title: RH4, sh4, P3I-Turbo, Rep1


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype,IFN-γ injected, male, rep2

status: Public on Mar 26 2026

type: SRA

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

country: USA

institute: National Institutue on Aging, NIH

description: Library name: SN22wtIFNm3_arc_atac

library_source: genomic single cell

data_processing:
Paired-end sequencing was performed on a NovaSeq 6000. Samples were processed using the cellranger count pipeline (v7.1.0) for gene expression data, including intronic reads, with the reference genome refdata-gex-mm10-2020-A. For ATAC-seq data, the cellranger-atac count pipeline (v2.0.0) was used with the refdata-cellranger-arc-mm10-2020-A-2.0.0 reference package.
Assembly: mm10
Supplementary files format and content: Cell ranger output files per sample: filtered_feature_bc_matrix.h5,  atac_cut_sites.bigwig, atac_fragments.tsv.gz

molecule: genomic DNA

organism: Mus musculus

source_name: substantia nigra

extract_protocol:
After 24 hours, striatum and substantia nigra were collected for nuclei purification using 10x Genomics single-cell nuclei isolation kit (PN-1000494)
20, 000 nuclei/sample were processed according to  Chromium next GEM Single cell Multiome ATAC+Gene Expression user guide (CG000338 Rev E). Chromium Single Cell Multiome  Gene Expression and ATAC libraries were sequenced using standard Illumina® paired-end sequencing with P5 and P7 primers.

treatment_protocol: C57Bl/6J WT and LRRK2 knockout mice (3 months old) received bilateral stereotaxic injections of mouse IFN-γ (20 ng/site) or PBS into the striatum and substantia nigra. Tissues were collected 24 hours post-injection.

tag: tissue

value: substantia nigra

tag: strain

value: C57Bl/6J (WT; Jax)

tag: Sex

value: male

tag: genotype

tag: treatment

value: recombinant mouse IFN-γ injected


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, IFN-γ injected, female, rep1

description: Library name: SN21wtIFNf3_arc_gex

library_source: transcriptomic single cell

molecule: total RNA

value: female


title: Alpha-beta neurons,Adult,rep3

city: Rehovot

first: Oren

last: Schuldiner

address: 234 Herzl Street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: ab_adult_J_3_S25

library_source: transcriptomic

data_processing:
Two sequencing runs of RNA were combined, yielding a mean of 22.5 million reads (single-read sequencing) and a minimum of 10 million reads per sample. The reads were aligned with STAR (DOI: 10.1093/bioinformatics/bts635) v2.5.2 to the reference genome of Drosophila melanogaster (DM6, UCSC). Gene annotations were obtained from FlyBase.org (Dmel r6.46). Gene expression levels were quantified using STAR.
Assembly: DM6
Supplementary files format and content: excel file includes read counts and differential gene expression analysis

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: All fly strains were reared under standard laboratory conditions at 25°C on molasses containing food. Males and females were chosen at random. Developmental stage is referred to in the relevant places while adult refers to 3-5 days post eclosion.

extract_protocol:
Brains were dissected a cold Ringer’s solution, incubated with collagenase/dispase mix at 29ºC, washed in dissociation solution, mechanically dissociated into single cells and transferred via 35um mesh. 1000 GFP+ positive cells were sorted directly into 100μl Pico-Pure RNA isolation kit extraction buffer followed by RNA extraction using the kit or stored in -80 for later use.
Libraries were prepared based on the smart-seq2 protocol (Picelli et al., 2014). Briefly, Reverse transcription was performed using Oligo-dT primers, followed by PCR.The amplified cDNA underwent library generation using Nextera XT (Illumina)

value: Brain

tag: cell type

value: Alpha-beta neurons

tag: time point

value: Adult


title: RH4, sh4, P3M-Turbo, Rep3

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

data_processing:
Trimmed with fastp toolkit, aligned with STAR RNA, Normalization by DEseq2
Assembly: GRch38 Ver 106
Supplementary files format and content: Normalized counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Cell Line

growth_protocol: Cells were grown in RPMI + 10%FBS at 37C and 5% CO2. All cells were grown in the presense of doxycycline to induce shRNA expression

extract_protocol:
Qiagen RNEasy
Library was prepared using Kapa stranded mRNA seq Kit

value: Cell Line

tag: cell line

value: Rhabdomyosarcoma


title: Alpha-beta neurons,Adult,rep4

description: Library name: ab_adult_J_4_S48


title: Alpha-beta neurons,Adult,rep2

description: Library name: ab_adult_J_2_S24


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, control, male, rep2

description: Library name: SN20koPBSm1_arc_gex

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)

value: PBS injected


title: RH4, sh4, P3M-Turbo, Rep2


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype, IFN-γ injected, female, rep1

description: Library name: SN21wtIFNf3_arc_atac


title: 933000320188569

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description: Library name: 933000320188569

data_processing:
Expression levels were quantified directly from FASTQ files using kallisto v0.48. Transcript sequences from GRCr8 RefSeq were used as reference. Isoform-level counts were summed per gene to get gene expression counts.
Assembly: GRCr8
Supplementary files format and content: Log2-transformed read counts per gene per sample in BED format. Start/end coordinates indicate only the gene's TSS coordinate.

organism: Rattus norvegicus

source_name: Rostromedial tegmental nucleus

growth_protocol: Outbred laboratory rats

extract_protocol:
Unknown
Unknown

value: Rostromedial tegmental nucleus


title: Alpha-beta neurons,Adult,rep1

description: Library name: ab_adult_J_1_S1


title: 933000320188588

description: Library name: 933000320188588


title: RH4, sh4, P3M-Turbo, Rep1


title: 933000320188383

description: Library name: 933000320188383


title: 933000320188590

description: Library name: 933000320188590


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 knockout, control, female, rep1

description: Library name: SN19koPBSf1_arc_gex


title: RH4, sh4, P3N2-Turbo, Rep3


title: Alpha-beta  neurons,30 hours after pupa formation,rep5

description: Library name: ab30H_6_S54

value: 30 hours after pupa formation


title: 933000320188452

description: Library name: 933000320188452


title: RH4, sh4, P3N2-Turbo, Rep2


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, control, female, rep1

description: Library name: SN19koPBSf1_arc_atac


title: RH4, sh4, P3N1-Turbo, Rep3


title: RH4, sh4, P3N2-Turbo, Rep1


title: 933000320188198

description: Library name: 933000320188198


title: 933000320188380

description: Library name: 933000320188380


title: Alpha-beta  neurons,30 hours after pupa formation,rep3

description: Library name: ab30E_4_S43


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype, control, male, rep2

description: Library name: SN18wtPBSm1_arc_atac


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 knockout, control, male, rep2

description: Library name: SN20koPBSm1_arc_atac


title: Alpha-beta  neurons,30 hours after pupa formation,rep2

description: Library name: ab30D_2_S19


title: RH4, sh4, P3N1-Turbo, Rep2


title: 933000320188186

description: Library name: 933000320188186


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, control, male, rep2

description: Library name: SN18wtPBSm1_arc_gex


title: Alpha-beta  neurons,30 hours after pupa formation,rep1

description: Library name: ab30D_1_S6


title: RH4, sh4, P3N1-Turbo, Rep1


title: multiome GEX-seq, mouse substantia nigra, Lrrk2 wildtype, control, female, rep1

description: Library name: SN17wtPBSf1_arc_gex


title: Alpha-beta  neurons,27 hours after pupa formation, rep 3

description: Library name: ab27D_3_S29

value: 27 hours after pupa formation


title: Alpha-beta  neurons,30 hours after pupa formation,rep4

description: Library name: ab30F_6_S30


title: 933000320188184

description: Library name: 933000320188184


title: RH4, sh4, P3F4-Turbo, Rep2


title: 933000320188053

description: Library name: 933000320188053


title: multiome ATAC-seq, mouse substantia nigra, Lrrk2 wildtype, control, female, rep1

description: Library name: SN17wtPBSf1_arc_atac


title: RH4, sh4, P3F4-Turbo, Rep3


title: 933000320187929

description: Library name: 933000320187929


title: Alpha-beta  neurons,27 hours after pupa formation, rep 4

description: Library name: ab27D_5_g1_S53


title: Alpha-beta  neurons,27 hours after pupa formation, rep 5

description: Library name: ab27J_6_S44


title: RH4, sh4, P3F4-Turbo, Rep1


title: 933000320187980

description: Library name: 933000320187980


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout IFN-γ injected, male, rep4

description: Library name: ST16koIFNm4_arc_atac

source_name: striatum

value: striatum


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, male, rep4

description: Library name: ST16koIFNm4_arc_gex


title: 933000320187590

description: Library name: 933000320187590


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 5

description: Library name: ab24I_6_S28

value: 24 hours after pupa formation


title: 933000320187759

description: Library name: 933000320187759


title: Alpha-beta  neurons,27 hours after pupa formation, rep 1

description: Library name: ab27D_1_S5


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 6

description: Library name: ab24L_8_S52


title: RH4, sh4, P3F1-Turbo, Rep3


title: RH4, sh4, P3F1-Turbo, Rep2


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, female, rep3

description: Library name: ST15koIFNf4_arc_atac


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 4

description: Library name: ab24F_5_S35


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, female, rep3

description: Library name: ST15koIFNf4_arc_gex


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype,IFN-γ injected, male, rep4

description: Library name: ST14wtIFNm5_arc_atac


title: 933000320187563

description: Library name: 933000320187563


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, IFN-γ injected, male, rep4

description: Library name: ST14wtIFNm5_arc_gex


title: 933000320187589

description:
Library name: 933000320187589
Original label before genotype mismatch fix: 933000320187579


title: RH4, shSCR, Turbo-NLS, Rep3


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 2

description: Library name: ab24D_2_S21


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 3

description: Library name: ab24F_4_S45


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, IFN-γ injected, female, rep3

description: Library name: ST13wtIFNf4_arc_gex


title: 933000320187460

description: Library name: 933000320187460


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype, IFN-γ injected, female, rep3

description: Library name: ST13wtIFNf4_arc_atac


title: RH4, shSCR, Turbo-NLS, Rep1


title: 933000320187049

description: Library name: 933000320187049


title: Alpha-beta  neurons, 21 hours after pupa formation, rep5

description: Library name: ab21F_4_S46

value: 21 hours after pupa formation


title: 933000320187031

description: Library name: 933000320187031


title: 933000320186858

description: Library name: 933000320186858


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, control, male, rep4

description: Library name: ST12koPBSm2_arc_gex


title: RH4, sh4, P3F1-Turbo, Rep1


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, control, male, rep4

description: Library name: ST12koPBSm2_arc_atac


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 1

description: Library name: ab24C_1_S4


title: Alpha-beta  neurons, 21 hours after pupa formation, rep4

description: Library name: ab21E_4_S51


title: RH4, sh4, Turbo-NLS, Rep1


title: 933000320186852

description: Library name: 933000320186852


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, control, female, rep3

description: Library name: ST11koPBSf2_arc_gex


title: RH4, sh4, Turbo-NLS, Rep3


title: RH4, sh4, Turbo-NLS, Rep2


title: 933000320186806

description: Library name: 933000320186806


title: Alpha-beta  neurons, 21 hours after pupa formation, rep2

description: Library name: ab21C_2_S22


title: Alpha-beta  neurons, 21 hours after pupa formation, rep1

description: Library name: ab21C_1_S3


title: PAO1-WT-3-1

city: Hongkong

first: Xin

last: Deng

state: 九龍

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

department: BMS

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO3
counts_WTexp.txt
PAO1-3-1

