title: ChipSeq_Md_E11.5_WT_H3K27me3

description:
Library name: Sample 20
Md , E11.5, WT,ChipSeq , H3K27me3

data_processing:
Reads were aligned to the mouse GRCm38/mm10 reference genome using the QuasR package (version 1.38.0) through the qAlign function.
BigWig files were generated using the qExportWig function from the QuasR package. The files contain CPM (Counts Per Million) values with a resolution of 100 base pairs and a scaling factor of 1e6.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files contain cpm values
Supplementary files format and content: wig files contain cpm values

extract_protocol:
Dissected tissue from E8.5 embryos (i.e. dorsal most portion of the neural plate) and from E10.5 and E11.5 embryos (i.e. FNP, Mx, Md and PA2) were micro-dissected and incubated in trypsin 0.5%/EDTA 1X at 37 °C for 10 minutes, rinsed (DMEM 1X/ FBS 10%, followed by two washes in ice-cold 1× DMEM), dissociated by pipetting, cross-linked with 1% formaldehyde in PBS 1X for 10 minutes at room temperature (RT) and quenched with glycine (final concentration 125 mM) for 5 minutes at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and rinsed in ice-cold PBS. CNCCs from E11.5 Wnt1::Cre;ROSARFP and Wnt1::Cre;ROSARFP;Ezh2 flox/flox (Ezh2cKO) embryos were filtered and collected by FACS.
ChIP-seq experiments with anti-H3K4me2 (Millipore, Cat. #07-030), anti-H3K27me3 (Millipore, Cat. # 07-449), anti-H3K27ac (abcam, ab4729) and anti-CTCF (Cell Signaling, CST 2899) antibodies were performed as described in Minoux et al., 2017 and Kessler et al., 2023.
ChIP-seq libraries were generated using bar-coded adapters (NEB, E7335) in combination with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370) according to manufacturers’ instructions. The quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end) or an Illumina NovaSeq 6000 machine (50 bp read length, paired-end) .

value: Md

value: Cranial neural crest cells


title: ChipSeq_FNP_E11.5_WT_H3K27me3

status: Public on Apr 08 2026

type: SRA

city: Basel

first: Filippo

address: Fabrikstrasse 24,

country: Switzerland

institute: FMI

description:
Library name: Sample 18
FNP , E11.5, WT,ChipSeq , H3K27me3

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: FNP

tag: tissue

value: FNP

tag: developmental stage

tag: cell type

tag: genotype

value: WT

tag: antibody

tag: batch


title: ChIPseq_Input_NebNextUltra

description:
Library name: Sample 22
Input, ChipSeq, NebNextUltra

source_name: Md


title: ChipSeq_PA2_E11.5_WT_H3K27me3

description:
Library name: Sample 21
PA2 , E11.5, WT,ChipSeq , H3K27me3


title: BIS_Discovery_149

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing:
ChAMP package in R environment
processed value definition: combat normalised beta methylation values (linked as supplementary file on the Series record)

label: Cy3, Cy5

organism: Homo sapiens

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: F

value: BIS

value: Blood cells


title: SCC7-T4

city: ShenZhen

first: Lin

last: Ma

state: Guangdong Province

address: Lihu Campus: Xueyuan Avenue, Nanshan District, Shenzhen

department: Medical School

country: China

institute: ShenZhen University

description: Library name: Sample 4

library_source: transcriptomic

data_processing:
The libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads. raw reads were obtained per sample. The raw reads in FASTQ format were processed using fastp to remove low-quality reads, yielding clean reads for downstream analysis.
The clean reads were aligned to the reference genome using HISAT2. Gene expression levels were quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and read counts per gene were obtained using HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA purity and concentration were measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), while RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The transcriptome library was constructed following the manufacturer's protocol using the VAHTS Universal V5 RNA-seq Library Prep Kit.

tag: cell line

value: OE

tag: ID

tag: treatment

value: IR+Olaparib

value: EIO


title: BIR_Discovery_145

value: M

value: BIR


title: BIS_Discovery_144


title: H3K27me3-WT_Lung_Flu_1

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

description: Library name: sample 7

data_processing:
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used.
Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5 million fragments as suggested by CUT&RUN protocol paper. We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates.
Assembly: mm10(GRCm38)
Supplementary files format and content: bigwig
Library strategy: Cut&Run

source_name: Lung

extract_protocol:
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens (or Lung). CD4 Treg cells  (CD4+GFP+) T cells were further sorted by FACS.
Libraries were prepared with precipitated DNA using KAPA Hyper Prep Kit (Kapa Biosystems). The library DNA was enriched by size selection with AMPure XP beads.

value: Lung

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAB #9733 Cell Signaling

value: Treg

value: Day 15 post Flu virus


title: ChipSeq_Md_E11.5_Ezh2cKO_H3K4me2

description:
Library name: Sample 16
Md , E11.5, Ezh2cKO,ChipSeq , H3K4me2


title: ChipSeq_Mx_E11.5_WT_H3K27me3

description:
Library name: Sample 19
Mx , E11.5, WT,ChipSeq , H3K27me3

source_name: Mx

value: Mx


title: H3K27me3-Kdm6b_Lung_Flu_2

description: Library name: sample 2

value: PBS


title: SCC7-T8

description: Library name: Sample 8

value: IR

value: EI


title: ChipSeq_PA2_E11.5_WT_H3K4me2

description:
Library name: Sample 13
PA2 , E11.5, WT,ChipSeq , H3K4me2

value: Cranial neural crest cells

value: WT


title: H3K27me3-Kdm6b_Lung_PBS_2

description: Library name: sample 5

value: Foxp3Cre x Kdm6bfl/fl


title: ChipSeq_FNP_E11.5_Ezh2cKO_H3K4me2

description:
Library name: Sample 14
FNP , E11.5, Ezh2cKO,ChipSeq , H3K4me2

value: FNP


title: SCC7-T5

description: Library name: Sample 5

value: OE


title: Kdm6b_Lung_Flu_2

description: Library name: sample 11

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore.
Paired-end reads were mapped by STAR(v2.7.9a) using parameters " --genomeLoad NoSharedMemory --readFilesCommand unpigz -c -p 4 --limitBAMsortRAM 67108864000 --outReadsUnmapped None --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMmapqUnique 60 --outSAMmultNmax 1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions WithinBAM SoftClip --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic"
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0).
RSEM was used to quantify read counts per gene.
Assembly: mm10
Supplementary files format and content: gene-based raw counts and TPM tsv

extract_protocol:
Cells were lysed with the TRIzol reagent and stored at -80C. Total RNA extraction, sequencing library preparation, and deep sequencing were conducted by the Hartwell Center at St. Jude Children’s Research Hospital according to standard protocols.
Libraries were constructed by the Hartwell Center at St. Jude Children’s Research Hospital according to standard protocols for RNA sequencing.


title: WT_Smp3

city: Pittsburgh

first: Wei

last: Du

state: Pennsylvania

address: 5051 Centre Ave

department: Division of Oncology

institute: University of Pittsburgh

description: Library name: Sample6

data_processing:
For analysis we used Rsubread (Bioconductor release 3.8; 7) to align sequence reads to reference genome and used edgeR and limma R packages (Bioconductor release 3.8) to normalize gene expression level to log2 transcripts per million (TPM).
Assembly: We aligned sequence reads to Mus Musculus genome reference sequence (GCF_000001635.27_GRCm39) downloaded from NCBI assembly database and mapped the aligned sequences to gene symbols.
Supplementary files format and content: After normalization, we contained only protein-coding genes and removed genes of which expression level is zero across all samples to get 26,938 genes for further pathway analysis.

molecule: polyA RNA

source_name: bone marrow mesenchymal stromal cell

growth_protocol: Heterozygous Hes1fl/+ mice in a C57BL/6 background were generated from the sperm purchased at Experimental Animal Division at RIKEN Bioresource Center (RBRC #: RBRC06047)

extract_protocol:
We used the standard procedure of Qiagen RNeasy kit to extract total RNA from the bone marrow MSC of the heterozygous Hes1fl/+ mice in a C57BL/6 background
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101)

treatment_protocol: Heterozygous Hes1fl/+ mice were interbred with Prx1Cre (Prrx1Cre) mice to generate MSC specific Hes1 deletion. Prx1Cre transgenic mice have the Prx1 promoter/enhancer directing Cre recombinase expression to early limb bud mesenchyme and a subset of craniofacial mesenchyme. The mice were back crossed for more than 10 times before the experiments listed below.

