title: Control 3

city: New York

first: Dr. Liang

last: Lei

state: NY

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology

institute: Columbia University

description: Library name: PR8

data_processing:
The fastq files were loaded into 10xGenomics cloud and mapped with Cell Ranger Count v9.0.0 onto Mouse library GRm39 2024-A.
Assembly: Mouse library GRm39 2024-A
Supplementary files format and content: RDS

source_name: Brain

extract_protocol:
Mouse tumor bearing quadrants were homogenized with nuclei isolated according to the Chromium Single Cell Nuclei Isolation Kit protocol (1000494).
Barcoding, library preparation and sequencing were performed by the JP Sulzberger Columbia Genome Center.

value: Brain

value: Control


title: Systemic Dexamethasone 3

status: Public on Jul 07 2026

type: SRA

country: USA

description: Library name: PR7

library_source: transcriptomic single cell

molecule: nuclear RNA

organism: Mus musculus

tag: tissue

tag: treatment

value: Systemic Dexamethasone


title: CED Dexamethasone 3

description: Library name: PR9

value: CED Dexamethasone


title: Control 2

description: Library name: PR6


title: Systemic Dexamethasone 2

description: Library name: PR4


title: CED Dexamethasone 2

description: Library name: PR5


title: CED Dexamethasone 1

description: Library name: PR3


title: Control 1

description: Library name: PR2


title: Systemic Dexamethasone 1

description: Library name: PR1


title: Neuron-PLA-2

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Library name: Sample 18

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Clean Data was mapped to the reference genome using STAR v2.7.9a.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: brain

extract_protocol:
Total RNA was harvested by Trizol reagent. 2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: brain

tag: genotype

value: PLAAT3-PEX11 overexpression


title: Neuron-PLA-1

description: Library name: Sample 17


title: Neuron-ctrl-2

description: Library name: Sample 16

value: WT


title: PLA1-1

description: Library name: Sample 13


title: Neuron-ctrl-1

description: Library name: Sample 15


title: PLA1-2

description: Library name: Sample14


title: Ctrl1-2

description: Library name: Sample 12


title: NSC-Pex7sh-2

description: Library name: Sample10

source_name: primary neural stem cell

tag: cell type

value: primary neural stem cell


title: NSC-Pex7sh-1

description: Library name: Sample9


title: NSC-Scramble-2

description: Library name: Sample8


title: NSC-Scramble-1

description: Library name: Sample7


title: E18

description: Library name: Sample6


title: E16

description: Library name: Sample5


title: E14

description: Library name: Sample4


title: E13

description: Library name: Sample3


title: E11

description: Library name: Sample1


title: E12

description: Library name: Sample2


title: Vestibular ganglion, WT, male, rep3

city: beijing

first: lucinda

last: liu

state: 北京Beijing

address: 7 Science Park Road ZGC Life Science Park

institute: nibs

description: Library name: WT_rep3

data_processing:
Raw sequencing data were processed using Cellranger (10x Genomics, v7.0.0)
Assembly: mouse reference genome (mm10-2020-A, refdata-gex-mm10-2020-A)
Supplementary files format and content: H5 file

molecule: polyA RNA

source_name: vestibular ganglion

extract_protocol:
Temporal bones from 4-week-old male/female C57BL/6J mice (4 mice per preparation; total n = 12 male mice for 3 preparations and 4 female mice for 1 preparation) were isolated in ice-cold dissection buffer (Hanks' Balanced Salt Solution (HBSS) supplemented with 2.5 mM HEPES, 30 mM D-glucose, 1 mM CaCl₂, 1 mM MgSO₄, and 4 mM NaHCO₃. pH 7.4). The vestibular ganglion was carefully dissected by removing the surrounding bony labyrinth and membranous tissues while preserving the ganglion attached to the vestibular nerve. Isolated vestibular ganglia were pooled in Leibovitz's L-15 containing 300 units/mL collagenase IV (ThermoFisher) and 20 kunitz/mL DNase I (Stem Cell Technologies), then incubated for 30 minutes at 37 °C. The collagenase solution was replaced with EBSS containing 30 units of papain (Worthington Biochemical), 1.5 mM L-cysteine, 0.5 mM EDTA, 15 mM HEPES, and 20 kunitz/mL DNase I, followed by incubation for an additional 30 minutes at 37 °C with periodic trituration. An equal volume of Leibovitz's containing 20% ovomucoid protease inhibitor (Worthington Biochemical) was added to stop digestion. The dissociated cells were passed through a 40 μm filter (pluriSelect) to remove debris, pelleted at 300 g for 5 minutes, washed twice with Neurobasal media containing 140 mM D-glucose, 122 mM Trehalose, 0.46 mM Kynurenic acid and 5.54 mg/mL BSA solution, and resuspended in DPBS/BSA solution. Cell concentration and viability were assessed using a Luna Fl automated counter with AO/PI staining (Logos Biosystems).
The cell suspension was processed using the Chromium Single Cell 3' v3 chemistry (10x Genomics). Briefly, cells were loaded onto a Chromium Controller to generate single-cell gel beads-in-emulsion (GEMs), where each cell was co-encapsulated with a uniquely barcoded gel bead in nanoliter-scale droplets. Following cell lysis and barcoding, reverse transcription was performed using the Chromium Single Cell v3 reagent kit (10x Genomics) to generate barcoded cDNA. The cDNA was then amplified by PCR and used to construct sequencing libraries according to the manufacturer's protocol. Sequencing was performed with Illumina (NovaSeq) according to the manufacturer's instructions (Illumina).

value: vestibular ganglion

tag: Sex

value: male

value: Wildtype


title: Vestibular ganglion, WT, female, rep4

description: Library name: WT_rep4

value: female


title: Vestibular ganglion, WT, male, rep2

description: Library name: WT_rep2


title: Kidney, TSC2 KO_6

city: Haining

first: Heng-Jia

last: Liu

state: Zhejiang

address: 718 East Haizhou Road

department: International Campus

institute: Zhejiang University - University of Edinburgh

description:
Library name: TSC2 KO_6
10x Genomics

data_processing:
Raw data were processed by CellRanger (v6.1.1) for sample demultiplexing, barcode processing, and UMI counting, with alignment to the mm10 reference mouse genome.
Assembly: GRCm38
Supplementary files format and content: tsv files including raw counts matrix of each samples

source_name: Kidney

extract_protocol:
The kidneys were minced and transferred into a pre-cooled Miltenyi C-tube containing a protease solution (5 mM CaCl2 [Invitrogen; AM9530G], 10 mg/mL B. Licheniformis protease [Sigma-Aldrich; P5380], 125 U/mL DNase I [Sigma-Aldrich; D5025], 1xPBS), then incubated with gentle rotation at 4 oC for 10 min. After incubation, the samples were run on Miltenyi gentleMACS brain_03 program for three times in a cold room (4 oC). The incubation was repeated with gentle rotation at 4 oC for 10 min. Single-cell dissociation was confirmed by microscopic examination followed by the addition of 3mL ice-cold PBS with 10% FBS. Cells were passed through a 70 µm strainer and filter was rinsed with 3 mL ice-cold PBS with 10%FBS. Then cells were centrifuged at 300 x g at 4 oC for 5 min and passed through 30 µm strainer for two times. Dead cells were removed using Dead Cell Removal MicroBeads (Miltenyi), then excess red blood cells were removed using Anti-Ter-119 MicroBeads (Miltenyi). Cells were resuspended in PBS with 0.04% BSA at 1000 cells/mL.
Single-cell suspensions were super-loaded onto a single lane (Chromium chip G, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. mRNA libraries were sequenced to an average of 50,000 reads per cell using Illumina Novaseq.

value: Kidney


title: Kidney, TSC2 KO_4

description:
Library name: TSC2 KO_4
10x Genomics


title: Vestibular ganglion, WT, male, rep1

description: Library name: WT_rep1


title: Kidney, TSC2 B7-H3 dKO_3

description:
Library name: TSC2 B7-H3 KO_3
10x Genomics


title: Kidney, TSC2 B7-H3 dKO_2

description:
Library name: TSC2 B7-H3 KO_2
10x Genomics


title: Kidney, TSC2 B7-H3 dKO_1

description:
Library name: TSC2 B7-H3 KO_1
10x Genomics


title: 50-sh-Acsf3_ZT3_REP3

city: Nantes

first: Daniel

last: Mauvoisin

address: 8 quai Moncousu

country: France

institute: Inserm

description: Library name: 50-sh-Acsf3_ZT3_REP3.fastq.gz

data_processing:
Raw reads were mapped using STAR on the GRCm38/mm10 genome assembly (Ensembl release 102). The BRB-seqTools suite (http://github.com/DeplanckeLab/BRB-seqTools) was subsequently applied to retrieve raw counts per gene.
Pipeline details have been published by Alpern et al. 2019 ( https://doi.org/10.1186/s13059-019-1671-x )
Assembly: GRCm38/mm10
Supplementary files format and content: Supplementary files format and content: tab-delimited umi count matrix

source_name: liver

extract_protocol:
RNA extraction was performed on frozen liver using Nucleozol following the manufacturer protocol (Macherey Nagel).
Pipeline details have been published by Alpern et al. 2019 ( https://doi.org/10.1186/s13059-019-1671-x )

value: liver

tag: zt

tag: replicate


title: Kidney, TSC2 KO_3

description:
Library name: TSC2 KO_3
10x Genomics


title: Kidney, TSC2 KO_2

description:
Library name: TSC2 KO_2
10x Genomics


title: Kidney WT_2

description:
Library name: WT_2
10x Genomics


title: Kidney WT_3

description:
Library name: WT_3
10x Genomics


title: Kidney, TSC2 KO_1

description:
Library name: TSC2 KO_1
10x Genomics


title: Kidney WT_1

description:
Library name: WT_1
10x Genomics


title: 42-sh-Acsf3_ZT3_REP2

description: Library name: 42-sh-Acsf3_ZT3_REP2.fastq.gz


title: Mouse, wild type, colon tissue, rep 3

city: College Station

first: Destiny

middle: A

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

description: Library name: WT-1355

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregaion were made using the Cell Ranger software v. 8.0.0.
To perform the mapping using the updated genome, we created an adaptation to the "Chromium Mouse Transcriptome Probe Set v1.0.1" (provided). Alternatively, samples can be mapped using 10X Genomics provided "refdata-gex-mm10-2020-A" reference with the "Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv" probe list.
Filtering and normalization were performed using scGEAToolbox. Cell type annotation was performed using PanglaoDB marker gene sets within scGEAToolbox with refinement in Seurat. Cell differentiation potency scores were computed using the CCAT algorithm.
Assembly: GRCm39-2024-A
Assembly: Chromium_Mouse_Transcriptome_Probe_Update2024.csv
Supplementary files format and content: tab separated value files and matrix files
Supplementary files format and content: R data file includes the normalized count matrices, UMAP embeddings, cell type annotation, and CellPotency scores for all cells in all samples.

