description:
tumor DNA from breast cancer patient S000868.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: tumor DNA from breast cancer patient S010922.l.d.mth.tsv

status: Public on Mar 03 2025

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing:
Beta values, representing the level of methylation, were computed in a sample-by-sample context using the minfi R package v1.44 function preprocessNoob() and next Infinium probe normalized using the approach described by PMID:26923702
processed value definition: beta-value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer

label_protocol: Standard Illumina protocol

extract_protocol: Tumor DNA was extracted from RNAlater preserved tissue using Qiagen AllPrep kit according to manufacturer's instructions.

tag: tissue

value: breast cancer

value: TNBC

tag: Sex

value: Female


title: Bulk sample for Individual 69

city: Exeter

first: Alice

last: Franklin

address: Stocker Road

country: United Kingdom

institute: University of Exeter

hyb_protocol: Nuclei samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Nuclei samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Raw data (IDAT files) were imported using the watermelon R package readEPIC function. Data was then pre-processed using dasen function.
Normalized beta values

label: Cy5 and Cy3

source_name: Pre-frontal cortex

label_protocol: 500 ng DNA from each nuclei sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gold Kit (Cambridge Bioscience, UK) according to the manufacturer's standard protocol.

extract_protocol: Genomic DNA was extracted from frozen nuclei aliquots using a modified proteinase K-based extraction method.

tag: cell type

value: Bulk

value: Pre-frontal cortex

tag: ID

value: F

tag: basename


title: Bulk sample for Individual 68

value: M


title: tumor DNA from breast cancer patient S010919.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010902.l.d.mth.tsv


title: Bulk sample for Individual 66


title: Bulk sample for Individual 65


title: tumor DNA from breast cancer patient S010832.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010710.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010611.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010605.l.d.mth.tsv


title: Bulk sample for Individual 62


title: Bulk sample for Individual 64


title: Bulk sample for Individual 67


title: tumor DNA from breast cancer patient S010602.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010491.l.d.mth.tsv


title: Bulk sample for Individual 60


title: Bulk sample for Individual 59


title: tumor DNA from breast cancer patient S010320.l.d.mth.tsv


title: Bulk sample for Individual 61


title: tumor DNA from breast cancer patient S010410.l.d.mth.tsv


title: Bulk sample for Individual 58


title: tumor DNA from breast cancer patient S010248.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010302.l.d.mth.tsv


title: Bulk sample for Individual 63


title: Bulk sample for Individual 55


title: tumor DNA from breast cancer patient S010229.l.d.mth.tsv


title: Bulk sample for Individual 57


title: tumor DNA from breast cancer patient S010563.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010086.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010115.l.d.mth.tsv


title: tumor DNA from breast cancer patient S009990.l.d.mth.tsv


title: tumor DNA from breast cancer patient S010039.l.d.mth.tsv


title: Bulk sample for Individual 53


title: Bulk sample for Individual 52


title: Bulk sample for Individual 51


title: Bulk sample for Individual 56


title: tumor DNA from breast cancer patient S009968.l.d.mth.tsv


title: Bulk sample for Individual 54


title: Bulk sample for Individual 50


title: Bulk sample for Individual 80


title: Bulk sample for Individual 48


title: tumor DNA from breast cancer patient S009893.l.d.mth.tsv


title: Bulk sample for Individual 47


title: Bulk sample for Individual 49


title: tumor DNA from breast cancer patient S011076.l.d.mth.tsv


title: tumor DNA from breast cancer patient S009860.l.d.mth.tsv


title: tumor DNA from breast cancer patient S009856.l.d.mth.tsv


title: tumor DNA from breast cancer patient S009931.l.d.mth.tsv


title: Bulk sample for Individual 45


title: Bulk sample for Individual 46


title: tumor DNA from breast cancer patient S009748.l.d.mth.tsv


title: Bulk sample for Individual 44


title: Bulk sample for Individual 43


title: Bulk sample for Individual 42


title: tumor DNA from breast cancer patient S009673.l.d.mth.tsv


title: tumor DNA from breast cancer patient S009560.l.d.mth.tsv


title: Bulk sample for Individual 37


title: tumor DNA from breast cancer patient S008912.l.d.mth.tsv


title: Bulk sample for Individual 36


title: Bulk sample for Individual 39


title: Bulk sample for Individual 40


title: tumor DNA from breast cancer patient S009831.l.d.mth.tsv


title: tumor DNA from breast cancer patient S009357.l.d.mth.tsv


title: Bulk sample for Individual 38


title: tumor DNA from breast cancer patient S009746.l.d.mth.tsv


title: tumor DNA from breast cancer patient S008796.l.d.mth.tsv


title: Bulk sample for Individual 41


title: Bulk sample for Individual 35


title: tumor DNA from breast cancer patient S008775.l.d.mth.tsv


title: Bulk sample for Individual 34


title: Bulk sample for Individual 33


title: tumor DNA from breast cancer patient S008732.l.d.mth.tsv


title: tumor DNA from breast cancer patient S008283.l.d.mth.tsv


title: Bulk sample for Individual 32


title: Bulk sample for Individual 31


title: Bulk sample for Individual 30


title: tumor DNA from breast cancer patient S009360.l.d.mth.tsv


title: Bulk sample for Individual 29


title: tumor DNA from breast cancer patient S008046.l.d.mth.tsv


title: Bulk sample for Individual 28


title: tumor DNA from breast cancer patient S007987.l.d.mth.tsv


title: Bulk sample for Individual 26


title: tumor DNA from breast cancer patient S008630.l.d.mth.tsv


title: Bulk sample for Individual 27


title: Bulk sample for Individual 25


title: tumor DNA from breast cancer patient S007723.l.d.mth.tsv


title: tumor DNA from breast cancer patient S006996.l.d.mth.tsv


title: Bulk sample for Individual 24


title: Klf6fl/fl:Lyz2cre-TNF-3

type: SRA

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

country: USA

institute: CWRU

description:
Library name: Sample 12
K6TNvsLysMTN.txt

library_source: transcriptomic

data_processing:
Pooled libraries were diluted, denatured, and loaded onto the Illumina NextSeq 550 System using a high output flowcell.
The aligned reads were then analyzed with Cufflinks (Version name: 2.2.1) to obtain gene-level expression data using the GENCODE gene annotation for M32 (Version-GRCm39) and reported as fragments per kilobase per million reads mapped (FPKM).
Differential expression analysis was also performed and significantly differentially expressed genes were defined using an adjusted p-value < 0.05 (FDR corrected).
Assembly: mm10
Supplementary files format and content: FPKM for each sample in TSV format.

molecule: total RNA

organism: Mus musculus

source_name: BMDMs

growth_protocol: BMDMs were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, 10 g/ml streptomycin, and 2 mM glutamine in a humidified incubator (5% CO2 and 37°C).

extract_protocol:
Total RNA was isolated from indicated samples using the High Pure RNA Isolation Kit (Roche)
cDNA library for RNAseq was generated from 150 ng of total RNA using the Illumina (San Diego, CA) TruSeq Stranded Total RNA kit with Ribo Zero Gold for rRNA removal according to the manufacturer’s protocol.

treatment_protocol: BMDMs were treated with 10ng/ml TNF for 6 hours in humidified incubator.

value: BMDMs

value: Macrophage

tag: genotype

tag: treatment

value: TNF


title: Bulk sample for Individual 23


title: tumor DNA from breast cancer patient S008068.l.d.mth.tsv


title: tumor DNA from breast cancer patient S008058.l.d.mth.tsv


title: tumor DNA from breast cancer patient S006938.l.d.mth.tsv


title: Klf6fl/fl:Lyz2cre-TNF-1

description:
Library name: Sample 10
K6TNvsLysMTN.txt


title: tumor DNA from breast cancer patient S009587.l.d.mth.tsv


title: tumor DNA from breast cancer patient S006848.l.d.mth.tsv


title: Bulk sample for Individual 21


title: Bulk sample for Individual 22


title: tumor DNA from breast cancer patient S006775.l.d.mth.tsv


title: Lyz2cre-TNF-2

description:
Library name: Sample 8
K6TNvsLysMTN.txt


title: Lyz2cre-TNF-1

description:
Library name: Sample 7
K6TNvsLysMTN.txt


title: Klf6fl/fl:Lyz2cre-TNF-2

description:
Library name: Sample 11
K6TNvsLysMTN.txt


title: Bulk sample for Individual 20


title: tumor DNA from breast cancer patient S006275.l2.d.mth.tsv


title: Klf6fl/fl:Lyz2cre-Control-3

description:
Library name: Sample 6
K6ConvsLysMCon.txt

value: Control


title: tumor DNA from breast cancer patient S007986.l.d.mth.tsv


title: Klf6fl/fl:Lyz2cre-Control-2

description:
Library name: Sample 5
K6ConvsLysMCon.txt


title: Klf6fl/fl:Lyz2cre-Control-1

description:
Library name: Sample 4
K6ConvsLysMCon.txt


title: Bulk sample for Individual 19


title: Lyz2cre-TNF-3

description:
Library name: Sample 9
K6TNvsLysMTN.txt


title: tumor DNA from breast cancer patient S005404.l3.d.mth.tsv


title: Lyz2cre-Control-3

description:
Library name: Sample 3
K6ConvsLysMCon.txt


title: Lyz2cre-Control-2

description:
Library name: Sample 2
K6ConvsLysMCon.txt


title: Bulk sample for Individual 18


title: Lyz2cre-Control-1

description:
Library name: Sample 1
K6ConvsLysMCon.txt


title: tumor DNA from breast cancer patient S004240.l2.d.mth.tsv


title: Bulk sample for Individual 17


title: tumor DNA from breast cancer patient S002798.l.d.mth.tsv


title: Bulk sample for Individual 16


title: Bulk sample for Individual 15


title: Bulk sample for Individual 12


title: Bulk sample for Individual 13


title: Female BALB/c infected mouse stomach 4

city: Houston

first: Jill

middle: E

last: Weatherhead

state: TX

address: 1102 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description: Library name: sample9

data_processing:
Raw reads were used with the nf-core/rnaseq pipeline (v3.14.0) to trim the adaptors and filter reads using fastp and salmon-based transcript pseudocounts were generated.
Salmon transcript pseudocounts (quant.sf files generated in the nf-core/rnaseq pipeline) were collapsed to the gene level using tximportData package and  the tx2gene.tsv file generated by the nf-core/rnaseq pipeline. The tx2gene.tsv file is found in the github associated with this accession, check the BioProject for the URL. The gene-level pseudocounts were imported to DEseq2 (v1.40.2) for differential expression gene analysis.
Assembly: GRCm39_109
Supplementary files format and content: tsv files, contains the raw salmon transcript pseudocounts in TPM for RNAseq samples using the GRCm39_109 assembly

molecule: polyA RNA

source_name: stomach

extract_protocol:
Stomach tissues from mice post multiple infections were collected 4 days p.i. into 1mL of 1x DNA/RNA Shield reagent (R1100-50, Zymo Research, Irvine, CA) in a 2mL ZR bashingbead lysis tube (S6012-50, Zymo Research, Irvine, CA). The tissues were lysed using a Precellys 24 homogenizer (03119.200.RD000, Bertin Technologies, Montigny-le-Bretonneux, France) using the 6m/sec setting for 40s. The homogenates were transferred to 1.5mL DNA LoBind tubes (022431021, Eppendorf, Hamburg, Germany) and shipped on dry ice to SeqCenter (Pittsburgh, PA) for RNA extraction, polyA purification, and RNA sequencing. RNA was extracted using the Quick-RNA miniprep kit (R1054, Zymo Research, Irvine, CA).
Library preparation was carried out by SeqCenter (Pittsburgh, PA) using the Illumina Stranded Total RNA Prep ligation with Ribo-Zero Plus kit and 10bp unique dula indices. Sequencing was performed on a NovaSeq X Plus for 150bp paired-end reads.

