title: FPBC patient 22

description:
DNA from breast cancer FFPE tissue
JW-SBC-37

tag: breast cancer subtype

tag: tumor histology

value: Grade I (well differentiated)


title: WT cells under glucose rich condition

status: Public on Aug 12 2026

type: SRA

city: Hachioji-shi

first: Yusuke

last: Tsuruta

state: Tokyo

address: Minamiosawa 1-1

department: Department of Chemistry, Graduate School of Science,

country: Japan

institute: Tokyo Metropolitan University

description:
Library name: WT_glu_plus
non-strand-specific

library_source: transcriptomic

data_processing:
RNA-seq reads were subjected to adapter-trimming and filtering using fastp (-q 20 -l 20 -3). Trimmed reads were aligned to the S. pombe genome (ASM294v2.30) using HISAT2. Properly paired alignments were extracted using SAMTools (samtools view -f 2). Reads mapped to each gene were counted using featureCounts. Gene annotation data that were available on January 4, 2025, were downloaded from PomBase. Only protein coding genes were considered. The read counts were normalized using Transcripts Per Million (TPM).
Assembly: ASM294v2.30
Supplementary files format and content: tab-delimited text file includes TPM normalized counts.

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

extract_protocol:
The total RNA was purified as described in R T Elder et al. (doi: 10.1073/pnas.80.9.2432).
The libraries were non-strand-specific and were prepared using poly(A) selection

tag: cell type

value: S. pombe cell culture

tag: genotype

value: WT

tag: treatment

value: glucose rich condition


title: Act32-Liq

city: Chicago

first: Jason

middle: M

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

country: USA

institute: University of Illinois at Chicago

description: Library name: 343-L

data_processing:
A custom FASTA database was generated containing all of the coding sequences (CDS) from reference genome GAS ATCC 12344 and CDS from HG316453.2, NC_002737.2, NC_006086.1, NC_007296.2, NC_008021.1, NC_008022.1, and NC_008024.1 that could not be found in the ATCC strain using BWA MEM v0.7.17 (49). Raw RNA-seq reads were aligned to this custom database using BWA MEM. The expression level of gene features (CDS regions from the reference) were quantitated using FeatureCounts v2.0.3 (55) as raw read counts of the stranded libraries. Differential analysis of quantitated gene features as compared with treatment (acute vs carrier) or sampling method (liquid vs swab) was performed using the software package edgeR (56, 57) on raw sequence counts. Prior to analysis, the data were filtered to remove any features that had less than 5 total counts summed across all samples. Data were normalized as counts per million and an additional normalization factor was computed using the trimmed mean of M-values (TMM) algorithm. Statistical tests were performed using the “exactTest” function in edgeR. Adjusted p-values (q-values) were calculated using the Benjamini-Hochberg false discovery rate (FDR) correction. Significant gene features were determined based on an FDR threshold of 0.05 (5%).
Assembly: Custom database, see above.
Supplementary files format and content: Tab delimited text file containing the counts for each gene (CDS) in the custom reference database for each sample.

molecule: cytoplasmic RNA

organism: Streptococcus pyogenes

source_name: Cultured bacteria

growth_protocol: For liquid samples, overnight cultures of GAS strains were grown in THY medium. In the morning, cultures were diluted 1:10 in fresh THY medium and grown at 37 °C static until the OD600 reached 0.4-0.6. Cells were then spun down and resuspended in 500 µL DNA/RNA Shield (Zymo) before storage at -80 °C until extraction. Swab samples were processed directly from -80C flash frozen swabs.

extract_protocol:
For liquid samples, pellets were resuspended in 200 µL lysis solution (TRIzol Max Bacterial Enhancement Reagent (ThermoFisher 16122012) which had been pre-heated to 95 °C mixed with 1 mg/mL lysozyme and 50 U/mL mutanolysin) and moved to a MagMAX prime bead beating tube (ThermoFisher A58155). For swabs, 500 µL DNA/RNA Shield was added to frozen swabs and then vortexed for 30-60 seconds. The tubes containing the swabs were then sonicated in a sonicator bath for 5 minutes to help with removing adherent cells. Following sonication, swabs were again vortexed for 30-60 seconds  and then the tubes were spun down for 5 minutes at 4 °C. The supernatant and swab were removed and the resulting pellet resuspended in 200 µL lysis solution and moved to MagMAX bead beating tubes as above. All samples were placed in an OMNI Bead Ruptor 12 (Omni International, 19-050A) and beat twice for 4 minutes each with a 30 second break in between. The mixtures were then incubated at 37 °C for 30 minutes to allow additional enzymatic lysis and then incubated at 95 °C for 5 minutes. RNA was then collected using the TRIzol Max Bacterial RNA Isolation kit (ThermoFisher 16096-040) per manufacturer’s instructions including the phase separation and RNA precipitation steps. RNA pellets were air dried and resuspended in 45 µL DEPC-treated water. The Turbo DNA-free kit (ThermoFisher AM1907) was used per manufacturer’s instructions to remove any remaining DNA in the sample. The final RNA quantity and quality were measured on a NanoDrop One. Depletion of eurkaryotic RNA was done on the RNA from the swab samples using the MICROEnrich kit (ThermoFisher AM1901) per manufacturer’s instructions. The final precipitation step was skipped and the samples were taken immediately into the MICROBExpress kit protocol (ThermoFisher AM1905) per manufacturer’s instructions to remove bacterial rRNA. For liquid cultures, bacterial rRNA was removed using the same MICROBExpress kit using 2-10 µg starting RNA in 15 µL or less volume.
RNA-seq libraries for samples sequenced on the Novaseq X: Libraries were prepared in house using the NEB Next Ultra II Directional RNA library prep kit (NEB E7765) per the manufacturer’s protocol for purified mRNA. mRNA input amounts ranged from 1-100 ng total. Briefly, rRNA depleted RNA in was first fragmented at 94°C for 10 minutes with random primers. First and then second strand cDNA was synthesized, followed by cDNA purification using SPRIselect beads. Ends were prepped and NEBNext adaptors were ligated to cDNA strands. Samples were again purified using SPRIselect beads, followed by PCR enrichment of adaptor ligated DNA using unique indexed forward and reverse primers. Samples were purified once more using SPRIselect beads, and library quality was analyzed using a NanoDrop, Qubit and Tapestation.  RNA-seq libraries for samples sequenced on the HiSeq 2500 were prepared in house using the Kapa Stranded RNASeq Library Preparation kit (KK8400) per manufacturers instructions for purified mRNA with input range of 10-100 ng total. RNA was fragmented at 94°C for 6 minutes with random primers. Illumina adapters were ligated and library quality analyzed using NanoDrop, Qubit, and Tapestation.

tag: cell line

value: Cultured bacteria


city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: LP_ATAC-SMARCB1-0h-2
library prep for ATAC-SMARCB1-0h-2 derived from ADLI-4-0-048-3-02__OCP_74G

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: .bed, .narrowPeak and unstranded.bw

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Paired-end libaries
ATAC-sequencing

value: iPSC

tag: editing strategy

value: Knock-in of inducible C-terminal degron

tag: altered gene_symbol

tag: time

tag: model system

tag: condition

value: DMSO

tag: parental cell_line


title: FPBC patient 27

type: genomic

city: Santa Monica

first: Melanie

last: Goldfarb

state: California

address: 2200 Santa Monica blvd

department: Surgical Oncology

institute: Saint Johns Cancer Institute

description:
DNA from breast cancer FFPE tissue
JW-SBC-42

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC 850K Beadchip using standard Illumina protocol

scan_protocol: The array was scanned with the iScan system from Illumina according to the manufacturer's guidelines.

data_processing:
Data normalization and quality control were performed using the R package ChAMP (v.2.36.0). Batch effects were tested and corrected using the ComBat function in ChAMP, and probes with a detection p-value above 0.01 were excluded. Probes targeting non-CG dinucleotides, single nucleotide polymorphisms, and chromosome Y were removed from downstream analyses
processed value definition: Beta-values, corrected for batch effect from the different sample origin and other potential batches in the arrays

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Breast Cancer

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from 10-15 um thick tissue sections by microdissection with a needle. Genomic DNA was isolated using the Quick-DNA FFPE Miniprep kit (#D3067; Zymo Research, CA.). Genomic DNA was quantified by Qubit® 3.0 Fluorometer (Q33216; Thermo Fisher Scientific, CA). Genomic DNA was converted with Sodium bisulfite using EZ DNA Methylation-Direct (#D5021, Zymo Research, CA), following the manufacturer's recommendations

tag: batcharray

value: Array 2

tag: tissue

value: Breast Cancer

tag: age at diagnosis

tag: Sex

value: Female

value: Invasive ductal carcinoma

tag: grade

value: Grade II (moderate/intermediate)


title: WT cells under glucose starved condition

description:
Library name: WT_glu_minus
non-strand-specific

value: glucose starved condition


title: Act45-Liq

description: Library name: 3000-L


title: Act37-Swab1

description: Library name: 1004-S

source_name: Oropharyngeal swab

value: Oropharyngeal swab


title: FPBC patient 29

description:
DNA from breast cancer FFPE tissue
JW-SBC-49

tag: breast cancer subtype


title: Car13-Swab3

description: Library name: 2005-4-S


description:
Library name: LP_ATAC-SMARCB1-0h-1
library prep for ATAC-SMARCB1-0h-1 derived from ADLI-4-0-048-3-02__OCP_74G


title: FPBC patient 20

description:
DNA from breast cancer FFPE tissue
JW-SBC-35

tag: tumor histology


title: FPBC patient 24

description:
DNA from breast cancer FFPE tissue
JW-SBC-39


description:
Library name: LP_ATAC-SMARCB1-6h-1
library prep for ATAC-SMARCB1-6h-1 derived from ADLI-4-0-048-3-02__OCP_74G

tag: cell type

value: Auxin


title: Act32-Swab1

description: Library name: 343-S


description:
Library name: LP_ATAC-SMARCB1-24h-2
library prep for ATAC-SMARCB1-24h-2 derived from ADLI-4-0-048-3-02__OCP_74G


title: Act33-Swab1

description: Library name: 359-S


title: tup11/12-d cells under glucose rich condition

description:
Library name: tup_glu_plus
non-strand-specific

tag: genotype


title: Act24-Swab1

description: Library name: 352-S


description:
Library name: LP_ATAC-SMARCC1-0h-1
library prep for ATAC-SMARCC1-0h-1 derived from ADLI-0-0-056-01__OCM_108


title: Act30-Swab1

description: Library name: 260-S


title: Act29-Swab1

description: Library name: 1001-S


title: FPBC patient 25

description:
DNA from breast cancer FFPE tissue
JW-SBC-40


description:
Library name: LP_ATAC-SMARCA5-24h-2
library prep for ATAC-SMARCA5-24h-2 derived from ADLI-4-0-050-3-02__OCP_74G


title: Act43-Swab1

description: Library name: 2006-S


title: SUDHL4 - BMS158_2.5 - D2 - rep3

status: Public on Aug 13 2026

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

description: Library name: 7357-CH-0162

data_processing:
We used featureCounts 2.0.6 to count the number of reads on gene level.
Assembly: GRCh38
Supplementary files format and content: readcount on gene level

source_name: cell line

extract_protocol:
Cells for RNAseq were prepared according to instructions from Discovery Life Sciences.
Five million cells per sample were collected, washed, fixed, and stored at -80 C prior to shipping to Discovery Life Sciences where downstream RNAseq was carried out.

