title: spinal cord - WT - p-S166-RIPK1

description:
GEN00197573 mm_WT-2_phR
DKO_1_2_phR_on_Ac_vs_KD_1_vs_KD_2_vs_WT_2_phR_on_Ac_peaks_on_DKO-2_phR.bed
Tbk1+/+; Tak1ΔM/+

value: Tbk1+/+; Tak1deltaM/+


title: D325A MEFs - vehicle - SMARCC2

status: Public on Jul 13 2022

type: SRA

city: Boston

first: Wanjin

last: Li

state: Massachusetts

address: 240 longwood Ave

department: Cell Biology

country: USA

institute: Harvard Medical School

library_source: genomic

data_processing:
Library strategy: CUT&Tag
For ATAC-seq, paired-end 41x41 bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500 to access open vs closed chromatin regions. Data was processed following ATAC-seq guidelines by Harvard FAS informatics. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --very-sensitive -k 10.
For RNA-seq, libraries were sequenced on an Illumina NextSeq500 instrument with paired 38bp reads. Reads were aligned to the mm9 UCSC mouse transcriptome with Salmon and expression values were determined with DESeq2.
For CUT&Tag,paired-end 41x41bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --local --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Genome_build: mm9 for mouse, hg19 for human
Supplementary_files_format_and_content: bigWig files were generated by deeptools version 3.0.2

molecule: genomic DNA

organism: Mus musculus

source_name: D325A MEFs - vehicle - SMARCC2

extract_protocol:
ATAC-seq was performed according to the standard protocol.
For RNA-seq, RNA was extracted from wildtype or Ripk1D325A/D325A;Ripk3-/- MEFs using Quick-RNA MiniPrep kit (Zymo Research) with the in-column DNase treatment. Libraries were prepared and sequenced by the Bauer Core facility at Harvard University.
For CUT&Tag, the nuclei were isolated and the protein enriched DNA regions were obtained using standard CUT&Tag protocol.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ripk1D325A/D325A;Ripk3-/- MEFs treated with vehicle or TNFα with or without Nec-1s

tag: genotype

tag: cell line

value: MEFs

tag: treatment

value: vehicle

tag: time

tag: cut&tag antibody


title: CAp13

city: Boise

first: Matthew

last: Goelzer

state: Idaho

address: 1910 University Drive

department: Materials Science and Engineering

institute: Boise State University

library_source: transcriptomic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on FASTQ files using FastQC
Paired end reads were aligned by STAR
Gene counts generated by DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: CSV files include raw counts and RPKM log2Fold Change for each gene per sample. Log2Fold for specific sample comparisons.

molecule: total RNA

source_name: Bone marrow derived MSC

extract_protocol:
TRIzol reagent (Invitrogen), extracted using Qiagen RNAeasy Kit.
mRNA version 2 library prep kit (Illumina)

tag: cell type

value: MSC

tag: passage

value: Passage 8

tag: media

value: Adipogneic Media

tag: sirna

value: Control siRNA

tag: doxycyline


title: WY96-3418, rep9

city: LINCOLN

first: Robert

middle: Bristow

last: Moore

state: NE

address: 1901 vine street

department: Biochemistry

institute: University of Nebraska - Lincoln

data_processing:
Trimmomatic was utilized to remove low-quality reads obtained by FastQC, and reads with less than 35 bp were removed from the analysis.
FastQC was applied again and alignments were obtained by using the TopHat2.
Bowtie 2 was utilized for indexing the genes.
Cufflink identified expressed genes and calculated transcript levels in the aligned reads within the TopHat2 generated Sequence Alignment/Map (SAM) formatted files.
Genes transcribed were measured using fragments per kilobase of exon per million (FPKM) reads.
Assembly: Francisella tularensis genome sequences were obtained from NCBI microbial genome database and had the following accession numbers: SCHU S4 (NC_006570.2), MA00-2987 (NZ_CP012372.1), WY96-3418 (NC_009257.1), and LVS (NC_07880.1).
Supplementary files format and content: Cufflinks FPKM data

organism: Francisella tularensis subsp. tularensis

growth_protocol: Bacterial strains were cultured in BHI broth to mid-log growth phase.

extract_protocol:
Total RNA was extracted using the FastRNA Pro Blue Kit (MP Biomedicals), and then RNA was treated with DNase I and column purified, as recommended by the respective manufacturer.
To produce the the RNA-Seq libraries, ScriptSeq v2 Complete Library Preparation Kit for Bacteria (Epicentre) was utilized according to the manufacturer's instructions and included Ribo-Zero Ribosomal RNA (rRNA) Reagents for Bacteria to remove rRNA.

treatment_protocol: To preserve RNA integrity, bacterial cultures were added to RNAprotect Bacteria Reagent (Qiagen), as recommended by the manufacturer.

tag: clade

value: Francisella tularensis subspecies tularensis subtype A.II

tag: strain


title: D325A MEFs - TNF 2h - SMARCC2

source_name: D325A MEFs - TNF 2h - SMARCC2

value: TNF


title: WY96-3418, rep8


title: WY96-3418, rep7


title: SNaM14

value: Growth Media

value: Sun1/2 siRNA


title: SAp14


title: Patient10-D7

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
Alignment and transcript counting: cellranger v6.0.1
Ambient contamination removal: cellbender v0.2.0
SNP-based demultiplexing: souporcell v2020.7
Genome_build: hg38
Supplementary_files_format_and_content: 10x format single cell gene expression matrices

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol: Viable cells were resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/μL. 40,000 cells were loaded onto a 10x Genomics Chromium™ instrument (10x Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium™ single cell 5’ library & gel bead kit and coupled scTCR-seq libraries were obtained using Chromium™ single cell V(D)J enrichment kit (human T cell) (10x Genomics). Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). Both scRNA-seq and scTCR-seq libraries were normalized to 4nM concentration and pooled in a volume ratio of 4:1. The pooled libraries were sequenced on Illumina NovaSeq S4 platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp.

value: Axi-cel

tag: sorting

value: CAR-neg

tag: timepoint

value: Day +7


title: Patient10-D7-CART

value: CAR-pos


title: WY96-3418, rep10


title: Patient10-Infusion

source_name: Infusion product

value: Day 0


title: Patient11-D7


title: WY96-3418, rep5


title: CAp14


title: D325A MEFs - TNF+Nec-1s 2h - BRG1

source_name: D325A MEFs - TNF+Nec-1s 2h - BRG1


title: WY96-3418, rep6


title: SApM11

value: Sun1/2 siRNA, Adipogneic Media


title: WY96-3418, rep4


title: WY96-3418, rep3


title: D325A MEFs - TNF 2h - BRG1

source_name: D325A MEFs - TNF 2h - BRG1


title: Patient9-D7-CART


title: D325A MEFs - vehicle - BRG1

source_name: D325A MEFs - vehicle - BRG1


title: D325A MEFs - TNF+Nec-1s 4h - BRG1

source_name: D325A MEFs - TNF+Nec-1s 4h - BRG1


title: WY96-3418, rep2


title: Patient10-Baseline

value: Day -30


title: D325A MEFs - TNF+Nec-1s 4h - p-S166-RIPK1

value: MEFs


title: Patient9-Infusion


title: Patient9-D7


title: WY96-3418, rep1


title: CNaM14


title: D325A MEFs - TNF 4h - BRG1

source_name: D325A MEFs - TNF 4h - BRG1


title: CNaM11


title: Patient9-Baseline

value: Day -5


title: D325A MEFs - TNF 4h - p-S166-RIPK1

source_name: D325A MEFs - TNF 4h - p-S166-RIPK1


title: SCHU S4, rep24

source_name: SCHU S4

value: Francisella tularensis subspecies tularensis subtype A.I

value: SCHU S4


title: Patient8-D7-CART


title: D325A MEFs - TNF+Nec-1s 2h - p-S166-RIPK1


title: D325A MEFs - TNF 2h - p-S166-RIPK1

source_name: D325A MEFs - TNF 2h - p-S166-RIPK1


title: SCHU S4, rep23


title: Patient8-Infusion


title: D325A MEFs - vehicle - p-S166-RIPK1

source_name: D325A MEFs - vehicle - p-S166-RIPK1

value: vehicle


title: SCHU S4, rep21


title: SCHU S4, rep22


title: Patient8-Baseline


title: CApM11

value: MSC

value: Passage 8

value: Adipogneic Media

value: Control siRNA


title: SCHU S4, rep20


title: Migratory DC no SFB

city: Columbus

first: Soo

last: Ngoi

state: OH

address: 460 W 12th Ave

department: Internal Medicine Hematology

institute: OSU

data_processing:
10X Genomics Cell Ranger pipeline
Genome_build: 10X Genomics mouse reference genome
Supplementary_files_format_and_content: Hierarchical Data Format 5

source_name: Immune cells

growth_protocol: Ex vivo primary cells

extract_protocol:
FACS-sorted CD11c+MHCII-high cells
Chromium Single Cell 3' Library v2 Kit (10x Genomics) according to manufacturer's protocol

treatment_protocol: Mice were orally gavaged with SFB-positive fecal material and sacrifice 5 days later

tag: tissue

value: Mesenteric lymph nodes

value: Dendritic cells


title: D325A MEFs - TNF+Nec-1s 4h - H3K4me1

source_name: D325A MEFs - TNF+Nec-1s 4h - H3K4me1


title: RNA-seq_MAFK-KO_PAL_12

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Single-read sequencing was performed using the NextSeq 500 (Illumina). Pair-end sequencing was performed using the NovaSeq 6000 (Illumina).
All data was analysed on the Galaxy platform (https://usegalaxy.eu/). Reads were trimmed with Trim Galore! (Galaxy version 0.4.3.1) and quality was assessed using FastQC (Galaxy version 0.72+galaxy1). Reads were aligned to the hg38 or mm10 version of the human and mouse genome, respectively, using STAR (Galaxy version 2.7.7a). Strand specificity and read counting was performed with Infer Experiment (Galaxy version 2.6.4.1) and featureCounts (Galaxy version 2.0.1), respectively. Next, we used DESeq2 (Galaxy version 2.11.40.6+galaxy1) for differential expression analysis and the resulting data was annotated with Annotate DESeq2/DEXSeq output tables (Galaxy version 1.1.0).
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Excel (xlsx) files containing DESeq2 outputs.

molecule: polyA RNA

source_name: Mouse hepatocytes

growth_protocol: FL83B mouse hepatocytes (ATCC®, #CRL-2390™) were grown in F-12K medium (Thermo Fisher Scientific, #21127030) supplemented with 10% fetal bovine serum (growth medium). Cells were maintained at 37°C, 95% O2 and 5% CO2.

extract_protocol:
Cells were collected in TRI Reagent (Sigma #T9424), following which RNA was purified using Direct-zol™ RNA MiniPrep (Zymo Research, #R2050).
Libraries from human liver tissue and wild type FL83B cells were prepared with TruSeq Stranded Total RNA Library Prep Gold (Illumina, #20020599). Libraries from knockout FL83B cells and their corresponding non-targeting controls were prepared with TruSeq Stranded mRNA Library Kit (Illumina, #20020595).

treatment_protocol: FL83B cells were incubated in 400 µM palmitate diluted in growth medium for 24 h. One percent BSA diluted in growth medium was used as control. Moreover, gene knockout was achieved by the CRISPR-Cas9 system, using non-targeting agRNA (control) and Tcf4 or Mafk sgRNA.

