title: Astrocyte LPS Serpine2 control 3

value: control


title: Astrocyte LPS Serpine2 knockout 2

status: Public on Feb 02 2026

type: SRA

city: Los Angeles

first: Ye

last: Zhang

state: CA

address: 635 Charles E Young Dr S

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
STAR alignment, v2.6.0c (astrocytes) & v2.7.8a (microglia)
HTSeq quantification
Assembly: GRCm38 (astrocytes) & GRCm39 (microglia)
Supplementary files format and content: tab-delimited text files of gene counts, labelled with Ensembl gene IDs

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
Mice were perfused for 10 minutes with phosphate buffered saline solution before dissection of the cerebral cortex (astrocytes) or whole brain (microglia).  For astrocytes, cortical tissue was roughly chopped then placed in a papain solution (12 units/mL) for enzymatic digestion at 34.5C for 45 minutes. Digested tissue was washed with ovomucoid inhibitor and mechanically digested via trituration.  Cells were spun down and resuspended in PBS with 0.02% bovine serum albumin, then passed through a mesh filter to generate a single cell suspension. Tissue for microglia was dounced, spun down through a Percoll solution, and then resuspended to get a single cell suspension. The final cell suspensions were incubated on various petri dishes (10-20 min/dish) that were coated with antibodies targeting a desired cell population.  Cells bound to each dish were rinsed with PBS, and RNA was harvested immediately with 700 uL of TRIzol before flash freezing in liquid nitrogen. RNA was purified for sequencing using the miRNeasy kit (Qiagen).
RNA libraries were constructed with the Ovation V2 system (Tecan) and the NEBNext Ultra RNA Library Prep Kit (New England Biolabs)

tag: tissue

value: cerebral cortex

tag: cell type

value: astrocyte

tag: genotype

value: Serpine2 knockout

tag: Sex

value: male


title: non DUX4 ETV6-RUNX1, control 7

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

country: France

institute: APHP Hôpital Robert Debré

description: Library name: 27206

data_processing:
Alignment is performed by STAR (https://github.com/alexdobin/STAR). The duplicate reads (e.g., paired-end reads in which the insert DNA molecules have identical start and end locations in the Human genome) are removed (sambamba tools).
Counting of reads per gene are performed by STAR with --quantMode GeneCounts option. Next, RawCount is normalized by the Transcripts Per Kilobase Million (TPM) method.
Assembly: hg38
Supplementary files format and content: txt file including TPM values for all samples
Supplementary files format and content: txt file including FPKM values for all samples

organism: Homo sapiens

source_name: Bone marrow

growth_protocol: mononucleated cells were obtained by Ficoll from fresh EDTA or Heparin Lithium tumoral bone marrow at ALL diagnosis

extract_protocol:
Qiagen miRNeasy kit
RNA were quantified and qualified using Fragment Analyzer®, Agilent®. A cDNA library was generated by reverse transcription of mRNA after poly(A) capture (NEBNext® Poly(A) mRNA Magnetic Isolation Modules, NEBNext® Ultra II RNA First Strand Synthesis Module & Directional RNA Second Strand Module, New England Biolabs®). Size selection and subsequent purification steps were carried out on magnetic beads (Sera-Mag magnetic beads®, GE Healthcare®). The library was prepared (NEBNext® Ultra II End repair/A-tailing module & Ligation module, New England Biolabs®) and amplified by PCR (KAPA Hifi HotStart ReadyMix, Roche®). The final library was qualified by capillary migration (Fragment Analyzer®, Agilent®) and quantified by qPCR (NEBNext® Custom 2X Library Quant Kit Master Mix, New England Biolabs®; QuantStudio 6 Flex Real-Time PCR System®, Life Technologies®). The libraries were sequenced in 'pair-end' (2 times 100 cycles) using SBS technology (Flow Cell S2, NovaSeq 6000®, Illumina®). Image analysis and base calling is performed using Illumina Real Time Analysis with default parameters.

value: Bone marrow

value: Mononucleated cells

tag: batch

tag: gender

value: M


title: C57Bl/6 cells diABZI treated 2

type: RNA

city: Beaverton

first: Victor

middle: Robert

last: DeFilippis

state: Oregon

address: 505 NW 185th Ave.

department: Vaccine and Gene Therapy Institute

institute: Oregon Health and Science University

hyb_protocol: Samples were hybridized with Clariom S arrays (Affymetrix) and scanned at the Oregon Health and Science University Integrated Genomics Core facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
Raw data were processed with the Transcriptome Analysis Console (Affymetrix) for background correction and RMA normalization as well as fold change calculation and statistical significance (FDR < 0.01).
RMA expression value derived from Transcriptome Analysis Console

label: biotin

source_name: Healthy male

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were grown in 12 well dishes in RPMI + 10% FCS.

extract_protocol: RNA was isolated from collected cell pellets using Zymo DNA free RNA isolation kits per the manufacturer's instructions.

treatment_protocol: Cells were treated for 6 h with DMSO (mock), 50 nM diABZI, 10µg/mL cGAMP, or 100 ng/mL LPS as indicated.

value: Bone Marrow Derived Dendritic Cells

tag: strain

value: C57Bl/6 mice

tag: treatment

value: diABZI treated


title: Ch2-S2-70E-B2

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

data_processing: Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.

label: EvaGreen

label_protocol: qPCR was performed using 96.96 BioMark™ Dynamic Arrays (Fluidigm®, South San Francisco, CA) enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions (Spurgeon et al. 2008). DNA intercalating dye based approach (EvaGreen ) was used for quantitative detection of qPCR products. Each qPCR experiment consisted of 30 amplification cycles (15s at 95°C, 5s at 70°C, 60s at 60°C). Ct values were calculated by the Real-Time PCR Analysis Software (Fluidigm).

growth_protocol: Fetal dorsal telencephalic ventricular neuroepithelium corresponding to the precursor projection neurons of the developing cerebral cortical plate were obtained by sterile microsurgical dissection from gestational day (GD) 12.5 C57/Bl6 mouse fetuses. This period corresponds to the late 1st trimester-equivalent period for cortical development in human pregnancy. Neuroepithelial cells collected from two entire litters at a time, were dispersed in a defined culture medium DMEM F12 (Invitrogen, #11039-047), 20 ng/ml Basic Fibroblast Growth Factor (bFGF, BD Biosciences, #354060), 20 ng/ml human recombinant Epidermal Growth factor (EGF, Invitrogen #47743-568), 0.15 ng/ml recombinant human Leukemia Inhibitory Factor (LIF, Alomone, #L-200), ITS (Insulin, Transferrin, Selenium) supplement (Invitrogen, #51500-056), 0.85 units/ml Heparin (Sigma-Aldrich, #H-4784), 20 nM progesterone (Sigma-Aldrich, #P7556) and cultured as non-adherent neurosphere aggregates. Independent replicates for the reported experiments were from neurospheres established from a total of six sets of neuroepithelium isolations, from 12 different pregnancies.

extract_protocol: Each neurosphere was imaged, prior to collection in 6ul of Cells Direct Lysis Buffer (Invitogen #117753-100) and stored at -80oC, prior to being processed for RT-qPCR using the Biomark HD system (protocol ADP 42), for mRNA expression across 96 genes. Single neurospheres were processed directly to reverse transcription and pre-amplification reaction (Fluidigm protocol ADP 42), without RNA extraction to minimize RNA loss.

treatment_protocol: Neurosphere cultures were randomly assigned to control and ethanol-exposed (120 mg/dl (26 mM), 320 mg/dl (70 mM) and 450mg/dl (100mM)) groups. The final ethanol concentration in the culture media was determined by gas chromatography (TRACE™ 1310, Thermo Fisher Scientific), from samples of the media collected at the beginning of the treatment at day 0, at day 3 for re-feeding and at day 5 before collection.

value: C57/Bl6 mouse

value: dorsal telencephalon

tag: developmental stage

tag: culture group

value: Set-A

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)

tag: neurosphere size group

value: L


title: Ch2-S2-70E-B12

source_name: fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: S


title: Ch2-S2-70E-B11


title: non DUX4 ETV6-RUNX1, control 8

description: Library name: 27250

treatment_protocol: mononucleated cells were obtained by Ficoll from fresh EDTA or Heparin Lithium tumoral bone marrow at ALL diagnosis

value: F


title: non DUX4 ETV6-RUNX1, control 6

description: Library name: 27018


title: Astrocyte LPS Serpine2 control 1

value: control


title: Ch2-S2-70E-B10


title: C57Bl/6 cells diABZI treated 1

description: RMA expression value derived from Transcriptome Analysis Console


title: Astrocyte LPS Serpine2 control 2

value: cerebral cortex


title: ctx_19

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Library name: ctx_19
E18.5 embryonic cortex 19

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v7.1.0
Assembly: Mus musculus mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: E18.5 embryonic cortex

extract_protocol:
Nuclei were isolated by pooling frozen brain tissue from samples of the same genotype. All procedures were performed on ice or at 4°C in an RNase-free environment. Briefly, frozen mouse brain cortex tissue was gently lysed in 3 mL of homogenization buffer (250 mM sucrose, 150 mM KCl, 30 mM MgCl₂, 60 mM Tris, 0.01% v/v Triton X-100, 0.001% v/v Digitonin, 0.01% v/v NP40, 1 mM DTT), supplemented with 0.2 U/mL RNase inhibitor (NEB, M0314) and a complete protease inhibitor cocktail (Roche, 11697498001). Lysis was performed using a Wheaton Dounce Tissue Grinder (30 strokes with pestle B). The lysate was filtered through a 40 µm cell strainer and centrifuged at 1,000 × g for 8 minutes to collect a nuclear pellet. To remove debris, the pellet was resuspended in 350 µL of homogenization buffer, mixed 1:1 with 50% iodixanol buffer (iodixanol 60% v/v in a buffer containing 250 mM sucrose, 150 mM KCl, 3 mM MgCl₂, 60 mM Tris), and layered over 600 µL of 29% iodixanol buffer (iodixanol 29% v/v in the same buffer). The sample was centrifuged at 13,500 × g for 20 minutes. The supernatant was discarded, and the nuclei were gently resuspended and washed in 1 mL of 1% BSA/PBS. Nuclear integrity and complete lysis were visually confirmed. Nuclei were manually counted and diluted to a concentration of 1,000 nuclei/µL in 1% BSA/PBS.
Single-nucleus RNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics), following the manufacturer’s instruction. Briefly, single nucleus gel-bead-in-emulsions (GEMs) were generated in Chromium Controller with NextGEM Chip G (10X Genomics). The first-strand cDNA was synthesized on-beads, followed by clean-up and amplification. The amplified cDNAs were examined in Bioanalyzer with High-Sensitivity DNA Chip (Agilent). Ten-ul of cDNAs were forwarded to the library preparation. The dual-indexed libraries were pooled and sequenced on the Illumina NovaSeq 6000 or NovaSeq X Plus sequencer (Illumina).