value: cell line

tag: treatment

tag: batch


title: Act47-Swab1

description: Library name: 3002-S

tag: cell line


title: Car13-Swab1

description: Library name: 2005-S


title: FPBC patient 21

description:
DNA from breast cancer FFPE tissue
JW-SBC-36


description:
Library name: LP_ATAC-SMARCA5-24h-1
library prep for ATAC-SMARCA5-24h-1 derived from ADLI-4-0-050-3-02__OCP_74G

tag: editing strategy

tag: altered gene_symbol


title: Act48-Swab1

description: Library name: 3003-S


title: FPBC patient 16

description:
DNA from breast cancer FFPE tissue
JW-SBC-30

value: Grade I (well differentiated)


title: FPBC patient 18

description:
DNA from breast cancer FFPE tissue
JW-SBC-32


description:
Library name: LP_ATAC-SMARCA5-0h-2
library prep for ATAC-SMARCA5-0h-2 derived from ADLI-4-0-050-3-02__OCP_74G

tag: time

tag: model system


title: Act46-Swab1

description: Library name: 3001-S


title: Act40-Swab1

description: Library name: 2002-S


title: Act41-Swab1

description: Library name: 2003-S


title: Act42-Liq

description: Library name: 2004-L


title: FPBC patient 19

description:
DNA from breast cancer FFPE tissue
JW-SBC-34


title: Act21-Swab1

description: Library name: 347-S


title: FPBC patient 15

description:
DNA from breast cancer FFPE tissue
JW-SBC-29


title: Act22-Swab1

description: Library name: 349_S


title: Act20-Swab1

description: Library name: 346-S


title: FPBC patient 14

description:
DNA from breast cancer FFPE tissue
JW-SBC-28

value: Grade III (poorly differentiated)


description:
Library name: LP_ATAC-SMARCA5-6h-1
library prep for ATAC-SMARCA5-6h-1 derived from ADLI-4-0-050-3-02__OCP_74G

tag: condition

tag: parental cell_line


title: FPBC patient 13

description:
DNA from breast cancer FFPE tissue
JW-SBC-27

tag: batcharray

tag: tissue


description:
Library name: LP_ATAC-SMARCA5-6h-2
library prep for ATAC-SMARCA5-6h-2 derived from ADLI-4-0-050-3-02__OCP_74G


title: Act49-Swab1

description: Library name: 3004-S


title: FPBC patient 17

description:
DNA from breast cancer FFPE tissue
JW-SBC-31

tag: age at diagnosis

tag: Sex


title: Act42-Swab1

description: Library name: 2004-S


title: Act39-Swab1

description: Library name: 2001-S


title: FPBC patient 12

description:
DNA from breast cancer FFPE tissue
JW-SBC-26

tag: breast cancer subtype

tag: grade


title: Car2-Swab1

description: Library name: 241-S


description:
Library name: LP_ATAC-SMARCA4-6h-2
library prep for ATAC-SMARCA4-6h-2 derived from ADLI-4-0-047-3-03__OCP_74G

tag: cell type


title: Act36-Swab1

description: Library name: 1003-S


description:
Library name: LP_ATAC-SMARCA5-0h-1
library prep for ATAC-SMARCA5-0h-1 derived from ADLI-4-0-050-3-02__OCP_74G


description:
Library name: LP_ATAC-SMARCA4-6h-1
library prep for ATAC-SMARCA4-6h-1 derived from ADLI-4-0-047-3-03__OCP_74G


title: FPBC patient 11

description:
DNA from breast cancer FFPE tissue
JW-SBC-25

tag: tumor histology


title: Act10-Swab1

description: Library name: 249-S


title: FPBC patient 10

description:
DNA from breast cancer FFPE tissue
JW-SBC-48


title: Act34-Liq

description: Library name: 360-L


title: Act40-Liq

description: Library name: 2002-L


description:
Library name: LP_ATAC-SMARCA4-0h-2
library prep for ATAC-SMARCA4-0h-2 derived from ADLI-4-0-047-3-03__OCP_74G


title: Act29-Liq

description: Library name: 1001-L


title: Act28-Liq

description: Library name: 1000-L


description:
Library name: LP_ATAC-SMARCA4-24h-2
library prep for ATAC-SMARCA4-24h-2 derived from ADLI-4-0-047-3-03__OCP_74G


title: Act24-Liq

description: Library name: 352-L


description:
Library name: LP_ATAC-SMARCA1-6h-2
library prep for ATAC-SMARCA1-6h-2 derived from ADLI-4-0-046-3-09__OCP_74G


title: Act49-Liq

description: Library name: 3004-L


title: Act41-Liq

description: Library name: 2003-L


title: Act38-Swab1

description: Library name: 2000-S


title: Act20-Liq

description: Library name: 346-L


title: FPBC patient 9

description:
DNA from breast cancer FFPE tissue
JW-SBC-47


title: FPBC patient 8

description:
DNA from breast cancer FFPE tissue
JW-SBC-45


description:
Library name: LP_ATAC-SMARCA4-24h-1
library prep for ATAC-SMARCA4-24h-1 derived from ADLI-4-0-047-3-03__OCP_74G


title: FPBC patient 7

description:
DNA from breast cancer FFPE tissue
JW-SBC-44


description:
Library name: LP_ATAC-SMARCA4-0h-1
library prep for ATAC-SMARCA4-0h-1 derived from ADLI-4-0-047-3-03__OCP_74G


title: FPBC patient 6

description:
DNA from breast cancer FFPE tissue
JW-SBC-24

value: Array 1


title: Act10-Liq

description: Library name: 249-L


title: Act35-Swab1

description: Library name: 1002-S


description:
Library name: LP_ATAC-SMARCA1-6h-1
library prep for ATAC-SMARCA1-6h-1 derived from ADLI-4-0-046-3-09__OCP_74G


title: Act22-Liq

description: Library name: 349-L


title: Act48-Liq

description: Library name: 3003-L


description:
Library name: LP_ATAC-SMARCA1-24h-2
library prep for ATAC-SMARCA1-24h-2 derived from ADLI-4-0-046-3-09__OCP_74G


title: Act11-Liq

description: Library name: 250-L


title: FPBC patient 5

description:
DNA from breast cancer FFPE tissue
JW-SBC-23


title: Act39-Liq

description: Library name: 2001-L


title: Act44-Liq

description: Library name: 2007-L


title: Act45-Swab1

description: Library name: 3000-S


title: FPBC patient 4

description:
DNA from breast cancer FFPE tissue
JW-SBC-22


description:
Library name: LP_ATAC-SMARCA1-0h-2
library prep for ATAC-SMARCA1-0h-2 derived from ADLI-4-0-046-3-09__OCP_74G


title: Car12-1-Liq

description: Library name: 351-L


description:
Library name: LP_ATAC-SMARCA1-24h-1
library prep for ATAC-SMARCA1-24h-1 derived from ADLI-4-0-046-3-09__OCP_74G


title: FPBC patient 3

description:
DNA from breast cancer FFPE tissue
JW-SBC-21


title: SPBC patient 13

description:
DNA from breast cancer FFPE tissue
JW-SBC-18


title: Act44-Swab1

description: Library name: 2007-S


title: Act38-Liq

description: Library name: 2000-L


title: FPBC patient 2

description:
DNA from breast cancer FFPE tissue
JW-SBC-20


title: SPBC patient 12

description:
DNA from breast cancer FFPE tissue
JW-SBC-16


description:
Library name: LP_ATAC-SMARCA1-0h-1
library prep for ATAC-SMARCA1-0h-1 derived from ADLI-4-0-046-3-09__OCP_74G


title: WT embryos, 69 hours post fertilization, biol rep 2

city: Lexington

first: Kaan Ihsan

last: Eskut

state: Kentucky

address: 195 Huguelet Dr.

department: Biology

institute: University of Kentucky

description:
Library name: hrs69_2
column name in raw counts:hrs69_2

data_processing:
RNA-seq reads from this study were aligned to the reference genome using HISAT2 v2.2.1
Gene expression was quantified from these alignments using StringTie v2.2.1
Assembly: UKy_Petmar_22M1.pri1.0
Supplementary files format and content: comma separated file with raw counts from stringtie v2.2.1

organism: Petromyzon marinus

source_name: Embryos

growth_protocol: Eggs and sperm were collected from mature adults by stripping gametes into crystallization dishes and containing 10% Holtfreter’s solution and incubated for 10 min to permit fertilization. After visually confirming activation, embryos were rinsed in distilled water to remove excess sperm and maintained in 10% Holtfreter’s solution at 18 °C throughout development.

extract_protocol:
Total RNA was extracted from two pools of approximately 100 snap frozen embryos for each condition, following the standard Trizol extraction protocol with the addition of 10 mM dithiothreitol(DTT) to the lysis reaction.
Library preparation and sequencing were conducted by Novogene using their "Plant and Animal Eukaryotic mRNA" pipeline.

value: Embryos

tag: genotype

value: Wildtype


title: WT embryos, 72 hours post fertilization, biol rep 1

description:
Library name: hrs72_1
column name in raw counts:hrs72_1


title: Act35-Liq

description: Library name: 1002-L

value: Cultured bacteria


title: WT embryos, 72 hours post fertilization, biol rep 2

description:
Library name: hrs72_2
column name in raw counts:hrs72_2


description:
Library name: LP_ATAC-RAD21-6h-1
library prep for ATAC-RAD21-6h-1 derived from ADLI-5-2-004-3-8-nAID22__OCP_210A

value: iPSC

value: Knock-in of inducible C-terminal degron


title: WT embryos, 69 hours post fertilization, biol rep 1

description:
Library name: hrs69_1
column name in raw counts:hrs69_1


title: SPBC patient 11

description:
DNA from breast cancer FFPE tissue
JW-SBC-15


title: WT embryos, 66 hours post fertilization, biol rep 1

description:
Library name: hrs66_1
column name in raw counts:hrs66_1


title: WT embryos, 66 hours post fertilization, biol rep 2

description:
Library name: hrs66_2
column name in raw counts:hrs66_2


title: WT embryos, 60 hours post fertilization, biol rep 2

description:
Library name: hrs60_2
column name in raw counts:hrs60_2


description:
Library name: LP_ATAC-RAD21-6h-2
library prep for ATAC-RAD21-6h-2 derived from ADLI-5-2-004-3-8-nAID22__OCP_210A


title: SPBC patient 10

description:
DNA from breast cancer FFPE tissue
JW-SBC-14


description:
Library name: LP_ATAC-RAD21-24h-2
library prep for ATAC-RAD21-24h-2 derived from ADLI-5-2-004-3-8-nAID22__OCP_210A


title: WT embryos, 60 hours post fertilization, biol rep 1

description:
Library name: hrs60_1
column name in raw counts:hrs60_1


description:
Library name: LP_ATAC-RAD21-24h-1
library prep for ATAC-RAD21-24h-1 derived from ADLI-5-2-004-3-8-nAID22__OCP_210A


title: FPBC patient 1

description:
DNA from breast cancer FFPE tissue
JW-SBC-13


title: WT embryos, 54 hours post fertilization, biol rep 2

description:
Library name: hrs54_2
column name in raw counts:hrs54_2


title: WT embryos, 54 hours post fertilization, biol rep 1

description:
Library name: hrs54_1
column name in raw counts:hrs54_1


title: WT embryos, 51 hours post fertilization, biol rep 2

description:
Library name: hrs51_2
column name in raw counts:hrs51_2


description:
Library name: LP_ATAC-RAD21-0h-1
library prep for ATAC-RAD21-0h-1 derived from ADLI-5-2-004-3-8-nAID22__OCP_210A

value: DMSO


title: SPBC patient 9

description:
DNA from breast cancer FFPE tissue
JW-SBC-12

value: Breast Cancer


description:
Library name: LP_ATAC-RAD21-0h-2
library prep for ATAC-RAD21-0h-2 derived from ADLI-5-2-004-3-8-nAID22__OCP_210A


title: WT embryos, 51 hours post fertilization, biol rep 1

description:
Library name: hrs51_1
column name in raw counts:hrs51_1


title: SPBC patient 8

description:
DNA from breast cancer FFPE tissue
JW-SBC-11

value: Female


description:
Library name: LP_ATAC-PRMT5-6h-2
library prep for ATAC-PRMT5-6h-2 derived from ADLI-5-2-011-1__OCP_210A


title: SPBC patient 7

description:
DNA from breast cancer FFPE tissue
JW-SBC-09

value: Invasive ductal carcinoma


title: WT embryos, 45 hours post fertilization, biol rep 2

description:
Library name: hrs45_2
column name in raw counts:hrs45_2


description:
Library name: LP_ATAC-PRMT5-6h-1
library prep for ATAC-PRMT5-6h-1 derived from ADLI-5-2-011-1__OCP_210A


