripheral blood mononuclear cells


title: NCC037, scRNA-seq

description: 10x Genomics


title: animal38_PBS_monogenic_female


title: NCC034, scRNA-seq

description: 10x Genomics


title: animal130_peptides1012_bigenic_male


title: NCC027, scRNA-seq

description: 10x Genomics


title: NCC022, scRNA-seq

description: 10x Genomics


title: NCC025, scRNA-seq

description: 10x Genomics


title: animal84_PBS_monogenic_female


title: animal124_PBS_bigenic_male


title: SAN 10xmultiome 2 (MO Sa2)

status: Public on May 22 2023

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
Raw sequencing reads were processed to aligned reads and fragments files using the PUMATAC pipeline. Briefly, cell barcodes were corrected using a pre-existing whitelist using scToolkit. TrimGalore was used to trim reads. Alignment to GRCh38 was performed using bwa-mem2. Cell barcode mutliplets were detected using scToolkit. Aligned reads were converted to fragments.tsv.gz using scToolkit.
library strategy: 10x Multiome
Assembly: GRCh38
Supplementary files format and content: "FULL" fragments.tsv.gz: tab-delimited bed-like fragments file with 5 fields: chromosome, start position, end position, cell barcode and count. Derived from the full sequencing data.
Supplementary files format and content: "FULL" fragments.tsv.gz.tbi: tabix index supplementary to full fragments.tsv.gz files.
Supplementary files format and content: "FIXEDCELLS" fragments.tsv.gz: tab-delimited bed-like fragments file with 5 fields: chromosome, start position, end position, cell barcode and count. Derived from the sequencing data downsampled to the fixed number of cells found in the full sequencing data.
Supplementary files format and content: "FIXEDCELLS" fragments.tsv.gz.tbi: tabix index supplementary to fixedcells fragments.tsv.gz files.
Supplementary files format and content: h5ad files: scanpy-generated hdf5 formated raw count matrices

source_name: Mixture of PBMC from 2 donors

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were purchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
PBMC were thawed as described above. Nuclei isolation was slightly different, including RNAse inhibitors to ensure RNA quality. Briefly, two pools of cells (technical replicates) were generated from these two donors by mixing 500,000 cells per donor, in total 1 million cells per pool. Cells were pelleted for 5 mins at 300 rcf at 4oC and washed twice in 1mL wash buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 1U/µL RNase inhibitor). After the second wash and final centrifugation, cells were resuspended 0.1 mL chilled Lysis buffer (10 mM Tris, HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA, 1 mM DTT, and incubated for 3 minutes on ice. Nuclei were washed 3 times in 1 mL wash buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 1U/µL RNase inhibitor) by spinning down at 500 g for 5 min.  After the last centrifugation cells were resuspended in chilled Nuclei buffer (Nuclei Buffer 1X, 1 mM DTT, 1U/µL RNAse inhibitor) calculated and loaded according to the Chromium Next GEM single cell multiome ATAC + GEX user guide (protocol CG000338 Rev A). For loading onto 10x chips we aimed for a recovery of 3000 nuclei. Following nuclei isolation and transposition, GEMs were generated using GEM Chip J. Post GEM clean-up and pre-amplification PCR were carried out as per user guide. For the ATACseq library 8 cycles of PCR were run, whilst 7 cycles of PCR were performed for cDNA amplification. Of the amplified cDNA 25 % of the material was used for gene expression library construction with 15 cycles of PCR for both technical replicates.

value: Mixture of PBMC from 2 donors

value: PBMC

value: Wild type


title: SAN 10xmultiome 1 (MO Sa1)


title: CNA 10xmultiome 2 (MO C2)


title: CNA 10xmultiome 1 (MO C1)


title: MDC mtscatac 2 (mtscATAC M2)

data_processing:
Raw sequencing reads were processed to aligned reads and fragments files using the PUMATAC pipeline. Briefly, cell barcodes were corrected using a pre-existing whitelist using scToolkit. TrimGalore was used to trim reads. Alignment to GRCh38 was performed using bwa-mem2. Cell barcode mutliplets were detected using scToolkit. Aligned reads were converted to fragments.tsv.gz using scToolkit.
Assembly: GRCh38
Supplementary files format and content: "FULL" fragments.tsv.gz: tab-delimited bed-like fragments file with 5 fields: chromosome, start position, end position, cell barcode and count. Derived from the full sequencing data.
Supplementary files format and content: "FULL" fragments.tsv.gz.tbi: tabix index supplementary to full fragments.tsv.gz files.
Supplementary files format and content: "FIXEDCELLS" fragments.tsv.gz: tab-delimited bed-like fragments file with 5 fields: chromosome, start position, end position, cell barcode and count. Derived from the sequencing data downsampled to the fixed number of cells found in the full sequencing data.
Supplementary files format and content: "FIXEDCELLS" fragments.tsv.gz.tbi: tabix index supplementary to fixedcells fragments.tsv.gz files.