treatment_protocol: no treatment

value: E18.5 embryonic cortex

value: no treatment


title: Astrocyte saline Serpine2 knockout 3

value: astrocyte

value: Serpine2 knockout

value: female


title: ctx_51

description:
Library name: ctx_51
E18.5 embryonic cortex 51

value: Cux2-Cre/WT; Atf4 fl/fl


title: Ch2-S2-25E-C9

value: M


title: C57Bl/6 cells mock treated 1

value: Bone Marrow Derived Dendritic Cells

value: C57Bl/6 mice

value: male

value: mock treated


title: non DUX4 ETV6-RUNX1, control 5

description: Library name: 26729

value: Bone marrow

value: Mononucleated cells


title: Ch2-S2-25E-C8

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-A

value: S


title: ctx_25

description:
Library name: ctx_25
E18.5 embryonic cortex 25

value: E18.5 embryonic cortex


title: non DUX4 ETV6-RUNX1, control 4

description: Library name: 26584

value: F


title: Ch2-S2-70E-B1


title: Ch2-S2-70E-A12


title: ctx_10

description:
Library name: ctx_10
E18.5 embryonic cortex 10

value: Cux2-Cre/Cre; Atf4 fl/fl

value: no treatment


title: non DUX4 ETV6-RUNX1, control 1

description: Library name: 16552


title: non DUX4 ETV6-RUNX1, control 3

description: Library name: 26418


title: ctx_50

description:
Library name: ctx_50
E18.5 embryonic cortex 50


title: non DUX4 ETV6-RUNX1, control 2

description: Library name: 22584


title: ctx_11

description:
Library name: ctx_11
E18.5 embryonic cortex 11


title: D97__moDC_Pos_DOC_Pos_Isotype

city: Hayward

first: Soonweng

last: Cho

address: 3928 Point Eden Way

institute: Arcus Biosciences

description: Library name: D97__moDC_Pos_DOC_Pos_Isotype

data_processing:
Raw reads were trimmed using Trimgalore with default parameters.
STAR 2-pass was used to align trimmed reads to the human reference genome, GRCh38 (Ensembl v104).
Salmon was used to quantify gene counts from aligned BAM files and tximport from txmeta R package was used to generate raw count matrix.
Assembly: GRCh38
Supplementary files format and content: Tab delimited file with raw counts from each sample.

molecule: polyA RNA

source_name: monocyte-derived dendritic cell

growth_protocol: Monocytes were isolated from LRS chambers from healthy human donors using negative selection (EasySep Human Monocyte Enrichment Kit) and differentiated into moDCs in RPMI 1640 media with 10% heat inactivated fetal bovine serum, 100 ng/mL GM-CSF, and 100 ng/mL IL-4 for 3 days.

extract_protocol:
Total RNA was extracted.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep following manufacturer's protocols.

treatment_protocol: Day 3 moDCs were treated with 100 nM AB598 or isotype control for 1 h followed by different combinations of 300 μM ATP,  A549 cells, and 0.1 µM docetaxel and co-cultured in RPMI 1640 media with 10% HI FBS, 100 ng/mL GM-CSF and 100 ng/mL IL-4 for another 3 days.

value: monocyte-derived dendritic cell

tag: donor


title: ctx_8

description:
Library name: ctx_8
E18.5 embryonic cortex 8


title: Astrocyte saline Serpine2 knockout 2

value: cerebral cortex

value: astrocyte

value: Serpine2 knockout


title: ctx_6

description:
Library name: ctx_6
E18.5 embryonic cortex 6


title: Ch2-S2-25E-C5


title: Ch2-S2-25E-C7

value: M


title: Astrocyte saline Serpine2 control 1

value: control

value: female


title: ctx_9

description:
Library name: ctx_9
E18.5 embryonic cortex 9

value: Cux2-Cre/WT; Atf4 fl/fl


title: Ch2-S2-25E-C4


title: Ch2-S2-25E-C3

value: L


title: D97__moDC_Pos_Isotype

description: Library name: D97__moDC_Pos_Isotype

value: Isotype


title: Astrocyte saline Serpine2 control 2

value: male


title: Astrocyte saline Serpine2 knockout 1


title: Ch2-S2-25E-C6

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-A


title: D97__moDC_Pos_DOC_Pos_AB598_Pos_ATP

description: Library name: D97__moDC_Pos_DOC_Pos_AB598_Pos_ATP


title: Astrocyte saline Serpine2 control 3


title: D97__moDC_Pos_DOC_Pos_AB598

description: Library name: D97__moDC_Pos_DOC_Pos_AB598


title: MMS synovium

city: Bunkyo-ku, Tokyo

first: Hisatoshi

last: Ishikura

state: Japan

department: Orthopaedic

country: Japan

institute: University of Tokyo

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger pipeline (version 2.0.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: synovium

extract_protocol:
Synovium from control and MMS D14 mice knees (20 knees respectively) were dissected, minced with scissors and transferred into RPMI-1640 (Nacalai Tesque) containing 0.2mg/ml Liberase TL (Sigma-Aldrich) and 0.1mg/ml DNaseⅠ (Roche) at 37℃ for 20 min with intermittent syringe homogenization. Cells were filtered through 100 µm and 40 µm cell strainers and 40 µm Flowmi cell strainer (Sigma-Aldrich).
For each synovium sample, single cell RNA libraries were generated using the 10x Genomics Chromium platform. Single cell suspensions were loaded onto the Chromium Single Cell system v3.1 (Ghromium Next GEM Single Cell 3’ Reagent Kits v3.1). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Following the GEM generation, the Gel bead is dissolved, primers are released, and any co-partitioned cell is lysed. Primers containing the poly(dT) sequence, Ilumina TurSeq Read1, Unique Molecular Identifier (UMI) and the 10x Barcode are mixed with the cell lysate and a Master Mix containing reverse transcription reagents. After incubation, the pooled barcoded cDNA was then cleaned up with DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Ilumina TruSeq Read2, P5, P7, i7 and i5 sample index were added via End Repair, A-tailing, Adaptor Ligation, and PCR.

value: synovium

value: Goblet cells

value: Wild type


title: D97__moDC_Pos_DOC_Pos_A549_Pos_Isotype

description: Library name: D97__moDC_Pos_DOC_Pos_A549_Pos_Isotype

value: monocyte-derived dendritic cell


title: ctx-94-96-97

description:
Library name: ctx-94-96-97
3 same genotype whole e11.5 embryonic cortex mix 94-96-97

value: Emx1-Cre; Atf4 fl/fl

value: no treatment


title: Ch2-S2-25E-C2


title: Control synovium

description: 10x Genomics


description: Library name: D97__moDC_Pos_DOC_Pos_A549_Pos_AB598_Pos_ATP


title: ctx-69-91-93

description:
Library name: ctx-69-91-93
3 same genotype whole e11.5 embryonic cortex mix 69-91-93

value: Atf4 fl/fl


title: D97__moDC_Pos_DOC_Pos_A549_Pos_AB598

description: Library name: D97__moDC_Pos_DOC_Pos_A549_Pos_AB598


title: Choroid plexus from an old gray mouse lemur #4

city: Sherbrooke

first: Mariano

last: Avino

address: 3201 Jean Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Sherbrooke University

description: Library name: CP-O4

data_processing:
Single-end fastq quality control, trimming and adpter-removal were performed with Trim Galore. Reads were aligned against gray mouse lemur genome (GCF_000165445.2_Mmur_3.0) with Rsubread.
Assembly: Mmur3
Supplementary files format and content: raw counts for each sample

organism: Microcebus murinus

source_name: choroid plexus

growth_protocol: All animals were born and housed in the breeding colony of the CNRS/MNHN laboratory in Brunoy (France). They were kept under standard captive conditions: temperature at 24–26 °C, 55% relative humidity, and an artificial photoperiod mimicking seasonal changes (short-day: 10h light/14h dark and long-day: 14h light/10h dark cycles). Lighting was provided by fluorescent lamps during the day (250–350 lux) and red dim light during the night. Food and water were provided ad libitum.

extract_protocol:
Following euthanasia by intraperitoneal injection of pentobarbital (70 mg/kg), brains were collected and briefly rinsed in phosphate-buffered saline (PBS). Choroid plexuses (CPs) were extracted and conserved at -80C until RNA extraction. Total RNAs were extracted from CP tissue using a hybrid technique combining the TRIzol reagent protocol (Invitrogen, Thermo Fisher Scientific) and the Quick-RNA™ Miniprep Kit (Zymo Research) was used. CP tissues were first homogenized in 500µL of cold TRIzol with ceramic beads using a high-speed tissue homogenizer and then 500µL of chloroform:isoamyl alcohol 24:1 (Sigma Aldrich) were added. Samples were vortexed for 20 seconds and incubated for 2 min at room temperature. The samples were then centrifuged at 10,000g for 18 min at 4°C. The aqueous phase, that contains RNAs, was transferred in a new Eppendorf tube. An equal volume of 100% ethanol was added and the mixture was then loaded into a Zymo-Spin™ IIICG Column from the Quick-RNA™ Miniprep Kit. Further steps were conducted according to the manufacturer’s protocol.
RNA-seq libraries were prepared using NEBNext® single cell/low input RNA library preparation Kit (New England Biolabs). Library preparation was initiated with 50ng of total RNA.

value: choroid plexus

tag: healthy/disease

value: healthy individual

tag: age (months)


title: ctx-72-74-76

description:
Library name: ctx-72-74-76
3 same genotype whole e11.5 embryonic cortex mix 72-74-76


title: Ch2-S2-25E-B9

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: S


title: Choroid plexus from an old gray mouse lemur #2

description: Library name: CP-O2


title: ctx-37-60-92

description:
Library name: ctx-37-60-92
3 same genotype whole e11.5 embryonic cortex mix 37-60-92


title: Choroid plexus from an old gray mouse lemur #3

description: Library name: CP-O3


title: ctx-40-59-89

description:
Library name: ctx-40-59-89
3 same genotype whole e11.5 embryonic cortex mix 40-59-89


title: Ch2-S2-25E-C1

value: M


title: D97__moDC_Pos_AB598

description: Library name: D97__moDC_Pos_AB598


title: Ch2-S2-25E-B8


title: Choroid plexus from an old gray mouse lemur #1

description: Library name: CP-O1


title: Ch2-S2-25E-B7


title: ctx-1-3-14

description:
Library name: ctx-1-3-14
3 same genotype whole e11.5 embryonic cortex mix 1-3-14


title: D94__moDC_Pos_Isotype

description: Library name: D94__moDC_Pos_Isotype


title: Ch2-S2-25E-B6


title: Choroid plexus from an adult gray mouse lemur #4

description: Library name: CP-A4

value: female


title: Ch2-S2-25E-B5


title: Liver_Treg_counts_GEX

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Library name: Liver_Treg_counts_GEX
scRNA-seq of liver Tregs, 8 weeks post CDAHFD or control diet

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.1.
GEX library was processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Liver_Treg_counts.csv

source_name: Liver

extract_protocol:
Muscle and colon were enzymatically dissociated and digested with collagenase II/dispase to single cell suspensions. Tregs from hindlimb muscles and colons of Foxp3Gfp, Foxp3-cre x Maffl/fl (MafΔTreg)  and Foxp3-cre x Mafwt/wt (Maf-wt) were sorted by flow cytometry 3 days post CTX injury. Single cells were then encapsulated in nanodroplets according to the 10x Genomics protocol.
10X Genomics library prep (3' V2 or 5' V3) Library were sequenced using a HiSeq500.