treatment_protocol: Infected with an inoculum of 2,500 embryonated Ascaris suum eggs twice weekly for 2 weeks. Tissue harvested 18 days after initial infection.

value: stomach

tag: infection

value: Ascaris suum


title: Female BALB/c infected mouse stomach 5

description: Library name: sample10


title: Bulk sample for Individual 14


title: White eye female 5

city: Grand Rapids

first: April

last: Rickle

state: MI

address: 333 Bostwick Avenue

department: Metabolism and Nutritional Programming

institute: Van Andel Institute

description:
Library name: WF5
Column name in normalized_counts_females.csv: WF5

data_processing:
Low-quality read ends were trimmed followed by adapter sequence removal using Trimgalore v0.6.1. The --quality and –length parameters were set to 20
Trimmed reads were then aligned to the r6.60 version of the Drosophila genome using STAR v2.5.4b57 with default parameters
ReadsPerGene.out.tab files were imported into R v4.4.158 to obtain a counts table
Assembly: Drosophila r6.60
Supplementary files format and content: .csv files include raw and normalized counts for each sample

organism: Drosophila melanogaster

source_name: Whole heads

extract_protocol:
Heads were collected under CO2 anesthesia and snap frozen in liquid nitrogen. Heads were then homogenized in 500 µL Trizol and RNA was extracted according to manufacturer's protocols. 500 ng of RNA was used for library construction.
RNA libraries for RNAseq were constructed using the Kapa mRNA HyperPrep kit according to manufacturer's instructions.

value: Whole heads

tag: genetic background

value: female

value: w-

tag: replicate


title: Female BALB/c infected mouse stomach 2

description: Library name: sample7


title: Female BALB/c infected mouse stomach 3

description: Library name: sample8


title: White eye female 4

description:
Library name: WF4
Column name in normalized_counts_females.csv: WF4


title: Female BALB/c infected mouse stomach 1

description: Library name: sample6


title: WAT_201

type: RNA

city: Tokyo

first: Naoki

last: Kobayashi

address: 1-21-1 Toyama, Shinjuku

department: Dept. of Molecular Diabetic Medicine

country: Japan

institute: National Center for Global Health and Medicine

hyb_protocol: labelled cRNA was hybridized onto the SurePrint G3 Human GE Microarray following the manufacturer's instructions.

scan_protocol: Hybridization signals were quantified using an Agilent Technologies Scanner G2505B

data_processing: Data analysis was conducted using Limma package implemented in R/Bioconductor with Bonferroni correction.

source_name: adipose

label_protocol: Cy3 labeled cRNA was prepared from extracted RNA using labeling kit, followed by RNAeasy column purification.

extract_protocol: Total RNA was extracted from adipose tissue samples using the Qiagen RNeasy Lipid Tissue Mini Kit following the manufacturer's instructions.

tag: age

tag: bmi


title: WAT_199

value: Male


title: Bulk sample for Individual 11


title: WAT_192


title: White eye female 3

description:
Library name: WF3
Column name in normalized_counts_females.csv: WF3


title: WAT_198


title: WAT_196


title: WAT_200


title: WAT_202


title: WAT_195


title: Female BALB/c naïve mouse stomach 5

description: Library name: sample5

treatment_protocol: PBS via oral gavage twice per week for 2 weeks. Tissue harvested 18 days after first gavage.

value: control


title: Bulk sample for Individual 10


title: WAT_191


title: White eye female 2

description:
Library name: WF2
Column name in normalized_counts_females.csv: WF2


title: WAT_197


title: WAT_194


title: WAT_193


title: Female BALB/c naïve mouse stomach 4

description: Library name: sample4


title: White eye female 1

description:
Library name: WF1
Column name in normalized_counts_females.csv: WF1


title: Female BALB/c naïve mouse stomach 3

description: Library name: sample3


title: tumor DNA from breast cancer patient S008907.l.d.mth.tsv

value: breast cancer

value: TNBC


title: Bulk sample for Individual 9

value: Bulk


title: Bulk sample for Individual 8

value: Pre-frontal cortex


title: White eye male 5

description:
Library name: WM5
Column name in normalized_counts_males.csv: WM5

value: male


title: WAT_190


title: Bulk sample for Individual 7

value: F


title: Female BALB/c naïve mouse stomach 2

description: Library name: sample2


title: WAT_189


title: WAT_188

value: Female


title: WAT_187


title: White eye male 3

description:
Library name: WM3
Column name in normalized_counts_males.csv: WM3


title: White eye male 2

description:
Library name: WM2
Column name in normalized_counts_males.csv: WM2


title: Bulk sample for Individual 5


title: Bulk sample for Individual 4

value: M


title: Bulk sample for Individual 3


title: White eye male 1

description:
Library name: WM1
Column name in normalized_counts_males.csv: WM1


title: C2_MDA594

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

description: Library name: C2_MDA594

library_source: genomic

data_processing:
The steps of data processing were as follows: (1) Discard a pair of reads if either one of them contains adapter contamination (>10 nucleotides aligned to the adapter, allowing ≤ 10% mismatches); (2) Discard a pair of reads if more than 10% of bases are uncertain (read as N) in either one of the reads; (3) Discard a pair of reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one of the reads. Total reads number, raw data, error rate, and percentage of reads with Q30 (the percent of bases with Phred-scaled quality scores greater than 30) were calculated and summarized. Filtered reads were used as clean data for subsequent analysis.
Assembly: Clean data were mapped to the reference genome (mm39) by Burrows-Wheeler Aligner (BWA) software to generate BAM files. Subsequently, Sambamba was used to sort BAM files according to chromosome position. Picard tools were then utilized to merge BAM files and mark duplicate reads. GATK HaplotypeCaller was used to call germline SNP and InDel, while the use of GATK VariantFiltration module was carried to filter germline SNP and InDel. Annovar was use to annotate variants
Supplementary files format and content: Excel xlsx format with annotated variants

source_name: Breast cancer Mouse Derived Allograft

extract_protocol:
DNeasy Blood & Tissue Kit (Qiagen)
The libraries were hybridized in the buffer with biotin-labeled probes, and magnetic beads with streptavidin were used to capture the exons of genes. Subsequently, non-hybridized fragments were washed out and probes were digested. The captured libraries were enriched by PCR amplification. The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms with PE150 strategy, according to the effective library concentration and the data amount required.

value: Breast cancer Mouse Derived Allograft


title: Bulk sample for Individual 6


title: Bulk sample for Individual 2


title: C1_MDA594

description: Library name: C1_MDA594


title: Red eye female 4

description:
Library name: RF4
Column name in normalized_counts_females.csv: RF4

value: w+


title: Female BALB/c naïve mouse stomach 1

description: Library name: sample1

value: stomach


title: T1_MDA594OR1

description: Library name: T1_MDA594OR1


title: MDA594OR2_1356_22_Olap_100_12L_90CF

description: Library name: ABA45016

data_processing:
RNA-seq reads were mapped against the mouse reference genome (GRCm39) with STAR 2.7.10a using ENCODE parameters
Genes were quantified with RSEM 1.3.1 using the gencode M36 annotation
Differential expression was performed with limma using the voom transformation of the counts
Assembly: RNA-seq reads were mapped against the mouse reference genome (GRCm39) with STAR 2.7.10a using ENCODE parameters.
Supplementary files format and content: Normalized logCPM
Supplementary files format and content: Excel xlsx format

extract_protocol:
RNeasy Mini Kit (#74106, Qiagen)
KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche)

value: Treated


title: White eye male 4

description:
Library name: WM4
Column name in normalized_counts_males.csv: WM4

value: Whole heads


title: Bulk sample for Individual 1


title: WAT_183


title: Red eye female 3

description:
Library name: RF3
Column name in normalized_counts_females.csv: RF3

value: female


title: WAT_184


title: WAT_181


title: Non-neuronal sample for Individual 107

value: Non-neuronal

tag: antibody


title: MDA594OR2_1356_22_Olap_100_11R_7A7D

description: Library name: ABA45015


title: WAT_186

value: Male


title: WAT_185


title: WAT_182


title: Red eye female 2

description:
Library name: RF2
Column name in normalized_counts_females.csv: RF2


title: Neuronal sample for Individual 107

value: Neuronal


title: Red eye female 1

description:
Library name: RF1
Column name in normalized_counts_females.csv: RF1


title: MDA594OR2_1303_22_Olap_100_11L_78FD

description: Library name: ABA44507


title: Non-neuronal sample for Individual 101


title: MDA594OR2_1356_22_Control_1R_7ED2

description: Library name: ABA45013

value: Control


title: Red eye male 5

description:
Library name: RM5
Column name in normalized_counts_males.csv: RM5


title: MDA594OR2_1356_22_Control_1L_7ED2

description: Library name: ABA45012


title: T2_MDA594OR2

description: Library name: T2_MDA594OR2


title: Neuronal sample for Individual 100


title: MDA594OR1_1346_22_Olap_100_11R_79F5

description: Library name: ABA45011


title: WAT_179


title: WAT_180


title: Red eye male 4

description:
Library name: RM4
Column name in normalized_counts_males.csv: RM4


title: Red eye male 3

description:
Library name: RM3
Column name in normalized_counts_males.csv: RM3


title: MDA594OR1_1325_22_Olap_100_11R_7985

description: Library name: ABA45002


title: WAT_178


title: WAT_177


title: Neuronal sample for Individual 101


title: Non-neuronal sample for Individual 106


title: Non-neuronal sample for Individual 100


title: WAT_176


title: MDA594OR1_1295_22_Olap_100_11L_740A

description: Library name: ABA44504


title: MDA594OR1_1346_22_Control_1R_7B69

description: Library name: ABA45010


title: Red eye male 1

description:
Library name: RM1
Column name in normalized_counts_males.csv: RM1


title: E. faecalis-C. albicans 48hr dual-species biofilm, rep 2

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: Library name: Dualspecies2

data_processing:
Sequencing was done on a NextSeq2000 giving 2x50bp reads.
Demultiplexing, quality control, and adapter trimming were performed with bcl-convert (v3.9.3).
Read mapping was performed with HISAT2.
Read quantification was performed using Subread's featureCounts functionality.
Read counts were loaded into R and were nomalized using edgeR's Trimmed Mean of M avlues (TMM) algorithm. Subsequent values were then converted to counts per million (cpm).  Differential expression analysis was performed using edgeR's exact test for differences between two groups of negative-binomial counts with an estimated dispersion values of 1.
Assembly: CP002621.1
Supplementary files format and content: The processed .csv data files indicate the number of reads obtained for each open reading frame (OG1RF_xxxxx) for each sample after each of two original raw data files (.fastq) were compiled and mapped against the E. faecalis OG1RF genome (CP002621.1) as described above.

organism: Enterococcus faecalis OG1RF

source_name: E. faecalis-C.albicans dualspecies biofilm

growth_protocol: E. faecalis cells were grown overnight, washed in PBS, and resuspended in BHI medium supplemented with 20mM glucose (BHIG).  These cultures were normalized to OD600 = 0.5.  Monospecies biofilms were initiated by adding 5mL of the E. faecalis suspension, while dualspecies biofilms were initiated by adding 2.5mL each of the E. faecalis and C. albians suspensions to the wells of a 6-well plate.