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Cells from each donor were subsequently pooled at a 1:1 ratio and after washing, cells were fixed in 1% formaldehyde (FA; ThermoFisher #28906) in PBS for 10 min at RT, quenched with glycine solution to a final concentration of 0.125 M before washing cells twice in PBS via centrifugation at 400 g, 5 min, 4 °C. Cells were subsequently treated with lysis buffer (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1% BSA) for 3 min on ice, followed by adding 1 mL of chilled wash buffer and inversion (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA) before centrifugation at 500 x g, 5 min, 4 °C.
mtscATAC-seq libraries were generated using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (v1.1, #1000175) according to the manufacturer’s instructions (CG000209). Briefly, following tagmentation, cells were loaded on a Chromium controller Single-Cell Instrument to generate single-cell Gel Bead-In-Emulsions (GEMs) followed by linear PCR as described in the protocol using a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). After breaking the GEMs, the barcoded tagmented DNA was purified and further amplified to enable sample indexing (11 cycles of PCR) and enrichment of mtscATAC-seq libraries. The final libraries were quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent).


title: MDC mtscatac 1 (mtscATAC M1)


title: CNAG HyDrop 2 (Hy C2)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
HyDrop was performed as previously described (De Rop et al. 2022), but with an updated barcoded hydrogel bead design and minor improvements in nuclei handling. Briefly, barcoded hydrogel beads were produced as described previously, but using 384 x 384 combinations of primers instead of the original method’s 96 x 96 x 96, resulting in a barcode sequence of 30 instead of 50 base pairs. 1 million PBMCs was counted, pelleted and resuspended in 200 μL of ATAC Lysis Buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 μM Pitstop in DMSO, 0.01% Digitonin) for 5 min. on ice. 1 mL of ATAC Nuclei Wash Buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm strainer (Flowmi). 25 000 PBMC nuclei were resuspended in 25 μL of ATAC Reaction Mix (10% DMF, 10% Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/μL Tn5, 70 μM Pitstop in DMSO, 0.1% Tween-20, 0.01% Digitonin) and incubated at 37 °C for 1 hour without shaking. To recover a targeted 3000 nuclei, 5625 tagmented nuclei were added to 48 μL of PCR mix (1.3X Phusion HF Buffer, 15% Optiprep, 1.3 mM dNTPs, 39 mM DTT, 0.065 U/μL Phusion HF Polymerase, 0.065 U/μL Deep Vent Polymerase, 0.013 U/μL ET SSB). PCR mix was co-encapsulated with 35 μL of freshly thawed HyDrop-ATAC beads in HFE-7500 Novac oil with EA-008 surfactant (RAN Biotech) on the Onyx microfluidics platform (Droplet Genomics). The resulting emulsion was collected in aliquots of 25 μL total volume and thermocycled according to the linear amplification program (72 °C 15 min., 98 °C 3 min., 12 amplification cycles of [98 °C 10 s, 63 °C 30 s, 72 °C 1 min.], followed by a final hold on 4 °C). 125 μL of recovery agent (20% PFO in HFE), 55 μL of GITC Buffer (5 M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4) and 5 μL of 1 M DTT was added to each separate aliquot of 50 μL thermocycled emulsion and incubated on ice for 5 minutes. 5 μL of Dynabeads was added to the aqueous phase and incubated for 10 minutes. Dynabeads were pelleted on a Nd magnet and washed twice with 80% EtOH. Elution was performed in 50 μL of EB-DTT-Tween (10 mM DTT, 0.1% Tween-20 in EB (10 mM Tris-HCl, pH 8.5)). A 1x Ampure bead purification was performed according to manufacturer’s recommendations. Elution was performed in 30 μL of EB-DTT (10 mM DTT in EB). Eluted library was further amplified in 100 μL of PCR mix (1x KAPA HiFi, 1 μM index i7 primer, 1 μM index i5 primer). Final library was purified in a 0.4x-1.2x double-sided Ampure purification and eluted in 25 μL of EB-DTT (10 mM DTT in EB) and quality-controlled on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies).


title: CNA mtscatac 2 (mtscATAC C2)


title: CNAG HyDrop 3 (Hy C3)


title: CNA mtscatac 1 (mtscATAC C1)


title: BIO ddseq 2 (ddSEQ Bi2)

source_name: PBMC

extract_protocol:
Cryopreserved PBMC cells were quickly thawed in a 37  °C water bath, rinsed with culture medium (RPMI medium supplemented with 15% FBS) and then treated with 0.2 U μl−1 DNase I (Thermo Fisher Scientific) in 5 mL of culture medium at 37 °C for 30 min. After DNase I treatment, cells were washed once with medium and then twice with ice-cold 1× PBS with 0.1% BSA. Cells were then filtered with a 35-μm cell strainer (Corning) and cell viability and concentration were measured with Trypan blue on the TC20 Automated Cell Counter (Bio-Rad).
For a detailed description of tagmentation protocols and buffer formulations, refer to the SureCell ATAC-Seq Library Prep Kit User Guide (17004620, Bio-Rad). Collected cells and tagmentation buffers were chilled on ice. Lysis was performed simultaneously with tagmentation. After washing, equal number of cells from each donor were mixed with Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1× PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (ATAC Tagmentation Buffer and Enzyme are both included in the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad)). The mix was split into two technical replicates and the cells were then mixed and agitated on a ThermoMixer (5382000023, Eppendorf) for 30 min at 37  °C. Tagmented cells were kept on ice before encapsulation.  Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). scATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed in a C1000 Touch thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad); PCR conditions were as follows: 37 °C for 30 min, 85 °C for 10 min, 72 °C for 5 min, 98 °C for 30 s, eight cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. Emulsions were broken and products were cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded amplicons were further amplified using a C1000 Touch thermal cycler with a 96-Deep Well Reaction Module; PCR conditions were as follows: 98 °C for 30 s, seven cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. PCR products were purified using Ampure XP beads. and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent).