value: bone marrow mesenchymal stromal cell

value: Wildtype mouse


title: WT_Smp2

description: Library name: Sample5


title: SCC7-T2

description: Library name: Sample 2

value: sham

value: ES


title: BIR_Discovery_137

value: F

value: BIR

value: Blood cells


title: ChipSeq_PA2_E11.5_Ezh2cKO_H3K4me2

description:
Library name: Sample 17
PA2 , E11.5, Ezh2cKO,ChipSeq , H3K4me2


title: ChipSeq_Mx_E11.5_Ezh2cKO_H3K4me2

description:
Library name: Sample 15
Mx , E11.5, Ezh2cKO,ChipSeq , H3K4me2


title: H3K27me3-Kdm6b_Lung_Flu_1

description: Library name: sample 1

value: Lung

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAB #9733 Cell Signaling

value: Treg


title: Kdm6b_Lung_Naive_2

description: Library name: sample 8

value: PBS


title: BIR_Discovery_142

value: M


title: H3K27me3-Kdm6b_Lung_Flu_3

description: Library name: sample 3


title: Kdm6b_Lung_Naive_3

description: Library name: sample 9


title: BIR_Discovery_143


title: SCC7-T3

description: Library name: Sample 3


title: ChipSeq_PA2_E11.5_Ezh2cKO_H3K27ac

description:
Library name: Sample 9
PA2 , E11.5, Ezh2cKO,ChipSeq , H3K27ac

value: Cranial neural crest cells


title: Hes1KO_Smp3

description: Library name: Sample3

value: Hes1 Knockout mouse


title: WT_Smp1

description: Library name: Sample4

value: WT


title: Kdm6b_Lung_Flu_3

description: Library name: sample 12

value: Foxp3Cre x Kdm6bfl/fl

value: Day 15 post Flu virus


title: SCC7-T1

description: Library name: Sample 1

value: OE


title: Hes1KO_Smp2

description: Library name: Sample2

value: bone marrow mesenchymal stromal cell


title: BIS_Discovery_141

value: BIS


title: Hes1KO_Smp1

description: Library name: Sample1


title: Kdm6b_Lung_Flu_1

description: Library name: sample 10


title: ChipSeq_FNP_E11.5_WT_H3K4me2

description:
Library name: Sample 10
FNP , E11.5, WT,ChipSeq , H3K4me2

value: FNP


title: Kdm6b_Lung_Naive_1

description: Library name: sample 7


title: BIS_Discovery_140

value: F


title: BIR_Discovery_139

value: BIR


title: ChipSeq_Md_E11.5_WT_H3K4me2

description:
Library name: Sample 12
Md , E11.5, WT,ChipSeq , H3K4me2

value: Md


title: BIS_Discovery_138

value: Blood cells


title: ChipSeq_Md_E11.5_HIRE1-del_H3K27me3

description:
Library name: Sample 27
Md , E11.5, HIRE1-del,ChipSeq , H3K27me3


title: ChipSeq_Md_E11.5_Control_H3K27me3

description:
Library name: Sample 29
Md , E11.5, Control,ChipSeq , H3K27me3

value: Control


title: WT_Lung_Flu_1

description: Library name: sample 4

value: Lung

value: Treg


title: WT_Lung_Flu_2

description: Library name: sample 5


title: ChipSeq_Md_E11.5_HIRE1-del_H3K27ac

description:
Library name: Sample 28
Md , E11.5, HIRE1-del,ChipSeq , H3K27ac


title: ChipSeq_Md_E11.5_Ezh2cKO_H3K27ac

description:
Library name: Sample 8
Md , E11.5, Ezh2cKO,ChipSeq , H3K27ac


title: BIR_Discovery_136


title: WT_Lung_Flu_3

description: Library name: sample 6


title: WT_Lung_Naive_3

description: Library name: sample 3

value: PBS


title: ChipSeq_Md_E11.5_WT_H3K27ac

description:
Library name: Sample 4
Md , E11.5, WT,ChipSeq , H3K27ac

value: Cranial neural crest cells


title: ChipSeq_Md_E11.5_Control_H3K27ac

description:
Library name: Sample 30
Md , E11.5, Control,ChipSeq , H3K27ac


title: ChipSeq_Mx_E11.5_WT_H3K4me2

description:
Library name: Sample 11
Mx , E11.5, WT,ChipSeq , H3K4me2

value: Mx


title: BIS_Discovery_135

value: M


title: BIS_Discovery_133


title: BIS_Discovery_134


title: ChipSeq_Mx_E11.5_WT_H3K27ac

description:
Library name: Sample 3
Mx , E11.5, WT,ChipSeq , H3K27ac

value: WT


title: ChipSeq_Mx_E11.5_Ezh2cKO_H3K27ac

description:
Library name: Sample 7
Mx , E11.5, Ezh2cKO,ChipSeq , H3K27ac


title: WT_Lung_Naive_2

description: Library name: sample 2


title: ChipSeq_PA2_E11.5_Control_H3K27me3

description:
Library name: Sample 25
PA2 , E11.5, Control,ChipSeq , H3K27me3


title: BIS_Discovery_131


title: ChipSeq_FNP_E11.5_Ezh2cKO_H3K27ac

description:
Library name: Sample 6
FNP , E11.5, Ezh2cKO,ChipSeq , H3K27ac


title: ChipSeq_PA2_E11.5_WT_H3K27ac

description:
Library name: Sample 5
PA2 , E11.5, WT,ChipSeq , H3K27ac


title: Normal, H3K4me3

city: Boston

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Sequenced reads were aligned against the mm9 reference genome using BWA. Alignments were filtered for for uniquely mapped reads and alignment duplicates were removed.
BigWig files were generated using deepTools with CPM and Input normalization.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Normal

growth_protocol: Cell lines were obtained as previously described (Sykes 2016; PMID: 27641501) and maintained in RPMI1640 (10% FBS), penicillin/streptomycin, 6 ng/ml rmIL-3, and approximately 100 ng/ml SCF.

extract_protocol:
Cells were crosslinked for 10 minutes in 1% formaldehyde at room temperature and quenched with 125mM Glycine.
ChIP was performed as previously described in Carey (2009). Antibodies used: H3K4me1 (Abcam ab8895), H3K4me3 (Millipore, 04-745), H3K27me3 (Cell Signaling Technology, C36B11), H3K27ac (Abcam ab4729). Samples were further processed for high throughput sequencing. Sequencing was performed on Illumina HiSeq 2500 instrument resulting in approximately 30 million paired-end 50 bp reads per sample

value: Normal Granulocyte-macrophage progenitors (GMP)

value: Normal


title: BIS_Discovery_129


title: BIR_Discovery_132


title: BIR_Discovery_130


title: ChipSeq_FNP_E11.5_WT_H3K27ac

description:
Library name: Sample 2
FNP , E11.5, WT,ChipSeq , H3K27ac


title: WT_Lung_Naive_1

description: Library name: sample 1


title: Line XIII WT Input Control

city: Davis

first: Paul

last: Knoepfler

state: CA

address: 1 Shields Ave

department: Cell biology and human anatomy

institute: UC Davis

description: Library name: Line XIII WT Input

data_processing:
Reads were trimmed of adapters using bbduk and aligned to the hg19 genome with bowtie2.
MACS2 was used to call peaks, with an input sample used as the background control and an FDR of .05.
Assembly: hg19
Supplementary files format and content: narrowPeak file with called peaks from MACS2

source_name: DIPG Line XIII WT

growth_protocol: Cells were grown in Tumor Stem Medium, which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen)

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde, lysed, and sonicated using a Bioruptor Pico (Diagenode) to generate chromatin fragments <500bp. For each ChIP, 20-30ug of sonicated chromatin was used and immunoprecipitated on magnetic Dynabeads (Pierce #88802). The following antibodies were used: IgG (Santa Cruz, #sc-2027), mouse anti-H3 (Upstate/EMD-Millipore, #05-499), rabbit anti-H3K4me3 (Millipore 04-745).
Libaries were prepared using the NEB Next Ultra II DNA Library Prep Kit

value: DIPG Line XIII WT

value: pediatric glioma tumor cells

tag: chip antibody


title: ChipSeq_Progenitors_E8.5_WT_H3K27ac

description:
Library name: Sample 1
NCCprogenitors , E8.5, WT,ChipSeq , H3K27ac

source_name: NCCprogenitors

value: NCCprogenitors


title: ChipSeq_PA2_E11.5_HIRE1-del_H3K27ac

description:
Library name: Sample 24
PA2 , E11.5, HIRE1-del,ChipSeq , H3K27ac


title: Kdm6b_CR_Treg_2

description: Library name: sample 14

source_name: Spleen and LNs

value: Spleen and LNs

value: Anti-Kdm6b/JMJD3 (Abcam, Cat # ab38113)


title: Line XIII WT H3K4me3 ChIP-seq

description: Library name: Line XIII WT H3K4me3


title: ChipSeq_PA2_E11.5_Control_H3K27ac

description:
Library name: Sample 26
PA2 , E11.5, Control,ChipSeq , H3K27ac


title: BIR_Discovery_128

value: F

value: BIR


title: BIR_Discovery_124

value: Blood cells


title: ChipSeq_PA2_E11.5_HIRE1-del_H3K27me3

description:
Library name: Sample 23
PA2 , E11.5, HIRE1-del,ChipSeq , H3K27me3


title: BIS_Discovery_125

value: BIS


title: Normal, Input

value: Input


title: Normal, H3K4me1


title: BIR_Discovery_127


title: TCR_3h_Kdm6b_2

description:
Library name: sample 20
rRNA depleted, stranded RNA

value: rTreg

value: Foxp3Cre x Kdm6bfl/fl

value: anti-CD3/CD28 for 3 hours


title: Normal, H3K27me3


title: Normal, H3K27ac


title: Early, clone 2, H3K4me3

source_name: Early, clone 2

value: Leukemic progenitor cells

value: Early, clone 2


title: ACHT + FANCG No Treatment Replicate 4

city: KINGSTON

first: NIALL

middle: GEORGE

last: HOWLETT

state: RI

address: 120 FLAGG ROAD

department: CELL AND MOLECULAR BIOLOGY

institute: UNIVERSITY OF RHODE ISLAND

description: Library name: AGN4

data_processing:
Reads trimmed to remove adaptor sequences and poor quality bases using Trimmomatic v.0.36. Trimmed reads mapped to hg19 ENSEMBL reference genome using STAR aligner v.2.5.2b. FeatureCounts subread package v.1.5.2 was run on BAM files. FeatureCounts output files used for downstream differential expression analysis using DESeq2.
Assembly: hg19 ENSEMBL reference genome
Supplementary files format and content: csv format; DESeq2 differential expression analysis

source_name: Skin

growth_protocol: Cells were cultured in DMEM medium supplemented with 20% fetal bovine serum, 2 mM L-glutamine, and 50 microM penicillin-streptomycin

extract_protocol:
Rneasy kit Qiagen
NEBNext Ultra II RNA library prep kit

treatment_protocol: No treatment

value: Skin

value: Skin fibroblast

value: No treatment


title: ACHT + FANCD2 No Treatment Replicate 3

description: Library name: AD2N3


title: ACHT + FANCD2 No Treatment Replicate 4

description: Library name: AD2N4


title: ACHT + FANCD2 No Treatment Replicate 1

description: Library name: AD2N1


title: ACHT + FANCD2 No Treatment Replicate 2

description: Library name: AD2N2


title: BIR_Discovery_123


title: Kdm6b_CR_Treg_1

description: Library name: sample 13

value: Treg


title: BIR_Discovery_126

value: M


title: TCR_3h_Kdm6b_1

description:
Library name: sample 19
rRNA depleted, stranded RNA

value: Spleen and LNs


title: TCR_3h_WT_2

description:
Library name: sample 16
rRNA depleted, stranded RNA


title: noTCR_Kdm6b_2

description:
Library name: sample 18
rRNA depleted, stranded RNA

value: PBS


title: BIS_Discovery_119

value: F


title: BIS_Discovery_122


title: BIR_Discovery_120

value: BIR


title: Early, clone 2, H3K4me1


title: ACHT + FANCG No Treatment Replicate 2

description: Library name: AGN2


title: Early, clone 2, H3K27me3


title: noTCR_Kdm6b_1

description:
Library name: sample 17
rRNA depleted, stranded RNA


title: noTCR_WT_2

description:
Library name: sample 14
rRNA depleted, stranded RNA


title: Early, clone 2, Input


title: BIR_Discovery_121

value: Blood cells


title: Early, clone 2, H3K27ac


title: ACHT + FANCG No Treatment Replicate 3

description: Library name: AGN3


title: ACHT + FANCG No Treatment Replicate 1

description: Library name: AGN1


title: Normal lung, Full ROI segment, ROI NL3R2

city: houston

first: Nirmal

last: Sharma

state: MAtx

address: Baylor college of medicine

institute: Baylor college of medicine

description:
Library name: DSP-1001660018222-B-B07
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24

data_processing:
Raw FASTQ files were processed using the NanoString GeoMx NGS Pipeline (DnD) to generate Digital Count Conversion (DCC) files containing probe-level count data.
DCC files were loaded into NanoString GeoMx DSP software for QC, filtering, and normalization. Third-quartile (Q3) normalization was applied for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: DCC files: NanoString Digital Count Conversion files containing probe-level read counts per area of illumination (AOI).
Supplementary files format and content: geomx_Q3_log2_normalized_matrix.csv: Q3 (upper quartile, 75th percentile) normalized, log2-transformed expression values for all genes across all samples.
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: NanoString Probe Kit Configuration file mapping probes to target genes for the Human WTA panel.
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
Paraffin-embedded human lung tissue sections (5 um) were placed on GeoMx slides. Tissue was deparaffinized and rehydrated. RNA targets were hybridized with the NanoString GeoMx Human Whole Transcriptome Atlas (WTA) probe panel. Fluorescently labeled antibodies against CD31, PanCK, and CD45 were applied for morphology-guided region of interest (ROI) selection using the GeoMx Digital Spatial Profiler (DSP).
UV-cleaved oligonucleotide tags from selected areas of illumination (AOIs) were collected, indexed, and PCR-amplified to generate sequencing libraries using the NanoString GeoMx NGS Library Prep kit per manufacturer instructions. Panel: (v1.0) Human NGS Whole Transcriptome Atlas RNA.