extract_protocol:
After a total of 48hrs incubation, the media was removed and the cells of each well were suspended in 1mL of RNA Protect Bacterial Reagent (Qiagen).  The biofilms were mechanically removed using a cell scraper, homogenized, and incubated for 5 min at room temperature.  Three technical replicates were combined in conical tubes and the cells harvested by centrifugation. These pellets were again suspended in 1mL RNAProtect Bacteria Reagent, supplemented with 10mg mL-1 lysozyme.  RNA was then extracted using the Purelink RNA Mini kit (ThermoFisher).
Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.  All sequencing and subsequent steps were performed by SeqCenter (formerly MiGS).

treatment_protocol: Media for all biofilms was refreshed at 24hrs.

tag: biofilm type

value: Dual species


title: Red eye male 2

description:
Library name: RM2
Column name in normalized_counts_males.csv: RM2


title: MDA594OR1_1325_22_Olap_100_11L_7985

description: Library name: ABA45001


title: Neuronal sample for Individual 106


title: Neuronal sample for Individual 105


title: WAT_175


title: Non-neuronal sample for Individual 105


title: MDA594OR1_1325_22_Control_1R_9059

description: Library name: ABA44509


title: E. faecalis-C. albicans 48hr dual-species biofilm, rep 1

description: Library name: Dualspecies1

value: E. faecalis-C.albicans dualspecies biofilm


title: Non-neuronal sample for Individual 127

value: Pre-frontal cortex


title: E. faecalis 48hr mono-species biofilm, rep 3

description: Library name: Monospecies3

source_name: E. faecalis monospecies biofilm

value: Mono species

value: E. faecalis monospecies biofilm


title: Neuronal sample for Individual 127

value: F


title: MDA594OR1_1325_22_Control_1L_9059

description: Library name: ABA44508


title: MDA594_1344_22_Olap_100_12L_7D4A

description: Library name: ABA45009


title: WAT_173

value: Female


title: WAT_172


title: WAT_170


title: WAT_169


title: Neuronal sample for Individual 104


title: MDA594_1328_22_Olap_100_11R_6C7D

description: Library name: ABA45007

value: Breast cancer Mouse Derived Allograft


title: E. faecalis 48hr mono-species biofilm, rep 2

description: Library name: Monospecies2


title: E. faecalis 48hr mono-species biofilm, rep 1

description: Library name: Monospecies1


title: WAT_174


title: MDA594_1328_22_Olap_100_11L_6C7D

description: Library name: ABA45005


title: Non-neuronal sample for Individual 104


title: MDA594_1344_22_Control_1L_88F8

description: Library name: ABA45008


title: WAT_171


title: shRMST SOX2 ChIP-seq rep 1

city: Toronto

first: Housheng

middle: Hansen

last: He

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
Library name: shRMST_SOX2_rep1
Pair-end 150bp

data_processing:
Quality of all raw sequencing data was verified with FastQC (v0.11.5). Fastp (v0.23.1) was used to trim adapters and polyG tails. Trimmed fastq was then mapped to GRCh38 human genome with Bowtie2 (v2.4.5) with -- very-sensitive-local parameter. Deduplication of PCR products was performed with picard (v2.10.9). Deduplicated SAM file was converted and sorted to BAM with samtools (v.1.14). Bigwig was generated from BAM with deepTools (v3.5.1) bamCoverage function, normalized to sequencing depth, and visualized in IGV (v2.5.2). ChIP peaks were called with MACS2 (v2.2.5) with -f BAMPE mode and FDR cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: SHP77 cells cultured in RPMI with 10% FBS and 1% penicillin-streptomycin. Cells were infected by shRNA lentivirus and selected with 3 ug/mL puromycin for 7 days.

extract_protocol:
NKX2-1 antibody (EMD Millipore, cat. #07-601) and SOX2 antibody (Abcam, cat. #ab97959) were used to perform ChIP-seq in 8 million SHP77 cells. ChIP DNA was decrosslinked at 65C overnight and purified with MinElute PCR purification kit (Qiagen, cat. #28006).
ChIP-seq library was generated with Takara ThruPLEX DNA-seq kit (cat. #R400677) according to the manufacturer’s protocol. SMARTer DNA Unique Dual Index Kit - 24U Set B (Takara, cat. #R400666) was used to index and multiplex the samples for sequencing. AMPure XP beads (Beckman Coulter, cat. #A63881) were used for library size selection to 200-500 bp and final library quality was evaluated on BioAnalyzer 2100 with Agilent high sensitivity DNA kit (cat. #5067-4626).

tag: cell line

value: SCLC cell line

value: circRMST shRNA

value: ChIP


title: shRMST SOX2 ChIP-seq rep 2

description:
Library name: shRMST_SOX2_rep2
Pair-end 150bp


title: Non-neuronal sample for Individual 126


title: shRMST NKX2-1 ChIP-seq rep 2

description:
Library name: shRMST_NKX_rep2
Pair-end 150bp


title: MDA594_1328_22_Control_1L_7DE0

description: Library name: ABA45003


title: WAT_168


title: shRMST NKX2-1 ChIP-seq rep 1

description:
Library name: shRMST_NKX_rep1
Pair-end 150bp


title: WAT_167


title: Neuronal sample for Individual 126


title: Non-neuronal sample for Individual 125


title: MDA594_1328_22_Control_1R_7DE0

description: Library name: ABA45004


title: Neuronal sample for Individual 125


title: MDA594_1295_22_Control_2R_D42C

description: Library name: ABA44503


title: WAT_164


title: Red eye female 5

description:
Library name: RF5
Column name in normalized_counts_females.csv: RF5

value: Whole heads

value: w+


title: Non-neuronal sample for Individual 124

value: Non-neuronal


title: MDA594_1303_22_Control_1L_7D71

description: Library name: ABA44506


title: WAT_165

value: Male


title: WAT_166


title: WAT_163


title: Non-neuronal sample for Individual 123


title: Neuronal sample for Individual 124

value: Neuronal


title: shGFP SOX2 ChIP-seq rep 2

description:
Library name: shGFP_SOX2_rep2
Pair-end 150bp

value: shGFP


title: M7-2

city: shenzhen

first: zhiguang

last: chang

address: No. 1068, Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

department: Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology

country: China

institute: Chinese Academy of Sciences

description:
Library name: M7-2
replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

source_name: spleen-derived CD8+T cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: spleen-derived CD8+T cell

value: The time-matched control group for the M4 group


title: M7-3

description:
Library name: M7-3
replicate biosample 3


title: M6-3

description:
Library name: M6-3
replicate biosample 3

value: The time-matched control group for the M3 group


title: shGFP SOX2 ChIP-seq rep 1

description:
Library name: shGFP_SOX2_rep1
Pair-end 150bp


title: shGFP NKX2-1 ChIP-seq rep 1

description:
Library name: shGFP_NKX_rep1
Pair-end 150bp


title: WAT_162


title: Neuronal sample for Individual 122

value: M

value: Pre-frontal cortex


title: M6-2

description:
Library name: M6-2
replicate biosample 2


title: M7-1

description:
Library name: M7-1
replicate biosample 1


title: WAT_159


title: WAT_161


title: WAT_158


title: Neuronal sample for Individual 121

value: F


title: J4-2RNA-2

description:
Library name: J4-2RNA-2
replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

source_name: Jurkat

value: Jurkat

value: WT

value: Pre-exposure (direct sample collection)


title: M6-1

description:
Library name: M6-1
replicate biosample 1


title: Non-neuronal sample for Individual 121


title: Neuronal sample for Individual 120


title: WAT_160


title: J4-1RNA

description:
Library name: J4-1RNA
replicate biosample 1


title: M5-3

description:
Library name: M5-3
replicate biosample 3

value: The time-matched control group for the M2 group


title: J4-2RNA

description:
Library name: J4-2RNA
replicate biosample 2


title: WAT_157


title: WAT_156


title: M5-2

description:
Library name: M5-2
replicate biosample 2


title: J3RNA-3

description:
Library name: J3RNA-3
replicate biosample 3

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: M5-1

description:
Library name: M5-1
replicate biosample 1


title: Neuronal sample for Individual 119


title: shGFP input

description:
Library name: shGFP_input
Pair-end 150bp

value: SCLC cell line

value: Input control


title: J3RNA-2

description:
Library name: J3RNA-2
replicate biosample 2


title: M4-3

description:
Library name: M4-3
replicate biosample 3


title: Non-neuronal sample for Individual 119

value: Non-neuronal


title: Non-neuronal sample for Individual 120


title: Neuronal sample for Individual 118


title: WAT_154

value: Female


title: WAT_153


title: J2-3RNA

description:
Library name: J2-3RNA
replicate biosample 3

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: WAT_155


title: WAT_152

value: Male


title: M4-2

description:
Library name: M4-2
replicate biosample 2

value: spleen-derived CD8+T cell


title: WAT_151


title: Neuronal sample for Individual 35

value: Neuronal


title: M3-3

description:
Library name: M3-3
replicate biosample 3


title: Non-neuronal sample for Individual 118


title: J2-2RNA

description:
Library name: J2-2RNA
replicate biosample 2


title: J2-1RNA

description:
Library name: J2-1RNA
replicate biosample 1


title: M3-2

description:
Library name: M3-2
replicate biosample 2


title: WAT_150


title: Non-neuronal sample for Individual 117


title: E. faecalis-C. albicans 48hr dual-species biofilm, rep 3

description: Library name: Dualspecies3

value: Dual species

value: E. faecalis-C.albicans dualspecies biofilm


title: J1RNA-3

description:
Library name: J1RNA-3
replicate biosample 3

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: M3-1

description:
Library name: M3-1
replicate biosample 1


title: Neuronal sample for Individual 117

value: F

value: Pre-frontal cortex


title: WAT_148


title: M4-1

description:
Library name: M4-1
replicate biosample 1


title: J1RNA-2

description:
Library name: J1RNA-2
replicate biosample 2

value: Jurkat

value: WT


title: M2-3

description:
Library name: M2-3
replicate biosample 3


title: WAT_147


title: Non-neuronal sample for Individual 63


title: M2-2

description:
Library name: M2-2
replicate biosample 2


title: WAT_145


title: WAT_144


title: WAT_146


title: M2-1

description:
Library name: M2-1
replicate biosample 1


title: Neuronal sample for Individual 116


title: Neuronal sample for Individual 63


title: J1RNA-1

description:
Library name: J1RNA-1
replicate biosample 1


title: nAD1-hipp-PRO

city: Chicago

first: David

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

description: Library name: A14-193_9_NT

library_source: other

data_processing:
FASTQs were processed using 10X SpaceRanger v2.1.1 and saved as Seurat objects for analysis
ST spots with more than 20% of reads attributed to mitochondrial genes in the mRNA assay were removed for FCX, TCX and PCX, and ST spots with more than 30% of reads attributed to mitochondrial genes in the mRNA assay were removed for HIPP.
ST spots with extreme low and high UMI counts in the mRNA assay were omitted on a per-sample basis
ST spots with extreme low mRNA Feature counts were removed on a per-sample basis
ST spots with zero cumulative protein expression were removed from both assays
The outermost edge ST spots of each slide were removed
ST spots not located on cortical or hippocampal tissue were removed from both assays
Raw mRNA counts were lognormalized using Seurat's NormalizeData()
Raw mRNA counts were transformed using SCTransform
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data files are Seurat objects containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are the SpaceRanger output files for each sample: aligned fiducials, scale factors, hires image, lowres image, detected tissue image, tissue positions list, and barcode fluorescence intensity from the spatial output folder, and the barcode, features, and matrix matrices from the filtered_feature_bc_matrix output folder
Library strategy: Spatial Proteogenomics

molecule: protein

source_name: Posterior Hippocampus

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene and Protein Expression for FFPE – Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging (CG000659, Rev B, 10x Genomics) protocol
Libraries were constructed according to the user guide for Visium CytAssist Spatial Gene and Protein Expression Reagent Kits (CG000494; Rev B; 10x Genomics).