title: WT embryos, 42 hours post fertilization, biol rep 2

description:
Library name: hrs42_2
column name in raw counts:hrs42_2


title: SPBC patient 6

description:
DNA from breast cancer FFPE tissue
JW-SBC-07

value: Grade II (moderate/intermediate)


description:
Library name: LP_ATAC-PRMT5-24h-2
library prep for ATAC-PRMT5-24h-2 derived from ADLI-5-2-011-1__OCP_210A


description:
Library name: LP_ATAC-PRMT5-24h-1
library prep for ATAC-PRMT5-24h-1 derived from ADLI-5-2-011-1__OCP_210A


title: WT embryos, 39 hours post fertilization, biol rep 2

description:
Library name: hrs39_2
column name in raw counts:hrs39_2


title: WT embryos, 42 hours post fertilization, biol rep 1

description:
Library name: hrs42_1
column name in raw counts:hrs42_1


title: WT embryos, 33 hours post fertilization, biol rep 2

description:
Library name: hrs33_2
column name in raw counts:hrs33_2


title: WT embryos, 36 hours post fertilization, biol rep 1

description:
Library name: hrs36_1
column name in raw counts:hrs36_1


description:
Library name: LP_ATAC-PRMT5-0h-1
library prep for ATAC-PRMT5-0h-1 derived from ADLI-5-2-011-1__OCP_210A


description:
Library name: LP_ATAC-NUP88-6h-2
library prep for ATAC-NUP88-6h-2 derived from ADLI-4-3-84-3-5__OCP_74G


title: SPBC patient 2

description:
DNA from breast cancer FFPE tissue
JW-SBC-03


title: SPBC patient 1

description:
DNA from breast cancer FFPE tissue
JW-SBC-02


title: WT embryos, 30 hours post fertilization, biol rep 2

description:
Library name: hrs30_2
column name in raw counts:hrs30_2


title: WT embryos, 24 hours post fertilization, biol rep 1

description:
Library name: hrs24_1
column name in raw counts:hrs24_1


description:
Library name: LP_ATAC-NUP88-24h-1
library prep for ATAC-NUP88-24h-1 derived from ADLI-4-3-84-3-5__OCP_74G


title: Abomasum,Lactation,Goat-3

city: Cerdanyola del Vallès

first: Diego

middle: Alonso

last: Vargas Donayre

state: Barcelona

address: Carrer de la Vall Moronta

department: Plant and Animal Genomics

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

description: Library name: AB3

data_processing:
Raw reads with less than 100 bp and less than 85% of bases with Q>30 were discarded using Fastp. SILVA database rRNA database release 138.2 was used to eliminate rRNA contamination.
Filtered reads were mapped to the goat reference genome  with STAR and transcript structure recovery was conducted with StringTie. Novel lncRNAs were characterized with an internal protocol
Gene level estimated counts and offsets matrices were generated using tximport. Count data was normalized to CPM with edgeR. Genes with a CPM value greater than 0.5 in at least 3 samples in a tissue were considered as expressed. Null expressed genes were removed. Tissue-specificty of each gene was measured by the tau-index.
Assembly: ARS1.2
Supplementary files format and content: 33tissues_gene_counts.tsv.gz , tab-delimited text file includes raw gene count.
Supplementary files format and content: 33tissues_gene_length.tsv.gz , tab-delimited text file includes gene count offset.
Supplementary files format and content: 33tissues_CPM.tsv.gz , tab-delimited text file includes processed CPM
Supplementary files format and content: lncRNAs.gtf.gz , gtf file including novel lncRNA
Supplementary files format and content: 33tissues_tau.tsv.gz , tab-delimited text file includes tau-index for each expressed gene

organism: Capra hircus

source_name: Abomasum

extract_protocol:
RNA was extracted using the RiboPure™ Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Strand-specific library construction was performed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina.

value: Abomasum


title: WT embryos, 21 hours post fertilization, biol rep 2

description:
Library name: hrs21_2
column name in raw counts:hrs21_2


title: WT embryos, 21 hours post fertilization, biol rep 1

description:
Library name: hrs21_1
column name in raw counts:hrs21_1


title: Lung,Dry,Goat-73

description: Library name: LU73

source_name: Lung

value: Lung


description:
Library name: LP_ATAC-NUP214-6h-2
library prep for ATAC-NUP214-6h-2 derived from ADLI-2-3-67-1-19__OCM_NLS21

value: Auxin


title: WT embryos, 15 hours post fertilization, biol rep 1

description:
Library name: hrs15_1
column name in raw counts:hrs15_1


title: Mammary Gland,Lactation,Goat-3

description: Library name: MG3

source_name: Mammary Gland

value: Mammary Gland


title: WT embryos, 12 hours post fertilization, biol rep 3

description:
Library name: hrs12_2_2
column name in raw counts:hrs12_2_2


description:
Library name: LP_ATAC-NUP214-6h-1
library prep for ATAC-NUP214-6h-1 derived from ADLI-2-3-67-1-19__OCM_NLS21


title: Mammary Gland,Lactation,Goat-6

description: Library name: MG6


title: WT embryos, 12 hours post fertilization, biol rep 1

description:
Library name: hrs12_1_2
column name in raw counts:hrs12_1_2


description:
Library name: LP_ATAC-NUP214-24h-2
library prep for ATAC-NUP214-24h-2 derived from ADLI-2-3-67-1-19__OCM_NLS21


title: WT embryos, 48 hours post fertilization, biol rep 2

description:
Library name: hrs48_2
column name in raw counts:hrs48_2


title: Mammary Gland,Dry,Goat-54

description: Library name: MG54


title: SPBC patient 5

description:
DNA from breast cancer FFPE tissue
JW-SBC-06


title: SPBC patient 4

description:
DNA from breast cancer FFPE tissue
JW-SBC-05


title: WT embryos, 39 hours post fertilization, biol rep 3

description:
Library name: hrs39_3
column name in raw counts:hrs39_3


description:
Library name: LP_ATAC-PRMT5-0h-2
library prep for ATAC-PRMT5-0h-2 derived from ADLI-5-2-011-1__OCP_210A


title: WT embryos, 9 hours post fertilization, biol rep 1

description:
Library name: hrs9_1
column name in raw counts:hrs9_1


description:
Library name: LP_ATAC-NUP214-24h-1
library prep for ATAC-NUP214-24h-1 derived from ADLI-2-3-67-1-19__OCM_NLS21


title: WT embryos, 27 hours post fertilization, biol rep 2

description:
Library name: hrs27_2
column name in raw counts:hrs27_2


description:
Library name: LP_ATAC-NUP88-24h-2
library prep for ATAC-NUP88-24h-2 derived from ADLI-4-3-84-3-5__OCP_74G


title: WT embryos, 6 hours post fertilization, biol rep 2

description:
Library name: hrs6_2
column name in raw counts:hrs6_2


title: Mammary Gland,Dry,Goat-64

description: Library name: MG64


title: WT embryos, 6 hours post fertilization, biol rep 1

description:
Library name: hrs6_1
column name in raw counts:hrs6_1


description:
Library name: LP_ATAC-NUP214-0h-2
library prep for ATAC-NUP214-0h-2 derived from ADLI-2-3-67-1-19__OCM_NLS21


title: WT embryos, 3 hours post fertilization, biol rep 2

description:
Library name: hrs3_2
column name in raw counts:hrs3_2


title: Mammary Gland,Dry,Goat-73

description: Library name: MG73


title: WT embryos, 18 hours post fertilization, biol rep 1

description:
Library name: hrs18_1
column name in raw counts:hrs18_1


description:
Library name: LP_ATAC-NUP88-0h-1
library prep for ATAC-NUP88-0h-1 derived from ADLI-4-3-84-3-5__OCP_74G


title: WT embryos, 3 hours post fertilization, biol rep 1

description:
Library name: hrs3_1
column name in raw counts:hrs3_1


title: WT embryos, 18 hours post fertilization, biol rep 2

description:
Library name: hrs18_2
column name in raw counts:hrs18_2


title: Mandibular lymph node,Lactation,Goat-2

description: Library name: MLN2

source_name: Mandibular lymph node

value: Mandibular lymph node


title: Vero cells treated with PBS

city: Okayama City

first: MAN

last: LIU

address: 2-5-1 Shikata-cho, Kita-ku

institute: Okayama University

description:
Library name: Mock_1
Column name in viral_readcount_matrix.tsv: Mock_1; column name in viral_meandepth_matrix.tsv: Mock_1

data_processing:
Raw sequencing reads were preprocessed using fastp (v1.1.0) with the options “-l 35 -x -y”.
After removal of host-derived reads, the remaining reads were assembled de novo using SPAdes (v4.2.0) with default parameters. Contigs of >=100 nt were extracted using SeqKit (v2.12.0).
To validate the assembled viral contig, clean reads from both the test sample and the mock control were mapped back to the NODE6 contig (GenBank accession: PZ180042) using Bowtie2 (v2.5.5) with the --very-sensitive option. Read depth at each nucleotide position was calculated using SAMtools (v1.23).
Genome coverage, mean depth, and the number of mapped reads were determined from the resulting alignment files. The read-depth profile across the NODE6 contig was visualized in R (v4.5.2) using ggplot2 (v4.0.2).
Clean reads from the tick-related sample mapped to the 4621-bp NODE6 sequence with 100% genome coverage, yielding 6800 mapped reads and a mean depth of 167.46-fold mean depth, whereas no reads in the mock control mapped to NODE6.
Assembly: NODE6 viral contig, GenBank accession PZ180042
Supplementary files format and content: viral_readcount_matrix.tsv is a tab-delimited matrix containing mapped read counts for NODE6 in each sample. Column names match the library names in the SAMPLES section.
Supplementary files format and content: viral_meandepth_matrix.tsv is a tab-delimited matrix containing the mean read depth for NODE6 in each sample. Column names match the library names in the SAMPLES section.
Supplementary files format and content: infect_depth.txt and mock_depth.txt contain per-base read depth values across the NODE6 contig for the infection sample and mock control, respectively.

organism: Chlorocebus sabaeus

source_name: Vero cell

growth_protocol: Vero cells were cultured in DMEM supplemented with 5% fetal bovine serum (FBS) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). The libraries were sequenced on the Illumina NovaSeq X Plus platform in paired-end 151-bp mode.

treatment_protocol: Vero cells inoculated with tick homogenate supernatant were used as sample Infection_1, whereas Vero cells inoculated with PBS and processed in parallel were used as sample Mock_1.

value: Vero cell

value: epithelial cells

value: WT

tag: treatment

value: PBS


title: WT embryos, 15 hours post fertilization, biol rep 2

description:
Library name: hrs15_2
column name in raw counts:hrs15_2

value: Embryos

value: Wildtype


title: Mandibular lymph node,Lactation,Goat-3

description: Library name: MLN3


title: replicateB_lowratio

city: Martinsried

first: Brenda

middle: A

last: Schulman

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: replicateB_lowratio

library_source: genomic

data_processing:
Data analysis was performed with the fastqgz_to_counts.py, process_experimnets.py and screen_analysis.py scripts from the Screen Processing repository by mhorlbeck (github).
Assembly: hg19
Supplementary files format and content: csv format with genetable
Library strategy: CRISPR Screen

source_name: Pleural effusion

extract_protocol:
Genomic DNA was isolated with the NucleoSpin Blood XL kit (Macherey-Nagel). For indexing, PCR amplification was performed with 50 µL Q5 High-Fidelity 2x Master Mix (NEB). The indexed library was 264 bp. Samples from the same sample were pooled and purified with SPRIbeads (SPRIselect, 323317, Beckman-Coulter).
Library was obatined from Addgene (83969).

