title: POA_P42_DES 12_3

value: Sprague-Dawley

value: female

value: DES 12 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT03_100 mg/kg_mouse1

status: Public on Mar 21 2023

type: SRA

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample G5-1

library_source: transcriptomic

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the mouse reference genome GRCm38 (mm10) using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCm38.86.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Gastrocnemius

growth_protocol: Ten weeks-old male C57BL/6N (21 ~ 26g) were supplied by OrientBio (Seongnam, Republic of Korea) and maintained in a polycarbonate cage (~5 mice per cage) in a specific pathogen-free animal laboratory facility under a controlled environment (22 ± 2°C temperature, 45 ± 10% humidity, 12 hr-12 hr dark and light cycle). They had a free access to standard chow and water and were acclimated for at least 1 week before experiments.

extract_protocol:
Total RNA extraction using the TRIzolTM reagent (Thermo Fisher Scientific, #15596018) according to the manufacturer’s guide.
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: The study protocol involving experimental animals was peer-reviewed by the Institutional Animal Care and Use Committee of Korea Institute of Oriental Medicine (Protocol No. 22-048) and all procedures of animal studies were conducted in accordance with the guidelines for the Care and Use of Laboratory Animals by the Ministry of Food and Drug Safety, Republic of Korea. After 1-week acclimation, the mice were randomly allocated to 5 groups (9-10 per group) and subject to behavior tests for baseline correction (D1). Then, mice received intraperitoneal (i.p.) injection of PBS (group 1, normal control) or 25 mg/kg dexamethasone (DEX, group 2 to 5) every day for 10 days. Thirty minutes after PBS or DEX injection, JGT at 100 (group 3) or 400 mg/kg (Group 4) were administered to mice by oral gavage. Group 1 and group 2 (vehicle control) received oral gavage of PBS. A positive control group received oral gavage of resveratrol (RsV, 200 mg/kg) instead of JGT. Water soluble DEX were dissolved in a sterile PBS, and JGT and RsV were resuspended in a sterile 0.5% CMC in PBS on the day of drug administration. One day after final behavioral assessments, mice were deeply anaesthetized by i.p. injection of 2% avertin in PBS (240 mg/kg). The whole bloods were collected from the heart in a 1.5 mL tube using a 23 gauged-1 mL syringe and kept for 1 h at room temperature. Skeletal muscle tissues like gastrocnemius (GA), soleus (SO), and tibialis anterior (TA) muscles were excised from the hindlimbs. The isolated muscle tissues were snap frozen on a dry-ice and stored at -80°C for RNA-seq analysis.

tag: tissue

value: Gastrocnemius

tag: treatment

value: DEX 25 mg/kg, JGT03 100mg/kg (30min after)

tag: time

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.24HR.IgG.Donor1

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

country: USA

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For Cut and Tag libraries, the CutRunTools pipeline (Zhu et al. 2020) was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: hg19, mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: CD8 Positive T-cells

growth_protocol: Human T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2

extract_protocol:
Epicypher's CUT&Tag protocol was used for nuclear extraction and probing chromatin localization.
Epicypher's CUT&Tag protocol was used to ampllify tagmented DNA from isolated genomic DNA with 14 PCR cycles. DNA purification was completed  using AMPure beads (1.3X). Library size distribution was determined using TapeStation D1000.

treatment_protocol: Cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.

tag: cell line

value: CD8 Positive T-cells

tag: cell type

value: Primary T cells

tag: chip antibody

tag: sample type

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P22_KTZ 6_4

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 102.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file include raw counts for annotations for all Sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: pre-optic area

extract_protocol:
At PND22, PND42 and PND90,  the pre-optic area (POA) and the mediobasal hypothalamus (MBH) were dissected and frozen. Total RNA was extracted from the MBH and POA using Universal RNA mini kit (Qiagen,Venlo, Netherlands) following the manufacturer’s instructions.
Libraries were prepared using Truseq® stranded mRNA Sample Preparation Kits (Illumina, CA, USA) following manufacturer’s instructions. Libraries were validated using QIAxcel Advanced System and quantified by qPCR using the KAPA library quantification kit. Libraries were multiplexed and sequenced on an Illumina NovaSeq6000 sequencer to generate more than ~25,000,000 paired-end reads (2 × 150 bases) per library.

treatment_protocol: Dams were exposed by oral gavage with either chemical or vehicle (corn oil) once daily from GD 7 until birth and from the day after birth until postnatal (PND) 22. Doses for DES were 0; 3; 6; 12 µg/kg bw/day and doses for KTZ were 0; 3; 6; 12 mg/kg bw/day.

tag: strain

tag: Sex

value: pre-optic area

tag: age

value: KTZ 6 mg/kg bw/day


title: Batch1_Gastrocnemius_JGT03_100 mg/kg_mouse5

description: sample G5-5


title: Batch1_Gastrocnemius_JGT02_400 mg/kg_mouse4

description: sample G4-4

value: DEX 25 mg/kg, JGT02 400mg/kg (30min after)


title: CutAndTag.human.CD8.Positive.Tcells.24HR.H3K27ac.Donor2

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 19A-2

type: genomic

city: University Park

first: Idan

last: Shalev

state: PA

address: 219 Biobehavioral Health Building, Penn State University

institute: Penn State University

description: No-stress session Time 2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
idat files were preprocessed and detection p-values were calculated using minfi (1.42.0). Beta values were obtained by generating a genomic set ratio object and normalization was performed using the minfi function preprocessNoob.
Noob Normalized Average Beta

label: Cy5 and Cy3

source_name: Participant 19, No-stress session, Time 2

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from PBMC samples using QIAmp mini kit (Qiagen) according to standard instructions.

value: PBMC

value: Female

tag: ela status

value: Control

tag: session

value: No-stress


title: 17B-3

description: Stress session Time 3

source_name: Participant 17, Stress session, Time 3

value: Male

value: Stress


title: POA_P42_KTZ 3_3

value: Sprague-Dawley

value: female

value: KTZ 3 mg/kg bw/day


title: POA_P42_DES 6_1

value: DES 6 ug/kg bw/day


title: 18A-3

description: Stress session Time 3

source_name: Participant 18, Stress session, Time 3

value: ELA


title: Batch1_Gastrocnemius_JGT02_400 mg/kg_mouse3

description: sample G4-3

value: Gastrocnemius

value: 10 days


title: 17B-2

description: Stress session Time 2

source_name: Participant 17, Stress session, Time 2


title: 17B-1

description: Stress session Time 1

source_name: Participant 17, Stress session, Time 1


title: Batch1_Gastrocnemius_JGT02_400 mg/kg_mouse2

description: sample G4-2


title: POA_P42_DES 3_2

value: pre-optic area

value: DES 3 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT02_400 mg/kg_mouse1

description: sample G4-1

value: DEX 25 mg/kg, JGT02 400mg/kg (30min after)


title: Batch1_Gastrocnemius_JGT02_100 mg/kg_mouse5

description: sample G3-5

value: DEX 25 mg/kg, JGT02 100mg/kg (30min after)


title: POA_P42_KTZ 3_2


title: CutAndTag.human.CD8.Positive.Tcells.24HR.BRD9.Donor1

value: CD8 Positive T-cells

value: Primary T cells

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Batch1_Gastrocnemius_JGT02_100 mg/kg_mouse4

description: sample G3-4


title: 17A-4

description: No-stress session Time 4

source_name: Participant 17, No-stress session, Time 4

value: PBMC

value: Control

value: No-stress


title: POA_P22_KTZ 6_3

value: Sprague-Dawley

value: KTZ 6 mg/kg bw/day


title: 17A-2

description: No-stress session Time 2

source_name: Participant 17, No-stress session, Time 2

value: Male


title: CutAndTag.human.CD8.Positive.Tcells.24HR.ARID1A.Donor2

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Gastrocnemius_JGT02_100 mg/kg_mouse3

description: sample G3-3


title: 17A-1

description: No-stress session Time 1

source_name: Participant 17, No-stress session, Time 1


title: POA_P42_KTZ 3_1

value: female

value: KTZ 3 mg/kg bw/day


title: POA_P42_DES 12_2

value: DES 12 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT02_100 mg/kg_mouse2

description: sample G3-2

value: Gastrocnemius

value: 10 days


title: 16B-4

description: Stress session Time 4

source_name: Participant 16, Stress session, Time 4

value: Female

value: ELA

value: Stress


title: Batch1_Gastrocnemius_JGT02_100 mg/kg_mouse1

description: sample G3-1

value: DEX 25 mg/kg, JGT02 100mg/kg (30min after)


title: CutAndTag.human.CD8.Positive.Tcells.0HR.SS18.Donor1

value: CD8 Positive T-cells

value: Primary T cells

value: Naïve CD8 Positive T cells from human donor 1


title: CutAndTag.human.CD8.Positive.Tcells.24HR.H3K27ac.Donor1

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: CutAndTag.human.CD8.Positive.Tcells.0HR.SS18.Donor2

value: Naïve CD8 Positive T cells from human donor 2


title: POA_P42_control_2

value: Sprague-Dawley

value: pre-optic area

value: vehicle


title: POA_P42_DES 12_1

value: female


title: Batch1_Gastrocnemius_vehicle(DEX)_mouse4

description: sample G2-4

value: DEX 25 mg/kg


title: CutAndTag.human.CD8.Positive.Tcells.0HR.SMARCA4.Donor2

value: SMARCA4 (CST, #49360S)


title: 16B-2

description: Stress session Time 2

source_name: Participant 16, Stress session, Time 2

value: PBMC


title: CutAndTag.human.CD8.Positive.Tcells.0HR.SMARCA4.Donor1


title: CutAndTag.human.CD8.Positive.Tcells.24HR.BRD9.Donor2

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Gastrocnemius_vehicle(DEX)_mouse3