value: Posterior Hippocampus

value: Non-Immunized AD (nAD)


title: nAD1-pcx-PRO

description: Library name: A14-193_4_NT

source_name: Left Inferior Parietal Lobule

value: Left Inferior Parietal Lobule


title: Non-neuronal sample for Individual 116


title: M1-2

description:
Library name: M1-2
replicate biosample 2

value: Pre-exposure (direct sample collection)


title: M1-1

description:
Library name: M1-1
replicate biosample 1


title: Non-neuronal sample for Individual 115

value: Non-neuronal


title: M1-3

description:
Library name: M1-3
replicate biosample 3


title: nAD1-tcx-PRO

description: Library name: A14-193_3_NT

source_name: Left Superior Temporal Gyrus

value: Left Superior Temporal Gyrus


title: nAD1-fcx-PRO

description: Library name: A14-193_1_NT

source_name: Left Middle Frontal Gyrus

value: Left Middle Frontal Gyrus


title: WAT_143

value: Male


title: shRMST input

description:
Library name: shRMST_input
Pair-end 150bp

value: SCLC cell line

value: circRMST shRNA

value: Input control


title: YDJ1936_rep2

city: Stanford

first: Christopher

middle: M

last: Jakobson

state: CA

address: 318 Campus Dr, Clark Center W350

department: Chemical and Systems Biology

institute: Stanford University School of Medicine

description: Library name: H9

data_processing:
Raw reads were trimmed of adaptors and filtered for quality by BGI.
Transcriptomic reads were pseudo-aligned to the genome using Kallisto.
TPMs were consolidated in prionTpmOutput.csv using MATLAB.
Assembly: Saccharomyces cerevisiae R64-1
Supplementary files format and content: prionTpmOutput.csv contains the estimated TPM per gene for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to exponential phase, harvested by centrifugation, and snap-frozen.

extract_protocol:
Total RNA was extracted from snap-frozen yeast cells and subjected to polyA selection.
Libraries were constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

tag: strain

value: prion of SMP1


title: WAT_142


title: Non-neuronal sample for Individual 122

value: M


title: Non-neuronal sample for Individual 85

value: F


title: nAD2-hipp-PRO

description: Library name: A11-170_9_NT


title: Non-neuronal sample for Individual 35

value: Pre-frontal cortex


title: WAT_140

value: Female


title: WAT_141


title: shGFP NKX2-1 ChIP-seq rep 2

description:
Library name: shGFP_NKX_rep2
Pair-end 150bp

value: shGFP

value: ChIP


title: nAD2-pcx-PRO

description: Library name: A11-170_4_NT

value: Non-Immunized AD (nAD)


title: Neuronal sample for Individual 85

value: Neuronal


title: YDJ2221_rep2

description: Library name: H6

value: prion of MRPL10


title: Neuronal sample for Individual 115


title: WAT_139


title: Non-neuronal sample for Individual 114

value: Non-neuronal


title: YDJ2221_rep1

description: Library name: H5


title: nAD2-tcx-PRO

description: Library name: A11-170_3_NT

value: Left Superior Temporal Gyrus


title: YDJ725_rep2

description: Library name: H8

value: prion of PSP1


title: WAT_138


title: nAD2-fcx-PRO

description: Library name: A11-170_1_NT

value: Left Middle Frontal Gyrus


title: Non-neuronal sample for Individual 45


title: YDJ1784_rep1

description: Library name: H3

value: prion of HEH2


title: nAD1-hipp-mRNA

description: Library name: A14-193_9

value: Posterior Hippocampus


title: WAT_136

value: Male


title: nAD1-pcx-mRNA

description: Library name: A14-193_4

value: Left Inferior Parietal Lobule


title: YDJ729_rep2

description: Library name: H2

value: prion of AZF1


title: Neuronal sample for Individual 114

value: M


title: Neuronal sample for Individual 65

value: Pre-frontal cortex


title: YDJ1784_rep2

description: Library name: H4


title: WAT_135


title: nAD1-fcx-mRNA

description: Library name: A14-193_1


title: WAT_137


title: WAT_134

value: Female


title: Non-neuronal sample for Individual 69

value: F


title: YDJ119_rep1

description: Library name: H11

value: prion of YFH1


title: WAT_129


title: Non-neuronal sample for Individual 65


title: nAD2-hipp-mRNA

description: Library name: A11-170_9

value: Non-Immunized AD (nAD)


title: WAT_133


title: YDJ1936_rep1

description: Library name: H10

value: prion of SMP1


title: Neuronal sample for Individual 69

value: Neuronal


title: WAT_127


title: nAD2-pcx-mRNA

description: Library name: A11-170_4


title: Neuronal sample for Individual 113


title: YDJ729_rep1

description: Library name: H1


title: Non-neuronal sample for Individual 113

value: Non-neuronal


title: nAD2-tcx-mRNA

description: Library name: A11-170_3

value: Left Superior Temporal Gyrus


title: J3RNA-1

description:
Library name: J3RNA-1
replicate biosample 1

value: Jurkat

value: WT

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: WAT_126


title: YDJ733_rep2

description: Library name: G9


title: WAT_125


title: A34995-hipp-hdst

description: Library name: A34995

data_processing:
Nuclei were segmented using StarDist v0.9.1
FASTQs were processed using 10X SpaceRanger v3.0.0
Expression from 2um binned filtered feature barcode matrices was mapped to segmented nuclei and converted to Seurat objects for analysis
Nuclei with more than 20% of reads attributed to mitochondrial genes were removed
Nuclei with fewer than 10 UMI counts were removed
Raw counts were lognormalized using Seurat's NormalizeData()
Raw counts were transformed using SCTransform
SCTransform data was integrated to correct for sample-level batch effects using Seurat's IntegrateLayers() with Harmony Integration
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data file is a Seurat object containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are SpaceRanger output files for each sample: aligned fiducials, hires image, lowres image, detected tissue image from the spatial output folder, and the barcode, features, and matrix matrices from the 2um binned filtered_feature_bc_matrix output folder
Library strategy: Spatial Transcriptomics

source_name: Hippocampus

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium HD FFPE Tissue Preparation Handbook (CG000684, Rev A, 10x Genomics)
Libraries were constructed according to the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG000685, Rev B, 10x Genomics)

value: Hippocampus

value: Non-immunized AD (nAD4)


title: YDJ1856_rep2

description: Library name: G8

value: prion of POL32


title: nAD1-tcx-mRNA

description: Library name: A14-193_3


title: YDJ1856_rep1

description: Library name: G7


title: Neuronal sample for Individual 112


title: nAD2-fcx-mRNA

description: Library name: A11-170_1

value: Left Middle Frontal Gyrus


title: A9-hipp-hdst

description: Library name: NMA22-300-A9

value: Non-immunized AD (nAD3)


title: YDJ721_rep2

description: Library name: G6

value: prion of MPH1


title: Neuronal sample for Individual 86

value: M

value: Pre-frontal cortex


title: WAT_123

value: Female


title: YDJ721_rep1

description: Library name: G5


title: YDJ119_rep2

description: Library name: H12

value: prion of YFH1


title: B9-hipp-hdst

description: Library name: NMA22-205-B9

value: lecanemab Immunized AD (LCMB)


title: Non-neuronal sample for Individual 112

value: F


title: Non-neuronal sample for Individual 67

value: Non-neuronal


title: WAT_121

value: Male


title: YDJ1577_rep2

description: Library name: G4

value: prion of HEH2


title: WAT_122


title: YDJ1577_rep1

description: Library name: G3


title: LCMB-hipp-mRNA

data_processing:
FASTQs were processed using 10X SpaceRanger v2.1.1 and saved as Seurat objects for analysis
ST spots with more than 20% of reads attributed to mitochondrial genes in the mRNA assay were removed for FCX, TCX and PCX, and ST spots with more than 30% of reads attributed to mitochondrial genes in the mRNA assay were removed for HIPP.
ST spots with extreme low and high UMI counts in the mRNA assay were omitted on a per-sample basis
ST spots with extreme low mRNA Feature counts were removed on a per-sample basis
ST spots with zero cumulative protein expression were removed from both assays
The outermost edge ST spots of each slide were removed
ST spots not located on cortical or hippocampal tissue were removed from both assays
Raw mRNA counts were lognormalized using Seurat's NormalizeData()
Raw mRNA counts were transformed using SCTransform
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data files are Seurat objects containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are the SpaceRanger output files for each sample: aligned fiducials, scale factors, hires image, lowres image, detected tissue image, tissue positions list, and barcode fluorescence intensity from the spatial output folder, and the barcode, features, and matrix matrices from the filtered_feature_bc_matrix output folder

value: Posterior Hippocampus

value: lecanemab Immunized AD (iAD)


title: Neuronal sample for Individual 67

value: Neuronal


title: LCMB-pcx-mRNA

value: Left Inferior Parietal Lobule


title: Non-neuronal sample for Individual 86


title: WAT_119


title: nAD3-hipp-mRNA

value: Non-Immunized AD (nAD)


title: Neuronal sample for Individual 94


title: WAT_118


title: nAD-pool1

description: Library name: CAA_pool

library_source: transcriptomic single cell

data_processing:
FASTQs were demultiplexed and processed using 10X CellRanger v7.2.0 and saved as Seurat objects for analysis
SoupX background contamination removal (contamination fraction was automatically estimated using SoupX::autoEstCont function and counts were adjusted using the SoupX::adjustCounts function with roundToInt = TRUE to return integer counts)
Cells with UMI counts less than 3 median absolute deviations below the median or feature counts less than 2 median absolute deviations below the median were removed on a pool and sample specific basis
Cells with more than 20% of reads reads attributed to mitochondrial genes were removed
DoubletFinder doublet removal (pool specific doublet formation rate based on 10xGenomics multiplet rate estimation, using 10 PCs and pN = 0.25)
Raw counts were lognormalized using Seurat's NormalizeData()
Raw counts were transformed using SCTransform, with mitochondrial read % being regressed out
SCTransform data was integrated to correct for sample and pool-level batch effects using Seurat's IntegrateLayers() with Harmony Integration
Assembly: GrCh38-2020-A
Supplementary files format and content: cellranger processed output files

source_name: Left Middle Frontal Gyrus, Left Superior Temporal Gyrus, Left Inferior Parietal Lobe, Posterior Hippocampus

extract_protocol:
For each sample, two FFPE scrolls of 25 µm were prepared and processed according to the "Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling" protocol (CG000632, 10x Genomics), employing pestle-based dissociation.
After dissociation and deparaffinization, the next steps involved probe hybridization, GEM generation, and library construction as outlined in the "Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples" manual (CG000527; Rev E; 10x Genomics).