value: Pleural effusion

tag: cell line

value: TDO2 reporter (sfGFP-P2A-mCherry-TDO2)

value: Tryptophan starvation

tag: batch


title: replicateB_highratio

description: Library name: replicateB_highratio


title: replicateA_lowratio

description: Library name: replicateA_lowratio


description:
Library name: LP_ATAC-NUP153-6h-1
library prep for ATAC-NUP153-6h-1 derived from ADLI-4-3-68-3-5__OCP_74G

value: iPSC

tag: editing strategy

value: Knock-in of inducible C-terminal degron

tag: altered gene_symbol


title: MLL-AF9/Flt3ITD/+ cells, STM9005, 3 days, rep3

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

description: Library name: MLLAF9_STM9005_3d_3

library_source: other

data_processing:
The mimseq command (--species Mmus --cluster-id 0.97 --threads 15 --min-cov 0.0005 --max-mismatches 0.075) within the conda mimseq package (version 1.3.8) was then used to obtain counts for each isodecoder as well as summarized counts for each anticodon and the proportion of misincorporation at the G46 position.
Assembly: mm39
Supplementary files format and content: csv file containing anticodon counts for each sample (1 file per cell line)
Supplementary files format and content: csv file containing isodecoder mismatch proportions and coverage at each nucleotide for each sample (1 file per cell line)

molecule: other

organism: Mus musculus

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) coupled with RNA Clean & Concentrator-100 column purifications (Zymo Research, R1019), following the RNA Clean & Concentrator manufacturer’s instructions.
Modification-induced misincorporation tRNA-seq (mim-tRNA-seq) was adapted from Behrens et al. (2021) to enable profiling tRNA levels as well as methylation levels at the G46 position of tRNAs. Total RNA (5 µg in 19 µl nuclease free water) was incubated for 45 min at 37°C with 1.5 µL 1 M Tris-HCl (pH 9.0) and 1 µL SUPERase.In Rnase Inhibitor (Invitrogen, AM2694) to deacylate tRNAs. This was then incubated for 30 min at 37°C with 67 µL nuclease-free water, 10 µL T4 PNK buffer and 1 µL T4 PNK (NEB, M0201L) to dephosphorylate the 3′ end of tRNAs. RNA was recovered by ethanol precipitation with 10 µL 3M sodium acetate (pH 5.2) and 2 µL GlycoBlue coprecipitant (Invitrogen, AM9516) and resuspended in 5 µL nuclease-free water. Abasic sites at m7G modified positions were generated by incubation for 40 min on ice with 3 µL 37 mM m7GTP (Jena Bioscience, NU-1122S), 5 µL 3M Tris-HCl (pH 8.2), 2 µL nuclease-free water and 15 µL 1M sodium borohydride (Pandolfini et al., 2019) (NaBH4, Merck, 21346). The reaction was stopped by adding quenching buffer (180 µL 1M sodium acetate (pH 4.5), 120 µL nuclease-free water, 2 µL GlycoBlue and 990 µL ethanol). RNA was recovered by ethanol precipitation. RNA was resolved by gel electrophoresis on a 10% TBE-Urea gel. tRNAs were selected by excising RNAs between 65-90 nucleotides and generated into libraries for sequencing as described previously by Behrens et al. (2021). Libraries were sequenced in a single-end 100 bp run mode (SE100) on a NextSeq 2000 (Illumina).

treatment_protocol: B16F10 and MLL-AF9/Flt3ITD/+ cells were treated with DMSO or 2 µM STM9005 for 3 days

value: Primary murine MLL-AF9/Flt3ITD/+ driven AML cell line

value: STM9005 3 days


description:
Library name: LP_ATAC-NUP153-24h-2
library prep for ATAC-NUP153-24h-2 derived from ADLI-4-3-68-3-5__OCP_74G

tag: time

tag: model system


title: MLL-AF9/Flt3ITD/+ cells, STM9005, 3 days, rep2

description: Library name: MLLAF9_STM9005_3d_2


description:
Library name: LP_ATAC-NUP153-24h-1
library prep for ATAC-NUP153-24h-1 derived from ADLI-4-3-68-3-5__OCP_74G

tag: condition

tag: parental cell_line


title: MLL-AF9/Flt3ITD/+ cells, STM9005, 3 days, rep1

description: Library name: MLLAF9_STM9005_3d_1


title: Mandibular lymph node,Dry,Goat-64

description: Library name: MLN64

tag: tissue


title: MLL-AF9/Flt3ITD/+ cells, DMSO, 3 days, rep3

description: Library name: MLLAF9_DMSO_3d_3

value: DMSO 3 days


title: MLL-AF9/Flt3ITD/+ cells, DMSO, 3 days, rep2

description: Library name: MLLAF9_DMSO_3d_2


title: Masseter muscle,Lactation,Goat-2

description: Library name: MM2

source_name: Masseter muscle

value: Masseter muscle


description:
Library name: LP_ATAC-NUP153-0h-2
library prep for ATAC-NUP153-0h-2 derived from ADLI-4-3-68-3-5__OCP_74G

value: DMSO


title: MLL-AF9/Flt3ITD/+ cells, DMSO, 3 days, rep1

description: Library name: MLLAF9_DMSO_3d_1


description:
Library name: LP_ATAC-NUP153-0h-1
library prep for ATAC-NUP153-0h-1 derived from ADLI-4-3-68-3-5__OCP_74G


title: B16F10 cells, STM9005, 3 days, rep2

description: Library name: B16F10_STM9005_3d_2

value: Melanoma


title: Masseter muscle,Lactation,Goat-6

description: Library name: MM6


title: B16F10 cells, STM9005, 3 days, rep1

description: Library name: B16F10_STM9005_3d_1


description:
Library name: LP_ATAC-NAT10-6h-2
library prep for ATAC-NAT10-6h-2 derived from ADLI-4-1-108-3-4__OCP_74G

value: Auxin


title: B16F10 cells, DMSO, 3 days, rep3

description: Library name: B16F10_DMSO_3d_3


description:
Library name: LP_ATAC-NAT10-6h-1
library prep for ATAC-NAT10-6h-1 derived from ADLI-4-1-108-3-4__OCP_74G


title: B16F10 cells, DMSO, 3 days, rep2

description: Library name: B16F10_DMSO_3d_2


title: B16F10 cells, DMSO, 3 days, rep1

description: Library name: B16F10_DMSO_3d_1


description:
Library name: LP_ATAC-NAT10-24h-3
library prep for ATAC-NAT10-24h-3 derived from ADLI-4-1-108-3-4__OCP_74G


title: RNA-seq of Prostate specific Pten and Nnmt KO_2-2

city: Philadelphia

first: Erick

last: Mitchell-Velasquez

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed using atria v4.0.0 (default parameters)
Sequence reads were aligned to the hg38 genome using STAR v2.7.11a (parameters - outSAMtype BAM SortedByCoordinate \ outFilterType BySJout, outSJfilterCountUniqueMin -1 2 2 2
--outSJfilterCountTotalMin -1 2 2 2 \ outFilterIntronMotifs RemoveNoncanonical, twopassMode Basic \ outSAMattributes NH NM MD, outSAMunmapped Within, outSAMmapqUnique 50, \ --quantMode GeneCounts)
Gene counts were calculated using featureCounts v 2.16.1 (parameters - s 2, extraAttributes - (chr,gene_name,gene_type), p ,M ,O)
Assembly: mm10 for mouse prostate cells or and hg38 for human cell line
Supplementary files format and content: Tab-limited file containing raw counts for each Sample

source_name: mouse prostate cells

growth_protocol: VCaP parental and NNMT cells were maintained in methionine free DMEM supplemented with 10% dialyzed FBS and 20 uM methionine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
cells were extracted from mouse prostate tissue using the Nature protocol established by Drost et. al (2016),  RNA was extracted using the Qiagen miRNeasy Mini Kit
RNA-seq libraries were made using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: 20 uM methionine for 14 days for in vitro studies  and 0.12% methionine diet for  in vivo studies

value: mouse prostate cells

value: prostate tissue

value: pten and nnmt ko

value: low methionine diet

value: 2 months


title: Medulla oblongata,Dry,Goat-54

description: Library name: MO54

source_name: Medulla oblongata

value: Medulla oblongata


description:
Library name: LP_ATAC-NAT10-24h-2
library prep for ATAC-NAT10-24h-2 derived from ADLI-4-1-108-3-4__OCP_74G


title: RNA-seq of Prostate specific Pten and Nnmt KO_2-1


title: Mandibular lymph node,Dry,Goat-54

description: Library name: MLN54

value: Mandibular lymph node


title: replicateA_highratio

description: Library name: replicateA_highratio

value: Pleural effusion

value: TDO2 reporter (sfGFP-P2A-mCherry-TDO2)

value: Tryptophan starvation


title: Medulla oblongata,Dry,Goat-64

description: Library name: MO64


title: RNA-seq of Prostate specific Pten and Nnmt KO_1-2


title: RNA-seq of Prostate specific Pten and Nnmt KO_1-1


description:
Library name: LP_ATAC-NAT10-0h-2
library prep for ATAC-NAT10-0h-2 derived from ADLI-4-1-108-3-4__OCP_74G

value: iPSC

value: Knock-in of inducible C-terminal degron


title: RNA-seq of Prostate specific Pten KO_2-2

value: pten ko


title: RNA-seq of Prostate specific Pten KO_2-1


title: RNA-seq of Prostate specific Pten KO_1-2


description:
Library name: LP_ATAC-NAT10-0h-1
library prep for ATAC-NAT10-0h-1 derived from ADLI-4-1-108-3-4__OCP_74G


title: Neck skin,Lactation,Goat-2

description: Library name: NSK2

source_name: Neck skin

value: Neck skin


title: RNA-seq of Prostate specific Pten KO_1-1


title: Neck skin,Lactation,Goat-3

description: Library name: NSK3


title: PAO1 deletefiuR mutant carrying empty pHERD20T vector biological replicate 2

city: shandong qingdao

first: Can

middle: can

last: wu

state: shandong province

address: State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road

country: China

institute: shandong university

description:
Library name: PAO1-deFiuR-20T-2
paired-end

data_processing:
Raw sequencing reads were processed using fastp to remove low-quality reads and obtain clean reads. Clean reads were aligned to the reference genome of Pseudomonas aeruginosa PAO1 using HISAT2. Gene expression levels were calculated as FPKM values, and read counts for each gene were generated using HTSeq-count. Principal component analysis (PCA) was performed using R to evaluate sample reproducibility. Differentially expressed genes were identified using DESeq2 with statistical thresholds of q value < 0.05 and fold change > 2 or < 0.5. Functional enrichment analyses, including GO and KEGG pathway analyses, were performed for differentially expressed genes.
Assembly: Pseudomonas aeruginosa PAO1 reference genome NC_002516.2
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts, FPKM expression values, and significant differential expression results. In the expression matrices, rows represent genes and columns represent individual RNA-seq samples. The differential expression file contains comparison identifiers, fold changes, log2 fold changes, adjusted P values, regulation directions, and functional annotations.
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts, FPKM expression values, and significant differential expression results. In the expression matrices, rows represent genes and columns represent individual RNA-seq samples. The differential expression file contains comparison identifiers, fold changes, log2 fold changes, adjusted P values, regulation directions, and functional annotations.

organism: Pseudomonas aeruginosa

source_name: bacterial culture

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA concentration and purity were determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit following the manufacturer's protocol.