source_name: colon

extract_protocol:
Mouse colon (30-35 mg) was minced, fixed and dissociated following the 10X Genomics Tissue Fixation & Dissociation for Chormium Fixed RNA Profiling protocol (CG000553). After cell counting, single cells were processed through the 10X Genomics Chromium Fixed RNA Profiling Reagent Kit (CG000527).
Library was prepped using the 10X Genomics Chromium Fixed RNA Profiling Reagent Kit (CG000527). Libraries were quanitated using Kapa quantification kit and pooled for sequencing.

value: colon

value: wild type


title: Mouse, wild type, colon tissue, rep 2

description: Library name: WT-1353


title: Mouse, NR4A1 KO, colon tissue, rep 4

description: Library name: NR4A1-KO-380

value: NR4A1 KO


title: Mouse, wild type, colon tissue, rep 1

description: Library name: WT-1332


title: Mouse, wild type, colon tissue, rep 4

description: Library name: WT-1362


title: Mouse, NR4A1 KO, colon tissue, rep 2

description: Library name: NR4A1-KO-374


title: CONV 1x10Gy_ID561_DG_Other_033

city: Genève

first: Marie-Catherine

last: Vozenin

address: Avenue de la Roseraie 53

department: Radio-Oncologie

country: Switzerland

institute: HUG

description:
Library name: DSP-1001660035574-F-H12
FFPE fixed samples GeoMx Nanostring

data_processing:
DSP data were analyzed in R 4.4.0 (2024) according to Nanostring recommendation, using their in-house tools, with the exception of normalization which was performed using the trimmed mean of M values (TMM) algorithm of edgeR. Other packages were used for data manipulation and plotting as well as gene set enrichment analysis.
First, quality control (QC) was performed for the segments using a set of thresholds on chosen descriptive statistics of the segment. Chosen parameters were used as recommended by Nanostring. Then a Grubb test was performed for gene QC, also using parameters recommended by Nanostring. Next, negative probes were used to evaluate the background of quantification and define limit of quantification thresholds for filtering. Segments that contain less than 5% of the genes above the gene detection threshold and genes that are found in less than 5% of the segments were removed from the analysis. After filtering, normalization was performed using the TMM method of the edgeR package. Robust gene detection rate within segments and cell type specificity were confirmed, enabling downstream analysis.
Data was split per region (CA1, CA3, DG, SO and Cortex) and differential gene expression was performed using a linear mixed model (LMM) with the irradiation modality set as the test variable and the slide number as the random intercept.
All scripts used for the analysis and plotting can be found at https://gitlab.unige.ch/lirr/nanostring_flash_mouse_brain.
Assembly: MW0R30722
Supplementary files format and content: dcc
Library strategy: Spatial Transcriptomics

extract_protocol:
24h post-treatment completion, whole brains were collected and stored at 4°C in 4% PFA for 48 hours before Formalin-Fixed Paraffin-Embedded (FFPE) before processing
FFPE tissue section of 5-µm were processed according to the provider standard protocol for the GeoMx Digital Spatial Profiler (DSP).Neurons were identified using NeuN  (1:100, Millipore ABN78) revealed with a secondary goat anti-rabbit Alexa 594 (1:1000, Abcam ab150080). Vessels and astrocytes were also stained using an antibodies cocktail composed of CD31 Alexa 488 (Vessels, 1/100, R&D FAB3628G) and GFAP Alexa 647 (Astrocytes, 1/100, Novus NBP2-3318). The nuclear marker Syto83 (Invitrogen 511364) was also used. Whole slides were imaged at x20 magnification and morphologic markers were used to select regions of interest (ROI). Automatic segmentation of ROI based on CD31, NeuN and GFAP markers was performed to define area of illumination (AOIs). AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides to be sequenced. Sequencing libraries were generated by PCR from the photo-released indexing oligos. Pooled libraries were single-sequenced at 27 base pairs and with the single-index workflow  on an Illumina NovaSeq S4 instrument.

treatment_protocol: Irradiation was performed using a prototype 6 MeV electron beam, Oriatron type 6e (eRT6; PMB Alcen), LINAC, available at Lausanne University Hospital and described previously. Dosimetry has been extensively described and published to ensure reproducible and reliable biological studies. Animals were randomized in 5 groups and were sham or whole brain irradiated using a single dose of 10 Gy or 3 fractions of 10 Gy delivered 48 hours apart. A 17-mm graphite applicator was used and CONV was delivered at 0.09 Gy/s whereas FLASH was delivered in 1 pulse of 5.6x106Gy/s.

value: Brain

tag: strain

value: Other

value: DG

value: CONV 1x10Gy

tag: batch


title: CONV 1x10Gy_ID561_DG_Neurones_032

description:
Library name: DSP-1001660035574-F-H10
FFPE fixed samples GeoMx Nanostring

value: Neurones


title: CONV 1x10Gy_ID561_CA1_Other_031

description:
Library name: DSP-1001660035574-F-H08
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_DG_Astrocytes_032

description:
Library name: DSP-1001660035574-F-H09
FFPE fixed samples GeoMx Nanostring

value: Astrocytes


title: CONV 1x10Gy_ID561_CA1_Other_030

description:
Library name: DSP-1001660035574-F-H07
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_CA1_Neurones_030

description:
Library name: DSP-1001660035574-F-H06
FFPE fixed samples GeoMx Nanostring


title: 23-sh-Ctl_ZT18_REP3

description: Library name: 23-sh-Ctl_ZT18_REP3.fastq.gz

value: sh-Ctl


title: CONV 1x10Gy_ID561_SO_Other_029

description:
Library name: DSP-1001660035574-F-H04
FFPE fixed samples GeoMx Nanostring

value: SO


title: CONV 1x10Gy_ID561_SO_Other_028

description:
Library name: DSP-1001660035574-F-H03
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_CA1_Astrocytes_030

description:
Library name: DSP-1001660035574-F-H05
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_SO_Astrocytes_028

description:
Library name: DSP-1001660035574-F-H01
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_CA3_Other_026

description:
Library name: DSP-1001660035574-F-G11
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_CA3_Other_027

description:
Library name: DSP-1001660035574-F-G12
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_CA3_Astrocytes_026

description:
Library name: DSP-1001660035574-F-G09
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_Cortex_Neurones_024

description:
Library name: DSP-1001660035574-F-G06
FFPE fixed samples GeoMx Nanostring

value: Cortex


title: CONV 1x10Gy_ID561_Cortex_Vessels_024

description:
Library name: DSP-1001660035574-F-G05
FFPE fixed samples GeoMx Nanostring

value: Vessels


title: CONV 1x10Gy_ID561_Cortex_Other_024

description:
Library name: DSP-1001660035574-F-G07
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_Cortex_Other_023

description:
Library name: DSP-1001660035574-F-G04
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_Cortex_Neurones_023

description:
Library name: DSP-1001660035574-F-G03
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_Cortex_Vessels_023

description:
Library name: DSP-1001660035574-F-G02
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_SO_Other_022

description:
Library name: DSP-1001660035574-F-G01
FFPE fixed samples GeoMx Nanostring

value: FLASH 1x10Gy


title: FLASH 1x10Gy_ID568_SO_Other_020

description:
Library name: DSP-1001660035574-F-F11
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_SO_Neurones_020

description:
Library name: DSP-1001660035574-F-F10
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA1_Neurones_019

description:
Library name: DSP-1001660035574-F-F07
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_SO_Astrocytes_020

description:
Library name: DSP-1001660035574-F-F09
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA1_Astrocytes_019

description:
Library name: DSP-1001660035574-F-F06
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_Cortex_Other_025

description:
Library name: DSP-1001660035574-F-G08
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA3_Other_017

description:
Library name: DSP-1001660035574-F-F04
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA3_Other_018

description:
Library name: DSP-1001660035574-F-F05
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA3_Neurones_017

description:
Library name: DSP-1001660035574-F-F03
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_DG_Neurones_015

description:
Library name: DSP-1001660035574-F-E11
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_DG_Astrocytes_015

description:
Library name: DSP-1001660035574-F-E10
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_DG_Other_016

description:
Library name: DSP-1001660035574-F-F01
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_Cortex_Other_014

description:
Library name: DSP-1001660035574-F-E09
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_Cortex_Other_013

description:
Library name: DSP-1001660035574-F-E08
FFPE fixed samples GeoMx Nanostring


title: Ctrl1-1

description: Library name: Sample 11

value: brain

value: WT


title: FLASH 1x10Gy_ID568_Cortex_Neurones_013

description:
Library name: DSP-1001660035574-F-E07
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_Cortex_Other_012

description:
Library name: DSP-1001660035574-F-E05
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_Cortex_Vessels_012

description:
Library name: DSP-1001660035574-F-E03
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_Cortex_Neurones_011

description:
Library name: DSP-1001660035574-F-E01
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_Cortex_Vessels_011

description:
Library name: DSP-1001660035574-F-D12
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_SO_Other_010

description:
Library name: DSP-1001660035574-F-D11
FFPE fixed samples GeoMx Nanostring


title: Kidney, TSC2 KO_5

description:
Library name: TSC2 KO_5
10x Genomics

value: Kidney


title: FLASH 1x10Gy_ID567_SO_Neurones_009

description:
Library name: DSP-1001660035574-F-D09
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_SO_Other_009

description:
Library name: DSP-1001660035574-F-D10
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA1_Other_008

description:
Library name: DSP-1001660035574-F-D07
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_SO_Astrocytes_009

description:
Library name: DSP-1001660035574-F-D08
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA1_Other_007

description:
Library name: DSP-1001660035574-F-D06
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA1_Neurones_007

description:
Library name: DSP-1001660035574-F-D05
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA1_Astrocytes_007

description:
Library name: DSP-1001660035574-F-D04
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA3_Other_005

description:
Library name: DSP-1001660035574-F-D02
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA3_Other_006