title: WAT_124


title: YDJ737_rep2

description: Library name: G12

value: prion of YCK3


title: nAD3-pcx-mRNA


title: Non-neuronal sample for Individual 44


title: YDJ737_rep1

description: Library name: G11


title: YDJ1712_rep2

description: Library name: G2

value: prion of ASH1


title: YDJ733_rep1

description: Library name: G10

value: prion of SMP1


title: WAT_117


title: WAT_116


title: Neuronal sample for Individual 84

value: M


title: YDJ1712_rep1

description: Library name: G1


title: WAT_114


title: NND-6

data_processing:
FASTQs were processed using 10X SpaceRanger v2.0.0 and saved as Seurat objects for analysis
ST spots with more than 20% of reads attributed to mitochondrial genes were removed
ST spots with extreme low and high UMI counts were omitted
ST spots with extreme low  Feature counts were removed on a per-sample basis
The outermost edge ST spots of each slide were removed
ST spots not located on tissue were removed
Raw counts were lognormalized using Seurat's NormalizeData()
Raw counts were transformed using SCTransform
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data file is a Seurat object containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are SpaceRanger output files for each sample: barcode fluorescence intensity (Extended amyloid-ß niche) for applicable  samples, aligned fiducials, scale factors, hires image, lowres image, detected tissue image, tissue positions list from the spatial output folder, and the barcode, features, and matrix matrices from the filtered_feature_bc_matrix output folder

source_name: Frontal Cortex

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking protocol (CG000520 Rev B, 10x Genomics)
Libraries were constructed according to the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495, Rev E, 10x Genomics)

value: Frontal Cortex

value: Non-Neurological Disease (NND)


title: nAD-LCMB-pool1

value: Left Middle Frontal Gyrus, Left Superior Temporal Gyrus, Left Inferior Parietal Lobe, Posterior Hippocampus


title: WAT_115


title: Non-neuronal sample for Individual 84

data_processing:
Raw data (IDAT files) were imported using the watermelon R package readEPIC function. Data was then pre-processed using dasen function.
Normalized beta values

source_name: Pre-frontal cortex

value: Pre-frontal cortex


title: Neuronal sample for Individual 111


title: YDJ745_rep2

description: Library name: F9

value: prion of SLI15


title: Neuronal sample for Individual 49


title: WAT_113


title: nAD-LCMB-pool2


title: YDJ1073_rep2

description: Library name: F8

value: prion of POL32


title: WAT_112

value: Female


title: NND-4


title: YDJ1073_rep1

description: Library name: F7


title: Non-neuronal sample for Individual 49

value: Non-neuronal


title: WAT_111

value: Male


title: Aerobic Exercise Training + Metformin #3

city: Madison

first: Matthew

middle: D

last: Bruss

state: WI

address: 201 West Lakeside Street

department: Medicine

institute: UW-Madison

description: Library name: AK_12N

data_processing:
Sequencing reads were adapter-trimmed using Skewer (v0.2.2b) (Jiang et al., 2014) and aligned to the Mus musculus GRCm38 genome assembly using STAR (v2.5.3a) (Dobin et al., 2013), a splice-junction-aware aligner.
Gene-level quantification of expected read counts was achieved using RSEM (v1.3.0; Li and Dewey, 2011) with annotation from Ensembl release 104.
Differential gene expression (DGE) analysis was conducted using edgeR (v3.34.0; Robinson et al., 2010). Prior to analysis, read counts were normalized using the trimmed mean of M-values (TMM) method to account for differences in library sizes (Robinson and Oshlack, 2010). Lowly expressed genes were filtered using edgeR’s filterByExpr function, requiring a minimum count-per-million (CPM) threshold of 10 in at least the smallest group of biological replicates.
Assembly: Mus musculus GRCm38 genome assembly
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Gastrocnemius

treatment_protocol: Mice allocated to AET (or AET + MET) were exercised on a 6-lane motorized treadmill (Columbus Instruments Exer 3/6 treadmill) 5 days/week, 60min/day for 8 weeks. For the AET + MET group, Metformin (Cayman chemical 13118) was provided in the drinking water at 2mg/mL and replaced weekly.

value: Gastrocnemius


title: nAD-4


title: NND-5


title: Non-neuronal sample for Individual 111


title: Aerobic Exercise Training + Metformin #1

description: Library name: AK_12L


title: YDJ1832_rep1

description: Library name: F5

value: prion of MGA1


title: Non-neuronal sample for Individual 110


title: Aerobic Exercise Training #2

description: Library name: AK_11R


title: YDJ1832_rep2

description: Library name: F6


title: WAT_109


title: Aerobic Exercise Training #1

description: Library name: AK_11L


title: Neuronal sample for Individual 110

value: Neuronal


title: WAT_110


title: YDJ121_rep1

description: Library name: F11

value: prion of VTS1


title: YDJ745_rep1

description: Library name: F10


title: WAT_108


title: YDJ1085_rep1

description: Library name: F1


title: Neuronal sample for Individual 41


title: Sedentary #3

description: Library name: AK_NDC3


title: Neuronal sample for Individual 39

value: F


title: WAT_107


title: YDJ1085_rep2

description: Library name: F2

value: prion of ASH1


title: Sedentary #1

description: Library name: AK_NDC1


title: YDJ1944_rep2

description: Library name: E9

value: prion of SCD5


title: Neuronal sample for Individual 109


title: BLaER, TriC CBS, 96h, rep 3

city: Goettingen

first: Yi

last: Zhu

address: Am Fassberg 11

country: Germany

institute: Max Planck Insitute for Multidisciplinary Sciences

description: viewpoint: cbs; each biological replicate has 3 technical replicates

data_processing:
*library strategy: Tri-C
Tri-C data were analyzed using the CapCruncher pipeline (Downes, D. J. et al., 2022)  (v.0.2.3) in capture mode.
A custom script was used to extract reads with two or more cis reporters. These reads were used to calculate multi-way interaction counts between reporter fragments for each viewpoint.
The interaction counts were binned in 1500, 2000, or 2500 bp bins and corrected for the number of restriction fragments present in each bin. The matrices were normalized for the total multi-way interaction counts within a 2 Mb region (which was corrected for the number of restriction fragments present in the region) surrounding the viewpoint.
Assembly: hg38
Supplementary files format and content: txt file: the coordinates and the read counts of restriction fragments pairs interacting with the viewpoint.

source_name: BLaER

extract_protocol: Tri-C experiments were performed in 3 biological replicates per condition following the published protocol (Downes, D. J. et al., 2022).

value: BLaER

value: Leukemia cell line

value: 96h, biological rep3


title: WAT_106


title: Neuronal sample for Individual 79

value: M


title: WAT_105


title: Non-neuronal sample for Individual 39

value: Pre-frontal cortex


title: BLaER, TriC CBS, 96h, rep 2

value: 96h, biological rep2


title: WAT_103


title: Sedentary #2

description: Library name: AK_NDC2


title: Non-neuronal sample for Individual 79


title: YDJ1816_rep1

description: Library name: E7

value: prion of PCL9


title: WAT_104

value: Female


title: YDJ715_rep2

description: Library name: E6


title: YDJ1816_rep2

description: Library name: E8


title: Neuronal sample for Individual 34


title: WAT_101


title: WAT_102


title: BLaER, TriC CBS, 24h, rep 3

value: 24h, biological rep3


title: YDJ715_rep1

description: Library name: E5


title: YDJ749_rep2

description: Library name: E4

value: prion of FRE1


title: Non-neuronal sample for Individual 33

value: Non-neuronal


title: BLaER, TriC CBS, 24h, rep 2

value: 24h, biological rep2


title: Non-neuronal sample for Individual 36


title: WAT_099


title: YDJ749_rep1

description: Library name: E3


title: Neuronal sample for Individual 33

value: Neuronal


title: WAT_098

value: Male


title: BLaER, TriC CBS, 0h, rep 3

value: 0h, biological rep3


title: Neuronal sample for Individual 36


title: WAT_097


title: BLaER, TriC CBS, 96h, rep 1

value: 96h, biological rep1


title: YDJ1078_rep2

description: Library name: E12

value: prion of UBX7


title: BLaER, TriC CBS, 0h, rep 2

value: BLaER

value: 0h, biological rep2


title: Neuronal sample for Individual 74


title: YDJ1078_rep1

description: Library name: E11


title: Non-neuronal sample for Individual 74


title: WAT_100


title: YDJ1944_rep1

description: Library name: E10

value: prion of SCD5


title: BLaER, TriC Enhancer, 96h, rep 3

description: viewpoint: enhancer; each biological replicate has 3 technical replicates

value: Leukemia cell line

value: 96h, biological rep3


title: YDJ661_rep2

description: Library name: E2

value: Naive


title: YDJ661_rep1

description: Library name: E1


title: Neuronal sample for Individual 88

value: F

value: Pre-frontal cortex


title: WAT_096

value: Female


title: WAT_095


title: BLaER, TriC Enhancer, 96h, rep 2

value: 96h, biological rep2


title: WAT_093


title: WAT_091


title: Non-neuronal sample for Individual 88

value: Non-neuronal


title: YDJ1079_rep2

description: Library name: D9


title: BLaER, TriC CBS, 24h, rep 1

value: 24h, biological rep1


title: Non-neuronal sample for Individual 75


title: Neuronal sample for Individual 75

value: Neuronal


title: BLaER, TriC Enhancer, 24h, rep 3

value: 24h, biological rep3


title: BLaER, TriC Enhancer, 24h, rep 2

value: 24h, biological rep2


title: YDJ126_rep2

description: Library name: D8

value: prion of PCL9


title: WAT_089


title: YDJ126_rep1

description: Library name: D7


title: WAT_092

value: Male


title: WAT_090


title: BLaER, TriC CBS, 0h, rep 1

value: BLaER

value: 0h, biological rep1


title: BLaER, TriC Enhancer, 96h, rep 1

value: 96h, biological rep1


title: YDJ124_rep2

description: Library name: D6

value: prion of MGA1


title: WAT_088


title: BLaER, TriC Enhancer, 0h, rep 3

value: Leukemia cell line

value: 0h, biological rep3


title: YDJ127_rep2

description: Library name: D4

value: prion of FRE1


title: Non-neuronal sample for Individual 108

value: M

value: Pre-frontal cortex


title: YDJ124_rep1

description: Library name: D5


title: YDJ127_rep1

description: Library name: D3


title: YDJ1768_rep2

description: Library name: D12

value: prion of STE5


title: BLaER, MCC bCBS, 96h, rep 6

description: viewpoint: bCBS

data_processing:
*library strategy: Micro-Capture-C (MCC)
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
Assembly: hg38
Supplementary files format and content: Normalized bigWig files

extract_protocol:
Multiple aliquots of 15 M cells were crosslinked in 10 mL of culture medium with 2% formaldehyde (ThermoFischer, 28908). Next, the cells were permeabilized by digitonin (0.0025%; Sigma-Aldrich, D141). Digestion was performed with MNase (NEB, M0247) in low Ca2+ MNase buffer (10 mM Tris-HCl pH 7.5, 10 mM CaCl2) for 1 h at 37 °C. After confirming efficient digestion, samples were ligated and de-crosslinked. DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, 69504).
Before sonication, samples were size-selected to remove fragments corresponding to mono-nucleosomes using Mag-Bind TotalPure NGS beads (Omega Bio-Tek, M1378-01). MCC libraries were sheared using a Covaris S220 Focused-Ultrasonicator to a mean size of 200 bp (time: 280 s, duty factor: 10%, peak incident power: 175 W, cycles per burst: 200). Afterwards, the sonicated DNA fragments were indexed using 2 µg of DNA per indexing reaction. To increase library complexity, each reaction was indexed in duplicate in 7 PCR cycles using Herculase II polymerase (Agilent, 600677). The duplicate reactions were pooled and the libraires were enriched for viewpoints of interest in a double capture procedure, using ssDNA 5’-biotinylated 120 nt oligonucleotides. Briefly, 2 separate hybridization reactions were performed for each condition, using 2 µg of each sample as input. Captured DNA was pulled down using M-270 Streptavidin Dynabeads (Invitrogen, 65305), and amplified in 12 PCR cycles. After library quality assessment with a fragment analyzer, the libraries were sequenced on the Illumina sequencing platform with 300 cycles paired-end reads.