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using hisat2.  The gene differential expression analysis was performed using DESeq2 R package.
Assembly: NC_002516.2
Supplementary files format and content: counts.txt contains read counts, depth.txt contains sequenicng depth

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cells

growth_protocol: RNA-seq(LB)

extract_protocol:
The Pseudomonas aeruginosa PAO1 WT strain and the PA sRNA over expression strains were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

treatment_protocol: grow until mid-log phase

value: bacterial cells

value: WT

value: grow until mid-log phase in LB


title: 933000320049191

description: Library name: 933000320049191


title: PAO1-WT-2-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO2
counts_WTexp.txt
PAO1-2-2


title: Alpha-beta  neurons, 21 hours after pupa formation, rep3

description: Library name: ab21E_3_S27


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype, control, female, rep3

description: Library name: ST9wtPBSf2_arc_atac

value: C57Bl/6J (WT; Jax)

value: female


title: Alpha-beta  neurons,18 hours after pupa formation, rep 4

description: Library name: ab18F_4_S47

value: Brain

value: Alpha-beta neurons

value: 18 hours after pupa formation


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, control, male, rep4

description: Library name: ST10wtPBSm2_arc_gex

value: male


title: Alpha-beta  neurons,18 hours after pupa formation, rep 3

description: Library name: ab18F_3_S26


title: 933000320049198

description: Library name: 933000320049198


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, control, female, rep3

description: Library name: ST11koPBSf2_arc_atac

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)


title: RH4, shSCR, Turbo-NLS, Rep2

value: Cell Line

value: Rhabdomyosarcoma


title: PAO1-WT-3-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO3
counts_WTexp.txt
PAO1-3-2


title: WT-EV-1-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
WTEV-1-1


title: 933000320049013

description:
Library name: 933000320049013
Original label before genotype mismatch fix: 933000320049025

value: Rostromedial tegmental nucleus


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype, control, male, rep4

description: Library name: ST10wtPBSm2_arc_atac

value: PBS injected


title: PAO1-WT-2-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO2
counts_WTexp.txt
PAO1-2-1


title: 933000320049180

description: Library name: 933000320049180


title: WT-EV-1-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
WTEV-1-2


title: 933000320049177

description: Library name: 933000320049177


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, control, female, rep3

description: Library name: ST9wtPBSf2_arc_gex

value: striatum


title: WT1-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
WT1-1.depth.txt
WT1-2.depth.txt
WT1-2_combined


title: Alpha-beta  neurons,18 hours after pupa formation, rep 5

description: Library name: ab18H_5_S50


title: 933000320048869

description: Library name: 933000320048869


title: Alpha-beta  neurons,18 hours after pupa formation, rep 2

description: Library name: ab18E_2_S23


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, male, rep2

description: Library name: ST8koIFNm3_arc_atac

value: recombinant mouse IFN-γ injected


title: 933000320048521

description: Library name: 933000320048521


title: Alpha-beta  neurons,18 hours after pupa formation, rep 1

description: Library name: ab18C_1_S2


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, IFN-γ injected, male, rep2

description: Library name: ST6wtIFNm3_arc_gex


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, female, rep1

description: Library name: ST7koIFNf3_arc_gex


title: Dx-IONP, L4

city: Ribeirão Preto

first: William

last: Lautert Dutra

state: SP

address: Av. Bandeirantes, 3900

department: Genetics Department

country: Brazil

institute: Universidade de São Paulo

description:
Library name: LIB023450_TRA00065756_S1_L004
Dx-IONP, L4

data_processing:
The raw reads’ quality control was measured using the FASTQC program. We quantified the expression of transcripts using the software Salmon v1.6.0 (Patro et al., 2017). The transcriptome index was built using the reference GRCz11 version of the zebrafish genome (http://ftp.ensembl.org/pub/current_fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz) and transcriptome (http://ftp.ensembl.org/pub/current_fasta/danio_rerio/cdna/Danio_rerio.GRCz11.cdna.all.fa.gz), downloaded from ENSEMBL, following the manual instruction. Further, the Tximport v1.22.0 package was used to import the transcription-level abundance and estimate raw counts (Soneson et al., 2015). The count data normalization, expression levels, and differential gene expression (DEG) analysis were executed using the in R (R Foundation for Statistical Computing, R v4.1.2 “Bird Hippie”) with DESeq2 v1.34.0 with treatment groups as design factors (Love et al., 2014; Zhu et al., 2019).
Assembly: GRCz11 version of the zebrafish genome
Supplementary files format and content: fastq

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA was extracted and purified from 20 embryos per group, of 120 hpf using RNeasy® Micro Kit and RNeasy® MinElute® Cleanup kit (Quiagen).
One RNA-Seq library was prepared with the embryos pull for each group condition (control, iron and nanoparticle), using Apollo Wafergen 324 system. Quality control was done using TapeStation and qPCR. Finally, the sequencing was performed using four lanes of a NextSeq 500 High-Throughput Sequencer at the Harvard Biopolymers Facility.

value: larvae

value: Dx-IONP, L4

tag: batch


title: PAO1-WT-1-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PAO1-1-1_depth.txt
PAO1-1-2_depth.txt,counts_WTexp.txt
PAO1-1-1

value: bacterial cells

value: WT


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, male, rep2

description: Library name: ST8koIFNm3_arc_gex


title: WT1-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
WT1-1.depth.txt
WT1-2.depth.txt
WT1-1_combined

value: grow until mid-log phase in LB


title: Dx-IONP, L3

description:
Library name: LIB023450_TRA00065756_S1_L003
Dx-IONP, L3

value: Dx-IONP, L3


title: PA4642.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA4642.1-2


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, IFN-γ injected, female, rep1

description: Library name: ST7koIFNf3_arc_atac

value: female


title: 933000320048482

description: Library name: 933000320048482


title: 933000320048353

description: Library name: 933000320048353


title: Dx-IONP, L1

description:
Library name: LIB023450_TRA00065756_S1_L001
Dx-IONP, L1

value: Dx-IONP, L1


title: Dx-IONP, L2

description:
Library name: LIB023450_TRA00065756_S1_L002
Dx-IONP, L2

value: Dx-IONP, L2


title: 933000320048514

description: Library name: 933000320048514


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, IFN-γ injected, female, rep1

description: Library name: ST5wtIFNf3_arc_gex

value: C57Bl/6J (WT; Jax)


title: IC, L4

description:
Library name: LIB023450_TRA00066136_S3_L004
IC, L4

value: IC, L4


title: 933000320047650

description: Library name: 933000320047650


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype,IFN-γ injected, male, rep2

description: Library name: ST6wtIFNm3_arc_atac

value: male


title: IC, L3

description:
Library name: LIB023450_TRA00066136_S3_L003
IC, L3

value: IC, L3


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype, IFN-γ injected, female, rep1

description: Library name: ST5wtIFNf3_arc_atac


title: 933000320047442

description: Library name: 933000320047442

value: Rostromedial tegmental nucleus


title: PA4640.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA4640.1-2


title: PA4640.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA4640.1-1


title: IC, L2

description:
Library name: LIB023450_TRA00066136_S3_L002
IC, L2

value: IC, L2


title: PA4642.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA4642.1-1


title: 933000320046633

description: Library name: 933000320046633


title: 933000320046650

description: Library name: 933000320046650


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, control, male, rep2

description: Library name: ST4koPBSm1_arc_atac

value: striatum

value: C57Bl/6J -Lrrk2tm1.1Cai/J (LRRK2 KO; Jax)

value: PBS injected


title: 933000320046780

description: Library name: 933000320046780


title: IC, L1

description:
Library name: LIB023450_TRA00066136_S3_L001
IC, L1

value: larvae

value: IC, L1


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, control, male, rep2

description: Library name: ST4koPBSm1_arc_gex


title: multiome ATAC-seq, mouse striatum, Lrrk2 knockout, control, female, rep1

description: Library name: ST3koPBSf1_arc_atac


title: PA4639.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA4639.1-1

value: bacterial cells


title: Control, L3

description:
Library name: LIB023450_TRA00066135_S2_L003
Control, L3

value: Control, L3


title: Control, L4

description:
Library name: LIB023450_TRA00066135_S2_L004
Control, L4

value: Control, L4


title: 933000320046567

description: Library name: 933000320046567


title: PA3471.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA3471.1-2

value: grow until mid-log phase in LB


title: multiome GEX-seq, mouse striatum, Lrrk2 knockout, control, female, rep1

description: Library name: ST3koPBSf1_arc_gex

value: female


title: 933000320046511

description: Library name: 933000320046511


title: PA3471.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA3471.1-1


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, control, male, rep2

description: Library name: ST2wtPBSm1_arc_gex


title: PA4639.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA4639.1-2


title: multiome GEX-seq, mouse striatum, Lrrk2 wildtype, control, female, rep1

description: Library name: ST1wtPBSf1_arc_gex


title: PA2736.2-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA2736.2-2


title: Control, L2

description:
Library name: LIB023450_TRA00066135_S2_L002
Control, L2

value: Control, L2


title: 933000320046459

description: Library name: 933000320046459


title: 933000320046487

description: Library name: 933000320046487


title: Control, L1

description:
Library name: LIB023450_TRA00066135_S2_L001
Control, L1

value: Control, L1


title: PA2736.2-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA2736.2-1


title: KIF23-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep4

city: Beijing

first: Gang

last: Wang

address: 5th, Yiheyuan Road, Beijing

country: China

institute: Peking University

description:
Library name: KIF23_Control_rep4
Column name: KIF23_Control_rep4

data_processing:
The sequencing reads for each library were aligned against the human genome assembly GRCh38 (hg38), downloaded from the Ensembl project, using HISAT2 (v2.1.0).
The results of alignments were sorted by read names. The read counts of each gene were measured with the matching gene annotation (v.87) from Ensembl by HTSeq v0.6.1, utilizing the option “-stranded no”.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited txt file contains counts of all genes from HEK293T cell lines stably expressing APEX2-ERM, APEX-NES, BIRC5-APEX2_L242F-EGFP, or KIF23-APEX2_L242F-EGFP

growth_protocol: The human embryonic kidney 293T (HEK293T) cell line and its derived cell lines were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). All cell lines were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Following APEX2 labeling, cells were lysed by the addition of TRIzol reagent, and total RNAs were extracted according to the manufacturer’s protocol. The extracted RNAs were then treated with DNase I at 37°C for 30 min to remove any contaminating genomic DNA, followed by purification using the RNA Clean & Concentrator kit. A 10 mL aliquot of purified RNA was reserved as the Input sample. The remained RNAs were subjected to affinity purification, and set as Enrich or Control samples.
Input, Enrich, and Control samples from each biological replicate experiment were subjected to library construction by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) with Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) according to manufacturer’s instructions.

treatment_protocol: HEK293T cells stably expressing APEX2-ERM or APEX2-NES at approximately 90% confluency were incubated with 0.5 mM Btn-Ph for 30 min at 37°C in an environment containing 5% CO2.  Cell-cycle synchronized HEK293T cells stably expressing BIRC5-APEX2_L242F-EGFP or KIF23-APEX2_L242F-EGFP at approximately 90% confluency were incubated with 0.5 mM Btn-Ph for 30 min at 37°C in an environment containing 5% CO2. Biotinylation was initiated by adding 1 mM H2O2 for 10 seconds, followed by treatment with a quencher solution containing 20 mM sodium ascorbate and 5 mM Trolox. After three rounds of quenching, the cells were lysed for RNA extraction.