title: TXG 10xv11 1 (v1.1 T1)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
Technical replicates were generated on the same day starting from the same freshly thawed nuclei suspension. scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits v1.1 User Guide (10x Genomics; CG000209 Rev D). Briefly, the Transposition Reaction was prepared by mixing the desired number of nuclei with ATAC Buffer (10x Genomics) and ATAC Enzyme (10x Genomics), and was then incubated for 60 min at 37 °C. Nuclei were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller with Chip H. After this, the DNA linear amplification was performed by incubating the GEMs at the following thermal cycling conditions: 72 °C for 5 minutes, 98 °C for 30 seconds, 12 cycles of 98 °C for 10 seconds, 59 °C for 30 seconds and 72 °C for 1 minute. GEMs were broken using the Recovery Agent (10x Genomics), and the resulting DNA was purified by sequential Dynabeads and SPRIselect reagent beads clean-ups. Libraries were indexed by PCR using the Single Index Kit N Set A (10x Genomics, PN-1000212), and incubating at the following thermal cycling conditions: 98 °C for 45 seconds, 10 cycles of 98 °C for 20 seconds, 67 °C for 30 seconds, 72 °C for 20 seconds with a final extension of 72 °C for 1 min. Sequencing libraries were subjected to a final bead clean-up SPRIselect reagent.


title: CNAG HyDrop 1 (Hy C1)


title: BIO ddseq 1 (ddSEQ Bi1)


title: CNA 10xv11c 2 (v1.1c C2)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. The PBMC pellet was thawed and suspended in NIB-HEPES prior to Dounce homogenization.
Technical replicates were generated on the same day starting from the same freshly thawed nuclei suspension. scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits v1.1 User Guide (10x Genomics; CG000209 Rev D). Briefly, the Transposition Reaction was prepared by mixing the desired number of nuclei with ATAC Buffer (10x Genomics) and ATAC Enzyme (10x Genomics), and was then incubated for 60 min at 37 °C. Nuclei were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller with Chip H. After this, the DNA linear amplification was performed by incubating the GEMs at the following thermal cycling conditions: 72 °C for 5 minutes, 98 °C for 30 seconds, 12 cycles of 98 °C for 10 seconds, 59 °C for 30 seconds and 72 °C for 1 minute. GEMs were broken using the Recovery Agent (10x Genomics), and the resulting DNA was purified by sequential Dynabeads and SPRIselect reagent beads clean-ups. Libraries were indexed by PCR using the Single Index Kit N Set A (10x Genomics, PN-1000212), and incubating at the following thermal cycling conditions: 98 °C for 45 seconds, 10 cycles of 98 °C for 20 seconds, 67 °C for 30 seconds, 72 °C for 20 seconds with a final extension of 72 °C for 1 min. Sequencing libraries were subjected to a final bead clean-up SPRIselect reagent.


title: CNA 10xv11 1 (v1.1 C1)


title: CNA 10xv11 2 (v1.1 C2)


title: CNA 10xv11c 1 (v1.1c C1)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
Technical replicates were generated on the same day starting from the same freshly thawed nuclei suspension. scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits v1.1 User Guide (10x Genomics; CG000209 Rev D). Briefly, the Transposition Reaction was prepared by mixing the desired number of nuclei with ATAC Buffer (10x Genomics) and ATAC Enzyme (10x Genomics), and was then incubated for 60 min at 37 °C. Nuclei were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller with Chip H. After this, the DNA linear amplification was performed by incubating the GEMs at the following thermal cycling conditions: 72 °C for 5 minutes, 98 °C for 30 seconds, 12 cycles of 98 °C for 10 seconds, 59 °C for 30 seconds and 72 °C for 1 minute. GEMs were broken using the Recovery Agent (10x Genomics), and the resulting DNA was purified by sequential Dynabeads and SPRIselect reagent beads clean-ups. Libraries were indexed by PCR using the Single Index Kit N Set A (10x Genomics, PN-1000212), and incubating at the following thermal cycling conditions: 98 °C for 45 seconds, 10 cycles of 98 °C for 20 seconds, 67 °C for 30 seconds, 72 °C for 20 seconds with a final extension of 72 °C for 1 min. Sequencing libraries were subjected to a final bead clean-up SPRIselect reagent.