value: 96h, rep6


title: YDJ1637_rep2

description: Library name: D2

value: Hsp104 cured YDJ128


title: WAT_085

data_processing: Data analysis was conducted using Limma package implemented in R/Bioconductor with Bonferroni correction.


title: BLaER, MCC bCBS, 96h, rep 4

description: viewpoint: bCBS

value: 96h, rep4


title: WAT_087


title: BLaER, TriC Enhancer, 0h, rep 2

value: 0h, biological rep2


title: YDJ1768_rep1

description: Library name: D11


title: Neuronal sample for Individual 44

extract_protocol: Genomic DNA was extracted from frozen nuclei aliquots using a modified proteinase K-based extraction method.

value: Neuronal

value: F


title: BLaER, TriC Enhancer, 24h, rep 1

value: 24h, biological rep1


title: WAT_086

value: Female


title: WAT_083


title: BLaER, MCC bCBS, 96h, rep 3

description: viewpoint: bCBS

value: BLaER

value: 96h, rep3


title: WAT_080

value: Male


title: BLaER, MCC bCBS, 96h, rep 2

description: viewpoint: bCBS

value: Leukemia cell line

value: 96h, rep2


title: YDJ1637_rep1

description: Library name: D1


title: YDJ1860_rep2

description: Library name: C9

value: prion of SAP1


title: YDJ1079_rep1

description: Library name: D10

value: prion of SCD5


title: BLaER, MCC bCBS, 24h, rep 6

description: viewpoint: bCBS

value: 24h, rep6


title: WAT_079


title: BLaER, TriC Enhancer, 0h, rep 1

value: 0h, biological rep1


title: BLaER, MCC bCBS, 24h, rep 5

description: viewpoint: bCBS

value: 24h, rep5


title: WAT_077


title: YDJ1728_rep1

description: Library name: C7

value: prion of PBP2


title: WAT_082


title: YDJ1084_rep2

description: Library name: C6

value: prion of KAP120


title: WAT_078


title: BLaER, MCC bCBS, 96h, rep 1

description: viewpoint: bCBS

value: 96h, rep1


title: BLaER, MCC bCBS, 24h, rep 3

description: viewpoint: bCBS

value: 24h, rep3


title: YDJ1084_rep1

description: Library name: C5


title: BLaER, MCC bCBS, 24h, rep 2

description: viewpoint: bCBS

value: 24h, rep2


title: BLaER, MCC bCBS, 24h, rep 4

description: viewpoint: bCBS

value: 24h, rep4


title: YDJ1728_rep2

description: Library name: C8


title: WAT_094


title: YDJ1928_rep1

description: Library name: C3

value: prion of BUD2


title: WAT_076


title: YDJ1928_rep2

description: Library name: C4


title: WAT_074


title: WAT_070


title: WAT_072


title: WAT_071

value: Female


title: YDJ1578_rep2

description: Library name: C2

value: Hsp70 Cured YDJ128


title: WAT_073

value: Male


title: BLaER, MCC bCBS, 0h, rep 4

description: viewpoint: bCBS

value: BLaER

value: Leukemia cell line

value: 0h, rep4


title: YDJ1888_rep2

description: Library name: C12

value: prion of SPC110


title: BLaER, MCC bCBS, 0h, rep 5

description: viewpoint: bCBS

value: 0h, rep5


title: YDJ1888_rep1

description: Library name: C11


title: YDJ1860_rep1

description: Library name: C10

value: prion of SAP1


title: BLaER, MCC bCBS, 0h, rep 3

description: viewpoint: bCBS

value: 0h, rep3


title: YDJ1077_rep2

description: Library name: B8

value: prion of PBP2


title: BLaER, MCC bCBS, 0h, rep 2

description: viewpoint: bCBS

value: 0h, rep2


title: WAT_069


title: BLaER, MCC ppCBS, 96h, rep 6

description: viewpoint: ppCBS

value: 96h, rep6


title: YDJ1578_rep1

description: Library name: C1


title: WAT_067


title: YDJ1077_rep1

description: Library name: B7


title: WAT_065


title: BLaER, MCC ppCBS, 96h, rep 5

description: viewpoint: ppCBS

value: 96h, rep5


title: WAT_068


title: WAT_063


title: YDJ2025_rep2

description: Library name: B6

value: prion of KAP95


title: BLaER, MCC bCBS, 24h, rep 1

description: viewpoint: bCBS

value: 24h, rep1


title: BLaER, MCC bCBS, 96h, rep 5

description: viewpoint: bCBS


title: BLaER, MCC bCBS, 0h, rep 1

description: viewpoint: bCBS

value: 0h, rep1


title: YDJ2025_rep1

description: Library name: B5


title: WAT_062

value: Female


title: WAT_061


title: WAT_066


title: WAT_060


title: BLaER, MCC ppCBS, 96h, rep 3

description: viewpoint: ppCBS

value: 96h, rep3


title: BLaER, MCC ppCBS, 96h, rep 2

description: viewpoint: ppCBS

value: 96h, rep2


title: YDJ741_rep1

description: Library name: B3

value: prion of BUD2


title: BLaER, MCC ppCBS, 96h, rep 4

description: viewpoint: ppCBS

value: BLaER

value: Leukemia cell line

value: 96h, rep4


title: WAT_059

value: Male


title: YDJ1904_rep1

description: Library name: B10

value: prion of RBS1


title: YDJ6351_rep2

description: Library name: B2

value: Hsp90 cured YDJ128


title: BLaER, MCC ppCBS, 24h, rep 6

description: viewpoint: ppCBS

value: 24h, rep6


title: BLaER, MCC ppCBS, 24h, rep 5

description: viewpoint: ppCBS

value: 24h, rep5


title: WAT_057


title: YDJ741_rep2

description: Library name: B4


title: YDJ6351_rep1

description: Library name: B1


title: YDJ1072_rep2

description: Library name: A9

value: prion of PUS4


title: BLaER, MCC ppCBS, 24h, rep 4

description: viewpoint: ppCBS

value: 24h, rep4


title: BLaER, MCC ppCBS, 24h, rep 3

description: viewpoint: ppCBS

value: 24h, rep3


title: YDJ1074_rep2

description: Library name: A8

value: prion of MRS3


title: WAT_053


title: WAT_052


title: BLaER, MCC ppCBS, 96h, rep 1

description: viewpoint: ppCBS

value: 96h, rep1


title: BLaER, MCC ppCBS, 24h, rep 2

description: viewpoint: ppCBS

value: 24h, rep2


title: YDJ1074_rep1

description: Library name: A7


title: WAT_055

value: Female


title: BLaER, MCC bCBS, 0h, rep 6

description: viewpoint: bCBS

value: 0h, rep6


title: WAT_051


title: YDJ1361_rep2

description: Library name: A6

value: prion of KAP95


title: BLaER, MCC ppCBS, 0h, rep 6

description: viewpoint: ppCBS

value: BLaER


title: YDJ1361_rep1

description: Library name: A5


title: WAT_046


title: BLaER, MCC ppCBS, 0h, rep 5

description: viewpoint: ppCBS

value: Leukemia cell line

value: 0h, rep5


title: BLaER, MCC ppCBS, 0h, rep 4

description: viewpoint: ppCBS

value: 0h, rep4


title: YDJ1792_rep1

description: Library name: A3

value: prion of AZF1


title: YDJ128_rep2

description: Library name: A2

value: Naive


title: BLaER, MCC ppCBS, 24h, rep 1

description: viewpoint: ppCBS

value: 24h, rep1


title: BLaER, MCC ppCBS, 0h, rep 2

description: viewpoint: ppCBS

value: 0h, rep2


title: YDJ4115_rep1

description: Library name: A11

value: prion of SNT1


title: YDJ1792_rep2

description: Library name: A4


title: BLaER, MCC Promoter, 96h, rep 6

description: viewpoint: promoter

value: 96h, rep6


title: BLaER, MCC ppCBS, 0h, rep 3

description: viewpoint: ppCBS

value: 0h, rep3


title: BLaER, MCC Promoter, 96h, rep 5

description: viewpoint: promoter

value: 96h, rep5


title: YDJ128_rep1

description: Library name: A1


title: YDJ4115_rep2

description: Library name: A12


title: BLaER, MCC Promoter, 96h, rep 4

description: viewpoint: promoter

value: 96h, rep4


title: YDJ1072_rep1

description: Library name: A10

value: prion of PUS4


title: BLaER, MCC Promoter, 96h, rep 3

description: viewpoint: promoter

value: 96h, rep3


title: BLaER, MCC ppCBS, 0h, rep 1

description: viewpoint: ppCBS

value: 0h, rep1


title: BLaER, MCC Promoter, 96h, rep 2

description: viewpoint: promoter

value: 96h, rep2


title: FB_13d1 [mRNA]

city: Wuhan

first: Weiwei

last: Zheng

state: Hubei

address: Shizishan Street No.1

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bactrocera dorsalis

source_name: fat body tissues

growth_protocol: B. dorsalis were maintained in our lab under a 12 h light: 12 h dark photoperiod at 28 °C and 70%-80% relative humidity. Adult flies were reared on artificial diets composed of 25% yeast extract and 75% sugar.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

tag: gender

value: female

value: fat body

tag: sample type

value: oriental fruit fly


title: O_13d2 [mRNA]

source_name: ovary tissues

tag: tissue

value: ovary


title: FB_13d2 [mRNA]


title: O_13d1 [mRNA]


title: BLaER, MCC Promoter, 24h, rep 6

description: viewpoint: promoter

value: BLaER

tag: cell type

value: Leukemia cell line

value: 24h, rep6


title: FB_9d2 [mRNA]

value: 9 d


title: BLaER, MCC Promoter, 24h, rep 5

description: viewpoint: promoter

value: 24h, rep5


title: FB_9d1 [mRNA]


title: O_9d2 [mRNA]


title: BLaER, MCC Promoter, 96h, rep 1

description: viewpoint: promoter

value: 96h, rep1


title: BLaER, MCC Promoter, 24h, rep 3

description: viewpoint: promoter

value: 24h, rep3


title: BLaER, MCC Promoter, 24h, rep 2

description: viewpoint: promoter

value: 24h, rep2


title: FB_5d1 [mRNA]

value: 5 d


title: O_9d1 [mRNA]


title: BLaER, MCC Promoter, 0h, rep 6

description: viewpoint: promoter

value: 0h, rep6


title: O_5d2 [mRNA]


title: FB_5d2 [mRNA]


title: BLaER, MCC Promoter, 0h, rep 5

description: viewpoint: promoter

value: 0h, rep5


title: BLaER, MCC Promoter, 0h, rep 4

description: viewpoint: promoter

value: 0h, rep4


title: BLaER, MCC Promoter, 24h, rep 4

description: viewpoint: promoter

value: 24h, rep4


title: FB_1d2 [mRNA]

value: 1 d

value: female


title: O_5d1 [mRNA]

value: oriental fruit fly


title: BLaER, MCC Promoter, 24h, rep 1

description: viewpoint: promoter

value: 24h, rep1


title: BLaER, MCC Promoter, 0h, rep 3

description: viewpoint: promoter

value: BLaER

value: 0h, rep3


title: FB_1d1 [mRNA]