value: Endogenously expressing KIF23-APEX2_L242F-EGFP via knock-in

value: Cell cycle synchronization


title: 933000320046325

description: Library name: 933000320046325


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype, control, female, rep1

description: Library name: ST1wtPBSf1_arc_atac

value: C57Bl/6J (WT; Jax)


title: 933000320046372

description: Library name: 933000320046372

value: Rostromedial tegmental nucleus


title: HC15 - mPCLS_IAV - IAV

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description: Library name: HC15

data_processing:
FASTQ reads were mapped on human (Ensembl GRCh38 v110) or mouse (Ensembl GRCm39 v110) genome with software HISAT2 (V2.2.1)
Gene quantification was obtained with summarizeOverlaps() method from R package GenomicAlignments.
Assembly: GRCh38 or GRCm39 from Ensembl v110
Supplementary files format and content: All processed files are tables in TSV format (Tab Separated Values);hs_counts.tsv contains read count matrix of human libraries;mm_counts.tsv contains read count matrix of mouse libraries; metadata.tsv contains a table of library metadata.

source_name: Lung - pcls

growth_protocol: PCLS generation in DMEM/F12

extract_protocol:
NucleoSpin RNA XS kit (Macherey-Nagel) for murine & human PCLS or trizol extraction for murine or human in vivo samples
Illumina TruSeqHT Stranded mRNA protocol except for mIV, mPCLS & hPCLS, RNA exome-seq human in vivo samples

treatment_protocol: Untreated or A/Netherlands/602/2009 (H1N1) for 48h or Spn (ATCC: (Klein) Chester 6303, serotype 3 for 24h

value: Lung - pcls

value: IAV

tag: specimen id

tag: specimen sex

value: Female

tag: specimen age


title: PA1367.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA1367.1-2


title: KIF23-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep3

description:
Library name: KIF23_Control_rep3
Column name: KIF23_Control_rep3


title: PA1367.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA1367.1-1


title: HC13 - mPCLS_IAV - IAV

description: Library name: HC13


title: PA2734.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA2734.1-1


title: KIF23-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep2

description:
Library name: KIF23_Control_rep2
Column name: KIF23_Control_rep2


title: HC14 - mPCLS_IAV - mock

description: Library name: HC14

value: mock


title: PA2734.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA2734.1-2


title: 933000320046322

description: Library name: 933000320046322


title: HC11 - mPCLS_IAV - IAV

description: Library name: HC11


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep3

description:
Library name: KIF23_Input_rep3
Column name: KIF23_Input_rep3


title: KIF23-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep1

description:
Library name: KIF23_Control_rep1
Column name: KIF23_Control_rep1


title: 933000320046309

description: Library name: 933000320046309


title: HC10 - mPCLS_IAV - mock

description: Library name: HC10


title: 933000320046316

description: Library name: 933000320046316


title: 933000320046291

description: Library name: 933000320046291


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep4

description:
Library name: KIF23_Input_rep4
Column name: KIF23_Input_rep4


title: PA1014.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA1014.1-1


title: PA1270.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA1270.1-2


title: HC12 - mPCLS_IAV - mock

description: Library name: HC12


title: PAO1-WT-1-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PAO1-1-1_depth.txt
PAO1-1-2_depth.txt,counts_WTexp.txt
PAO1-1-2

value: WT


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep4

description:
Library name: KIF23_Enrich_rep4
Column name: KIF23_Enrich_rep4


title: PA1270.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA1270.1-1


title: 933000320046286

description: Library name: 933000320046286


title: multiome ATAC-seq, mouse striatum, Lrrk2 wildtype, control, male, rep2

description: Library name: ST2wtPBSm1_arc_atac

value: striatum

value: male

value: PBS injected


title: 933000320046296

description: Library name: 933000320046296


title: PA0982.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA0982.1-1

value: bacterial cells


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep1

description:
Library name: KIF23_Input_rep1
Column name: KIF23_Input_rep1


title: 933000320046287

description: Library name: 933000320046287


title: HC06 - mIV - IAV

description: Library name: HC06

source_name: Lung - in vivo

value: Lung - in vivo

value: mIV


title: PA0982.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA0982.1-2

value: grow until mid-log phase in LB


title: PA0806.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA0806.1-2


title: 933000320045980

description: Library name: 933000320045980


title: PA1014.1-2-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA1014.1-2


title: 933000320046163

description: Library name: 933000320046163


title: HC01 - mIV - mock

description: Library name: HC01


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep3

description:
Library name: KIF23_Enrich_rep3
Column name: KIF23_Enrich_rep3


title: HC04 - mIV - IAV

description: Library name: HC04


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep2

description:
Library name: KIF23_Enrich_rep2
Column name: KIF23_Enrich_rep2


title: HC03 - mIV - mock

description: Library name: HC03


title: HC05 - mIV - IAV

description: Library name: HC05


title: 933000320045935

description: Library name: 933000320045935


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep2

description:
Library name: KIF23_Input_rep2
Column name: KIF23_Input_rep2


title: CC fate marker in non-reprogramming and reprogramming CCs, rna_aer030, L3, Repro_CC

city: Hamburg

first: Baris

last: Tursun

address: Martin-Luther-King-Platz 3

country: Germany

institute: Universität Hamburg

description: Library name: rna_aer030

data_processing:
RNA-seq data were processed using the PiGx-RNA-seq pipeline (v0.1.0).
Transcript quantification was performed against the WBcel235 reference transcriptome (Ensembl release 94) using Salmon (v0.13.1) with default parameters.
Assembly: WBcel235
Supplementary files format and content: raw_counts.tsv: tab-delimeted text file with the per-gene quantifications via Salmon
Supplementary files format and content: normalized_counts.tsv: tab-delimeted text file with the read counts normalized by library size via DESeq2

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Background of germline-less animals carrying the temperature-sensitive glp-4(bn2) allele was used. For the dissociation of L3 worms (strains BAT2087 and BAT 2088) a mixed population was grown at 15°C, bleached and eggs were placed on unseeded plates at 25°C. Approximately 24 h later, plates were provided with food and worms grown to the L3 stage.

extract_protocol:
The protocol by Kaletsky et al., 2016 (Kaletsky, et al. 2016) was used with modifications to dissociate coelomocyte cells from L3 worms. Pelleted animals were washed with 1-2x volume of lysis buffer, pulse spun and the supernatant was removed. Lysis buffer was then added up to ~4-10x volume of the animal pellet, and the lysis reaction was run for 6.5 minutes at RT whilst rotating at 20 rpm. 2x volume of ice-cold M9 was added, and the sample was spun at 1000 g for 30 seconds at 4 °C. The supernatant was removed, and the resulting pellet was washed a further 6 times. M9 was then added up to 200 uL and mixed in a 1:1 ratio with pronase (20 mg/mL, warmed at 37 °C) at RT. 1x volume of chitinase (1 U/mL) was added, and the L3-chitinase mix was spun at 1300 g for 1 minute. The supernatant was then removed, and 4x volume chitinase (1 U/mL in egg buffer) was added and incubated at RT, rotating at 20 rpm for 1 hour. 2.5 volumes of PBS+2% FBS were then added to stop the reaction, and chitinase-treated worms were spun at 900 g for 3 minutes at 4 C. The supernatant was removed, and PBS+2% FBS was added up to 400 uL. For mechanical dissociation, 10 minutes of pipetting per sample, with a 1-minute break between each minute of pipetting, was applied. The pipette was pressed against the bottom of the tube whilst sucking up liquid and samples were aspirated into the remaining sample. A 10-um filter was wetted with PBS + 2% FBS and used to filter the dissociated cells. The filtered cells were pelleted at 1000 g for 5 min at 4 °C, and the supernatant was removed. Dissociation by pipetting and preparation for FACs sorting was then performed as described for the dissociation of embryos. Dissociated cells were resuspended in 1x PBS and filtered through a Corning™ Falcon™ Test Tube with Cell Strainer Snap Cap (35 mm nylon net). Cells were sorted out using either a BD FACS ARIA III or BD FACSARIA FUSION FACs machine. Sorted cells were collected in a 1.5 mL Eppendorf tube containing 50 mL PBS and the RNase inhibitor Ribolock at a final concentration of 1 U/mL.Samples were diluted 1 in 10 with Trizol (15596026 LIFE technologies) and glycoblue was added at 1 to 1000 to ensure that RNA pellets were visible following isolation. Samples were then vortexed for 30 seconds, incubated at RT for 5 mins and flash frozen in liquid nitrogen. 0.2x volume of chloroform was added to the sample, followed by 30 seconds of vortexing and 5 minutes of incubation at RT. Samples were then centrifuged at 12,000 g for 15 minutes at 4 °C. The clear aqueous layer was isolated and an equal volume of isopropanol was added. Samples were then inverted ten times and kept at -20 °C overnight. Samples were then centrifuged at 12,000 g for 30 minutes at 4 °C and the supernatant was discarded. The RNA + glycoblue pellet was then washed with 1 mL 75% ethanol, shaken briefly, and centrifuged at 7,500 g for 5 minutes at 4 °C. The supernatant was then discarded, and pellets were air-dried for 10 minutes at RT. RNA was resuspended in 20-25 mL RNase-free water.
Poly(A) RNA was selected for using the NEXTflex™ Poly(A) Beads Kit (BIOO SCIENTIFIC) according to the manufacturer’s instructions. RNA-seq libraries were prepared using the NEXTflex™ Rapid Directional qRNA-Seq™ Kit (BIOO SCIENTIFIC) according to the manufacturer’s instructions.

treatment_protocol: No separate treatment was applied beyond the temperature shift and growth to the L3 stage.

value: whole worm

value: coelomocyte cells (FACS sorted, unc-122prom::GFP positive)

value: BAT2088 barIs177; barIs115; glp-4 (bn2) I barIs177[unc-122prom::gfp]; barIs115[coel or unc-122prom_che-1_2xFLAG_3 UNC-54 UTR (dBT633) + myo-2prom::mCherry (dBT187)]; glp-4 (bn2) I


title: HC02 - mIV - mock

description: Library name: HC02


title: PA0806.1-1-OE

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
counts_allOEsRNA.txt
PA0806.1-1


title: Anti-H4K12la  oligodendrocyte precursor cell-C3-2

city: Xi'an

first: Yuan

last: Zhang

address: No. 620, West Chang'an Avenue, Chang'an District

institute: Shaanxi Normal University

description:
Library name: C3-2_h4k12la
anti-H4K12la

library_source: genomic

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: brain

growth_protocol: Neonatal C57BL/6 mouse brain tissue (postnatal days 0–3, mixed sex) was rapidly dissociated in HBSS. OPCs were isolated using the Neural Tissue Dissociation Kit Ran and CD140a (PDGFRα) MicroBead Kit, seeded into poly-D-lysine–coated 6-well plates, and maintained in DMEM/F12 containing 20 ng/mL PDGF-AA, 2% B27, 20 ng/mL bFGF, 2 mM GlutaMAX, and 1% N2.