title: TXG 10xv2 2 (v2 T2)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits v2 User Guide (10x Genomics; CG000496 Rev B ). Briefly, the Transposition Reaction was prepared by mixing the desired number of nuclei with ATAC Buffer (10x Genomics) and ATAC Enzyme (10x Genomics), and was then incubated for 30 min at 37 °C. Nuclei were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller with Chip H. Sample v2 T1 was the only sample for which Chromium X was used. After this, the DNA linear amplification was performed by incubating the GEMs at the following thermal cycling conditions: 72 °C for 5 minutes, 98 °C for 30 seconds, 12 cycles of 98 °C for 10 seconds, 59 °C for 30 seconds and 72 °C for 1 minute. GEMs were broken using the Recovery Agent (10x Genomics), and the resulting DNA was purified by sequential Dynabeads and SPRIselect reagent beads clean-ups. Libraries were indexed by PCR using the Single Index Kit N Set A, and incubating at the following thermal cycling conditions: 98 °C for 45 seconds, 8 cycles of 98 °C for 20 seconds, 67 °C for 30 seconds, 72 °C for 20 seconds with a final extension of 72 °C for 1 min. Sequencing libraries were subjected to a final bead clean-up SPRIselect reagent.]


title: CNA 10xv2 1 (v2 C1)


title: VIB 10xv1 2 (v1 V2)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Unless specified otherwise in technology-specific methods sections, nuclei isolation was performed according to the 10x Genomics demonstrated protocol “Nuclei Isolation for Single Cell ATAC Sequencing”. Briefly, 1 million cells from the cell mix were transferred to a 1.5 mL microcentrifuge tube and centrifuged at 500 rcf for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet and 100 µL of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette mixed 10 times. Samples were then incubated on ice for 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette mixed. Nuclei were centrifuged at 500 rcf for 5 min at 4 °C and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 925-2300 nuclei/µL, suitable for a Target Nuclei Recovery of 3000.
scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits v1.0 User Guide (10x Genomics; CG000001 Rev D). Briefly, the Transposition Reaction was prepared by mixing the desired number of nuclei with ATAC Buffer (10x Genomics) and ATAC Enzyme (10x Genomics), and was then incubated for 60 min at 37 °C. Nuclei were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller. After this, the DNA linear amplification was performed by incubating the GEMs at the following thermal cycling conditions: 72 °C for 5 minutes, 98 °C for 30 seconds, 12 cycles of 98 °C for 10 seconds, 59 °C for 30 seconds and 72 °C for 1 minute. GEMs were broken using the Recovery Agent (10x Genomics), and the resulting DNA was purified by sequential Dynabeads and SPRIselect reagent beads clean-ups. Libraries were indexed by PCR using the Single Index Kit, and incubating at the following thermal cycling conditions: 98 °C for 45 seconds, 10 cycles of 98 °C for 20 seconds, 67 °C for 30 seconds, 72 °C for 20 seconds with a final extension of 72 °C for 1 min. Sequencing libraries were subjected to a final bead clean-up SPRIselect reagent.


title: CNA 10xv2 2 (v2 C2)


title: TXG 10xv2 1 (v2 T1)


title: VIB 10xmultiome 2 (MO V2)


title: OHS s3atac 2 (s3 O2)

extract_protocol:
The PBMC pellet was thawed and suspended in NIB-HEPES prior to Dounce homogenization.
s3-ATAC was then performed as described previously (Mulqueen et al. 2021). Briefly, nuclei were flow sorted via a Sony SH800 to remove debris and attain an accurate count per well before PCR in 1x TD buffer. Immediately following sorting completion, the plate was sealed and spun down for 5 min at 500 r.c.f. and 4  °C to ensure nuclei were within the buffer. Nucleosomes and remaining transposases were then denatured with the addition 1 µL of 0.1% SDS (roughly 0.01% final concentration) per well. Then 4 µL of NPM (Nextera XT Kit, Illumina Inc.) per well was subsequently added to perform gap-fill on tagmented gDNA, with an incubation at 72  °C for 10 min. Next, 1.5 µL of 1 µM A14-LNA-ME oligo was then added to supply the template for adapter switching. The polymerase-based adapter switching was then performed with the following conditions: initial denaturation at 98  °C for 30 s, ten cycles of 98  °C for 10 s, 59  °C for 20 s and 72  °C for 10 s. The plate was then held at 10  °C. After adapter switching 1% (v/v) Triton-X 100 in ultrapure H2O (Sigma 93426) was added to quench persisting SDS. The following was then combined per well for PCR: 16.5 µL of sample, 2.5 µL of indexed i7 primer at 10 µM, 2.5 µL of indexed i5 primer at 10 µM, 3 µL of ultrapure H2O, 25 µL of NEBNext Q5U 2× Master mix (New England Biolabs M0597S) and 0.5 µL of 100× SYBR Green I (Thermo Scientific S7563) for a 50 µL of reaction per well. A real-time PCR was performed on a Bio-Rad CFX with the following conditions, measuring SYBR fluorescence every cycle: 98  °C for 30 s; 16–18 cycles of 98  °C for 10 s, 55  °C for 20 s, 72  °C for 30 s, fluorescent reading, 72  °C for 10 s. After fluorescence passes an exponential growth and begins to inflect, the samples were held at 72  °C for another 30 s then stored at 4  °C. Amplified libraries were then cleaned by pooling 25 µL per well into a 15 mL conical tube and cleaned via a Qiaquick PCR purification column following the manufacturer’s protocol (Qiagen 28106). The pooled sample was eluted in 50 µL 10 mM Tris-HCl, pH 8.0. Library molecules then went through a size selection via SPRI selection beads (Mag-Bind TotalPure NGS Omega Biotek M1378-01). Next, 50 µL of vortexed and fully suspended room temperature SPRI beads were combined with the 50-µL library (1× clean up) and incubated at room temperature for 5 min. The reaction was then placed on a magnetic rack and once cleared, the supernatant was removed. The remaining pellet was rinsed twice with 100 µL of fresh 80% ethanol. After ethanol was pipetted out, the tube was spun down and placed back on the magnetic rack to remove any lingering ethanol. Next, 31 µL of 10 mM Tris-HCl, pH 8.0 were then used to resuspend the beads off the magnetic rack and allowed to incubate for 5 min at room temperature. The tube was again placed on the magnetic rack and once cleared, the full volume of supernatant was moved to a clean tube. DNA was then quantified by Qubit double-stranded DNA High-sensitivity assay following the manufacturer’s instructions (Thermo Fisher Q32851). Libraries were then diluted to 2 ng µL−1 and run on an Agilent Tapestation 4150 D5000 tape (Agilent 5067-5592). Library molecule concentration within the range of 100–1,000 base pairs (bp) was then used for final dilution of the library to 1 nM.