value: lung

tag: sample type

value: Normal

tag: segment

value: Full ROI

tag: roi

tag: slide

tag: nuclei


title: Normal lung, Full ROI segment, ROI NL3R3

description:
Library name: DSP-1001660018222-B-B08
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24


title: Normal lung, Full ROI segment, ROI NL3R1

description:
Library name: DSP-1001660018222-B-B06
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24


title: Astrocytes, sepsis 3

city: hefei

first: mei

last: bin

state: anhui

address: Meishan Road Campus, No. 81, Meishan Road

institute: Anhui medical university

description:
Library name: Sample 6
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing , barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (http://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: hippocampus

extract_protocol:
Mice were deeply anesthetized with isoflurane and then perfused transcardially with ice-cold physiological saline. After that, the hippocampal tissues of the mice were removed and placed in a sterile environment. Wash twice with pre-cooled RPMI 1640+0.04%BSA medium. The tissue was fully cut into small pieces of about 0.5mm3 with surgical scissors and put into PBS with 1.5 mg/ml collagenase IV and 1 mg/ml DNase I , and digested by enzymatic digestion in a constant temperature incubator at 37℃ for 30-60 min, and mixed inversely every 5-10min. The digested cell suspension was filtered by BD 40μm cell screen for 1-2 times, centrifuged at 4℃ and 300g for 5min. After the precipitation was suspended with appropriate medium, the same volume of red blood cell lysate was added, mixed, left for 10 min at 4℃, cell suspension 300g centrifuged for 5min, and the supernatant was discarded. The precipitation was washed in the medium once, centrifuged at 300g for 5min, and the supernatant was discarded. The cell precipitation was suspended in the medium of 100μl, and the cell concentration and viability were calculated by Luna cell counter.
According to the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Operation manual for computer and library construction. The constructed library was sequenced using Illumina Nova 6000 PE150 platform.

value: hippocampus

value: Astrocyte

tag: age

value: 7-9 weeks old

value: WT

value: male


title: TCR_3h_WT_1

description:
Library name: sample 15
rRNA depleted, stranded RNA

tag: tissue

value: rTreg

value: anti-CD3/CD28 for 3 hours


title: Early, clone 1, H3K4me1

source_name: Early, clone 1

value: Leukemic progenitor cells

value: Early, clone 1


title: noTCR_WT_1

description:
Library name: sample 13
rRNA depleted, stranded RNA

value: Spleen and LNs


title: Early, clone 1, H3K4me3


title: Early, clone 1, H3K27me3


title: BIR_Discovery_117

value: M


title: Astrocytes, sepsis 2

description:
Library name: Sample 5
10x Genomics


title: BIS_Discovery_118

value: BIS


title: BIS_Discovery_116


title: Normal lung, Tumor segment, ROI NL3P3

description:
Library name: DSP-1001660018222-B-B05
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24

value: Tumor


title: Aggressive, clone 2, H3K4me3

source_name: Aggressive, clone 2

value: Aggressive, clone 2


title: BIS_Discovery_115

value: Blood cells


title: Normal lung, cd31 segment, ROI NL3E2

description:
Library name: DSP-1001660018222-B-B01
GeoMx WTA, Normal, cd31, slide Normal_11.15.24

value: lung

value: Normal


title: Astrocytes, sham surgery 3

description:
Library name: Sample 3
10x Genomics

value: hippocampus


title: Normal lung, cd31 segment, ROI NL3E3

description:
Library name: DSP-1001660018222-B-B02
GeoMx WTA, Normal, cd31, slide Normal_11.15.24


title: Normal lung, Tumor segment, ROI NL3P1

description:
Library name: DSP-1001660018222-B-B03
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24


title: Astrocytes, sham surgery 2

description:
Library name: Sample 2
10x Genomics

value: Astrocyte


title: Normal lung, Tumor segment, ROI NL3P2

description:
Library name: DSP-1001660018222-B-B04
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24


title: Early, clone 1, Input

value: Input


title: BIS_Discovery_112


title: BIS_Discovery_113


title: BIR_Discovery_114

value: F

value: BIR


title: Astrocytes, sepsis 1

description:
Library name: Sample 4
10x Genomics

value: 7-9 weeks old

value: WT

value: male


title: Sample_HP2_igG

city: Guangzhou

first: shuyi

last: kuang

state: Guangdong

address: ShaTai southern load

institute: Southern Medical Univercity

description: Library name: Sample8

data_processing:
The fastq files were trimmed using trimmomatic and aligned to mm10 with bowtie2 using parameters --end-to-end --very-sensitive --no-mixed --no-discordant. Duplicates were removed using Picard tools (MarkDuplicates). Low quality reads were removed using samtools. Peaks were called using MACS2 version 2.2.7.1. Differentially bound sites were identified using DiffBind (R statistical package).
Assembly: mm10
Supplementary files format and content: narrowPeak, Peak were calling using MACS v2.
Library strategy: CUT&Tag

source_name: Placenta

extract_protocol:
For the CUT&Tag experiments, nuclei isolation was performed according to the published protocol by using a minimum of 105 nuclei. Nuclei were resuspended in 200 μL antibody buffer containing 1 μg FOXO1 antibody or IgG and then incubated at 4ºC overnight.
Qubit Flex was used for initial quantitation after the library was constructed, and the library size range was checked using an Agilent 4200 Tapestation to ensure the inserted fragment size. After qualified library inspection, different libraries were pooled according to the requirements of effective concentration and target data volume.

value: Placenta

value: decidual PMN-MDSCs

value: Wild type

value: Healthy pregancy group


title: Sample_HP2_FoxO1

description: Library name: Sample7


title: Normal lung, cd31 segment, ROI NL3E1

description:
Library name: DSP-1001660018222-B-A12
GeoMx WTA, Normal, cd31, slide Normal_11.15.24


title: Astrocytes, sham surgery 1

description:
Library name: Sample 1
10x Genomics


title: Aggressive, clone 2, H3K4me1

value: Leukemic progenitor cells


title: BIR_Discovery_111


title: Early, clone 1, H3K27ac

value: Early, clone 1


title: Normal lung, Full ROI segment, ROI NL2R2

description:
Library name: DSP-1001660018222-B-A10
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24

value: Full ROI


title: Aggressive, clone 2, H3K27me3

value: Aggressive, clone 2


title: Aggressive, clone 2, H3K27ac


title: Normal lung, Full ROI segment, ROI NL2R3

description:
Library name: DSP-1001660018222-B-A11
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24

value: lung

value: Normal


title: BIS_Discovery_110

value: M

value: BIS

value: Blood cells


title: BIS_Discovery_109


title: Sample_HP1_igG

description: Library name: Sample6


title: Aggressive, clone 2, Input

value: Input


title: BIS_Discovery_108


title: Normal lung, Tumor segment, ROI NL2P3

description:
Library name: DSP-1001660018222-B-A08
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24

value: Tumor


title: Aggressive, clone 1, H3K4me1

source_name: Aggressive, clone 1

value: Aggressive, clone 1


title: Aggressive, clone 1, H3K4me3


title: Sample_A2_igG

description: Library name: Sample4

value: Advanced pregancy group


title: Aggressive, clone 1, H3K27me3


title: BIS_Discovery_104


title: Sample_A2_FoxO1

description: Library name: Sample3

value: Placenta


title: Sample_HP1_FoxO1

description: Library name: Sample5

value: decidual PMN-MDSCs


title: Normal lung, Full ROI segment, ROI NL2R1

description:
Library name: DSP-1001660018222-B-A09
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24


title: Normal lung, Tumor segment, ROI NL2P1

description:
Library name: DSP-1001660018222-B-A06
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24


title: BIS_Discovery_106


title: Sample_A1_FoxO1

description: Library name: Sample1

value: Wild type


title: Aggressive, clone 1, Input


title: BIS_Discovery_105


title: BIS_Discovery_107


title: Normal lung, Tumor segment, ROI NL2P2

description:
Library name: DSP-1001660018222-B-A07
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24


title: Aggressive, clone 1, H3K27ac


title: Normal lung, cd31 segment, ROI NL2E2

description:
Library name: DSP-1001660018222-B-A04
GeoMx WTA, Normal, cd31, slide Normal_11.15.24


title: Normal lung, cd31 segment, ROI NL2E3

description:
Library name: DSP-1001660018222-B-A05
GeoMx WTA, Normal, cd31, slide Normal_11.15.24


title: BIR_Discovery_103

value: F

value: BIR


title: Sample_A1_igG

description: Library name: Sample2


title: Early, Smad1, replicate 3

data_processing:
Transcriptome mapping was performed with STAR using the Ensembl annotation of the mm9 reference genome.
Read counts for individual genes were generated using HTSeq. Only genes with CPM > 1 for at least one sample were included in the analyses.
Assembly: mm9
Supplementary files format and content: Table with RPKM values for each sample

source_name: Leukemic progenitor cells

extract_protocol:
RNA was extracted using TRIzol LS Reagent
Sequencing libraries were prepared using polyA-selection followed by NEBNext Ultra Directional RNA library preparation protocol (New England Biolabs). Sequencing was performed on Illumina HiSeq 2500 instrument, resulting in approximately 30 million 50 bp reads per sample.