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

treatment_protocol: DMEM/F12 containing 2% B27 and 1% N2, supplemented with either propionic acid (PA, 10 μM) or vehicle.

value: brain

value: oligodendrocyte precursor cell

value: Genomic DNA

value: propionic acid


title: BIRC5-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep3

description:
Library name: BIRC5_Control_rep3
Column name: BIRC5_Control_rep3

value: Endogenously expressing BIRC5-APEX2_L242F-EGFP via knock-in

value: Cell cycle synchronization


title: CC fate marker in non-reprogramming and reprogramming CCs, rna_aer029, L3, WT_CC

description: Library name: rna_aer029

value: BAT2087 barIs177; glp-4 (bn2) I barIs177[unc-122prom::gfp]; glp-4 (bn2) I


title: KIF23-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep1

description:
Library name: KIF23_Enrich_rep1
Column name: KIF23_Enrich_rep1

value: Endogenously expressing KIF23-APEX2_L242F-EGFP via knock-in


title: 933000320046160

description: Library name: 933000320046160

value: Rostromedial tegmental nucleus


title: BIRC5-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep4

description:
Library name: BIRC5_Control_rep4
Column name: BIRC5_Control_rep4


title: BIRC5-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep2

description:
Library name: BIRC5_Control_rep2
Column name: BIRC5_Control_rep2


title: 933000320045819

description: Library name: 933000320045819


title: BIRC5-APEX2_L242F-EGFP, omit H2O2, post-enrichment, rep1

description:
Library name: BIRC5_Control_rep1
Column name: BIRC5_Control_rep1


title: CC fate marker in non-reprogramming and reprogramming CCs, rna_aer028, L3, Repro_CC

description: Library name: rna_aer028


title: Anti-H4K12la  oligodendrocyte precursor cell-Vehicle-2

description:
Library name: Vehicle-2_h4k12la
anti-H4K12la

value: vehicle


title: CC fate marker in non-reprogramming and reprogramming CCs, rna_aer027, L3, WT_CC

description: Library name: rna_aer027


title: 933000320045638

description: Library name: 933000320045638


title: Anti-H4K12la  oligodendrocyte precursor cell-C3-1

description:
Library name: C3-1_h4k12la
anti-H4K12la


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep4

description:
Library name: BIRC5_Input_rep4
Column name: BIRC5_Input_rep4


title: 933000120138546

description: Library name: 933000120138546


title: CC fate marker in non-reprogramming and reprogramming CCs, rna_aer022, L3, Repro_CC

description: Library name: rna_aer022


title: Anti-H4K12la  oligodendrocyte precursor cell-Vehicle-1

description:
Library name: Vehicle-1_h4k12la
anti-H4K12la


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep3

description:
Library name: BIRC5_Input_rep3
Column name: BIRC5_Input_rep3


title: spleen, transport stress+Mtb

city: wuhan

first: xiaojuan

last: gou

address: 1 Shizishan Street, Hongshan District, Wuhan City, Hubei Province

department: College of Veterinary medicine

institute: Huazhong Agricultural University

description:
Library name: L4_FL
L4_FL_RSEC_MolsPerCell.csv

data_processing:
Raw data were processed using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) pipeline (v1.11)
Assembly: mm10
Supplementary files format and content: Comma-separated values cell-gene matrix files

source_name: spleen

extract_protocol:
Mouse spleen single cell suspension was obtained. The tissue was digested with 3mg protease XXIII and 30U/ml papin, and single cells were suspended with 0.5% BSA.
Single-cell mRNA library was performed by the BD Rhapsody Single-Cell Analysis System (BD Biosciences, USA). Firstly，single-cell suspension in BSA was loaded into a BD Rhapsody cartridge with >200, 000 microwells. Secondly, single-cell mRNA was captured by magnetic beads with barcoded capture oligos.Then, magnetic beads were collected for cDNA synthesis and library construction following the BD Rhapsody single cell 3’ whole transcriptome amplification (WTA) workflow. Finally, the libraries were sequenced on Illumina NovaSeq 6000 (Illumina, USA) with 300-bp reads (150-bp paired-end reads).

treatment_protocol: The mice were subjected to TS for 3 h (8:30 am to 11:30 am) per day for 8 days as follows: Minimal handing was used to insert a group of 10 mice into the restraint device, consisting of a closed transparent 500 mL plastic bottle, to restric its activity. Large breathing holes around the bottle provide adequate ventilation. The bottles containing the mice were transferred to a temperature-controlled shaker and shaken at 90-120 rpm/min at 35-36 °C. The mice were dried and placed in their original cages with free access to food and water after TS.

value: spleen


title: 933000120138519

description: Library name: 933000120138519


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep2

description:
Library name: BIRC5_Input_rep2
Column name: BIRC5_Input_rep2


title: 933000120138480

description: Library name: 933000120138480


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, pre-enrichment, rep1

description:
Library name: BIRC5_Input_rep1
Column name: BIRC5_Input_rep1


title: CC fate marker in non-reprogramming and reprogramming CCs, rna_aer021, L3, WT_CC

description: Library name: rna_aer021


title: spleen, Mtb

description:
Library name: L3_FL
L3_FL_RSEC_MolsPerCell.csv


title: 933000120138468

description: Library name: 933000120138468


title: UPN500_fibro_SNPa

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, ligated, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing: Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.3 (ChAS) software with filters set at 400 Kb for Copy Number Alterations (CNAs) and 10 Mb for copy neutral Loss Of Heterozygosity (cnLOH). Our data refer to NetAffx Build 20211122 (hg19) database

label: Biotin

source_name: Fibroblast cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis

tag: cytogenetics

value: Not Available

tag: mutations

value: NBN c.37G>A, p.Asp13Asn   LIG4 c.2465C>T, p.Ser822Leu

tag: age


title: 933000120117316

description: Library name: 933000120117316


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep4

description:
Library name: BIRC5_Enrich_rep4
Column name: BIRC5_Enrich_rep4


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep3

description:
Library name: BIRC5_Enrich_rep3
Column name: BIRC5_Enrich_rep3


title: Adrenal gland, Mtb, rep2

description:
Library name: AG_RU4
PVN_PG_AG_allcount.csv

source_name: Adrenal gland

value: Adrenal gland


title: spleen, control

description:
Library name: L1_FL
L1_FL_RSEC_MolsPerCell.csv


title: UPN502_BM_SNPa

source_name: Unsorted Bone Marrow Cells

value: IDH2 c.419G>A, p.Arg140Gln   DNMT3A c.2645G>A, p.Arg882His


title: UPN501_BM_SNPa


title: KO_sample_3

city: Shanghai

first: Honglian

last: Yu

address: No. 279, Zhouzhu Highway

institute: Shanghai University of Medicine and Health Sciences

description: Library name: KO3_lib

data_processing:
Raw sequencing data quality was evaluated using FastQC. Reads were processed to remove adapters and low-quality bases using Trimmomatic to obtain clean reads.
Clean reads were aligned to the reference genome using HISAT2.
Gene expression levels were estimated using StringTie , and expression was quantified as read counts and normalized to FPKM/TPM.
Assembly: GRCm39
Supplementary files format and content: The all_count.txt file contains the raw read counts for all genes across the samples.

source_name: testis

extract_protocol:
Total RNA was extracted from tissue samples using appropriate extraction methods. RNA quality and concentration were rigorously assessed before library construction.
Sequencing libraries were generated using standard protocols. Briefly, mRNA was purified from total RNA using oligo-dT enrichment. Fragmentation was carried out, followed by double-stranded cDNA synthesis. The fragments were subjected to end repair, dA-tailing, adapter ligation, and PCR amplification. Libraries were sequenced on an Illumina platform using a PE150 (paired-end 150bp) strategy.

value: testis

value: syna knockout

value: untreated


title: UPN501_fibro_SNPa


title: Adrenal gland, Mtb, rep1

description:
Library name: AG_RU1
PVN_PG_AG_allcount.csv


title: UPN500_BM_SNPa

value: CSF3R c.2245C>T, p.Gln749*   ASXL1 c.1534C>T, p.Gln512*   SRSF2 c.284C>G, p.Pro95Arg  NBN c.37G>A, p.Asp13Asn   LIG4 c.2465C>T, p.Ser822Leu


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep1

description:
Library name: BIRC5_Enrich_rep1
Column name: BIRC5_Enrich_rep1


title: 933000120138374

description: Library name: 933000120138374


title: KO_sample_2

description: Library name: KO2_lib


title: APEX2_L242F-NES, Btn-An labeling, pre-enrichment, rep3

description:
Library name: NES_Input_rep3
Column name: NES_Input_rep3

value: Stably expressing APEX2_L242F-NES

value: No additional treatment


title: Adrenal gland, transport stress+Mtb, rep1

description:
Library name: AG_RS1
PVN_PG_AG_allcount.csv


title: APEX2_L242F-NES, Btn-An labeling, pre-enrichment, rep2

description:
Library name: NES_Input_rep2
Column name: NES_Input_rep2


title: nkMN_31_CUT&RUN_PAX8

address: Piazzale G. Menghini, 9

description: Library name: nkMN_31_CUT_RUN_PAX8

data_processing:
Sequenced reads were trimmed for adaptor sequences using trimmomatic
Reads were aligned against hg19 build of the human genome using bowtie2 with --dovetail option
Peak calling pipeline used SEACR software with -relaxed option and IgG negative control as background
Assembly: hg19
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

source_name: Frozen viable mononuclear bone marrow cells

extract_protocol:
CUT&RUN was performed on frozen viable mononuclear bone marrow cells (10% DMSO) obtained after Ficoll separation
CUT&RUN libraries were prepared by using the SimpleChIP ChIP-seq DNA Library Prep Kit following manufacturer’s instructions (Cell Signaling Technology) and sequenced on Illumina Miseq using manufacturer’s recommended protocol for 75 bp paired-end read runs with v3 cartridge (Illumina San Diego, CA).

tag: karyotype

value: DNMT3A, IDH2, NPM1, PTPN11

tag: diagnosis

value: AML


title: WT_control_3

description: Library name: WT3_lib

tag: tissue

value: wild type


title: spleen, transport stress

description:
Library name: L2_FL
L2_FL_RSEC_MolsPerCell.csv


title: nkMN_31_CUT&RUN_IgG

description: Library name: nkMN_31_CUT_RUN_IgG

value: Frozen viable mononuclear bone marrow cells


title: Adrenal gland, control, rep2

description:
Library name: AG_PU4
PVN_PG_AG_allcount.csv


title: Adrenal gland, transport stress+Mtb, rep2

description:
Library name: AG_RS4
PVN_PG_AG_allcount.csv


title: WT_control_1

description:
Library name: WT1_lib
Excluded from downstream differential expression analysis due to outlier profile as revealed by sample correlation clustering.