description: sample G2-3

value: Gastrocnemius

value: 10 days


title: 17A-3

description: No-stress session Time 3

source_name: Participant 17, No-stress session, Time 3

value: Male

value: Control

value: No-stress


title: POA_P42_control_1


title: 16B-1

description: Stress session Time 1

source_name: Participant 16, Stress session, Time 1

value: Female

value: ELA

value: Stress


title: POA_P90_KTZ 3_5

value: KTZ 3 mg/kg bw/day


title: Batch1_Gastrocnemius_vehicle(DEX)_mouse2

description: sample G2-2


title: CutAndTag.human.CD8.Positive.Tcells.24HR.ARID1A.Donor1

value: CD8 Positive T-cells

value: Primary T cells

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: 16A-4

description: No-stress session Time 4

source_name: Participant 16, No-stress session, Time 4


title: Batch1_Gastrocnemius_vehicle(DEX)_mouse1

description: sample G2-1


title: 16A-3

description: No-stress session Time 3

source_name: Participant 16, No-stress session, Time 3


title: CutAndTag.human.CD8.Positive.Tcells.0HR.PBRM1.Donor1

value: Naïve CD8 Positive T cells from human donor 1


title: Batch1_Gastrocnemius_non-treat_mouse4

description: sample G1-4

source_name: Gastrocnemius

value: non-treat


title: 16A-2

description: No-stress session Time 2

source_name: Participant 16, No-stress session, Time 2


title: 16A-1

description: No-stress session Time 1

source_name: Participant 16, No-stress session, Time 1


title: POA_P42_DES 3_1

source_name: pre-optic area

value: Sprague-Dawley

value: female

value: pre-optic area

value: DES 3 ug/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.0HR.IgG.Donor2

source_name: CD8 Positive T-cells

value: Naïve CD8 Positive T cells from human donor 2


title: POA_P90_KTZ 6_4

value: KTZ 6 mg/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.0HR.IgG.Donor1


title: 15A-4

description: Stress session Time 4

source_name: Participant 15, Stress session, Time 4

value: PBMC

value: Male

value: Control


title: Batch1_Gastrocnemius_non-treat_mouse5

description: sample G1-5

value: Gastrocnemius

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.0HR.H3K27ac.Donor2


title: POA_P90_DES 12_4

value: DES 12 ug/kg bw/day


title: Batch1_Gastrocnemius_non-treat_mouse2

description: sample G1-2


title: POA_P90_DES 12_3


title: 15A-2

description: Stress session Time 2

source_name: Participant 15, Stress session, Time 2

value: Stress


title: CutAndTag.human.CD8.Positive.Tcells.0HR.H3K27ac.Donor1

value: CD8 Positive T-cells

value: Primary T cells


title: CutAndTag.human.CD8.Positive.Tcells.0HR.PBRM1.Donor2.Rep2


title: CutAndTag.human.CD8.Positive.Tcells.0HR.PBRM1.Donor2.Rep1


title: 15A-1

description: Stress session Time 1

source_name: Participant 15, Stress session, Time 1


title: POA_P90_DES 6_5

value: DES 6 ug/kg bw/day


title: 16B-3

description: Stress session Time 3

source_name: Participant 16, Stress session, Time 3

value: Female

value: ELA


title: POA_P90_KTZ 12_5

value: Sprague-Dawley

value: female

value: KTZ 12 mg/kg bw/day


title: 14B-4

description: Stress session Time 4

source_name: Participant 14, Stress session, Time 4


title: POA_P90_DES 3_4

value: pre-optic area

value: DES 3 ug/kg bw/day


title: POA_P90_KTZ 6_5

value: KTZ 6 mg/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.0HR.BRD9.Donor2

value: Naïve CD8 Positive T cells from human donor 2


title: CutAndTag.human.CD8.Positive.Tcells.0HR.BRD9.Donor1

value: Naïve CD8 Positive T cells from human donor 1


title: Batch1_water extract of JGT (Low dose)_rep3

description: sample 3-3-3

growth_protocol: A C2C12 murine myoblast cell (CRL-1772) was purchased from American Type Culture Collection (Manassas, VA, USA) and maintained in a growth medium (GM, Dulbecco’s Modified Eagle Medium with 4.5 gr/L glucose (DMEM) supplemented with 10% heat-inactivated fetal bovine serum, 100 I.U penicillin and 100 microgr/mL streptomycin at 37°C in a humidified 5% CO2 incubator. For differentiation to myotubes, GM was replaced with differentiation medium (DM, DMEM supplemented with 2% heat-inactivated horse serum, 100 I.U penicillin and 100 microgr/mL streptomycin) when myoblasts were grown to 80-90% confluence. The DM was replaced with a fresh one every 2 days for total 5-7 days. A basal medium and supplements used for C2C12 cell culture were purchased from Thermo Fisher Scientific.

treatment_protocol: A hot water extract of Jakyak-gamcho-tang (JGT) was manufactured and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). In brief, dried Paeoniae radix (450 g) and Glycyrrhizae radix et rhizoma (450 g) at 1:1 weight ratio were pulverized and subjected to extraction in a hot distilled water (9 L) for 3 h in a reflux extraction system (MS-DM609, MTOPS, Seoul, Republic of Korea). The extract solution was filtered through a 53 micrometer mesh filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea) and then lyophilized in a LP-20 freeze dryer (Ilshin-Bio-Base, Dongduchen, Republic of Korea) to get a final JGT extract (219.9 g, 24.4 % yield). The JGT extract was finely homogenized and packed in a foil ziplock bag containing desiccant silica gels. For in vitro studies, homogenous JGT (100 mg) was vigorously voltexed for 30 min at room temperature in a 10 mL phosphate-buffered saline (PBS, Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 micrometer membrane to get a JGT stock solution (10 mg/mL). The JGT stock solution was aliquoted in a small volume and stored at -80°C until used. For RNA extraction, first, a JGT concentration exhibiting 80% cell viability in myotubes was calculated using a 4-parameter logistic curve fit and determined to be 500 microgr/mL as the maximum tolerable dose for RNA sequencing analysis. Then, C2C12 myoblasts were differentiated for 6 days on 6-well culture plates and then treated with increasing doses of JGT (20, 100, and 500 microgr/mL) for 24 h. A vehicle control was treated with 0.1% DMSO. After 24-h treatment, total RNA was extracted.

value: JGT 20 microg/mL


title: Batch1_water extract of JGT (Medium dose)_rep3

description: sample 3-3-2

value: JGT 100 microg/mL


title: 14B-3

description: Stress session Time 3

source_name: Participant 14, Stress session, Time 3

value: PBMC

value: Male

value: Control


title: 14B-2

description: Stress session Time 2

source_name: Participant 14, Stress session, Time 2

value: Stress


title: Batch1_Gastrocnemius_non-treat_mouse3

description: sample G1-3

value: Gastrocnemius

value: non-treat

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.0HR.ARID1A.Donor2

value: CD8 Positive T-cells

value: Primary T cells


title: POA_P90_KTZ 3_4

value: Sprague-Dawley

value: female

value: KTZ 3 mg/kg bw/day


title: Batch1_water extract of JGT (High dose)_rep3

description: sample 3-3-1

value: JGT 500 microg/mL


title: Batch1_water extract of JGT (Low dose)_rep2

description: sample 3-2-3


title: CutAndTag.human.CD8.Positive.Tcells.0HR.ARID1A.Donor1


title: 14B-1

description: Stress session Time 1

source_name: Participant 14, Stress session, Time 1


title: POA_P90_DES 12_2

value: pre-optic area

value: DES 12 ug/kg bw/day


title: Batch1_Gastrocnemius_non-treat_mouse1

description: sample G1-1


title: Batch1_water extract of JGT (Medium dose)_rep2

description: sample 3-2-2


title: POA_P90_DES 3_3

value: DES 3 ug/kg bw/day


title: 13A-4

description: Stress session Time 4

source_name: Participant 13, Stress session, Time 4


title: Batch1_water extract of JGT (High dose)_rep2

description: sample 3-2-1


title: POA_P90_control_3

value: vehicle


title: 13A-3

description: Stress session Time 3

source_name: Participant 13, Stress session, Time 3

value: PBMC


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.FHT1015.Donor1

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
Output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
Assembly: hg19, mm10
Supplementary files format and content: bigWig, broadPeak

source_name: CD8 Positive T-Cells

growth_protocol: Human and mouse T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2.

extract_protocol:
Regions of tagmented genomic DNA were purified Qiagen's MinElute DNA purification Kit.
Custom PCR primers were used to amplify tagmented DNA for a total of 7 cycles to prevent over amplification.

treatment_protocol:
Human cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.Mouse cells were activated with Mouse T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat#11453D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.
Cells were treated with inhibitors (Compound 14 and FHT1015) on Day 3 and Day 6 and taken down for one timepoint at Day9.  Cells were treated with degraders (ACBI1 and AU-15330, 100nM) on Day 3 and Day 6 and taken down for one timepoint at Day9.

value: CD8 Positive T-Cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1 treated with FHT1015 100 nM


title: POA_P90_KTZ 12_4

value: KTZ 12 mg/kg bw/day


title: Batch1_water extract of JGT (Low dose)_rep1

description: sample 3-1-3

value: JGT 20 microg/mL


title: 13A-2

description: Stress session Time 2

source_name: Participant 13, Stress session, Time 2

value: Male

value: Control

value: Stress


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.FHT1015.Donor2

value: Primary T cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2 treated with FHT1015 100 nM


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.Compound14.Donor2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2 treated with compound 14 100 nM


title: POA_P90_control_4

value: Sprague-Dawley

value: female


title: Batch1_water extract of JGT (Medium dose)_rep1

description: sample 3-1-2

value: JGT 100 microg/mL


title: 13A-1

description: Stress session Time 1

source_name: Participant 13, Stress session, Time 1


title: POA_P22_DES 12_2

value: pre-optic area

value: DES 12 ug/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.Compound14.Donor1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1 treated with compound 14 100 nM


title: Batch1_water extract of JGT (High dose)_rep1

description: sample 3-1-1

value: JGT 500 microg/mL


title: Batch1_vehicle_rep3

description: sample A1-1-6

value: 0.1percent DMSO


title: 12B-4

description: Stress session Time 4

source_name: Participant 12, Stress session, Time 4

value: PBMC

value: ELA


title: ATACseq.human.CD8.Positive.Tcells.48HR.Donor1.Rep2

value: CD8 Positive T-Cells

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 1 replicate 2


title: POA_P90_KTZ 12_3

value: KTZ 12 mg/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.Day9.Transient.Donor2