tag: tissue/cell type

value: FL83B hepatocytes

tag: condition

value: PAL

value: Mafk sgRNA


title: Patient7-Infusion

value: Axi-cel

value: Day 0


title: D325A MEFs - TNF 4h - H3K4me1

source_name: D325A MEFs - TNF 4h - H3K4me1

tag: genotype

value: TNF


title: RNA-seq_MAFK-KO_PAL_11


title: Patient7-D7-CART

value: CAR-pos

value: Day +7


title: Patient8-D7

value: CAR-neg


title: SCHU S4, rep18

value: Francisella tularensis subspecies tularensis subtype A.I

value: SCHU S4


title: D325A MEFs - TNF+Nec-1s 2h - H3K4me1

source_name: D325A MEFs - TNF+Nec-1s 2h - H3K4me1

tag: cell line

value: MEFs


title: SCHU S4, rep19


title: Resident DC +SFB


title: Patient7-D7

tag: treatment


title: SCHU S4, rep17


title: RNA-seq_CON_PAL_9_J78.4

value: non-targeting sgRNA


title: D325A MEFs - TNF 2h - H3K4me1

source_name: D325A MEFs - TNF 2h - H3K4me1

tag: time


title: D325A MEFs - vehicle - H3K4me1

source_name: D325A MEFs - vehicle - H3K4me1

value: vehicle

tag: cut&tag antibody


title: Migratory DC +SFB

tag: cell type


title: SNaM11

source_name: Bone marrow derived MSC

value: MSC

tag: passage

value: Passage 8

value: Growth Media

value: Sun1/2 siRNA


title: RNA-seq_CON_PAL_8_J78.4

value: FL83B hepatocytes

value: PAL


title: SCHU S4, rep16


title: Patient6-D7-CART

source_name: Peripheral blood

value: Axi-cel


title: D325A MEFs - TNF+Nec-1s 3h rep3

data_processing:
For ATAC-seq, paired-end 41x41 bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500 to access open vs closed chromatin regions. Data was processed following ATAC-seq guidelines by Harvard FAS informatics. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --very-sensitive -k 10.
For RNA-seq, libraries were sequenced on an Illumina NextSeq500 instrument with paired 38bp reads. Reads were aligned to the mm9 UCSC mouse transcriptome with Salmon and expression values were determined with DESeq2.
For CUT&Tag,paired-end 41x41bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --local --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Genome_build: mm9 for mouse, hg19 for human
Supplementary_files_format_and_content: bigWig files were generated by deeptools version 3.0.2

source_name: D325A MEFs - TNF+Nec-1s 3h rep3


title: RNA-seq_CON_PAL_7_J78.4


title: RNA-seq_MAFK-KO_6

value: BSA

value: Mafk sgRNA


title: SCHU S4, rep15


title: RNA-seq_MAFK-KO_PAL_10


title: Patient6-D7


title: D325A MEFs - TNF+Nec-1s 3h rep2

source_name: D325A MEFs - TNF+Nec-1s 3h rep2


title: Patient6-Baseline

value: Day -30


title: SCHU S4, rep14


title: D325A MEFs - TNF+Nec-1s 3h rep1

source_name: D325A MEFs - TNF+Nec-1s 3h rep1


title: SCHU S4, rep13


title: Patient5-Infusion

source_name: Infusion product

value: Day 0


title: RNA-seq_MAFK-KO_4


title: Patient4-D7

value: Day +7


title: D325A MEFs - TNF 3h rep2

source_name: D325A MEFs - TNF 3h rep2

value: TNF


title: RNA-seq_CON_3_J78.4


title: SCHU S4, rep12

source_name: SCHU S4

value: Francisella tularensis subspecies tularensis subtype A.I

value: SCHU S4


title: D325A MEFs - TNF 3h rep3

source_name: D325A MEFs - TNF 3h rep3

value: MEFs


title: D325A MEFs - TNF 3h rep1

source_name: D325A MEFs - TNF 3h rep1


title: RNA-seq_CON_2_J78.4

value: non-targeting sgRNA


title: SCHU S4, rep11


title: Patient4-Infusion


title: SCHU S4, rep10


title: Patient3-Infusion


title: RNA-seq_CON_1_J78.4


title: D325A MEFs - TNF+Nec-1s 2h rep2

source_name: D325A MEFs - TNF+Nec-1s 2h rep2


title: D325A MEFs - TNF+Nec-1s 2h rep3

source_name: D325A MEFs - TNF+Nec-1s 2h rep3


title: Patient2-D7


title: RNA-seq_TCF4-KO_PAL_11

source_name: Mouse hepatocytes

value: Tcf4 sgRNA


title: Patient2-Infusion


title: RNA-seq_TCF4-KO_PAL_12


title: SCHU S4, rep9


title: D325A MEFs - TNF+Nec-1s 2h rep1

source_name: D325A MEFs - TNF+Nec-1s 2h rep1


title: SCHU S4, rep8


title: D325A MEFs - TNF 2h rep3

source_name: D325A MEFs - TNF 2h rep3


title: RNA-seq_TCF4-KO_PAL_10


title: SCHU S4, rep6


title: 231 shSmyca#1_rep3

city: Taipei

first: Ruey-Hwa

last: Chen

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to hg38 whole genome using Tophat v2.0.12 with parameters mismatch=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Cole et al., Bioinformatics, 2009.
Genome_build: hg38
Supplementary_files_format_and_content: reads counts/fpkm

source_name: Breast cancer cell lines

growth_protocol: MDA-MB231 cells expressing Control or Smyca shRNAs were maintained following ATCC instructions

extract_protocol:
The RNA was extracted using Trizol reagent following manufacture's instruction.
RNA libraries were prepared for sequencing following standard Illumina protocols

tag: knockdown

value: Smyca


title: D325A MEFs - TNF 2h rep2

source_name: D325A MEFs - TNF 2h rep2


title: RNA-seq_CON_PAL_9_J78.3


title: RNA-seq_MAFK-KO_5


title: SCHU S4, rep5


title: RNA-seq_CON_PAL_8_J78.3


title: SCHU S4, rep4


title: D325A MEFs - TNF 2h rep1

source_name: D325A MEFs - TNF 2h rep1


title: 231 shSmyca#1_rep1


title: RNA-seq_CON_PAL_7_J78.3


title: RNA-seq_TCF4-KO_6


title: Patient1-Infusion


title: D325A MEFs - vehicle rep1

source_name: D325A MEFs - vehicle rep1

value: vehicle


title: SCHU S4, rep7


title: SCHU S4, rep2


title: 231 shCtrl_rep2

value: Ctrl


title: SCHU S4, rep3


title: SCHU S4, rep1


title: 231 shCtrl_rep1


title: RNA-seq_TCF4-KO_4

value: FL83B hepatocytes


title: MA00-2987, rep24


title: D325A MEFs - TNF+Nec-1s 4h

source_name: D325A MEFs - TNF+Nec-1s 4h


title: IL-1b+NPX_OC-C_repeat3

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome mm10 by HISAT2 aligner (version 2.1.0)
Gene counts were quantified by htseq-count (version 0.11.2)
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using Python

source_name: OC-C

growth_protocol: The differentiated AD, FT and OC microtissues were cultured in the microJoint chip for 4 weeks, with the tissue-specific medium streams perfused at the top and a shared stream of "simulated synovial fluid" perfused at the bottom.

extract_protocol:
Cylindrical microtissues were biopsy-punched (Electron Microscopy Sciences, Hatfield, PA) from the tissue inserts. Because of their biphasic nature, osteochondral microtissues were cut into three equal sections under an Olympus dissecting microscope (Olympus, Waltham, MA) and the top and bottom sections were used to extract “bone” and “cartilage” RNA, respectively. The microtissues were crushed in QIAzol lysis buffer (Qiagen, Germantown, MD), and RNA was extracted using an RNeasy Plus Universal Kit (Qiagen, Germantown, MD) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After culturing the microtissues in the microJoint for 4 weeks, the proinflammatory cytokine IL-1β (10 ng/mL; PeproTech, Rocky Hill, NJ) was introduced in the FM stream to challenge the FT for 7 days, leading to the generation of an inflamed microJoint. For the drug treatment group, after a 3-day IL-1β treatment of the FT, naproxen sodium (NPX; Sigma, St. Louis, MO) was added at 5 μM to all medium streams and remained for 4 days. IL-1β treatment continued for another 4 days as well (7 days treatment in total). After the 1 week of IL-1β treatment, with or without the use of NPX, the microtissues were collected for RNA extraction.

tag: microtissue

value: OC-C

tag: model


title: D325A MEFs - vehicle rep3

source_name: D325A MEFs - vehicle rep3


title: RNA-seq_CON_3_J78.3


title: MA00-2987, rep23

tag: clade


title: IL-1b+NPX_OC-C_repeat2


title: RNA-seq_CON_2_J78.3


title: D325A MEFs - TNF+Nec-1s 2h

source_name: D325A MEFs - TNF+Nec-1s 2h


title: MA00-2987, rep21

tag: strain


title: RNA-seq_CON_1_J78.3


title: D325A MEFs - TNF 2h

source_name: D325A MEFs - TNF 2h


title: 231 shCtrl_rep3


title: IL-1b+NPX_OC-C_repeat1


title: 231 shSmyca#1_rep2


title: IL-1b+NPX_OC-O_repeat3

source_name: OC-O

value: OC-O


title: D325A MEFs - vehicle rep2

source_name: D325A MEFs - vehicle rep2


title: D325A MEFs - vehicle

source_name: D325A MEFs - vehicle


title: IL-1b+NPX_OC-O_repeat2


title: MA00-2987, rep19


title: MA00-2987, rep20


title: RNA-seq_PAL_3

value: PAL


title: RNA-seq_PAL_2


title: D325A MEFs - TNF 4h

source_name: D325A MEFs - TNF 4h


title: SEV1

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

country: China

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Sample 4

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: primary neurons

growth_protocol: Primary cortical neurons were prepared from the brains of C57 mice on embryonic day (E14.5) as described by Gerard et al 2012.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina NovaSeq 6000.

treatment_protocol: The cells were treated with 3% sevoflurane, plus 21% O2, and 5% CO2 2 h a day for three consecutive days. Control conditions included 21% O2, and 5% CO2.

tag: srtain

value: cortex


title: RNA-seq_PAL_1

source_name: Mouse hepatocytes


title: SEV2

description: Sample 5


title: IL-1b+NPX_FT_repeat3

source_name: FT

value: FT


title: MA00-2987, rep18


title: RNA-seq_BSA_3

value: BSA


title: IL-1b+NPX_OC-O_repeat1


title: IL-1b+NPX_FT_repeat2


title: CON1

description: Sample 1


title: RNA-seq_BSA_2


title: CON2

description: Sample 2


title: SEV3

description: Sample 6


title: IL-1b+NPX_AD_repeat3

source_name: AD

value: AD


title: MA00-2987, rep15


title: MA00-2987, rep16


title: CON3

description: Sample 3


title: IL-1b+NPX_AD_repeat2


title: MA00-2987, rep17


title: RNA-seq_BSA_1


title: MA00-2987, rep12


title: PAL_2

data_processing:
Pair-end sequencing of the libraries was performed using the Illumina NextSeq 500.
All data was analysed on the Galaxy platform (https://usegalaxy.eu/). Reads were trimmed with Cutadapt (Galaxy version: 1.16.5) and quality was assessed using FastQC (Galaxy version 0.72+galaxy1). Reads were aligned to the hg38 or mm10 version of the human and mouse genome, respectively, using Bowtie2 (Galaxy version 2.3.4.3+galaxy0). Low quality reads (phred < 30) were filtered out with Filter (Galaxy Version 2.4.1) and duplicated reads were removed with MarkDuplicates (Galaxy version 2.18.2.2). Next, we used Genrich (Galaxy version 0.5+galaxy2) for peak calling (q-value < 0.05), while ChIPseeker (Galaxy version, #1.18.0+galaxy1) was used to annotate peaks.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Excel (xlsx) files containing Genrich outputs.

extract_protocol:
Nuclei from human liver (15 mg) were isolated using with the Nuclei EZ Prep kit (Sigma-Aldrich, #NUC101) and a glass dounce homogenizer (25 strokes with lose pastel and 25 strokes with tight pastel in ice-cold Nuclei EZ Lysis Buffer). Nuclei were filter through a 40 μm cell strainer and counted before ATAC-seq. On the other hand, Fl83B mouse hepatocytes were seeded in 60 mm plates 24 h before BSA or PAL treatment. Nuclei from human liver and mouse hepatocytes were then used for ATAC-seq as previously described (PMID: 28846090).
Library preparation was performed as previously described (PMID: 28846090).

treatment_protocol: FL83B cells were incubated in 400 µM palmitate diluted in growth medium for 24 h. One percent BSA diluted in growth medium was used as control.


title: MA00-2987, rep13


title: PAL_3


title: IL-1b_OC-C_repeat3


title: IL-1b+NPX_FT_repeat1


title: IL-1b+NPX_AD_repeat1


title: BSA_3


title: MA00-2987, rep10


title: RNA-seq_TCF4-KO_5


title: MA00-2987, rep11


title: PAL_1


title: MA00-2987, rep22


title: MA00-2987, rep14


title: BSA_1


title: MA00-2987, rep8


title: IL-1b_OC-O_repeat2


title: ARcKO_DHT_rep4

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

country: Japan

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed using Trimmomatic (version 0.33) to remove poor quality reads.
Read data was then aligned to the mouse genome (mm10) with Hisat2 (version 2.1.0)
The aligned reads were used for the transcript quantification by using featureCounts from the subread package (version 1.6.5)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Th2 differentiated cells

growth_protocol: For Th2 differentiation, naive CD4 T cells were cultured with 10 mg/ml plate bound anti-CD3 antibody (145-2C11, Bio X Cell) and 8 mg/ml soluble anti-CD28 antibody (37.51, Bio X Cell), 20 ng/ml human IL-2 (BioLegend), 10 ng/ml mouse IL-4 (BioLegend), 5 ng/ml anti-IFN-g antibody in RPMI 1640 medium containing 10% FBS, 50 mM 2-mercaptethanol, and 10 mM HEPES (pH 7.4).