title: WT_control_2

description: Library name: WT2_lib


title: Mon7_1_CUT&RUN_IgG

description: Library name: Mon7_1_CUT_RUN_IgG

value: CSF3R, ASXL1, SRSF2, NBN, LIG4

value: MDS


title: APEX2_L242F-NES, Btn-An labeling, pre-enrichment, rep1

description:
Library name: NES_Input_rep1
Column name: NES_Input_rep1


title: nkMN_31_CUT&RUN_IKZF1

description: Library name: nkMN_31_CUT_RUN_IKZF1


title: APEX2-ERM, Btn-Ph labeling, pre-enrichment, rep3

description:
Library name: ERM_APEX-seq_Input_rep3
Column name: ERM_APEX-seq_Input_rep3

value: Stably expressing APEX2-ERM


title: Adrenal gland, transport stress, rep2

description:
Library name: AG_PS4
PVN_PG_AG_allcount.csv


title: BIRC5-APEX2_L242F-EGFP, Btn-An labeling, post-enrichment, rep2

description:
Library name: BIRC5_Enrich_rep2
Column name: BIRC5_Enrich_rep2

value: Endogenously expressing BIRC5-APEX2_L242F-EGFP via knock-in

value: Cell cycle synchronization


title: KO_sample_1

description: Library name: KO1_lib


title: hypophysis, Mtb, rep2

description:
Library name: PG_RU4
PVN_PG_AG_allcount.csv

source_name: hypophysis

value: hypophysis


title: Mon7_1_CUT&RUN_IKZF1

description: Library name: Mon7_1_CUT_RUN_IKZF1


title: Adrenal gland, transport stress, rep1

description:
Library name: AG_PS1
PVN_PG_AG_allcount.csv

value: Adrenal gland


title: Ptpn6 KO 48 hrs -1

city: South San Francisco

first: Xingyue

middle: Monica

last: Ge

address: 1 DNA Way

institute: Genentech

description: Library name: LIB5451398

data_processing:
Reads were aligned to the mm10 mouse genome with GSNAP aligner. Normalization was based on the nRPKM method. Differential expression was performed using voom+limma.
Assembly: mm10
Supplementary files format and content: .tab (gene count)

source_name: Bone marrow-derived macrophage

growth_protocol: Bone marrow (BM) was harvested from tibiae and femurs of mice. Total BM cells were plated in BMDM culture media [DMEM High Glucose, 10% FBS (VWR), GlutaMAX (Gibco) and penicillin/streptomycin (Gibco) supplemented with 50ng/mL recombinant murine M-CSF (Genentech)] at a density of 0.5x106 cells/ml in 150mm non-TC treated Petri dishes (VWR) in a volume of 20 ml per dish. After two days, 20 ml fresh BMDM culture media was added without removal of media. On day 4, all media was removed and 20 ml fresh BMDM culture media added. On day 5, cells were gently scraped from dishes using a rubber policeman and transferred to a 50 ml conical tube. The Petri dish was washed once with 20 ml 1X PBS and cells harvested via centrifugation. Cells were resuspended in 10mL 1X PBS and counted, after which they were centrifuged once again for transfection and re-plating.

extract_protocol:
Total RNA was isolated using RNeasy Plus Universal Mini kit (Qiagen).
RNA-seq libraries were generated using Tru-seq RNA Library Prep Kit v2 (Illumina) and sequenced using a Hiseq4000 (Illumina).

treatment_protocol: To prepare each guide RNA, the Alt-R crRNA and Alt-tracrRNA (IDT) were reconstituted to 100 µM with Nuclease-Free Duplex Buffer (IDT).  To prepare the crRNA/XT-tracrRNA duplexes, the two oligos were mixed at equimolar concentrations in a sterile PCR tube. Oligos were annealed by heating at 95°C for 5 min followed directly by hybridization for 15 min at room temperature in a PCR thermocycler. The mix was then placed on ice or frozen at -20°C until further use. In either a sterile PCR strip or 1.5 ml tube, the annealed crRNA-tracrRNA duplexes were mixed with Cas9 (Alt-R S.p. HiFi Cas9 Nuclease V3) at a 3:1 molar ratio. HiFi Cas9 was selected to minimize potential for off-target editing. Cas9 protein and guide RNAs were complexed by incubation at room temperature for at least 10 min. 3-5x106 cells per reaction were resuspended in 20 µl of P3 primary nucleofection solution (Lonza).  The cell suspension was then added to each Cas9-RNP complex and pipetted up and down 3-5 times gently to mix.  The cell suspension was then immediately loaded into the supplied nucleofector cassette strip (Lonza). The strip was inserted into the Lonza 4D-Nucleofector (4D-Nucleofector Core Unit: Lonza, AAF-1002B; 4D-Nucleofector X Unit: AAF-1002X) and electroporated with the Buffer P3, CM-137 condition.  The cassette strip was removed and 150-180 µl of pre-warmed medium was immediately added into each cassette well.  The cell suspension was then re-plated for downstream assays.  Electroporated cells were plated at a density of 20,000 cells per 1.9 cm2 (i.e. 20,000 cells per well of a 24-well plate). Cells were fed every 1-2 days with a 50% media change using a supplementation medium containing 100 mg/mL CSF-1 to account for rapid consumption of CSF-1 in the cultures. Cells were maintained for 7 days. We performed RNA-seq analysis of BMDMs treated with gPtpn6, Rraga, or control guides, each at 4 hrs, 24 hrs, or 48 hrs after the time of last CSF-1 supplementation.

value: Bone marrow-derived macrophage

value: gPtpn6 48 hrs


title: Mon7_1_CUT&RUN_PAX8

description: Library name: Mon7_1_CUT_RUN_PAX8


title: Ptpn6 KO 48 hrs -2

description: Library name: LIB5451399


title: APEX2-ERM, Btn-Ph labeling, post-enrichment, rep3

description:
Library name: ERM_APEX-seq_Enrich_rep3
Column name: ERM_APEX-seq_Enrich_rep3


title: Ptpn6 KO 48 hrs -3

description: Library name: LIB5451400


title: Library

description:
Library name: Sample25
F54_S25_L001_R1_001

data_processing:
Screen analysis was performed using MAGECK-MLE to identify genes selectively enriched or depleted compared to the control.
Supplementary files format and content: Includes sgRNA counts for each targeted gene (row) for each sample (column)
Library strategy: CRISPR Screen

growth_protocol: Cells were grown in DMEM + 10% FBS and maintained in 2 µg/ml doxycycline to sustain P3F1 depletion throughout the screen.

extract_protocol:
Cell pellets were lysed in 1 ml DNAzol by vigorous pipetting according to the manufacturer’s protocol (Molecular Research Center Inc.). DNA was precipitated in 0.5 ml 200-proof ethanol (VWR), followed by a second precipitation in 2.5 ml 200-proof ethanol. Precipitated DNA was pelleted by centrifugation at 20,000 g, washed twice with 75% ethanol, and solubilized in 0.5 ml of water.
To minimize PCR amplification bias, sgRNA sequences from each sample were amplified in triplicate and pooled at each step. First-round PCR was performed using 50–100 µg gDNA, Hotstart Taq (Takara), and 1 µM each of CRISPR F1 and CRISPR R1 primers (IDT). Thermal cycling conditions were: 95 °C for 5 minutes; 18 cycles of 95 °C for 30 seconds, 60 °C for 30 seconds, 72 °C for 30 seconds; final extension at 72 °C for 5 minutes. Amplicons from the same sample were pooled, and a second PCR was performed to add sample barcodes and Illumina adaptors using 20 µl of PCR1 and 0.5 µM CRISPR R2 plus barcoded forward primers. Thermal cycling conditions were: 95 °C for 5 minutes; 20 cycles of 95 °C for 15 seconds, 58 °C for 30 seconds, 72 °C for 30 seconds; final extension at 72 °C for 5 minutes. Second-round PCR products were pooled at equal concentrations and purified using Ampure XP Beads according to the manufacturer’s protocol (Beckman Coulter).

treatment_protocol: For each replicate, 1.2 × 10⁷ cells were infected at an MOI of 0.3 to ensure predominantly single lentiviral integration events. Infections were performed across six wells of a 6-well plate, with 1 ml of the appropriate media containing virus at a predetermined concentration to achieve the target MOI, supplemented with 8 µg/ml polybrene (MilliporeSigma), and spun at 800 × g for 1 hour. After 6 hours of culture at 37 °C, cells were washed with 1× Phosphate Buffered Saline (PBS; Sodium Chloride, 0.137 M; Potassium Chloride, 0.0027 M; Sodium Phosphate Dibasic, 0.01 M; Potassium Phosphate Monobasic, 0.0018 M) and the media was replaced. After 18 hours, infections were pooled into a 15 cm culture dish and selected with 150 µg/ml hygromycin (Thermo Fisher Scientific). Cells were continuously passaged under selection for 1 week, after which 1 × 10⁶ cells were pelleted and snap frozen as the initial sample. An additional 1 × 10⁶ cells were maintained under continuous passage for 2 weeks for final samples and subsequently pelleted and snap frozen.

value: rhabdomyosarcoma

value: CRISPR Library


title: APEX2-ERM, Btn-Ph labeling, post-enrichment, rep2

description:
Library name: ERM_APEX-seq_Enrich_rep2
Column name: ERM_APEX-seq_Enrich_rep2


title: P3I_Fin_2

description:
Library name: Sample23
F52_S23_L001_R1_001


title: APEX2-ERM, Btn-Ph labeling, post-enrichment, rep1

description:
Library name: ERM_APEX-seq_Enrich_rep1
Column name: ERM_APEX-seq_Enrich_rep1


title: P3I_Fin_1

description:
Library name: Sample22
F50_S22_L001_R1_001


title: APEX2-ERM, Btn-Ph labeling, pre-enrichment, rep1

description:
Library name: ERM_APEX-seq_Input_rep1
Column name: ERM_APEX-seq_Input_rep1


title: Adrenal gland, control, rep1

description:
Library name: AG_PU1
PVN_PG_AG_allcount.csv


title: hypophysis, Mtb, rep1

description:
Library name: PG_RU1
PVN_PG_AG_allcount.csv


title: Control 48 hrs -3

description: Library name: LIB5451394

value: gControl

value: gControl 48 hrs


title: Rraga KO 48 hrs -1

description: Library name: LIB5451395

value: gRraga

value: gRraga 48 hrs


title: Rraga KO 48 hrs -3

description: Library name: LIB5451397


title: hypophysis, control, rep2

description:
Library name: PG_PU4
PVN_PG_AG_allcount.csv


title: hypophysis, control, rep1

description:
Library name: PG_PU1
PVN_PG_AG_allcount.csv


title: P3I_Fin_3

description:
Library name: Sample24
F53_S24_L001_R1_001


title: hypophysis, transport stress+Mtb, rep1

description:
Library name: PG_RS1
PVN_PG_AG_allcount.csv


title: APEX2-ERM, omit probe, post-enrichment, rep3

description:
Library name: ERM_APEX-seq_Control_rep3
Column name: ERM_APEX-seq_Control_rep3

value: No additional treatment


title: Control 48 hrs -2

description: Library name: LIB5451393


title: APEX2-ERM, omit probe, post-enrichment, rep2

description:
Library name: ERM_APEX-seq_Control_rep2
Column name: ERM_APEX-seq_Control_rep2


title: APEX2-ERM, omit probe, post-enrichment, rep1

description:
Library name: ERM_APEX-seq_Control_rep1
Column name: ERM_APEX-seq_Control_rep1


title: Rraga KO 48 hrs -2

description: Library name: LIB5451396


title: hypophysis, transport stress, rep2

description:
Library name: PG_PS4
PVN_PG_AG_allcount.csv


title: P3FM3_Fin_1

description:
Library name: Sample19
F47_S19_L001_R1_001


title: hypophysis, transport stress, rep1

description:
Library name: PG_PS1
PVN_PG_AG_allcount.csv


title: APEX2-NES, Btn-Ph labeling, pre-enrichment, rep3

description:
Library name: NES_APEX-seq_Input_rep3
Column name: NES_APEX-seq_Input_rep3

value: Stably expressing APEX2-NES


title: P3FM3_Fin_3

description:
Library name: Sample21
F49_S21_L001_R1_001


title: Ptpn6 KO 4 hrs -3

description: Library name: LIB5451391

value: gPtpn6 4 hrs


title: Ptpn6 KO 4 hrs -2

description: Library name: LIB5451390


title: APEX2-NES, Btn-Ph labeling, pre-enrichment, rep2

description:
Library name: NES_APEX-seq_Input_rep2
Column name: NES_APEX-seq_Input_rep2