description:
Library name: DSP-1001660035574-F-D03
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA3_Neurones_005

description:
Library name: DSP-1001660035574-F-D01
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_CA3_Astrocytes_005

description:
Library name: DSP-1001660035574-F-C12
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_DG_Other_004

description:
Library name: DSP-1001660035574-F-C11
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_DG_Other_003

description:
Library name: DSP-1001660035574-F-C10
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_DG_Neurones_003

description:
Library name: DSP-1001660035574-F-C09
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_DG_Astrocytes_003

description:
Library name: DSP-1001660035574-F-C08
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_Cortex_Neurones_002

description:
Library name: DSP-1001660035574-F-C06
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_Cortex_Vessels_002

description:
Library name: DSP-1001660035574-F-C05
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID567_Cortex_Other_001

description:
Library name: DSP-1001660035574-F-C04
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_SO_Other_018

description:
Library name: DSP-1001660035574-F-C03
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_SO_Neurones_018

description:
Library name: DSP-1001660035574-F-C02
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_CA1_Other_017

description:
Library name: DSP-1001660035574-F-B12
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_CA1_Neurones_017

description:
Library name: DSP-1001660035574-F-B11
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_CA3_Neurones_016

description:
Library name: DSP-1001660035574-F-B08
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_CA3_Other_016

description:
Library name: DSP-1001660035574-F-B09
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_DG_Astrocytes_015

description:
Library name: DSP-1001660035574-F-B04
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_Cortex_Other_014

description:
Library name: DSP-1001660035574-F-B03
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_Cortex_Neurones_014

description:
Library name: DSP-1001660035574-F-B02
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_Cortex_Vessels_014

description:
Library name: DSP-1001660035574-F-B01
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_Cortex_Neurones_013

description:
Library name: DSP-1001660035574-F-A11
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID560_Cortex_Vessels_013

description:
Library name: DSP-1001660035574-F-A10
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_CA1_Other_012

description:
Library name: DSP-1001660035574-F-A09
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_CA1_Neurones_012

description:
Library name: DSP-1001660035574-F-A08
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_CA1_Astrocytes_012

description:
Library name: DSP-1001660035574-F-A07
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_SO_Neurones_011

description:
Library name: DSP-1001660035574-F-A05
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_SO_Astrocytes_011

description:
Library name: DSP-1001660035574-F-A04
FFPE fixed samples GeoMx Nanostring


title: TTchem, Parental_siCTRL_REP2

status: Public on Jul 08 2026

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Library name: CTRL_REP2
Nascent RNA

library_source: other

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.3 with the STAR (Dobin et al., 2012)
RPKM normalised bigwig files generated using deepTools bamCoverage function with options: --normalizeUsing RPKM --exactScaling –effectiveGenomeSize (Ramirez et al., 2014)
NOTE: The 11 nt UMIs are provided in separate 'R2' fastq files
Assembly: GRCh38
Supplementary files format and content: bigwig files for forward and reverse strands

molecule: other

organism: Homo sapiens

source_name: HEK293 FlpIn-TREx

extract_protocol:
As descriebd in Gregersen et al., 2020, Nat Protoc.
NEBNext Ultra II Direcional RNA Library Prep Kit for Illumina with UMI Adaptors

tag: cell line

value: HEK293 FlpIn-TREx

value: Parental


title: Rhesus macaque airway epithelial cells, Wood smoke, Recovery, S2

city: Davis

first: Hong

last: Ji

state: California

address: One Shields Avenue

department: California National Primate Research Center

institute: University of California, Davis

description:
Library name: Sample 22
Column name in raw_counts_All_Samples.csv: WSR_2

data_processing:
Quality control performed using FastQC
Adapter and quality trimming performed using Trim Galore (adapter stringency = 6, quality cutoff = 20, 10 bp trimmed from 5′ ends, minimum length = 50 bp)
Reads aligned to the rhesus macaque transcriptome (Mmul10) using Bowtie2
Transcript quantification performed using RSEM
Gene-level counts generated using tximport for downstream analysis
Assembly: Mmul10
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

organism: Macaca mulatta

source_name: Airway epithelium

growth_protocol: Primary tracheobronchial epithelial cells isolated from adult female rhesus macaques were expanded and cultured on Transwell inserts. Upon reaching confluence, cells were differentiated at air–liquid interface using BEGM:DMEM (1:1) supplemented with retinoic acid, with media changes every 2–3 days.

extract_protocol:
Cells were lysed using buffer RLT with beta-mercaptoethanol. RNA was extracted using the Qiagen AllPrep DNA/RNA Micro Kit according to manufacturer’s instructions. RNA quantity was measured using Qubit fluorometry.
Poly-A selected RNA libraries were prepared from 0.5 µg total RNA per sample using standard protocols. RNA quality (RIN ≥ 7) was confirmed prior to library preparation.

treatment_protocol: Differentiated primary tracheobronchial epithelial cells cultured at air–liquid interface were exposed to filtered air or diluted whole wood smoke for 6 hours per day for 1 day or 5 consecutive days. A subset of cells exposed for 5 days was allowed to recover for 7 days under standard culture conditions prior to sample collection.

value: Airway epithelium

value: female

tag: age days

tag: weight kgs

tag: animal id

tag: time

value: Recovery


title: CONV 1x10Gy_ID560_Cortex_Other_013

description:
Library name: DSP-1001660035574-F-A12
FFPE fixed samples GeoMx Nanostring

value: Brain

value: Other


title: FLASH 1x10Gy_ID565_CA3_Other_010

description:
Library name: DSP-1001660035574-F-A03
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_CA3_Neurones_010

description:
Library name: DSP-1001660035574-F-A02
FFPE fixed samples GeoMx Nanostring

value: Neurones


title: FLASH 1x10Gy_ID565_CA3_Astrocytes_010

description:
Library name: DSP-1001660022432-E-H12
FFPE fixed samples GeoMx Nanostring

value: Astrocytes


title: FLASH 1x10Gy_ID565_DG_Other_009

description:
Library name: DSP-1001660022432-E-H11
FFPE fixed samples GeoMx Nanostring

value: DG


title: Mouse, NR4A1 KO, colon tissue, rep 3

description: Library name: NR4A1-KO-376

value: colon

value: NR4A1 KO


title: FLASH 1x10Gy_ID565_DG_Neurones_009

description:
Library name: DSP-1001660022432-E-H10
FFPE fixed samples GeoMx Nanostring


title: Mouse, NR4A1 KO, colon tissue, rep 1

description: Library name: NR4A1-KO-372


title: CONV 1x10Gy_ID561_DG_Other_032

description:
Library name: DSP-1001660035574-F-H11
FFPE fixed samples GeoMx Nanostring

value: CONV 1x10Gy


title: FLASH 1x10Gy_ID565_DG_Astrocytes_009

description:
Library name: DSP-1001660022432-E-H09
FFPE fixed samples GeoMx Nanostring

value: FLASH 1x10Gy


title: FLASH 1x10Gy_ID565_Cortex_Other_008

description:
Library name: DSP-1001660022432-E-H08
FFPE fixed samples GeoMx Nanostring

value: Cortex


title: CONV 1x10Gy_ID561_CA3_Neurones_026

description:
Library name: DSP-1001660035574-F-G10
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID561_SO_Neurones_028

description:
Library name: DSP-1001660035574-F-H02
FFPE fixed samples GeoMx Nanostring

value: SO


title: FLASH 1x10Gy_ID565_Cortex_Neurones_008

description:
Library name: DSP-1001660022432-E-H07
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_Cortex_Vessels_008

description:
Library name: DSP-1001660022432-E-H06
FFPE fixed samples GeoMx Nanostring

value: Vessels


title: FLASH 1x10Gy_ID565_Cortex_Other_007

description:
Library name: DSP-1001660022432-E-H05
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_Cortex_Neurones_007

description:
Library name: DSP-1001660022432-E-H04
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_Cortex_Vessels_007

description:
Library name: DSP-1001660022432-E-H03
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_SO_Other_006

description:
Library name: DSP-1001660022432-E-H02
FFPE fixed samples GeoMx Nanostring

value: CTRL


title: CTRL_ID564_SO_Neurones_006

description:
Library name: DSP-1001660022432-E-H01
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA1_Other_021

description:
Library name: DSP-1001660035574-F-F12
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID565_SO_Other_011

description:
Library name: DSP-1001660035574-F-A06
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA1_Other_019

description:
Library name: DSP-1001660035574-F-F08
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_SO_Astrocytes_006

description:
Library name: DSP-1001660022432-E-G12
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_CA1_Other_005

description:
Library name: DSP-1001660022432-E-G11
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_CA1_Neurones_005

description:
Library name: DSP-1001660022432-E-G10
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_CA1_Astrocytes_005

description:
Library name: DSP-1001660022432-E-G09
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_CA3_Other_004

description:
Library name: DSP-1001660022432-E-G08
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_CA3_Neurones_004

description:
Library name: DSP-1001660022432-E-G07
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_CA3_Astrocytes_004

description:
Library name: DSP-1001660022432-E-G06
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_DG_Other_003

description:
Library name: DSP-1001660022432-E-G05
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_DG_Neurones_003

description:
Library name: DSP-1001660022432-E-G04
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_CA3_Astrocytes_017

description:
Library name: DSP-1001660035574-F-F02
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_DG_Other_015

description:
Library name: DSP-1001660035574-F-E12
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_DG_Astrocytes_003

description:
Library name: DSP-1001660022432-E-G03
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_Cortex_Neurones_002

description:
Library name: DSP-1001660022432-E-G01
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_Cortex_Other_002

description:
Library name: DSP-1001660022432-E-G02
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_Cortex_Neurones_001

description:
Library name: DSP-1001660022432-E-F10
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_Cortex_Vessels_001

description:
Library name: DSP-1001660022432-E-F09
FFPE fixed samples GeoMx Nanostring


title: FLASH 1x10Gy_ID568_Cortex_Neurones_012

description:
Library name: DSP-1001660035574-F-E04
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_CA1_Other_018

description:
Library name: DSP-1001660022432-E-F08
FFPE fixed samples GeoMx Nanostring

value: CONV 3x10Gy


title: FLASH 1x10Gy_ID568_Cortex_Vessels_013

description:
Library name: DSP-1001660035574-F-E06
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_Cortex_Other_001

description:
Library name: DSP-1001660022432-E-F11
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_CA1_Astrocytes_018