extract_protocol:
Th2 cells were lysed with Buffer LTR (Qiagen), and RNA was purified with RNeasy Micro Kit (QIAGEN). Double strand cDNA was synthesized using SMART-Seq HT kit for Sequencing (Takara), and sequencing libraries were constructed with Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were stimulated with 10 nM dihydrotestosterone (DHT) (Sigma) from day 4 for 48 hours.

tag: age

value: lymph node

value: Th2 cells


title: IL-1b_OC-C_repeat2


title: IL-1b_OC-C_repeat1


title: BSA_2

tag: tissue


title: ARcKO_DHT_rep3


title: ARcKO_DHT_rep2


title: ARcKO_DHT_rep1


title: MA00-2987, rep6

value: Francisella tularensis subspecies tularensis subtype A.I


title: IL-1b_FT_repeat3


title: IEC12C

city: Xi'an

first: Hai

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: induced endothelial cells, stage day 12

extract_protocol:
Seperated cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: induced endothelial cells

tag: time of_differentiation

value: stage day 12


title: IL-1b_OC-O_repeat3


title: IEC12B


title: IL-1b_OC-O_repeat1


title: MA00-2987, rep7


title: IEC12A


title: WT_DHT_rep3

value: AR-flox/y


title: IL-1b_FT_repeat1


title: IEC4C

source_name: induced endothelial cells, stage day 4

value: stage day 4


title: IEC4B


title: MA00-2987, rep9


title: WT_DHT_rep4


title: WT_DHT_rep2


title: MA00-2987, rep5


title: IL-1b_FT_repeat2


title: MA00-2987, rep4


title: KLF2-cKO.3

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the GRCm38 mouse genome with HISAT2 2.1.0
Gene-wise counts were generated with featureCounts 1.6.4
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Combined table with summarized gene-wise counts for each sample generated with featureCounts

source_name: mLN IgA P1 plasma cell

extract_protocol:
IgA plasma cells were FACS-purified from 2 pooled mLN per sample (CD138+ TACI+ IgA+ CD19+ B220+) and sorted directly into Trizol (Qiagen) Lysis reagent. Total RNA was isolated with the RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Low input kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.


title: WT_DHT_rep1


title: MA00-2987, rep3


title: IL-1b_AD_repeat2


title: BEND79

city: Honolulu

first: Vedbar

middle: S

last: Khadka

state: HI

address: 651 IIalo Street

institute: JABSOM Bioinformatics Core, University of Hawaii

data_processing:
hisat2-build was used too index genome (Bos_taurus.ARS-UCD1.2.dna.toplevel.fa)
hisat2 was used to align against the genome
samtools was used to sort SAM files
htseq_counts was used to produce raw counts
DESeq2 was used for differential gene expression analysis
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: xlsx; contains raw read counts and DESeq2 results

organism: Bos taurus

source_name: Uterus

extract_protocol:
Total RNA was isolated from frozen tissues (60-100 mg) using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The total RNA concentration was determined using NanoDrop One (Thermo Fisher Scientific, Madison, WI). RNA quality was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France).
RNA libraries were prepared for sequencing using standard lllumina protocols

value: Pregnant


title: IEC2A

source_name: induced endothelial cells, stage day 2

value: stage day 2


title: MA00-2987, rep1


title: Control_OC-C_repeat2

source_name: OC-C

value: Control


title: KLF2-cKO.1


title: IL-1b_AD_repeat1


title: IEC2B


title: WTcre.3


title: KLF2-cKO.2


title: Control_OC-O_repeat3


title: BEND78


title: MA00-2987, rep2


title: WTcre.2


title: Control_OC-C_repeat3

value: OC-C


title: IL-1b_AD_repeat3


title: IEC4A


title: Control_OC-C_repeat1


title: BEND74

value: Non-Pregnant


title: AOCB

source_name: porcine endothelial cell lines

value: porcine endothelial cells

value: final


title: IEC2C


title: H54_7H9_replicate2

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

data_processing:
Raw RNA-sequencing reads with a Phred-scaled quality score greater than 20 were aligned to the reference genome M. tuberculosis H37Rv (NC_000962.3) using Bowtie 2.
The number of reads mapped to annotated features (n=4,008) in the reference NCBI GenBank assembly GCF_000195955.2 was counted using feature-count.
The read counts were normalized using DESeq2.
Fold-changes with a false-discovery rate (FDR) less than 0.05 were considered significantly differentially expressed.
Assembly: M. tuberculosis H37Rv (NC_000962.3)
Supplementary files format and content: text files include FPKM values for each Sample

organism: Mycobacterium tuberculosis

extract_protocol:
A total of 5μg RNA was treated with DNase I (New England BioLabs, USA). The total RNA was depleted of the ribosomal-RNAs (rRNA) using Ribo-Zero-Magnetic-Kit (epicentre). The rRNA-depleted RNA was fragmented into 130-170 nucleotides and transcribed into cDNA using Superscript II (Invitrogen, USA). The cDNA was then poly-adenylated and ligated to the sequencing adapters. The resulting libraries were quantitated by real-time quantitative PCR (qPCR) and amplified on the cBot for cluster generation (TruSeq PE Cluster Kit v3-cBot-HS).
TruSeq PE Cluster Kit v3-cBot-HS

value: 7H9 medium


title: BEND76


title: H112_NR_replicate2

value: multi-stress condition


title: AOCA


title: BEND73


title: BEND72


title: BEND75


title: WTcre.1


title: Control_OC-O_repeat2

value: OC-O


title: AOCC


title: BEND77


title: H54_NR_replicate1


title: Control_OC-O_repeat1


title: H54_NR_replicate2


title: BEND05

value: Cyclic


title: H112_7H9_replicate2


title: Control_FT_repeat2

value: FT


title: Control_FT_repeat3


title: H112_NR_replicate1


title: Control_AD_repeat3

value: AD


title: Control_AD_repeat2


title: BEND06


title: Control_FT_repeat1


title: Flybrain_rehydrated_2

city: Durham

first: Vincent

last: Croset

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
We obtained 3.419 billion reads, and used CellRanger 3.1.0 to map these to the FB2018_06 Drosophila melanogaster genome assembly (v6.25) (Thurmond et al., 2019) and create digital gene expression (DGE) matrices.
Assembly: FB2018_06 Drosophila melanogaster genome assembly (v6.25)
Supplementary files format and content: Digital Gene Expression Matrices (.h5) representing the number of individual transcripts detected for each gene in each cell.  A seurat object named  Thirst2_SCT_trimPlus.Robj contained QC , filtered,   normalised and batch corrected data  for all samples with cell type annotations per cell barcode included

organism: Drosophila melanogaster

source_name: Brain (dissociated)

growth_protocol: Flies were raised on standard cornmeal food under a 12:12 light:dark cycle at 60% humidity and 25°C

extract_protocol:
For each sample, 24 central brains from mixed sexes (1:1) were individually dissected in ice-cold DPBS (Gibco, 14190–086) and immediately transferred into 1 mL toxin-supplemented Schneider’s medium (tSM: Gibco, 21720–001 + 50 mM d(-)-2- amino-5-phosphonovaleric acid, 20 mM 6,7-dinitroquinoxaline-2,3-dione and 0.1 mM tetrodotoxin) on ice. Brains were washed once with 1 mL tSM and incubated in tSM containing 1.11 mg/mL papain (Sigma, P4762) and 1.11 mg/mL collagenase I (Sigma, C2674). Brains were washed once more with tSM and subsequently triturated with flame-rounded 200 mL pipette tips. Dissociated brains were resuspended into 1 mL PBS + 0.01% BSA and filtered through a 10 mm CellTrix strainer (Sysmex, 04-0042-2314). Cell concentration was measured using a disposable Fuchs-Rosenthal haemocytometer (VWR, 631–1096) under a Leica DMIL LED Fluo microscope. A typical preparation from 24 brains yielded ~600,000 cells.
mRNA barcoding and library preparation were performed using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), following manufacturer’s instructions. For each sample, we targeted an 8,000 cell recovery. Libraries were sequenced with NovaSeq 6000 (Illumina)

treatment_protocol: For dehydration, animals were placed into vials containing a ~2cm layer of Drierite topped with a piece of cotton and a dried sucrose-coated filter paper. Vials were kept in a sealed container with a layer of Drierite at the bottom for indicated time. (Re-)hydrated flies were placed into a vial containing 1% agar and a wet piece of sucrose-coated filter paper.

tag: condition

value: Rehydrated

value: Brain


title: Flybrain_rehydrated_1

tag: genotype


title: Flybrain_6h_deprived_1

value: Thirsty (6h)


title: Flybrain_12h_deprived_1

value: Thirsty (12h)


title: Flybrain_6h_deprived_2


title: Flybrain_12h_deprived_2


title: H54_7H9_replicate1


title: BEND04


title: BEND03


title: WT_96h

status: Public on Jul 12 2022

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
The clean reads were aligned to mm10 by bowtie2 with default parameter and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes (DEG) were calculated using DESeq2
Genome_build: mm10

source_name: in vitro Th17

growth_protocol: For the in vivo isolated CD4+ T cells, naïve CD4+ T cells from Rorc_fl/fl (WT) or Cd4_cre Rorc_fl/fl (RorcCd4) mice were transferred into Tcrbd-/- reciepient mice for 6 weeks, and the CD4+ T cells were isolated from colon lamina propria for sequencing. For in vitro polarized Th17 cells, Rorc_fl/fl (WT) or ERT2_cre Rorc_fl/fl (RorcERT2) naïve CD4+ T cells were activated with plate-bound anti-CD3 and anti-CD28 and cultured with TGF-β, IL-6, IL-1β and IL-23 for 3 days, and then treated with 4-OHT for another 48 or 96 hours.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: The cells were re-stimulated with PMA and ionomycin for 2 hours before RNA extraction for in vivo isolated T cells, and re-stimulated with anti-CD3 for 4 hours before RNA-extraction for in vitro cultured Th17 cells.


title: H112_7H9_replicate1


title: WT_colitis_rep2

source_name: colon CD4+ T cells


title: Flybrain_sated_2

value: Sated


title: Control_AD_repeat1


title: Sample 2C_Mutant strain

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

institute: University Of Miami

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned using Bowtie 2
Reads were counted using htseq-count
Assembly: NC_000913.3
Supplementary files format and content: Read counts per gene

organism: Escherichia coli

source_name: MG1655 rph+

growth_protocol: Wild-type and mutant cells were grown to early log phase in rich defined medium, transferred to a 42C water bath for 30 min, then harvested for RNA preparation

extract_protocol:
RNA was isolated using the hot phenol method
Ribosomal RNA was depleted using a bacterial rRNA depletion kit (New England Biolabs, cat # E7850) using the manufacturer's protocol. Libraries were constructed using Ultra II RNA library prep kit (New England Biolabs, cat # E7770) using the manufacturer's protocol.

tag: cell line

value: MG1655 rph+

value: Bacteria

value: ornts


title: Flybrain_sated_1


title: RorcERT2_96h

value: ERT2cre Rorc_fl/fl


title: WT_48h


title: RorcCd4_colitis_rep2

value: Cd4_cre Rorc_fl/fl


title: RorcERT2_48h


title: RorcCd4_colitis_rep1


title: Sample 1B_WT strain

value: Wild-type

tag: treatment


title: WT_colitis_rep1


title: Sample 2D_Mutant strain


title: Sample 2A_Mutant strain


title: Sample 2B_Mutant strain


title: Sample 1C_WT strain


title: nasal_prox1_1440

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description: Nasal Prox1+ cells