value: Leukemic progenitor cells

value: Smad1 overexpression


title: WT-1-10X

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines /latest/what-is-cell-ranger) using default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
The tissue was placed in a petri dish on ice and cut into small pieces of 2-4 mm. The pieces were infused with the RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI/enzyme mix, attached to the sleeve of the gentleMACS Octo Dissociator and run program. After termination of the program, the suspension was passed through a 70um straine and spun down at 300 x g for 10 min at 4 °C, removed the supernatant and added 10 times volume 1 x Red Blood CellLysis Solution(130-094-183, Miltenyi Biotec) to lytic red blood cells in the refrigerator at 4 °C for 10 min, then added 10 ml 1 x PBS+0.04 % BSA and the resulting suspension was centrifuged at 300 x g for 10 min.
Library was performed accordimg to the manufacter's instructions (single cell 5'v2 protocol. 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Immediately following GEM generation, the Gel Bead is dissolved, primers are released, and any co- partitioned cell is lysed. Primer than contains an Illumina TruSeq Read 1 (Read 1 sequencing primer), 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence are mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces Barcoded, fulllength cDNA from poly-adenylated mRNA.After incubation, GEMs are broken and pooled fractions are recovered. Silane magnetic beads are used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction.Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. TruSeq Read 1 (Read 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (Read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 450bp.

value: Spleen

value: WT


title: WT-2-10XTCR


title: Normal lung, cd31 segment, ROI NL2E1

description:
Library name: DSP-1001660018222-B-A03
GeoMx WTA, Normal, cd31, slide Normal_11.15.24

value: lung

value: Normal


title: BIR_Discovery_102

source_name: Blood cells

value: M


title: BIR_Discovery_100

value: Blood cells


title: Early, control, replicate 1

value: Control


title: BIR_Discovery_101


title: Early, Smad1, replicate 2


title: KO-1-10XTCR

value: KO


title: Normal lung, Full ROI segment, ROI NL1R2

description:
Library name: DSP-1001660018221-A-H12
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24

value: Full ROI


title: BIS_Discovery_99

value: BIS


title: Normal lung, Full ROI segment, ROI NL1R3

description:
Library name: DSP-1001660018222-B-A02
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24


title: Normal lung, Tumor segment, ROI NL1P2

description:
Library name: DSP-1001660018221-A-H09
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24

value: Tumor


title: Normal lung, Full ROI segment, ROI NL1R1

description:
Library name: DSP-1001660018221-A-H11
GeoMx WTA, Normal, Full ROI, slide Normal_11.15.24


title: KO-1-10XBCR


title: WT-2-10XBCR


title: Early, control, replicate 3


title: BIS_Discovery_98


title: KO-1-10X


title: Early, Smad1, replicate 1


title: CD4+ T cells treated with MAPK13-IN-1 2

city: wuhan

first: wang

last: yi

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Peak locations were determined using the MACS algorithm (v1.4.2) .
Assembly: mm10
Supplementary files format and content: bigWig, narrow peak (except for Input sample)

source_name: spleen

extract_protocol: ChIP-seq libraries were prepared through DNA fragmentation, end repair, dA-tailing, adaptor ligation, PCR amplification, and subsequent selection of fragments ranging from 200 to 500 bp using gel electrophoresis on a 2% agarose gel. After undergoing quality control testing, the chip library was sequenced on an Illumina HiSeq sequencer.

value: spleen

value: CD4+ T cells


title: Aggressive, Plag1 overexpression, replicate 5

value: Plag1 overexpression


title: Normal lung, Tumor segment, ROI NL1P3

description:
Library name: DSP-1001660018221-A-H10
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24


title: Normal lung, Tumor segment, ROI NL1P1

description:
Library name: DSP-1001660018221-A-H08
GeoMx WTA, Normal, Tumor, slide Normal_11.15.24


title: CD4+ T cells treated with MAPK13-IN-1 1


title: Early, control, replicate 2


title: Aggressive, Plag1 overexpression, replicate 4


title: BIR_Discovery_96

value: BIR


title: BIR_Discovery_97


title: Normal lung, cd31 segment, ROI NL1E3

description:
Library name: DSP-1001660018221-A-H07
GeoMx WTA, Normal, cd31, slide Normal_11.15.24


title: CD4+ T cells treated with DMSO 2

value: DMSO


title: BIR_Discovery_95


title: Aggressive, Plag1 overexpression, replicate 3

value: Leukemic progenitor cells


title: BIR_Discovery_93


title: BIR_Discovery_92

value: F


title: Non-CLAD lung, Full ROI segment, ROI NC9R2

description:
Library name: DSP-1001660018221-A-H03
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24

value: Non-CLAD


title: Aggressive, control, replicate 3


title: BIS_Discovery_94


title: CD4+ T cells treated with DMSO 1


title: Aggressive, Irx5 overexpression, replicate 3

value: Irx5 overexpression


title: T21, R23874

city: New York City

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: R23874

data_processing:
Raw sequencing reads were processed using the RAPiD-nf pipeline, with alignment to the GRCh38 reference genome performed using STAR v2.7.3a.
Alignment quality was assessed with RSeQC and Picard. PCR duplicates were marked but not removed prior to quantification.
Gene-level counts were generated using featureCounts (Subread v2.0.1) with GENCODE v32 annotations.
Counts were normalized usingthe VOOM method from the limma package (v3.48.3), and log2-transformed expression matrices were created seperately for DLPFC and hippocampus.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: tab-delimited text file (T21_raw_counts.txt) includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from frozen dorosolateral prefrontal cortex and hippocampal tissues using the AllPrep DNA/RNA Mini Kit, and only samples with RIN ≥ 9.0 were included.
RNA-seq libraries were generatred from 300 ng of high-quality total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

value: Hippocampus

tag: karyotype

tag: rin

tag: gestational age

tag: race

value: Caucasian


title: T21, R23872

description: Library name: R23872


title: Non-CLAD lung, Full ROI segment, ROI NC9R3

description:
Library name: DSP-1001660018221-A-H04
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24

value: lung


title: Normal lung, cd31 segment, ROI NL1E1

description:
Library name: DSP-1001660018221-A-H05
GeoMx WTA, Normal, cd31, slide Normal_11.15.24

value: Normal


title: Non-CLAD lung, Full ROI segment, ROI NC9R1

description:
Library name: DSP-1001660018221-A-H02
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24


title: T21, R23875

description: Library name: R23875

value: M


title: Normal lung, cd31 segment, ROI NL1E2

description:
Library name: DSP-1001660018221-A-H06
GeoMx WTA, Normal, cd31, slide Normal_11.15.24


title: Aggressive, Irx5 overexpression, replicate 1


title: T21, R23877

description: Library name: R23877


title: BIR_Discovery_91

value: Blood cells


title: Aggressive, control, replicate 2

value: Control


title: BIS_Discovery_90

value: BIS


title: T21, R23871

description: Library name: R23871


title: Aggressive, Irx5 overexpression, replicate 2


title: Non-CLAD lung, Tumor segment, ROI NC9P3

description:
Library name: DSP-1001660018221-A-H01
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24

value: Tumor


title: Aggressive, control, replicate 1


title: Non-CLAD lung, Tumor segment, ROI NC9P2 002

description:
Library name: DSP-1001660018221-A-G12
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: BIS_Discovery_89


title: BIS_Discovery_88


title: BIR_Discovery_85


title: Non-CLAD lung, CD31 segment, ROI NC9E3

description:
Library name: DSP-1001660018221-A-G09
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: Cancer heart 5, A16-14570

city: West Lafayette

first: Andrea

last: Pires dos Santos

address: 625 Harrison St.

institute: Purdue University

description:
Library name: Cardiac sample 11
Column name in miRNA_expression_raw.txt: A16-14570
miRNA_expression_raw.txt
miRNA_expression_norm.txt

data_processing:
CLC Genomics Workbench 21.0.4
Assembly: CanFam3.1.101
Supplementary files format and content: raw counts for each sample.
Supplementary files format and content: normalized counts for each sample.

organism: Canis lupus familiaris

source_name: Heart

extract_protocol:
miRNeasy FFPE Kit (Qiagen)
QIAseq miRNA Library Kit (QIAGEN). A total of 100ng total RNA was converted into miRNA NGS libraries.

value: Heart


title: BIR_Discovery_84


title: Cancer heart 2, A15-13889

description:
Library name: Cardiac sample 8
Column name in miRNA_expression_raw.txt: A15-13889
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: T21, R23870

description: Library name: R23870


title: Cancer heart 3, A16-10141

description:
Library name: Cardiac sample 9
Column name in miRNA_expression_raw.txt: A16-10141
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: Cancer heart 6, A21-10585

description:
Library name: Cardiac sample 12
Column name in miRNA_expression_raw.txt: A21-10585
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: T21, R23866

description: Library name: R23866


title: T21, R23867

description: Library name: R23867


title: Cancer heart 4, A16-11970

description:
Library name: Cardiac sample 10
Column name in miRNA_expression_raw.txt:  A16-11970
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: T21, R23868

description: Library name: R23868


title: Non-CLAD lung, Tumor segment, ROI NC9P2

description:
Library name: DSP-1001660018221-A-G11
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: BIS_Discovery_87


title: Non-CLAD lung, CD31 segment, ROI NC9E1

description:
Library name: DSP-1001660018221-A-G07
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: Non-CLAD lung, CD31 segment, ROI NC9E2

description:
Library name: DSP-1001660018221-A-G08
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: T21, R23864

description: Library name: R23864


title: BIR_Discovery_86


title: T21, R23869

description: Library name: R23869


title: Non-CLAD lung, Tumor segment, ROI NC9P1

description:
Library name: DSP-1001660018221-A-G10
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: Non-CLAD lung, Full ROI segment, ROI NC6R3

description:
Library name: DSP-1001660018221-A-G06
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24

value: Full ROI


title: Cancer heart 1, A13-3550

description:
Library name: Cardiac sample 7
Column name in miRNA_expression_raw.txt: A13-3550
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: BIS_Discovery_83


title: T21, R23861

description: Library name: R23861


title: T21, R23854

description: Library name: R23854


title: BIS_Discovery_82


title: BIR_Discovery_80

value: BIR


title: Healthy heart 5, 5-RVM-6

description:
Library name: Cardiac sample 5
Column name in miRNA_expression_raw.txt: 5-RVM-6
miRNA_expression_raw.txt
miRNA_expression_norm.txt

value: Visceral hemangiosarcoma


title: BIR_Discovery_81


title: Non-CLAD lung, Tumor segment, ROI NC6P3

description:
Library name: DSP-1001660018221-A-G03
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: Non-CLAD lung, Full ROI segment, ROI NC6R2

description:
Library name: DSP-1001660018221-A-G05
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24