value: bacterial culture


title: PAO1 deletefiuR mutant carrying empty pHERD20T vector biological replicate 1

department: State Key Laboratory of Microbial Technology

description:
Library name: PAO1-deFiuR-20T-1
paired-end


title: PAO1 carrying pHERD20T-fiuI biological replicate 2

description:
Library name: PAO1-FiuI-20T-2
paired-end

value: PAO1 carrying pHERD20T-fiuI


title: Neck skin,Lactation,Goat-6

description: Library name: NSK6


title: PAO1 carrying pHERD20T-fiuI biological replicate 1

description:
Library name: PAO1-FiuI-20T-1
paired-end


description:
Library name: LP_ATAC-HDAC3-24h-3
library prep for ATAC-HDAC3-24h-3 derived from ADLI-4-1-115-3-8__OCP_74G

value: Auxin


title: Neurohypophysis,Lactation,Goat-2

description: Library name: NYP2

source_name: Neurohypophysis

value: Neurohypophysis


title: PAO1 carrying empty pHERD20T vector biological replicate 2

description:
Library name: PAO1-20T-2
paired-end

value: PAO1 carrying empty pHERD20T vector


title: PAO1 carrying empty pHERD20T vector biological replicate 1

description:
Library name: PAO1-20T-1
paired-end


description:
Library name: LP_ATAC-HDAC3-24h-1
library prep for ATAC-HDAC3-24h-1 derived from ADLI-4-1-115-3-8__OCP_74G


title: Neurohypophysis,Lactation,Goat-3

description: Library name: NYP3


title: PAO1 deletePA1774 mutant biological replicate 1

description:
Library name: dePA1774_1
paired-end

value: PAO1 deletePA1774 mutant


description:
Library name: LP_ATAC-HDAC3-0h-2
library prep for ATAC-HDAC3-0h-2 derived from ADLI-4-1-115-3-8__OCP_74G

value: DMSO


title: PAO1 deletePA3351 mutant biological replicate 2

description:
Library name: dePA3351_2
paired-end

value: PAO1 deletePA3351 mutant


description:
Library name: LP_ATAC-HDAC3-6h-1
library prep for ATAC-HDAC3-6h-1 derived from ADLI-4-1-115-3-8__OCP_74G


description:
Library name: LP_ATAC-NUP214-0h-1
library prep for ATAC-NUP214-0h-1 derived from ADLI-2-3-67-1-19__OCM_NLS21


title: Neurohypophysis,Lactation,Goat-6

description: Library name: NYP6


title: PAO1 deletePA3351 mutant biological replicate 1

description:
Library name: dePA3351_1
paired-end


description:
Library name: LP_ATAC-HDAC3-0h-1
library prep for ATAC-HDAC3-0h-1 derived from ADLI-4-1-115-3-8__OCP_74G


title: Vero cells treated with tick homogenate

description:
Library name: Infection_1
Column name in viral_readcount_matrix.tsv: Infection_1; column name in viral_meandepth_matrix.tsv: Infection_1

value: Vero cell

value: epithelial cells

value: WT

value: tick homogenate


description:
Library name: LP_ATAC-NUP153-6h-2
library prep for ATAC-NUP153-6h-2 derived from ADLI-4-3-68-3-5__OCP_74G


title: PAO1 wild type biological replicate 2

description:
Library name: PAO1_WT_2
paired-end

value: PAO1 wild type


title: Adrenal gland (cortex),Dry,Goat-73

description: Library name: AGC73

source_name: Adrenal gland (cortex)

value: Adrenal gland (cortex)


title: PAO1 wild type biological replicate 1

description:
Library name: PAO1_WT_1
paired-end


title: Neurohypophysis,Dry,Goat-64

description: Library name: NYP64


description:
Library name: LP_ATAC-FOXM1-6h-2
library prep for ATAC-FOXM1-6h-2 derived from ADLI-2-1-015-1-13__OCM_NLS21

value: iPSC

value: Knock-in of inducible C-terminal degron


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H12

city: Princeton

first: Bruce

last: Wang

address: Carl Icahn Lab

institute: Princeton University

description:
Library name: delta_del_160_library_3_H12
M3-Seq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, alignment, data processing, were performed from the raw basecalls using custom scripts here: https://github.com/brwaang55/m3seq_scripts. Raw basecall files were converted into bam files, which were demultiplexed for the data here.
The data files here were then aligned to a combined Pa011 and PaMx41 genome, and processed using M3-Seq scripts
Assembly: Pseu_aeru_BWH011_V1, ASM275751v1
Supplementary files format and content: Single-cell matrices (csv).

source_name: Bacterial cells

growth_protocol: Cells were grown in LB culture until OD=0.3.

extract_protocol: Libraries were constructed following the M3-Seq protocol.

treatment_protocol: At OD=0.3, cells were infected with PaMx41 Deltaacb2 at an MOI=2.

value: Bacterial cells

value: Pa011 DeltaCBASS

value: Phage infected


title: PAO1 deletePA1774 mutant biological replicate 2

description:
Library name: dePA1774_2
paired-end

value: bacterial culture


description:
Library name: LP_ATAC-FOXM1-6h-1
library prep for ATAC-FOXM1-6h-1 derived from ADLI-2-1-015-1-13__OCM_NLS21

value: Auxin


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H11

description:
Library name: delta_del_160_library_3_H11
M3-Seq


title: Omasum,Lactation,Goat-2

description: Library name: OM2

source_name: Omasum

value: Omasum


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H9

description:
Library name: delta_del_160_library_3_H9
M3-Seq


description:
Library name: LP_ATAC-FOXM1-24h-2
library prep for ATAC-FOXM1-24h-2 derived from ADLI-2-1-015-1-13__OCM_NLS21


title: E. coli 0.25x MIC Corramycin rep 1, 45 min

city: Saarbrücken

first: Franziska

last: Fries

state: Saarland

address: Campus E8 1

department: Microbial Natural Products

institute: Helmholtz Institute for Pharmaceutical Research Saarland

description:
Library name: Sampe 19
Forward and reverse reads are denoted by R1 and R2.

data_processing:
Raw sequencing data was analyzed using Geneious Prime (version 2023.1.1). Reads were mapped to the reference sequence (NCBI NZ_CP009072.1 and NC_000962.3) and mRNA abundances were quantified as transcripts per million (TPM) prior to differential gene expression analysis with DESeq2.
Assembly: NCBI NZ_CP009072.1 (E. coli ATCC25922), NCBI NC_000962.3 (Mtb H37Rv)
Supplementary files format and content: csv files include raw transcript counts and normalized counts RPKM, TPM
Supplementary files format and content: xlsx files contain differential expression tables for the different samples, organized by organism (each with different sheets for the different conditions).

organism: Escherichia coli

growth_protocol: E. coli ATCC25922 was grown overnight in cation-adjusted Mueller-Hinton broth (MHB2) at 37 °C with shaking. The next morning, the culture was sub-cultured 1:100 in fresh MHB2 and grown until log-phase, after which the culture was adjusted to an OD600 of 0.5. M. tuberculosis H37Ra was grown in Middlebrook 7H9 medium supplemented with 10% OADC until log-phase was reached. Single cells were prepared by syringing and the culture was adjusted to an OD600 of 0.5.

extract_protocol:
For E. coli, 500 µL of samples were centrifuged at 5,000 g, RT, 10 min. The supernatant was removed and pellets were dissolved in TE buffer (100 mM Tris, 1 mM EDTA, pH 8.0) containing 15 mg/mL lysozyme and 20 µL of proteinase K (Qiagen). Samples were mechanically disrupted with acid-washed glass beads (one spatula tip of sizes 150-212 µm, 212-300 µm and 425-600 µm, respectively) using the TissueLyser II (Qiagen) at a frequency of 1/s for 5 min. 700 µL QIAzol lysis reagent (Qiagen) were added and samples were disrupted for another two cycles with the TissueLyser II. Subsequently, total RNA was extracted using the RNeasy mini kit (Qiagen). For Mtb, 7 mL of samples were drawn and total RNA was extracted following a protocol consisting of mechanical disruption with the FastPrep machine (MP Biomedicals, Irvine, CA, USA) and extraction using the RNeasy mini kit (Qiagen).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Preparation Kit.

treatment_protocol: For E. coli, bacteria were treated with 0.125x, 0.25x or 0.5x MIC of corramycin, or DMSO (control) for either 15 min or 45 min. Each condition was performed in triplicates. For M. tuberculosis, bacteria were exposed to 0.5x, 1x or 2x MIC of corramycin, or DMSO (control) for either 6 h or 24 h. Each condition was performed in triplicates.

value: bacterial strain


title: B16F10 cells, STM9005, 3 days, rep3

description: Library name: B16F10_STM9005_3d_3

value: Melanoma

value: STM9005 3 days


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H8

description:
Library name: delta_del_160_library_3_H8
M3-Seq


title: Omasum,Lactation,Goat-3

description: Library name: OM3


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H7

description:
Library name: delta_del_160_library_3_H7
M3-Seq


description:
Library name: LP_ATAC-FOXM1-24h-1
library prep for ATAC-FOXM1-24h-1 derived from ADLI-2-1-015-1-13__OCM_NLS21


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H6

description:
Library name: delta_del_160_library_3_H6
M3-Seq


title: Masseter muscle,Dry,Goat-54

description: Library name: MM54

value: Masseter muscle


title: Omasum,Lactation,Goat-6

description: Library name: OM6


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H5

description:
Library name: delta_del_160_library_3_H5
M3-Seq


description:
Library name: LP_ATAC-FOXM1-0h-2
library prep for ATAC-FOXM1-0h-2 derived from ADLI-2-1-015-1-13__OCM_NLS21

value: DMSO


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H4

description:
Library name: delta_del_160_library_3_H4
M3-Seq


title: Omasum,Dry,Goat-54

description: Library name: OM54


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H3

description:
Library name: delta_del_160_library_3_H3
M3-Seq


title: Medulla oblongata,Lactation,Goat-6

description: Library name: MO6

value: Medulla oblongata


description:
Library name: LP_ATAC-FOXM1-0h-1
library prep for ATAC-FOXM1-0h-1 derived from ADLI-2-1-015-1-13__OCM_NLS21


title: Pif1-FRB, pGAL-AID-FKBP12 in rrm3 ung1 With HU, + galactose, + rapamycin, 2days

city: New York

first: Shaili

last: Regmi

address: 100 Washington Sq E

institute: New York University

description: Library name: sr5965_5_13

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 using an SP flow cell with 150 bp paired-end reads (300 cycle v1.5 kit). Reads were basecalled using Picard IlluminaBasecallsToFastq v2.23.8 with APPLY_EAMSS_FILTER set to false and demultiplexed using Pheniqs v2.1.0.
Paired reads were aligned to the custom W303-1A RAD5+ reference genome using BWA-MEM v0.7.17 with default parameters.
BAM files were coordinate-sorted and indexed using SAMtools v1.14. Alignments bearing secondary (XA:Z:) or supplementary/chimeric (SA:Z:) tags were removed, and reads with mapping quality (MAPQ) >= 30, excluding unmapped/secondary/supplementary/duplicate flags (3332) and requiring the properly paired flag (2), were retained. PCR duplicates were identified and removed using Picard MarkDuplicates v2.27.5 with the REMOVE_DUPLICATES=true option.
Deduplicated BAM files were indexed and pileup files generated using SAMtools mpileup against the custom reference genome. SNPs were called from the pileups using VarScan v2.4.2 (p-value threshold 0.95, minimum variant allele frequency 0.001, VCF output, other parameters default).
Assembly: custom (YTT166_VF.fasta)
Supplementary files format and content: Variant Call Format (VCF) file generated using VarScan v2.4.2

organism: Saccharomyces cerevisiae

source_name: W303 RAD5+ haploid

extract_protocol:
DNA was extracted as described in Hennion,M., Theulot,B., Arbona,J.-M., Audit,B. and Hyrien,O. (2022) FORK-seq: Single-Molecule Profiling of DNA Replication. In Devaux,F. (ed), Yeast Functional Genomics, Methods in Molecular Biology. Springer US, New York, NY, Vol. 2477, pp. 107–128.
Sequencing libraries were prepared using Illumina DNA Prep Kit (20049005) and barcoded using IDT for Illumina Nextera DNA UD Indexes (20026934) according to the manufacturer’s instructions (Illumina, Inc.).

value: W303 RAD5+ haploid

value: MATa, Pif1-V5-linkerV2-FRB::HYG, rrm3::G418, leu2-3,112::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: Omasum,Dry,Goat-64

description: Library name: OM64


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H2

description:
Library name: delta_del_160_library_3_H2
M3-Seq


title: Pif1-FRB, pGAL-AID-FKBP12 in rrm3 ung1 With HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_05


title: Omasum,Dry,Goat-73

description: Library name: OM73


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well H1

description:
Library name: delta_del_160_library_3_H1
M3-Seq


description:
Library name: LP_ATAC-FOXA1-6h-2
library prep for ATAC-FOXA1-6h-2 derived from ADLI-5-1-125-3-10__OCP_210A


description:
Library name: LP_ATAC-FOXA1-6h-1
library prep for ATAC-FOXA1-6h-1 derived from ADLI-5-1-125-3-10__OCP_210A


title: Pif1-FRB, pGAL-AID-FKBP12 in ung1 With HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_5_12

value: MATa, Pif1-V5-linkerV2-FRB::HYG, leu2-3::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: Ovary,Lactation,Goat-2

description: Library name: OV2

source_name: Ovary

value: Ovary


title: E. coli 0.125x MIC Corramycin rep 3, 45 min

description:
Library name: Sample 18
Forward and reverse reads are denoted by R1 and R2.