treatment_protocol: Mice were injected them with 0.03 mL per muscle of Naja mossambica cardiotoxon (0.03 mg/mL) in one or more hindlimb muscles

tag: source nane

value: Liver Tregs, 8 weeks post CDAHFD or control diet

value: Liver

tag: genetics

tag: age weeks

value: 8 weeks post


title: Choroid plexus from an adult gray mouse lemur #3

description: Library name: CP-A3

tag: cell type

value: male


title: D94__moDC_Pos_DOC_Pos_Isotype

description: Library name: D94__moDC_Pos_DOC_Pos_Isotype


title: D94__moDC_Pos_DOC_Pos_AB598_Pos_ATP

description: Library name: D94__moDC_Pos_DOC_Pos_AB598_Pos_ATP


title: D97__moDC_Pos_AB598_Pos_ATP

description: Library name: D97__moDC_Pos_AB598_Pos_ATP


title: Choroid plexus from an adult gray mouse lemur #2

description: Library name: CP-A2

tag: Sex


title: Brg1KD_rep2_PCMC

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

description: Library name: Brg1KD_rep2_PCMC

library_source: genomic

data_processing:
Promoter-capture micro-C matrices were downsampled across replicas to obtain matrices with equal contacts. We obtained loops using CHiCAGO (Cairns et al., 2016) pipeline with 20 kb resolution. The loops from both replicas were combined using pgltools intersect. These loops were compared to the Hi-C loops obtained from the control samples using bedtools (Quinlan & Hall, 2010). Differential loop analysis was performed using the CHiCAGO (Cairns et al., 2016) pipeline on combined replicas. We considered p < 0.5 as the threshold for loop change. The up, down, and unchanged loops identified in this analysis were used for downstream analysis. To remove any potential biases, we resized the loop anchors to 10 kb by calculating the mid coordinates and expanding 5 kb downstream and 5 kb upstream. We used these loops coordinates to perform aggregated peak analysis on the Hi-C contact matrices using GENOVA (van der Weide et al., 2021) with default options. All enrichment analysis of promoter capture micro-C loops with different data sets with genomic features were performed using bedtools (Quinlan & Hall, 2010).
Assembly: mm10
Supplementary files format and content: bedpe contain loop calls from CHICAGO analysis
Library strategy: Capture-C

molecule: genomic DNA

source_name: E14 mESC

growth_protocol: E14TG2a (E14) mouse embryonic stem (ES) cells derived from male Mus musculus were cultured under standard conditions. Cells were maintained on tissue culture-treated plates pre-coated with 0.2% gelatin and incubated at 37°C in a humidified atmosphere containing 5% CO₂. The culture medium consisted of high-glucose Dulbecco’s Modified Eagle Medium (DMEM; Sigma, D5796), supplemented with 10% fetal bovine serum (Sigma), 2 mM L-glutamine (Corning), 0.1 mM β-mercaptoethanol (Acros Organics), 1X nonessential amino acids (Corning), and leukemia inhibitory factor (LIF; prepared in-house). Cells were passaged every 48 hours using trypsin-EDTA (Corning, 25-053-Cl) at a dilution of approximately 1:8 in fresh medium. Mycoplasma contamination was routinely assessed by PCR, and culture space was treated with anti-mycoplasma solution (LookOut® DNA Erase Spray, Sigma) to minimize contamination risk. All experiments were conducted using ES cells between passages 18 and 26.

extract_protocol:
chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde. The crosslinked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to chromatin capture beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends. After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified
Purified DNA was used as input for sequencing library preparation using Illumina-adapters. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification. The library was then enriched for promoter regions using Dovetail® Pan Promoter Enrichment Kit (CP3-PP-002) following manufacturer instructions.

treatment_protocol: Endoribonuclease-digested short interfering RNAs (esiRNAs) were generated as previously described. Briefly, target gene regions were selected based on sequence uniqueness using the DEQOR algorithm. For esiRNA synthesis, T7 templates were generated using cDNA derived from wild-type murine E14 embryonic stem (ES) cells for Smarca4 and Ino80, and from the pLJM1-EGFP plasmid (Addgene, Plasmid #19319), for control EGFP esiRNAs. The dsRNAs were in vitro transcribed using T7 polymerase (homemade; 5.5 hr at 37°C, followed by an annealing stage lowering the temperature 0.1°C/s down to 25 °C), digested with ShortCut RNase III (NEB), then purified using a PureLink RNA Mini Kit (Invitrogen) with a modified purification strategy. Briefly, lysis buffer was added to a 1:1 volume ratio and isopropanol was then added to a final concentration of 40%. Following a 15 sec vortex, the samples were loaded to silica columns (Epoch Life Science) and centrifugated (1 min, 11,000 xg). Isopropanol was added to the flow-through at a 1:1 volume. Following a 15 sec vortex, the samples were applied to new silica columns and centrifugated (1 min, 11,000 xg). This was repeated until the entire sample was applied to the column. After a 500 µL wash with Wash buffer 2, the samples were eluted using ultrapure nuclease-free water (Ambion). Transient transfections were performed in 10 cm plates using Lipofectamine 3000 (Invitrogen). Briefly, 3.5 µg of esiRNAs and 25 µL of Lipofectamine were incubated in 2 mL of OptiMEM (Gibco) for 20 min. Then, 3.5X105 cells in 4 mL of culture media were added to the transfection mixture and plated onto 10 cm plates. After 16-18 hr, the media was removed, and fresh media was added. Samples were harvested 48 hr post transfection using trypsin. Following a 1X PBS (Corning) wash, cells were processed or flash-frozen and held at -80°C.

tag: cell line

value: E14 mESC

value: embryonic stem cells

tag: genotype

value: wild type

value: Smarca4 esiRNA KD

tag: batch


title: Ino80KD_rep2_PCMC

description: Library name: Ino80KD_rep2_PCMC

tag: treatment

value: Ino80 esiRNA KD


title: Ino80KD_rep1_PCMC

description: Library name: Ino80KD_rep1_PCMC


title: D94__moDC_Pos_DOC_Pos_AB598

description: Library name: D94__moDC_Pos_DOC_Pos_AB598

value: monocyte-derived dendritic cell


title: Choroid plexus from an adult gray mouse lemur #1

description: Library name: CP-A1


title: Ch2-S2-25E-B4

tag: strain

value: C57/Bl6 mouse

tag: tissue

value: dorsal telencephalon

tag: developmental stage

value: Set-A


title: Ch2-S2-25E-B3

tag: culture group

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)


title: D94__moDC_Pos_DOC_Pos_A549_Pos_Isotype

description: Library name: D94__moDC_Pos_DOC_Pos_A549_Pos_Isotype

tag: donor


title: Choroid plexus from a young gray mouse lemur #3

description: Library name: CP-Y3

value: choroid plexus

tag: healthy/disease

value: healthy individual

tag: age (months)


title: D94__moDC_Pos_DOC_Pos_A549_Pos_AB598

description: Library name: D94__moDC_Pos_DOC_Pos_A549_Pos_AB598


title: Ch2-S2-25E-B12

tag: neurosphere size group

value: S


title: Control_rep1_PCMC

description: Library name: Control_rep1_PCMC

value: control esiRNA KD


title: Ch2-S2-25E-B2

value: M


title: Choroid plexus from a young gray mouse lemur #4

description: Library name: CP-Y4


title: Brg1KD_rep1_PCMC

description: Library name: Brg1KD_rep1_PCMC


description: Library name: D94__moDC_Pos_DOC_Pos_A549_Pos_AB598_Pos_ATP


title: Control_rep2_PCMC

description: Library name: Control_rep2_PCMC


title: Choroid plexus from a young gray mouse lemur #1

description: Library name: CP-Y1

value: female


title: Choroid plexus from a young gray mouse lemur #2

description: Library name: CP-Y2


title: D94__moDC_Pos_AB598_Pos_ATP

description: Library name: D94__moDC_Pos_AB598_Pos_ATP


title: Ch2-S2-25E-B10


title: Ch2-S2-25E-B11


title: D94__moDC_Pos_AB598

description: Library name: D94__moDC_Pos_AB598


title: D2.0R shCXCL10 rep3

city: Bristol

first: Qiang

last: Lan

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

description: Library name: sh10_3

data_processing:
All sequencing reads were processed for quality control, removal of low-quality reads, adaptor sequence and ribosomal RNA by RSeQC (v5.0.1), Cutadapt (v4.8)  and Fastq Screen (v0.11.3) . The filtered reads were aligned against Mus_musculus GRCm39.110 genome using STAR (v2.7.10a) and summarized with htseq-count (v0.11.2)  using gene annotation.
Assembly: Mus_musculus GRCm39.110
Supplementary files format and content: count matrix

growth_protocol: cell lines were maintained in high glucose Dulbecco’s Modifier Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S, Life Technologies – Invitrogen) and 1% Non-essential Amino Acid (NEAA)

extract_protocol:
Total RNA was extracted from adherent cells using the RNA Plus extraction kit (Machery-Nagel), following the manufacturer’s protocol
Illumina Strand mRNA

value: breast cancer cell line

value: CXCL10 knockdown


title: Ino80KD_rep1_HiC

description: Library name: Ino80KD_rep1_HiC

data_processing:
Raw fastq files for each replicate were aligned to the mm10 genome using BWA and the resulting sam files were downsampled to the smallest for each replicate using SAMtools . The datasets were then processed with different tools to obtain matrices in the desired formats. Juicer 2.0  was used to obtain matrices in the Juicer format (hic files). Matrices from the two biological replicates were combined using the mega.sh script from Juicer. nf-core/hic was used to obtain matrices in the cooler format (cool files). Replicas were combined using the merge command from the cooler library. HOMER was used to generate tag directories, the default HiC pipeline and options from HOMER were used to perform downstream analyses. Tag directories from two biological replicas were combined using the makeTagDirectory command from HOMER. To obtain HiCExplorer format matrices (h5 files), we converted raw Juicer matrices of the corresponding resolutions to FAN-C format using the FAN-C command fanc to-fanc, the FAN-C matrices were then exported to cooler matrices using fanc to-cooler and later converted to HiCExplorer format using the HiCExplorer command hicConvertFormat. Finally, we normalized the matrices using the hicCorrectMatrix command from HiCExplorer. All genomic feature enrichment analyses and genomic feature list manipulations were performed using bedtools
Compartment analysis: To identify compartments, we first performed a PCA analysis with HOMER using the runHiCpca.pl script (default settings) on the combined tag directories at a 25 kb resolution, then the compartments were called using findHiCCompartments.pl (default settings). Pearson correlation matrices were obtained using 250 kb resolution FAN-C matrices and the fanc compartments command. Browser tracks were generated in UCSC genome browser.
Subcompartment analysis: Subcompartment analysis was performed using CALDER2  at 50 kb resolution on matrices generated using Juicer2. To compute the subcompartment change percentages, we recorded the subcompartment assignment of the central position of each subcompartment found in Smarca4 KD or Ino80 KD samples and compared the assignment in the control sample. To analyze the ratio of subcompartment switches associated with specific genomic features we, similarly, recorded the subcompartment assignment for each location associated with each feature in Smarca4 KD or Ino80 KD samples and compared it to the one observed in the control sample. To obtain the observed/expected ratio of chromatin opening or closing, for each feature, we divided the number of subcompartments that switched to a more active state or a more inactive state over an average of 1,000 randomized genomic locations. Randomized genomic locations were generated using bedtools shuffle for each genomic feature analyzed. Browser tracks were generated in UCSC genome browser.
TAD analysis: TAD boundaries were calculated with the hicFindTADs command from HiCExplorer v3.7.2, using 10 kb resolution HiCExplorer matrices and the following settings:  correctForMultipleTesting fdr, minBoundaryDistance 80000, minDepth 80000, maxDepth 800000, step 25000, and thresholdComparisons 0.05. Differential TADs were calculated using two independent approaches: 1) with the hicDifferentialTAD command from HiCExplorer v3.7.2 using the results from the aforementioned hicFindTADs analysis and the following settings: mode all, modeReject all, pValue 0.05; 2) TADCompare with default settings on Juicer-generated 25 kb resolution raw matrices. Insulation was calculated on 25 kb resolution cooler format matrices using the _find_insulating_boundaries_dense command from cooltools v0.7.0 at 125 kb resolution. To compare the insulation values at TAD boundaries associated with BRG1 or INO80 binding, we used a list of TAD boundaries obtained with hicFindTADs and intersected them with CTCF, BRG1 or INO80 binding locations using bedtools.
Loop analysis: Hi-C loops were identified using Mustache using 10 kb resolution, FDR=0.01, and otherwise default settings. Differential Hi-C loops were obtained using diff_mustache.py using 10 kb resolution and an FDR=0.01.
Assembly: mm10
Supplementary files format and content: hic file with interactions
Supplementary files format and content: bed with loop interactions