description:
Library name: DSP-1001660022432-E-F06
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_SO_Other_017

description:
Library name: DSP-1001660022432-E-F05
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_CA1_Neurones_018

description:
Library name: DSP-1001660022432-E-F07
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_SO_Neurones_017

description:
Library name: DSP-1001660022432-E-F04
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_CA3_Other_016

description:
Library name: DSP-1001660022432-E-F02
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_DG_Other_015

description:
Library name: DSP-1001660022432-E-E11
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_CA3_Astrocytes_016

description:
Library name: DSP-1001660022432-E-E12
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_DG_Neurones_015

description:
Library name: DSP-1001660022432-E-E10
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_Cortex_Other_014

description:
Library name: DSP-1001660022432-E-E08
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_DG_Astrocytes_015

description:
Library name: DSP-1001660022432-E-E09
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_Cortex_Neurones_014

description:
Library name: DSP-1001660022432-E-E07
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_Cortex_Other_013

description:
Library name: DSP-1001660022432-E-E05
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID564_Cortex_Vessels_002

description:
Library name: DSP-1001660022432-E-F12
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_Cortex_Neurones_013

description:
Library name: DSP-1001660022432-E-E04
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_Cortex_Vessels_014

description:
Library name: DSP-1001660022432-E-E06
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_Cortex_Vessels_013

description:
Library name: DSP-1001660022432-E-E03
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_CA1_Neurones_012

description:
Library name: DSP-1001660022432-E-E01
FFPE fixed samples GeoMx Nanostring

value: FLASH 3x10Gy


title: FLASH 3x10Gy_ID558_CA1_Astrocytes_012

description:
Library name: DSP-1001660022432-E-D12
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_SO_Other_011

description:
Library name: DSP-1001660022432-E-D11
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_CA3_Other_010

description:
Library name: DSP-1001660022432-E-D08
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_CA3_Neurones_010

description:
Library name: DSP-1001660022432-E-D07
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_SO_Astrocytes_011

description:
Library name: DSP-1001660022432-E-D09
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_DG_Other_009

description:
Library name: DSP-1001660022432-E-D05
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_DG_Neurones_009

description:
Library name: DSP-1001660022432-E-D04
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_Cortex_Other_008

description:
Library name: DSP-1001660022432-E-D02
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_DG_Astrocytes_009

description:
Library name: DSP-1001660022432-E-D03
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_CA3_Astrocytes_010

description:
Library name: DSP-1001660022432-E-D06
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_Cortex_Neurones_008

description:
Library name: DSP-1001660022432-E-D01
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_Cortex_Vessels_008

description:
Library name: DSP-1001660022432-E-C12
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_Cortex_Other_007

description:
Library name: DSP-1001660022432-E-C11
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_Cortex_Neurones_007

description:
Library name: DSP-1001660022432-E-C10
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_SO_Other_006

description:
Library name: DSP-1001660022432-E-C08
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_Cortex_Vessels_007

description:
Library name: DSP-1001660022432-E-C09
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_CA1_Other_005

description:
Library name: DSP-1001660022432-E-C05
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_SO_Astrocytes_006

description:
Library name: DSP-1001660022432-E-C06
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_SO_Neurones_006

description:
Library name: DSP-1001660022432-E-C07
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_CA1_Astrocytes_005

description:
Library name: DSP-1001660022432-E-C03
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_CA1_Neurones_005

description:
Library name: DSP-1001660022432-E-C04
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_CA3_Other_004

description:
Library name: DSP-1001660022432-E-C02
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_CA3_Astrocytes_004

description:
Library name: DSP-1001660022432-E-B12
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_DG_Neurones_003

description:
Library name: DSP-1001660022432-E-B10
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_Cortex_Other_002

description:
Library name: DSP-1001660022432-E-B08
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_DG_Astrocytes_003

description:
Library name: DSP-1001660022432-E-B09
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_Cortex_Neurones_002

description:
Library name: DSP-1001660022432-E-B07
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_Cortex_Neurones_001

description:
Library name: DSP-1001660022432-E-B04
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_Cortex_Vessels_001

description:
Library name: DSP-1001660022432-E-B03
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_Cortex_Vessels_002

description:
Library name: DSP-1001660022432-E-B06
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_SO_Other_017

description:
Library name: DSP-1001660022432-E-A11
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_SO_Neurones_017

description:
Library name: DSP-1001660022432-E-A10
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_CA3_Other_016

description:
Library name: DSP-1001660022432-E-A08
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_SO_Astrocytes_017

description:
Library name: DSP-1001660022432-E-A09
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_CA3_Neurones_016

description:
Library name: DSP-1001660022432-E-A07
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_CA3_Astrocytes_016

description:
Library name: DSP-1001660022432-E-A06
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_DG_Neurones_015

description:
Library name: DSP-1001660022432-E-A04
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_DG_Astrocytes_015

description:
Library name: DSP-1001660022432-E-A03
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_Cortex_Other_014

description:
Library name: DSP-1001660022432-E-A02
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_Cortex_Neurones_014

description:
Library name: DSP-1001660022431-D-H12
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_Cortex_Vessels_014

description:
Library name: DSP-1001660022431-D-H11
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_Cortex_Other_013

description:
Library name: DSP-1001660022431-D-H10
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_Cortex_Vessels_013

description:
Library name: DSP-1001660022431-D-H08
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_Cortex_Neurones_013

description:
Library name: DSP-1001660022431-D-H09
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_CA1_Other_012

description:
Library name: DSP-1001660022431-D-H07
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_CA1_Astrocytes_012

description:
Library name: DSP-1001660022431-D-H05
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_SO_Neurones_011

description:
Library name: DSP-1001660022431-D-H03
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_SO_Other_011

description:
Library name: DSP-1001660022431-D-H04
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_SO_Astrocytes_011

description:
Library name: DSP-1001660022431-D-H02
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_CA3_Other_010

description:
Library name: DSP-1001660022431-D-H01
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_CA3_Neurones_010

description:
Library name: DSP-1001660022431-D-G12
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_CA3_Astrocytes_010

description:
Library name: DSP-1001660022431-D-G11
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_DG_Other_009

description:
Library name: DSP-1001660022431-D-G10
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_CA1_Neurones_018

description:
Library name: DSP-1001660022432-E-B01
FFPE fixed samples GeoMx Nanostring


title: Treated with 7,17-diHDPAn-3 Sample8

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

description: Library name: S_8_plusgata_1

data_processing:
Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.  Base calls are transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis - sample de-multiplexing and alignment to the Zebrafish genome - is performed using Illumina's CASAVA 1.8.2 software suite. The data is returned to the user if the sample error rate is less than 2% and the distribution of reads per sample in a lane is within reasonable tolerance. Data is retained on the cluster for at least 6 months, after which it is transferred to a tape backup system. For RNA-seq data analysis, low quality reads were trimmed, and adaptor contamination was removed using Trim Galore (v0.5.0). Trimmed reads were mapped to the Zebrafish reference genome (GRCz11) using HISAT2 (v2.1.0). Gene expression levels were quantified using StringTie (v1.3.3b). Differentially expressed genes were identified using DESeq2 (v 1.22.1).
Assembly: Zebrafish reference genome: Danio rerio (GRCz11)
Supplementary files format and content: Gene level count data; gene_count_matrix.csv

organism: Danio rerio

source_name: Embryo

extract_protocol:
Total RNA was isolated from control and embryos treated with 7,17-diHDPAn-3 with Quick-RNA Miniprep Kit (Zymo Research), and cDNA was synthesized using iScript reverse transcription supermix (Bio-Rad). Total RNA quality was determined by measuring the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel, which measures the ratio of ribosomal peaks.
Using the SMARTer Stranded Total RNA-Seq Kit v3- Pico Input Mammalian from Takara and a normalized RNA input between 250pg-10ng, the RNA was first fragmented prior to first strand cDNA synthesis. Next indexing and PCR1 was performed. After bead clean-up, ribosomal cDNA was depleted by ZapR v3 in the presence of mammalian specific R-probes. Next, fragments that were not cleaved in the depletion step were enriched in a second PCR before a final bead clean-up was performed. Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/µl were used for sequencing. Sample concentrations were normalized to 2.0 nM and loaded onto an Illumina NovaSeq flow cell at a concentration that yields 25 million passing filter clusters per sample. Samples were sequenced using 100bp paired-end sequencing on an Illumina NovaSeq according to Illumina protocols. The 10bp unique dual index was read during additional sequencing reads that automatically follow the completion of read 1. Data generated during sequencing runs was simultaneously transferred to the Yale Center for Genome Analysis (YCGA) cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time.

value: Embryo

value: erythrocyte progenitors and erythrocytes

value: embryos treated with 7,17-diHDPAn-3


title: FLASH 3x10Gy_ID557_DG_Astrocytes_009

description:
Library name: DSP-1001660022431-D-G08
FFPE fixed samples GeoMx Nanostring

value: Brain


title: FLASH 3x10Gy_ID557_DG_Neurones_009

description:
Library name: DSP-1001660022431-D-G09
FFPE fixed samples GeoMx Nanostring

value: Neurones


title: FLASH 3x10Gy_ID557_Cortex_Other_008

description:
Library name: DSP-1001660022431-D-G07
FFPE fixed samples GeoMx Nanostring

value: Other


title: FLASH 3x10Gy_ID557_Cortex_Neurones_008

description:
Library name: DSP-1001660022431-D-G06
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_Cortex_Vessels_008

description:
Library name: DSP-1001660022431-D-G05
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_Cortex_Other_007

description:
Library name: DSP-1001660022431-D-G04
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_Cortex_Neurones_007

description:
Library name: DSP-1001660022431-D-G03
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_Cortex_Vessels_007

description:
Library name: DSP-1001660022431-D-G02
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID551_DG_Other_015

description:
Library name: DSP-1001660022432-E-A05
FFPE fixed samples GeoMx Nanostring

value: DG


title: CTRL_ID559_SO_Neurones_006

description:
Library name: DSP-1001660022431-D-F12
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_SO_Other_006

description:
Library name: DSP-1001660022431-D-G01
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_SO_Astrocytes_006

description:
Library name: DSP-1001660022431-D-F11
FFPE fixed samples GeoMx Nanostring

value: Astrocytes


title: CTRL_ID559_CA1_Other_005

description:
Library name: DSP-1001660022431-D-F10
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID557_CA1_Neurones_012