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 2


title: POA_P90_KTZ 3_3

value: KTZ 3 mg/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.Day9.Transient.Donor1

value: Primary T cells

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 1


title: 12B-2

description: Stress session Time 2

source_name: Participant 12, Stress session, Time 2

value: Male

value: Stress


title: Batch1_vehicle_rep2

description: sample A1-1-5


title: POA_P90_DES 6_4

source_name: pre-optic area

value: Sprague-Dawley

value: female

value: DES 6 ug/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.Day9.Transient.DMSO.Donor4.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with DMSO technical replicate 2


title: Batch1_vehicle_rep1

description: sample A1-1-4


title: ATACseq.human.CD8.Positive.Tcells.Day9.Transient.DMSO.Donor4.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with DMSO technical replicate 1


title: POA_P22_DES 12_1

value: pre-optic area

value: DES 12 ug/kg bw/day


title: Batch1_non-treat_rep3

description: sample A1-1-3

value: non-treat


title: 12B-1

description: Stress session Time 1

source_name: Participant 12, Stress session, Time 1

value: PBMC

value: ELA


title: 11A-3

description: Stress session Time 3

source_name: Participant 11, Stress session, Time 3

value: Control


title: POA_P90_DES 3_2

value: DES 3 ug/kg bw/day


title: 11A-4

description: Stress session Time 4

source_name: Participant 11, Stress session, Time 4


title: Batch1_non-treat_rep2

description: sample A1-1-2


title: 11A-2

description: Stress session Time 2

source_name: Participant 11, Stress session, Time 2


title: POA_P90_DES 12_1


title: POA_P90_DES 6_3


title: ATACseq.human.CD8.Positive.Tcells.Day9.Transient.DMSO.Donor3.Rep2

value: CD8 Positive T-Cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with DMSO technical replicate 2


title: Batch1_non-treat_rep1

description: sample A1-1-1


title: 11A-1

description: Stress session Time 1

source_name: Participant 11, Stress session, Time 1


title: ATACseq.human.CD8.Positive.Tcells.Day9.Transient.DMSO.Donor3.Rep1

value: Primary T cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with DMSO technical replicate 1


title: 9A-3

description: Stress session Time 3

source_name: Participant 9, Stress session, Time 3

value: Male

value: Stress


title: 9A-2

description: Stress session Time 2

source_name: Participant 9, Stress session, Time 2


title: POA_P90_KTZ 6_3

value: Sprague-Dawley

value: female

value: KTZ 6 mg/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.Day9.Chronic.Donor2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2


title: ATACseq.human.CD8.Positive.Tcells.Day9.Chronic.Donor1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1


title: ATACseq.human.CD8.Positive.Tcells.Day6.Donor2

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 2


title: brain, tauP301L, 45d, rep10, sample2

city: Leuven

first: Patrik

last: Verstreken

address: Herestraat 49

institute: VIB-KU Leuven

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp10_20220502_45d_tauP301L_sample2

library_source: transcriptomic single cell

data_processing:
Pooled sequencing data from 10x libraries was demultiplexed and index-hopping-filter v1.0.1 (10x Genomics) applied. Feature-barcode matrices were computed with Cell Ranger (v4.0.0, 10x Genomics). The fraction of contaminating ambient RNA was automatically determined and corrected with soupX (v1.5.2). Subsequently, individual ambient RNA corrected matrices were loaded into scanpy (v1.8.1) and concatenated into one dataset. Quality control steps included filtering of cells from 5 day old animals at a minimum of 800, 25/45 day old animals 600 detected genes as well as a maximum of 20 000 counts and 15% mitochondrial content.
Reads from the adapted Smart-seq3 libraries were preprocessed with fastp (v0.20.0) followed by alignment and counting with STARsolo (STAR v2.7.9).
Assembly: 4th 2020 FlyBase Drosophila melanogaster release (r6.35)
Supplementary files format and content: tab-delim text and matrix files

organism: Drosophila melanogaster

source_name: entire brains

growth_protocol: light-controlled incubator at 25°C and 12-hour light-dark cycle, standard corn meal and molasses food

extract_protocol:
For 10x library preparation cells were first counted with the FLUNA-FL Dual Fluorescence Cell Counter and viability determined with Acridine Orange/Propidium Iodide dyes (Logos biosystems), which was >93% for all samples, typically 98-100%. We targeted 10 000 captured cells per genotype and sample with Chromium v3.1 chemistry (10x Genomics). For adapted Smart-seq3, 400 GFP+ C2_3 neurons were FAC-sorted for each sample.
For the 5d and 25d 10x datasets, single-cell encapsulation was carried out with the 10x Chromium Next GEM chip; for the 45d 10x dataset with a custom HyDrop chip. Library preparation followed the 10x Single cell 3’ reagent kit v3.1 user guide (CG000204 Rev D). Briefly, reverse transcription was performed on a C1000 Touch Thermal Cycler (Bio Rad) at 53°C 45 min and 85°C 5 min with a 4°C hold, followed by breakage of the single-cell emulsion, Dynabeads MyOne SILAN clean-up and cDNA amplification at 98°C 3 min, 13 cycles of 98°C 3 min - 63°C 20 s - 72°C 1 min, with a final 72°C 1 min extension and 4°C hold. Amplified cDNA was cleaned with SPRIselect (Beckman Coulter). Thereafter cDNA was enzymatically fragmented, followed by end-repair, A-tailing, SPRIselect clean-up, adapter ligation and another SPRIselect clean-up was carried out prior to PCR amplification of the ligation products incorporating unique sample indices at 98°C 45 s, 15 cycles 98°C 20 s - 54°C 30 s - 72°C 20 s - with a final 72°C 1 min extension and 4°C hold. SPRIselect clean-up of the amplified libraries was carried out. At different check points the quality of cDNA and final sequencing library was evaluated using Qubit (ThermoFisher) and Bioanalyzer (Agilent). Libraries were first sequenced shallow to determine library complexity and subsequently sequenced deeper to achieve ~80% sequencing saturation. For the FAC-sorted bulk RNAseq of C2_3 neurons we followed the Smart-seq3 protocol with increased lysis buffer to 7.5 µl including the sorted cell volume, the RT mix volume to 2.5 µl and the final cDNA amplified product to 25 µl in total. Tn5 concentration increased to the Smart-seq2 protocol.
10x Genomics v3.1 scRNAseq and adapted Smart-seq3 for bulk RNAseq

value: entire brains

tag: genotype

value: nsyb-QF2w > tau[P301L]


title: 9A-1

description: Stress session Time 1

source_name: Participant 9, Stress session, Time 1

value: PBMC

value: ELA


title: brain, tauP301L, 45d, rep10, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp10_20220502_45d_tauP301L_sample1


title: POA_P90_KTZ 3_2

value: pre-optic area

value: KTZ 3 mg/kg bw/day


title: brain, mini_ctrl, 45d, rep10, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp10_20220502_45d_mini_ctrl_sample1

value: nsyb-QF2w > mini-w+


title: ATACseq.human.CD8.Positive.Tcells.72HR.Donor2

value: CD8 Positive T-Cells

value: Primary T cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 8A-3

description: Stress session Time 3

source_name: Participant 8, Stress session, Time 3

value: Male

value: Control

value: Stress


title: brain, tauP301L, 45d, rep9, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp9_20220425__45d_tauP301L_sample2


title: POA_P90_KTZ 6_2

value: Sprague-Dawley

value: female

value: KTZ 6 mg/kg bw/day


title: brain, tauP301L, 45d, rep9, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp9_20220425__45d_tauP301L_sample1


title: POA_P90_KTZ 3_1


title: 8A-1

description: Stress session Time 1

source_name: Participant 8, Stress session, Time 1


title: POA_P90_DES 6_2

value: DES 6 ug/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.72HR.Donor1

source_name: CD8 Positive T-Cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: 8A-4

description: Stress session Time 4

source_name: Participant 8, Stress session, Time 4


title: 7B-4

description: Stress session Time 4

source_name: Participant 7, Stress session, Time 4


title: POA_P90_KTZ 12_1

value: KTZ 12 mg/kg bw/day


title: brain, mini_ctrl, 45d, rep9, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp9_20220425__45d_mini_ctrl_sample2

value: entire brains


title: ATACseq.human.CD8.Positive.Tcells.48HR.Donor1

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: ATACseq.human.CD8.Positive.Tcells.48HR.Donor2

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 7B-3

description: Stress session Time 3

source_name: Participant 7, Stress session, Time 3

value: PBMC

value: ELA


title: brain, mini_ctrl, 45d, rep9, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp9_20220425__45d_mini_ctrl_sample1

value: nsyb-QF2w > mini-w+


title: ATACseq.human.CD8.Positive.Tcells.3HR.Donor2

value: CD8 Positive T-Cells

value: Primary T cells

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: brain, tauP301L, 45d, rep8, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp8_20220421__45d_tauP301L_sample2

value: nsyb-QF2w > tau[P301L]


title: 7B-2

description: Stress session Time 2

source_name: Participant 7, Stress session, Time 2

value: Male

value: Stress


title: ATACseq.human.CD8.Positive.Tcells.Day6.Donor1

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 1


title: ATACseq.human.CD8.Positive.Tcells.3HR.Donor1

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P90_KTZ 12_2

source_name: pre-optic area

value: Sprague-Dawley

value: female

value: pre-optic area


title: brain, mini_ctrl, 45d, rep10, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp10_20220502_45d_mini_ctrl_sample2

value: entire brains


title: POA_P22_DES 6_1

value: DES 6 ug/kg bw/day


title: 7B-1

description: Stress session Time 1

source_name: Participant 7, Stress session, Time 1


title: POA_P90_control_2

value: vehicle


title: brain, tauP301L, 45d, rep8, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp8_20220421__45d_tauP301L_sample1


title: ATACseq.human.CD8.Positive.Tcells.24HR.Donor2

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: POA_P90_KTZ 6_1

value: KTZ 6 mg/kg bw/day


title: ATACseq.human.CD8.Positive.Tcells.24HR.Donor1

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P22_KTZ 6_2


title: 6A-3

description: Stress session Time 3

source_name: Participant 6, Stress session, Time 3

value: PBMC

value: Control


title: brain, mini_ctrl, 45d, rep8, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp8_20220421__45d_mini_ctrl_sample1

value: nsyb-QF2w > mini-w+


title: brain, mini_ctrl, 45d, rep8, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp8_20220421__45d_mini_ctrl_sample2


title: 6A-4

description: Stress session Time 4

source_name: Participant 6, Stress session, Time 4


title: 6A-2

description: Stress session Time 2

source_name: Participant 6, Stress session, Time 2


title: POA_P90_DES 6_1


title: POA_P22_KTZ 12_1

value: KTZ 12 mg/kg bw/day


title: brain, tauP301L, 45d, rep7, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp7_20220412__45d_tauP301L_sample2

value: nsyb-QF2w > tau[P301L]


title: ATACseq.human.CD8.Positive.Tcells.0HR.Donor1

value: CD8 Positive T-Cells

value: Primary T cells

value: Naive CD8 Positive T cells from human donor 1


title: POA_P22_KTZ 6_1

value: Sprague-Dawley


title: brain, tauP301L, 45d, rep7, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp7_20220412__45d_tauP301L_sample1


title: POA_P90_DES 3_1

value: female

value: DES 3 ug/kg bw/day


title: 5B-4

description: Stress session Time 4

source_name: Participant 5, Stress session, Time 4

value: Male

value: ELA

value: Stress


title: IMR90 MYC shSF3B1 RNA-seq, rep3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets were aligned to the hg38 human genome using STAR v2.5.2b  with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2  was used to analyze differential gene expression.
rMAT v4.0.2 was used to identify alternative splicing events
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: IMR90 cells

growth_protocol: IMR90 human primary cells cultured in EMEM+10%FBS+1%Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Quality and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with  Ribo-Zero Gold treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (300 cycles) Illumina platform.