extract_protocol:
5X106 cells were crosslinked using formaldehyde (1% final concentration) for 10 min at RT. The reaction was quenched using glycine (130 mM final concentration). After a PBS wash, the cell pellets were frozen and stored at -80°C. Cells were resuspended in ice-cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2 % NP-40) with protease inhibitors (Thermo Scientific) and incubated on ice for 15 min. The lysate was homogenized using dounce homogenization and nuclei were pelleted at 2,500 xg at RT. The nuclei were then washed with and resuspended in ice-cold NEBuffer 3.1 (NEB). SDS was then added (0.1% final concentration) and the nuclei were incubated at 65°C for 10 min. SDS was quenched by adding Triton X-100 (1% final concentration). DpnII (50,000 U, NEB) was added, and chromatin digestion was carried out overnight at 37°C. End repair was performed at 23°C for 5 hr using Klenow Fragment (3'→5' exo-, 50 U, NEB), NEBuffer 3.1 (0.112 X), 28 nM of each dCTP, dGTP. dTTP, and biotin-14-dATP. Blunt ligation was performed at 16°C for 4 hr using T4 DNA ligase (60 U, Invitrogen) and ligation buffer (1X, Invitrogen), Triton X-100 (1%) and BSA (1 mg/mL). Crosslinks were reversed at 65°C overnight, and protein was degraded using proteinase K. The DNA was extracted using phenol-chloroform (Invitrogen). Biotin removal from unligated ends was performed at 20°C for 4 hr using 5 µg of DNA, 5 U T4 DNA Pol, NEBuffer 2.1 (1X, NEB), 25 nM dATP, and 25 nM dGTP. DNA was sheared to obtain 200-300 bp fragments sizes using a sonicator (Covaris). DNA size fractionation was performed using AMPure XP magnetic beads (Beckman Coulter) as described by the manufacturer.
End repair was performed at 20°C for 30 min using 50 µL of size-selected DNA elute, T4 DNA pol (7.5 U, NEB), T4 polynucleotide kinase (25 U, NEB), Klenow DNA pol (2.5 U, NEB), ligation buffer (1X, NEB). Biotin DNA pulldown was performed using 1 µg of end-repaired DNA, MyOne streptavidin C1-coated beads (Invitrogen), according to manufacturer instructions. The beads were resuspended in 41 µL TE. A-tailing was then performed at 37°C for 30 min, followed by addition of Klenow fragment (3’ -> 5’ exo-, 15 U, NEB), dATP (0.2 nM), and NEBuffer 2.1 (1X). After a wash with ligation buffer, the beads were resuspended in 36.25 µL ligation buffer. Adapter ligation was then performed at RT for 2 hr with the addition of T4 ligase (4 U), ATP (0.2 mM), paired ended adapters (5 µL of 15 µM annealed adapters, 5’ ligation buffer (2.75 µL). After washing twice with tween wash buffer (TWB; 5 mM Tris-HCl [pH=8.0], 0.5 mM EDTA, 1 M NaCl, 0.05% Tween), the beads were resuspended in Binding Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). Following a wash with NEBuffer 2.1, beads were resuspended in 20 µL of NEBuffer 2.1. The library of ligated fragments was then PCR amplified for 6 cycles using 6 µL of beads, 2 µL of 10 µM adapter primers (G19-PE Primer 1.0 and 2.0), 25mM dNTPs, 10X PfU buffer, and 2 µL PfuUltra in a 30 µL reaction and the following conditions: 98°C for 3 min, 5 cycles of: 98°C for 20 sec, 60°C for 30 sec, and 72°C; and a final amplification at 72°C for 5 min. Finally, the PCR products were combined, and primer dimers were removed using AMPure XP beads.

value: E14 mESC


title: D91__moDC_Pos_DOC_Pos_Isotype

description: Library name: D91__moDC_Pos_DOC_Pos_Isotype


title: D2.0R shCXCL10 rep1

description: Library name: sh10_1


title: Brg1KD_rep1_HiC

description: Library name: Brg1KD_rep1_HiC

value: embryonic stem cells


title: Ino80KD_rep2_HiC

description: Library name: Ino80KD_rep2_HiC

value: wild type


title: D91__moDC_Pos_DOC_Pos_AB598_Pos_ATP

description: Library name: D91__moDC_Pos_DOC_Pos_AB598_Pos_ATP


title: D2.0R sh Control rep4

description: Library name: shC_4

value: knockdown control


title: D91__moDC_Pos_Isotype

description: Library name: D91__moDC_Pos_Isotype

value: Isotype


title: Ch2-S2-25E-B1


title: Control_rep2_HiC

description: Library name: Control_rep2_HiC


title: Ch2-S2-100E-C9


title: Ch2-S2-100E-C8

value: L


title: Ch2-S2-100E-C6

value: C57/Bl6 mouse


title: D91__moDC_Pos_DOC_Pos_AB598

description: Library name: D91__moDC_Pos_DOC_Pos_AB598

value: monocyte-derived dendritic cell


title: Brg1KD_rep2_HiC

description: Library name: Brg1KD_rep2_HiC

value: Smarca4 esiRNA KD


title: Ch2-S2-100E-C7

value: dorsal telencephalon

value: Set-A


title: D2.0R shCXCL10 rep2

description: Library name: sh10_2


title: D91__moDC_Pos_DOC_Pos_A549_Pos_Isotype

description: Library name: D91__moDC_Pos_DOC_Pos_A549_Pos_Isotype


title: Control_rep1_HiC

description: Library name: Control_rep1_HiC


title: Ch2-S2-100E-C5

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)


title: D2.0R sh Control rep3

description: Library name: shC_3


title: Day28_3

city: Chicago

first: Yudai

last: Miyashita

state: IL

address: Simpson Querrey 5-402-C 303 E Superior Street

department: Thoracic Surgery

institute: Northwestern Univesity

description: Library name: AB-24-29

data_processing:
Raw sequencing data were processed using Cell Ranger (version 8.0.1) for demultiplexing, alignment to the mm10 reference genome, and generation of gene-barcode matrices.
Assembly: Mus musculus
Supplementary files format and content: The processed data files include gene-barcode matrices (barcodes.tsv, features.tsv, matrix.mtx) and Seurat objects for downstream analysis.
Supplementary files format and content: Data are provided in TSV format for raw counts and RDS format for Seurat-processed files.

source_name: Lung

extract_protocol:
Single-cell suspensions were prepared from harvested lung tissues at resting, Day 7, and Day 28 post-transplantation using enzymatic digestion and mechanical dissociation.
Single-cell RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3 according to the manufacturer's instructions.

treatment_protocol: Mice underwent orthotopic left lung transplantation. No immunosuppressive, antibiotic, or anti-inflammatory therapy was administered during the study.

value: Lung


description: Library name: D91__moDC_Pos_DOC_Pos_A549_Pos_AB598_Pos_ATP


title: Day28_2

description: Library name: AB-24-28


title: D2.0R wildtype rep2

description: Library name: WT_2

value: wildtype


title: D91__moDC_Pos_AB598

description: Library name: D91__moDC_Pos_AB598


title: D2.0R sh Control rep2

description: Library name: shC_2


title: Day7_2

description: Library name: AB-24-22


title: Ch2-S2-100E-C3

value: M


title: Day7_3

description: Library name: AB-24-23


title: D2.0R wildtype rep4

description: Library name: WT_4


title: Day7_1

description: Library name: AB-24-21


title: D2A1 wildtype rep2

description: Library name: D2A1_2


title: D91__moDC_Pos_DOC_Pos_A549_Pos_AB598

description: Library name: D91__moDC_Pos_DOC_Pos_A549_Pos_AB598


title: D4221__moDC_Pos_DOC_Pos_Isotype

description: Library name: D4221__moDC_Pos_DOC_Pos_Isotype


title: Ch2-S2-100E-C2

value: S


title: Day28_1

description: Library name: AB-24-27


title: S8_Single-cell RNA-seq of mouse intestine (Cre-positive)

city: Houston

first: Akira

last: Yamamoto

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: S8
Cre-positive mouse intestine

data_processing:
Sequencing data were generated using paired-end sequencing on an Illumina NovaSeq X Plus platform.
Raw sequencing reads were processed using CellRanger to generate gene-barcode count matrices.
Filtered feature-barcode matrices were used for downstream analysis.
Quality control, normalization, clustering, and downstream analyses were performed using Seurat in R (version 4.4.2).
Assembly: mm10
Supplementary files format and content: Processed data include filtered gene-barcode count matrices (matrix.mtx, features.tsv, barcodes.tsv) generated by CellRanger.

source_name: Intestine

growth_protocol: Mice were maintained under standard laboratory conditions until tissue collection.

extract_protocol:
Intestinal epithelial cells were isolated from intestinal tissue and dissociated into a single-cell suspension.
Single-cell RNA-seq libraries were prepared from single-cell suspensions using the 10x Chromium Next GEM Single Cell 3' GEM v3.1 Library Prep according to the manufacturer's instructions.

treatment_protocol: At day 6 post-transplant, mice were sacrificed and intestinal tissue was collected for analysis.

value: Intestine

value: Cre-positive


title: resting3

description: Library name: AB-24-20


title: D4221__moDC_Pos_DOC_Pos_AB598

description: Library name: D4221__moDC_Pos_DOC_Pos_AB598


title: D2.0R wildtype rep3

description: Library name: WT_3

value: breast cancer cell line


title: Ch2-S2-100E-B6


description: Library name: D4221__moDC_Pos_DOC_Pos_A549_Pos_Isotype


title: S6_Single-cell RNA-seq of mouse intestine (Cre-negative)

description:
Library name: S6
Cre-negative mouse intestine

value: Cre-negative


title: sample f3 (B2M KO, CD40-treated, replicate 2) HTO

first: Amy

last: Huang

address: 25 Shattuck St

department: Immunology

description:
Hashtag-derived oligonucleotide (HTO)
sample_f3_barcodes.tsv.gz
sample_f3_features.tsv.gz
sample_f3_matrix.mtx.gz

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (v.3.0.0) pipeline with feature barcoding (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis). For replicate 1 samples, generation of FASTQ files were performed with bcl2fastq (v2.20.0.422)
Assembly: mm10
Supplementary files format and content: Gzipped tab-separated values files and matrix files

molecule: protein

source_name: Tumor

extract_protocol:
B16 tumors were resected from mice and mechanically minced prior to treatment with collagenase and DNAse for 10 minutes at 37C. The cells were washed and filtered through 70 micron filters to obtain single cell suspensions, then labeled with CD45+ MACS beads per the manufacturers instructions. CD45+ cells were isolated on LS columns by positive selection. Cells from each mouse were counted, labeled with hashtag antibodies, and pooled together per experimental group. Pooled cells from each experimental group were loaded onto a single lane of the 10x Chromium controller at the appropriate cell number needed for a calculated post-deconvolution doublet rate of less than 5%.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol with feature barcoding, 10x Genomics).