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 1000 genes), potential dead cells (>10% mitochondrial gene percentage) and contaminating Prox1- cells were removed for EC datasets. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasal Prox1+ cells from Prox1-GFP mouse

source_name: Nasal Prox1+ cells

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasal Prox1+ cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

value: Nasal Prox1+ cells

value: FVB


title: nasal_prox1_1426

description: Nasal Prox1+ cells


title: nasal_prox1_1439

description: Nasal Prox1+ cells


title: nasal_prox1_1425

description: Nasal Prox1+ cells


title: nasal_prox1_1434

description: Nasal Prox1+ cells


title: nasal_prox1_1433

description: Nasal Prox1+ cells


title: nasal_prox1_1437

description: Nasal Prox1+ cells


title: nasal_prox1_1422

description: Nasal Prox1+ cells


title: nasal_prox1_1424

description: Nasal Prox1+ cells


title: nasal_prox1_1419

description: Nasal Prox1+ cells


title: nasal_prox1_1438

description: Nasal Prox1+ cells


title: nasal_prox1_1423

description: Nasal Prox1+ cells


title: nasal_prox1_1432

description: Nasal Prox1+ cells


title: nasal_prox1_1429

description: Nasal Prox1+ cells


title: nasal_prox1_1413

description: Nasal Prox1+ cells


title: nasal_prox1_1430

description: Nasal Prox1+ cells


title: nasal_prox1_1415

description: Nasal Prox1+ cells


title: nasal_prox1_1428

description: Nasal Prox1+ cells


title: Sample 1D_WT strain


title: nasal_prox1_1427

description: Nasal Prox1+ cells


title: nasal_prox1_1407

description: Nasal Prox1+ cells


title: Sample 1A_WT strain


title: nasal_prox1_1402

description: Nasal Prox1+ cells


title: nasal_prox1_1421

description: Nasal Prox1+ cells


title: nasal_prox1_1435

description: Nasal Prox1+ cells


title: nasal_prox1_1436

description: Nasal Prox1+ cells


title: nasal_prox1_1420

description: Nasal Prox1+ cells


title: nasal_prox1_1398

description: Nasal Prox1+ cells


title: nasal_prox1_1396

description: Nasal Prox1+ cells


title: nasal_prox1_1394

description: Nasal Prox1+ cells


title: nasal_prox1_1418

description: Nasal Prox1+ cells


title: nasal_prox1_1417

description: Nasal Prox1+ cells


title: nasal_prox1_1404

description: Nasal Prox1+ cells


title: nasal_prox1_1431

description: Nasal Prox1+ cells


title: nasal_prox1_1410

description: Nasal Prox1+ cells


title: nasal_prox1_1416

description: Nasal Prox1+ cells


title: nasal_prox1_1414

description: Nasal Prox1+ cells


title: nasal_prox1_1388

description: Nasal Prox1+ cells


title: nasal_prox1_1387

description: Nasal Prox1+ cells


title: nasal_prox1_1409

description: Nasal Prox1+ cells


title: nasal_prox1_1408

description: Nasal Prox1+ cells


title: nasal_prox1_1393

description: Nasal Prox1+ cells


title: nasal_prox1_1411

description: Nasal Prox1+ cells


title: nasal_prox1_1405

description: Nasal Prox1+ cells


title: nasal_prox1_1406

description: Nasal Prox1+ cells


title: nasal_prox1_1403

description: Nasal Prox1+ cells


title: nasal_prox1_1383

description: Nasal Prox1+ cells


title: nasal_prox1_1401

description: Nasal Prox1+ cells


title: nasal_prox1_1382

description: Nasal Prox1+ cells


title: nasal_prox1_1379

description: Nasal Prox1+ cells


title: nasal_prox1_1378

description: Nasal Prox1+ cells


title: nasal_prox1_1399

description: Nasal Prox1+ cells


title: nasal_prox1_1381

description: Nasal Prox1+ cells


title: nasal_prox1_1380

description: Nasal Prox1+ cells


title: nasal_prox1_1400

description: Nasal Prox1+ cells


title: nasal_prox1_1385

description: Nasal Prox1+ cells


title: nasal_prox1_1372

description: Nasal Prox1+ cells


title: nasal_prox1_1370

description: Nasal Prox1+ cells


title: nasal_prox1_1412

description: Nasal Prox1+ cells


title: nasal_prox1_1397

description: Nasal Prox1+ cells


title: nasal_prox1_1395

description: Nasal Prox1+ cells


title: nasal_prox1_1392

description: Nasal Prox1+ cells


title: nasal_prox1_1391

description: Nasal Prox1+ cells


title: nasal_prox1_1366

description: Nasal Prox1+ cells


title: nasal_prox1_1390

description: Nasal Prox1+ cells


title: nasal_prox1_1389

description: Nasal Prox1+ cells


title: nasal_prox1_1360

description: Nasal Prox1+ cells


title: nasal_prox1_1359

description: Nasal Prox1+ cells


title: nasal_prox1_1358

description: Nasal Prox1+ cells


title: nasal_prox1_1386

description: Nasal Prox1+ cells


title: nasal_prox1_1355

description: Nasal Prox1+ cells


title: nasal_prox1_1384

description: Nasal Prox1+ cells


title: nasal_prox1_1353

description: Nasal Prox1+ cells


title: nasal_prox1_1349

description: Nasal Prox1+ cells


title: nasal_prox1_1375

description: Nasal Prox1+ cells


title: nasal_prox1_1374

description: Nasal Prox1+ cells


title: nasal_prox1_1373

description: Nasal Prox1+ cells


title: nasal_prox1_1371

description: Nasal Prox1+ cells


title: nasal_prox1_1369

description: Nasal Prox1+ cells


title: nasal_prox1_1346

description: Nasal Prox1+ cells


title: nasal_prox1_1345

description: Nasal Prox1+ cells


title: nasal_prox1_1368

description: Nasal Prox1+ cells


title: nasal_prox1_1367

description: Nasal Prox1+ cells


title: nasal_prox1_1376

description: Nasal Prox1+ cells


title: nasal_prox1_1377

description: Nasal Prox1+ cells


title: nasal_prox1_1365

description: Nasal Prox1+ cells


title: nasal_prox1_1334

description: Nasal Prox1+ cells


title: nasal_prox1_1337

description: Nasal Prox1+ cells


title: nasal_prox1_1335

description: Nasal Prox1+ cells


title: nasal_prox1_1363

description: Nasal Prox1+ cells


title: nasal_prox1_1331

description: Nasal Prox1+ cells


title: nasal_prox1_1361

description: Nasal Prox1+ cells


title: nasal_prox1_1362

description: Nasal Prox1+ cells


title: nasal_prox1_1333

description: Nasal Prox1+ cells


title: nasal_prox1_1357

description: Nasal Prox1+ cells


title: nasal_prox1_1354

description: Nasal Prox1+ cells


title: nasal_prox1_1356

description: Nasal Prox1+ cells


title: nasal_prox1_1330

description: Nasal Prox1+ cells


title: nasal_prox1_1352

description: Nasal Prox1+ cells


title: nasal_prox1_1350

description: Nasal Prox1+ cells


title: nasal_prox1_1351

description: Nasal Prox1+ cells


title: nasal_prox1_1364

description: Nasal Prox1+ cells


title: nasal_prox1_1348

description: Nasal Prox1+ cells


title: nasal_prox1_1347

description: Nasal Prox1+ cells


title: nasal_prox1_1344

description: Nasal Prox1+ cells


title: nasal_prox1_1324

description: Nasal Prox1+ cells


title: nasal_prox1_1326

description: Nasal Prox1+ cells


title: nasal_prox1_1343

description: Nasal Prox1+ cells


title: nasal_prox1_1323

description: Nasal Prox1+ cells


title: nasal_prox1_1342

description: Nasal Prox1+ cells


title: nasal_prox1_1320

description: Nasal Prox1+ cells


title: nasal_prox1_1340

description: Nasal Prox1+ cells


title: nasal_prox1_1318

description: Nasal Prox1+ cells


title: nasal_prox1_1316

description: Nasal Prox1+ cells


title: nasal_prox1_1339

description: Nasal Prox1+ cells


title: nasal_prox1_1341

description: Nasal Prox1+ cells


title: nasal_prox1_1338

description: Nasal Prox1+ cells


title: nasal_prox1_1313

description: Nasal Prox1+ cells


title: nasal_prox1_1336

description: Nasal Prox1+ cells


title: nasal_prox1_1311

description: Nasal Prox1+ cells


title: nasal_prox1_1332

description: Nasal Prox1+ cells


title: nasal_prox1_1309

description: Nasal Prox1+ cells


title: nasal_prox1_1329

description: Nasal Prox1+ cells


title: nasal_prox1_1328

description: Nasal Prox1+ cells


title: nasal_prox1_1300

description: Nasal Prox1+ cells


title: nasal_prox1_1325

description: Nasal Prox1+ cells


title: nasal_prox1_1327

description: Nasal Prox1+ cells


title: nasal_prox1_1322

description: Nasal Prox1+ cells


title: nasal_prox1_1319

description: Nasal Prox1+ cells


title: nasal_prox1_1321

description: Nasal Prox1+ cells


title: nasal_prox1_1294

description: Nasal Prox1+ cells


title: nasal_prox1_1296

description: Nasal Prox1+ cells


title: nasal_prox1_1293

description: Nasal Prox1+ cells


title: nasal_prox1_1292

description: Nasal Prox1+ cells


title: nasal_prox1_1317

description: Nasal Prox1+ cells


title: nasal_prox1_1315

description: Nasal Prox1+ cells


title: nasal_prox1_1289

description: Nasal Prox1+ cells


title: nasal_prox1_1290

description: Nasal Prox1+ cells


title: nasal_prox1_1314

description: Nasal Prox1+ cells


title: nasal_prox1_1312

description: Nasal Prox1+ cells


title: nasal_prox1_1310

description: Nasal Prox1+ cells


title: nasal_prox1_1308

description: Nasal Prox1+ cells


title: nasal_prox1_1287

description: Nasal Prox1+ cells


title: nasal_prox1_1307

description: Nasal Prox1+ cells


title: nasal_prox1_1306

description: Nasal Prox1+ cells


title: nasal_prox1_1286

description: Nasal Prox1+ cells


title: nasal_prox1_1305

description: Nasal Prox1+ cells


title: nasal_prox1_1302

description: Nasal Prox1+ cells


title: nasal_prox1_1301

description: Nasal Prox1+ cells


title: nasal_prox1_1285

description: Nasal Prox1+ cells


title: nasal_prox1_1304

description: Nasal Prox1+ cells


title: nasal_prox1_1299

description: Nasal Prox1+ cells


title: nasal_prox1_1298

description: Nasal Prox1+ cells


title: nasal_prox1_1278

description: Nasal Prox1+ cells


title: nasal_prox1_1280

description: Nasal Prox1+ cells


title: nasal_prox1_1297

description: Nasal Prox1+ cells


title: nasal_prox1_1276

description: Nasal Prox1+ cells


title: nasal_prox1_1295

description: Nasal Prox1+ cells


title: nasal_prox1_1275

description: Nasal Prox1+ cells


title: nasal_prox1_1273

description: Nasal Prox1+ cells


title: nasal_prox1_1270

description: Nasal Prox1+ cells


title: nasal_prox1_1291

description: Nasal Prox1+ cells


title: nasal_prox1_1303

description: Nasal Prox1+ cells


title: nasal_prox1_1288

description: Nasal Prox1+ cells


title: nasal_prox1_1264

description: Nasal Prox1+ cells


title: nasal_prox1_1272

description: Nasal Prox1+ cells


title: nasal_prox1_1284

description: Nasal Prox1+ cells


title: nasal_prox1_1283

description: Nasal Prox1+ cells


title: nasal_prox1_1258

description: Nasal Prox1+ cells


title: nasal_prox1_1259

description: Nasal Prox1+ cells


title: nasal_prox1_1257

description: Nasal Prox1+ cells


title: nasal_prox1_1267

description: Nasal Prox1+ cells


title: nasal_prox1_1281

description: Nasal Prox1+ cells


title: nasal_prox1_1277

description: Nasal Prox1+ cells


title: nasal_prox1_1279

description: Nasal Prox1+ cells


title: nasal_prox1_1271

description: Nasal Prox1+ cells


title: nasal_prox1_1268

description: Nasal Prox1+ cells


title: nasal_prox1_1269

description: Nasal Prox1+ cells


title: nasal_prox1_1251

description: Nasal Prox1+ cells


title: nasal_prox1_1266

description: Nasal Prox1+ cells


title: nasal_prox1_1249

description: Nasal Prox1+ cells


title: nasal_prox1_1282

description: Nasal Prox1+ cells


title: nasal_prox1_1246

description: Nasal Prox1+ cells


title: nasal_prox1_1244

description: Nasal Prox1+ cells


title: nasal_prox1_1265

description: Nasal Prox1+ cells


title: nasal_prox1_1263

description: Nasal Prox1+ cells


title: nasal_prox1_1243

description: Nasal Prox1+ cells


title: nasal_prox1_1262

description: Nasal Prox1+ cells


title: nasal_prox1_1260

description: Nasal Prox1+ cells


title: nasal_prox1_1261

description: Nasal Prox1+ cells


title: nasal_prox1_1238

description: Nasal Prox1+ cells


title: nasal_prox1_1274