title: hypothalamus, Mtb, rep2

description:
Library name: PVN_RU2
PVN_PG_AG_allcount.csv

source_name: hypothalamus

value: hypothalamus


title: Control 48 hrs -1

description: Library name: LIB5451392


title: APEX2-NES, Btn-Ph labeling, pre-enrichment, rep1

description:
Library name: NES_APEX-seq_Input_rep1
Column name: NES_APEX-seq_Input_rep1


title: hypothalamus, Mtb, rep1

description:
Library name: PVN_RU1
PVN_PG_AG_allcount.csv


title: Ptpn6 KO 4 hrs -1

description: Library name: LIB5451389


title: P3N1_Fin_1

description:
Library name: Sample16
F44_S16_L001_R1_001


title: P3F1_Fin_3

description:
Library name: Sample15
F43_S15_L001_R1_001


title: P3N2_Fin_2

description:
Library name: Sample17
F45_S17_L001_R1_001


title: P3FM3_Fin_2

description:
Library name: Sample20
F48_S20_L001_R1_001


title: APEX2-NES, Btn-Ph labeling, post-enrichment, rep2

description:
Library name: NES_APEX-seq_Enrich_rep2
Column name: NES_APEX-seq_Enrich_rep2


title: Rraga KO 4 hrs -3

description: Library name: LIB5451388

value: gRraga 4 hrs


title: APEX2-NES, Btn-Ph labeling, post-enrichment, rep3

description:
Library name: NES_APEX-seq_Enrich_rep3
Column name: NES_APEX-seq_Enrich_rep3


title: hypothalamus, transport stress+Mtb, rep1

description:
Library name: PVN_RS1
PVN_PG_AG_allcount.csv


title: P3F1_Fin_2

description:
Library name: Sample14
F42_S14_L001_R1_001


title: hypothalamus, transport stress+Mtb, rep2

description:
Library name: PVN_RS2
PVN_PG_AG_allcount.csv


title: APEX2-NES, Btn-Ph labeling, post-enrichment, rep1

description:
Library name: NES_APEX-seq_Enrich_rep1
Column name: NES_APEX-seq_Enrich_rep1


title: Rraga KO 4 hrs -2

description: Library name: LIB5451387


title: P3F1_Fin_1

description:
Library name: Sample13
F41_S13_L001_R1_001


title: APEX2-ERM, Btn-Ph labeling, pre-enrichment, rep2

description:
Library name: ERM_APEX-seq_Input_rep2
Column name: ERM_APEX-seq_Input_rep2

value: Stably expressing APEX2-ERM


title: Rraga KO 4 hrs -1

description: Library name: LIB5451386


title: Control 4 hrs -3

description: Library name: LIB5451385

value: gControl 4 hrs


title: hypothalamus, control, rep2

description:
Library name: PVN_PU2
PVN_PG_AG_allcount.csv


title: hypophysis, transport stress+Mtb, rep2

description:
Library name: PG_RS4
PVN_PG_AG_allcount.csv

value: hypophysis


title: APEX2_L242F-ERM, Btn-An labeling, pre-enrichment, rep3

description: Column name: ERM_Input_rep3

data_processing:
The sequencing reads for each library were aligned against the human genome assembly GRCh38 (hg38), downloaded from the Ensembl project, using HISAT2 (v2.1.0).
The results of alignments were sorted by read names. The read counts of each gene were measured with the matching gene annotation (v.87) from Ensembl by HTSeq v0.6.1, utilizing the option “-stranded no”.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited txt file contains counts of all genes from HEK293T cell lines stably expressing APEX2_L242F-ERM or APEX2_L242F-NES

extract_protocol:
Following APEX2_L242F-mediated labeling, cells were lysed by the addition of TRIzol reagent, and total RNAs were extracted according to the manufacturer’s protocol. The extracted RNAs were then treated with DNase I at 37°C for 30 min to remove any contaminating genomic DNA, followed by purification using the RNA Clean & Concentrator kit. A 10 mL aliquot of purified RNA was reserved as the Input sample. The remained RNAs were subjected to affinity purification, and set as Enrich or Control samples.
Input, Enrich, and Control samples from each biological replicate experiment were subjected to library construction by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) with Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) according to manufacturer’s instructions.

treatment_protocol: HEK293T cells stably expressing APEX2_L242F-ERM or APEX2_L242F-NES at approximately 90% confluency were incubated with 5 mM Btn-An for 30 min at 37°C in an environment containing 5% CO2. Biotinylation was initiated by adding 1 mM H2O2 for 10 seconds, followed by treatment with a quencher solution containing 20 mM sodium ascorbate and 5 mM Trolox. After three rounds of quenching, the cells were lysed for RNA extraction.

value: Stably expressing APEX2_L242F-ERM


title: P3N3_Fin_3

description:
Library name: Sample18
F46_S18_L001_R1_001


title: P3I_Init_3

description:
Library name: Sample12
F40_S12_L001_R1_001


title: APEX2_L242F-ERM, Btn-An labeling, pre-enrichment, rep2

description: Column name: ERM_Input_rep2


title: hypothalamus, transport stress, rep2

description:
Library name: PVN_PS2
PVN_PG_AG_allcount.csv


title: P3I_Init_2

description:
Library name: Sample11
F39_S11_L001_R1_001


title: Control 4 hrs -2

description: Library name: LIB5451384

value: Bone marrow-derived macrophage


title: hypothalamus, transport stress, rep1

description:
Library name: PVN_PS1
PVN_PG_AG_allcount.csv


title: APEX2_L242F-ERM, Btn-An labeling, pre-enrichment, rep1

description: Column name: ERM_Input_rep1


title: Control 4 hrs -1

description: Library name: LIB5451383


title: APEX2_L242F-ERM, Btn-An labeling, post-enrichment, rep3

description: Column name: ERM_Enrich_rep3


title: P3FM3_Init_3

description:
Library name: Sample9
F37_S9_L001_R1_001


title: mice bone marrow, G1-C replicate 3, scRNAseq

first: Jing

last: Wen

address: 3147 Biomedical Sciences Wy

department: CMM

institute: UCSD

description: 10x genomics

data_processing:
Single cell RNA samples were processed using Cellranger (version 6.0.1) with the reference genome mm10. Individual samples were processed and analyzed in Seurat (version 4.3) for quality control. Cells with <500 or >6000 expressed genes or >15% mitochondrial genes were removed. Doublets were detected and removed from each sample using Scrublet with an automatic threshold, considering an expected doublet rate of 6% for all samples. Ambient RNA contamination was accounted for by running SoupX on each sample using its automated algorithm to estimate contamination rates.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcode.tsv, features.tsv, matrix.mtx)

source_name: bone marrow

extract_protocol:
Bone marrow cells were isolated from tibia and femur bones following removal of surrounding muscle. Joints were cut using a scalpel and the exposed BM was flushed from the ends of bones using a 25-gauge needle and a 3 ml syringe filled with 2% FBS PBS. Clumps were gently disaggregated using a needle-less syringe and passed through a 70 μm cell strainer. The cell suspension was pelleted by centrifugation at 500 g for 5 min at room temperature.
For 10X, single cells were processed with chromium next GEM single cell 3’ HT reagent kits v3.1 (dual index) following the manufacturer’s protocol.