value: Tumor

value: C57BL/6 B2M KO

value: CD40 agonist

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1 Antibody; TotalSeq-B0302 anti-mouse Hashtag 2 Antibody; TotalSeq-B0303 anti-mouse Hashtag 3 Antibody


title: D91__moDC_Pos_AB598_Pos_ATP

description: Library name: D91__moDC_Pos_AB598_Pos_ATP

tag: cell type

value: monocyte-derived dendritic cell


title: D2A1 wildtype rep3

description: Library name: D2A1_3

tag: cell line


title: Ch2-S2-100E-C1

value: C57/Bl6 mouse


title: S5_Single-cell RNA-seq of mouse intestine (Cre-positive)

description:
Library name: S5
Cre-positive mouse intestine

tag: genotype


title: D4221__moDC_Pos_Isotype

description: Library name: D4221__moDC_Pos_Isotype

value: Isotype


title: D4221__moDC_Pos_DOC_Pos_A549_Pos_AB598

description: Library name: D4221__moDC_Pos_DOC_Pos_A549_Pos_AB598


title: sample d4 (B2M KO, isotype-treated, replicate 2) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_d4_barcodes.tsv.gz
sample_d4_features.tsv.gz
sample_d4_matrix.mtx.gz

value: isotype


title: Ch2-S2-100E-C4

value: dorsal telencephalon

value: Set-A


title: Ch2-S2-100E-B8

value: L


title: D4221__moDC_Pos_DOC_Pos_AB598_Pos_ATP

description: Library name: D4221__moDC_Pos_DOC_Pos_AB598_Pos_ATP


title: Ch2-S2-100E-B7

value: S


title: D4221__moDC_Pos_AB598

description: Library name: D4221__moDC_Pos_AB598


title: resting2

description: Library name: AB-24-19

value: Lung


title: S2_Single-cell RNA-seq of mouse intestine (Cre-positive)

description:
Library name: S2
Cre-positive mouse intestine

value: Intestine

value: Cre-positive


title: Ch2-S2-100E-B9


title: D2A1 wildtype rep1

description: Library name: D2A1_1

value: breast cancer cell line

value: wildtype


title: Ch2-S2-100E-B12

value: M


title: S7_Single-cell RNA-seq of mouse intestine (Cre-negative)

description:
Library name: S7
Cre-negative mouse intestine

value: Cre-negative


title: resting1

description: Library name: AB-24-18


title: D2634__moDC_Pos_Isotype

description: Library name: D2634__moDC_Pos_Isotype


title: sample c1-1 (WT, CD40-treated, technical replicate 1) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_c1_1_barcodes.tsv.gz
sample_c1_1_features.tsv.gz
sample_c1_1_matrix.mtx.gz

value: Tumor

value: C57BL/6 WT

value: CD40 agonist

value: HTO


title: Ch2-S2-100E-B5

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: C57/Bl6 mouse


title: Ch2-S2-100E-B11


title: Ch2-S2-100E-B4


title: Ch2-S2-100E-B10


title: sample f1 (B2M KO, CD40-treated, replicate 1) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_f1_barcodes.tsv.gz
sample_f1_features.tsv.gz
sample_f1_matrix.mtx.gz

value: C57BL/6 B2M KO

value: TotalSeq-B0301 anti-mouse Hashtag 1 Antibody; TotalSeq-B0302 anti-mouse Hashtag 2 Antibody; TotalSeq-B0303 anti-mouse Hashtag 3 Antibody


description: Library name: D4221__moDC_Pos_DOC_Pos_A549_Pos_AB598_Pos_ATP

value: monocyte-derived dendritic cell


title: S4_Single-cell RNA-seq of mouse intestine (Cre-negative)

description:
Library name: S4
Cre-negative mouse intestine


title: sample d1 (B2M KO, isotype-treated, replicate 1) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_d1_barcodes.tsv.gz
sample_d1_features.tsv.gz
sample_d1_matrix.mtx.gz

value: isotype


title: S3_Single-cell RNA-seq of mouse intestine (Cre-positive)

description:
Library name: S3
Cre-positive mouse intestine


title: sample c1-2 (WT, CD40-treated, technical replicate 2) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_c1_barcodes.tsv.gz
sample_c1_2_features.tsv.gz
sample_c1_2_matrix.mtx.gz


title: D4221__moDC_Pos_AB598_Pos_ATP

description: Library name: D4221__moDC_Pos_AB598_Pos_ATP


title: D2634__moDC_Pos_DOC_Pos_AB598

description: Library name: D2634__moDC_Pos_DOC_Pos_AB598


title: sample f3 (B2M KO, CD40-treated, replicate 2) GEX

description:
RNA
sample_f3_barcodes.tsv.gz
sample_f3_features.tsv.gz
sample_f3_matrix.mtx.gz

value: RNA


title: S1_Single-cell RNA-seq of mouse intestine (Cre-negative)

description:
Library name: S1
Cre-negative mouse intestine


title: Ch2-S2-100E-B2

value: dorsal telencephalon

value: Set-A


title: Ch2-S2-100E-A12


title: Ch2-S2-100E-B3

value: S


title: D2634__moDC_Pos_DOC_Pos_Isotype

description: Library name: D2634__moDC_Pos_DOC_Pos_Isotype


title: CSDS + aerobic exercise mouse hippocampus RNA-seq_ME6

city: Chengdu

first: Xia

last: Jiang

state: Sichuan province

address: West China School of Public Health and West China Fourth Hospital, Sichuan University, No.16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China

department: Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.

country: China

institute: Sichuan University

description:
Library name: ME6
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress and aerobic exercise intervention.

data_processing:
Raw sequencing reads were trimmed and quality-filtered using fastp with default parameters.
Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 in strand-specific mode.
Gene expression quantification was performed using RSEM.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data include a gene-level read count matrix generated from RNA-seq, with genes in rows and individual samples in columns.

source_name: Hippocampus

growth_protocol: Adolescent male C57BL/6J mice were housed under specific pathogen-free conditions; temperature 22 ± 2 °C; humidity 45 ± 15%; 12-h light/dark cycle; food and water were provided ad libitum.

extract_protocol:
For each group (CG, MG, and ME), six mice were randomly selected. Hippocampal tissues were rapidly dissected, snap-frozen in liquid nitrogen, and stored at −80 °C. Total RNA was extracted using the MJZol total RNA extraction kit (Majorbio, Shanghai, China) according to the manufacturer’s instructions. RNA concentration and purity were assessed with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was evaluated using an Agilent 5300 Bioanalyzer (Agilent Technologies, USA). Only high-quality RNA samples with an RNA Integrity Number (RIN) ≥ 7 were used for library preparation.
RNA-seq libraries were prepared using the Stranded mRNA Prep and Ligation protocol (Illumina, USA), including poly(A) RNA enrichment, fragmentation, cDNA synthesis, adaptor ligation, and PCR amplification. Libraries were sequenced on the Illumina NovaSeq X Plus platform.

treatment_protocol: Mice were randomly assigned to control (CG), chronic social defeat stress (CSDS) model (MG), or CSDS plus aerobic exercise intervention (ME) groups. CSDS was performed using a resident–intruder paradigm. Mice in the ME group received aerobic exercise training starting one week before CSDS and continuing throughout the stress exposure period.

value: Hippocampus

value: WT

value: Chronic social defeat stress (CSDS) + aerobic exercise

tag: batch

value: Batch 1


title: CSDS + aerobic exercise mouse hippocampus RNA-seq_ME3

description:
Library name: ME3
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress and aerobic exercise intervention.

tag: treatment


title: sample a4 (WT, isotype-treated, replicate 2) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_a4_barcodes.tsv.gz
sample_a4_features.tsv.gz
sample_a4_matrix.mtx.gz

value: Tumor


title: CSDS + aerobic exercise mouse hippocampus RNA-seq_ME2

description:
Library name: ME2
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress and aerobic exercise intervention.


title: sample a1 (WT, isotype-treated, replicate 1) HTO

description:
Hashtag-derived oligonucleotide (HTO)
sample_a1_barcodes.tsv.gz
sample_a1_features.tsv.gz
sample_a1_matrix.mtx.gz

value: C57BL/6 WT


title: CSDS + aerobic exercise mouse hippocampus RNA-seq_ME5

description:
Library name: ME5
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress and aerobic exercise intervention.


title: CSDS + aerobic exercise mouse hippocampus RNA-seq_ME4

description:
Library name: ME4
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress and aerobic exercise intervention.


title: Ch2-S2-100E-B1

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

tag: strain

value: L


title: D2634__moDC_Pos_DOC_Pos_AB598_Pos_ATP

description: Library name: D2634__moDC_Pos_DOC_Pos_AB598_Pos_ATP


title: CSDS mouse hippocampus RNA-seq_MG6

description:
Library name: MG6
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress.

tag: tissue

value: Chronic social defeat stress (CSDS)


title: D2634__moDC_Pos_AB598

description: Library name: D2634__moDC_Pos_AB598


title: CSDS mouse hippocampus RNA-seq_MG5

description:
Library name: MG5
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress.


description: Library name: D2634__moDC_Pos_DOC_Pos_A549_Pos_Isotype


title: Ch2-S2-0E-C9

value: C57/Bl6 mouse

tag: developmental stage


description: Library name: D2634__moDC_Pos_DOC_Pos_A549_Pos_AB598_Pos_ATP


title: Ch2-S2-0E-C5

tag: culture group

value: M


title: sample f1 (B2M KO, CD40-treated, replicate 1) GEX

description:
RNA
sample_f1_barcodes.tsv.gz
sample_f1_features.tsv.gz
sample_f1_matrix.mtx.gz

value: C57BL/6 B2M KO

value: CD40 agonist


title: Ch2-S2-0E-C8

tag: ethanol (etoh) treatment


title: sample d4 (B2M KO, isotype-treated, replicate 2) GEX

description:
RNA
sample_d4_barcodes.tsv.gz
sample_d4_features.tsv.gz
sample_d4_matrix.mtx.gz

value: isotype


title: sample d1 (B2M KO, isotype-treated, replicate 1) GEX

description:
RNA
sample_d1_barcodes.tsv.gz
sample_d1_features.tsv.gz
sample_d1_matrix.mtx.gz

value: RNA


title: CSDS mouse hippocampus RNA-seq_MG4

description:
Library name: MG4
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress.


title: D2634__moDC_Pos_DOC_Pos_A549_Pos_AB598

description: Library name: D2634__moDC_Pos_DOC_Pos_A549_Pos_AB598

value: monocyte-derived dendritic cell


title: CSDS + aerobic exercise mouse hippocampus RNA-seq_ME1

description:
Library name: ME1
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress and aerobic exercise intervention.


title: D2633__moDC_Pos_DOC_Pos_Isotype

description: Library name: D2633__moDC_Pos_DOC_Pos_Isotype


title: sample a1 (WT, isotype-treated, replicate 1) GEX

description:
RNA
sample_a1_barcodes.tsv.gz
sample_a1_features.tsv.gz
sample_a1_matrix.mtx.gz


title: D2634__moDC_Pos_AB598_Pos_ATP

description: Library name: D2634__moDC_Pos_AB598_Pos_ATP


title: CSDS mouse hippocampus RNA-seq_MG3

description:
Library name: MG3
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress.


title: Ch2-S2-0E-C7

value: dorsal telencephalon

value: Set-A

tag: neurosphere diameter (um)


title: Ch2-S2-0E-C6


title: sample c1-2 (WT, CD40-treated, technical replicate 2) GEX

description:
RNA
sample_c1_barcodes.tsv.gz
sample_c1_2_features.tsv.gz
sample_c1_2_matrix.mtx.gz


title: sample c1-1 (WT, CD40-treated, technical replicate 1) GEX

description:
RNA
sample_c1_1_barcodes.tsv.gz
sample_c1_1_features.tsv.gz
sample_c1_1_matrix.mtx.gz


title: D2633__moDC_Pos_DOC_Pos_AB598

description: Library name: D2633__moDC_Pos_DOC_Pos_AB598

tag: donor


title: CSDS mouse hippocampus RNA-seq_MG2

description:
Library name: MG2
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress.

value: Hippocampus


title: D2633__moDC_Pos_Isotype

description: Library name: D2633__moDC_Pos_Isotype

value: Isotype


title: Ch2-S2-0E-C10

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: S


title: sample a4 (WT, isotype-treated, replicate 2) GEX

description:
RNA
sample_a4_barcodes.tsv.gz
sample_a4_features.tsv.gz
sample_a4_matrix.mtx.gz


title: D2633__moDC_Pos_DOC_Pos_AB598_Pos_ATP

description: Library name: D2633__moDC_Pos_DOC_Pos_AB598_Pos_ATP


title: Ch2-S2-0E-C4


title: CSDS mouse hippocampus RNA-seq_MG1

description:
Library name: MG1
Hippocampal tissue collected from adolescent male C57BL/6J mice subjected to chronic social defeat stress.

value: WT

value: Batch 1


title: Ch2-S2-0E-C3


description: Library name: D2633__moDC_Pos_DOC_Pos_A549_Pos_Isotype


title: Control mouse hippocampus RNA-seq_CG6

description:
Library name: CG6
Hippocampal tissue collected from adolescent male C57BL/6J mice under control conditions.

value: No treatment


title: Control mouse hippocampus RNA-seq_CG5

description:
Library name: CG5
Hippocampal tissue collected from adolescent male C57BL/6J mice under control conditions.


title: D2633__moDC_Pos_DOC_Pos_A549_Pos_AB598

description: Library name: D2633__moDC_Pos_DOC_Pos_A549_Pos_AB598


title: Control mouse hippocampus RNA-seq_CG4

description:
Library name: CG4
Hippocampal tissue collected from adolescent male C57BL/6J mice under control conditions.