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G12

description:
Library name: 119_del_160_library_3_G12
M3-Seq


description:
Library name: LP_ATAC-FOXA1-24h-2
library prep for ATAC-FOXA1-24h-2 derived from ADLI-5-1-125-3-10__OCP_210A

value: iPSC

value: Knock-in of inducible C-terminal degron


title: Pif1-FRB, pGAL-AID-FKBP12 in ung1 With HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_04


title: Ovary,Lactation,Goat-3

description: Library name: OV3


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G11

description:
Library name: 119_del_160_library_3_G11
M3-Seq

value: Bacterial cells


description:
Library name: LP_ATAC-FOXA1-24h-1
library prep for ATAC-FOXA1-24h-1 derived from ADLI-5-1-125-3-10__OCP_210A


title: Pif1-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_4_16


title: Ovary,Dry,Goat-54

description: Library name: OV54


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G10

description:
Library name: 119_del_160_library_3_G10
M3-Seq

value: Phage infected


description:
Library name: LP_ATAC-FOXA1-0h-3
library prep for ATAC-FOXA1-0h-3 derived from ADLI-5-1-125-3-10__OCP_210A


title: Pif1-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_4_12


title: Ovary,Dry,Goat-73

description: Library name: OV73


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G9

description:
Library name: 119_del_160_library_3_G9
M3-Seq


description:
Library name: LP_ATAC-FOXA1-0h-2
library prep for ATAC-FOXA1-0h-2 derived from ADLI-5-1-125-3-10__OCP_210A


title: Pif1-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, no rapamycin, 1day

description: Library name: sr5965_4_04


title: Medulla oblongata,Dry,Goat-73

description: Library name: MO73


title: Adrenal gland(medulla),Dry,Goat-54

description: Library name: AGM54

source_name: Adrenal gland(medulla)

value: Adrenal gland(medulla)


description:
Library name: LP_ATAC-CHD4-6h-2
library prep for ATAC-CHD4-6h-2 derived from ADLI-0-0-040-1-3__OCM_108

value: Auxin


title: Pineal gland,Lactation,Goat-2

description: Library name: PG2

source_name: Pineal gland

value: Pineal gland


title: Sgs1-FRB, pGAL-AID-FKBP12 in hrq1 ung1 With HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_5_14

value: MATa, Sgs1-V5-linkerV2-FRB::HYG, hrq1::G418, leu2-3,112::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G8

description:
Library name: 119_del_160_library_3_G8
M3-Seq


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G7

description:
Library name: 119_del_160_library_3_G7
M3-Seq


description:
Library name: LP_ATAC-CHD4-6h-1
library prep for ATAC-CHD4-6h-1 derived from ADLI-0-0-040-1-3__OCM_108


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G6

description:
Library name: 119_del_160_library_3_G6
M3-Seq


title: Sgs1-FRB, pGAL-AID-FKBP12 in hrq1 ung1 With HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_06


title: Pineal gland,Lactation,Goat-3

description: Library name: PG3


title: Sgs1-FRB, pGAL-AID-FKBP12 in ung1 With HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_02

value: MATa, Sgs1-V5-linkerV2-FRB::HYG, leu2-3::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: Sgs1-FRB, pGAL-AID-FKBP12 in ung1 With HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_5_10


description:
Library name: LP_ATAC-CHD4-0h-2
library prep for ATAC-CHD4-0h-2 derived from ADLI-0-0-040-1-3__OCM_108


title: Sgs1-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_4_14


description:
Library name: LP_ATAC-CHD4-24h-1
library prep for ATAC-CHD4-24h-1 derived from ADLI-0-0-040-1-3__OCM_108


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G5

description:
Library name: 119_del_160_library_3_G5
M3-Seq


title: Pineal gland,Dry,Goat-64

description: Library name: PG64


description:
Library name: LP_ATAC-HDAC3-6h-3
library prep for ATAC-HDAC3-6h-3 derived from ADLI-4-1-115-3-8__OCP_74G


description:
Library name: LP_ATAC-CHD4-24h-2
library prep for ATAC-CHD4-24h-2 derived from ADLI-0-0-040-1-3__OCM_108


title: Pineal gland,Dry,Goat-54

description: Library name: PG54


title: Pineal gland,Lactation,Goat-6

description: Library name: PG6


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G3

description:
Library name: 119_del_160_library_3_G3
M3-Seq


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G4

description:
Library name: 119_del_160_library_3_G4
M3-Seq


description:
Library name: LP_ATAC-CHD4-0h-1
library prep for ATAC-CHD4-0h-1 derived from ADLI-0-0-040-1-3__OCM_108


title: Sgs1-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_4_10


title: Pineal gland,Dry,Goat-73

description: Library name: PG73


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G1

description:
Library name: 119_del_160_library_3_G1
M3-Seq


title: Rostral colliculus,Lactation,Goat-2

description: Library name: RC2

source_name: Rostral colliculus

value: Rostral colliculus


title: Sgs1-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, no rapamycin, 1day

description: Library name: sr5965_4_02


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H12

description:
Library name: delta_del_160_library_2_H12
M3-Seq

value: Pa011 DeltaCBASS


title: Rrm3-FRB, pGAL-AID-FKBP12 in pif1-m2 ung1 With HU Rep2, + galactose, + rapamycin, 2days

description: Library name: sr5965_8_07

value: MATa, Rrm3-V5-linkerV2-FRB::HYG, pif1-m2::G418, leu2-3,112::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+ #2


description:
Library name: LP_ATAC-CHAF1A-6h-2
library prep for ATAC-CHAF1A-6h-2 derived from ADLI-4-2-085-3__OCP_74G


description:
Library name: LP_ATAC-CHAF1A-6h-1
library prep for ATAC-CHAF1A-6h-1 derived from ADLI-4-2-085-3__OCP_74G


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 3, well G2

description:
Library name: 119_del_160_library_3_G2
M3-Seq


title: Rostral colliculus,Lactation,Goat-3

description: Library name: RC3


description:
Library name: LP_ATAC-CHAF1A-24h-2
library prep for ATAC-CHAF1A-24h-2 derived from ADLI-4-2-085-3__OCP_74G


title: Rrm3-FRB, pGAL-AID-FKBP12 in pif1-m2 ung1 With HU Rep1, + galactose, + rapamycin, 2days

description: Library name: sr5965_5_16

value: MATa, Rrm3-V5-linkerV2-FRB::HYG, pif1-m2::G418, leu2-3,112::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H11

description:
Library name: delta_del_160_library_2_H11
M3-Seq


description:
Library name: LP_ATAC-CHAF1A-0h-2
library prep for ATAC-CHAF1A-0h-2 derived from ADLI-4-2-085-3__OCP_74G

value: DMSO


title: Rrm3-FRB, pGAL-AID-FKBP12 in pif1-m2 ung1 With HU Rep1, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_08

value: W303 RAD5+ haploid


title: Adrenal gland(medulla),Dry,Goat-64

description: Library name: AGM64


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H9

description:
Library name: delta_del_160_library_2_H9
M3-Seq


description:
Library name: LP_ATAC-CHAF1A-0h-1
library prep for ATAC-CHAF1A-0h-1 derived from ADLI-4-2-085-3__OCP_74G


title: Rostral colliculus,Dry,Goat-64

description: Library name: RC64


title: Rrm3-FRB, pGAL-AID-FKBP12 in ung1 With HU Rep2, + galactose, + rapamycin, 2days

description: Library name: sr5965_8_06

value: MATa, Rrm3-V5-linkerV2-FRB::HYG, leu2-3::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+ #2


title: Rostral colliculus,Lactation,Goat-6

description: Library name: RC6


title: Rrm3-FRB, pGAL-AID-FKBP12 in ung1 With HU Rep1, + galactose, + rapamycin, 2days

description: Library name: sr5965_5_11

value: MATa, Rrm3-V5-linkerV2-FRB::HYG, leu2-3::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H10

description:
Library name: delta_del_160_library_2_H10
M3-Seq


description:
Library name: LP_ATAC-CHAF1A-24h-1
library prep for ATAC-CHAF1A-24h-1 derived from ADLI-4-2-085-3__OCP_74G

value: iPSC


title: Rrm3-FRB, pGAL-AID-FKBP12 in ung1 With HU Rep1, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_03


description:
Library name: LP_ATAC-ARID3B-6h-2
library prep for ATAC-ARID3B-6h-2 derived from ADLI-0-0-054-3-12__OCM_108

value: Knock-in of inducible C-terminal degron


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H8

description:
Library name: delta_del_160_library_2_H8
M3-Seq

value: Bacterial cells


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H7

description:
Library name: delta_del_160_library_2_H7
M3-Seq

value: Phage infected


title: Rostral colliculus,Dry,Goat-73

description: Library name: RC73


title: Rhinencephalon,Lactation,Goat-6

description: Library name: RHI6

source_name: Rhinencephalon

value: Rhinencephalon


title: Rhinencephalon,Dry,Goat-54

description: Library name: RHI54


description:
Library name: LP_ATAC-ARID3B-6h-1
library prep for ATAC-ARID3B-6h-1 derived from ADLI-0-0-054-3-11__OCM_108

value: Auxin


title: Rrm3-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_4_15


title: WT embryos, 33 hours post fertilization, biol rep 1

description:
Library name: hrs33_1
column name in raw counts:hrs33_1

source_name: Embryos

value: Embryos

value: Wildtype


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H6

description:
Library name: delta_del_160_library_2_H6
M3-Seq


title: Rrm3-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_4_11


title: Rhinencephalon,Dry,Goat-64

description: Library name: RHI64


description:
Library name: LP_ATAC-ARID3B-24h-2
library prep for ATAC-ARID3B-24h-2 derived from ADLI-0-0-054-3-10__OCM_108


title: Rrm3-FRB, pGAL-AID-FKBP12 in ung1 No HU, + galactose, no rapamycin, 1day

description: Library name: sr5965_4_03


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H5

description:
Library name: delta_del_160_library_2_H5
M3-Seq


title: Rhinencephalon,Dry,Goat-73

description: Library name: RHI73


description:
Library name: LP_ATAC-ARID3B-24h-1
library prep for ATAC-ARID3B-24h-1 derived from ADLI-0-0-054-3-09__OCM_108


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H4

description:
Library name: delta_del_160_library_2_H4
M3-Seq


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 With HU, + galactose, + rapamycin, 2days

description: Library name: sr5965_5_09

value: MATa, Hrq1-V5-linkerV2-FRB::HYG, leu2-3::LEU2-pGal1-AID-V5-linkerV2-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


description:
Library name: LP_ATAC-ARID3B-0h-2
library prep for ATAC-ARID3B-0h-2 derived from ADLI-0-0-054-3-08__OCM_108


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H3

description:
Library name: delta_del_160_library_2_H3
M3-Seq


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H2

description:
Library name: delta_del_160_library_2_H2
M3-Seq


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 With HU, + galactose, no rapamycin, 2days

description: Library name: sr5965_5_01


description:
Library name: LP_ATAC-ARID3B-0h-1
library prep for ATAC-ARID3B-0h-1 derived from ADLI-0-0-054-3-07__OCM_108


title: msk_pooledseq_polyIII-H1 derived Definitive endoderm (stage 1)

description:
Library name: PolyIII_DE_40KO
gene barcode-H1 derived Definitive endoderm (stage 1)