treatment_protocol: Cells were subjected to subsequent lentiviral transduction with doxycycline (dox) inducible c-MYC oncogene vector and short hairpin RNA against SF3B1 splicing factor. After selection for pure populations of transduced cells, MYC was induced by 1 ug/ml dox and cells were harvested 24 hours afterwards into Trizol reagent.

value: Normal lung fibroblasts

tag: genotype (overexpression)

value: MYC

tag: genotype (knockdown)


title: brain, mini_ctrl, 45d, rep7, sample1

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp7_20220412__45d_mini_ctrl_sample1

value: entire brains


title: IMR90 MYC shSF3B1 RNA-seq, rep2


title: POA_P22_KTZ 3_3

value: pre-optic area

value: KTZ 3 mg/kg bw/day


title: 5B-3

description: Stress session Time 3

source_name: Participant 5, Stress session, Time 3

value: PBMC


title: IMR90 MYC shSF3B1 RNA-seq, rep1


title: POA_P22_KTZ 3_2


title: ATACseq.human.CD8.Positive.Tcells.0HR.Donor2

value: Naive CD8 Positive T cells from human donor 2


title: 5B-2

description: Stress session Time 2

source_name: Participant 5, Stress session, Time 2


title: IMR90 MYC RNA-seq, rep3

value: control


title: POA_P22_KTZ 3_1


title: 6A-1

description: Stress session Time 1

source_name: Participant 6, Stress session, Time 1

value: Control


title: IMR90 MYC RNA-seq, rep2


title: 5A-4

description: No-stress session Time 4

source_name: Participant 5, No-stress session, Time 4

value: No-stress


title: POA_P90_control_1

value: vehicle


title: 5A-3

description: No-stress session Time 3

source_name: Participant 5, No-stress session, Time 3


title: IMR90 MYC RNA-seq, rep1


title: MBH_P22_DES 6_5

source_name: medio-basal hypothalamus

value: Sprague-Dawley

value: medio-basal hypothalamus

value: DES 6 ug/kg bw/day


title: MBH_P22_DES 6_4

value: female


title: brain, mini_ctrl, 45d, rep7, sample2

description:
BGI MGISEQ-2000, Illumina NextSeq 2000
10x Genomics v3.1
45d_dataset_soupX_corrected.mtx
45d_dataset_barcodes.tsv
45d_dataset_genes.tsv
45d_meta_data.tsv
exp7_20220412__45d_mini_ctrl_sample2

source_name: entire brains

value: nsyb-QF2w > mini-w+


title: 5A-2

description: No-stress session Time 2

source_name: Participant 5, No-stress session, Time 2

value: Male

value: ELA


title: IMR90 control RNA-seq, rep3

value: Normal lung fibroblasts


title: IMR90 control RNA-seq, rep2


title: MBH_P22_DES 3_5

value: DES 3 ug/kg bw/day


title: sham,  scRNAseq

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Jingxi Street, Baiyun District

department: Department of Anesthesiology

country: China

institute: Nanfang hospital, Southern Medical University

description: 10x Genomics

data_processing:
Beads with unique molecular identifiers (UMI) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized into the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin.
Briefly, 10× beads were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD).
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2×150 chemistry.
The FASTQ files were generated by using the 10× Genomics Cell Ranger toolkit (v.3.0.1), which were extracted barcodes and UMI, filtered and mapped reads to the GRCh38 reference genome, and obtained a matrix containing normalized gene counts versus cells per sample. Then we further analyzed these outputs using Seurat (v.4.1.2) for quality control and downstream analysis with default parameters, unless otherwise indicated. We removed out low-quality cells according to the following quality control procedures: (1) cells with less than 200 genes or more than 3000 genes and genes expressed in less than 3 cells were removed. (2) over 10% of mitochondrial-derived UMI counts were filtered out. After quality control, the datasets were log-normalized. The top 2000 highly variable genes (HVGs) were chosen for canonical correlation analysis and the first 30 reduced dimensions were adopted for integration anchors. Finally, a total of 53484 single cells were applied in downstream analyses, including 16345, 11056, 16246 and 9837 single cells on postoperative days 1, 3 and 7 and sham surgery groups, respectively.
Then the data were scaled using the ScaleData function. Principal components analysis (PCA) was performed, and we selected the top 30 PCs for clustering cells with a resolution parameter of 1.0. The same PCs were used to generate the Uniform manifold approximation and projection (UMAP). Each cluster was annotated based on high expression of known marker genes and visualized by FeaturePlot function. Cldn5, Ly6c1, Ly6a, Itm2a (Endothelial Cells); Cldn11, Mag, Opalin, Ermn, Mog (Oligodendrocytes); Acta2, Des, Tpm2, Filip1l (Vascular Smoothmuscle Cells); Ttr, Clic6, Sostdc1, Car12, Prlr, Htr2c (Choroid plexus cells); VKcnj8, Atp13a5, Anpep, Abcc9, Cd248 (Pericytes); Hexb, C1qa, Tmem119, GRP34, OLFML3 (Microglia); Rtn1, Sox4 (Neuron); F3, Gja1, Slc1a3, Gjb6(Astrocyte); Calml4, Chchd10, Clu (Ependymal); Olig1, Olig2, Pdgfra, Tnr, C1ql1, Matn4 (Oligodendrocyte progenitor cells); Cd8a, Klrd1, Cd4 (T cells); Trem1, Mmp8 (Neutrophil); Cd14, Cd86 (Monocyte); Cd19, Cd79a (B cells).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Brain

extract_protocol:
After 1, 3, and 7 days of ischemia-reperfusion, mice were anesthetized, fixed, and perfused with ice-cold PBS to remove blood. The ischemic hemisphere (tMCAO ipsilateral brain) and ipsilateral hemisphere (Sham ipsilateral brain) were immediately dissected, minced with a scalpel, and digested with papain (Worthington, Biochemical Corporation, USA) at 37°C for 30 minutes. During incubation, the minced brain tissue was gently shaken four times with a 10 ml pipette. After incubation, the tissue was centrifuged at 300g for 5 min at RT. The supernatant is then discarded and the cell pellet is resuspended in DNase diluted albumin inhibitor solution. Afterwards, the suspended single cells were passed through a pre-wetted (with HBSS) 40 μm cell strainer and centrifuged at 300 g for 5 min at 4°C. The cell pellet was then resuspended in 10 ml of 30% Percoll in PBS and centrifuged at 700 g for 10 min. After removing the fraction of myelin debris floating on the surface, the pelleted cells were immediately resuspended with FACS buffer (PBS, 1% BSA). Cells were loaded onto 10x Genomics Chromium chips according to the manufacturer's instructions.
Beads with unique molecular identifiers (UMI) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized into the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2×150 chemistry

value: Brain

value: male

value: sham,  scRNAseq

value: 8 weeks old

value: total RNA


title: MBH_P22_DES 3_4


title: tMCAO, day 7, scRNAseq

description: 10x Genomics

value: tMCAO, day 7


title: MOLM-13 A88G RNA-seq #4

data_processing:
RNA-seq datasets were aligned to the hg38 human genome using STAR  with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2 was used to analyze differential gene expression.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: MOLM-13 cells

growth_protocol: MOLM-13 were cultured in RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 10% FBS and 1% penicillin streptomycin. All cells were grown at 37oC with 5% CO2 and routinely tested for mycoplasma infection (Universal Mycoplasma Detection Kit, ATCC).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Quality and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with Ribo-Zero Gold treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was done using the NextSeq 500/550 High Output v2.5 kit (75 cycles) Illumina platform.

treatment_protocol: CRISPR/Cas9 editing of the SF3B1 5’UTR A88 was carried using a gRNA oligonucleotide designed with the CRISPR-Cas9 gRNA Design checker (Integrated DNA Technologies). Functional CRISPR-Cas9 complexes were assembled with Alt-R® CRISPR-Cas9 guide RNA kit (Integrated DNA Technologies) in the presence of homology repair template. Cells were transfected by nucleofection using the SE Cell Line 4D-NucleofectorTM X Kit L (Lonza) with the FF-120 Nucleofector Program, and transferred to a 24-well plate with pre-heated cell culture media for 48 hrs before analysis. The editing efficiency was validated by Sanger sequencing.

value: Acute myeloid leukemia cell


title: 4B-3

description: Stress session Time 3

source_name: Participant 4, Stress session, Time 3

value: PBMC

value: Stress


title: 5B-1

description: Stress session Time 1

source_name: Participant 5, Stress session, Time 1


title: 4B-4

description: Stress session Time 4

source_name: Participant 4, Stress session, Time 4


title: 5A-1

description: No-stress session Time 1

source_name: Participant 5, No-stress session, Time 1

value: No-stress


title: MBH_P22_control_5

value: Sprague-Dawley

value: medio-basal hypothalamus

value: vehicle


title: MOLM-13 A88G RNA-seq #3


title: 4B-2

description: Stress session Time 2

source_name: Participant 4, Stress session, Time 2

value: Male


title: tMCAO, day 3, scRNAseq

description: 10x Genomics

value: tMCAO, day 3


title: tMCAO, day 1, scRNAseq

description: 10x Genomics

value: tMCAO, day 1


title: 4B-1

description: Stress session Time 1

source_name: Participant 4, Stress session, Time 1

value: ELA


title: 4A-4

description: No-stress session Time 4

source_name: Participant 4, No-stress session, Time 4


title: MBH_P22_control_4

value: female


title: MBH_P22_control_3


title: MOLM-13 A88G RNA-seq #1


title: IMR90 control RNA-seq, rep1

source_name: IMR90 cells

value: Normal lung fibroblasts

value: control


title: MOLM-13 WT RNA-seq #4

value: WT


title: MBH_P22_control_2


title: MEF, rSeV-N5T, 8dpi

city: New York

first: Skyler

middle: Andrew

last: Uhl

state: New York

address: 1 Gustave L. levy Pl.