title: Ch2-S2-0E-C2


title: SGf Rep.1

first: Nourhan

last: Abdelfattah

state: TX

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

data_processing:
The 75-nt single-end (SE75) sequence reads were mapped to the mouse mm9 genome using the BWA algorithm (RRID:SCR_010910) with default settings.  Duplicate reads were removed, and only uniquely mapped reads (mapping quality ≥25) were used for further analysis. Known motifs were identified with the findMotifsGenome program in HOMER (v4.11; RRID:SCR_010881) using default parameters
Assembly: mm9
Supplementary files format and content: BigWig and NarrowPeak

source_name: MB

extract_protocol:
Flash frozen fSMO;GFAP-cre MB tissues from males and females were sent to Active Motif (Carlsbad, CA) for ChIP-Seq analysis, using a previously ChIP validated anti-YAP1 antibody (US Biological, Salem, MA; # Y1200-01D- RRID:AB_2927438).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 instrument.

value: MB

tag: Sex

value: Female


title: pooled input Rep.1


title: SGf Rep.2

description: 2_08MK_012BHMRI_Fsmo-MB-Female_YAP1_mm_i86

value: Male


title: D2633__moDC_Pos_AB598_Pos_ATP

description: Library name: D2633__moDC_Pos_AB598_Pos_ATP


title: Ch2-S2-0E-B8

value: C57/Bl6 mouse

value: M


title: SGm Rep.1


title: Ch2-S2-0E-B9


description: Library name: D2633__moDC_Pos_DOC_Pos_A549_Pos_AB598_Pos_ATP


title: SGm Rep.2

description: 1_08MJ_012BHMRI_Fsmo-MB-Male_YAP1_mm_i85


title: Ch2-S2-0E-B7


title: D2633__moDC_Pos_AB598

description: Library name: D2633__moDC_Pos_AB598


title: Control mouse hippocampus RNA-seq_CG3

description:
Library name: CG3
Hippocampal tissue collected from adolescent male C57BL/6J mice under control conditions.


title: pooled input Rep.2


title: Control mouse hippocampus RNA-seq_CG1

description:
Library name: CG1
Hippocampal tissue collected from adolescent male C57BL/6J mice under control conditions.


title: Ch2-S2-0E-B6


title: Ch2-S2-0E-C1


title: Control mouse hippocampus RNA-seq_CG2

description:
Library name: CG2
Hippocampal tissue collected from adolescent male C57BL/6J mice under control conditions.


title: Ch2-S2-0E-B5


title: A549 cells hCoV229E infected+ selinexor treatment 48h 2

city: Braunschweig

first: Fakhar

last: Waqas

address: Inhoffenstr

country: Germany

institute: Helmholtz Zentrum für Infektionsforshcung GmbH

description:
Bulk RNA sequencing of A549 cells infected and selinexor treated
2674InfSEL48h

data_processing:
Large sets of high‐throughput sequencing reads were mapped against the Homo sapiens hg38 reference genome via STAR 2.7.3a tool.
DESeq2 was used to normalize the counts of each gene to account for differences in sequencing depth and low count variability. The DESeq2 normalization metric is based on the median of ratios method.
Following normalization, DESeq2 was run in a pairwise manner, identifying significantly differentially expressed genes with higher levels of expression in the unstimulated group in comparison to the stimulated group of both WT and KO cells.
Assembly: human reference genome (hg19, GRCh38)
Supplementary files format and content: normalized count csv file

source_name: A549 cells

growth_protocol: A549 cells were seeded in 12-well plate usingDMEM media supplemented with 10% FCS and 1% Glutamax

extract_protocol:
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 100 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 5 x107 reads per RNA sample.

treatment_protocol: A549 cells were seeded in 12-well plate and infected with hCoV-229E at MOI 0.3 and treated with 0.1 µM of BARD, 100 µM of 4OI and 1 µM of SEL for 24 hours and 48 hours.

value: A549 cells

value: hCoV229E infected+ SEL


title: A3P9-3

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

description: Library name: A3P9-3_S12

data_processing:
CLC Genomics Workbench 24.0.5 (Qiagen)
Reads from FASTq files were filtered for quality and aligned to the GRCh38  version of the reference human genome
The data were normalised using the TMM method (trimmed Mean of M-values)
DE analysis was performed using Generalized Linear Model (GLM) and Trimmed mean of M-values (TMM) normalized counts (CPM) were used as input data, considering significant Benjamini-Hochberg adjusted p-values ≤ 0.05
Assembly: GRCh38 human genome
Supplementary files format and content: CPM

growth_protocol: Huh-7 cell line was maintained in Modified Eagle’s Medium 101 (MEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% penicillin/streptomycin 102 solution (10,000 U/mL and 10 mg/mL, respectively), 1% L-glutamine 200 mM, and 1% non- 103 essential amino acids 100× solution

extract_protocol:
RNAeasy Kit (Qiagen)
library preparation of mRNAs from liver tissues was obtained using TruSeq Stranded mRNA (Illumina).

treatment_protocol: Cells were washed with phosphate-buffered saline (PBS) and fresh culture  medium was added to each plate and then transfected with ANGPTL3-siRNA  Pre-designed human ANGPTL3-siRNA pooled: C, or PCSK9-siRNA  or both sRNA together, or scramble-siRNA purchased from Thermo- 112 Scientific. The siRNA were mixed to obtain a 50 mM stock solution in nuclease free water. 113 Silencing was performed with Lipofectamine™ 3000 Transfection Reagent (Thermo- 114 Scientific, Waltham, Massachusetts, USA, Catalog number: L3000001) according to 115 manufacturer’s instructions. C

value: Liver

value: human hepatocellular carcinoma

value: cell line

value: ANGPTL3-siRNA and PCSK9-siRNA


title: A549 cells hCoV229E infected+ selinexor treatment 48h 3

description:
Bulk RNA sequencing of A549 cells infected and selinexor treated
2676InfSEL48h


title: A3P9-2

description: Library name: A3P9-2_S11


title: A3P9-1

description: Library name: A3P9-1_S10


title: E22-2 homo Stim_rep2

city: Columbus

first: Ankita

last: Saini

state: Ohio

address: 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University Wexner Medical Center

description: Library name: ATAC_16

data_processing:
Sequencing data were mapped to mm10 using Bowtie2. BigWig files were created from BAM files using deepTools package.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Mnk3_E22-2 homo

extract_protocol:
Nuclei were isolated from freshly harvested cells. The nuclei were then subjected to transposition reactions for 30 minutes using Tagment DNA TDE1 Enzyme (Illumina, 20034197). Purified DNA was then amplified to generate libraries using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-2001).
Libraries generated using Nextera XT DNA Library Preparation Kit

treatment_protocol: Cells were either stimulated with 10ng/ml each of IL-1b+IL-23 or left untreated for ~16 hours

value: Mnk3_E22-2 homo

value: Stim with IL1b+IL23


title: Ch2-S2-0E-B3

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

data_processing: Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.

extract_protocol: Each neurosphere was imaged, prior to collection in 6ul of Cells Direct Lysis Buffer (Invitogen #117753-100) and stored at -80oC, prior to being processed for RT-qPCR using the Biomark HD system (protocol ADP 42), for mRNA expression across 96 genes. Single neurospheres were processed directly to reverse transcription and pre-amplification reaction (Fluidigm protocol ADP 42), without RNA extraction to minimize RNA loss.

value: dorsal telencephalon

value: Set-A

value: L


title: A549 cells hCoV229E infected+ selinexor treatment 48h 1

description:
Bulk RNA sequencing of A549 cells infected and selinexor treated
2673InfSEL48h

value: WT


title: E22-1 homo Stim_rep2

description: Library name: ATAC_15

source_name: Mnk3_E22-1 homo

value: Mnk3_E22-1 homo


title: PCSK9-3

description: Library name: PCSK9-3_S9


title: E22-2-WT Stim_rep2

description: Library name: ATAC_14


title: A549 cells hCoV229E infected+ 4-octyl itaconate treatment 48h 3

description:
Bulk RNA sequencing of A549 cells infected and 4-octyl itaconate treated
2672Inf4OI48h

value: hCoV229E infected+ 4OI


title: PCSK9-1

description: Library name: PCSK9-1_S7


title: Ch2-S2-0E-B2


title: PCSK9-2

description: Library name: PCSK9-2_S8


title: Ch2-S2-0E-B12

value: S


title: Ch2-S2-0E-B4

value: C57/Bl6 mouse


title: A549 cells hCoV229E infected+ 4-octyl itaconate treatment 48h 1

description:
Bulk RNA sequencing of A549 cells infected and 4-octyl itaconate treated
2669Inf4OI48h


title: Ang3_3

description: Library name: Ang3-3_S6


title: Ang3_2

description: Library name: Ang3-2_S5


title: E22-2 homo Ctrl_rep2

description: Library name: ATAC_12

value: Ctrl


title: E22-1-WT Stim_rep2

description: Library name: ATAC_13


title: A549 cells hCoV229E infected+ 4-octyl itaconate treatment 48h 2

description:
Bulk RNA sequencing of A549 cells infected and 4-octyl itaconate treated
2670Inf4OI48h

value: A549 cells


title: A549 cells hCoV229E infected+ Bardoxolone treatment 48h 2

description:
Bulk RNA sequencing of A549 cells infected and bardoxolone treated
2667InfBARD48h

value: hCoV229E infected+ BARD


title: A549 cells hCoV229E infected+ Bardoxolone treatment 48h 3

description:
Bulk RNA sequencing of A549 cells infected and bardoxolone treated
2668InfBARD48h


title: E22-1 homo Ctrl_rep2

description: Library name: ATAC_11


title: CTRL3

description: Library name: CTRL-3_S3

value: Liver

value: scramble-siRNA


title: Ch2-S2-0E-B1


title: Ch2-S2-0E-B11

value: M


title: E22-2-WT Ctrl_rep2

description: Library name: ATAC_10


title: Ang3_1

description: Library name: Ang3-1_S4

value: human hepatocellular carcinoma

value: cell line


title: A549 cells hCoV229E infected 48h 3

description:
Bulk RNA sequencing of A549 cells infected
2664Infection48h

value: hCoV229E infected


title: CTRL1

description: Library name: CTRL-1_S1


title: A549 cells hCoV229E infected+ Bardoxolone treatment 48h 1

description:
Bulk RNA sequencing of A549 cells infected and bardoxolone treated
2665InfBARD48h


title: E22-1-WT Ctrl_rep2

description: Library name: ATAC_09


title: E22-1 homo Stim_rep1

description: Library name: ATAC_07

value: Stimulated with IL-1b+IL-23


title: Ch2-S2-0E-B10

value: dorsal telencephalon

value: Set-A


title: A549 cells hCoV229E infected 48h 2

description:
Bulk RNA sequencing of A549 cells infected
2663Infection48h

value: WT


title: E22-2 homo Stim_rep1

description: Library name: ATAC_08

value: Mnk3_E22-2 homo


title: Ch1-S3-70E-A9

value: Set-B


title: Ch2-S2-0E-A12

value: L


title: A549 cells hCoV229E infected 48h 1

description:
Bulk RNA sequencing of A549 cells infected
2661Infection48h


title: Ch1-S3-70E-A8

value: C57/Bl6 mouse

value: S


title: MGHPDL002_021213, anti-PD-1

city: Philadelphia

first: Yeqing

last: Chen

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
After sequencing, paired fastq files were aligned to GRCh37 reference genome by STAR with default settings.
After obtaining the BAM files, read counts were summarized by featureCounts with the setting that only paired-ended, non-chimeric, high-quality reads (mapping quality >= 20) reads were counted.
The R package edgeR was used to normalize sequencing depths and gene lengths, generating RPKMs (Reads Per Kilobase of transcript per Million mapped reads).
Assembly: GRCh37
Supplementary files format and content: Comma-separated value (CSV) file includes raw counts for each sample.

source_name: Melanoma

extract_protocol:
RNA was extracted from fresh frozen tumors using the Qiagen Rneasy Mini kit.
RNA libraries were prepare with 250ng RNA per sample following the standard Illumina protocals.