description:
Library name: DSP-1001660022431-D-H06
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_CA1_Astrocytes_005

description:
Library name: DSP-1001660022431-D-F08
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_CA1_Neurones_005

description:
Library name: DSP-1001660022431-D-F09
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_CA3_Astrocytes_004

description:
Library name: DSP-1001660022431-D-F05
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_CA3_Other_004

description:
Library name: DSP-1001660022431-D-F07
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_CA3_Neurones_004

description:
Library name: DSP-1001660022431-D-F06
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_DG_Other_003

description:
Library name: DSP-1001660022431-D-F04
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_DG_Neurones_003

description:
Library name: DSP-1001660022431-D-F03
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_DG_Astrocytes_003

description:
Library name: DSP-1001660022431-D-F02
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_Cortex_Neurones_002

description:
Library name: DSP-1001660022431-D-E12
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_Cortex_Other_002

description:
Library name: DSP-1001660022431-D-F01
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_Cortex_Vessels_002

description:
Library name: DSP-1001660022431-D-E11
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_Cortex_Neurones_001

description:
Library name: DSP-1001660022431-D-E09
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_Cortex_Other_001

description:
Library name: DSP-1001660022431-D-E10
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID559_Cortex_Vessels_001

description:
Library name: DSP-1001660022431-D-E08
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_SO_Other_018

description:
Library name: DSP-1001660022431-D-E07
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_SO_Neurones_018

description:
Library name: DSP-1001660022431-D-E06
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_SO_Astrocytes_018

description:
Library name: DSP-1001660022431-D-E05
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_CA1_Other_017

description:
Library name: DSP-1001660022431-D-E04
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_CA1_Neurones_017

description:
Library name: DSP-1001660022431-D-E03
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_CA1_Astrocytes_017

description:
Library name: DSP-1001660022431-D-E02
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_CA3_Other_016

description:
Library name: DSP-1001660022431-D-E01
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_CA3_Neurones_016

description:
Library name: DSP-1001660022431-D-D12
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_CA3_Astrocytes_016

description:
Library name: DSP-1001660022431-D-D11
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_DG_Neurones_015

description:
Library name: DSP-1001660022431-D-D09
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_DG_Other_015

description:
Library name: DSP-1001660022431-D-D10
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_SO_Astrocytes_017

description:
Library name: DSP-1001660022432-E-F03
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_DG_Astrocytes_015

description:
Library name: DSP-1001660022431-D-D08
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_Cortex_Other_014

description:
Library name: DSP-1001660022431-D-D07
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_Cortex_Neurones_014

description:
Library name: DSP-1001660022431-D-D06
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_Cortex_Vessels_014

description:
Library name: DSP-1001660022431-D-D05
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_Cortex_Other_013

description:
Library name: DSP-1001660022431-D-D04
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID553_CA3_Neurones_016

description:
Library name: DSP-1001660022432-E-F01
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_CA3_Other_012

description:
Library name: DSP-1001660022431-D-D01
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_CA1_Other_012

description:
Library name: DSP-1001660022432-E-E02
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_CA3_Neurones_012

description:
Library name: DSP-1001660022431-D-C12
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_Cortex_Vessels_013

description:
Library name: DSP-1001660022431-D-D02
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_DG_Other_011

description:
Library name: DSP-1001660022431-D-C10
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_CA3_Astrocytes_012

description:
Library name: DSP-1001660022431-D-C11
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_DG_Astrocytes_011

description:
Library name: DSP-1001660022431-D-C08
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_SO_Other_010

description:
Library name: DSP-1001660022431-D-C07
FFPE fixed samples GeoMx Nanostring


title: CONV 3x10Gy_ID550_Cortex_Neurones_013

description:
Library name: DSP-1001660022431-D-D03
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_DG_Neurones_011

description:
Library name: DSP-1001660022431-D-C09
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_SO_Neurones_010

description:
Library name: DSP-1001660022431-D-C06
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID558_SO_Neurones_011

description:
Library name: DSP-1001660022432-E-D10
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_CA1_Other_009

description:
Library name: DSP-1001660022431-D-C04
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_CA1_Neurones_009

description:
Library name: DSP-1001660022431-D-C03
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_Cortex_Other_008

description:
Library name: DSP-1001660022431-D-C01
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_Cortex_Neurones_008

description:
Library name: DSP-1001660022431-D-B12
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_SO_Astrocytes_010

description:
Library name: DSP-1001660022431-D-C05
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_Cortex_Other_007

description:
Library name: DSP-1001660022431-D-B10
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_Cortex_Neurones_007

description:
Library name: DSP-1001660022431-D-B09
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_Cortex_Vessels_008

description:
Library name: DSP-1001660022431-D-B11
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_Cortex_Vessels_007

description:
Library name: DSP-1001660022431-D-B08
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_SO_Other_006

description:
Library name: DSP-1001660022431-D-B07
FFPE fixed samples GeoMx Nanostring


title: FLASH 3x10Gy_ID555_CA1_Astrocytes_009

description:
Library name: DSP-1001660022431-D-C02
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_SO_Neurones_006

description:
Library name: DSP-1001660022431-D-B06
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_CA3_Neurones_004

description:
Library name: DSP-1001660022432-E-C01
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_SO_Astrocytes_006

description:
Library name: DSP-1001660022431-D-B05
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_CA1_Astrocytes_005

description:
Library name: DSP-1001660022431-D-B02
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_CA1_Other_005

description:
Library name: DSP-1001660022431-D-B04
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_CA3_Other_004

description:
Library name: DSP-1001660022431-D-B01
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_CA3_Neurones_004

description:
Library name: DSP-1001660022431-D-A12
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_DG_Other_003

description:
Library name: DSP-1001660022431-D-A10
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_DG_Neurones_003

description:
Library name: DSP-1001660022431-D-A09
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_CA3_Astrocytes_004

description:
Library name: DSP-1001660022431-D-A11
FFPE fixed samples GeoMx Nanostring


title: CONV 1x10Gy_ID563_DG_Other_003

description:
Library name: DSP-1001660022432-E-B11
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_DG_Astrocytes_003

description:
Library name: DSP-1001660022431-D-A08
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_Cortex_Other_002

description:
Library name: DSP-1001660022431-D-A07
FFPE fixed samples GeoMx Nanostring


title: CTRL_ID554_Cortex_Neurones_002

description:
Library name: DSP-1001660022431-D-A06
FFPE fixed samples GeoMx Nanostring


title: ZJ22, 0h, rep3

city: Shanghai

first: yangxuan

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS), Chinese Academy of Sciences

description: Library name: ZJ22_0h_3

data_processing:
The raw reads were trimmed with Trimmomatic v.0.39 with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 LEADING:20 TRAILING:20 MINLEN:50.
Clean reads were then aligned to the TAIR10 transcriptome using Hisat2 v2.2.1.
Expression levels were extracted for each gene using TPMCalculator v0.0.3 and featureCounts v2.0.6.
Assembly: Oryza_sativa.IRGSP-1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Oryza sativa

source_name: leaf

extract_protocol:
Around  5-6 leaves were pooled as one replicate. Total RNAs were extracted with the RNAprep Pure Plant Plus Kit Kit (TIANGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TransNGS Fast RNA-Seq Library Prep Kit for Illumina  following the manufacturer’s instructions.

treatment_protocol: The leaves of ZJ22 and bui1 plants following Xoo inoculation were sampled at 0h, 6h, 12h, 24h and 48h for transcriptome analysis.

value: leaf

value: Xoo inoculation

tag: time point


title: CONV 1x10Gy_ID563_Cortex_Other_001

description:
Library name: DSP-1001660022432-E-B05
FFPE fixed samples GeoMx Nanostring

value: CONV 1x10Gy


title: CTRL_ID554_Cortex_Vessels_002

description:
Library name: DSP-1001660022431-D-A05
FFPE fixed samples GeoMx Nanostring

value: Cortex


title: CTRL_ID554_Cortex_Neurones_001

description:
Library name: DSP-1001660022431-D-A03
FFPE fixed samples GeoMx Nanostring


title: SB3_2

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description:
Library name: sample 12
biol rep 3

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using trim_galore v0.6.10. Index of the reference genome was built using Hisat2 v2.2.1 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.2.1.
featureCounts v2.1.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: xls files include FPKM values for each sample

source_name: spleen and lymph nodes

growth_protocol: CD4+ T cells that from WT and SKI knockout mice were co-cultured in complete RPMI 1640 medium in the presence of anti-CD3 antibody and antigen prensenting cells. Cell mixture were kept in an incubator for 3 days

extract_protocol:
RNA was harvested using ZYMO Direct-zol RNA microprep kit, sequencing library containing >= 10 ng RNA of each sample
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. (Novogene Co., Ltd)

value: spleen and lymph nodes

value: KO

value: Medium with SB


title: SB2_2

description:
Library name: sample 11
biol rep 2


title: CTRL_ID554_Cortex_Vessels_001

description:
Library name: DSP-1001660022431-D-A02
FFPE fixed samples GeoMx Nanostring

value: Vessels

value: CTRL


title: SB1_2

description:
Library name: sample 10
biol rep 1


title: SB3_1

description:
Library name: sample 9
biol rep 3

value: WT


title: CONV 3x10Gy_ID551_CA1_Other_018

description:
Library name: DSP-1001660022432-E-B02
FFPE fixed samples GeoMx Nanostring

value: CONV 3x10Gy


title: CTRL_ID554_Cortex_Other_001

description:
Library name: DSP-1001660022431-D-A04
FFPE fixed samples GeoMx Nanostring


title: SB2_1

description:
Library name: sample 8
biol rep 2


title: SB1_1

description:
Library name: sample 7
biol rep 1


title: Ctr3_2

description:
Library name: sample 6
biol rep 3

value: Medium


title: Ctr2_2

description:
Library name: sample 5
biol rep 2


title: Ctr1_2

description:
Library name: sample 4
biol rep 1


title: CONV 3x10Gy_ID551_CA1_Astrocytes_018

description:
Library name: DSP-1001660022432-E-A12
FFPE fixed samples GeoMx Nanostring

value: Brain


title: Ctr3_1

description:
Library name: sample 3
biol rep 3


title: Ctr2_1

description:
Library name: sample 2
biol rep 2


title: Ctr1_1

description:
Library name: sample 1
biol rep 1


title: Granulosa cells - PRAKO - WT rep 3

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

description: Library name: AWT3

data_processing:
Overrepresented adapters were checked using FastQC and adapters were trimmed using AdapterRemoval when required.
Quasi-aligment of dataset to the GENCODE mouse transcriptome and transcript quantification via Salmon.
Expression profiles and differential gene expression were assessed with limma and edgeR.
Assembly: mm10
Supplementary files format and content: txt, TPM count from Salmon

source_name: peri-ovulatory granulosa cells

growth_protocol: 21-27 days old mice

extract_protocol:
cells from 2-3 mice were pooled together per replicate. Total RNA was extracted using the Monarch RNA Extraction Kit (NEB) and DNase-treated.
Library preparation was through the mRNA-seq Illumina Truseq Strandard mRNA kit (Illumina). Paired-end sequencing was on the NovaSeq 6000 S1 Sequencing System (Illumina).