title: VIB 10xv1 1 (v1 V1)


title: OHS s3atac 1 (s3 O1)


title: CNA 10xv11 3 (v1.1 C3)


title: EPF HyDrop 4 (Hy E4)


title: VIB HyDrop 1 (Hy V1)


title: VIB HyDrop 1 (Hy V2)


title: EPF HyDrop 2 (Hy E2)


title: VIB 10xmultiome 1 (MO V1)


title: EPF HyDrop 1 (Hy E1)


title: VIB 10xv2 2 (v2 V2)


title: BRO mtscatac 2 (mtscATAC Br2)

extract_protocol:
Cryopreserved human PBMCs from a male and female donor were puchased from AllCells and (AllCells, Lot #3030456 and 3030663). Cryopreserved PBMC were thawed according to the 10x Genomics demonstrated protocol CG00039 ("Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing"). Briefly, 1 mL of frozen cells was rapidly thawed in a 37 °C water bath and transferred to a 50 mL tube using a 1000 µL wide bore tip. Next, 1 mL of 37 °C pre-warmed medium supplemented with 10% FBS (Thermo Fisher Scientific) was added drop-wise while gently swirling the sample. After 1 minute of incubation at room temperature, 2, 4, 8 and 16 mL of medium with 10% FBS were added drop-wise with 1 minute of incubation at room-temperature inbetween. The cell suspension was then centrifuged at 300 g for 5 min. at room temperature. The pellet was resuspended in 10 mL of medium with 10% FBS, and cells were counted. Cells from each donor were subsequently pooled at a 1:1 ratio and after washing,  cells were also washed, and 250,000 live cells were sorted using SytoxBlue at 1:1000 dilution as a live/dead cell stain. Sorting did not take place for samples mt M1-2 and mt C1-2. cells were fixed in 1% formaldehyde (FA; ThermoFisher #28906) in PBS for 10 min at RT, quenched with glycine solution to a final concentration of 0.125 M before washing cells twice in PBS via centrifugation at 400 g, 5 min, 4 °C. Cells were subsequently treated with lysis buffer (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1% BSA) for 3 min on ice, followed by adding 1 mL of chilled wash buffer and inversion (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA) before centrifugation at 500 x g, 5 min, 4 °C.
mtscATAC-seq libraries were generated using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (v1.1, #1000175) according to the manufacturer’s instructions (CG000209). Briefly, following tagmentation, cells were loaded on a Chromium controller Single-Cell Instrument to generate single-cell Gel Bead-In-Emulsions (GEMs) followed by linear PCR as described in the protocol using a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). After breaking the GEMs, the barcoded tagmented DNA was purified and further amplified to enable sample indexing (11 cycles of PCR) and enrichment of mtscATAC-seq libraries. The final libraries were quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent).


title: VIB 10xv2 1 (v2 V1)


title: STA 10xv11 2 (v1.1 St2)


title: BRO mtscatac 1 (mtscATAC Br1)


title: STA 10xv11 1 (v1.1 St1)


title: UCS ddseq 2 (ddSEQ U2)


title: HAR ddseq 1 (ddSEQ H1)


title: BIO ddseq 3 (ddSEQ Bi3)


title: UCS ddseq 1 (ddSEQ U1)


title: WT HEK 293T, 8H 991, rep 2 ESRRA_WT_8H_991_2_S11

status: Public on May 08 2023

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: WT HEK 293T, 8H 991, rep 2

data_processing:
Raw RNA sequencing reads in FASTQ files were quality-tested using FASTQC and mapped to the human reference genome (GRCh38) with STAR aligner with default parameters .
Raw or TPM (Transcripts Per Million) gene expression levels were quantified across all the exons of the top isoform in RefSeq with  analyzeRepeats.pl in HOMER
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