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: TruSeq stranded total RNA, with RiboZero Gold

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Host reads aligned to Homo sapiens HG19 reference genome assembly and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Viral reads were aligned to viral reference genome via Bowtie 2 using custom app on illumina basespace, Integrative Genomics Viewer (IGV) 2.15.2 was then used to generate a .csv files comparing individual base calls per aligned read to each nucleotide in the reference sequence
Assembly: hg19
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence

source_name: MEF

extract_protocol:
Trizol phenol chloroform or Qiagen Rneasy kit
Poly-A enrichment and TruSeq stranded OR TruSeq stranded Total RNA with RiboZero Gold

value: MEF

value: embryonic fibroblasts

value: rSeV-N5T (MOI=5) --- 8dpi


title: MBH_P22_KTZ 3_5

value: KTZ 3 mg/kg bw/day


title: 4A-3

description: No-stress session Time 3

source_name: Participant 4, No-stress session, Time 3

value: PBMC


title: MBH_P22_DES 12_5

value: DES 12 ug/kg bw/day


title: MOLM-13 WT RNA-seq #3

value: Acute myeloid leukemia cell


title: MOLM-13 WT RNA-seq #2


title: MBH_P22_KTZ 3_4

value: Sprague-Dawley

value: medio-basal hypothalamus


title: MOLM-13 A88G RNA-seq #2


title: MOLM-13 WT RNA-seq #1


title: 4A-1

description: No-stress session Time 1

source_name: Participant 4, No-stress session, Time 1

value: Male

value: No-stress


title: 4A-2

description: No-stress session Time 2

source_name: Participant 4, No-stress session, Time 2


title: 3B-4

description: No-stress session Time 4

source_name: Participant 3, No-stress session, Time 4

value: Control


title: MBH_P22_DES 12_4

source_name: medio-basal hypothalamus


title: MBH_P22_DES 3_3

value: DES 3 ug/kg bw/day


title: LPS 7d BM-derived macrophages.1

city: Nashville

first: wei

last: han

address: 1161 21ST Ave S

department: pulmonary medicine

institute: vanderbilt university medical center

description:
5341-WH-33
BM.2.LPS.7D

data_processing:
RNA sequencing was performed on an Illumina NovaSeq6000 system with a paired-end mRNA library prep, PE-150, with 30 million reads
Fastq files were checked for quality issues using FastQC (v0.11.9) and trimmed with Trimmomatic (v0.39) to remove low quality bases with default options.
Reads from Fastq files were aligned to the mouse reference genome (GRCm38) using HISAT2(v2.1.0) with default parameters.
Number of reads per gene was performed using feature Counts (v2.0.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for all samples

source_name: Lung

extract_protocol:
Total RNA was isolated from resident AMs and BM-derived macrophages macrophages using RNeasy Mini Kit (Cat. 741014, Qiagen), followed by DNA digestion (Cat. AM1906, Thermo Fisher Scientific).
Quality checks of RNA, mRNA enrichment, and cDNA library preparation utilizing stranded mRNA (polyA selected) were conducted at Vanderbilt Technologies for Advanced Genomics

value: Lung

value: BM-derived macrophage

value: LPS


title: LPS 7d BM-derived macrophages.2

description:
5341-WH-34
BM.3.LPS.7D


title: LPS 7d BM-derived macrophages.3

description:
5341-WH-20
BM.4.LPS.7D


title: LPS 3d BM-derived macrophages.3

description:
5341-WH-28
BM.3.LPS.3D


title: LPS 3d BM-derived macrophages.4

description:
5341-WH-30
BM.4.LPS.3D


title: LP1_OR12D2_sgrna2_rep2

first: Constantine

last: Mitsiades

state: MA

address: 450 Brookline Avenue Dept. of Medical Oncology

institute: Dana-Farber Cancer Institute, Harvard Medical School

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package
Raw counts for all samples were generated using STAR (Dobin et al., 29, 1, 15-21, Bioinformatics 2012)
Assembly: gchr38.84
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Multiple Myeloma

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LP1 cells were stably transduced with a construct for dCas9-Vp64 after lentiviral sgRNA transduction packaged with the pXPR-502 construct (RRID:Addgene_96923). LP1 cells transduced with POU2AF1 sgRNA for CRISPR-based activation of POU2AF1or control OR genes were pelleted down at 0.25MLN cells triplicate and immediately frozen (-80ºC). RNA was extracted by RNeasy plus mini kit(Qiagen 74134) according to instruction. In addition, ERCCRNA spike-in mix(Thermo Fisher 4456740) was added at very first step of extraction (RLT extraction).

value: Multiple Myeloma

value: OR12D2 sgRNA2 GAATGTCTGTCACTCCCAAG


title: LPS 3d BM-derived macrophages.2

description:
5341-WH-12
BM.2.LPS.3D


title: LP1_OR12D2_sgrna2_rep1

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor edgeR package
Raw counts for all samples were generated using STAR (Dobin et al., 29, 1, 15-21, Bioinformatics 2012)
Assembly: gchr38.84
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample


title: MBH_P22_DES 6_3

value: female

value: DES 6 ug/kg bw/day


title: 3B-2

description: No-stress session Time 2

source_name: Participant 3, No-stress session, Time 2


title: Adjacent normal tissue, sample 5N

type: RNA

city: Zunyi

first: Handong

last: Huang

state: 贵州

address: 149 Dalian Road

institute: Affiliated Hospital of Zunyi Medical University

description: Tissue sample was snap-frozen immediately following resection and stored at −80°C until subsequent use. CRC diagnose was histologically confirmed by two experienced pathologists.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Adjacent normal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tissue samples were snap-frozen immediately following resection and stored at −80°C until subsequent use.

extract_protocol: RNAiso Plus extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Colorectal cancer and adjacent normal tissues were frozen by liquid nitrogen and ground.

tag: gender

value: male

tag: tumor stage

value: pT4aN0M0, II B


title: MBH_P22_DES 6_2

tag: tissue


title: 3B-1

description: No-stress session Time 1

source_name: Participant 3, No-stress session, Time 1

value: PBMC


title: LPS 3d BM-derived macrophages.1

description:
5341-WH-9
BM.1.LPS.3D

tag: treatment


title: 3A-4

description: Stress session Time 4

source_name: Participant 3, Stress session, Time 4

value: Stress

tag: time


title: MBH_P22_DES 3_2

value: Sprague-Dawley


title: 3B-3

description: No-stress session Time 3

source_name: Participant 3, No-stress session, Time 3


title: LPS 1d BM-derived macrophages.5

description:
6483-WH-26
BM.9.LPS.1D


title: LP1_OR6S1_sgrna1_rep3

tag: cell line

value: OR6S1 sgRNA1 GACCTGCAATTGGATAAACT


title: MBH_P22_DES 3_1

value: medio-basal hypothalamus


title: LP1_OR6S1_sgrna1_rep2

tag: cell type


title: LP1_OR12D2_sgrna2_rep3


title: LP1_OR6S1_sgrna1_rep1


title: 3A-2

description: Stress session Time 2

source_name: Participant 3, Stress session, Time 2

value: Male


title: Adjacent normal tissue, sample 4N

value: pT4aN1bM0, III B


title: CRC tissue, sample 5Ca

source_name: CRC tissue


title: LPS 1d BM-derived macrophages.4

description:
6483-WH-25
BM.8.LPS.1D


title: LPS 1d BM-derived macrophages.2

description:
6483-WH-23
BM.6.LPS.1D


title: MBH_P22_control_1

value: vehicle


title: CRC tissue, sample 4Ca


title: CRC tissue, sample 6Ca

value: pT3N0M0, II A


title: Adjacent normal tissue, sample 6N


title: LPS 1d BM-derived macrophages.1

description:
6483-WH-22
BM.5.LPS.1D

value: Lung

value: BM-derived macrophage


title: 3A-3

description: Stress session Time 3

source_name: Participant 3, Stress session, Time 3

value: Control


title: LPS 1d BM-derived macrophages.3

description:
6483-WH-24
BM.7.LPS.1D

value: LPS


title: MBH_P22_KTZ 12_5

value: female

value: KTZ 12 mg/kg bw/day


title: LP1_POU2AF1_sgrna2_rep3

value: Multiple Myeloma

value: POU2AF1 sgRNA 2 TGGCTGCAGAAACGTTGCAC


title: LP1_POU2AF1_sgrna2_rep2


title: MBH_P22_DES 12_3

value: DES 12 ug/kg bw/day


title: 2B-4

description: No-stress session Time 4

source_name: Participant 2, No-stress session, Time 4

value: PBMC

value: No-stress


title: LP1_POU2AF1_sgrna2_rep1


title: MBH_P90_DES 12_5

value: Sprague-Dawley


title: 3A-1

description: Stress session Time 1

source_name: Participant 3, Stress session, Time 1

value: Stress


title: MBH_P90_DES 3_5

value: medio-basal hypothalamus

value: DES 3 ug/kg bw/day


title: 2B-3

description: No-stress session Time 3

source_name: Participant 2, No-stress session, Time 3

value: Male


title: LP1_POU2AF1_sgrna1_rep2

value: POU2AF1 sgRNA 1 GCGCACAGTGGGGTGACAGG


title: LPS 7d resident AM.4

description:
5341-WH-24
AM.4.LPS.7D

value: Lung

value: Resident AM


title: LPS 7d resident AM.2

description:
5341-WH-22
AM.2.LPS.7D


title: LPS 7d resident AM.1

description:
5341-WH-21
AM.1.LPS.7D


title: LP1_POU2AF1_sgrna1_rep3


title: 2B-2

description: No-stress session Time 2

source_name: Participant 2, No-stress session, Time 2

value: Control


title: 2B-1

description: No-stress session Time 1

source_name: Participant 2, No-stress session, Time 1


title: LPS 7d resident AM.3

description:
5341-WH-23
AM.3.LPS.7D

value: LPS


title: MBH_P90_control_5

value: female

value: vehicle


title: 2A-4

description: Stress session Time 4

source_name: Participant 2, Stress session, Time 4


title: LP1_POU2AF1_sgrna1_rep1

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute). Differential gene expression analysis for the RNA-seq data using the bioconductor edgeR package. Raw counts for all samples were generated using STAR (Dobin et al., 29, 1, 15-21, Bioinformatics 2012)
Assembly: gchr38.84
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: Multiple Myeloma