description: Nasal Prox1+ cells


title: nasal_prox1_1240

description: Nasal Prox1+ cells


title: nasal_prox1_1242

description: Nasal Prox1+ cells


title: nasal_prox1_1255

description: Nasal Prox1+ cells


title: nasal_prox1_1254

description: Nasal Prox1+ cells


title: nasal_prox1_1256

description: Nasal Prox1+ cells


title: nasal_prox1_1252

description: Nasal Prox1+ cells


title: nasal_prox1_1250

description: Nasal Prox1+ cells


title: nasal_prox1_1253

description: Nasal Prox1+ cells


title: nasal_prox1_1231

description: Nasal Prox1+ cells


title: nasal_prox1_1232

description: Nasal Prox1+ cells


title: nasal_prox1_1230

description: Nasal Prox1+ cells


title: nasal_prox1_1229

description: Nasal Prox1+ cells


title: nasal_prox1_1225

description: Nasal Prox1+ cells


title: nasal_prox1_1226

description: Nasal Prox1+ cells


title: nasal_prox1_1248

description: Nasal Prox1+ cells


title: nasal_prox1_1247

description: Nasal Prox1+ cells


title: nasal_prox1_1245

description: Nasal Prox1+ cells


title: nasal_prox1_1241

description: Nasal Prox1+ cells


title: nasal_prox1_1236

description: Nasal Prox1+ cells


title: nasal_prox1_1234

description: Nasal Prox1+ cells


title: nasal_prox1_1235

description: Nasal Prox1+ cells


title: nasal_prox1_1224

description: Nasal Prox1+ cells


title: nasal_prox1_1222

description: Nasal Prox1+ cells


title: nasal_prox1_1237

description: Nasal Prox1+ cells


title: nasal_prox1_1218

description: Nasal Prox1+ cells


title: nasal_prox1_1221

description: Nasal Prox1+ cells


title: nasal_prox1_1220

description: Nasal Prox1+ cells


title: nasal_prox1_1228

description: Nasal Prox1+ cells


title: nasal_prox1_1239

description: Nasal Prox1+ cells


title: nasal_prox1_1215

description: Nasal Prox1+ cells


title: nasal_prox1_1216

description: Nasal Prox1+ cells


title: nasal_prox1_1233

description: Nasal Prox1+ cells


title: nasal_prox1_1227

description: Nasal Prox1+ cells


title: nasal_prox1_1205

description: Nasal Prox1+ cells


title: nasal_prox1_1208

description: Nasal Prox1+ cells


title: nasal_prox1_1206

description: Nasal Prox1+ cells


title: nasal_prox1_1212

description: Nasal Prox1+ cells


title: nasal_prox1_1213

description: Nasal Prox1+ cells


title: nasal_prox1_1214

description: Nasal Prox1+ cells


title: nasal_prox1_1207

description: Nasal Prox1+ cells


title: nasal_prox1_1217

description: Nasal Prox1+ cells


title: nasal_prox1_1219

description: Nasal Prox1+ cells


title: nasal_prox1_1204

description: Nasal Prox1+ cells


title: nasal_prox1_1209

description: Nasal Prox1+ cells


title: nasal_prox1_1211

description: Nasal Prox1+ cells


title: nasal_prox1_1203

description: Nasal Prox1+ cells


title: nasal_prox1_1223

description: Nasal Prox1+ cells


title: nasal_prox1_1199

description: Nasal Prox1+ cells


title: nasal_prox1_1200

description: Nasal Prox1+ cells


title: nasal_prox1_1201

description: Nasal Prox1+ cells


title: nasal_prox1_1202

description: Nasal Prox1+ cells


title: nasal_prox1_1196

description: Nasal Prox1+ cells


title: nasal_prox1_1197

description: Nasal Prox1+ cells


title: nasal_prox1_1193

description: Nasal Prox1+ cells


title: nasal_prox1_1190

description: Nasal Prox1+ cells


title: nasal_prox1_1195

description: Nasal Prox1+ cells


title: nasal_prox1_1188

description: Nasal Prox1+ cells


title: nasal_prox1_1191

description: Nasal Prox1+ cells


title: nasal_prox1_1192

description: Nasal Prox1+ cells


title: nasal_prox1_1189

description: Nasal Prox1+ cells


title: nasal_prox1_1210

description: Nasal Prox1+ cells


title: nasal_prox1_1186

description: Nasal Prox1+ cells


title: nasal_prox1_1183

description: Nasal Prox1+ cells


title: nasal_prox1_1185

description: Nasal Prox1+ cells


title: nasal_prox1_1182

description: Nasal Prox1+ cells


title: nasal_prox1_1181

description: Nasal Prox1+ cells


title: nasal_prox1_1174

description: Nasal Prox1+ cells


title: nasal_prox1_1180

description: Nasal Prox1+ cells


title: nasal_prox1_1175

description: Nasal Prox1+ cells


title: nasal_prox1_1173

description: Nasal Prox1+ cells


title: nasal_prox1_1178

description: Nasal Prox1+ cells


title: nasal_prox1_1177

description: Nasal Prox1+ cells


title: nasal_prox1_1172

description: Nasal Prox1+ cells


title: nasal_prox1_1169

description: Nasal Prox1+ cells


title: nasal_prox1_1176

description: Nasal Prox1+ cells


title: nasal_prox1_1168

description: Nasal Prox1+ cells


title: nasal_prox1_1171

description: Nasal Prox1+ cells


title: nasal_prox1_1166

description: Nasal Prox1+ cells


title: nasal_prox1_1165

description: Nasal Prox1+ cells


title: nasal_prox1_1167

description: Nasal Prox1+ cells


title: nasal_prox1_1187

description: Nasal Prox1+ cells


title: nasal_prox1_1194

description: Nasal Prox1+ cells


title: nasal_prox1_1163

description: Nasal Prox1+ cells


title: nasal_prox1_1164

description: Nasal Prox1+ cells


title: nasal_prox1_1162

description: Nasal Prox1+ cells


title: nasal_prox1_1160

description: Nasal Prox1+ cells


title: nasal_prox1_1161

description: Nasal Prox1+ cells


title: nasal_prox1_1170

description: Nasal Prox1+ cells


title: nasal_prox1_1159

description: Nasal Prox1+ cells


title: nasal_prox1_1155

description: Nasal Prox1+ cells


title: nasal_prox1_1156

description: Nasal Prox1+ cells


title: nasal_prox1_1154

description: Nasal Prox1+ cells


title: nasal_prox1_1152

description: Nasal Prox1+ cells


title: nasal_prox1_1179

description: Nasal Prox1+ cells


title: nasal_prox1_1198

description: Nasal Prox1+ cells


title: nasal_prox1_1150

description: Nasal Prox1+ cells


title: nasal_prox1_1184

description: Nasal Prox1+ cells


title: nasal_prox1_1153

description: Nasal Prox1+ cells


title: nasal_prox1_1146

description: Nasal Prox1+ cells


title: nasal_prox1_1149

description: Nasal Prox1+ cells


title: nasal_prox1_1143

description: Nasal Prox1+ cells


title: nasal_prox1_1142

description: Nasal Prox1+ cells


title: nasal_prox1_1141

description: Nasal Prox1+ cells


title: nasal_prox1_1158

description: Nasal Prox1+ cells


title: nasal_prox1_1139

description: Nasal Prox1+ cells


title: nasal_prox1_1147

description: Nasal Prox1+ cells


title: nasal_prox1_1140

description: Nasal Prox1+ cells


title: nasal_prox1_1157

description: Nasal Prox1+ cells


title: nasal_prox1_1148

description: Nasal Prox1+ cells


title: nasal_prox1_1134

description: Nasal Prox1+ cells


title: nasal_prox1_1137

description: Nasal Prox1+ cells


title: nasal_prox1_1135

description: Nasal Prox1+ cells


title: nasal_prox1_1151

description: Nasal Prox1+ cells


title: nasal_prox1_1132

description: Nasal Prox1+ cells


title: nasal_prox1_1130

description: Nasal Prox1+ cells


title: nasal_prox1_1133

description: Nasal Prox1+ cells


title: nasal_prox1_1145

description: Nasal Prox1+ cells


title: nasal_prox1_1131

description: Nasal Prox1+ cells


title: nasal_prox1_1128

description: Nasal Prox1+ cells


title: nasal_prox1_1129

description: Nasal Prox1+ cells


title: nasal_prox1_1127

description: Nasal Prox1+ cells


title: nasal_prox1_1124

description: Nasal Prox1+ cells


title: nasal_prox1_1144

description: Nasal Prox1+ cells


title: nasal_prox1_1125

description: Nasal Prox1+ cells


title: nasal_prox1_1126

description: Nasal Prox1+ cells


title: nasal_prox1_1123

description: Nasal Prox1+ cells


title: nasal_prox1_1122

description: Nasal Prox1+ cells


title: nasal_prox1_1138

description: Nasal Prox1+ cells


title: nasal_prox1_1120

description: Nasal Prox1+ cells


title: nasal_prox1_1119

description: Nasal Prox1+ cells


title: nasal_prox1_1121

description: Nasal Prox1+ cells


title: nasal_prox1_1117

description: Nasal Prox1+ cells


title: nasal_prox1_1118

description: Nasal Prox1+ cells


title: nasal_prox1_1115

description: Nasal Prox1+ cells


title: nasal_prox1_1114

description: Nasal Prox1+ cells


title: nasal_prox1_1116

description: Nasal Prox1+ cells


title: nasal_prox1_1136

description: Nasal Prox1+ cells


title: nasal_prox1_1112

description: Nasal Prox1+ cells


title: nasal_prox1_1102

description: Nasal Prox1+ cells


title: nasal_prox1_1111

description: Nasal Prox1+ cells


title: nasal_prox1_1110

description: Nasal Prox1+ cells


title: nasal_prox1_1097

description: Nasal Prox1+ cells


title: nasal_prox1_1105

description: Nasal Prox1+ cells


title: nasal_prox1_1109

description: Nasal Prox1+ cells


title: nasal_prox1_1098

description: Nasal Prox1+ cells


title: nasal_prox1_1108

description: Nasal Prox1+ cells


title: nasal_prox1_1106

description: Nasal Prox1+ cells


title: nasal_prox1_1091

description: Nasal Prox1+ cells


title: nasal_prox1_1093

description: Nasal Prox1+ cells


title: nasal_prox1_1103

description: Nasal Prox1+ cells


title: nasal_prox1_1113

description: Nasal Prox1+ cells


title: nasal_prox1_1104

description: Nasal Prox1+ cells


title: nasal_prox1_1100

description: Nasal Prox1+ cells


title: nasal_prox1_1101

description: Nasal Prox1+ cells


title: nasal_prox1_1099

description: Nasal Prox1+ cells


title: nasal_prox1_1081

description: Nasal Prox1+ cells


title: nasal_prox1_1084

description: Nasal Prox1+ cells


title: nasal_prox1_1082

description: Nasal Prox1+ cells


title: nasal_prox1_1095

description: Nasal Prox1+ cells


title: nasal_prox1_1089

description: Nasal Prox1+ cells


title: nasal_prox1_1094

description: Nasal Prox1+ cells


title: nasal_prox1_1078

description: Nasal Prox1+ cells


title: nasal_prox1_1075

description: Nasal Prox1+ cells


title: nasal_prox1_1107

description: Nasal Prox1+ cells


title: nasal_prox1_1086

description: Nasal Prox1+ cells


title: nasal_prox1_1087

description: Nasal Prox1+ cells


title: nasal_prox1_1074

description: Nasal Prox1+ cells


title: nasal_prox1_1077

description: Nasal Prox1+ cells


title: nasal_prox1_1076

description: Nasal Prox1+ cells


title: nasal_prox1_1096

description: Nasal Prox1+ cells


title: nasal_prox1_1080

description: Nasal Prox1+ cells


title: nasal_prox1_1072

description: Nasal Prox1+ cells


title: nasal_prox1_1083

description: Nasal Prox1+ cells


title: nasal_prox1_1070

description: Nasal Prox1+ cells


title: nasal_prox1_1090

description: Nasal Prox1+ cells


title: nasal_prox1_1071

description: Nasal Prox1+ cells


title: nasal_prox1_1088

description: Nasal Prox1+ cells


title: nasal_prox1_1073

description: Nasal Prox1+ cells


title: nasal_prox1_1065

description: Nasal Prox1+ cells


title: nasal_prox1_1061

description: Nasal Prox1+ cells


title: nasal_prox1_1064

description: Nasal Prox1+ cells


title: nasal_prox1_1063

description: Nasal Prox1+ cells


title: nasal_prox1_1085

description: Nasal Prox1+ cells


title: nasal_prox1_1058

description: Nasal Prox1+ cells


title: nasal_prox1_1066

description: Nasal Prox1+ cells


title: nasal_prox1_1057

description: Nasal Prox1+ cells


title: nasal_prox1_1067

description: Nasal Prox1+ cells


title: nasal_prox1_1068

description: Nasal Prox1+ cells


title: nasal_prox1_1062

description: Nasal Prox1+ cells


title: nasal_prox1_1079

description: Nasal Prox1+ cells


title: nasal_prox1_1055

description: Nasal Prox1+ cells


title: nasal_prox1_1060

description: Nasal Prox1+ cells


title: nasal_prox1_1052

description: Nasal Prox1+ cells


title: nasal_prox1_1069

description: Nasal Prox1+ cells


title: nasal_prox1_1050

description: Nasal Prox1+ cells


title: nasal_prox1_1056

description: Nasal Prox1+ cells


title: rlt1/2 rep2 (MNaseseq)