value: bone marrow

tag: strain

value: mRNA vaccine


title: P3FM3_Init_1

description:
Library name: Sample7
F35_S7_L001_R1_001

value: rhabdomyosarcoma

value: CRISPR Library


title: mice bone marrow, G1-C replicate 2, scRNAseq

description: 10x genomics


title: P3FM3_Init_2

description:
Library name: Sample8
F36_S8_L001_R1_001


title: APEX2_L242F-ERM, Btn-An labeling, post-enrichment, rep1

description: Column name: ERM_Enrich_rep1


title: Ptpn6 KO 24 hrs -2

description: Library name: LIB5451381

value: gPtpn6 24 hrs


title: Ptpn6 KO 24 hrs -1

description: Library name: LIB5451380


title: P3N3_Init_3

description:
Library name: Sample6
F34_S6_L001_R1_001


title: Ptpn6 KO 24 hrs -3

description: Library name: LIB5451382


title: P3I_Init_1

description:
Library name: Sample10
F38_S10_L001_R1_001


title: mice bone marrow, G1-C replicate 1, scRNAseq

description: 10x genomics


title: hypothalamus, control, rep1

description:
Library name: PVN_PU1
PVN_PG_AG_allcount.csv


title: mice bone marrow, RBD replicate 3, scRNAseq

description: 10x genomics


title: APEX2_L242F-ERM, omit probe, post-enrichment, rep3

description: Column name: ERM_Control_rep3


title: Rraga KO 24 hrs -3

description: Library name: LIB5451379

value: gRraga

value: gRraga 24 hrs


title: APEX2_L242F-ERM, omit probe, post-enrichment, rep2

description: Column name: ERM_Control_rep2

value: No additional treatment


title: APEX2_L242F-ERM, omit probe, post-enrichment, rep1

description: Column name: ERM_Control_rep1


title: Rraga KO 24 hrs -2

description: Library name: LIB5451378


title: mice bone marrow, RBD replicate 2, scRNAseq

description: 10x genomics


title: mice bone marrow, RBD replicate 1, scRNAseq

description: 10x genomics


title: P3N1_Init_1

description:
Library name: Sample4
F32_S4_L001_R1_001


title: APEX2_L242F-NES, Btn-An labeling, post-enrichment, rep3

description: Column name: NES_Enrich_rep3

value: Stably expressing APEX2_L242F-NES


title: Rraga KO 24 hrs -1

description: Library name: LIB5451377


title: P3N2_Init_2

description:
Library name: Sample5
F33_S5_L001_R1_001


title: mice bone marrow, GFP replicate 3, scRNAseq

description: 10x genomics


title: P3F1_Init_3

description:
Library name: Sample3
F31_S3_L001_R1_001


title: Control 24 hrs -3

description: Library name: LIB5451376

value: gControl

value: gControl 24 hrs


title: APEX2_L242F-NES, Btn-An labeling, post-enrichment, rep2

description: Column name: NES_Enrich_rep2


title: P3F1_Init_2

description:
Library name: Sample2
F30_S2_L001_R1_001


title: Control 24 hrs -2

description: Library name: LIB5451375


title: APEX2_L242F-NES, Btn-An labeling, post-enrichment, rep1

description: Column name: NES_Enrich_rep1


title: Control 24 hrs -1

description: Library name: LIB5451374


title: P3F1_Init_1

description:
Library name: Sample1
F29_S1_L001_R1_001


title: APEX2_L242F-ERM, Btn-An labeling, post-enrichment, rep2

description: Column name: ERM_Enrich_rep2


title: 4, Canis lupus familiaris, AdiposeSubcutaneousAxillary

status: Public on Mar 25 2026

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox000004

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read counts mapped to human

organism: Canis lupus familiaris

source_name: AdiposeSubcutaneousAxillary

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

value: AdiposeSubcutaneousAxillary


title: 307, Canis lupus familiaris, BrainCerebellum

description: Library name: itox000307

source_name: BrainCerebellum

value: BrainCerebellum


title: 304, Canis lupus familiaris, BrainAmygdala

description: Library name: itox000304

source_name: BrainAmygdala

value: BrainAmygdala


title: mice bone marrow, GFP replicate 1, scRNAseq

description: 10x genomics


title: 302, Canis lupus familiaris, BrainAmygdala

description: Library name: itox000302


title: 313, Canis lupus familiaris, BrainCingulateCortex

description: Library name: itox000313

source_name: BrainCingulateCortex

value: BrainCingulateCortex


title: 308, Canis lupus familiaris, BrainCerebellum

description: Library name: itox000308


title: 303, Canis lupus familiaris, BrainAmygdala

description: Library name: itox000303


title: 3, Canis lupus familiaris, AdiposeSubcutaneousAxillary

description: Library name: itox000003


title: 315, Canis lupus familiaris, BrainCingulateCortex

description: Library name: itox000315


title: 316, Canis lupus familiaris, BrainCorpusCallosum

description: Library name: itox000316

source_name: BrainCorpusCallosum

value: BrainCorpusCallosum


title: 318, Canis lupus familiaris, BrainCorpusCallosum

description: Library name: itox000318


title: 21, Canis lupus familiaris, AdrenalCortexAndMedulla

description: Library name: itox000021

source_name: AdrenalCortexAndMedulla

value: AdrenalCortexAndMedulla


title: 301, Canis lupus familiaris, BrainAmygdala

description: Library name: itox000301


title: 305, Canis lupus familiaris, BrainAmygdala

description: Library name: itox000305


title: 306, Canis lupus familiaris, BrainCerebellum

description: Library name: itox000306


title: 310, Canis lupus familiaris, BrainCerebellum

description: Library name: itox000310


title: 309, Canis lupus familiaris, BrainCerebellum

description: Library name: itox000309


title: 311, Canis lupus familiaris, BrainCingulateCortex

description: Library name: itox000311


title: 314, Canis lupus familiaris, BrainCingulateCortex

description: Library name: itox000314


title: 312, Canis lupus familiaris, BrainCingulateCortex

description: Library name: itox000312


title: mice bone marrow, GFP replicate 2, scRNAseq

description: 10x genomics

value: bone marrow


title: 362, Canis lupus familiaris, BrainOccipitalCortex

description: Library name: itox000362

source_name: BrainOccipitalCortex

value: BrainOccipitalCortex


title: 363, Canis lupus familiaris, BrainOccipitalCortex

description: Library name: itox000363


title: 364, Canis lupus familiaris, BrainOccipitalCortex

description: Library name: itox000364


title: 377, Canis lupus familiaris, BrainStriatum

description: Library name: itox000377

source_name: BrainStriatum

value: BrainStriatum


title: 379, Canis lupus familiaris, BrainStriatum

description: Library name: itox000379


title: 373, Canis lupus familiaris, BrainSeptum

description: Library name: itox000373

source_name: BrainSeptum

value: BrainSeptum


title: 367, Canis lupus familiaris, BrainSON

description: Library name: itox000367

source_name: BrainSON

value: BrainSON


title: 372, Canis lupus familiaris, BrainSeptum

description: Library name: itox000372


title: 365, Canis lupus familiaris, BrainOccipitalCortex

description: Library name: itox000365


title: 368, Canis lupus familiaris, BrainSON

description: Library name: itox000368


title: 366, Canis lupus familiaris, BrainOccipitalCortex

description: Library name: itox000366


title: 370, Canis lupus familiaris, BrainSON

description: Library name: itox000370


title: 380, Canis lupus familiaris, BrainStriatum

description: Library name: itox000380


title: 371, Canis lupus familiaris, BrainSeptum

description: Library name: itox000371


title: 317, Canis lupus familiaris, BrainCorpusCallosum

description: Library name: itox000317


title: 378, Canis lupus familiaris, BrainStriatum

description: Library name: itox000378


title: 375, Canis lupus familiaris, BrainSeptum

description: Library name: itox000375


title: 383, Canis lupus familiaris, BrainSubstantiaNigra

description: Library name: itox000383

source_name: BrainSubstantiaNigra

value: BrainSubstantiaNigra


title: 382, Canis lupus familiaris, BrainSubstantiaNigra

description: Library name: itox000382


title: 682, Canis lupus familiaris, EpididymisTail

description: Library name: itox000682

source_name: EpididymisTail

value: EpididymisTail


title: 679, Canis lupus familiaris, EpididymisHead

description: Library name: itox000679

source_name: EpididymisHead

value: EpididymisHead


title: 376, Canis lupus familiaris, BrainStriatum

description: Library name: itox000376


title: 374, Canis lupus familiaris, BrainSeptum

description: Library name: itox000374


title: 48, Canis lupus familiaris, ArteryAortaThoracic

description: Library name: itox000048

source_name: ArteryAortaThoracic

value: ArteryAortaThoracic


title: 369, Canis lupus familiaris, BrainSON

description: Library name: itox000369


title: 49, Canis lupus familiaris, ArteryAortaThoracic

description: Library name: itox000049


title: 683, Canis lupus familiaris, EpididymisTail

description: Library name: itox000683


title: 381, Canis lupus familiaris, BrainSubstantiaNigra

description: Library name: itox000381


title: 684, Canis lupus familiaris, EpididymisTail

description: Library name: itox000684


title: 690, Canis lupus familiaris, EsophagusGastroesophagealJunction

description: Library name: itox000690

source_name: EsophagusGastroesophagealJunction

value: EsophagusGastroesophagealJunction


title: 691, Canis lupus familiaris, EsophagusGastroesophagealJunction

description: Library name: itox000691


title: 692, Canis lupus familiaris, EsophagusGastroesophagealJunction

description: Library name: itox000692


title: 50, Canis lupus familiaris, ArteryAortaThoracic

description: Library name: itox000050


title: 714, Canis lupus familiaris, EyeChoroid

description: Library name: itox000714

source_name: EyeChoroid

value: EyeChoroid


title: 681, Canis lupus familiaris, EpididymisHead

description: Library name: itox000681


title: 717, Canis lupus familiaris, EyeCornea

description: Library name: itox000717

source_name: EyeCornea

value: EyeCornea


title: 718, Canis lupus familiaris, EyeCornea

description: Library name: itox000718


title: 689, Canis lupus familiaris, EsophagusGastroesophagealJunction

description: Library name: itox000689


title: 715, Canis lupus familiaris, EyeChoroid

description: Library name: itox000715


title: 53, Canis lupus familiaris, ArteryAortaThoracic

description: Library name: itox000053


title: 719, Canis lupus familiaris, EyeCornea

description: Library name: itox000719


title: 721, Canis lupus familiaris, EyeCornea

description: Library name: itox000721


title: 727, Canis lupus familiaris, EyeIrisCiliaryBody

description: Library name: itox000727

source_name: EyeIrisCiliaryBody

value: EyeIrisCiliaryBody


title: 734, Canis lupus familiaris, EyeOpticNerve

description: Library name: itox000734

source_name: EyeOpticNerve

value: EyeOpticNerve


title: 733, Canis lupus familiaris, EyeOpticNerve

description: Library name: itox000733


title: 680, Canis lupus familiaris, EpididymisHead

description: Library name: itox000680


title: 729, Canis lupus familiaris, EyeIrisCiliaryBody

description: Library name: itox000729


title: 735, Canis lupus familiaris, EyeOpticNerve

description: Library name: itox000735


title: 716, Canis lupus familiaris, EyeChoroid

description: Library name: itox000716


title: 720, Canis lupus familiaris, EyeCornea

description: Library name: itox000720


title: 731, Canis lupus familiaris, EyeIrisCiliaryBody

description: Library name: itox000731


title: 732, Canis lupus familiaris, EyeOpticNerve

description: Library name: itox000732


title: 728, Canis lupus familiaris, EyeIrisCiliaryBody

description: Library name: itox000728


title: 781, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000781

source_name: GangliaCeliac

value: GangliaCeliac


title: 54, Canis lupus familiaris, ArteryTibial

description: Library name: itox000054

source_name: ArteryTibial

value: ArteryTibial


title: 784, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000784


title: 785, Canis lupus familiaris, GangliaDorsalRootL4

description: Library name: itox000785


title: 786, Canis lupus familiaris, GangliaDorsalRootL4

description: Library name: itox000786


title: 780, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000780


title: 782, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000782


title: 730, Canis lupus familiaris, EyeIrisCiliaryBody

description: Library name: itox000730


title: 783, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000783


title: 790, Canis lupus familiaris, GanglionSuperiorCervical

description: Library name: itox000790

source_name: GanglionSuperiorCervical

value: GanglionSuperiorCervical


title: 791, Canis lupus familiaris, GanglionSuperiorCervical

description: Library name: itox000791


title: 793, Canis lupus familiaris, GanglionSuperiorCervical

description: Library name: itox000793


title: 788, Canis lupus familiaris, GangliaDorsalRootL4

description: Library name: itox000788


title: 787, Canis lupus familiaris, GangliaDorsalRootL4

description: Library name: itox000787


title: 913, Canis lupus familiaris, KidneyMedulla

description: Library name: itox000913

source_name: KidneyMedulla

value: KidneyMedulla


title: 792, Canis lupus familiaris, GanglionSuperiorCervical

description: Library name: itox000792


title: 914, Canis lupus familiaris, KidneyMedulla

description: Library name: itox000914


title: 795, Canis lupus familiaris, GanglionSuperiorCervical

description: Library name: itox000795


title: 915, Canis lupus familiaris, KidneyMedulla

description: Library name: itox000915


title: 794, Canis lupus familiaris, GanglionSuperiorCervical

description: Library name: itox000794


title: 942, Canis lupus familiaris, LiverRightMedialLobe

description: Library name: itox000942

source_name: LiverRightMedialLobe

value: LiverRightMedialLobe


title: 917, Canis lupus familiaris, KidneyMedulla

description: Library name: itox000917