treatment_protocol: mice were injected with 5 IU eCG, following by 5 IU hCG after 46 hours. After 8 hours of hCG mice were culled for granulosa cell collection.

value: peri-ovulatory granulosa cells

value: 5IU eCG per mouse for 46 hours, then 5IU hCG per mouse for 8 hours


title: Granulosa cells - PRAKO - WT rep 1

description: Library name: AWT1


title: Granulosa cells - PRAKO - WT rep 4

description: Library name: AWT4


title: Granulosa cells - PRAKO - WT rep 2

description: Library name: AWT2


title: Granulosa cells - PRAKO - KO rep 3

description: Library name: AKO3


title: Granulosa cells - PRAKO - KO rep 2

description: Library name: AKO2


title: Granulosa cells - PRAKO - KO rep 4

description: Library name: AKO4


title: 3_Ubc13 flox/flox Alb positive_1

city: Osong-eup, Heungdeok-gu

first: WANG

last: FENG

state: Cheongju-si, Chungcheongbuk-do

address: Osongsaengmyeong ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea

country: South Korea

institute: chungbun national university

description:
Library name: 3_Ubc13 flox/flox Alb positive_1
Column name in raw_counts.text: Aub1

data_processing:
Read Alignment: Sequencing reads were aligned to the genome or transcriptome using Bowtie2.
Transcript Assembly and Abundance Estimation: Aligned reads were used to assemble transcripts and estimate their abundance.
Differential Expression Analysis: Differentially expressed genes (DEGs) were identified based on read counts. TMM+CPM normalization was applied using EdgeR within the R/Bioconductor framework, ensuring accurate expression level comparisons.
Data Visualization: For data mining and visualization, the results were processed in ExDEGA (Ebiogen Inc.), allowing comprehensive graphical representation of findings.
Assembly: mm10 (the Mouse Genome Assembly, GRCm38)
Supplementary files format and content: Processed data file is in format of text file containing ID, Gene Symbol, Treated Group/Control Group, Control Group, Treated Group, C2, C4, B3, B5, Entrez ID, Gene ID, Chromosome, Start, End, Width, Strand, p_id, Transcript ID, tss_id, bioType, Aliases, Description, and NCBI Search.

source_name: Liver

extract_protocol:
RNA was extracted from liver tissues and cells using the Hybrid-R kit (Geneall, Cat. 305-101), according to the manufacturer’s instructions.
Murine primary hepatocyte RNA sequencing was performed with the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) following the manufacturer's protocol. cDNA libraries were prepared with an oligo-dT primer for first-strand synthesis and a random primer for second-strand synthesis, then purified using magnetic beads. Final libraries were amplified to include adapter sequences and purified post-PCR. Sequencing was performed as single-end 75 bp reads on an Illumina NextSeq 550.  Reads were aligned with Bowtie2 to the genome or transcriptome. Transcripts were assembled, and differential expression was analyzed with EdgeR using TMM+CPM normalization. Gene classification utilized DAVID and Medline databases, with data visualization by ExDEGA (Ebiogen Inc.).

value: Liver

value: Hepatic Ubc13 deletion liver

value: Normal diet


title: 4_Ubc13 flox/flox Alb positive_2

description:
Library name: 4_Ubc13 flox/flox Alb positive_2
Column name in raw_counts.text: Aub2


title: Granulosa cells - PRAKO - KO rep 1

description: Library name: AKO1


title: 2_Ubc13 flox/flox Alb negative_2

description:
Library name: 2_Ubc13 flox/flox Alb negative_2
Column name in raw_counts.text: WT2


title: 1_Ubc13 flox/flox Alb negative_1

description:
Library name: 1_Ubc13 flox/flox Alb negative_1
Column name in raw_counts.text: WT1


title: mm_rna_folb_CD23creBRWD1_cre-minus.3

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to reference genome mm9 in a splice-aware manner using STAR. Gene expression was quantified using featureCounts against UCSC genes, with Ensembl IG genes from mm10 converted to mm9 coordinates with UCSC liftOver.
Assembly: mm9
Supplementary files format and content: tab-delimited text file of raw counts per gene

source_name: Follicular B cells B220+ CD93+ CD21+ CD23+

extract_protocol:
Total RNA was isolated using a RNeasy kit (Qiagen).
Libraries were prepared by the University of Chicago Genomics Facility before sequencing.

treatment_protocol: Follicular B cell samples were isolated from mouse spleens. Follicular B cells were flow sorted as B220+ CD93+ CD21+ CD23+. Follicular B cells from Cd23-Cre Brwd1fl/fl mice were also sorted as tdTomato+. For Germinal Center B cell samples, mice were immunized intraperitoneally with 10^9 sheep red blood cells in PBS, then boosted with 10^9 sheep red blood cells 5 days later. On day 14, germinal center B cells were isolated from spleens. Germinal Center B cells were sorted as B220+ GL7+ CD95+ tdTomato+. LZ cells were defined as CXCR4- CD83+. DZp cells were defined as CXCR4+ CD83+. DZd B cells were defined as CXCR4+ CD83-.

value: Cells were isolated from spleens


title: mm_rna_folb_CD23creBRWD1_cre-minus.1

value: Follicular B cells B220+ CD93+ CD21+ CD23+


title: mm_rna_folb_CD23creBRWD1_cre-minus.2


title: mm_rna_folb_CD23creBRWD1_cre-plus_tdtomato-plus.3

source_name: Follicular B cells B220+ CD93+ CD21+ CD23+ tdTomato+

value: Cd23-Cre Brwd1fl/fl


title: mm_rna_folb_CD23creBRWD1_cre-plus_tdtomato-plus.2

value: Follicular B cells B220+ CD93+ CD21+ CD23+ tdTomato+


title: whole body of the Drosophila treated (cisplatin 50mg/ml + NPTiO2 50mg/ml), sample 3  Reads 1 and 2

city: Rio de Janeiro

first: Cristiano

middle: Nascimento

last: Costa

state: Rio de Janeiro

address: Rua Senador Furtado, 121/125

department: education department

country: Brazil

institute: Instituto Federal do Rio de Janeiro

description:
Library name: Sample 12
CIS_NPTIO2_3

data_processing:
Sequencing was performed on an Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA) using the NextSeq 500/550 high-output kit v2.5 (150 cycles) (Illumina, USA), generating 2 × 75-bp reads.
raw sequence data was analyzed using the FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Reads shorter than 20 nucleotides after trimming were removed using the Trimmomatic tool (Bolger; Lohse; Usadel, 2014).
alignment quality was evaluated using Samtools (Li et al., 2009)
the number of reads mapped to each gene was quantified using HT-seq Count tool (Anders; Pyl; Huber, 2015)
Assembly: aligned to the reference genome of Drosophila melanogaster ASM2977511v1, date: April 17Th, 2023 (BioProject, NCBI), using the BWA aligner
Supplementary files format and content: format fastaq.gz
Supplementary files format and content: format fastaq.gz

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: standard cornmeal-yeast-agar medium (BRENT; OSTER, 1974); maintained in an incubator at 25 °C and humidity between 70% and 80%, with a 12-hour light cycle

extract_protocol:
Female flies were used for the RNA-Seq experiment.RNA extraction was carried outarroed by c Trizol™ reagent (ThermoFisher™ Scientific, Waltham, Massachusetts, USA) and macerated. Total RNA extraction was made according to the manufacturer’s instructions.
mRNA sequencing libraries were constructed using the Illumina Stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, USA), according to the manufacturer’s protocol. The quality of libraries was verified using the Agilent TapeStation 4200 System (Agilent Technologies, USA) according to the manufacturer’s instructions.

treatment_protocol: Control group was treated with a standard medium enriched with a mixture of yeast, water, and a green food coloring dye. Treatment groups were treated with the same culture medium but with the following aqueous solutions instead of water: CIS group – aqueous cisplatin solution (50µg/ml); NPTIO2 group -  aqueous NPTiO2 solution (50µg/ml); CIS/NPTIO2 group – cisplatin aqueous solution (50µg/ml) and NPTiO2 aqueous solution (50µg/ml) simultaneously. Flies were kept in this condition for 3 (three) days.