title: 2A-3

description: Stress session Time 3

source_name: Participant 2, Stress session, Time 3


title: LPS 3d resident AM.2

description:
5341-WH-32
AM.2.LPS.3D

source_name: Lung


title: MBH_P42_control_5

source_name: medio-basal hypothalamus


title: MBH_P42_KTZ 6_5

value: KTZ 6 mg/kg bw/day


title: 2A-2

description: Stress session Time 2

source_name: Participant 2, Stress session, Time 2


title: LPS 3d resident AM.3

description:
5341-WH-16
AM.4.LPS.3D


title: MBH_P42_control_4


title: RNASeq_D9_G_rep3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
16-P8D9_S16
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt

data_processing:
RNA-Seq paired reads were aligned to the hg38 genome with Hisat2 (v2.1.0) using the Ensembl annotation (v95).
Reads in genes were counted using featurecounts, with multimapping reads fractionally assigned using --fraction and -M.
For HOTAIR knockdown experiments, RNA-Seq reads in genes were counted with HTseq.
Low abundance genes were filtered out of further analysis using edgeR's function "filterByExpr".
Normalisation between library sizes to get FPKM values was done using the trimmed mean of M-values method.
Normalisation for differential expression was by limma-voom (Law et al. 2014) and tests calculated by lmFit and eBayes.
Calculations of changing expression over time were done pairwise Prolif  v day0, day0 v day1, day1 v day3 and day3 v day9; first within each donor and then combined across donors.
Transcript quantification from RNA-Seq reads was conducted with salmon v1.3.0 (--numBootstraps 20 --gcBias) on an index of the ensembl transcriptome plus additional HOTAIR transcripts from refseq (NR_003716.3, NR_047517.1, NR_047518.1) and from the lncRNA sections of the ucsc browser (TCONS_00079053_HOTAIR, TCONS_00079054_HOTAIR, TCONS_00079056_HOTAIR, TCONS_00079057_HOTAIR, TCONS_00079058_HOTAIR, TCONS_00079061_HOTAIR).
Genome_build: hg38 (GRCh38) ensembl95
Supplementary_files_format_and_content: *.bw: Bigwig RNAseq coverage file generated with deeptools bamCoverage (binsize 10bp).
Supplementary_files_format_and_content: Raw read counts per gene, one column per sample.
Supplementary_files_format_and_content: FPKM for each gene passing the filtering threshold in each sample.
Supplementary_files_format_and_content: TPM for each transcript in each gluteal sample.

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were isolated from subcutaneous liposuction material. Cells were cultured under proliferative conditions in DMEM/F12 containing 10% fetal calf serum, 10 ng/ml epidermal growth factor (Sigma-Aldrich E9644) and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-7 were used in three independent differentiations into the adipocyte lineage.

extract_protocol:
For RNA-seq, total mRNA was isolated from cells at aforementioned stages of differentiation using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol:
Two days before induction of differentiation, proliferating cells (day-2 [day minus 2] stage) were harvested and processed for RNA extraction.
For adipogenic differentiation, harvested day-2 cells were reseeded in DMEM/F12/10% serum without growth factors. Adipogenesis was induced 48 h later (on day 0; D0) by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was left with the cells for the 3 days of differentiation. Cells were collected on day0, day 1, day 3 and day9 (D0, D1, D3, D9) and processed for RNA extraction.
For transient knockdown, proliferating cells were electroporated with Nucleofector (Lonza) using the Human Mesenchymal Stem Cell NucleofectorTM Kit (Lonza). Two siRNAs (Silencer select from Ambion) were used - siHOTAIR 1: N272221, siHOTAIR 2: N272230. Electroporated cells were plated and cultured for 72 h in proliferative conditions before harvesting for RT-PCR and RNA-FISH.

tag: time point

tag: adipose depot

value: Gluteal

tag: culture

value: Cultured in vitro

tag: sirna probe


title: LPS 3d resident AM.1

description:
5341-WH-31
AM.1.LPS.3D


title: RNASeq_D3_G_rep3

description:
15-P8D3_S15
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: 2A-1

description: Stress session Time 1

source_name: Participant 2, Stress session, Time 1

value: PBMC

tag: Sex

tag: age


title: RNASeq_D1_G_rep3

description:
14-P8D1_S14
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: MBH_P42_DES 12_5

tag: strain

value: Sprague-Dawley

value: DES 12 ug/kg bw/day


title: RNASeq_PROLIF_A_rep1

description:
1-19200_S5
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab

value: day-2 (proliferating)

value: Abdominal subcutaneous


title: MBH_P42_KTZ 6_4

value: medio-basal hypothalamus


title: MBH_P42_KTZ 12_5

value: KTZ 12 mg/kg bw/day


title: LPS 1d resident AM.2

description:
5341-WH-27
AM.2.LPS.1D

value: Lung


title: MBH_P42_DES 3_5

value: DES 3 ug/kg bw/day


title: 1B-4

description: Stress session Time 4

source_name: Participant 1, Stress session, Time 4

value: Male

tag: ela status

value: ELA

tag: session

value: Stress


title: 1B-2

description: Stress session Time 2

source_name: Participant 1, Stress session, Time 2


title: RNASeq_PROLIF_G_rep3

description:
12-KD3NT_S12
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: 1B-1

description: Stress session Time 1

source_name: Participant 1, Stress session, Time 1


title: MBH_P42_KTZ 3_5

value: female

value: KTZ 3 mg/kg bw/day


title: RNASeq_D9_G_rep2

description:
11-P6D9_S11
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: No LPS resident AM.3

description:
4645-WH-3
Young.3.AM

value: Resident AM

value: No treatment


title: LPS 1d resident AM.1

description:
5341-WH-26
AM.1.LPS.1D

value: LPS


title: 1A-4

description: No-stress session Time 4

source_name: Participant 1, No-stress session, Time 4

value: PBMC

value: No-stress


title: RNASeq_D3_G_rep2

description:
10-P6D3_S10
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt

value: Gluteal

value: Cultured in vitro


title: RNASeq_D1_G_rep2

description:
9-P6D1_S9
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: MBH_P42_DES 12_4

value: Sprague-Dawley

value: DES 12 ug/kg bw/day


title: 1A-3

description: No-stress session Time 3

source_name: Participant 1, No-stress session, Time 3


title: No LPS resident AM.2

description:
4645-WH-2
Young.2.AM


title: MBH_P42_DES 6_5

value: medio-basal hypothalamus

value: DES 6 ug/kg bw/day


title: LPS 1d resident AM.4

description:
5341-WH-8
AM.4.LPS.1D

value: Lung


title: MBH_P22_KTZ 12_4

value: KTZ 12 mg/kg bw/day


title: 1A-1

description: No-stress session Time 1

source_name: Participant 1, No-stress session, Time 1

value: Male

value: ELA


title: Naïve

city: La Jolla

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
The single-end reads that passed Illumina filters were subsequently filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were aligned with the mm10 reference genome using STAR (v 2.6.1) and the RefSeq gene annotation downloaded from the University of California - Santa Cruz Genome Bioinformatics site.
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via the SAMtools  to generate SAM files.
Read counts to each genomic feature were obtained with the featureCounts (v 1.6.5) using the default option along with a minimum quality cut off (Phred > 10)
After removing absent features (zero counts in all samples), the raw counts were imported to R/Bioconductor package DESeq2 (v 1.24.0)
Assembly: mm10
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: Spleen

extract_protocol:
Cells were directly sorted into 1.7 mL microtubes containing 500 μL Trizol LS buffer. RNA extraction was performed using miRNeasy micro kits for downstream RNA-SmartSeq2 input requirements (Rosales et al. 2013).
cDNA was purified using AMPure XP beads. O0.5 nanogram cDNA was used to prepare a standard Nextera XT sequencing library (Illumina Nextera XT DNA sample preparation kit and index kit). Samples were sequenced using a HiSeq2500 (Illumina) with single-end sequencing.

value: Spleen

tag: genotype

value: Cas9-Tg, SMARTA TCR-Tg

value: LCMV infection of recipient mice


title: MBH_P42_KTZ 3_4

value: female

value: KTZ 3 mg/kg bw/day


title: LPS 1d resident AM.3

description:
5341-WH-7
AM.3.LPS.1D

value: Resident AM

value: LPS


title: IL3_mature_3

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

data_processing:
Sequencing was performed by using Illumina Novaseq 6000 (Illumina, USA). Adapter trimming of sequencing data was performed by using cutadapt 3.4, and trimmed reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 8 -N 1 -L 16 –very-sensitive-local –seed 656565 –nofw. Then, read counts of each gene in each samples were counted by using awk, sort, and uniq -c commands. Resulted gene-expression count data was summarized by same Gene Symbol and all of the expression table was full-outer joined by Gene Symbol by using dplyr-1.0.7 package.
Normalization of count data and differential expression analysis were performed by utilizing R package TCC v 1.32.0 (Sun et al. BMC BioInformatics 2013).
Supplementary files format and content: GRCm38 release-101
Supplementary files format and content: Tab-separated values files

source_name: bone marrow

extract_protocol:
CD34-CLEC12Ahi pre-basophils and CD34-CLEC12Alo mature basophils were isolated from the bone marrow of TNP-IgE sensitized mice by using FACS AriaIII (BD Biosciences). Isolated cells were separately cultured ex vivo in the presence of 10ng/mL of OVA (Control), 10 ng/mL of TNP-conjugated OVA (TNP-OVA), or 10ng/mL of recombinant murine IL-3 (BioLegend) for 4h and were lysed by lithium  dodecyl sulfate buffer.
Library construction for bulk-RNA sequencing was conducted according to the previous study (Ogawa et al. Biochem Biophys Res Commun. 2022; doi: 10.1016/j.bbrc.2022.02.090.). Briefly, 100ng of amplified cDNA libraries were subjected to Illumina library construction by using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Fragmentation, end-repair, dA-tailing, adaptor ligation, and barcoding PCR were sequentially conducted according to the manufacturer’s instruction.