value: fat body


title: BLaER, MCC Promoter, 0h, rep 2

description: viewpoint: promoter

value: Leukemia cell line

value: 0h, rep2


title: O_1d2 [mRNA]

value: ovary


title: O_1d1 [mRNA]

value: 1 d post-eclosion


title: BLaER subclone CTCF-AID, CTCF_ChIP _96h_depl_rep2

data_processing:
ChIPmentation data were analyzed with the NGseqBasic pipeline (Jelena Telenius et al., 2018).
For MED26 and SMC1A ChIPmentation, BigWig files were generated using deeptools (v.3.3.0) bamCoverage funtion with RPKM normalization and a binning size of 10bp.
For CTCF ChIPmentation, BigWig files were normalized with spike-in.
Covarege tracks of replicates were merged using UCSC bigWigMerge.
Assembly: hg38
Supplementary files format and content: bigWig files: reads coverage

extract_protocol:
Aliquots of 1.5 M cells were crosslinked in a single fixation reaction with 1% formaldehyde for 10 min at room temperature, quenched with ice-cold glycine at a final concentration of 125 mM, and washed 2 times with ice-cold PBS. Fixed cells were first gently lysed with Farnham lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) to isolate nuclei, which was followed by nuclear lysis with 0.5% SDS buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% SDS). Then, chromatin was fragmented, using an optimized procedure for each target. In the CTCF ChIPmentation experiments, chromatin was fragmented by sonication (time: 7 min, duty factor: 5 %, peak incident power: 140 W, cycles per burst: 200). In MED26 and SMC1A ChIPmentation experiments, chromatin was first fragmented by a titrated amount of MNase (2.5 Kunitz) and then gently sonicated (time: 1 min, duty factor: 2 %, peak incident power: 105 W, cycles per burst: 200). To perform immunoprecipitation, a mixture of Protein A (10008D, Invitrogen) and Protein G Dynabeads (10003D, Invitrogen) in 1:1 ratio was blocked with 0.5 % BSA, washed and pre-incubated with 2 µg of primary antibody (CTCF: Diagenode, C15410210-50; SMC1A: Abcam, ab9262; MED26: Bethyl Laboratories, A302-370) and 1 µg of spike-in antibody (Biozol, 61686) for 6 h, at 4 °C. Sheared chromatin was diluted in IP buffer, and added along with 50 ng Drosophila spike-in chromatin to the bead-bound antibodies. The samples were incubated overnight on a rotator at 4 °C, and washed with stringent buffers the next morning.
Sequencing adapters were added to the bead-bound DNA by Tagmentation with the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197). After washes, the bead-bound samples were de-crosslinked overnight at 65 °C in the presence of proteinase K (0.2 mg/mL, final) and cleaned with 1.8x volume of Mag-Bind TotalPure NGS beads (Omega Bio-Tek, M1378-01). The tagmented DNA was used for library preparation with the NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541).

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, auxin, rep2


title: BLaER, MCC Promoter, 0h, rep 1

description: viewpoint: promoter

value: 0h, rep1


title: FB_13d2 [miRNA]

description: Processed data.xlsx

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 1 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: B. dorsalis were maintained in our lab under a 12 h light: 12 h dark photoperiod at 28 °C and 70%-80% relative humidity. Adult flies were reared on artificial diets composed of 25% yeast extract and 75% sugar.


title: BLaER subclone CTCF-AID, CTCF_ChIP _96h_depl_rep1

value: 96h, auxin, rep1


title: FB_13d1 [miRNA]

description: Processed data.xlsx


title: WAT_021

source_name: adipose

extract_protocol: Total RNA was extracted from adipose tissue samples using the Qiagen RNeasy Lipid Tissue Mini Kit following the manufacturer's instructions.

tag: Sex

value: Male


title: WAT_018


title: WAT_022

value: Female


title: WAT_027


title: WAT_026


title: WAT_035


title: WAT_031


title: WAT_040


title: WAT_045


title: WAT_025


title: WAT_037


title: WAT_043


title: WAT_038


title: WAT_023


title: WAT_049


title: WAT_042


title: WAT_032


title: WAT_041


title: WAT_016


title: WAT_036


title: WAT_030


title: WAT_012


title: WAT_028


title: WAT_024


title: WAT_020


title: WAT_029


title: WAT_033


title: WAT_019


title: WAT_015


title: BLaER subclone CTCF-AID, CTCF_ChIP _96h_control_rep2

tag: genotype

value: 96h, no treatment control, rep2


title: O_13d2 [miRNA]

description: Processed data.xlsx

value: female


title: BLaER, MED26_ChIP_96h_rep2

tag: treatment

value: 96h, rep2


title: FB_9d1 [miRNA]

description: Processed data.xlsx

value: 9 d

value: oriental fruit fly


title: O_13d1 [miRNA]

description: Processed data.xlsx


title: BLaER, MED26_ChIP_96h_rep1

value: BLaER

value: 96h, rep1


title: FB_9d2 [miRNA]

description: Processed data.xlsx

value: fat body


title: BLaER, MED26_ChIP_72h_rep2

value: Leukemia cell line

value: 72h, rep2


title: O_9d1 [miRNA]

description: Processed data.xlsx

value: ovary


title: BLaER subclone CTCF-AID, CTCF_ChIP _96h_control_rep1

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: 96h, no treatment control, rep1


title: O_9d2 [miRNA]

description: Processed data.xlsx


title: BLaER, MED26_ChIP_72h_rep1

value: 72h, rep1


title: BLaER, MED26_ChIP_72h_rep3

value: 72h, rep3


title: FB_5d2 [miRNA]

description: Processed data.xlsx

value: 5 d


title: BLaER, MED26_ChIP_24h_rep2

value: 24h, rep2


title: EpiDermFT, ZDL, rep 2

city: Dallas

first: William

last: Swindell

address: 6201 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

description: Library name: ZDL_2

data_processing:
TrimGalore was used for adaptor removal and quality trimming of reads.
Reads corresponding to rRNA were filtered out using bbmap.
The set of filtered and quality-trimmed reads were mapped to the hg38 genome using tophat2.
Read counts for hg38 genes were generated using htseq-count
FPKM values were estimated using cufflinks.
Assembly: hg38
Supplementary files format and content: txt file

source_name: EpiDermFT

growth_protocol: EpiDermFT tissues were obtained from MatTek on 07/26/22 and permitted to equilibrate overnight in a cell culture incubator. Cultures were fed every other day in accordance with manufacturer specifications.

extract_protocol:
After the treatment period, tissues were rinsed and RNA extraction was performed using the commercial RNeasy Plus Mini kit (Qiagen, Germantown, MD; cat. no. 74134). The QiaCube Connect robotic station was utilized to ensure a standardized extraction process.
RNA libraries for RNA-seq were generated following a standard workflow with mRNA enrichment, mRNA fragmentation and random priming following by first and second strand cDNA synthesis with end repair, 5' phosphorylation and dA-tailing. Sequencing was subsequently carried out following adaptor ligation and PCR enrichment.

treatment_protocol: Test materials were dissolved in DMSO diluted with distilled water to a final concen-tration of 100 µg/ml. Test materials were then added to the apical surface of Epi-DermFT tissues (3 µl/cm2) for 24 hours.

value: EpiDermFT

value: normal (wild type)

value: ZDL

tag: batch


title: BLaER, MED26_ChIP_24h_rep3

value: 24h, rep3


title: BLaER, MED26_ChIP_96h_rep3

value: 96h, rep3


title: FB_5d1 [miRNA]

description: Processed data.xlsx

value: female

value: oriental fruit fly


title: EpiDermFT, ZDL, rep 3

description: Library name: ZDL_3


title: O_5d1 [miRNA]

description: Processed data.xlsx


title: EpiDermFT, ZDL, rep 1

description: Library name: ZDL_1


title: FB_1d2 [miRNA]

description: Processed data.xlsx

value: 1 d

value: fat body


title: WAT_008

value: Male


title: O_5d2 [miRNA]

description: Processed data.xlsx

value: ovary


title: WAT_009


title: WAT_007


title: WAT_003


title: WAT_004


title: WAT_001

value: Female


title: FB_1d1 [miRNA]

description: Processed data.xlsx


title: BLaER, MED26_ChIP_12h_rep3

value: BLaER

value: Leukemia cell line

value: 12h, rep3


title: WAT_006


title: EpiDermFT, CDL, rep 3

description: Library name: CDL_3

value: CDL


title: BLaER, MED26_ChIP_12h_rep2

value: 12h, rep2


title: EpiDermFT, CDL, rep 2

description: Library name: CDL_2

value: EpiDermFT


title: BLaER, MED26_ChIP_24h_rep1

value: 24h, rep1


title: O_1d1 [miRNA]

description: Processed data.xlsx

value: 1 d post-eclosion


title: MDX594OR Olaparib.

description: Library name: MDX594OR Olaparib

data_processing:
single-cell T-cell receptor (scTCR-seq) data were analyzed through the CellRanger Single-Cell Software Suite (v6.0.1)
sequencing of the 5' GEX- and TCR-enriched was carried out on an Illumina NovaSeq 6000 Sequencing System (RRID:SCR_016387) sequencer to obtain approximately 40,000 and 5,000 read pairs per cell, respectively.
Low-quality cells were excluded if presented a mitochondrial percentage exceeding 15% or 10% and/or fewer than 200 genes or 500 genes, for mouse and human respectively. Scrublet was used to detect potential doublets and remove corresponding cells. In the scTCRseq analysis, “TCR clonotype” refers to a unique TCR sequence. To assess the degree of expansion, TCR clonotypes were classified as follows: “Single” if the TCR clonotype was expressed by 1 T cells, “Small” for 1 to 5 T cells, “Medium” for 5 to 10 T cells, “Large” for 10 to 30 T cells and “Hyper expanded” for more than 30 T cells
Assembly: Sequencing reads from mouse  cells were mapped with the genome references for mouse (gex-mm10).
Supplementary files format and content: csv containint contig annotations
Library strategy: TCR-Seq

source_name: Breast cancer Mouse Derived Allograft

extract_protocol:
Single-cells were loaded to the 10×Genomics Chromium Controller to be partitioned into Gel Beads-in-emulsion (GEMs). The cDNA sequencing libraries were prepared using the Chromium Single Cell 5´ Library and Gel Bead Kit (10X Genomics, Cat. N. 1000006) following manufacturer's instructions. Briefly, after GEM generation and reverse transcription (RT), GEM-RT were cleaned up and cDNA was amplified during 13 cycles to be subjected to quality control and quantification on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies).
To construct the Gene expression (GEX) library, 25-50 ng of the amplified cDNA were fragmented, end repaired, A-tailed, and sample indexed using the Chromium Single Cell 5’ Library Construction Kit (10x genomics, 1000020). For the V(D)J library, T cell receptor sequences were enriched from the amplified cDNA with the Chromium Single Cell V(D)J Enrichment Kits (PN-1000005)

value: Breast cancer Mouse Derived Allograft


title: BLaER, MED26_ChIP_0h_rep2

value: 0h, rep2


title: BLaER, MED26_ChIP_0h_rep3

value: 0h, rep3


title: EpiDermFT, CDL, rep 1

description: Library name: CDL_1

value: normal (wild type)


title: EpiDermFT, LYS, rep 3

description: Library name: LYS_3

value: LYS


title: EpiDermFT, LYS, rep 1

description: Library name: LYS_1


title: BLaER, MED26_ChIP_0h_rep1

value: 0h, rep1


title: MDX594OR Vehicle.