value: whole body

value: Oregon

value: metabolic response

value: single


title: whole body of the Drosophila treated (cisplatin 50mg/ml + NPTiO2 50mg/ml), sample 1  Reads 1 and 2

description:
Library name: Sample 10
CIS_NPTIO2_1


title: Tn 7H9 r1

first: Ruiqing

last: Ma

address: 2901 Caolang Rd., Jinshan District

institute: Shanghai Public Health Clinical Center

description:
Library name: pro-rep 1
input

library_source: genomic

data_processing:
Basecalling: Illumina GA Pipeline v1.8
Transit v3.0, Transit Pre-Processor (TPP) step for read aligment, Resampling -a for pairwise comparison
Assembly: NC_000962, Mycobacterium tuberculosis H37Rv, complete genome
Supplementary files format and content: *.xlsx files generated by Transit contain log2FoldChange and p-value of the comparison results between two conditions

molecule: genomic DNA

organism: Mycobacterium tuberculosis

extract_protocol:
CTAB genome extraction method
Tn-seq

tag: sample group

value: Tn 7H9


title: whole body of the Drosophila treated (NPTiO2) 50mg/ml), sample 1 Reads 1 and 2

description:
Library name: Sample 7
NPTIO2_1


title: mm_rna_folb_CD23creBRWD1_cre-plus_tdtomato-plus.1


title: whole body of the Drosophila treated (NPTiO2) 50mg/ml), sample 2 Reads 1 and 2

description:
Library name: Sample 8
NPTIO2_2


title: whole body of the Drosophila treated (cisplatin 50mg/ml + NPTiO2 50mg/ml), sample 2 Reads 1 and 2

description:
Library name: Sample 11
CIS_NPTIO2_2


title: whole body of the Drosophila treated (cisplatin 50mg/ml), sample 3 Reads 1 and 2

description:
Library name: Sample 6
CIS3


title: whole body of the Drosophila treated (cisplatin 50mg/ml), sample 2 Reads 1 and 2

description:
Library name: Sample 5
CIS2


title: whole body of the Drosophila treated (NPTiO2) 50mg/ml), sample 3 Reads 1 and 2

description:
Library name: Sample 9
NPTIO2_3


title: whole body of the Drosophila treated (cisplatin 50mg/ml), sample 1 Reads 1 and 2

description:
Library name: Sample 4
CIS1


title: non-treated Drosophila sample 3 Reads 1 and 2

description:
Library name: Sample 3
CONTROL3


title: non-treated Drosophila sample 2 Reads 1 and 2

description:
Library name: Sample 2
CONTROL2


title: non-treated Drosophila sample 1 Reads 1 and 2

description:
Library name: Sample 1
CONTROL1


title: CUTandTAG, NIPBL, ctrl, AlFx

city: Tokyo

first: Shoin

last: Tei

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

description: Library name: CUTandTAG_NIPBL_ctrl_AlFx

data_processing:
Reads were aligned to human (hg38) and E. coli genomes with Bowtie2 (version 2.5.3) using Churros (version 1.5.0). Normalization factors were calculated from the ratio of E. coli spike-in to human reads. Redundant reads were removed, and read counts were normalized by the normalization factors with parse2wig+ (version 1.20.0). Visualization was carried out with drompa+ PC_SHARP (version 1.17.2) and deepTools(version 3.5.1).
Assembly: hg38
Supplementary files format and content: BigWIg
Library strategy: CUT&Tag

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium containing 10% FBS, penicillin, and streptomycin solution (Wako) at 37 C with 5% CO2.

extract_protocol:
Cells were crosslinked with 0.3% formaldehyde for 2 min, quenched with 225 mM glycine for 5 min. The crosslinked cells were washed once with cold PBS and resuspended in wash buffer [20 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, 1× cOmplete EDTA-free (Roche)]. Concanavalin A–conjugated magnetic beads were prepared by incubating Dynabeads MyOne T1 (Invitrogen) with biotinylated concanavalin A (Type IV; Merck Sigma-Aldrich) in bead wash buffer [PBS (pH 6.8) containing 0.01% Tween-20]44. Cells were immobilized on concanavalin A–coated magnetic beads and incubated in antibody buffer [wash buffer supplemented with 0.1% Triton X-100, 2 mM EDTA, and 100 μg mL⁻¹ BSA (NEB)] containing the appropriate primary antibody for 2 h at room temperature, followed by incubation with secondary antibody for 1 h at room temperature. Cells were washed once with TX-wash buffer [wash buffer containing 0.1% Triton X-100] and once with 300-TX-wash buffer [TX-wash buffer containing 300 mM NaCl], and then incubated with CUTANA™ pAG-Tn5 (EpiCypher). Tagmentation was performed at 37 °C for 1 h in tagmentation buffer [300-TX-wash buffer supplemented with 10 mM MgCl2 and 5 ng mL⁻¹ CUTANA™ E. coli spike-in DNA (EpiCypher)]. DNA was released in 2x release buffer [20 mM HEPES-KOH (pH 7.5), 20 mM EDTA, 2% SDS, and 2.5 μg mL⁻¹ proteinase K (Roche)] and incubated at 55 °C for 2 h.
DNA was purified using a QIAquick PCR purification kit (QIAGEN), amplified with indexed primers, size-selected using SPRIselect beads (Beckman Coulter).

treatment_protocol: Treatment with 1 μM 5-Ph-IAA (Merck Sigma Aldrich) for 2 h was performed to deplete RAD21. Cells were detached from a culture dish by Accutase (Thermo Fisher Scientific) and incubated on ice for 15 min in dig-wash buffer [20 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.05% digitonin, 0.5 mM spermidine, 1 mM DTT, 1x cOmplete EDTA-free (Roche)] for permeabilization. The cells were washed twice with Dig-wash buffer and resuspended in reaction buffer [20 mM HEPES-KOH (pH 7.5), 75 mM NaCl, 5 mM MgCl2, 0.05% digitonin, 10% glycerol, 1 mM DTT, 1x cOmplete EDTA-free] and incubated at 25°C for 10 min with or without 1 mM ATP. For AlFx, 1 mM AlCl3 and 5 mM NaF were added after the incubation with 1 mM ATP for 5 min and the cells were further incubated for 5 min.

value: ATP, AlFx


title: CUTandTAG, NIPBL, ctrl, ATP

description: Library name: CUTandTAG_NIPBL_ctrl_ATP

value: ATP


title: CUTandTAG, NIPBL, ctrl

description: Library name: CUTandTAG_NIPBL_ctrl

value: DMSO


title: CUTandTAG, RPB1, aux2, AlFx

description: Library name: CUTandTAG_RPB1_aux2_AlFx

value: AUxin2, ATP, AlFx


title: CUTandTAG, RPB1, aux2, ATP

description: Library name: CUTandTAG_RPB1_aux2_ATP

value: Auxin2, ATP


title: CUTandTAG, RPB1, ctrl, AlFx

description: Library name: CUTandTAG_RPB1_ctrl_AlFx


title: CUTandTAG, RPB1, ctrl, ATP

description: Library name: CUTandTAG_RPB1_ctrl_ATP


title: CUTandTAG, RAD21, aux2

description: Library name: CUTandTAG_RAD21_aux2


title: CUTandTAG, RPB1, ctrl

description: Library name: CUTandTAG_RPB1_ctrl


title: CUTandTAG, RAD21, aux2, ATP

description: Library name: CUTandTAG_RAD21_aux2_ATP


title: CUTandTAG, RAD21, ctrl, AlFx

description: Library name: CUTandTAG_RAD21_ctrl_AlFx


title: CUTandTAG, RAD21, aux2, AlFx

description: Library name: CUTandTAG_RAD21_aux2_AlFx


title: CUTandTAG, RAD21, ctrl

description: Library name: CUTandTAG_RAD21_ctrl


title: L1, P0 mys-1, CUT&Tag, replicate 1

city: Hangzhou

first: Lianfeng

last: Wu

state: Please select a state below

address: 600 Dunyu road

institute: Westlake University

description: Library name: NTY390-1

data_processing:
The Illumina adapters and low-complexity adapters were removed from the reads by Trim Galore! (version 0.6.6), cutadapt (version 4.2). The reads were mapped to the C. elegans genome ce11 by bowtie2 (version 2.4.1) with option “-X 2000”. The unmapped reads were further mapped to the Drosophila genome dm6 by bowtie2 (version 2.4.1) with option “-X 2000”. PCR duplicates were removed by sambamba (version 0.8.2) with option “--overflow-list-size 600000”. Alignments were further filtered by sambamba (version 0.8.2) with option “-F 1804”. NormalizeFactor was calculated as: 10000/(number of alignments mapped to spike-in genome). The average NormalizeFactor of two biological replicates was used for all the following analyses.
Assembly: ce11
Supplementary files format and content: bigWig for each sample
Library strategy: CUT&Tag

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans (N2) were maintained on nematode growth media (NGM) seeded with Escherichia coli OP50 as food source under standard culture conditions at 20°C

extract_protocol:
Approximately 100,000 embryos or L1 larvae were pelleted in ddH2O, snap-frozen in liquid nitrogen Frozen worm pellets were crushed to isolate single nuclei in MACS Buffer (10 mM Tris-HCl pH 7.4, 3 mM MgAc2, 5 mM CaCl2, 2 mM EDTA, 0.6 mM DTT, 1×Protease Inhibitor Cocktail) and were filtered through 30 µm Cell-Tric. After centrifugation (500 × g, 10 min, 4°C), pellets were permeabilized in OMNI Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% digitonin) for 15 min on ice, then washed twice with PBSI (PBS with 1× protease inhibitor). Nuclei were counted under microscope with Hoechst staining For each sample, 5 × 105 nuclei were combined with 5 × 102 Drosophila S2 cells (as spike-in control). Nuclei-spike-in mixtures were resuspended in MED Buffer #1 (20 mM HEPES, 271 mM NaCl, 2% BSA, 0.5 mM Spermidine, 0.01% Digitonin, 2 mM EDTA, 1×Protease Inhibitor Cocktail) containing 1 µL Bridged Protein A-Tn5 and 2 µg H4K16ac antibody (Abcam ab109463), and incubated overnight at 4°C. Nuclei were washed in MED Buffer #2 (MED Buffer #1 without EDTA), incubated in 10 mM MgCl2, at 550 rpm for 1 h at 37 °C for tagmentation, and then terminated by adding 10 mM EDTA. The nuclei were lysed in 500 mM NaCl, 1% SDS and protease K at 55 °C, 850 rpm for at least 2 h followed by column purification of DNA. Libraries were prepared using NEBNext® High-Fidelity 2X PCR Master Mix and Nextera N5/N7 primers for PCR ampliﬁcation according to recommended cycle number, followed by post-PCR clean-up with SPRIselect Beads and fragments distribution analysis. Biological duplicates per group were prepared for CUT&Tag and sent for sequencing on Illumina NovaSeq 6000.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300  bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Parental generation (P0) hermaphrodites were fed with HT115(DE3) bacteria, with empty vector L4440 or mys-1 RNAi from the L1 larval stage until Day 1 of adulthood. P0 adults were then bleached to isolate embryos (F1) in M9 buffer. The F1 early-stage were collected immediately after bleach (embryo 0 h), 6h after bleach (embryo 6 h) and 24 h after bleach (L1).