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: counts and feature counts as h5ad files

extract_protocol: Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1, Illunmina NovaSeq 6000

value: ESC

value: CRISPR/Cas9 method

value: ARID1A, PRR12, TCF4, TCF7L2, CDKN1C, SOX11, PAX6, MEIS1, SIX3, HES1, ISL1, KLF11, PBX1, NOTCH2, CBX4, JMJD6, MORC3, NOTCH1, SMARCC2, SMARCD3, MEF2C, NR2F1, NR2F2, POU3F2, TET1, SETD1B, FOXP2, MEN1, HNF1B, PAX4, PTF1A, SYT4, ZNF800, CTNNBIP1, HEY1, VEZF1, ZNF608, RB1, RCOR2, SOX17

value: 3 days

value: Definitive endoderm (stage 1)


title: Reticulum,Lactation,Goat-3

description: Library name: RT3

source_name: Reticulum

value: Reticulum


title: Adrenal gland(medulla),Dry,Goat-73

description: Library name: AGM73

value: Adrenal gland(medulla)


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library 2, well H1

description:
Library name: delta_del_160_library_2_H1
M3-Seq

value: Pa011 DeltaCBASS


title: msk_pooledseq_polyIII-H1 derived ESC (stage 0)

description:
Library name: PolyIII_ES_40KO
gene barcode-H1 derived ESC (stage 0)

value: -1 day

value: ESC (stage 0)


title: Reticulum,Dry,Goat-64

description: Library name: RT64


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep2, + galactose, + rapamycin, 2days

description: Library name: sr5965_4_13

value: W303 RAD5+ haploid


title: Reticulum,Lactation,Goat-6

description: Library name: RT6


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G12

description:
Library name: 119_del_160_library_2_G12
M3-Seq

value: Bacterial cells

value: Phage infected


title: msk_pooledseq_larry-H1 derived Definitive endoderm (stage 1)

description:
Library name: LARRY_DE_40KO
cell barcode-H1 derived Definitive endoderm (stage 1)


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep2, + galactose, no rapamycin, 2days

description: Library name: sr5965_4_09


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep2, + galactose, + rapamycin, 1day

description: Library name: sr5965_4_05


title: msk_pooledseq_larry-H1 derived ESC (stage 0)

description:
Library name: LARRY_ES_40KO
cell barcode-H1 derived ESC (stage 0)


title: Reticulum,Dry,Goat-73

description: Library name: RT73


title: Rumen,Lactation,Goat-3

description: Library name: RU3

source_name: Rumen

value: Rumen


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep2, + galactose, no rapamycin, 1day

description: Library name: sr5965_4_01


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G11

description:
Library name: 119_del_160_library_2_G11
M3-Seq


title: Neurohypophysis,Dry,Goat-54

description: Library name: NYP54

value: Neurohypophysis


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G10

description:
Library name: 119_del_160_library_2_G10
M3-Seq


title: Rumen,Lactation,Goat-6

description: Library name: RU6


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep1, + galactose, + rapamycin, 2days

description: Library name: sr5965_3_13

value: MATa, Hrq1-V5-FRB::HYG, leu2-3,112::LEU2-pGal1-AID-V5-FKBP12-2xNLS, ung1::TRP, tor1-1::HIS3, fpr1::NatMX4, ade2-1 can1-100 his3-11,15 trp1-1 ura3-1 RAD5+


title: msk_pooledseq_transcriptome-H1 derived ESC (stage 0)

description:
Library name: mRNA_ES_40KO
transcriptome library-H1 derived ESC (stage 0)


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep1, + galactose, + rapamycin, 1day

description: Library name: sr5965_3_12


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G9

description:
Library name: 119_del_160_library_2_G9
M3-Seq


title: msk_pooledseq_transcriptome-H1 derived Definitive endoderm (stage 1)

description:
Library name: mRNA_DE_40KO
transcriptome library-H1 derived Definitive endoderm (stage 1)


title: Rumen,Dry,Goat-54

description: Library name: RU54


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G8

description:
Library name: 119_del_160_library_2_G8
M3-Seq


title: HC10

city: Nanjing

first: Ruixi

last: Ye

state: Jiangsu

address: 南京市栖霞区仙林大道163号

institute: Nanjing University

description: Library name: HC10

data_processing:
Sequence reads failing to meet quality control criteria (quality scores < 25 or length < 18 nucleotides) were excluded. Clean reads were mapped sequentially against non-coding RNA databases: (i) miRBase v22 for miRNAs, (ii) GtRNAdb 21 of hg19 for genomic tRNAs, (iii) rRNA databases from NCBI, and (iv) piRBase v3.0 for piRNAs.
Supplementary files format and content: tab-delimited text file includes raw and CPM normalized counts for each Sample

source_name: peripheral venous blood

extract_protocol:
Total RNA was extracted from serum using the RNA Simple Total RNA Kit (Tiangen Biotech, Beijing, Cat. no. 4992858) following the manufacturer’s protocol.
Small-RNA libraries were prepared using the VAHTS Small RNA Library Prep Kit (Vazyme, Nanjing) and sequenced on an Illumina NovaSeq 6000 platform using the NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles).

value: peripheral venous blood

value: Male

tag: disease state

value: healthy control


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep1, + galactose, no rapamycin, 1day

description: Library name: sr5965_3_11


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G7

description:
Library name: 119_del_160_library_2_G7
M3-Seq


title: HC9

address: 南京市栖霞区仙林大道163号

description: Library name: HC9

tag: Sex


title: Rumen,Dry,Goat-64

description: Library name: RU64


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G6

description:
Library name: 119_del_160_library_2_G6
M3-Seq


title: Rumen,Dry,Goat-73

description: Library name: RU73


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep1, no galactose, + rapamycin, 1day

description: Library name: sr5965_3_10


title: HC8

address: 南京市栖霞区仙林大道163号

description: Library name: HC8


title: Adenohypophysis,Lactation,Goat-2

description: Library name: AYP2

source_name: Adenohypophysis

value: Adenohypophysis


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G5

description:
Library name: 119_del_160_library_2_G5
M3-Seq


title: pGAL-Hrq1KA-AID in hrq1 ung1 Rep2

description: Library name: sr5965_8_05

value: MATa, hrq1::NAT, ung1::TRP, pESC-URA-Hrq1-K318A-AID, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: Hrq1-FRB, pGAL-AID-FKBP12 in ung1 No HU Rep1, no galactose, no rapamycin, 1day

description: Library name: sr5965_3_09


title: HC7

address: 南京市栖霞区仙林大道163号

description: Library name: HC7

value: Female


title: Subcutaneous fat,Lactation,Goat-2

description: Library name: SF2

source_name: Subcutaneous fat

value: Subcutaneous fat


title: pGAL-Hrq1-AID in hrq1 ung1 Rep2

description: Library name: sr5965_8_04

value: MATa, hrq1::NAT, ung1::TRP, pESC-URA-Hrq1-AID, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G4

description:
Library name: 119_del_160_library_2_G4
M3-Seq


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G3

description:
Library name: 119_del_160_library_2_G3
M3-Seq


title: Subcutaneous fat,Lactation,Goat-3

description: Library name: SF3


title: HC6

address: 南京市栖霞区仙林大道163号

description: Library name: HC6


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G2

description:
Library name: 119_del_160_library_2_G2
M3-Seq


title: pGAL-AID in hrq1 ung1 Rep2

description: Library name: sr5965_8_03

value: MATa, hrq1::NAT, ung1::TRP, pESC-URA-AID, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: Subcutaneous fat,Dry,Goat-54

description: Library name: SF54


title: Subcutaneous fat,Dry,Goat-64

description: Library name: SF64


title: pGAL-EV in hrq1 ung1 Rep2

description: Library name: sr5965_8_02

value: MATa, hrq1::NAT, ung1::TRP, pESC-URA, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: HC5

address: 南京市栖霞区仙林大道163号

description: Library name: HC5


title: HC4

address: 南京市栖霞区仙林大道163号

description: Library name: HC4


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, library2, well G1

description:
Library name: 119_del_160_library_2_G1
M3-Seq


title: pGAL-Hrq1-AID in hrq1 Rep2

description: Library name: sr5965_8_01

value: MATa, hrq1::NAT, pESC-URA-Hrq1-AID, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: HC3

address: 南京市栖霞区仙林大道163号

description: Library name: HC3


title: Spleen,Lactation,Goat-2

description: Library name: SP2

source_name: Spleen

value: Spleen


title: pGAL-Hrq1KA-AID in hrq1 ung1 Rep1

description: Library name: sr5965_3_08

value: W303 RAD5+ haploid


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H12

description:
Library name: delta_del_160_library_1_H12
M3-Seq

value: Bacterial cells

value: Pa011 DeltaCBASS

value: Phage infected


title: Spleen,Lactation,Goat-3

description: Library name: SP3


title: HC2

address: 南京市栖霞区仙林大道163号

description: Library name: HC2


title: HC1

address: 南京市栖霞区仙林大道163号

description: Library name: HC1


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H11

description:
Library name: delta_del_160_library_1_H11
M3-Seq


title: pGAL-Hrq1-AID in hrq1 ung1 Rep1

description: Library name: sr5965_3_07


title: Spleen,Lactation,Goat-6

description: Library name: SP6


title: CRC10

address: 南京市栖霞区仙林大道163号

description: Library name: CRC10

value: colorectal cancer


title: pGAL-AID in hrq1 ung1 Rep1

description: Library name: sr5965_3_06


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H10

description:
Library name: delta_del_160_library_1_H10
M3-Seq


title: Spleen,Dry,Goat-54

description: Library name: SP54


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H9

description:
Library name: delta_del_160_library_1_H9
M3-Seq


title: CRC9

address: 南京市栖霞区仙林大道163号

description: Library name: CRC9

value: peripheral venous blood


title: pGAL-EV in hrq1 ung1 Rep1

description: Library name: sr5965_3_05


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H8

description:
Library name: delta_del_160_library_1_H8
M3-Seq


title: Spleen,Dry,Goat-64

description: Library name: SP64


title: CRC8

address: 南京市栖霞区仙林大道163号

description: Library name: CRC8


title: Spleen,Dry,Goat-73

description: Library name: SP73


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H7

description:
Library name: delta_del_160_library_1_H7
M3-Seq


title: pGAL-Hrq1KA-AID in hrq1 Rep1

description: Library name: sr5965_3_04

value: MATa, hrq1::NAT, pESC-URA-Hrq1-K318A-AID, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: CRC7

address: 南京市栖霞区仙林大道163号

description: Library name: CRC7


title: pGAL-Hrq1-AID in hrq1 Rep1

description: Library name: sr5965_3_03


title: Thyroid,Lactation,Goat-2

description: Library name: THY2

source_name: Thyroid

value: Thyroid


title: CRC6

address: 南京市栖霞区仙林大道163号

description: Library name: CRC6

value: Male


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H6

description:
Library name: delta_del_160_library_1_H6
M3-Seq


title: pGAL-AID in hrq1 Rep1

description: Library name: sr5965_3_02

value: MATa, hrq1::NAT, pESC-URA-AID, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: Thyroid,Dry,Goat-54

description: Library name: THY54


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H5

description:
Library name: delta_del_160_library_1_H5
M3-Seq


title: CRC5

address: 南京市栖霞区仙林大道163号

description: Library name: CRC5

value: Female


title: Thyroid,Dry,Goat-64

description: Library name: THY64


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H4

description:
Library name: delta_del_160_library_1_H4
M3-Seq


title: CRC4

address: 南京市栖霞区仙林大道163号

description: Library name: CRC4


title: Xenium P1 Female_Rep2

type: RNA

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

description: FFPE single-cell spatial transcriptomics

hyb_protocol: Probe hybridization was performed at 50°C overnight using the pre-designed, 247-probe Xenium Mouse Brain Gene Expression base panel in tandem with a custom 100-probe add-on panel. On the next day, slides underwent wash steps to remove any unhybridized probes, followed by a 2-h ligation step at 37°C to anneal probes to their specific mRNA target. Probes were then enzymatically amplified via rolling circle amplification PCR for 2-h at 37°C. After subsequent washing, quenching steps were performed to reduce background autofluorescence, followed by a DAPI nuclear stain. The slide cassettes were then loaded onto the Xenium Analyzer instrument for quantification.