city: New Haven

first: Emma

middle: Tung

last: Corcoran

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

data_processing:
RNA-seq: Paired-end reads were filtered and trimmed using Trim Galore! (version 0.5.0) with default options for quality (https://github.com/FelixKrueger/TrimGalore). The resulting data sets were aligned to the Araport11 genome using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Protein-coding genes were defined as described in the Araport11 genome annotation. The program featureCounts (version 1.6.4) was used to count the paired-end fragments overlapping with the annotated protein-coding genes. Differential expression analysis of protein-coding genes was performed using DESeq2 version 1.26 on raw read counts to obtain normalized fold changes and Padj-values for each gene. Genes were considered to be differentially expressed if they showed >1.5-fold-change and Padj-value <0.05.
MNase-seq: Paired-end reads were filtered and trimmed using Trim Galore! (version 0.5.0) with default options for quality (https://github.com/FelixKrueger/TrimGalore). Bowtie2 version 2.4.2 was used to align the reads to the Araport11 genome with the --very-sensitive parameter. Duplicate reads were removed using Picard toolkit version 2.9.0 (MarkDuplicates with REMOVE_DUPLICATES=true) and the insertion size was filtered from 140 bp to 160 bp using SAMtools version 1.11. The average nucleosome occupancy corresponding to the regions 1-kb upstream and downstream of the TSS of all protein-coding genes was calculated using the bamCoverage (--MNase parameter specified) and computeMatrix functions of deepTools2 version 2.7.15. Normalization was performed by scaling with the effective library size calculated by the calcNormFactors function using edgeR version 3.28.1.
Genome_build: RNA-seq: Araport11   MNase-seq: Araport11
Supplementary_files_format_and_content: RNA-seq bigwig: BPM of RNAseq over the genome using deeptools.
Supplementary_files_format_and_content: MNase-seq bigwig: Nucleosome positions from MNaseseq data using deeptools (see MNaseseq processing)

organism: Arabidopsis thaliana

source_name: 4-week-old leaves

growth_protocol: Arabidopsis plants were grown under cool white fluorescent lights (~100 umol m-2 s-1) in short day conditions (8 h light/16 h dark).

extract_protocol:
MNase-digested DNA was collected as described previously (Pajoro et al., 2018) with the following modifications: 2 g of leaf tissue from 4-week-old plants grown in short-day conditions was ground in liquid nitrogen and resuspended in 20 ml of lysis buffer for 15 minutes at 4°C. The resulting slurry was filtered through a 40 μm cell strainer into a 50 ml tube. Samples were centrifuged for 20 minutes at 3200g. The resulting pellets were resuspended in 10 ml of HBB buffer and centrifuged for 10 minutes at 1500g. Pellets were successively washed in 5 ml wash buffer and 5 ml reaction buffer. MNase-seq library preparation was performed using the KAPA Hyper Library Preparation kit (KAPA Biosystems, Part#KK8504). For each biological replicate, pooled leaf tissue from three plants was used.
Libraries were validated using Agilent Bioanalyzer 2100 Hisense DNA assay and quantified using the KAPA Library Quantification Kit for Illumina® Platforms kit. Sequencing was done on an Illumina NovaSeq 6000 using the S4 XP workflow.

tag: ecotype

value: leaves

value: 6 weeks

value: rlt1/2 mutant


title: rlt1/2 rep1 (MNaseseq)

value: 5 weeks


title: arid5 rep2 (MNaseseq)

value: 4 weeks

value: arid5 mutant


title: nasal_prox1_1059

description: Nasal Prox1+ cells


title: nasal_prox1_1049

description: Nasal Prox1+ cells


title: nasal_prox1_1053

description: Nasal Prox1+ cells


title: nasal_prox1_1051

description: Nasal Prox1+ cells


title: nasal_prox1_1054

description: Nasal Prox1+ cells


title: nasal_prox1_1048

description: Nasal Prox1+ cells


title: rH4R17A-1 rep2 (MNaseseq)

value: rH4R17A-1 mutant


title: rH4-2 rep2 (MNaseseq)

value: rH4-2 mutant


title: nasal_prox1_1092

description: Nasal Prox1+ cells


title: rH4-2 rep1 (MNaseseq)


title: arid5 rep1 (MNaseseq)


title: nasal_prox1_1040

description: Nasal Prox1+ cells


title: nasal_prox1_1043

description: Nasal Prox1+ cells


title: nasal_prox1_1041

description: Nasal Prox1+ cells


title: rlt1/2 rep1 (RNAseq)

extract_protocol:
Leaves of 4-week-old plants grown in short day were frozen in liquid nitrogen, ground with a mortar and pestle, and then RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). For each biological replicate, pooled leaf tissue from three plants was used.
Library preparation was performed at the Yale Center for Genome Analysis (YCGA) using Illumina’s TruSeq Stranded Total RNA with Ribo-Zero Plant in which samples were normalized with a total RNA input of 1 ug and library amplification with 8 PCR cycles.


title: nasal_prox1_1038

description: Nasal Prox1+ cells


title: nasal_prox1_1046

description: Nasal Prox1+ cells


title: nasal_prox1_1044

description: Nasal Prox1+ cells


title: nasal_prox1_1045

description: Nasal Prox1+ cells


title: rH4R17A-1 rep1 (MNaseseq)


title: nasal_prox1_1047

description: Nasal Prox1+ cells


title: arid5 rep1 (RNAseq)


title: nasal_prox1_1035

description: Nasal Prox1+ cells


title: rH4R17A-1 rep2 (RNAseq)


title: Col0 rep2 (MNaseseq)

value: wild type


title: nasal_prox1_1042

description: Nasal Prox1+ cells


title: nasal_prox1_1039

description: Nasal Prox1+ cells


title: nasal_prox1_1032

description: Nasal Prox1+ cells


title: pie1 rep2 (RNAseq)

value: pie1 mutant


title: Col0 rep1 (MNaseseq)

growth_protocol: Arabidopsis plants were grown under cool white fluorescent lights (~100 umol m-2 s-1) in short day conditions (8 h light/16 h dark).


title: rlt1/2 rep2 (RNAseq)


title: pie1 rep1 (RNAseq)


title: nasal_prox1_1030

description: Nasal Prox1+ cells


title: nasal_prox1_1036

description: Nasal Prox1+ cells


title: rH4-2 rep2 (RNAseq)


title: nasal_prox1_1034

description: Nasal Prox1+ cells


title: rH4R17A-2 rep2 (RNAseq)

value: rH4R17A-2 mutant


title: rH4-2 rep1 (RNAseq)

data_processing:
RNA-seq: Paired-end reads were filtered and trimmed using Trim Galore! (version 0.5.0) with default options for quality. The resulting data sets were aligned to The Arabidopsis Information Resource (TAIR10) genome using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Protein-coding genes were defined as described in the TAIR10 annotation gff3 file. The program featureCounts (version 1.6.4) was used to count the paired-end fragments overlapping with the annotated protein-coding genes. Differential expression analysis of protein-coding genes was performed using DESeq2 version 1.26 on raw read counts to obtain normalized fold changes and Padj-values for each gene. Genes were considered to be differentially expressed if they showed > +1.5-fold-change and Padj-value < 0.05.
MNase-seq: Paired-end reads were filtered and trimmed using Trim Galore! (version 0.5.0) with default options for quality. Bowtie2 version 2.4.2 was used to align the reads to The Arabidopsis Information Resource (TAIR10) genome with the --very-sensitive parameter. Duplicate reads were removed using Picard toolkit version 2.9.0 (MarkDuplicates with REMOVE_DUPLICATES=true) and the insertion size was filtered from 140 bp to 160 bp using SAMtools version 1.11. The average nucleosome occupancy corresponding to the regions 1-kb upstream and downstream of the TSS of all protein-coding genes was calculated using the bamCoverage (--MNase parameter specified) and computeMatrix functions of deepTools2 version 2.7.15. Normalization was performed by scaling with the effective library size calculated by the calcNormFactors function using edgeR version 3.28.1.
Genome_build: RNA-seq: TAIR10  MNase-seq: TAIR10
Supplementary_files_format_and_content: RNA-seq bigwig: BPM of RNAseq over the genome using deeptools.
Supplementary_files_format_and_content: MNase-seq bigwig: Nucleosome positions from MNaseseq data using deeptools (see MNaseseq processing)

growth_protocol: Arabidopsis plants were grown under cool?white fluorescent lights (~100 ?mol m?2 s?1) in short?day conditions (8 h light/16 h dark).


title: rH4R17A-1 rep1 (RNAseq)


title: nasal_prox1_1028

description: Nasal Prox1+ cells


title: chr11/17 rep2 (RNAseq)

value: chr11/17 mutant


title: rH4-1 rep1 (RNAseq)

value: rH4-1 mutant


title: nasal_prox1_1037

description: Nasal Prox1+ cells


title: nasal_prox1_1026

description: Nasal Prox1+ cells


title: nasal_prox1_1027

description: Nasal Prox1+ cells


title: Col0 rep2 (RNAseq)


title: nasal_prox1_1033

description: Nasal Prox1+ cells


title: nasal_prox1_1031

description: Nasal Prox1+ cells


title: rH4R17A-2 rep1 (RNAseq)


title: chr11/17 rep1 (RNAseq)


title: nasal_prox1_1029

description: Nasal Prox1+ cells


title: rH4-1 rep2 (RNAseq)


title: nasal_prox1_1022

description: Nasal Prox1+ cells


title: nasal_prox1_1023

description: Nasal Prox1+ cells


title: nasal_prox1_1021

description: Nasal Prox1+ cells


title: nasal_prox1_1024

description: Nasal Prox1+ cells


title: Col0 rep1 (RNAseq)


title: arid5 rep2 (RNAseq)


title: EC-102

city: University

first: Zhiqiang

last: Pan

state: MS

address: 1558 University Ave

institute: USDA-ARS-NPURU

description: Treated with Citral for 24 h

data_processing:
Raw RNA-Seq data sequenced with Illumina HiSeq were imported into CLC Genomics Workbench version 7.0 as fastq files.
The raw reads underwent different types of trimming in the following sequential order: quality trimming, ambiguity trimming, adapter trimming, and length trimming.
The trimmed reads were them mapped against the Arabidopsis thaliana (Col-0 TAIR 10) reference sequence using CLC Genomics Workbench
The data was filtered using JMP Genomics version 7.0, and the filtered data was normalized using the TMM method.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: Roots

growth_protocol: Sterile square Petri dishes (100x15 mm) were prepared with 0.44% macro-and micronutrients and 1% sucrose in 0.8% agar. Twenty-four seeds were sown per plate, which were sealed with tape and placed in a growth chamber at 22 ºC and 16/8 h light/ dark photoperiod under light intensity of 120 µmol/m2sec.

extract_protocol:
Total RNAs were isolated from flash frozen Arabidopsis tissues using an RNeasy plant mini kit (Qiagen) according to the manufacturer’s instructions.
Library construction, quantification and qualification were performed by Global Biologics (Columbia, MO) using 1 ug  RNA and the IlluminaTruSeq RNA Library Preparation Kits.

treatment_protocol: Plants were grown on agar plates for 14 days in a growth chamber and then treated at 7 h after the beginning of the photoperiod by adding 8 mL per plate of the IC50 concentration (21 µM) of t-chalcone. After treatment, plants were incubated for 0, 1, 3, 6, 12 and 24 h.