title: Healthy heart 4, 4-RVF-5

description:
Library name: Cardiac sample 4
Column name in miRNA_expression_raw.txt: 4-RVF-5
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: BIS_Discovery_78


title: T21, R23846

description: Library name: R23846


title: T21, R23843

description: Library name: R23843


title: Non-CLAD lung, Full ROI segment, ROI NC6R1

description:
Library name: DSP-1001660018221-A-G04
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24


title: BIR_Discovery_79


title: Healthy heart 1, 1-RVF-1

description:
Library name: Cardiac sample 1
Column name in miRNA_expression_raw.txt: 1-RVF-1
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: Healthy heart 3, 3-RVF-3

description:
Library name: Cardiac sample 3
Column name in miRNA_expression_raw.txt: 3-RVF-3
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: Non-CLAD lung, CD31 segment, ROI NC6E3

description:
Library name: DSP-1001660018221-A-F12
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: T21, R23842

description: Library name: R23842


title: Non-CLAD lung, Tumor segment, ROI NC6P1

description:
Library name: DSP-1001660018221-A-G01
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: T21, R23844

description: Library name: R23844


title: Healthy heart 6, 7-RVF-7

description:
Library name: Cardiac sample 6
Column name in miRNA_expression_raw.txt: 7-RVF-7
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: BIR_Discovery_76


title: BIS_Discovery_77


title: Non-CLAD lung, Tumor segment, ROI NC6P2

description:
Library name: DSP-1001660018221-A-G02
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: Healthy heart 2, 2-RVM-2

description:
Library name: Cardiac sample 2
Column name in miRNA_expression_raw.txt: 2-RVM-2
miRNA_expression_raw.txt
miRNA_expression_norm.txt


title: BIR_Discovery_75


title: Control, R23876

description: Library name: R23876


title: Non-CLAD lung, CD31 segment, ROI NC6E1

description:
Library name: DSP-1001660018221-A-F10
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: BIS_Discovery_73


title: T21, R23835

description: Library name: R23835


title: T21, R23831

description: Library name: R23831


title: RL cells, treated with linperlisib (32 µM) plus chiglitazar (16 µM), replicate 2

city: Xiamen

first: Wenqin

last: Wang

address: Xiang'an South Road No. 422, Xiang'an District

institute: Xiamen University

description:
Library name: Combination_2
Column name in raw_Count.txt: Combination_2

data_processing:
Raw base call files were converted to FASTQ format and demultiplexed by the sequencing service provider.
Adapter sequences, reads containing excessive unknown bases, and low-quality reads were removed to obtain clean reads for downstream analysis.
Clean reads were aligned to the human reference genome using a splice-aware aligner with default or recommended parameters.
Gene-level read counts were generated by summarizing uniquely mapped reads to annotated genes based on a current human gene annotation database.
The processed file “raw_count.txt” was generated by summarizing uniquely mapped reads at the gene level to obtain raw read counts for each gene in each sample, and by merging these counts with gene annotation information (Ensembl ID, gene symbol/ID, genomic coordinates, gene biotype, and Gene Ontology terms).
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: The processed data file “raw_count.txt” is a tab-delimited text file containing a gene-by-sample matrix. Each row corresponds to one gene (identified by “AccID”), and each of the twelve sample columns (“Chiglitazar_1”, “Chiglitazar_2”, “Chiglitazar_3”, “Combination_1”, “Combination_2”, “Combination_3”, “Control_1”, “Control_2”, “Control_3”, “Linperlisib_1”, “Linperlisib_2”, “Linperlisib_3”) contains the raw (unnormalized) read count for that gene in the corresponding RL sample.

source_name: hematopoietic and lymphoid tissue

growth_protocol: RL cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 medium (HyClone, Thermo Scientific, MA, USA) supplemented with 10% fetal bovine serum (FBS), 100 μg/mL streptomycin, and 100 U/mL penicillin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂ and passaged regularly to keep them in logarithmic growth phase.

extract_protocol:
Total RNA was isolated from RL cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
mRNA was enriched from total RNA using oligo(dT) beads to capture polyadenylated transcripts. Purified mRNA was fragmented and used as template for first-strand cDNA synthesis with random primers and M-MuLV reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. Double-stranded cDNA was end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Adapter-ligated fragments of approximately 200 bp were size-selected with AMPure XP beads and amplified by PCR to generate sequencing libraries. Libraries were quality-controlled by qPCR quantification and fragment size assessment, pooled, and subjected to 150 bp paired-end sequencing on an Illumina platform by HaploX Biotechnology (Shenzhen, China).

treatment_protocol: For transcriptome profiling, 1 × 10⁶ RL cells per condition were seeded and allowed to recover overnight. Cells were then treated for 24 h with 0.1% DMSO (vehicle control), linperlisib (32 μM), chiglitazar (16 μM), or the combination of linperlisib (32 μM) plus chiglitazar (16 μM) before RNA extraction.

value: hematopoietic and lymphoid tissue

value: RL

tag: cell type

value: Follicular Lymphoma

tag: batch


title: BIS_Discovery_72

data_processing:
ChAMP package in R environment
processed value definition: combat normalised beta methylation values (linked as supplementary file on the Series record)

extract_protocol: precipitation with sodium acetate

tag: Sex

value: F


title: RL cells, treated with linperlisib (32 µM) plus chiglitazar (16 µM), replicate 1

description:
Library name: Combination_1
Column name in raw_Count.txt: Combination_1

tag: cell line


title: RL cells, treated with chiglitazar (16 µM), replicate 2

description:
Library name: Chiglitazar_2
Column name in raw_Count.txt: Chigliatzar_2

tag: treatment

value: treated with chiglitazar (16 µM)


title: RL cells, treated with linperlisib (32 µM) plus chiglitazar (16 µM), replicate 3

description:
Library name: Combination_3
Column name in raw_Count.txt: Combination_3


title: RL cells, treated with chiglitazar (16 µM), replicate 3

description:
Library name: Chiglitazar_3
Column name in raw_Count.txt: Chigliatzar_3


title: Control, R23981

description: Library name: R23981

value: Hippocampus

value: Caucasian


title: Non-CLAD lung, CD31 segment, ROI NC6E2

description:
Library name: DSP-1001660018221-A-F11
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24

value: lung

value: Non-CLAD


title: Non-CLAD lung, Full ROI segment, ROI NC4R3

description:
Library name: DSP-1001660018221-A-F09
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24


title: Non-CLAD lung, Full ROI segment, ROI NC4R1

description:
Library name: DSP-1001660018221-A-F07
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24


title: Control, R23873

description: Library name: R23873

value: M


title: BIS_Discovery_74

value: Blood cells


title: T21, R23852

description: Library name: R23852


title: Non-CLAD lung, Full ROI segment, ROI NC4R2

description:
Library name: DSP-1001660018221-A-F08
GeoMx WTA, Non-CLAD, Full ROI, slide Non-Clad_11.13.24


title: RL cells, treated with chiglitazar (16 µM), replicate 1

description:
Library name: Chiglitazar_1
Column name in raw_Count.txt: Chigliatzar_1


title: BIS_Discovery_71

value: BIS


title: RL cells, treated with linperlisib (32 µM), replicate 3

description:
Library name: Linperlisib_3
Column name in raw_Count.txt: Linperlisib_3

value: treated with linperlisib (32 µM)


title: Non-CLAD lung, Tumor segment, ROI NC4P3

description:
Library name: DSP-1001660018221-A-F06
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24

value: Tumor


title: Control, R23863

description: Library name: R23863

value: Control


title: Non-CLAD lung, Tumor segment, ROI NC4P1

description:
Library name: DSP-1001660018221-A-F04
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: BIS_Discovery_70


title: Control, R23865

description: Library name: R23865


title: RL cells, treated with linperlisib (32 µM), replicate 2

description:
Library name: Linperlisib_2
Column name in raw_Count.txt: Linperlisib_2


title: Non-CLAD lung, Tumor segment, ROI NC4P2

description:
Library name: DSP-1001660018221-A-F05
GeoMx WTA, Non-CLAD, Tumor, slide Non-Clad_11.13.24


title: RL cells, treated with 0.1% DMSO, replicate 3

description:
Library name: Control_3
Column name in raw_Count.txt: Control_3

value: treated with 0.1% DMSO


title: BIS_Discovery_69


title: RL cells, treated with 0.1% DMSO, replicate 2

description:
Library name: Control_2
Column name in raw_Count.txt: Control_2


title: BIS_Discovery_68


title: RL cells, treated with linperlisib (32 µM), replicate 1

description:
Library name: Linperlisib_1
Column name in raw_Count.txt: Linperlisib_1


title: Control, R23862

description: Library name: R23862


title: BIR_Discovery_67

value: BIR


title: Control, R23860

description: Library name: R23860


title: BIS_Discovery_66


title: Non-CLAD lung, CD31 segment, ROI NC4E2

description:
Library name: DSP-1001660018221-A-F02
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: BIS_Discovery_65


title: Control, R23858

description: Library name: R23858


title: RL cells, treated with 0.1% DMSO, replicate 1

description:
Library name: Control_1
Column name in raw_Count.txt: Control_1

value: hematopoietic and lymphoid tissue


title: Control, R23859

description: Library name: R23859


title: Non-CLAD lung, CD31 segment, ROI NC4E3

description:
Library name: DSP-1001660018221-A-F03
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: CLAD lung, Full ROI segment, ROI C6R3

description:
Library name: DSP-1001660018221-A-E12
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.12.24

value: CLAD

value: Full ROI


title: Non-CLAD lung, CD31 segment, ROI NC4E1

description:
Library name: DSP-1001660018221-A-F01
GeoMx WTA, Non-CLAD, CD31, slide Non-Clad_11.13.24


title: Control, R23857

description: Library name: R23857


title: BIR_Discovery_64


title: Control, R23856

description: Library name: R23856

value: F


title: Control, R23853

description: Library name: R23853


title: H1299, LMNB2 KO, SC35 TSA, rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
All TSA reads in FASTQ format were aligned to the GRCh38.p13.103 human genome using Bowtie2 (v.2.4.4) and removed redundant reads.
After confirmed the consistency between each replicate, we pooled extended reads and generated the bigwig track for visualization with IGV (v.2.8.7).
All bigwig files were generated from sorted bam files using deepTools (v 3.5.1).
Assembly: GRCh38.p13.103
Supplementary files format and content: normalized Bigwig, 100bp
Supplementary files format and content: smoothed Bigwig, 20kb
Library strategy: TSA-seq

source_name: Lung

growth_protocol: All the cell culture reagents used in the present study were purchased from Welgene (Seoul, Republic of Korea). H1299 (human non-small cell lung carcinoma) cells were purchased from the Korean Cell Line Bank (Seoul, Republic of Korea). H1299 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin at 37 °C in an incubator with 5% CO2 in a humidified atmosphere. For synchronization at G1/S, cells were cultured in the presence of 2mM thymidine (Sigma) for 18hrs, washed three times with phosphate-buffered saline (PBS) and released in fresh medium without thymidine for 9 hrs. After another 16 hrs in thymidine, cells were provided for experiments.