source_name: kidney

growth_protocol: HEK 293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was extracted from cells using the QIAGEN RNeasy Plus mini kit

value: kidney

tag: time

value: ESRRA WT


title: HAR ddseq 2 (ddSEQ H2)


title: WT HEK 293T, 4H 991, rep 1 ESRRA_WT_4H_991_1_S7

description: WT HEK 293T, 4H 991, rep 1

tag: cell line


title: WT HEK 293T, 8H 991, rep 3 ESRRA_WT_8H_991_3_S12

description: WT HEK 293T, 8H 991, rep 3


title: BIO ddseq 4 (ddSEQ Bi4)


title: WT HEK 293T, 8H 991, rep 1 ESRRA_WT_8H_991_1_S10

description: WT HEK 293T, 8H 991, rep 1


title: EPF HyDrop 3 (Hy E3)


title: WT HEK 293T, 4H 991, rep 2 ESRRA_WT_4H_991_2_S8

description: WT HEK 293T, 4H 991, rep 2


title: WT HEK 293T, 24H 991, rep 2 ESRRA_WT_24H_991_2_S17

description: WT HEK 293T, 24H 991, rep 2


title: WT HEK 293T, 2H 991, rep 2 ESRRA_WT_2H_991_2_S5

description: WT HEK 293T, 2H 991, rep 2


title: WT HEK 293T, 24H 991, rep 3 ESRRA_WT_24H_991_3_S18

description: WT HEK 293T, 24H 991, rep 3


title: WT HEK 293T, 2H 991, rep 1 ESRRA_WT_2H_991_1_S4

description: WT HEK 293T, 2H 991, rep 1


title: WT HEK 293T, 2H 991, rep 3 ESRRA_WT_2H_991_3_S6

description: WT HEK 293T, 2H 991, rep 3


title: WT HEK 293T, 16H 991, rep 3 ESRRA_WT_16H_991_3_S15

description: WT HEK 293T, 16H 991, rep 3


title: WT HEK 293T, 16H 991, rep 2 ESRRA_WT_16H_991_2_S14

description: WT HEK 293T, 16H 991, rep 2


title: WT HEK 293T, 16H 991, rep 1 ESRRA_WT_16H_991_1_S13

description: WT HEK 293T, 16H 991, rep 1


title: WT HEK 293T, DMSO, rep 2 ESRRA_WT_0H_DMSO_2_S2

description: WT HEK 293T, DMSO, rep 2

value: DMSO


title: WT HEK 293T, DMSO, rep 3 ESRRA_WT_0H_DMSO_3_S3

description: WT HEK 293T, DMSO, rep 3


title: WT HEK 293T, DMSO, rep 1 ESRRA_WT_0H_DMSO_1_S1

description: WT HEK 293T, DMSO, rep 1


title: ESRRA KO, HEK 293T, 8H 991, rep 3 ESRRA_KO_8H_991_3_S30

description: ESRRA KO, HEK 293T, 8H 991, rep 3

value: ESRRA Knock out


title: ESRRA KO, HEK 293T, 4H 991, rep 3 ESRRA_KO_4H_991_3_S27

description: ESRRA KO, HEK 293T, 4H 991, rep 3


title: ESRRA KO, HEK 293T, 8H 991, rep 2 ESRRA_KO_8H_991_2_S29

description: ESRRA KO, HEK 293T, 8H 991, rep 2


title: WT HEK 293T, 4H 991, rep 3 ESRRA_WT_4H_991_3_S9

description: WT HEK 293T, 4H 991, rep 3


title: WT HEK 293T, 24H 991, rep 1 ESRRA_WT_24H_991_1_S16

description: WT HEK 293T, 24H 991, rep 1


title: ESRRA KO, HEK 293T, 4H 991, rep 1 ESRRA_KO_4H_991_1_S25

description: ESRRA KO, HEK 293T, 4H 991, rep 1


title: ESRRA KO, HEK 293T, 2H 991, rep 3 ESRRA_KO_2H_991_3_S24

description: ESRRA KO, HEK 293T, 2H 991, rep 3


title: ESRRA KO, HEK 293T, 2H 991, rep 1 ESRRA_KO_2H_991_1_S22

description: ESRRA KO, HEK 293T, 2H 991, rep 1


title: ESRRA KO, HEK 293T, 24H 991, rep 3 ESRRA_KO_24H_991_3_S36

description: ESRRA KO, HEK 293T, 24H 991, rep 3


title: ESRRA KO, HEK 293T, 2H 991, rep 2 ESRRA_KO_2H_991_2_S23

description: ESRRA KO, HEK 293T, 2H 991, rep 2


title: ESRRA KO, HEK 293T, 24H 991, rep 2 ESRRA_KO_24H_991_2_S35

description: ESRRA KO, HEK 293T, 24H 991, rep 2


title: ESRRA KO, HEK 293T, 24H 991, rep 1 ESRRA_KO_24H_991_1_S34

description: ESRRA KO, HEK 293T, 24H 991, rep 1


title: ESRRA KO, HEK 293T, DMSO, rep 3 ESRRA_KO_0H_DMSO_3_S21

description: ESRRA KO, HEK 293T, DMSO, rep 3