treatment_protocol: C57BL/6J WT mice were intravenously sensitized with 300 μg of TNP-specific IgE (TNP-IgE) 1 day prior to the experiment.

value: bone marrow

value: basophil

value: C57BL/6J WT

value: stimulated with 10ng/mL recombinant murine IL-3 for 4hr


title: gMll1 Tfh rep3

value: Mll1-knockdown (gMll1), LCMV infection of recipient mice


title: RNASeq_D0_G_rep3

description:
13-P8D0_S13
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt

value: day0 (induction of differentiation)

value: Gluteal

value: Cultured in vitro


title: gMll1 Th1 rep3


title: gMll1 Tfh rep2


title: MBH_P22_KTZ 12_3

value: Sprague-Dawley

value: medio-basal hypothalamus

value: KTZ 12 mg/kg bw/day


title: IL3_mature_1


title: MBH_P42_KTZ 12_4


title: IL3_mature_2


title: gMll1 Tfh rep1

value: Spleen

value: Cas9-Tg, SMARTA TCR-Tg


title: IL3_prebaso_3


title: No LPS resident AM.1

description:
4645-WH-1
Young.1.AM

value: Lung

value: No treatment


title: gMll1 Th1 rep1


title: IL3_prebaso_2


title: Old_MSC_scRNAseq_77

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

description: Single cell RNA-seq of bone marrow CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell from old mice

data_processing:
Sequencing was performed using an Illumina HiSeq2000 system. Sequence reads were aligned to the murine genome mm9 using RNA-seq Unified Mapper (RUM) version 2.0.4, and transcripts were assembled using Cufflinks version 2.1.1.
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Young and old MSCs (CD45-Ter119-CD31-CD140a+LepR+) were isolated with a FACSAria II cell sorter from 10-week-old and 2-year-old mice, respectively. Single-cell cDNA synthesis was performed with a C1 Single-Cell Auto Prep System (Fluidigm)
Reverse transcription and preamplification were performed according to the manufacturer’s instructions using a SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech) and a C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq (Fluidigm). For RNA controls, tubes #1, #4, and #7 of ArrayControl RNA Spikes (Thermo Fisher Scientific) were mixed at a ratio of 100:10:1, and the RNA Spikes mixture was diluted 1:10000 in C1 Loading Reagent (Fluidigm). Sorted MSCs were diluted in Suspension Reagent to ~1000 cells/µL and loaded into a C1-Single-Cell Auto Prep IFC for mRNA-seq (5-10 μm). After loading the cells, the integrated fluidic circuit (IFC) was observed microscopically using an IN Cell Analyzer 6000 (GE Healthcare) to ensure that single cells were captured in each well. Wells with 0, >1, or shrunken cells were excluded. A total of 83 of the 96 wells for young MSCs and 79 of the 96 wells for old MSCs were considered valid. The thermal cycling conditions for cell lysis, reverse transcription, and preamplification were as follows: 72°C for 3 min, 4°C for 10 min, and 25°C for 10 min for cell lysis; 42°C for 90 min and 70°C for 10 min for reverse transcription; 95°C for 1 min and 5 cycles at 95°C for 20 s, 58°C for 4 min, and 68°C for 6 min, 9 cycles at 95°C for 20 s, 64°C for 30 s, and 68°C for 6 min, 7 cycles at 95°C for 30 s, 64°C for 30 s, and 68°C for 7 min, and 1 cycle at 72°C for 10 min for preamplification; and holding at 4°C until harvest. Amplified cDNA (approximately 3.5 μL) from each well was diluted with 10 μL of C1 DNA Dilution Reagent (Fluidigm) and frozen at -30°C until use. The sample in each well was further diluted 1:2 with C1 Harvest Reagent and subjected to tagmentation and Illumina sequencing library preparation using a Nextera XT DNA Sample Preparation Kit (Illumina) and a Nextera XT DNA Sample Preparation Index Kit (96 indices, Illumina). Then, 2.5 μL of Tagment DNA Buffer, 1.25 μL of Amplification Tagment Mix and 1.25 μL of the diluted cDNA sample were mixed and incubated at 55°C for 10 min in a thermal cycler. The tagmentation reaction was then stopped by adding 1.25 μL of neutralizing buffer (NT buffer). Next, the samples were subjected to PCR amplification. A 6.25 μL aliquot of each sample was mixed with NPM buffer, and 1.25 μL each of Index Primer 1 and Index Primer 2. The thermal cycling conditions were as follows: 72°C for 3 min, 95°C for 30 s, 12 cycles at 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 1 cycle at 72°C for 5 min. A 1 μL aliquot from each well of amplified DNA was processed by two rounds of mixing and cleanup with AMPure XP beads (Beckman Coulter), and DNA was then eluted with 144 μL of DNA suspension buffer.

value: Bone marrow

value: 24 month old


title: Old_MSC_scRNAseq_75

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: Old_MSC_scRNAseq_76


title: Old_MSC_scRNAseq_74


title: gCd8 Tfh rep3

value: Wild-type (control gCd8), LCMV infection of recipient mice


title: IL3_prebaso_1

value: bone marrow

value: basophil

value: C57BL/6J WT


title: MBH_P42_KTZ 12_3

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 102.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file include raw counts for annotations for all Sample

value: female


title: TNP_mature_3

value: stimulated with 10ng/mL TNP-OVA for 4hr


title: MBH_P42_KTZ 6_3

value: KTZ 6 mg/kg bw/day


title: Old_MSC_scRNAseq_78


title: gCd8 Th1 rep3


title: Old_MSC_scRNAseq_72


title: MBH_P22_KTZ 12_2

value: Sprague-Dawley


title: TNP_mature_2


title: MBH_P42_DES 6_4

value: medio-basal hypothalamus

value: DES 6 ug/kg bw/day


title: gMll1 Th1 rep2

value: Spleen

value: Mll1-knockdown (gMll1), LCMV infection of recipient mice


title: Old_MSC_scRNAseq_71


title: TNP_mature_1


title: gCd8 Tfh rep2

value: Cas9-Tg, SMARTA TCR-Tg


title: MBH_P42_KTZ 6_2


title: MBH_P42_DES 3_4

value: DES 3 ug/kg bw/day


title: Old_MSC_scRNAseq_70

value: Bone marrow


title: gCd8 Th1 rep2


title: MBH_P42_DES 6_3


title: MBH_P42_DES 6_2


title: TNP_prebaso_2


title: MBH_P42_DES 3_3


title: Old_MSC_scRNAseq_69

value: 24 month old


title: MDCK, rSeV-N5T, 8dpi

organism: Canis lupus familiaris

source_name: MDCK

value: MDCK

value: kidney epithelial cells

value: WT

value: rSeV-N5T (MOI=5) --- 8dpi


title: MBH_P22_KTZ 6_5


title: gCd8 Tfh rep1

value: Wild-type (control gCd8), LCMV infection of recipient mice


title: Old_MSC_scRNAseq_73

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: brain, tauP301L, 25d, rep6

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp6_20201202_25d_tauP301L

source_name: entire brains

value: entire brains

value: nsyb-QF2w > tau[P301L]


title: TNP_prebaso_1

value: bone marrow

value: basophil

value: C57BL/6J WT

value: stimulated with 10ng/mL TNP-OVA for 4hr


title: gCd8 Th1 rep1

value: Spleen


title: Control_mature_2

value: stimulated with 10ng/mL OVA for 4hr


title: Old_MSC_scRNAseq_67


title: MBH_P42_KTZ 12_2

value: Sprague-Dawley

value: female

value: medio-basal hypothalamus

value: KTZ 12 mg/kg bw/day


title: Old_MSC_scRNAseq_68

value: Bone marrow

value: 24 month old


title: Old_MSC_scRNAseq_66


title: Control_mature_1


title: brain, asynA53T, 25d, rep6

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp6_20201202_25d_asynA53T

value: nsyb-QF2w > asyn[A53T]


title: TNP_prebaso_3


title: Old_MSC_scRNAseq_64


title: MBH_P42_KTZ 6_1

value: KTZ 6 mg/kg bw/day


title: brain, smGdP, 25d, rep6

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp6_20201202_25d_smGdP

value: nsyb-QF2w > smGdP


title: MBH_P42_KTZ 12_1


title: Control_prebaso_2


title: brain, mini_ctrl, 25d, rep6

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp6_20201202_25d_mini_ctrl

value: entire brains

value: nsyb-QF2w > mini-w+


title: MBH_P42_KTZ 3_3

value: KTZ 3 mg/kg bw/day


title: Old_MSC_scRNAseq_63

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: brain, tauP301L, 25d, rep5

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp5_20201126_25d_tauP301L

value: nsyb-QF2w > tau[P301L]


title: Old_MSC_scRNAseq_62


title: Control_mature_3

value: bone marrow

value: basophil

value: C57BL/6J WT


title: Control_prebaso_1

value: stimulated with 10ng/mL OVA for 4hr


title: Old_MSC_scRNAseq_65


title: MBH_P42_DES 12_3

value: Sprague-Dawley

value: female

value: DES 12 ug/kg bw/day


title: brain, asynA53T, 25d, rep5

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp5_20201126_25d_asynA53T


title: Old_MSC_scRNAseq_61

value: Bone marrow


title: Old_MSC_scRNAseq_59

value: 24 month old


title: MBH_P42_DES 6_1

value: medio-basal hypothalamus

value: DES 6 ug/kg bw/day


title: MBH_P22_KTZ 6_4

value: KTZ 6 mg/kg bw/day


title: Old_MSC_scRNAseq_58


title: Old_MSC_scRNAseq_60


title: MBH_P42_DES 3_2

value: DES 3 ug/kg bw/day


title: brain, smGdP, 25d, rep5

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp5_20201126_25d_smGdP

value: entire brains

value: nsyb-QF2w > smGdP


title: brain, mini_ctrl, 25d, rep5

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp5_20201126_25d_mini_ctrl

value: nsyb-QF2w > mini-w+


title: IL-3-simulation_03

data_processing:
Sequencing data generated by Illumina Novaseq 6000 (Illumina, USA) was subjected to adaptor trimming by Cutadapt-3.4.
Trimmed reads were aligned against murine reference RNA sequences (GRCm39 RefSeq RNA) by utilizing bowtie2 .
Supplementary files format and content: mm38
Supplementary files format and content: Tab-separated values files

source_name: bone marrow-derived basophils

extract_protocol:
Bone marrow-derived basophils were stimulated with 10 ng/mL IL-3 or control PBS for 6 hours and subjected to RNA extraction by using Nucleospin RNA Plus XS (Macherey Nagel)
Library construction for bulk-RNA sequencing was conducted according to the previous study (Ogawa et al. Biochem Biophys Res Commun. 2022). Briefly, 100ng of amplified cDNA libraries were subjected to Illumina library construction by using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Fragmentation, end-repair, dA-tailing, adaptor ligation, and barcoding PCR were sequentially conducted according to the manufacturer’s instruction.