description: Library name: MDX594OR Vehicle


title: MDX594 Olaparib.

description: Library name: MDX594 Olaparib


title: EpiDermFT, LYS, rep 2

description: Library name: LYS_2


title: EpiDermFT, CTL, rep 3

description: Library name: CTL_3

value: CTL


title: O_1d2 [miRNA]

description: Processed data.xlsx

value: 1 d

value: female

value: ovary

value: oriental fruit fly


title: MDX594 Vehicle.

description: Library name: MDX594 Vehicle


title: BLaER, SMC1A_ChIP_96h_rep2

value: BLaER

value: Leukemia cell line

value: 96h, rep2


title: BLaER, SMC1A_ChIP_96h_rep3

value: 96h, rep3


title: BLaER, MED26_ChIP_12h_rep1

value: 12h, rep1


title: EpiDermFT, CTL, rep 1

description: Library name: CTL_1

value: EpiDermFT


title: ZFP661 OE (replicate 2), WAPL ChIP

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211 6 Center Drive

institute: NIH/NICHD

description: Library name: ZFP661_2_WAPL

data_processing:
Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
To generate ChIP signal (i.e., bigwig) files, deepTools (v3.5.1) was used with the parameters “--normalizeUsing CPM --binSize 10 –extendReads” (CPM represents counts per million) and with chrM and regions on ENCODE blacklist excluded. The ChIP signals were normalized by subtracting the ChIP input in each biological replicate.
Assembly: mm10
Supplementary files format and content: bigwig signal files (.bw)

source_name: R1 mESC

growth_protocol: Cells were cultured in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.4M glycine for 5 min
ChIP assays were performed according to the ENCODE protocol with modifications. For anti-WAPL ChIP (Proteintech, 16370-1-AP), 20 million cells per ChIP were used, with 5 μg of antibody for each ChIP. ChIP DNA was purified, and 10 μl of the ChIP DNA was used as input to construct the ChIP library using the ThruPLEX DNA-Seq Kit (Takara, R400676). The input DNA from the same biological replicate was used to construct the corresponding ChIP input library.

value: R1 mESC

value: mouse embryonic stem cells

value: ZFP661 OE

tag: chip antibody

value: WAPL(Proteintech, 16370-1-AP)


title: ZFP661 OE (replicate 1), WAPL ChIP

description: Library name: ZFP661_1_WAPL


title: BLaER, SMC1A_ChIP_96h_rep1

value: 96h, rep1


title: BLaER, SMC1A_ChIP_72h_rep3

value: 72h, rep3


title: ZFP661 OE (replicate 2), ChIP Input

description: Library name: ZFP661_2_input_WAPL

value: Input control


title: EpiDermFT, CTL, rep 2

description: Library name: CTL_2

value: normal (wild type)

value: CTL


title: RNA-seq of isolated C57BL/6 RAB27aKO 3 mature neutrophils treated with CpG for 6h

city: La Jolla

first: Mouad

last: Ait Kbaich

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

data_processing:
Dr. Tom multi-omics data mining system
Raw sequencing data in FASTQ format was processed and analyzed using BGI's Dr.Tom system
Reads were filtered using SOAPnuke 50 to remove those containing sequencing adapters, having a low-quality base ratio exceeding 20%, or an unknown base ratio greater than 5%
Clean reads were then mapped to the reference genome using Bowtie2
Gene expression levels were quantified using RSEM (v1.2.28) obtaining read count, FPKM, and TPM values
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text file includes FPKM, TPM and counts for each sample

source_name: Bone Marrow

growth_protocol: Isolated mature neutrophil were resuspended in phenol red-free RPMI and either stimulated with CpG-B (5µM) (ODN 1826; InvivoGen) or vehicle for 6 hours

extract_protocol:
Bone marrow–derived mature neutrophils were isolated by positive selection using Anti-Ly6G MicroBeads
The library construction and sequencing procedures were executed at Shenzhen BGI Genomics Co.

treatment_protocol: Neutrophils were stimulated with 5 µM CpG-B or left untreated and incubated for 6h at 37C and RNA was isolated using Qiagen RNeasy Mini Kit and sequenced by BGI Genomics using Illumina HISEQ4000

value: Bone Marrow

value: Ly6G+ Mature Neutrophils

value: CpG


title: RNA-seq of isolated C57BL/6 RAB27aKO 2 mature neutrophils treated with CpG for 6h


title: BLaER, SMC1A_ChIP_72h_rep2

value: BLaER

value: Leukemia cell line

value: 72h, rep2


title: RNA-seq of isolated C57BL/6 RAB27aKO 1 mature neutrophils treated with CpG for 6h


title: ZFP661 OE (replicate 1), ChIP Input

description: Library name: ZFP661_1_input_WAPL


title: BLaER, SMC1A_ChIP_72h_rep1

value: 72h, rep1


title: EV control (replicate 2), WAPL ChIP

description: Library name: EV2_WAPL

value: EV control


title: EV control (replicate 1), WAPL ChIP

description: Library name: EV1_WAPL

value: R1 mESC


title: BLaER, SMC1A_ChIP_24h_rep3

value: 24h, rep3


title: RNA-seq of isolated C57BL/6 RAB27aKO 2 mature neutrophils


title: RNA-seq of isolated C57BL/6 RAB27aKO 1 mature neutrophils


title: EV control (replicate 2), ChIP Input

description: Library name: EV2_input_WAPL

value: mouse embryonic stem cells


title: BLaER, SMC1A_ChIP_24h_rep1

value: 24h, rep1


title: RNA-seq of isolated C57BL/6 wild-type 3 mature neutrophils treated with CpG for 6h

value: Wild-Type


title: RNA-seq of isolated C57BL/6 wild-type 2  mature neutrophils treated with CpG for 6h


title: RNA-seq of isolated C57BL/6 RAB27aKO 3 mature neutrophils


title: BLaER, SMC1A_ChIP_12h_rep3

value: 12h, rep3


title: ZFP661 OE, ATAC-seq (replicate 2)

description: Library name: ATAC_OE_ZFP661_replicate_2

data_processing:
Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. The resulting clean reads were mapped onto the mouse genome (mm10) using BWA with default parameters, and only uniquely mapped reads (with tag X0:i:1) were retained for downstream analyses.
The ATAC-seq cutting sites were detected using Genrich (v0.6) with the parameters '-r -e chrM,chrY -j -y,' and the 10bp flanking regions of the cutting sites were used as chromatin accessible regions.
Assembly: mm10
Supplementary files format and content: bed files (bed.gz)

extract_protocol:
Cells were treated with 200 U of DNase (from the Worthington Papain Dissociation System) for 30 minutes at 37°C, and then washed twice with 1X DPBS.
Cells were counted using the Countess II Automated Cell Counter, and 80,000 cells were used for each ATAC-seq assay. ATAC-seq libraries were constructed using the Active Motif ATAC-seq Kit (cat: 53150) following the provided protocol.

value: ZFP661 OE


title: BLaER, SMC1A_ChIP_12h_rep2

value: 12h, rep2


title: ZFP661 OE, ATAC-seq (replicate 1)

description: Library name: ATAC_OE_ZFP661_replicate_1


title: BLaER, SMC1A_ChIP_24h_rep2

value: 24h, rep2


title: EV control (replicate 1), ChIP Input

description: Library name: EV1_input_WAPL

value: Input control


title: RNA-seq of isolated C57BL/6 wild-type 1 mature neutrophils treated with CpG for 6h

value: Bone Marrow

value: Ly6G+ Mature Neutrophils


title: EV control, ATAC-seq (replicate 2)

description: Library name: ATAC_OE_EV_control_replicate_2


title: RNA-seq of isolated C57BL/6 wild-type 2 mature neutrophils


title: BLaER, SMC1A_ChIP_12h_rep1

value: BLaER

value: 12h, rep1


title: RNA-seq of isolated C57BL/6 wild-type 3 mature neutrophils


title: BLaER, SMC1A_ChIP_0h_rep3

value: Leukemia cell line

value: 0h, rep3


title: BLaER, SMC1A_ChIP_0h_rep2

value: 0h, rep2


title: BLaER, CaptureC_set2_promoter, 96h, biological replicate 2

description: each biological replicate has 4 technical replicates

data_processing:
*library strategy: Capture-C
Capture-C data were analyzed using the CapCruncher pipeline (Downes, D. J. et al., 2022)  (v.0.2.3) in capture mode.
Assembly: hg38
Supplementary files format and content: normalized bigWig files

extract_protocol: Capture-C experiments were performed in 2 biological replicates per condition following the published protocol (Downes, D. J. et al., 2022).

value: 96h, biological rep2, promoter viewpoints set 2


title: Aorta, LXR

city: New Haven

first: Carlos

last: Fernandez-Hernando

address: 10 Amistad St

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcod processing, gene counting and aggregation were made using the CellRanger software (version 7.1.0, 10x Genomics)
Assembly: custom reference mouse genome mm10 that include eGFP and tdTomato marker sequences
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aorta

extract_protocol:
Aortas were harvested from WT and LXRiSMC mice and digested in 1.5mg/ml collagenase A (10103578001, Roche) + 0.5 mg/ml elastase (6365, Worthington) buffer at 37oC for 45 minutes with gentle shaking.
eGFP+ and tdTomato+ cells were encapsulated into droplets and processed following manufacturer’s specifications using 10X Genomics GemCode technology. Equal numbers of cells per sample were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMs) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the Single-Cell 3′ Reagent Kits version 2 (10X Genomics).

value: Aorta

value: immune and vascular cells

value: 16 weeks of Western diet feeding


title: EV control, ATAC-seq (replicate 1)

description: Library name: ATAC_OE_EV_control_replicate_1

value: R1 mESC

value: mouse embryonic stem cells

value: EV control


title: BLaER, SMC1A_ChIP_0h_rep1

value: 0h, rep1


title: RNA-seq of isolated C57BL/6 wild-type 1 mature neutrophils

value: Wild-Type


title: Left lung_Niave_Wild type_Male_5

city: Chapel Hill

last: McPeek

state: NC

address: 125 Mason Farm Rd. CB:7248

institute: University of North Carolina

data_processing:
Paired-end sequencing output were processed by Illumina bcl2fastq used for basecalling.
Sequence reads in FASTQ files were mapped to GRCm39 reference genome with GENCODE vM29 gene annotation by STAR, to generate BAM files.
Gene expression estimates were made as counts, and TPMs, by StringTie from BAM files and GENCODE vM27 annotation.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with gene information, counts, and columns as samples
Supplementary files format and content: tab-delimited text file with gene information, TPMs, and columns as samples

source_name: Left lung

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol:
Naïve left lung: Naïve mice were euthanized by isoflurane overdose immediently prior to tissue collection. The left lung was collected and immediently flash frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.
Pneumonic left lung: Mice were inoculated with Streptococcus pneumoniae (1.74 ± 0.14 x 10^6 bacterium) by intratracheal instillation into the left lung. 24 hours post inoculation, mice were euthanized by isoflurane overdose and the left lung was collected and flash frozen in liquid nitrogen. Tissue was stored at -80°C prior to RNA isolation.

value: Left lung

value: Wild type

value: Male

value: Naïve


title: Left lung_Niave_Wild type_Male_4


title: BLaER, CaptureC_set2_promoter, 0h, biological replicate 2

value: BLaER

value: 0h, biological rep2, promoter viewpoints set 2


title: BLaER, CaptureC_set2_promoter, 96h, biological replicate 1

value: Leukemia cell line

value: 96h, biological rep1, promoter viewpoints set 2


title: Left lung_Niave_Wild type_Male_2