title: ESRRA KO, HEK 293T, DMSO, rep 1 ESRRA_KO_0H_DMSO_1_S19

description: ESRRA KO, HEK 293T, DMSO, rep 1


title: ESRRA KO, HEK 293T, 16H 991, rep 2 ESRRA_KO_16H_991_2_S32

description: ESRRA KO, HEK 293T, 16H 991, rep 2


title: ESRRA KO, HEK 293T, 16H 991, rep 1 ESRRA_KO_16H_991_1_S31

description: ESRRA KO, HEK 293T, 16H 991, rep 1


title: siPGC1a, HEK 293T, 4H 991, rep 3 siPGC1a_4H_991_3_S27

description: siPGC1a, HEK 293T, 4H 991, rep 3

value: PGC1a knockdown


title: siPGC1a, HEK 293T, 4H 991, rep 1 siPGC1a_4H_991_1_S25

description: siPGC1a, HEK 293T, 4H 991, rep 1


title: siPGC1a, HEK 293T, 4H 991, rep 2 siPGC1a_4H_991_2_S26

description: siPGC1a, HEK 293T, 4H 991, rep 2


title: siPGC1a, HEK 293T, 8H 991, rep 2 siPGC1a_8H_991_2_S29

description: siPGC1a, HEK 293T, 8H 991, rep 2


title: ESRRA KO, HEK 293T, 16H 991, rep 3 ESRRA_KO_16H_991_3_S33

description: ESRRA KO, HEK 293T, 16H 991, rep 3


title: siPGC1a, HEK 293T, 8H 991, rep 3 siPGC1a_8H_991_3_S30

description: siPGC1a, HEK 293T, 8H 991, rep 3


title: ESRRA KO, HEK 293T, 8H 991, rep 1 ESRRA_KO_8H_991_1_S28

description: ESRRA KO, HEK 293T, 8H 991, rep 1


title: siPGC1a, HEK 293T, 2H 991, rep 3 siPGC1a_2H_991_3_S24

description: siPGC1a, HEK 293T, 2H 991, rep 3


title: siPGC1a, HEK 293T, 2H 991, rep 2 siPGC1a_2H_991_2_S23

description: siPGC1a, HEK 293T, 2H 991, rep 2


title: siPGC1a, HEK 293T, 8H 991, rep 1 siPGC1a_8H_991_1_S28

description: siPGC1a, HEK 293T, 8H 991, rep 1


title: siPGC1a, HEK 293T, 2H 991, rep 1 siPGC1a_2H_991_1_S22

description: siPGC1a, HEK 293T, 2H 991, rep 1


title: siPGC1a, HEK 293T, 24H 991, rep 2 siPGC1a_24H_991_2_S35

description: siPGC1a, HEK 293T, 24H 991, rep 2


title: ESRRA KO, HEK 293T, 4H 991, rep 2 ESRRA_KO_4H_991_2_S26

description: ESRRA KO, HEK 293T, 4H 991, rep 2


title: siPGC1a, HEK 293T, 16H 991, rep 2 siPGC1a_16H_991_2_S32

description: siPGC1a, HEK 293T, 16H 991, rep 2


title: siPGC1a, HEK 293T, 16H 991, rep 3 siPGC1a_16H_991_3_S33

description: siPGC1a, HEK 293T, 16H 991, rep 3


title: siPGC1a, HEK 293T, 16H 991, rep 1 siPGC1a_16H_991_1_S31

description: siPGC1a, HEK 293T, 16H 991, rep 1


title: siPGC1a, HEK 293T, DMSO, rep 2 siPGC1a_0H_DMSO_2_S20

description: siPGC1a, HEK 293T, DMSO, rep 2


title: siPGC1a, HEK 293T, DMSO, rep 3 siPGC1a_0H_DMSO_3_S21

description: siPGC1a, HEK 293T, DMSO, rep 3


title: siControl, HEK 293T, 8H 991, rep 2 siCont_8H_991_2_S11

description: siControl, HEK 293T, 8H 991, rep 2

value: siCont


title: siControl, HEK 293T, 4H 991, rep 2 siCont_4H_991_2_S8

description: siControl, HEK 293T, 4H 991, rep 2


title: siPGC1a, HEK 293T, DMSO, rep 1 siPGC1a_0H_DMSO_1_S19

description: siPGC1a, HEK 293T, DMSO, rep 1


title: siControl, HEK 293T, 8H 991, rep 1 siCont_8H_991_1_S10

description: siControl, HEK 293T, 8H 991, rep 1


title: siControl, HEK 293T, 8H 991, rep 3 siCont_8H_991_3_S12

description: siControl, HEK 293T, 8H 991, rep 3


title: siPGC1a, HEK 293T, 24H 991, rep 3 siPGC1a_24H_991_3_S36

description: siPGC1a, HEK 293T, 24H 991, rep 3


title: siControl, HEK 293T, 2H 991, rep 2 siCont_2H_991_2_S5

description: siControl, HEK 293T, 2H 991, rep 2


title: siControl, HEK 293T, 24H 991, rep 3 siCont_24H_991_3_S18

description: siControl, HEK 293T, 24H 991, rep 3