tag: agent

value: Citral

tag: time point


title: EC-101

description: Treated with Citral for 24 h


title: nasal_prox1_1017

description: Nasal Prox1+ cells

tag: cell type


title: EC-100

description: Treated with Citral for 24 h


title: EC-076

description: Treated with 0.1percent EtOH ctrl for 12 h

value: 0.1percent EtOH ctrl


title: EC-086

description: Treated with 0.1percent EtOH ctrl for 24 h

source_name: Shoots


title: nasal_prox1_1018

description: Nasal Prox1+ cells

value: Nasal Prox1+ cells


title: nasal_prox1_1019

description: Nasal Prox1+ cells

value: FVB


title: EC-091

description: Treated with Citral for 24 h


title: EC-082

description: Treated with Citral for 12 h


title: nasal_prox1_1014

description: Nasal Prox1+ cells


title: MCF-10A (control)

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

institute: SUNY Upstate Medical University

description:
control
AMc020817-J_S10_L002

data_processing:
alignment by Bowtie2
Peak-calling by MACS2
Consensus peak (shared by all replicates for each cell line) identification by DiffBind
Assembly: hg19
Supplementary files format and content: BED file
Library strategy: Break-seq

source_name: mammary

growth_protocol: MCF-7 Cells grown in DMEM (Corning#10-013-CV) media containing 10% FBS (Gemini#100-106) and 1X Penstrep (Corning#30-002-CI).  Cells were split at 70-80% confluency and expanded to obtain >4x10^7 cells before harvest.  MCF-10A cells were grown in medium171 (Life Technologies #W171500) containing MEGS (Life Technologies #S0155).  Cells were split at 95%-100% confluency and expanded to obtain >4x10^7 cells.  Samples were collected from two biological replicates each of which by two technical replicates.

extract_protocol:
10^6 PBS-washed cells were embedded in 0.5% Incert low-melting point agarose in PBS and cast into plugs (0.5cmx1cmx1.5mm).  Plugs were then incubated in  6 ml lysis buffer (0.5M EDTA, 1% Sarkosyl, 200ug/ml Proteinase K) at 50 degree celcius for 48 h, with a buffer exchange at 24 h.  Plugs were then washed three times, for 1 h each, with 6 ml TE at room temperature.
The DNA in TE-washed agarose plugs was then in-gel end-labeled with biotinylated dNTP mix (1 mM dTTP, dCTP, dGTP, 0.84 mM dATP, 0.16 mM Biotin-14-dATP) using End-It Kit (Epicentre). Plugs were then treated with beta-Agarase (NEB) to digest agarose and release DNA. DNA sample was then sonicated using a Covaris M220 using the snap-cap DNA 300bp shearing protocol.  DNA was then processed using a PCR Cleanup Kit (Qiagen) and run on agarose gel to verify the fragmentation pattern of DNA and quantified on a Nanodrop. 10-11 μg of DNA was then end-repaired using a regular End-It kit and purified by the PCR Clean-up Kit.  The DNA was then A-tailed by A-tail Kit or exo-Klenow (NEB) and purified by PCR Clean-up kit, followed by quantification on a Nanodrop.  M270 Dynabeads (Life Technologies) were used to purify biotinylated DNA.  DNA bound to beads was calculated by measuring the quantity of DNA in the flow through.  DNA-bound beads were then resuspended in a T4-ligase mix containing Illumina adaptors.  400 ng of DNA bound to beads was used for PCR amplification using KAPA Hotstart Ready Mix (KAPA).  Each sample was given a specific index primer for multiplexing.  PCR product was then run on agarose gel to verify amplification and quantity.  AMPure beads (Agencourt) were used to remove free adaptors and the final product was analyzed on agarose gel. Break-seq libraries were sequenced on Illumina Hi-Seq 2500 with 100 or 150 bp paired-end reads, followed by Break-seq data analysis.

value: mammary

value: no treatment


title: nasal_prox1_1020

description: Nasal Prox1+ cells


title: nasal_prox1_1016

description: Nasal Prox1+ cells


title: MCF-10A, 1B

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-G_S7_L002

tag: biological replicate no.

tag: technical replicate no.


title: nasal_prox1_1010

description: Nasal Prox1+ cells


title: MCF-7 (control)

description:
control
AMc020817-E_S5_L001


title: MCF-7, 2A

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-C_S3_L001


title: nasal_prox1_1015

description: Nasal Prox1+ cells


title: nasal_prox1_1009

description: Nasal Prox1+ cells


title: MCF-10A, 2B

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-I_S9_L002


title: MCF-7, 1B

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-B_S2_L001


title: nasal_prox1_1013

description: Nasal Prox1+ cells


title: nasal_prox1_1005

description: Nasal Prox1+ cells


title: MCF-7, 2B

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-D_S4_L001


title: nasal_prox1_1012

description: Nasal Prox1+ cells


title: nasal_prox1_1025

description: Nasal Prox1+ cells


title: nasal_prox1_1007

description: Nasal Prox1+ cells


title: MCF-7, 1A

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-A_S1_L001


title: nasal_prox1_1006

description: Nasal Prox1+ cells


title: nasal_prox1_1008

description: Nasal Prox1+ cells


title: MCF-10A, 2A

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-H_S8_L002


title: nasal_prox1_1000

description: Nasal Prox1+ cells


title: MCF-10A, 1

description:
RNA-seq
AMc030717-I
BrCa_RNAseq_featureCounts_hg19.exon.txt
BrCa_RNAseq_alltagswithFDR.txt

data_processing:
alignment by STARfusion aligner
read count calculation by FeatureCount
identification of differentially expressed genes by edgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing feature counts for all samples
Supplementary files format and content: tab-delimited text file containing Log2 transformed ratio of average feature counts from MCF-7 to that from MCF-10A (MCF-7/MCF-10A)

extract_protocol:
5x10^E6 cells were harvested for RNA-seq.
RNA was extracted using the Qiagen RNeasy Plus Mini Kit. The RNA was run on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip to assess RNA quality and quantity.  1 µg of total RNA was used as input to the Illumina TruSeq Stranded Total RNA Library Prep Kit Ribo Zero Gold H/M/R.  Library size was assessed using the DNA 1000 chip on the Bioanalyzer, and the libraries were quantified using a Qubit fluorometer.  Pair-end sequencing was run on an Illumina NextSeq 500 instrument.  Four replicates were processed for treatment/conditions out of which three were biological replicates.


title: nasal_prox1_1003

description: Nasal Prox1+ cells


title: MCF-10A, 1A

description:
Break-seq
Labeled DNA double strand breaks
AMc020817-F_S6_L001


title: nasal_prox1_1004

description: Nasal Prox1+ cells


title: nasal_prox1_997

description: Nasal Prox1+ cells


title: MCF-10A, 2

description:
RNA-seq
AMc030717-J
BrCa_RNAseq_featureCounts_hg19.exon.txt
BrCa_RNAseq_alltagswithFDR.txt


title: WSU-DLCL2 DMSO

city: Summit

first: Rida

last: Khan

state: NJ

address: 556 Morris Ave

department: Knowledge Science Research, IPS

institute: Bristol-Myers Squibb

data_processing:
STAR genomic mapping
Salmon gene pseudocount quantification
MACS peaks finding
GSVA pathway variation analysis
N/A
Assembly: hg38
Supplementary files format and content: .xlsx matrix table containing supplementary processed data for all samples

source_name: DLBCL cell line

growth_protocol: DLBCL (TMD8, U2932, WSU-DLCL2, SUDHL-4, OCI-LY18, RL, WILL1, Pfeiffer, SUDHL-8, Riva) were obtained from ATCC and DSMZ, authenticated through use of AmpFLSTR (ThermoFisher) and cultured in RPMI-1640 containing 10% fetal bovine serum (FBS), 1% Penicillin/Streptomycin and 1 mM sodium pyruvate.

extract_protocol: Not provided

treatment_protocol: DLBCL cell lines were treated with DMSO, Lenalidomide or CC-122 (avadomide) for 18 hours and harvested, mRNA extracted and then subjected to RNAseq

value: DLBCL cell line

value: WSU

value: DMSO


title: nasal_prox1_999

description: Nasal Prox1+ cells


title: MCF-10A

description: DNA-seq

data_processing:
alignment by Bowtie2
copy number analysis by QDNAseq
chromosome rearrangement identification by Socrates
Assembly: hg19
Supplementary files format and content: BED file generated by QDNAseq
Supplementary files format and content: tab-delimited text file generated by Socrates

extract_protocol:
Two replicates of 10^7 cells were harvested, and 5 × 106 cells were used to make each agarose plug for DNA-seq.
Genomic DNA was isolated from agarose plug to simulate the exact conditions for Break-seq samples, and to provide an appropriate control. DNA isolation was performed identically to Break-seq samples, except that the first step of End-repair with biotinylated dNTPs was omitted.


title: nasal_prox1_1011

description: Nasal Prox1+ cells


title: nasal_prox1_996

description: Nasal Prox1+ cells


title: nasal_prox1_1001

description: Nasal Prox1+ cells


title: MCF-7

description: DNA-seq


title: WSU-DLCL2 Len

value: Lenalidomide


title: TMD8 Ava


title: TMD8 DMSO


title: nasal_prox1_1002

description: Nasal Prox1+ cells


title: nasal_prox1_995

description: Nasal Prox1+ cells


title: MCF-7, 1

description:
RNA-seq
AMc030717-G
BrCa_RNAseq_featureCounts_hg19.exon.txt
BrCa_RNAseq_alltagswithFDR.txt


title: MCF-7, 2

description:
RNA-seq
AMc030717-H
BrCa_RNAseq_featureCounts_hg19.exon.txt
BrCa_RNAseq_alltagswithFDR.txt


title: nasal_prox1_994

description: Nasal Prox1+ cells


title: nasal_prox1_993

description: Nasal Prox1+ cells


title: WSU-DLCL2 Ava


title: nasal_prox1_992

description: Nasal Prox1+ cells


title: nasal_prox1_998

description: Nasal Prox1+ cells


title: TMD8 Len


title: YSH259

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

description: Liver cancer

data_processing:
The low quality sequence reads with less than 30 PHRED score and adapter sequence reads were trimmed using a Trim Galore tool
Sequence reads were mapped to the human reference genome (hg38) using TopHat2 tool with default parameters
RNA abundance was estimated by as the FPKM values according to GENCODE database (version 27) using Cufflinks tool
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include log2(FPKM+1) values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Intrahepatic cholangiocarcinoma

extract_protocol:
Total RNA was extracted from each sample using the RNeasy total RNA extraction kit (Qiagen) according to manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: molecular subtype