extract_protocol:
Cells were treated with trypsin for 5 min and immediately cross-linked by adding sample volume of 8% paraformaldehyde freshly prepared in calcium and magnesium free (CMF)-PBS for 20 min at 37°C. After quenching unreacted aldehyde with glycine at a final concentration of 0.125 M, cells were transferred to tubes for subsequent reaction. Cells were permeabilized for 1 hour in CMF-PBS containing 0.7% saponin and rinsed with CMF-PBS. To quench endogenous peroxidases, cells were incubated in 1.5% H2O2 (#216763, Sigma) in CMF-PBS for 1 hour at RT and washed using washing buffer (0.1% saponin in CMF-PBS). Samples are incubated for 1 hour in a blocking solution (5% normal goat serum and 0.2% saponin in CMF-PBS). Primary antibodies were diluted in blocking solution and samples were incubated for 24 hours at 4°C. After washing with washing buffer, cells were resuspended in blocking solution containing secondary antibody and incubated for 24 hours at 4°C. To label tyramide under different conditions, cells were resuspended in Buffer A indicated in Supplementary Figure S3A and same volume of Buffer B was added. For TSA v1.0, the labeling was done at RT for 10 min, but for TSA v2.0, total two rounds of reactions were performed at RT for 30 min each. Among cells, small portion was used to confirm TSA labeling with Streptavidin-PE and remaining cells were subjected to modified gDNA isolation method. Because tyramide preferentially labeled proteins over DNA, avoiding protein contamination is necessary to efficiently purify biotinylated DNA. Thus, we performed two different DNA purification methods. First, tyramide labeled cells were lysed by using PureLink™ Genomic Digestion Buffer (K182301, Invitrogen), followed by 1 hour of RNase (350 ng/μl) reaction at 37°C and 6 hours of Proteinase K (1 μg/μl) reaction at 55°C. After adding NaCl solution (200 mM), samples were incubated at 65°C for an overnight period to reverse protein-DNA crosslinks. Then, gDNA was extracted by using UltraPure™ Phenol: Chloroform: Isoamyl alcohol (PCI; 15593049, Invitrogen), followed by EtOH precipitation. gDNA was dissolved in distilled water (W4502, Sigma) and sheared using a bioruptor sonicator (Diagenode) at high power for 30 cycles (30s on / 30s off). For the 2nd round of purification, the AMPure magnetic beads (A63881, Beckman Coulter, CA, USA) were used to remove all protein contaminants from the biotinylated DNA. After bead purification, the samples were sheared again until the size of DNA fragments were ranged from 100 to 300 bp. Biotinylated DNA fragments were isolated by using Dynabeads M-270 streptavidin (65305, Invitrogen) according to the manufacturer's instructions. Immobilized DNA fragments were eluted in TSA elution buffer (10 mM Tris, 10 mM EDTA, 0.5% SDS, 1 μg/μl proteinase K, and 0.6 mM biotin) and final round of DNA extraction with PCI and subsequent EtOH precipitation was performed before proceeding to library preparation.
The Kapa Hyper Prep kit (KK8502, Kapa Biosystems/ 07962347001, Roche) was used to create the TSA-seq library. To summarize, 15 ng of input and TSA-enriched DNA were end-repaired, 3’-end A-tailed, and ligated with KAPA Unique Dual-Indexed Adapter Kit (KK8727, Kapa Biosystems/ 08861919702, Roche) before being amplified. The Illumina HiSeq X Ten platform was used for paired-end sequencing of all TSA libraries.

value: Lung

value: Epithelial

tag: genotype

value: LMNB2 KO


title: BIR_Discovery_60


title: BIS_Discovery_63


title: BIR_Discovery_62


title: H1299, LMNB2 KO, SC35 TSA, rep1


title: CLAD lung, Tumor segment, ROI C6P3

description:
Library name: DSP-1001660018221-A-E09
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.12.24

value: lung

tag: sample type


title: H1299, Input, rep1

value: Wild type


title: H1299, LMNB1 KO, SC35 TSA, rep1

value: LMNB1 KO


title: H1299, LMNB1 KO, SC35 TSA, rep2


title: CLAD lung, Full ROI segment, ROI C6R2

description:
Library name: DSP-1001660018221-A-E11
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.12.24

tag: segment


title: Control, R23851

description: Library name: R23851

value: Hippocampus

value: M

value: Caucasian


title: Control, R23850

description: Library name: R23850


title: H1299, Control, SC35 TSA, rep2


title: BIS_Discovery_61

value: BIS

value: Blood cells


title: CLAD lung, Full ROI segment, ROI C6R1

description:
Library name: DSP-1001660018221-A-E10
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.12.24

tag: roi


title: CLAD lung, Tumor segment, ROI C6P2

description:
Library name: DSP-1001660018221-A-E08
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.12.24

value: Tumor

tag: slide


title: CLAD lung, Tumor segment, ROI C6P1

description:
Library name: DSP-1001660018221-A-E07
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.12.24

tag: nuclei


title: BIR_Discovery_59

value: BIR


title: H1299, Control, SC35 TSA, rep1


title: BIR_Discovery_58


title: spinal health patient,Ctrl_6

city: Beijing

first: Qing

last: Sun

address: Datun road, No.15th

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Before read mapping, we applied fastp with default parameter to filtering the adaptor sequence and removing the low quality reads to achieve the clean data. The clean reads were then aligned to human genome (GRCh38) using the Bismark. Methylation levels of a C within an aligned read were gauged by the ratio of reads that contained a methylated C at that location versus all the reads that covered the location, and resulted in an assignment to one of five levels. The number of Cs and Ts, corresponding to methylated andunmethylated Cs in the original sequence, for each cytosine position in the reference genome was used to calculate its methylation status.
Based on the calculated P-value at each CpG site, we implemented a simple procedure in DSS for calling DMRs based on the approximate Wald test P-values described above.  Called DMRs must exceed 100bp and cover more than three CpG sites. Meanwhile, the CpG sites in the DMR with P-values less than 0.00005 must exceed 80% . Regions satisfying the above criteria will be reported as DMRs.
Assembly: GRCh38
Supplementary files format and content: bw format files  contain each chromosome for each  Meth_Site

source_name: spinal bone

extract_protocol:
The whole-genome DNA was extracted with an Magbind Aminal Tissue DNA Kit (Methylome Biotech) following the instructions
Libraries for whole-genome bisulfite sequencing (WGBS) were prepared according to Methylome-Seq ssDNA Lib Prep Kit (For Illumina) protocol (Methylome Biotech)

value: spinal bone


title: BIS_Discovery_54

city: Nuthetal

first: Heike

last: Vogel

institute: German Institute of Human Nutrition Potsdam-Rehbruecke


title: BIR_Discovery_55


title: Control, R23848

description: Library name: R23848

value: Control


title: Control, R23849

description: Library name: R23849


title: Control, R23841

description: Library name: R23841


title: CLAD lung, cd45 segment, ROI C6L1

description:
Library name: DSP-1001660018221-A-E04
GeoMx WTA, CLAD, cd45, slide Clad 2_11.12.24

value: CLAD


title: spinal health patient,Ctrl_4


title: spinal health patient,Ctrl_5


title: CLAD lung, cd31 segment, ROI C6E3

description:
Library name: DSP-1001660018221-A-E03
GeoMx WTA, CLAD, cd31, slide Clad 2_11.12.24


title: CLAD lung, cd31 segment, ROI C6E1

description:
Library name: DSP-1001660018221-A-E01
GeoMx WTA, CLAD, cd31, slide Clad 2_11.12.24


title: spinal health patient,Ctrl_3


title: CLAD lung, cd45 segment, ROI C6L2

description:
Library name: DSP-1001660018221-A-E05
GeoMx WTA, CLAD, cd45, slide Clad 2_11.12.24


title: Control, R23845

description: Library name: R23845


title: spinal health patient,Ctrl_2


title: Control, R23839

description: Library name: R23839


title: BIR_Discovery_56

value: F


title: BIR_Discovery_57


title: CLAD lung, Full ROI segment, ROI C5R3

description:
Library name: DSP-1001660018221-A-D12
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.12.24

value: Full ROI


title: Control, R23847

description: Library name: R23847


title: Control, R23838

description: Library name: R23838


title: CLAD lung, cd31 segment, ROI C6E2

description:
Library name: DSP-1001660018221-A-E02
GeoMx WTA, CLAD, cd31, slide Clad 2_11.12.24


title: Control, R23855

description: Library name: R23855


title: BIR_Discovery_52


title: BIR_Discovery_53


title: spinal health patient,Ctrl_1


title: CLAD lung, Full ROI segment, ROI C5R1

description:
Library name: DSP-1001660018221-A-D10
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.12.24


title: CLAD lung, Full ROI segment, ROI C5R2

description:
Library name: DSP-1001660018221-A-D11
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.12.24


title: BIR_Discovery_50


title: congenital scoliosis patient,CS_5


title: Control, R23837

description: Library name: R23837


title: Control, R23836

description: Library name: R23836


title: Control, R23833

description: Library name: R23833


title: Control, R23834

description: Library name: R23834


title: CLAD lung, Tumor segment, ROI C5P2

description:
Library name: DSP-1001660018221-A-D08
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.12.24


title: CLAD lung, Tumor segment, ROI C5P3

description:
Library name: DSP-1001660018221-A-D09
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.12.24


title: CLAD lung, Tumor segment, ROI C5P1

description:
Library name: DSP-1001660018221-A-D07
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.12.24


title: BIS_Discovery_48


title: Control, R23832

description: Library name: R23832


title: congenital scoliosis patient,CS_6


title: congenital scoliosis patient,CS_4


title: BIS_Discovery_51


title: BIR_Discovery_49


title: BIS_Discovery_47


title: CLAD lung, cd45 segment, ROI C5L2

description:
Library name: DSP-1001660018221-A-D06
GeoMx WTA, CLAD, cd45, slide Clad 2_11.12.24


title: BIS_Discovery_46


title: T21, R23830

description: Library name: R23830

source_name: DLPFC

value: DLPFC


title: Control, R23829

description: Library name: R23829


title: congenital scoliosis patient,CS_3


title: congenital scoliosis patient,CS_2


title: congenital scoliosis patient,CS_1


title: congenital scoliosis patient,CS_7


title: BIS_Discovery_44


title: CLAD lung, cd31 segment, ROI C5E2

description:
Library name: DSP-1001660018221-A-D03
GeoMx WTA, CLAD, cd31, slide Clad 2_11.12.24


title: T21, R23827

description: Library name: R23827


title: CLAD lung, cd31 segment, ROI C5E3

description:
Library name: DSP-1001660018221-A-D04
GeoMx WTA, CLAD, cd31, slide Clad 2_11.12.24


title: CLAD lung, cd45 segment, ROI C5L1

description:
Library name: DSP-1001660018221-A-D05
GeoMx WTA, CLAD, cd45, slide Clad 2_11.12.24


title: Day 2 naphthalene Sca1pos 2

first: margherita

last: paschini

address: 1 blackfan circle, Karp Building

department: Hem/Onc

institute: Boston Children's Hospital

description: Library name: epi_IW22

data_processing:
10X Genomics Cell Ranger 3.1.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Assembly: mm10-1.2.0
Supplementary files format and content: h5 files for each library

extract_protocol:
Lungs were extracted from mice at 2 or 7 days after injection, dissociated into single-cell suspension, and enriched via FACS.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 3 and 3.1

treatment_protocol: Adult mice were given intraperitoneal injections of 200 mg/kg naphthalene in corn oil or corn oil control (of equal volume).