title: siControl, HEK 293T, 24H 991, rep 1 siCont_24H_991_1_S16

description: siControl, HEK 293T, 24H 991, rep 1


title: siControl, HEK 293T, 16H 991, rep 2 siCont_16H_991_2_S14

description: siControl, HEK 293T, 16H 991, rep 2


title: siControl, HEK 293T, 16H 991, rep 3 siCont_16H_991_3_S15

description: siControl, HEK 293T, 16H 991, rep 3


title: siControl, HEK 293T, 4H 991, rep 1 siCont_4H_991_1_S7

description: siControl, HEK 293T, 4H 991, rep 1


title: siControl, HEK 293T, 2H 991, rep 1 siCont_2H_991_1_S4

description: siControl, HEK 293T, 2H 991, rep 1


title: siControl, HEK 293T, DMSO, rep 3 siCont_0H_DMSO_3_S3

description: siControl, HEK 293T, DMSO, rep 3


title: siControl, HEK 293T, 16H 991, rep 1 siCont_16H_991_1_S13

description: siControl, HEK 293T, 16H 991, rep 1


title: siControl, HEK 293T, 24H 991, rep 2 siCont_24H_991_2_S17

description: siControl, HEK 293T, 24H 991, rep 2


title: siControl, HEK 293T, DMSO, rep 2 siCont_0H_DMSO_2_S2

description: siControl, HEK 293T, DMSO, rep 2


title: siControl, HEK 293T, DMSO, rep 1 siCont_0H_DMSO_1_S1

description: siControl, HEK 293T, DMSO, rep 1


title: WT HEK 293T, 8H 991, rep 1 TFEB_TFE3_DWT_8H_991_1_S10

description: WT HEK 293T, 8H 991, rep 1

value: TFEB+TFE3 WT


title: siPGC1a, HEK 293T, 24H 991, rep 1 siPGC1a_24H_991_1_S34

description: siPGC1a, HEK 293T, 24H 991, rep 1


title: WT HEK 293T, 4H 991, rep 3 TFEB_TFE3_DWT_4H_991_3_S9

description: WT HEK 293T, 4H 991, rep 3


title: ESRRA KO, HEK 293T, DMSO, rep 2 ESRRA_KO_0H_DMSO_2_S20

description: ESRRA KO, HEK 293T, DMSO, rep 2


title: WT HEK 293T, 8H 991, rep 2 TFEB_TFE3_DWT_8H_991_2_S11

description: WT HEK 293T, 8H 991, rep 2


title: siControl, HEK 293T, 4H 991, rep 3 siCont_4H_991_3_S9

description: siControl, HEK 293T, 4H 991, rep 3


title: WT HEK 293T, 8H 991, rep 3 TFEB_TFE3_DWT_8H_991_3_S12

description: WT HEK 293T, 8H 991, rep 3


title: WT HEK 293T, 4H 991, rep 2 TFEB_TFE3_DWT_4H_991_2_S8

description: WT HEK 293T, 4H 991, rep 2


title: siControl, HEK 293T, 2H 991, rep 3 siCont_2H_991_3_S6

description: siControl, HEK 293T, 2H 991, rep 3


title: WT HEK 293T, 24H 991, rep 1 TFEB_TFE3_DWT_24H_991_1_S16

description: WT HEK 293T, 24H 991, rep 1


title: WT HEK 293T, 2H 991, rep 2 TFEB_TFE3_DWT_2H_991_2_S5

description: WT HEK 293T, 2H 991, rep 2


title: WT HEK 293T, 24H 991, rep 3 TFEB_TFE3_DWT_24H_991_3_S18

description: WT HEK 293T, 24H 991, rep 3


title: WT HEK 293T, 4H 991, rep 1 TFEB_TFE3_DWT_4H_991_1_S7

description: WT HEK 293T, 4H 991, rep 1


title: WT HEK 293T, 2H 991, rep 3 TFEB_TFE3_DWT_2H_991_3_S6

description: WT HEK 293T, 2H 991, rep 3


title: WT HEK 293T, 16H 991, rep 2 TFEB_TFE3_DWT_16H_991_2_S14

description: WT HEK 293T, 16H 991, rep 2


title: WT HEK 293T, 24H 991, rep 2 TFEB_TFE3_DWT_24H_991_2_S17

description: WT HEK 293T, 24H 991, rep 2


title: WT HEK 293T, 16H 991, rep 3 TFEB_TFE3_DWT_16H_991_3_S15

description: WT HEK 293T, 16H 991, rep 3


title: WT HEK 293T, DMSO, rep 2 TFEB_TFE3_DWT_0H_DMSO_2_S2

description: WT HEK 293T, DMSO, rep 2


title: TFEB+TFE3 KO HEK 293T, 4H 991, rep 2 TFEB_TFE3_DKO_4H_2_S26

description: TFEB+TFE3 KO HEK 293T, 4H 991, rep 2

value: TFEB+TFE3 Knock out


title: WT HEK 293T, 16H 991, rep 1 TFEB_TFE3_DWT_16H_991_1_S13

description: WT HEK 293T, 16H 991, rep 1