tag: disease state

value: ICC


title: SUDHL-4 Len


title: SUDHL-4 DMSO


title: U2932 Len


title: SUDHL-4 Ava


title: YSH255

description: Liver cancer


title: nasal_prox1_985

description: Nasal Prox1+ cells

tag: strain


title: nasal_prox1_991

description: Nasal Prox1+ cells


title: YSH254

description: Liver cancer


title: nasal_prox1_986

description: Nasal Prox1+ cells


title: YSH253

description: Liver cancer


title: nasal_prox1_989

description: Nasal Prox1+ cells


title: U2932 DMSO


title: nasal_prox1_990

description: Nasal Prox1+ cells


title: nasal_prox1_984

description: Nasal Prox1+ cells


title: nasal_prox1_982

description: Nasal Prox1+ cells


title: nasal_prox1_983

description: Nasal Prox1+ cells


title: nasal_prox1_981

description: Nasal Prox1+ cells


title: U2932 Ava


title: nasal_prox1_980

description: Nasal Prox1+ cells


title: YSH258

description: Liver cancer


title: nasal_prox1_987

description: Nasal Prox1+ cells


title: nasal_prox1_979

description: Nasal Prox1+ cells


title: nasal_prox1_988

description: Nasal Prox1+ cells


title: YSH250

description: Liver cancer


title: YSH251

description: Liver cancer


title: YSH257

description: Liver cancer


title: YSH249

description: Liver cancer


title: YSH248

description: Liver cancer


title: nasal_prox1_977

description: Nasal Prox1+ cells


title: YSH256

description: Liver cancer


title: YSH247

description: Liver cancer


title: nasal_prox1_976

description: Nasal Prox1+ cells


title: nasal_prox1_975

description: Nasal Prox1+ cells


title: nasal_prox1_973

description: Nasal Prox1+ cells


title: YSH242

description: Liver cancer


title: nasal_prox1_972

description: Nasal Prox1+ cells


title: YSH243

description: Liver cancer


title: YSH252

description: Liver cancer


title: YSH245

description: Liver cancer


title: YSH241

description: Liver cancer


title: nasal_prox1_971

description: Nasal Prox1+ cells


title: YSH238

description: Liver cancer


title: YSH239

description: Liver cancer


title: YSH240

description: Liver cancer


title: nasal_prox1_970

description: Nasal Prox1+ cells


title: nasal_prox1_967

description: Nasal Prox1+ cells


title: nasal_prox1_966

description: Nasal Prox1+ cells


title: nasal_prox1_978

description: Nasal Prox1+ cells


title: nasal_prox1_974

description: Nasal Prox1+ cells


title: nasal_prox1_969

description: Nasal Prox1+ cells


title: nasal_prox1_965

description: Nasal Prox1+ cells


title: YSH236

description: Liver cancer


title: nasal_prox1_968

description: Nasal Prox1+ cells


title: YSH235

description: Liver cancer


title: YSH246

description: Liver cancer


title: YSH237

description: Liver cancer


title: YSH234

description: Liver cancer


title: nasal_prox1_963

description: Nasal Prox1+ cells


title: nasal_prox1_964

description: Nasal Prox1+ cells


title: nasal_prox1_961

description: Nasal Prox1+ cells


title: nasal_prox1_960

description: Nasal Prox1+ cells


title: nasal_prox1_962

description: Nasal Prox1+ cells


title: nasal_prox1_958

description: Nasal Prox1+ cells


title: YSH231

description: Liver cancer


title: YSH232

description: Liver cancer


title: YSH229

description: Liver cancer


title: nasal_prox1_955

description: Nasal Prox1+ cells


title: YSH244

description: Liver cancer


title: nasal_prox1_953

description: Nasal Prox1+ cells


title: YSH224

description: Liver cancer


title: YSH233

description: Liver cancer


title: YSH223

description: Liver cancer


title: nasal_prox1_957

description: Nasal Prox1+ cells


title: nasal_prox1_951

description: Nasal Prox1+ cells


title: YSH225

description: Liver cancer


title: nasal_prox1_950

description: Nasal Prox1+ cells


title: YSH230

description: Liver cancer


title: YSH227

description: Liver cancer


title: nasal_prox1_949

description: Nasal Prox1+ cells


title: nasal_prox1_956

description: Nasal Prox1+ cells


title: nasal_prox1_959

description: Nasal Prox1+ cells


title: YSH218

description: Liver cancer


title: nasal_prox1_952

description: Nasal Prox1+ cells


title: nasal_prox1_947

description: Nasal Prox1+ cells


title: YSH226

description: Liver cancer


title: YSH216

description: Liver cancer


title: nasal_prox1_945

description: Nasal Prox1+ cells


title: YSH214

description: Liver cancer


title: YSH219

description: Liver cancer


title: nasal_prox1_944

description: Nasal Prox1+ cells


title: nasal_prox1_942

description: Nasal Prox1+ cells


title: YSH221

description: Liver cancer


title: YSH220

description: Liver cancer


title: nasal_prox1_954

description: Nasal Prox1+ cells


title: YSH228

description: Liver cancer


title: nasal_prox1_939

description: Nasal Prox1+ cells


title: nasal_prox1_943

description: Nasal Prox1+ cells


title: YSH222

description: Liver cancer


title: YSH208

description: Liver cancer


title: nasal_prox1_946

description: Nasal Prox1+ cells


title: YSH207

description: Liver cancer


title: YSH206

description: Liver cancer


title: nasal_prox1_935

description: Nasal Prox1+ cells


title: YSH213

description: Liver cancer


title: nasal_prox1_934

description: Nasal Prox1+ cells


title: YSH205

description: Liver cancer


title: nasal_prox1_933

description: Nasal Prox1+ cells


title: YSH215

description: Liver cancer


title: YSH217

description: Liver cancer


title: nasal_prox1_932

description: Nasal Prox1+ cells


title: nasal_prox1_948

description: Nasal Prox1+ cells


title: YSH209

description: Liver cancer


title: YSH212

description: Liver cancer


title: YSH211

description: Liver cancer


title: nasal_prox1_937

description: Nasal Prox1+ cells


title: nasal_prox1_940

description: Nasal Prox1+ cells


title: YSH200

description: Liver cancer

source_name: Hepatocellular carcinoma

value: HCC


title: YSH210

description: Liver cancer


title: YSH201

description: Liver cancer


title: nasal_prox1_938

description: Nasal Prox1+ cells


title: nasal_prox1_929

description: Nasal Prox1+ cells


title: YSH204

description: Liver cancer


title: nasal_prox1_927

description: Nasal Prox1+ cells


title: nasal_prox1_931

description: Nasal Prox1+ cells


title: YSH199

description: Liver cancer


title: YSH203

description: Liver cancer


title: YSH197

description: Liver cancer


title: nasal_prox1_926

description: Nasal Prox1+ cells


title: nasal_prox1_928

description: Nasal Prox1+ cells


title: YSH196

description: Liver cancer


title: YSH194

description: Liver cancer


title: nasal_prox1_923

description: Nasal Prox1+ cells


title: YSH193

description: Liver cancer


title: nasal_prox1_924

description: Nasal Prox1+ cells


title: nasal_prox1_922

description: Nasal Prox1+ cells


title: YSH192

description: Liver cancer


title: YSH191

description: Liver cancer


title: nasal_prox1_921

description: Nasal Prox1+ cells


title: YSH198

description: Liver cancer


title: nasal_prox1_941

description: Nasal Prox1+ cells


title: YSH189

description: Liver cancer


title: YSH188

description: Liver cancer


title: YSH186

description: Liver cancer


title: nasal_prox1_919

description: Nasal Prox1+ cells


title: nasal_prox1_925

description: Nasal Prox1+ cells


title: nasal_prox1_918

description: Nasal Prox1+ cells


title: nasal_prox1_917

description: Nasal Prox1+ cells


title: nasal_prox1_916

description: Nasal Prox1+ cells


title: nasal_prox1_914

description: Nasal Prox1+ cells


title: YSH184

description: Liver cancer


title: nasal_prox1_915

description: Nasal Prox1+ cells


title: YSH185

description: Liver cancer


title: YSH183

description: Liver cancer


title: nasal_prox1_912

description: Nasal Prox1+ cells


title: YSH179

description: Liver cancer


title: YSH178

description: Liver cancer


title: YSH180

description: Liver cancer


title: YSH190

description: Liver cancer


title: YSH177

description: Liver cancer


title: nasal_prox1_910

description: Nasal Prox1+ cells


title: nasal_prox1_920

description: Nasal Prox1+ cells


title: nasal_prox1_909

description: Nasal Prox1+ cells


title: nasal_prox1_911

description: Nasal Prox1+ cells


title: YSH176

description: Liver cancer


title: nasal_prox1_930

description: Nasal Prox1+ cells


title: YSH174

description: Liver cancer


title: YSH175

description: Liver cancer


title: nasal_prox1_908

description: Nasal Prox1+ cells


title: nasal_prox1_907

description: Nasal Prox1+ cells


title: YSH172

description: Liver cancer


title: YSH171

description: Liver cancer


title: nasal_prox1_905

description: Nasal Prox1+ cells


title: nasal_prox1_904

description: Nasal Prox1+ cells


title: nasal_prox1_913

description: Nasal Prox1+ cells


title: nasal_prox1_903

description: Nasal Prox1+ cells


title: YSH168

description: Liver cancer


title: YSH167

description: Liver cancer


title: nasal_prox1_902

description: Nasal Prox1+ cells


title: YSH170

description: Liver cancer


title: nasal_prox1_901

description: Nasal Prox1+ cells


title: YSH164

description: Liver cancer


title: YSH163

description: Liver cancer


title: nasal_prox1_897

description: Nasal Prox1+ cells


title: YSH161

description: Liver cancer


title: YSH166

description: Liver cancer


title: nasal_prox1_898

description: Nasal Prox1+ cells


title: YSH173

description: Liver cancer


title: nasal_prox1_906

description: Nasal Prox1+ cells


title: nasal_prox1_899

description: Nasal Prox1+ cells


title: nasal_prox1_896

description: Nasal Prox1+ cells


title: YSH158

description: Liver cancer


title: nasal_prox1_895

description: Nasal Prox1+ cells


title: nasal_prox1_900

description: Nasal Prox1+ cells


title: YSH155

description: Liver cancer


title: YSH160

description: Liver cancer


title: YSH159

description: Liver cancer


title: nasal_prox1_894

description: Nasal Prox1+ cells


title: nasal_prox1_893

description: Nasal Prox1+ cells


title: YSH165

description: Liver cancer


title: YSH157

description: Liver cancer


title: nasal_prox1_891

description: Nasal Prox1+ cells


title: nasal_prox1_889

description: Nasal Prox1+ cells


title: nasal_prox1_888

description: Nasal Prox1+ cells


title: YSH076

description: Liver cancer


title: YSH077

description: Liver cancer


title: YSH154

description: Liver cancer


title: YSH153

description: Liver cancer


title: YSH074

description: Liver cancer


title: YSH152

description: Liver cancer


title: nasal_prox1_885

description: Nasal Prox1+ cells


title: nasal_prox1_884

description: Nasal Prox1+ cells


title: YSH078

description: Liver cancer


title: nasal_prox1_887

description: Nasal Prox1+ cells


title: YSH202

description: Liver cancer


title: nasal_prox1_892

description: Nasal Prox1+ cells


title: YSH075

description: Liver cancer


title: nasal_prox1_883

description: Nasal Prox1+ cells


title: YSH073

description: Liver cancer


title: nasal_prox1_890

description: Nasal Prox1+ cells


title: nasal_prox1_882

description: Nasal Prox1+ cells


title: YSH072

description: Liver cancer


title: nasal_prox1_880

description: Nasal Prox1+ cells


title: YSH070

description: Liver cancer


title: nasal_prox1_881

description: Nasal Prox1+ cells


title: YSH071

description: Liver cancer


title: nasal_prox1_879

description: Nasal Prox1+ cells


title: nasal_prox1_886

description: Nasal Prox1+ cells


title: YSH068

description: Liver cancer


title: YSH069

description: Liver cancer


title: YSH067

description: Liver cancer


title: nasal_prox1_877

description: Nasal Prox1+ cells


title: nasal_prox1_878

description: Nasal Prox1+ cells


title: YSH065

description: Liver cancer


title: nasal_prox1_875

description: Nasal Prox1+ cells


title: nasal_prox1_874

description: Nasal Prox1+ cells


title: nasal_prox1_872

description: Nasal Prox1+ cells


title: YSH066

description: Liver cancer


title: YSH063

description: Liver cancer


title: nasal_prox1_876

description: Nasal Prox1+ cells


title: YSH064

description: Liver cancer


title: YSH061

description: Liver cancer


title: nasal_prox1_868

description: Nasal Prox1+ cells


title: nasal_prox1_870

description: Nasal Prox1+ cells


title: nasal_prox1_871

description: Nasal Prox1+ cells


title: nasal_prox1_867

description: Nasal Prox1+ cells


title: YSH059

description: Liver cancer


title: nasal_prox1_869

description: Nasal Prox1+ cells


title: YSH060

description: Liver cancer


title: YSH062

description: Liver cancer


title: nasal_prox1_866

description: Nasal Prox1+ cells


title: YSH058

description: Liver cancer


title: YSH057

description: Liver cancer


title: YSH056

description: Liver cancer


title: nasal_prox1_873

description: Nasal Prox1+ cells


title: nasal_prox1_864

description: Nasal Prox1+ cells


title: nasal_prox1_865

description: Nasal Prox1+ cells


title: YSH054

description: Liver cancer


title: YSH055

description: Liver cancer


title: YSH053

description: Liver cancer


title: nasal_prox1_863

description: Nasal Prox1+ cells


title: nasal_prox1_862

description: Nasal Prox1+ cells


title: nasal_prox1_861

description: Nasal Prox1+ cells


title: YSH051

description: Liver cancer


title: nasal_prox1_859

description: Nasal Prox1+ cells


title: nasal_prox1_860

description: Nasal Prox1+ cells


title: YSH049

description: Liver cancer


title: YSH030

description: Liver cancer


title: YSH037

description: Liver cancer


title: nasal_prox1_857

description: Nasal Prox1+ cells


title: nasal_prox1_858

description: Nasal Prox1+ cells


title: YSH022

description: Liver cancer


title: YSH019

description: Liver cancer


title: nasal_prox1_855

description: Nasal Prox1+ cells


title: nasal_prox1_853

description: Nasal Prox1+ cells


title: nasal_prox1_852

description: Nasal Prox1+ cells