value: Epithelial

value: Wildtype

value: 200 mg/kg naphthalene


title: Control, R23826

description: Library name: R23826


title: Day 2 naphthalene Sca1pos 1

description: Library name: epi_IW21

value: lung


title: CLAD lung, Full ROI segment, ROI C7R3

description:
Library name: DSP-1001660018221-A-D01
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.7.24


title: CLAD lung, cd31 segment, ROI C5E1

description:
Library name: DSP-1001660018221-A-D02
GeoMx WTA, CLAD, cd31, slide Clad 2_11.12.24


title: Day 2 naphthalene Sca1neg 1

description: Library name: epi_IW15


title: BIR_Discovery_42

address: Arthur-Scheunert-Allee 114-116


title: Hi-C_PA2_E11.5_Hoxa2PTE-42kb-del

city: Basel

first: Filippo

address: Fabrikstrasse 24,

institute: FMI

description:
Library name: Sample 1
PA2 , E11.5, Hoxa2PTE-42kb-del, HiC

data_processing:
All Hi-C datasets were analyzed using the HiCUP pipeline (version 0.6.1).
The interaction matrices .hic were generated using Juicer (version 1.6)
Assembly: GRCm38/mm10
Supplementary files format and content: hic file contains HiC matrices

extract_protocol:
Tissue from E8.5, E10.5 and E11.5 embryos was dissociated as described for RNA-seq. Then the dissociated cells were cross-linked with 2% paraformaldehyde for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and resuspended in cold 1× PBS. CNCCs from Wnt1::Cre;ROSARFP and Ezh2cKO embryos were filtered and collected by FACS. Cells were spun down (1600 rpm, 10 minutes, 4°C), supernatant removed, and cell pellets were flash-frozen and stored at -80°C.
The input material per Hi-C experiment was 1-2 × 106 cells. Cells were incubated in 500 µL ice-cold lysis buffer (10 mM Tris-HCl pH 8, 0.2% (vol/vol) NP-40, 10 mM NaCl,1× protease inhibitor cocktail (Roche)) for 30 min with periodical mixing, followed by centrifugation to pellet nuclei (760xg, 5 min., 4°C). Cell nuclei were resuspended in 179 µL ice-cold 1.25× NEBuffer 2, 5.5 µL of 10% SDS was added, and nuclei were incubated at 37°C, shaking at 950 rpm, for 1 hour. Then 37.5 µL of 10% Triton X-100 was added and cell nuclei incubated at 37°C, shaking at 950 rpm, for 1 hour. A 5 μL aliquot was taken as a control for undigested chromatin (stored at − 20 °C). For HindIII digestion 5 µL of HindIII enzyme (NEB, cat. no. R0104T) was added, incubated 6 hours at 37°C shaking at 950 rpm, followed by addition of another 5 µL of HindIII and overnight incubation at 37°C shaking at 950 rpm. A 5 μL aliquot was taken to test digestion efficiency (stored at − 20 °C). To fill in and biotinylate the restriction fragment overhangs 30 µL of biotinylation master mix (6 µL 10× NEBuffer 2, 2 µL H2O, 1.5 µL 10 mM dATP, 1.5 µL 10 mM dGTP, 1.5 µL 10 mM dTTP, 37.5 µL 0.4 mM biotin-14-dATP, and 10 µL 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L)) was added, incubated for 75 min at 37°C mixing regularly by pipetting, and then placed on ice. Next, 227 µL ligation master mix (100 µL 10× ligation buffer (NEB B0202), 10 µL 10 mg/mL BSA, 344 µL nuclease-free H2O) and 12.5 µL 1U/µL T4 DNA ligase (Invitrogen 15224-024) was added for overnight blunt end ligation in a water bath at 16°C. The next day ligated samples were incubated for a further 30 min at room temperature. The re-ligated chromatin products and test aliquots were de-cross-linked for at least 6 hours by adding 50 µL and 2.5 μL proteinase K (10 mg/mL), incubated at 65 °C. Afterwards, 6 µL or 0.5 μL of 10 mg/ml RNase A was added to the samples and test aliquots, respectively, and incubated for 60 min at 37 °C. Next, chromatin was precipitated by adding 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) (PC) to the samples and test aliquots, vigorously shaking them, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to a new 15 mL tube. To reduce loss of DNA 1 mL of TLE buffer (10 mM Tris HCl (pH 8.0), 0.1 mM EDTA) was added to tube containing PC and residual chromatin, tube was vigorously mixed, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to the 15 mL tube. One tenth volume of 3 M sodium acetate was added to the chromatin sample mixed by vortexing, followed by the addition of 3 volumes 100% ethanol and vortexing to mix. The samples were frozen at − 80 °C for at least 2h. The precipitated chromatin was isolated by centrifugation at maximum speed for 45 min at 4 °C. The chromatin pellet was washed twice with 2mL freshly prepared 70% ethanol and centrifuged at maximum speed for 15 min at 4 °C in between washes. Finally, the chromatin pellet was dried at room temperature and resuspended in 100 μL TLE buffer. To check the Hi-C library DNA, 1:50 dilution of the sample, and the undigested and digested controls were loaded on a 1.5% agarose gel. The DNA concentration of the Hi-C library was determined using Qubit™ dsDNA HS assay kit. 5 µg DNA (split into two 5 µg aliquots) were used for library preparation. The next steps were performed per 5 µg aliquot. The DNA was sonicated using Covaris S220 (peak incidence power: 175W; duty factor: 10%; cycles per burst: 200; time: 120s) in a volume of 130 µL in a Covaris microTUBE to obtain 100 – 1000 bp long DNA fragments. End repair, dATP-tailing and Adapter ligation was performed on beads. For this, 100 µL of Dynabeads™ MyOne™ Streptavidin T1 (Invitrogen) were washed twice with 400 µL Tween Buffer (TWB; 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) and resuspended in 400 µL 2× binding buffer (2×BB; 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). The volume of the sonicated DNA was increased to 400 µL with TLE. DNA was mixed with washed beads (800 µL total volume) and incubated at RT for 45 min rotating at 5 rpm. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by a wash with 400 µL 1×BB, then with 100 µL 1×ligation buffer, and resuspended in 50 µL 1× ligation buffer. For end repair each aliquot was mixed on ice with 50 µL 2.5 mM dNTP mix (12.5 μL of 10 mM of each dNTP), 18 μL of T4 DNA Polymerase (NEB M0203), 18 μL of T4 PNK (NEB M0201), 3.7 μL of DNA polymerase I large fragment (Klenow; NEB M0210), and 360.1 μL of H2O, and then incubated at 20°C for 60 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 500 µL TLE and resuspended in 415 µL TLE. For dATP-tailing each aliquot was mixed with 50 µL 10× NEBuffer 2, 5 µL 10 mM dATG and 20 µL 5 U/µL Klenow exo-minus, and then incubated at 37°C for 30 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 200 µL 1× ligation buffer and resuspended in 100 µL 1× ligation buffer. For Hi-C 10 µL 15 µM TruSeq DNA Sgl index adapters (Illumina, Cat. No. 20016329) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1× BB, one wash with 200 µL 1×BB, one wash with 100 µL 1× NEBuffer 2, one wash with 50 µL 1× NEBuffer 2 and resuspended in 50 µL 1× NEBuffer 2. For Hi-C library amplification a reaction master mix was prepared, reaction volume per PCR tube was 25 µL (PCHi-C: 5 µL 5× Herculase II reaction buffer (Agilent), 0.25 µL 100 mM dNTPs, 2 µL PE PCR primer 1.0 {Schoenfelder, 2018}, 2 µL PE PCR primer 2.0 {Schoenfelder, 2018}, 0.5 µL Polymerase (Herculase, Agilent), 2.5 µL Hi-C DNA on beads, 12.75 µL nuclease-free H2O; Hi-C: 12.5 µL KAPA HiFi HotStart ReadyMix (Roche), 2.5 µL Illumina primer mix (contained in KAPA HiFi HotStart Library Amplification Kit), 2.5 µL Hi-C DNA on beads, 7.5 µL nuclease-free H2O) and PCR was run under the following conditions: 30s at 98 °C; 6-7 cycles of: 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 7 min at 72 °C. Post-amplification PCR reactions per sample were pooled and DNA was cleaned up using AMPure XP beads and eluted in nuclease-free H2O. Obtained DNA was used directly for Hi-C sequencing.