treatment_protocol: Bone marrow cells were cultured in the presence of 0.3 ng/mL for 7days, followed by enrichment of basophils by using biotinylated anti-CD49b antibody and streptavidin-conjugated beads.

value: bone marrow-derived basophils

value: stimulated with 10ng/mL IL-3


title: brain, tauP301L, 25d, rep4

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp4_20201123_25d_tauP301L

value: nsyb-QF2w > tau[P301L]


title: PDAC_Subq_tumor_GB1275

city: St. Louis

first: David

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous PDAC tumor

extract_protocol:
PDAC tissues were taken from vehicle-treated, GB1275-treated KP2 Subq pancreatic tumors, 14 days post-treatment. Immune cells (CD45+) were sorted by an Aria-II cell sorter (BD Biosciences). Each sample was generated from a pool of three mice/treatment group and two total libraries were sequenced.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: subcutaneous PDAC tumor

value: CD45+ Cells

value: p48-CRE; LSL-KrasG12D/wt; p53flox/flox


title: PDAC_Subq_tumor_Vehicle

description: 10x Genomics

value: Vehicle


title: IL-3-simulation_02

value: basophil

value: C57BL/6J WT


title: Control_prebaso_3

value: bone marrow

value: stimulated with 10ng/mL OVA for 4hr


title: Old_MSC_scRNAseq_57

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow

value: 24 month old


title: MBH_P42_control_3

source_name: medio-basal hypothalamus

extract_protocol:
At PND22, PND42 and PND90,  the pre-optic area (POA) and the mediobasal hypothalamus (MBH) were dissected and frozen. Total RNA was extracted from the MBH and POA using Universal RNA mini kit (Qiagen,Venlo, Netherlands) following the manufacturer’s instructions.
Libraries were prepared using Truseq® stranded mRNA Sample Preparation Kits (Illumina, CA, USA) following manufacturer’s instructions. Libraries were validated using QIAxcel Advanced System and quantified by qPCR using the KAPA library quantification kit. Libraries were multiplexed and sequenced on an Illumina NovaSeq6000 sequencer to generate more than ~25,000,000 paired-end reads (2 × 150 bases) per library.

value: Sprague-Dawley

value: female

value: medio-basal hypothalamus

value: vehicle


title: brain, asynA53T, 25d, rep4

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp4_20201123_25d_asynA53T

data_processing:
Pooled sequencing data from 10x libraries was demultiplexed and index-hopping-filter v1.0.1 (10x Genomics) applied. Feature-barcode matrices were computed with Cell Ranger (v4.0.0, 10x Genomics). The fraction of contaminating ambient RNA was automatically determined and corrected with soupX (v1.5.2). Subsequently, individual ambient RNA corrected matrices were loaded into scanpy (v1.8.1) and concatenated into one dataset. Quality control steps included filtering of cells from 5 day old animals at a minimum of 800, 25/45 day old animals 600 detected genes as well as a maximum of 20 000 counts and 15% mitochondrial content.
Reads from the adapted Smart-seq3 libraries were preprocessed with fastp (v0.20.0) followed by alignment and counting with STARsolo (STAR v2.7.9).
Assembly: 4th 2020 FlyBase Drosophila melanogaster release (r6.35)
Supplementary files format and content: tab-delim text and matrix files

value: entire brains

value: nsyb-QF2w > asyn[A53T]


title: PBS-simulation_03

value: bone marrow-derived basophils

value: stimulated with PBS


title: MBH_P22_KTZ 6_3

value: KTZ 6 mg/kg bw/day


title: brain, smGdP, 25d, rep4

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp4_20201123_25d_smGdP

value: nsyb-QF2w > smGdP


title: brain, mini_ctrl, 25d, rep4

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp4_20201123_25d_mini_ctrl

value: nsyb-QF2w > mini-w+


title: Old_MSC_scRNAseq_55


title: IL-3-simulation_01

value: basophil

value: C57BL/6J WT

value: stimulated with 10ng/mL IL-3


title: PBS-simulation_02


title: Old_MSC_scRNAseq_56

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell


title: PBS-simulation_01


title: Old_MSC_scRNAseq_54

value: Bone marrow


title: MBH_P42_KTZ 3_1

value: KTZ 3 mg/kg bw/day


title: MBH_P42_DES 12_2

value: Sprague-Dawley

value: DES 12 ug/kg bw/day


title: MBH_P42_DES 12_1

value: female

value: medio-basal hypothalamus


title: Spleen mature basophil_03

data_processing:
Sequencing data generated by Illumina Novaseq 6000 (Illumina, USA) was subjected to adaptor trimming by Cutadapt-3.4.
Trimmed reads were aligned against murine reference RNA sequences (GRCm39 RefSeq RNA) by utilizing bowtie2-2.4.2 .
Supplementary files format and content: mm39
Supplementary files format and content: Tab-separated values files

source_name: spleen

extract_protocol:
Basophil progenitors, immature basophils and mature basophils were isolated from the bone marrow and mature basophils were isolated from the spleen by FACS sorting.
Library construction for bulk-RNA sequencing was conducted according to the previous study (Ogawa et al. Biochem Biophys Res Commun. 2022). Briefly, 100ng of amplified cDNA libraries were subjected to Illumina library construction by using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Fragmentation, end-repair, dA-tailing, adaptor ligation, and barcoding PCR were sequentially conducted according to the manufacturer’s instruction.

value: spleen


title: brain, tauP301L, 5d, rep3

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp3_20201116_5d_tauP301L

value: entire brains

value: nsyb-QF2w > tau[P301L]


title: Spleen mature basophil_02


title: Old_MSC_scRNAseq_52

value: 24 month old


title: MBH_P42_DES 3_1

value: DES 3 ug/kg bw/day


title: brain, mini_ctrl, 5d, rep3

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp3_20201116_5d_mini_ctrl


title: MBH_P42_control_2

value: vehicle


title: brain, smGdP, 5d, rep3

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp3_20201116_5d_smGdP

value: nsyb-QF2w > smGdP


title: brain, asynA53T, 5d, rep3

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp3_20201116_5d_asynA53T

value: nsyb-QF2w > asyn[A53T]


title: Spleen mature basophil_01

value: basophil

value: C57BL/6J WT


title: MBH_P42_KTZ 3_2


title: Old_MSC_scRNAseq_51

description: Single cell RNA-seq of bone marrow CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell from old mice


title: brain, tauP301L, 5d, rep2

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp2_20200923_5d_tauP301L


title: BM mature basophil_03

value: bone marrow


title: MBH_P42_control_1


title: Old_MSC_scRNAseq_49

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow


title: brain, asynA53T, 5d, rep2

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp2_20200923_5d_asynA53T


title: MBH_P90_KTZ 3_5

value: Sprague-Dawley

value: KTZ 3 mg/kg bw/day


title: brain, smGdP, 5d, rep2

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp2_20200923_5d_smGdP


title: BM mature basophil_01


title: BM mature basophil_02


title: Old_MSC_scRNAseq_53


title: MBH_P90_KTZ 12_5

value: female

value: KTZ 12 mg/kg bw/day


title: BM immature basophil_03


title: Old_MSC_scRNAseq_46


title: MBH_P90_KTZ 6_5

value: medio-basal hypothalamus

value: KTZ 6 mg/kg bw/day


title: brain, mini_ctrl, 5d, rep2

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp2_20200923_5d_mini_ctrl

value: entire brains

value: nsyb-QF2w > mini-w+


title: Old_MSC_scRNAseq_50

value: 24 month old


title: BM immature basophil_02


title: brain, tauP301L, 5d, rep1

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp1_20200618_5d_tauP301L

value: nsyb-QF2w > tau[P301L]


title: MBH_P90_KTZ 6_4


title: Old_MSC_scRNAseq_45


title: brain, asynA53T, 5d, rep1

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp1_20200618_5d_asynA53T


title: brain, smGdP, 5d, rep1

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp1_20200618_5d_smGdP

value: nsyb-QF2w > smGdP


title: BM immature basophil_01


title: BM BaP_03


title: brain, mini_ctrl, 5d, rep1

description:
10x Genomics v3.1
5_25d_dataset_soupX_corrected.mtx
5_25d_dataset_uncorrected_UMI.mtx
5_25d_dataset_barcodes.tsv
5_25d_dataset_genes.tsv
5_25d_meta_data.tsv
exp1_20200618_5d_mini_ctrl


title: Old_MSC_scRNAseq_43


title: Old_MSC_scRNAseq_44


title: MBH_P90_DES 12_3

value: DES 12 ug/kg bw/day


title: MBH_P90_DES 6_5

value: DES 6 ug/kg bw/day


title: Old_MSC_scRNAseq_48


title: Old_MSC_scRNAseq_47


title: MBH_P90_DES 3_4

value: DES 3 ug/kg bw/day


title: BM BaP_01

value: bone marrow

value: basophil

value: C57BL/6J WT


title: 1B-3

description: Stress session Time 3

data_processing:
idat files were preprocessed and detection p-values were calculated using minfi (1.42.0). Beta values were obtained by generating a genomic set ratio object and normalization was performed using the minfi function preprocessNoob.
Noob Normalized Average Beta

source_name: Participant 1, Stress session, Time 3

extract_protocol: Genomic DNA was extracted and purified from PBMC samples using QIAmp mini kit (Qiagen) according to standard instructions.

value: PBMC

value: Male

value: ELA

value: Stress


title: Old_MSC_scRNAseq_42

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: Bone marrow


title: Old_MSC_scRNAseq_41