value: Melanoma


title: E22-2-WT Stim_rep1

description: Library name: ATAC_06


title: MGHBI1_102512, anti-CTLA-4


title: A549 cells control 48h 3

description:
Bulk RNA sequencing of A549 cells untreated
2648Control48h

value: A549 cells

value: untreated


title: Ch1-S3-70E-A7

first: Rajanikanth

last: Vadigepalli


title: Ch1-S3-70E-A6


title: MGHBI1_092712, anti-CTLA-4


title: A549 cells control 48h 2

description:
Bulk RNA sequencing of A549 cells untreated
2647Control48h


title: E22-2 homo Ctrl_rep1

description: Library name: ATAC_04

value: Untreated


title: E22-1-WT Stim_rep1

description: Library name: ATAC_05


title: MGHBI1_022613, anti-CTLA-4


title: Ch1-S3-70E-A5


title: E22-1 homo Ctrl_rep1

description: Library name: ATAC_03

value: Mnk3_E22-1 homo


title: E22-2-WT Ctrl_rep1

description: Library name: ATAC_02


title: A549 cells hCoV229E infected+ selinexor treatment 24h 3

description:
Bulk RNA sequencing of A549 cells infected and selinexor treated
2612InfSEL24h

value: hCoV229E infected+ SEL


title: MGH272_022916, anti-PD-1


title: A549 cells control 48h 1

description:
Bulk RNA sequencing of A549 cells untreated
2646Control48h


title: A549 cells hCoV229E infected+ 4-octyl itaconate treatment 24h 3

description:
Bulk RNA sequencing of A549 cells infected and 4-octyl itaconate treated
2608Inf4OI24h

value: hCoV229E infected+ 4OI


title: A549 cells hCoV229E infected+ selinexor treatment 24h 2

description:
Bulk RNA sequencing of A549 cells infected and selinexor treated
2610InfSEL24h


title: Ch1-S3-70E-A2

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: M


title: Ch1-S3-70E-A3


title: A549 cells hCoV229E infected+ selinexor treatment 24h 1

description:
Bulk RNA sequencing of A549 cells infected and selinexor treated
2609InfSEL24h


title: E22-1-WT Ctrl_rep1

description: Library name: ATAC_01


title: MGH212_091214, anti-CTLA-4


title: CTRL2

description: Library name: CTRL-2_S2

value: Liver

value: human hepatocellular carcinoma

value: cell line

value: scramble-siRNA


title: Stim_IgGRb_rep2

description: Library name: AS20

data_processing:
The Nextflow cutandrun pipeline was used to analyze the data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
The assay was performed using CUTANA™ ChIC/CUT&RUN (EpiCypher, 14-1048) with following antibodies: Runx3 (Clone 2B3; Invitrogen, MA5-17169), mouse IgG control (Diagenode, C15400001-100), RORγt (Abcam, ab207082), and rabbit IgG control (Diagenode, C15410206).
The libraries were made using CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001).

treatment_protocol: Mnk3 cells were either stimulated with 10ng/ml each of IL-1b+IL-23 or left untreated for ~16 hours

value: Stim with IL-1b+IL-23


title: MGH208_081915, anti-PD-1


title: MGH272_020415, anti-PD-1


title: A549 cells hCoV229E infected+ 4-octyl itaconate treatment 24h 2

description:
Bulk RNA sequencing of A549 cells infected and 4-octyl itaconate treated
2606Inf4OI24h

value: WT


title: Stim_IgGMo_rep2

description: Library name: AS19


title: MGH212_091015-1, anti-CTLA-4


title: Ch1-S3-70E-A11

value: dorsal telencephalon

value: Set-B


title: Stim_Rorc_rep2

description: Library name: AS18


title: Ch1-S3-70E-A4

value: C57/Bl6 mouse


title: A549 cells hCoV229E infected+ 4-octyl itaconate treatment 24h 1

description:
Bulk RNA sequencing of A549 cells infected and 4-octyl itaconate treated
2605Inf4OI24h


title: MGH148_123114-1, anti-PD-1

value: Melanoma


title: Ch1-S3-70E-A1

value: L


title: MGH98_FFPE_090716-1, anti-PD-1


title: Stim_Rnx3_rep2

description: Library name: AS17


title: A549 cells hCoV229E infected+ Bardoxolone treatment 24h 3

description:
Bulk RNA sequencing of A549 cells infected and bardoxolone treated
2604InfBARD24h

value: A549 cells

value: hCoV229E infected+ BARD


title: Ch1-S3-70E-A10


title: Ch1-S3-25E-A9


title: Ctrl_IgGRb_rep2

description: Library name: AS15

value: Untreated


title: A549 cells hCoV229E infected+ Bardoxolone treatment 24h 2

description:
Bulk RNA sequencing of A549 cells infected and bardoxolone treated
2603InfBARD24h


title: Ctrl_IgGMo_rep2

description: Library name: AS14


title: MGH98_090716, anti-PD-1


title: Ch1-S3-25E-A8


title: Ch1-S3-25E-A7


title: A549 cells hCoV229E infected+ Bardoxolone treatment 24h 1

description:
Bulk RNA sequencing of A549 cells infected and bardoxolone treated
2602InfBARD24h


title: A549 cells hCoV229E infected 24h 2

description:
Bulk RNA sequencing of A549 cells infected
2599Infection24h

value: hCoV229E infected


title: Ctrl_Rnx3_rep2

description: Library name: AS12


title: A549 cells hCoV229E infected 24h 3

description:
Bulk RNA sequencing of A549 cells infected
2600Infection24h


title: MGH98_030314, anti-PD-1


title: MGH42_101714, anti-CTLA-4


title: Ctrl_Rorc_rep2

description: Library name: AS13


title: Ch1-S3-25E-A5

value: S


title: A549 cells hCoV229E infected 24h 1

description:
Bulk RNA sequencing of A549 cells infected
2597Infection24h


title: Ch1-S3-25E-A6


title: Ch1-S3-25E-A3


title: Stim_IgGMo_rep1

description: Library name: AS9

value: Stimulated IL-1b+IL-23


title: Ch1-S3-25E-A4

value: M


title: Sort-purified (CD4+/Ly5.1-/CD44+) CD4 T cells isolated from tdLN Input Control

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: Library name: CD4_250k_input_Ln

data_processing:
Sequence reads were aligned to the mouse reference genome (GRCm38.p6) using the nf-core/cutandrun pipeline v3.2.2 with default parameters. In brief, reads were quality-checked with FastQC v0.12.1, trimmed with TrimGalore v0.6.6. and aligned with Bowtie2 v2.4.4. Alignments were de-duplicated using Picard MarkDuplicates v3.1.0. Peaks were called using MACS3 v3.0.3 in paired-end mode with input control, using a q-value threshold of 0.01. Signal tracks (bigWig) were generated using deepTools bamCoverage v3.5.1 with BPM normalization and 50 bp bin size.
Assembly: GRCm38
Supplementary files format and content: BigWig files for each sample
Supplementary files format and content: MACS3 peak calls for each sample (except input)
Library strategy: CUT&RUN

source_name: tdLN

growth_protocol: Naive WT TCRSMARTA transgenic CD4 T cells were transferred to cytoxan-treated B16-GP61 tumor-bearing mice. Naïve WT TCRTAG CD8 T cells were transferred to ASTxAlbCre liver tumor mice

extract_protocol:
After flow sorting, samples were fixed with PFA, quenched with Glycine and transferred to a BSA-coated 96 well plate. Cells were washed and resuspended in buffer (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine, + 2uM EDTA in H2O) containing anti-TOX, anti-H3K4me3 (positive control) or no antibody (negative input control) overnight. The following day, cells were resuspended in buffer (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in H2O)  containing pAG-MNase (CELL SIGNALING) for 1 hour before wash and incubation in calcium-containing buffer (0.05% w/v Saponin, 1X Roche Complete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS + CaCl2 2uM) for 30 minutes. After incubation, STOP buffer (0.05% w/v Saponin, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS+ 20uM EDTA + 4uM EGTA) was added to the samples, supernatant was collected, and DNA was isolated with the MiniElute Kit. DNA fragments were digested with Proteinase K (Thermo Fisher, cat. EO0491) under addition of 0.1% SDS for 4h at 65°C.
Library prep was conducted on the product using a KAPA HyperPrep Kit (Kapa Biosystems, cat. KK8504). The final product was cleaned by AMPure XP beads (Beckman Coulter catalog no. A63882).

treatment_protocol: Mice received WT TCRSMARTA or TCRTAG

value: tdLN

tag: tumor type

value: CD4 T cells

tag: t cells

value: Polyclonal endogenous activated (CD44+) CD4 T cells


title: MGH42_032113, anti-CTLA-4


title: Sort-purified (CD8+/Ly5.1-/CD44+) CD8 T cells isolated from liver tumors Input Control

description: Library name: Input_CD8

value: Liver

value: ASTxAlbCre

value: CD8 T cells

value: polyclonal endogenous activated (CD44+) CD8 T cells


title: A549 cells control 24h 2

description:
Bulk RNA sequencing of A549 cells untreated
2582Control24h

value: WT

value: untreated


title: MGH98_051514, anti-PD-1

value: Melanoma


title: A549 cells control 24h 3

description:
Bulk RNA sequencing of A549 cells untreated
2583Control24h

value: A549 cells


title: Stim_Rnx3_rep1

description: Library name: AS7


title: Stim_Rorc_rep1

description: Library name: AS8


title: Stim_IgGRb_rep1

description: Library name: AS10


title: A549 cells control 24h 1

description:
Bulk RNA sequencing of A549 cells untreated
2581Control24h


title: Ch1-S3-25E-A11

address: 1 University of New Mexico

institute: University of New Mexico

source_name: fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-B

tag: neurosphere size group

value: L


title: Sort-purified (CD8+/Ly5.1+/CD44+/PD1hi) TCRTAG CD8 T cells isolated from liver tumors 20 days post transfer replicate #3

description: Library name: Tox_CD8_Liver_2

value: TCRTAG transgenic CD8 T cells


title: Ctrl_IgGRb_rep1

description: Library name: AS5

value: Control


title: ChIP-seq, HEK293T cells, Input, VPA-treated, Rep3

city: Tokyo

first: Yutaka

last: Saito

department: Artificial Intelligence Research Center (AIRC)

institute: National Institute of Advanced Industrial Science and Technology (AIST)

data_processing:
Raw ChIP-seq reads were aligned to Hg38 reference genome, or GRCh38 (GRCh38 Genome Reference Consortium Human Reference 38) from UCSC (without alternative contigs) using Bowtie2.
CTCF and H3K27ac peaks were called using MACS (version 3.0.0a7) using the following parameters: callpeak -g hs -f BAMPE -B --seed 1985. Input samples were used as the background.
Differential peak analysis was performed using DiffBind R package to identify differentially changed peaks (log2(fold change)>1 or <-1 and FDR < 0.05).
Assembly: hg38
Supplementary files format and content: the narrowpeak formatted file contains peaks obtained from MACS

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed according to a protocol published by Agilent technologies (Santa Clara, CA, http://www.agilent.com), with the following modifications. Briefly, 293T cells untreated (CTRL) or treated with 1 mM VPA for 1 day (VPA) were fixed by 1% formaldehyde solution for 10 min. After harvesting the fixed cells, the cells were lysed in lysis buffer, and sonicated using Misonix XL2020 sonicator (MISONIX Inc., NY, http://misonix.com) until the DNA fragments were 200–600 base pairs in length. 3.0% of the total volume was stored as input at −20°C, until use. Immunoprecipitation was performed at 4°C, overnight with antibodies described bellow. DNA/beads was washed with a low salt buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% sodium dodecyl sulfate (SDS), 1% Triton X-100) once, and then further washed with a high-salt buffer (20 mM Tris-HCl pH 7.4, 400 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) once before washing with a RIPA buffer. Immune complexes were disrupted with direct elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) and the covalent links between immunoprecipitates and input chromatin were disrupted by incubation at 65°C for overnight. DNA was further incubated with RNaseA and proteinase K (Nacalai Tesque), purified by phenol extraction, and ethanol precipitated. DNA pellets were dissolved in Tris-EDTA (TE) buffer (10 mM Tris-HCl, 1 mM EDTA pH8.0). The antibodies were used anti-CTCF(3418S, Cell Signaling Technology) and Acetyl-Histone H3 (Lys27) (H3K27ac, 8173S, Cell Signaling Technology)
A sequencing library was prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) according to the manufacturer's instructions.