scan_protocol: Instrument buffers and reagents were prepared as according to the Xenium Analyzer User Guide (10X Genomics). Following instrument initialization, slides and consumables were loaded onto the Xenium Analyzer, and regions of interest were selected after a preliminary sample scan. Once the Xenium Analyzer run began, slides underwent iterative rounds of image acquisition where probe-specific fluorescent oligos were added, hybridized to the amplified probe sequence, imaged and gently removed. After approximately 2 days of on-instrument imaging and analysis, Xenium data was collected for downstream analysis.

data_processing: Xenium In Situ Analyzer performs automated onboard analysis which includes DAPI-based segmentation of nuclei via deep-learning, then expansion of the segmentation masks. A cell-by-gene matrix of segmented nuclei is generated for analysis. Post-processing in R with custom scripts and Seurat.

source_name: whole-brain section

extract_protocol: Emrbyo and postnatal brains collected on corresponding developmental timepoint and drop-fixed in 10% Neutral Buffered Formalin (NBF) at 4°C for 24 hours, followed by three 5-minute 1X PBS washes and dehydration in 70%, 50% and 30% ethanol for 1 hour at room temperature. Samples were stored in 70% ethanol at 4 degrees until paraffin embedding and sectioning which was performed by the Diagnostic and Research Histology Laboratory at UBC.

value: WT mouse


title: pGAL-EV in hrq1 Rep1

description: Library name: sr5965_3_01

value: MATa, hrq1::NAT, pESC-URA, ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H3

description:
Library name: delta_del_160_library_1_H3
M3-Seq

source_name: Bacterial cells


title: Thyroid,Dry,Goat-73

description: Library name: THY73


title: CRC3

address: 南京市栖霞区仙林大道163号

description: Library name: CRC3


title: Xenium P1 Female_Rep1


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H2

description:
Library name: delta_del_160_library_1_H2
M3-Seq


title: Abomasum,Lactation,Goat-6

description: Library name: AB6

source_name: Abomasum

value: Abomasum


title: CRC2

address: 南京市栖霞区仙林大道163号

description: Library name: CRC2


title: Xenium P1 Male_Rep2


title: Adenohypophysis,Dry,Goat-64

description: Library name: AYP64

value: Adenohypophysis


title: Pa011 DeltaCBASS infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well H1

description:
Library name: delta_del_160_library_1_H1
M3-Seq


title: CRC1

address: 南京市栖霞区仙林大道163号

description: Library name: CRC1


title: Adenohypophysis,Dry,Goat-73

description: Library name: AYP73


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G12

description:
Library name: 119_del_160_library_1_G12
M3-Seq


title: Xenium P1 Male_Rep1


title: Xenium E18.5 Female_Rep2


title: Bridge (brainstem),Lactation,Goat-2

description: Library name: BRG2

source_name: Bridge (brainstem)

value: Bridge (brainstem)


title: Treat 3

city: Shanghai

first: Haixia

last: Gao

address: No. 1585 Yuanguo Road, Building 1A, Anting Town, Jiading District

institute: Shanghai University

description: Library name: Sample 6

data_processing:
Raw paired-end fastq reads were quality controlled with FastQC v0.11.9; Trimmomatic v0.39 was used to trim adapters and filter low-quality reads with Q < 20, reads shorter than 50 bp were discarded to generate clean reads.
Assembly: GRCh38 (hg38), Homo sapiens primary assembly from NCBI RefSeq
Supplementary files format and content: Tab-delimited .txt file named all.fpkm_anno.txt, containing gene ID, gene symbol and normalized FPKM expression values of all 6 sequencing samples; each sample column name corresponds to the library name recorded in SAMPLES sheet.

source_name: primary human T lymphocyte

extract_protocol:
Total RNA was extracted from cell pellets using TRIzol reagent following the manufacturer’s standard protocol. RNA integrity and purity were assessed via agarose gel electrophoresis and Nanodrop spectrophotometry; only high-quality intact RNA samples were retained for library construction.
PolyA-tailed mRNA was enriched from total RNA via oligo(dT) magnetic beads. Purified mRNA was fragmented, followed by first-strand and second-strand cDNA synthesis. End repair, A-tailing, adapter ligation and PCR amplification were performed to construct Illumina paired-end RNA-seq libraries.

value: primary human T lymphocyte


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G11

description:
Library name: 119_del_160_library_1_G11
M3-Seq


title: Treat 2

description: Library name: Sample 5


title: Xenium E18.5 Female_Rep1


title: Treat 1

description: Library name: Sample 4


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G10

description:
Library name: 119_del_160_library_1_G10
M3-Seq


title: Bridge (brainstem),Dry,Goat-54

description: Library name: BRG54


title: Xenium E18.5 Male_Rep2


title: Bridge (brainstem),Dry,Goat-64

description: Library name: BRG64


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G9

description:
Library name: 119_del_160_library_1_G9
M3-Seq


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G8

description:
Library name: 119_del_160_library_1_G8
M3-Seq


title: Xenium E18.5 Male_Rep1


title: Ctr 3

description: Library name: Sample 3


title: Ctr 2

description: Library name: Sample 2


title: Abomasum,Dry,Goat-54

description: Library name: AB54


title: Xenium E15.5 Female_Rep2


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G7

description:
Library name: 119_del_160_library_1_G7
M3-Seq


title: Bridge (brainstem),Dry,Goat-73

description: Library name: BRG73


title: Ctr 1

description: Library name: Sample 1


title: Xenium E15.5 Female_Rep1


title: Cerebellar hemisphere,Lactation,Goat-2

description: Library name: CHM2

source_name: Cerebellar hemisphere

value: Cerebellar hemisphere


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G6

description:
Library name: 119_del_160_library_1_G6
M3-Seq

value: Bacterial cells


title: [GEX] Post_Tx2

city: Jongno-gu, Seoul

first: Soyoung

last: Jeong

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

description:
Library name: Post_Tx2
GEX

data_processing:
Raw sequencing reads were aligned to the human reference genome using Cellranger v7.1.0. Further analysis was conducted on R using the Seurat package. SoupX was used to remove ambient RNA. For preprocessing and quality control, cells were filtered using gene counts between 200 and 5,000, and a mitochondrial gene percentage threshold of under ten percent. Doublets were removed using scDblFinder. For CTRL1, CTRL2, GPP1, and GPP2, samples were multiplexed with a single 10x Genomics Chromium GEM and original sequencing FASTQ files were deposited. For Post_Tx1 and Post_Tx2, samples were multiplexed. To remove individual samples from an independent study, cell barcodes corresponding to each sample were used to subset the original Cell Ranger alignment BAM file. FASTQ files deposited were regenerated from the barcode-restricted BAM using 10x Genomics bamtofastq (v1.4.1). The deposited FASTQ files therefore contain sequencing reads associated with cells analyzed in the present study.
Assembly: GRCh38
Supplementary files format and content: rds, processed and annotated seurat object

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using density-gradient centrifugation with Cell Preparation Tubes. Isolated PBMCs were cryopreserved in CellBanker I and stored in liquid nitrogen until use.
Cells were then loaded onto the Chromium Controller. cDNA generation and gene expression library construction were conducted according to the manufacturer’s protocols (10x Genomics user guide CG000330) using the Chromium Next GEM Single Cell 5’ Kit v2 (PN-1000263) and Library Construction Kit (PN-1000190). The quality of final libraries was checked on Agilent TapeStation 4150 (Agilent Technologies). Libraries were pooled and paired-end sequenced on an Illumina NovaSeq 6000.

treatment_protocol: GPP1 was treated with ustekinumab (IL-12/23 blockade), and GPP2 was treated with secukinumab (IL-17A blockade).

value: Blood

value: Secukinumab

tag: timepoint

value: 6 mo post Tx

tag: library type

value: RNA


title: Xenium E15.5 Male_Rep2


title: Cerebellar hemisphere,Lactation,Goat-3

description: Library name: CHM3


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G5

description:
Library name: 119_del_160_library_1_G5
M3-Seq

value: Phage infected


title: Cerebellar hemisphere,Lactation,Goat-6

description: Library name: CHM6


title: Xenium E12.5 Female_Rep2

source_name: whole embryo section


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G4

description:
Library name: 119_del_160_library_1_G4
M3-Seq


title: Cerebellar hemisphere,Dry,Goat-54

description: Library name: CHM54


title: [HTO CTRL1, CTRL2, GPP1, GPP2

description:
Library name: GPP_P_HTO
HTO

value: Baseline

value: HTO


title: [GEX] Post_Tx1

description:
Library name: Post_Tx1
GEX

value: Ustekinumab


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G3

description:
Library name: 119_del_160_library_1_G3
M3-Seq


title: Xenium E12.5 Female_Rep1


title: Xenium E15.5 Male_Rep1


title: Cerebellar hemisphere,Dry,Goat-64

description: Library name: CHM64


title: [GEX] CTRL1, CTRL2, GPP1, GPP2

description:
Library name: GPP_P_GEX
GEX


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G2

description:
Library name: 119_del_160_library_1_G2
M3-Seq


title: HASMC hypertensive hydrostatic pressure replicate 3

city: Shinjyuku

first: Takahiro

last: Kusume

address: 6-1-1, Shinjyuku

institute: Tokyo medical university

description: Library name: Pressure_H_3

data_processing:
Raw reads were assessed using FastQC (v0.11.7).
Adapter sequences and low-quality bases were removed using Trimmomatic (v0.38).
Trimmed reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0).
Gene-level read counts were generated using featureCounts (v1.6.3).
FPKM and TPM values were calculated from mapped reads.
Assembly: hg38
Supplementary files format and content: RawCount_Matrix_ann.txt contains gene-level read counts.
Supplementary files format and content: TPM_Matrix_ann.txt contains TPM-normalized expression values.

source_name: Aorta

growth_protocol: Human aortic smooth muscle cells were purchased from Kurabo (KS-4009, Kurabo, Osaka, Japan) and maintained in HuMedia-SG2 medium (KS2170, Kurabo) containing 5% fetal bovine serum (FBS), insulin (5 μg /ml), human epidermal growth factor (0.5 ng/ml), human basic fibroblast growth factor (2 ng/ml), gentamicin (50 μg /ml) and amphotericin B (50 ng/ml) with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, the Netherlands).
RNA-seq libraries were prepared from total RNA using poly(A) selection with the NE Next Poly(A) mRNA Magnetic Isolation Module, followed by library construction using the NE Next Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: Cells were cultured under control (no mechanical loading), cyclic stretch (10%), normotensive cyclic hydrostatic pressure (120/60 mmHg), or hypertensive cyclic hydrostatic pressure (180/120 mmHg) conditions for 24 h before RNA extraction.

value: Aorta

value: Human aortic smooth muscle cells

tag: cell type

value: vascular smooth muscle cell

value: WT

value: Cyclic hydrostatic pressure (180/120 mmHg, 1Hz)


title: Xenium E12.5 Male_Rep2

value: WT mouse


title: Cerebellar hemisphere,Dry,Goat-73

description: Library name: CHM73


title: Pa011 infected with PaMx41 Deltaacb at MOI=2, 160 minutes post infection, well G1

description:
Library name: 119_del_160_library_1_G1
M3-Seq


title: Xenium E12.5 Male_Rep1


title: Colon,Lactation,Goat-2

description: Library name: CO2

source_name: Colon

value: Colon


title: HASMC hypertensive hydrostatic pressure replicate 2

description: Library name: Pressure_H_2


title: HASMC hypertensive hydrostatic pressure replicate 1

description: Library name: Pressure_H_1