title: 943, Canis lupus familiaris, LiverRightMedialLobe

description: Library name: itox000943


title: 916, Canis lupus familiaris, KidneyMedulla

description: Library name: itox000916


title: 945, Canis lupus familiaris, LiverRightMedialLobe

description: Library name: itox000945


title: 10, Canis lupus familiaris, AdiposeVisceralOmentum

description: Library name: itox000010

source_name: AdiposeVisceralOmentum

value: AdiposeVisceralOmentum


title: 789, Canis lupus familiaris, GangliaDorsalRootL4

description: Library name: itox000789


title: 9, Canis lupus familiaris, AdiposeVisceralOmentum

description: Library name: itox000009


title: 946, Canis lupus familiaris, LiverRightMedialLobe

description: Library name: itox000946


title: 16, Canis lupus familiaris, AdiposeWhiteReproductive

description: Library name: itox000016

source_name: AdiposeWhiteReproductive

value: AdiposeWhiteReproductive


title: 22, Canis lupus familiaris, AdrenalCortexAndMedulla

description: Library name: itox000022

source_name: AdrenalCortexAndMedulla

value: AdrenalCortexAndMedulla


title: 23, Canis lupus familiaris, AdrenalCortexAndMedulla

description: Library name: itox000023


title: 289, Canis lupus familiaris, Bcells

description: Library name: itox000289

source_name: Bcells

value: Bcells


title: 291, Canis lupus familiaris, BoneMarrow

description: Library name: itox000291

source_name: BoneMarrow

value: BoneMarrow


title: 385, Canis lupus familiaris, BrainTemporalCortex

description: Library name: itox000385

source_name: BrainTemporalCortex

value: BrainTemporalCortex


title: 386, Canis lupus familiaris, BrainTemporalCortex

description: Library name: itox000386


title: 290, Canis lupus familiaris, BoneMarrow

description: Library name: itox000290


title: 387, Canis lupus familiaris, BrainTemporalCortex

description: Library name: itox000387


title: 293, Canis lupus familiaris, BoneMarrow

description: Library name: itox000293


title: 389, Canis lupus familiaris, BrainTemporalCortex

description: Library name: itox000389


title: 17, Canis lupus familiaris, AdrenaMedulla

description: Library name: itox000017

source_name: AdrenaMedulla

value: AdrenaMedulla


title: 388, Canis lupus familiaris, BrainTemporalCortex

description: Library name: itox000388


title: 288, Canis lupus familiaris, Bcells

description: Library name: itox000288


title: 394, Canis lupus familiaris, BrainThalamus

description: Library name: itox000394

source_name: BrainThalamus

value: BrainThalamus


title: 944, Canis lupus familiaris, LiverRightMedialLobe

description: Library name: itox000944


title: 391, Canis lupus familiaris, BrainThalamus

description: Library name: itox000391


title: 392, Canis lupus familiaris, BrainThalamus

description: Library name: itox000392


title: 428, Canis lupus familiaris, Cervix

description: Library name: itox000428

source_name: Cervix

value: Cervix


title: 393, Canis lupus familiaris, BrainThalamus

description: Library name: itox000393


title: 390, Canis lupus familiaris, BrainThalamus

description: Library name: itox000390


title: 395, Canis lupus familiaris, BrownFat

description: Library name: itox000395

source_name: BrownFat

value: BrownFat


title: 693, Canis lupus familiaris, EsophagusGastroesophagealJunction

description: Library name: itox000693

source_name: EsophagusGastroesophagealJunction

value: EsophagusGastroesophagealJunction


title: 292, Canis lupus familiaris, BoneMarrow

description: Library name: itox000292


title: 5, Canis lupus familiaris, AdiposeSubcutaneousAxillary

description: Library name: itox000005

source_name: AdiposeSubcutaneousAxillary

value: AdiposeSubcutaneousAxillary


title: 384, Canis lupus familiaris, BrainSubstantiaNigra

description: Library name: itox000384

source_name: BrainSubstantiaNigra

value: BrainSubstantiaNigra


title: 429, Canis lupus familiaris, Cervix

description: Library name: itox000429


title: 697, Canis lupus familiaris, EsophagusMucosa

description: Library name: itox000697

source_name: EsophagusMucosa

value: EsophagusMucosa


title: 698, Canis lupus familiaris, EsophagusMuscularis

description: Library name: itox000698

source_name: EsophagusMuscularis

value: EsophagusMuscularis


title: 695, Canis lupus familiaris, EsophagusMucosa

description: Library name: itox000695


title: 696, Canis lupus familiaris, EsophagusMucosa

description: Library name: itox000696


title: 699, Canis lupus familiaris, EsophagusMuscularis

description: Library name: itox000699


title: 694, Canis lupus familiaris, EsophagusMucosa

description: Library name: itox000694


title: 700, Canis lupus familiaris, EsophagusMuscularis

description: Library name: itox000700


title: 51, Canis lupus familiaris, ArteryAortaThoracic

description: Library name: itox000051

source_name: ArteryAortaThoracic

value: ArteryAortaThoracic


title: 701, Canis lupus familiaris, EsophagusMuscularis

description: Library name: itox000701


title: 712, Canis lupus familiaris, EyeChoroid

description: Library name: itox000712

source_name: EyeChoroid

value: EyeChoroid


title: 6, Canis lupus familiaris, AdiposeSubcutaneousAxillary

description: Library name: itox000006


title: 711, Canis lupus familiaris, EyeChoroid

description: Library name: itox000711


title: 52, Canis lupus familiaris, ArteryAortaThoracic

description: Library name: itox000052


title: 7, Canis lupus familiaris, AdiposeSubcutaneousAxillary

description: Library name: itox000007


title: 802, Canis lupus familiaris, GutCecum

description: Library name: itox000802

source_name: GutCecum

value: GutCecum


title: 804, Canis lupus familiaris, GutCecum

description: Library name: itox000804


title: 806, Canis lupus familiaris, GutCecum

description: Library name: itox000806


title: 803, Canis lupus familiaris, GutCecum

description: Library name: itox000803


title: 805, Canis lupus familiaris, GutCecum

description: Library name: itox000805


title: 702, Canis lupus familiaris, EsophagusMuscularis

description: Library name: itox000702


title: 807, Canis lupus familiaris, GutCecum

description: Library name: itox000807


title: 813, Canis lupus familiaris, GutDuodenum

description: Library name: itox000813

source_name: GutDuodenum

value: GutDuodenum


title: 899, Canis lupus familiaris, KidneyCortex

description: Library name: itox000899

source_name: KidneyCortex

value: KidneyCortex


title: 811, Canis lupus familiaris, GutColonTransverse

description: Library name: itox000811

source_name: GutColonTransverse

value: GutColonTransverse


title: 8, Canis lupus familiaris, AdiposeVisceralOmentum

description: Library name: itox000008

source_name: AdiposeVisceralOmentum

value: AdiposeVisceralOmentum


title: 808, Canis lupus familiaris, GutColonTransverse

description: Library name: itox000808


title: 901, Canis lupus familiaris, KidneyCortex

description: Library name: itox000901


title: 820, Canis lupus familiaris, GutIleum

description: Library name: itox000820

source_name: GutIleum

value: GutIleum


title: 18, Canis lupus familiaris, AdrenalCortexAndMedulla

description: Library name: itox000018

source_name: AdrenalCortexAndMedulla

value: AdrenalCortexAndMedulla


title: 815, Canis lupus familiaris, GutDuodenum

description: Library name: itox000815


title: 816, Canis lupus familiaris, GutDuodenum

description: Library name: itox000816


title: 818, Canis lupus familiaris, GutDuodenum

description: Library name: itox000818


title: 809, Canis lupus familiaris, GutColonTransverse

description: Library name: itox000809


title: 903, Canis lupus familiaris, KidneyCortex

description: Library name: itox000903


title: 912, Canis lupus familiaris, KidneyMedulla

description: Library name: itox000912

source_name: KidneyMedulla

value: KidneyMedulla


title: 810, Canis lupus familiaris, GutColonTransverse

description: Library name: itox000810


title: 900, Canis lupus familiaris, KidneyCortex

description: Library name: itox000900


title: 20, Canis lupus familiaris, AdrenalCortexAndMedulla

description: Library name: itox000020


title: 812, Canis lupus familiaris, GutColonTransverse

description: Library name: itox000812


title: 814, Canis lupus familiaris, GutDuodenum

description: Library name: itox000814


title: 19, Canis lupus familiaris, AdrenalCortexAndMedulla

description: Library name: itox000019


title: 1, Canis lupus familiaris, AdiposeRepro

description: Library name: itox000001

source_name: AdiposeRepro

value: AdiposeRepro


title: 902, Canis lupus familiaris, KidneyCortex

description: Library name: itox000902


title: 2, Canis lupus familiaris, AdiposeSubcutaneousAxillary

description: Library name: itox000002


title: 821, Canis lupus familiaris, GutIleum

description: Library name: itox000821


title: 819, Canis lupus familiaris, GutIleum

description: Library name: itox000819


title: 817, Canis lupus familiaris, GutDuodenum

description: Library name: itox000817


title: 822, Canis lupus familiaris, GutIleum

description: Library name: itox000822


title: 11, Canis lupus familiaris, AdiposeVisceralOmentum

description: Library name: itox000011


title: 13, Canis lupus familiaris, AdiposeWhiteReproductive

description: Library name: itox000013

source_name: AdiposeWhiteReproductive

value: AdiposeWhiteReproductive


title: 12, Canis lupus familiaris, AdiposeVisceralOmentum

description: Library name: itox000012


title: 342, Canis lupus familiaris, BrainION

description: Library name: itox000342

source_name: BrainION

value: BrainION


title: 341, Canis lupus familiaris, BrainION

description: Library name: itox000341


title: 346, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000346

source_name: BrainInfenorparietal

value: BrainInfenorparietal


title: 345, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000345


title: 348, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000348


title: 350, Canis lupus familiaris, BrainMotorCortex

description: Library name: itox000350

source_name: BrainMotorCortex

value: BrainMotorCortex


title: 343, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000343


title: 344, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000344


title: 347, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000347


title: 352, Canis lupus familiaris, BrainMotorCortex

description: Library name: itox000352


title: 349, Canis lupus familiaris, BrainInfenorparietal

description: Library name: itox000349


title: 351, Canis lupus familiaris, BrainMotorCortex

description: Library name: itox000351


title: 354, Canis lupus familiaris, BrainMotorCortex

description: Library name: itox000354


title: 355, Canis lupus familiaris, BrainMotorCortex

description: Library name: itox000355


title: 361, Canis lupus familiaris, BrainOccipitalCortex

description: Library name: itox000361

source_name: BrainOccipitalCortex

value: BrainOccipitalCortex


title: 359, Canis lupus familiaris, BrainNucleiAccumbens

description: Library name: itox000359

source_name: BrainNucleiAccumbens

value: BrainNucleiAccumbens


title: 353, Canis lupus familiaris, BrainMotorCortex

description: Library name: itox000353


title: 58, Canis lupus familiaris, ArteryTibial

description: Library name: itox000058

source_name: ArteryTibial

value: ArteryTibial


title: 765, Canis lupus familiaris, GallBladder

description: Library name: itox000765

source_name: GallBladder

value: GallBladder


title: 357, Canis lupus familiaris, BrainNucleiAccumbens

description: Library name: itox000357


title: 356, Canis lupus familiaris, BrainNucleiAccumbens

description: Library name: itox000356


title: 358, Canis lupus familiaris, BrainNucleiAccumbens

description: Library name: itox000358


title: 360, Canis lupus familiaris, BrainNucleiAccumbens

description: Library name: itox000360


title: 768, Canis lupus familiaris, GallBladder

description: Library name: itox000768


title: 766, Canis lupus familiaris, GallBladder

description: Library name: itox000766


title: 778, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000778

source_name: GangliaCeliac

value: GangliaCeliac


title: 779, Canis lupus familiaris, GangliaCeliac

description: Library name: itox000779


title: 825, Canis lupus familiaris, GutJejunum

description: Library name: itox000825

source_name: GutJejunum

value: GutJejunum


title: 823, Canis lupus familiaris, GutJejunum

description: Library name: itox000823


title: 462, Canis lupus familiaris, AoEC

description: Library name: itox000462

source_name: AoEC

value: AoEC


title: 767, Canis lupus familiaris, GallBladder

description: Library name: itox000767


title: 827, Canis lupus familiaris, GutJejunum

description: Library name: itox000827


title: 826, Canis lupus familiaris, GutJejunum

description: Library name: itox000826


title: 764, Canis lupus familiaris, GallBladder

description: Library name: itox000764


title: 829, Canis lupus familiaris, HeartArteryCoronary

description: Library name: itox000829

source_name: HeartArteryCoronary

value: HeartArteryCoronary


title: 832, Canis lupus familiaris, HeartArteryCoronary

description: Library name: itox000832


title: 830, Canis lupus familiaris, HeartArteryCoronary

description: Library name: itox000830


title: 836, Canis lupus familiaris, HeartAtrialAppendage

description: Library name: itox000836

source_name: HeartAtrialAppendage

value: HeartAtrialAppendage


title: 838, Canis lupus familiaris, HeartLeftAtrium

description: Library name: itox000838

source_name: HeartLeftAtrium

value: HeartLeftAtrium


title: 831, Canis lupus familiaris, HeartArteryCoronary

description: Library name: itox000831