value: human embryonic kidney cells

tag: antibody

value: valproic acid (VPA)


title: ChIP-seq, HEK293T cells, Input, VPA-treated, Rep2

tag: cell type


title: Ch1-S3-25E-A2

value: M


title: Ctrl_IgGMo_rep1

description: Library name: AS4

tag: cell line


title: Sort-purified (CD8+/Ly5.1+/CD44+/PD1hi) TCRTAG CD8 T cells isolated from liver tumors 20 days post transfer replicate #2

description: Library name: Tox_CD8_Liver_1

value: Liver

tag: genotype


title: Sort-purified (CD8+/Ly5.1+/CD44+/PD1hi) TCRTAG CD8 T cells isolated from liver tumors 20 days post transfer replicate #1

description: Library name: CD8_100k_Tox_liver_1

value: ASTxAlbCre


title: Ch1-S3-25E-A10

value: S


title: ChIP-seq, HEK293T cells, Input, VPA-treated, Rep1


title: Ch1-S3-100E-A9


title: Ch1-S3-25E-A1


title: Ctrl_Rorc_rep1

description: Library name: AS3


title: Ch1-S3-100E-A8


title: ChIP-seq, HEK293T cells, Input, untreated, Rep3


title: Old tail epidermis, H3K9me2, biol rep 3

city: Baltimore

first: Andrew

middle: Paul

last: Feinberg

state: Maryland

address: 855 N. Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

description: Library name: O-3_epidermis_H3K9me2

data_processing:
Base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bowtie2
bamCoverage function from DeepTools
Assembly: mm10
Supplementary files format and content: bigWig files with RPKM normalized signal

source_name: Tail epidermis

extract_protocol:
ChIP-Seq, Zymo ChIP Clean and Concentrator kit
NEBNext Ultra II

treatment_protocol: Epidermis isolated from tail skin with dispase treatment, flash frozen and stored at -80 °C.

value: Tail epidermis

tag: chip antibody

tag: age at_time_of_sample_collection

value: 22 months

tag: batch


title: Sort-purified (CD4+/Ly5.1+/CD44+/PD1hi) TCRSMARTA CD4 T cells isolated from tdLN 7 days post transfer replicate #2

description: Library name: Tox_CD4_LN_1

tag: tissue

value: tdLN

value: CD4 T cells

value: WT

value: TCRSMARTA transgenic CD4 T cells


title: Ctrl_Rnx3_rep1

description: Library name: AS2

tag: treatment


title: Ch1-S3-100E-A7

city: Albuquerque

tag: strain

value: C57/Bl6 mouse

value: dorsal telencephalon

tag: developmental stage

tag: culture group


title: Old tail epidermis, H3K9me2, biol rep 2

description: Library name: O-2_epidermis_H3K9me2


title: Sort-purified (CD4+/Ly5.1+/CD44+/PD1hi) TCRSMARTA CD4 T cells isolated from tdLN 7 days post transfer replicate #1

description: Library name: CD4_353k_Tox_Ln


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2+/PD1hi/LAG3hi/CD39hi) TOX WT TCRSMARTA CD4 T cells isolated from tdLN replicate #4

description: Library name: WT-7

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs.
Reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR. Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M17).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

growth_protocol: Naïve WT and KO TCRSMARTA transgenic CD4 T cells were transferred into cytoxan-treated B16-GP61 tumor-bearing B6 mice

extract_protocol:
Cells were sorted directly into Trizol LS. Extraction was performed using Rneasy mini kit (Qiagen) per manufacturer's instructions. Total RNA underwent amplification using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing (12 cycles of amplification for 2-10 ng of total RNA).
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina Hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 4000, in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).

treatment_protocol: Tumor-bearing mice received congenically marked WT (Ly5.12) and KO (Ly5.1) TCRSMARTA

tag: cd4 t cells


title: ChIP-seq, HEK293T cells, Input, untreated, Rep1


title: ChIP-seq, HEK293T cells, Input, untreated, Rep2


title: Old tail epidermis, H3K9me2, biol rep 1

description: Library name: O-1_epidermis_H3K9me2


title: ChIP-seq, HEK293T cells, CTCF, VPA-treated, Rep3

value: CTCF


title: Sort-purified (CD4+/Ly5.1+/CD44+/PD1hi) TCRSMARTA CD4 T cells isolated from tdLN 7 days post transfer replicate #3

description: Library name: Tox_CD4_LN_2


title: Ch1-S3-100E-A6

value: Set-B

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2+/PD1hi/LAG3hi/CD39hi) TOX WT TCRSMARTA CD4 T cells isolated from tdLN replicate #2

description: Library name: WT-5


title: Ch1-S3-100E-A5


title: Ch1-S3-100E-A4


title: ChIP-seq, HEK293T cells, CTCF, VPA-treated, Rep2


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2+/PD1hi/LAG3hi/CD39hi) TOX WT TCRSMARTA CD4 T cells isolated from tdLN replicate #3

description: Library name: WT-6


title: Young tail epidermis, H3K9me2, biol rep 1

description: Library name: Y-1_epidermis_H3K9me2

value: 3 months


title: Young tail epidermis, H3K9me2, biol rep 3

description: Library name: Y-3_epidermis_H3K9me2


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2+/PD1hi/LAG3hi/CD39hi) TOX WT TCRSMARTA CD4 T cells isolated from tdLN replicate #1

description: Library name: WT-2


title: Young tail epidermis, H3K9me2, biol rep 2

description: Library name: Y-2_epidermis_H3K9me2


title: ChIP-seq, HEK293T cells, CTCF, VPA-treated, Rep1

value: human embryonic kidney cells


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #6

description: Library name: KO-8

value: KO


title: ChIP-seq, HEK293T cells, CTCF, untreated, Rep3


title: Ch1-S3-100E-A3

value: L


title: Ch1-S3-100E-A2


title: ChIP-seq, HEK293T cells, CTCF, untreated, Rep2


title: Ch1-S3-100E-A10

value: M


title: Mouse, conventional PAR1b-knockout, immortalized mouse embryonic fibroblasts

city: Sapporo

first: Naoko

last: Murata-Kamiya

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

description: Library name: iMEF_KO

data_processing:
The libraries were sequenced using paired-end sequencing (150 bp x 2 paired-end) on an Illumina NovaSeq X Plus.
Raw sequencing reads were trimmed to remove Illumina Nextera adapter sequence using the Skewer (version 0.2.2) with “-f sanger -t 1 -m pe -x” options.
The trimmed reads were then aligned to the mouse reference genome (GRCm38/mm10) using the Bowtie2 (version 2.3.4.2) with “-N 1 -X 2000” options.
The PCR duplicates were marked and removed using the MarkDuplicates tool in Picard (version 2.18.11).
Chromatin accessible regions (ATAC-peaks) were identified using the MACS2 (version 2.1.2) callpeak command with parameters “--shift -75 --extsize 150 -- nomodel -q 0.01”.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Mouse embryo

growth_protocol: DMEM containing D-glucose (4.5 g/L), 10% fetal bovine serum (FBS) and antibiotics. Cells were cultured at 37C with 5% CO2.

extract_protocol:
Nuclei were extructed using hypotonic lysis buffer.
The ATAC-seq libraries were constructed using Active Motif ATAC-seq Kit (Cat. No. 53150) according to the manufacture’s instructions (Version B6).

value: Mouse embryo

value: Mouse embryonic fibroblasts

value: Conventional PAR1b-knockout


title: Ch1-S3-100E-A11


title: Mouse, wild-type, immortalized mouse embryonic fibroblasts

description: Library name: iMEF_WT

value: Wild-type


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #5

description: Library name: KO-6

value: tdLN


title: ChIP-seq, HEK293T cells, CTCF, untreated, Rep1


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #4

description: Library name: KO-4

value: CD4 T cells


title: KPS.3

city: Stony Brook

first: Harold

last: Bien

address: 100 Nicolls Road

institute: Stony Brook University

description: Library name: RZL3_9

data_processing:
Sequence reads were quantified with GC bias trimming using Salmon
Trimmed sequence reads were mapped to the GrCM39/mm39 reference genome
Assembly: GrCM39/mm39
Supplementary files format and content: tab-delimited sf files including name, length, effective length, transcripts per million, and total number of reads

source_name: KPS

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina with the Ploy(A) mRNA Magnetic Isolation Module

value: KPS

value: lung adenocarcinoma

value: STK11 knockout


title: Ch1-S3-100E-A1

value: C57/Bl6 mouse

value: dorsal telencephalon


title: KPS.2

description: Library name: RZL3_8


title: Ch1-S3-0E-A9

value: Set-B

value: S


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #2

description: Library name: KO-2

value: TCRSMARTA transgenic CD4 T cells


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #3

description: Library name: KO-3

value: KO


title: KPS.1

description: Library name: RZL3_7


title: ChIP-seq, HEK293T cells, H3K27ac, VPA-treated, Rep3

value: human embryonic kidney cells

value: valproic acid (VPA)


title: ChIP-seq, HEK293T cells, H3K27ac, VPA-treated, Rep1


title: ChIP-seq, HEK293T cells, H3K27ac, VPA-treated, Rep2


title: Ch1-S3-0E-A7

value: M


title: ChIP-seq, HEK293T cells, H3K27ac, untreated, Rep3


title: KPA.2

description: Library name: RZL3_5

source_name: KPA

value: KPA

value: PIK3CA knockout


title: ChIP-seq, HEK293T cells, H3K27ac, untreated, Rep2


title: Sort-purified (CD4+/Ly5.1+/Ly5.2+/PD1hi/LAG3hi/CD39hi) TOX WT TCRSMARTA CD4 T cells isolated from tdLN replicate #2

description: Library name: WT-2

data_processing:
Data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium, n.d.): Reads were aligned to the mouse reference genome (version GRCm38) with BWA-backtrack. Post-alignment filtering was done with samtools and Picard tools  to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin, peak calling was performed with MACS2. The narrowPeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01.
Coverage files (bigWig) were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --blackListFileName mm10.blacklist --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40.
Assembly: mm10
Supplementary files format and content: BigWig files for each sample

growth_protocol: Naïve WT and KO TCRSMARTA transgenic CD4 T cells were transferred into cytoxan-treated B16-GP61 tumor-bearing mice

extract_protocol:
Cells were sorted and frozen in 10% DMSO/FCS. Frozen cells were thawed, washed in PBS, and lysed. Transposition was performed at 42°C for 45 min. DNA was purified with the MinElute PCR purification kit (Qiagen)
DNA was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5Å~ ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

value: WT


title: Sort-purified (CD4+/Ly5.1+/Ly5.2+/PD1hi/LAG3hi/CD39hi) TOX WT TCRSMARTA CD4 T cells isolated from tdLN replicate #1

description: Library name: WT-1

value: tdLN


title: Ch1-S3-0E-A8


title: RNA, Sort-purified (CD4+/Ly5.1+/Ly5.2-/PD1lo/LAG3lo/CD39lo) TOX KO TCRSMARTA CD4 T cells isolated from tdLN replicate #1

description: Library name: KO-1

value: CD4 T cells


title: ChIP-seq, HEK293T cells, H3K27ac, untreated, Rep1


title: KPA.1

description: Library name: RZL3_4


title: Ch1-S3-0E-A5


title: Ch1-S3-0E-A6


title: KP.3

description: Library name: RZL3_3

source_name: KP

value: KP

value: Kras G12D, Tp53 null