tag: developmental stages

value: whole worm

value: mys-1 RNAi in P0

value: batch 1


title: CUTandTAG, RPB1, aux2

description: Library name: CUTandTAG_RPB1_aux2


title: L1, P0 mys-1, CUT&Tag, replicate 2

description: Library name: NTY390-2


title: CUTandTAG, RAD21, ctrl, ATP

description: Library name: CUTandTAG_RAD21_ctrl_ATP


title: E6, P0 mys-1, CUT&Tag, replicate 2

description: Library name: NTY389-2

source_name: embryo

value: embyro 6 h

value: embryo


title: L1, P0 control, CUT&Tag, replicate 2

description: Library name: NTY387-2

value: control RNAi in P0


title: E6, P0 mys-1, CUT&Tag, replicate 1

description: Library name: NTY389-1


title: L1, P0 control, CUT&Tag, replicate 1

description: Library name: NTY387-1


title: E6, P0 control, CUT&Tag, replicate 2

description: Library name: NTY386-2


title: Ad, P0 mys-1, replicate 1

description: Library name: ML1

data_processing:
The sequencing reads were de-multiplexed using bcl2fastq and quantified using kallisto 0.46.0, with default parameters to WormBase reference genome (WS274).
Assembly: WS274
Supplementary files format and content: gene-counts

extract_protocol:
Total RNA was extraced from Trizol following manufacturer's instructions
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300  bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Parental generation (P0) hermaphrodites were fed with HT115(DE3) bacteria, with empty vector L4440 or mys-1 RNAi from the L1 larval stage until Day 1 of adulthood. P0 adults were then bleached to isolate embryos (F1) in M9 buffer. The F1 early-stage were collected immediately after bleach (embryo 0 h), 6h after bleach (embryo 6 h) and 24 h after bleach (L1). The F1 embryos were also transferred  onto L4440 plates and grown for 70 hours to collect adult. All samples were frozen in Trizol.

value: Adult

value: batch 3


title: E6, P0 control, CUT&Tag, replicate 1

description: Library name: NTY386-1


title: E0, P0 control, CUT&Tag, replicate 2

description: Library name: NTY385-2

value: embyro 0 h


title: E0, P0 control, CUT&Tag, replicate 1

description: Library name: NTY385-1


title: Ad, P0 mys-1, replicate 2

description: Library name: ML2


title: Ad, P0 mys-1, replicate 3

description: Library name: ML3


title: Ad, P0 control, replicate 3

description: Library name: LL3


title: Ad, P0 control, replicate 2

description: Library name: LL2


title: L1, P0 mys-1, replicate 2

description: Library name: L1-M-2

value: batch 2


title: L1, P0 mys-1, replicate 1

description: Library name: L1-M-1


title: L1, P0 control, replicate 2

description: Library name: L1-L-2


title: L1, P0 control, replicate 1

description: Library name: L1-L-1


title: E6, P0 mys-1, replicate 4

description: Library name: M4-6


title: E6, P0 mys-1, replicate 1

description: Library name: M1-6


title: E6, P0 mys-1, replicate 3

description: Library name: M3-6


title: E6, P0 control, replicate 3

description: Library name: L3-6


title: E6, P0 mys-1, replicate 2

description: Library name: M2-6


title: E0, P0 mys-1, replicate 4

description: Library name: M4-0


title: E0, P0 mys-1, replicate 3

description: Library name: M3-0


title: E6, P0 control, replicate 2

description: Library name: L2-6


title: E6, P0 control, replicate 1

description: Library name: L1-6


title: E0, P0 mys-1, replicate 2

description: Library name: M2-0


title: E0, P0 mys-1, replicate 1

description: Library name: M1-0


title: E0, P0 control, replicate 4

description: Library name: L4-0


title: E0, P0 control, replicate 2

description: Library name: L2-0


title: Nasal epithelial brushing, pediatric ICU control Control_023

type: genomic

city: Little Rock

first: James

middle: Garrett

last: Williams

state: AR

address: 13 Children's Way

department: Pediatrics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulfite-converted, amplified DNA was enzymatically fragmented and hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip, followed by single-base extension and staining, per the Illumina Infinium HD Methylation Assay protocol (CCHMC DNA Sequencing and Genotyping Core).

scan_protocol: BeadChips were imaged on the Illumina iScan system.

data_processing:
IDAT files were processed in R (v4.5.0) with the sesame package. openSesame was run with prep='QCDPB' (quality masking, channel/dye-bias correction, noob background correction, and pOOBAH detection-p masking) on platform EPICv2 using a pinned local manifest; beta values were computed with getBetas. Probes flagged by the EPICv2 KYCG mask (cross-reactive and SNP-affected) and probes with detection p-value > 0.05 were removed. Replicate EPICv2 probes were collapsed to one value per CpG by averaging (limma::avereps on the base CpG identifier). M-values were computed as log2(beta/(1-beta)). Cell-type composition was estimated with EpiDISH, and M-values were adjusted for composition (limma::removeBatchEffect) for downstream analyses. The submitted processed matrix contains normalized beta values per CpG per sample.
[processed value definition] Beta value = methylated signal / (methylated + unmethylated signal), ranging from 0 (unmethylated) to 1 (fully methylated), after noob/dye-bias correction and pOOBAH detection-p masking (sesame getBetas). NA indicates a probe that failed detection in that sample.

label: Cy3 and Cy5

source_name: nasal epithelium

label_protocol: Standard Illumina Infinium HD Methylation Assay. Genomic DNA was bisulfite-converted and whole-genome amplified per the manufacturer's protocol.

extract_protocol: Nasal brushes were thawed on ice in 1:100 beta-mercaptoethanol to reduce mucus disulfide bonds, passed through a QIAshredder (Qiagen), and treated with DNase. Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen) and quantified on a Qubit Flex fluorometer (Thermo Fisher Scientific).

tag: tissue

value: nasal epithelium

tag: condition

value: PICU control without lung disease


title: Nasal epithelial brushing, pediatric ICU control Control_022


title: E0, P0 control, replicate 3

description: Library name: L3-0

tag: genotype

tag: treatment


title: Nasal epithelial brushing, PARDS subject ARDS_045

value: PARDS


title: Nasal epithelial brushing, PARDS subject ARDS_039


title: Nasal epithelial brushing, PARDS subject ARDS_037


title: Nasal epithelial brushing, PARDS subject ARDS_036


title: Nasal epithelial brushing, PARDS subject ARDS_034


title: Nasal epithelial brushing, PARDS subject ARDS_032


title: Nasal epithelial brushing, PARDS subject ARDS_031


title: Nasal epithelial brushing, PARDS subject ARDS_030


title: Nasal epithelial brushing, PARDS subject ARDS_026


title: Nasal epithelial brushing, PARDS subject ARDS_023


title: Nasal epithelial brushing, PARDS subject ARDS_018


title: Nasal epithelial brushing, PARDS subject ARDS_016


title: Nasal epithelial brushing, PARDS subject ARDS_019


title: Nasal epithelial brushing, PARDS subject ARDS_015


title: Nasal epithelial brushing, PARDS subject ARDS_004


title: Nasal epithelial brushing, PARDS subject ARDS_010


title: Nasal epithelial brushing, PARDS subject ARDS_003


title: Nasal epithelial brushing, PARDS subject ARDS_002


title: Nasal epithelial brushing, PARDS subject ARDS_001


title: BMAL2_SEV_2

city: St Louis

first: Carolina

middle: B

last: Lopez

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: BMAL2_SEV_2

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers,  and grouped by gene_id. Final gene counts were annotated with gene biotype and  other metadata extracted from the reference GTF file.  Sample-sample correlations  for sample-sample heatmap and PCA were calculated on normalized counts  (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression  was done with edgeR v4.0.16 using standard practice including filtering for  low-expressed genes with edgeR::filterByExprwith default values. Functional  enrichment, when available, is performed using gene set enrichment analysis with  gseapy v0.12 using the MSigDB Hallmark gene set.
Assembly: GRCh38
Supplementary files format and content: fastq sequencing files
Supplementary files format and content: csv gene expression tables
Supplementary files format and content: csv gene set enrichment tables

source_name: BMAL2 A549

growth_protocol: A549 human lung epithelial cells (ATCC CCL-185) were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1 mM sodium pyruvate, and 50 μg/mL gentamicin at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
RNA was extracted by Kingfisher (Thermofisher) with MagMax Mirvana Total RNA isolation kit (Thermofisher, A27828).
Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

treatment_protocol: Cells were infected with Sendai Virus (MOI 1.5) for 24 hours

value: BMAL2 A549

tag: cell type

value: lung epithelial cells

value: SeV infected


title: LATS+Y/Ti_3

city: Miami

first: xiaomin

last: cai

state: Florida

address: Rosenstiel Medical Science Building 1600 NW, 10th Ave.

institute: University of Miami

description: Library name: L3

data_processing:
Raw FASTQ files were processed in a Linux (Ubuntu 22.04) environment. Reads were aligned to the Mus musculus GRCm38 reference genome using HISAT2. Gene-level read counts were generated using featureCounts with the GENCODE vM25 annotation (gencode.vM25.annotation.gtf).
Assembly: Mus musculus GRCm38
Supplementary files format and content: The processed data file is a gene-level raw count matrix generated by featureCounts.

source_name: mouse knee joint tissue

extract_protocol:
For the first set, total RNA was extracted from mouse knee joint cartilage tissue using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. For the second and third sets, total RNA was extracted from mouse knee joint tissues using a modified Trizol/RNeasy. Knee tissues were cryogenically homogenized using stainless steel beads, lysed in TRIzol reagent, treated with Proteinase K, subjected to chloroform extraction, and purified using RNeasy spin columns (Qiagen).
For the first set, Sequencing libraries were then prepared according to the manufacturer’s protocol and sequenced by Innomics Inc. on the DNBSEQ platform using paired-end 100-bp reads.  For the second and third sets, Sequencing libraries were prepared according to the manufacturer’s protocol and sequenced by Admera Health, LLC on an Illumina platform using paired-end 150-bp reads.

value: mouse knee joint tissue


title: BMAL2_SEV_1

description: Library name: BMAL2_SEV_1


title: LATS+Y/Ti_2

description: Library name: L2


title: LATS+Y/Ti_1

description: Library name: L1


title: BMAL2_3

description: Library name: BMAL2_3

value: mock


title: Ad, P0 control, replicate 1

description: Library name: LL1

value: whole worm


title: PKC+Y/Ti_3

description: Library name: K3


title: BMAL2_1

description: Library name: BMAL2_1


title: PKC+Y/Ti_2

description: Library name: K2


title: CTRL_SEV_3

description: Library name: CTRL_SEV_3


title: PKC+Y/Ti_1

description: Library name: K1


title: CTRL_SEV_2

description: Library name: CTRL_SEV_2


title: Y/Ti_3

description: Library name: J3


title: CTRL_SEV_1

description: Library name: CTRL_SEV_1