tag: developmental stage

value: Cranial neural crest cells


title: T21, R23828

description: Library name: R23828

tag: tissue

value: M


title: T21, R23824

description: Library name: R23824

tag: karyotype

value: Caucasian


title: T21, R23825

description: Library name: R23825

tag: rin


title: BIR_Discovery_45


title: CLAD lung, Full ROI segment, ROI C7R2

description:
Library name: DSP-1001660018221-A-C12
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.7.24


title: BIS_Discovery_43

value: BIS


title: BIS_Discovery_41

value: Blood cells


title: CLAD lung, Full ROI segment, ROI C7R1

description:
Library name: DSP-1001660018221-A-C11
GeoMx WTA, CLAD, Full ROI, slide Clad 2_11.7.24


title: BIR_Discovery_39


title: PCHi-C_PA2_E11.5_Hoxa2PTE-42kb-del_2

description:
Library name: Sample 2
PA2 , E11.5, Hoxa2PTE-42kb-del, PCHiC, BioRep 2

data_processing:
All PCHiC datasets were analyzed using the HiCUP pipeline (version 0.6.1).
Significant interactions were identified using the CHiCAGO pipeline (version 1.26.0) with recommended parameters for six-cutter restriction enzymes: minFragLen = 150, maxFragLen = 40,000, maxLBrownEst = 1,500,000, and binsize = 20,000.
Assembly: GRCm38/mm10
Supplementary files format and content: WashU text file contains Chicago Significant interactions
Library strategy: Capture-C

extract_protocol:
Tissue from E8.5, E10.5 and E11.5 embryos was dissociated as described for RNA-seq. Then the dissociated cells were cross-linked with 2% paraformaldehyde for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and resuspended in cold 1× PBS. CNCCs from Wnt1::Cre;ROSARFP and Ezh2cKO embryos were filtered and collected by FACS. Cells were spun down (1600 rpm, 10 minutes, 4°C), supernatant removed, and cell pellets were flash-frozen and stored at -80°C.
Promoter capture Hi-C was performed as described previously {Schoenfelder, 2018}  with adaptations to our system. The input material per PCHi-C experiment was 2.5 – 5 × 10^6 cells. Cells were incubated in 1mL ice-cold lysis buffer (10 mM Tris-HCl pH 8, 0.2% (vol/vol) NP-40, 10 mM NaCl,1× protease inhibitor cocktail (Roche)) for 30 min with periodical mixing, followed by centrifugation to pellet nuclei (760xg, 5 min., 4°C). Cell nuclei were resuspended in 358 µL ice-cold 1.25× NEBuffer 2, 11 µL of 10% SDS was added, and nuclei were incubated at 37°C, shaking at 950 rpm, for 1 hour. Then 75 µL of 10% Triton X-100 was added and cell nuclei incubated at 37°C, shaking at 950 rpm, for 1 hour. A 5 μL aliquot was taken as a control for undigested chromatin (stored at − 20 °C). For HindIII digestion 10 µL of HindIII enzyme (NEB, cat. no. R0104T) was added, incubated 6 hours at 37°C shaking at 950 rpm, followed by addition of another 10 µL of HindIII and overnight incubation at 37°C shaking at 950 rpm. A 5 μL aliquot was taken to test digestion efficiency (stored at − 20 °C). To fill in and biotinylate the restriction fragment overhangs 60 µL of biotinylation master mix (6 µL 10× NEBuffer 2, 2 µL H2O, 1.5 µL 10 mM dATP, 1.5 µL 10 mM dGTP, 1.5 µL 10 mM dTTP, 37.5 µL 0.4 mM biotin-14-dATP, and 10 µL 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L)) was added, incubated for 75 min at 37°C mixing regularly by pipetting, and then placed on ice. Next, 454 µL ligation master mix (100 µL 10× ligation buffer (NEB B0202), 10 µL 10 mg/mL BSA, 344 µL nuclease-free H2O) and 25 µL 1U/µL T4 DNA ligase (Invitrogen 15224-024) was added for overnight blunt end ligation in a water bath at 16°C. The next day ligated samples were incubated for a further 30 min at room temperature. The re-ligated chromatin products and test aliquots were de-cross-linked for at least 6 hours by adding 100 μL and 2.5 μL proteinase K (10 mg/mL), incubated at 65 °C. Afterwards, 12 μL or 0.5 μL of 10 mg/ml RNase A was added to the samples and test aliquots, respectively, and incubated for 60 min at 37 °C. Next, chromatin was precipitated by adding 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) (PC) to the samples and test aliquots, vigorously shaking them, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to a new 15 mL tube. To reduce loss of DNA 1 mL of TLE buffer (10 mM Tris HCl (pH 8.0), 0.1 mM EDTA) was added to tube containing PC and residual chromatin, tube was vigorously mixed, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to the 15 mL tube. One tenth volume of 3 M sodium acetate was added to the chromatin sample mixed by vortexing, followed by the addition of 3 volumes 100% ethanol and vortexing to mix. The samples were frozen at − 80 °C for at least 2h. The precipitated chromatin was isolated by centrifugation at maximum speed for 45 min at 4 °C. The chromatin pellet was washed twice with 2mL freshly prepared 70% ethanol and centrifuged at maximum speed for 15 min at 4 °C in between washes. Finally, the chromatin pellet was dried at room temperature and resuspended in 100 μL TLE buffer. To check the Hi-C library DNA, 1:50 dilution of the sample, and the undigested and digested controls were loaded on a 1.5% agarose gel. The DNA concentration of the Hi-C library was determined using Qubit™ dsDNA HS assay kit.For PCHi-C 10 µg DNA (split into two 5 µg aliquots) were used for library preparation. The next steps were performed per 5 µg aliquot. The DNA was sonicated using Covaris S220 (peak incidence power: 175W; duty factor: 10%; cycles per burst: 200; time: 120s) in a volume of 130 µL in a Covaris microTUBE to obtain 100 – 1000 bp long DNA fragments. End repair, dATP-tailing and Adapter ligation was performed on beads. For this, 100 µL of Dynabeads™ MyOne™ Streptavidin T1 (Invitrogen) were washed twice with 400 µL Tween Buffer (TWB; 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) and resuspended in 400 µL 2× binding buffer (2×BB; 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). The volume of the sonicated DNA was increased to 400 µL with TLE. DNA was mixed with washed beads (800 µL total volume) and incubated at RT for 45 min rotating at 5 rpm. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by a wash with 400 µL 1×BB, then with 100 µL 1×ligation buffer, and resuspended in 50 µL 1× ligation buffer. For end repair each aliquot was mixed on ice with 50 µL 2.5 mM dNTP mix (12.5 μL of 10 mM of each dNTP), 18 μL of  T4 DNA Polymerase (NEB M0203), 18 μL of T4 PNK (NEB M0201), 3.7 μL of DNA polymerase I large fragment (Klenow; NEB M0210), and 360.1 μL of H2O, and then incubated at 20°C for 60 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 500 µL TLE and resuspended in 415 µL TLE. For dATP-tailing each aliquot was mixed with 50 µL 10× NEBuffer 2, 5 µL 10 mM dATG and 20 µL 5 U/µL Klenow exo-minus, and then incubated at 37°C for 30 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 200 µL 1× ligation buffer and resuspended in 100 µL 1× ligation buffer. For PCHi-C adaptor ligation 4 µL 15 µM pre-annealed PE adapters (described in Schoenfelder et al., 2018) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. For Hi-C 10 µL 15 µM TruSeq DNA Sgl index adapters (Illumina, Cat. No. 20016329) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1× BB, one wash with 200 µL 1×BB, one wash with 100 µL 1× NEBuffer 2, one wash with 50 µL 1× NEBuffer 2 and resuspended in 50 µL 1× NEBuffer 2. At this point all aliquots per PCHi-C sample were pooled. For on-bead PCHi-C library amplification a reaction master mix was prepared, reaction volume per PCR tube was 25 µL (PCHi-C: 5 µL 5× Herculase II reaction buffer (Agilent), 0.25 µL 100 mM dNTPs, 2 µL PE PCR primer 1.0 {Schoenfelder, 2018}, 2 µL PE PCR primer 2.0 {Schoenfelder, 2018}, 0.5 µL Polymerase (Herculase, Agilent), 2.5 µL Hi-C DNA on beads, 12.75 µL nuclease-free H2O; Hi-C: 12.5 µL KAPA HiFi HotStart ReadyMix (Roche), 2.5 µL Illumina primer mix (contained in KAPA HiFi HotStart Library Amplification Kit), 2.5 µL Hi-C DNA on beads, 7.5 µL nuclease-free H2O) and PCR was run under the following conditions: 30s at 98 °C; 6-7 cycles of: 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 7 min at 72 °C. Post-amplification PCR reactions per sample were pooled and DNA was cleaned up using AMPure XP beads and eluted in nuclease-free H2O. Obtained DNA was used directly for Hi-C sequencing or for promoter-capture as described in Schoenfelder et al., 2018. Sequencing was performed on an Illumina NextSeq 500 (75bp read length, paired-end).


title: T21, R23823

description: Library name: R23823

tag: gestational age


title: BIR_Discovery_40


title: PCHi-C_PA2_E11.5_Hoxa2PTE-42kb-del_1

description:
Library name: Sample 1
PA2 , E11.5, Hoxa2PTE-42kb-del, PCHiC, BioRep 1


title: CLAD lung, Tumor segment, ROI C7P3

description:
Library name: DSP-1001660018221-A-C10
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.7.24

value: Tumor


title: BIS_Discovery_38


title: BIR_Discovery_36

value: BIR


title: CLAD lung, CD45 segment, ROI C7L1

description:
Library name: DSP-1001660018221-A-C05
GeoMx WTA, CLAD, CD45, slide Clad 2_11.7.24


title: BIS_Discovery_37


title: CLAD lung, Tumor segment, ROI C7P1

description:
Library name: DSP-1001660018221-A-C08
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.7.24


title: T21, R23820

description: Library name: R23820

tag: race


title: T21, R23821

description: Library name: R23821


title: BIS_Discovery_33


title: CLAD lung, Tumor segment, ROI C7P2

description:
Library name: DSP-1001660018221-A-C09
GeoMx WTA, CLAD, Tumor, slide Clad 2_11.7.24


title: PCHi-C_Md_E11.5_Hoxa2PTE-36kb-del_2BioRep

description:
Library name: Sample 20
Md , E11.5, Hoxa2PTE-36kb-del, PCHiC, BioRep 2

source_name: Md

value: Md

tag: cell type


title: PCHi-C_PA2_E11.5_Ezh2cKO_1BioRep

description:
Library name: Sample 17
PA2 , E11.5, Ezh2cKO, PCHiC, BioRep 1

tag: batch


title: PCHi-C_Md_E11.5_Hoxa2PTE-36kb-del_1BioRep

description:
Library name: Sample 19
Md , E11.5, Hoxa2PTE-36kb-del, PCHiC, BioRep 1


title: CLAD lung, CD45 segment, ROI C7L3

description:
Library name: DSP-1001660018221-A-C07
GeoMx WTA, CLAD, CD45, slide Clad 2_11.7.24

source_name: lung


title: T21, R23817

description: Library name: R23817

tag: Sex


title: PCHi-C_PA2_E11.5_Hoxa2PTE-36kb-del_1BioRep

description:
Library name: Sample 21
PA2 , E11.5, Hoxa2PTE-36kb-del, PCHiC, BioRep 1


title: T21, R23822

description: Library name: R23822


title: BIR_Discovery_34


title: PCHi-C_PA2_E11.5_Hoxa2PTE-36kb-del_2BioRep

description:
Library name: Sample 22
PA2 , E11.5, Hoxa2PTE-36kb-del, PCHiC, BioRep 2


title: T21, R23819

description: Library name: R23819


title: CLAD lung, cd31 segment, ROI C7E3

description:
Library name: DSP-1001660018221-A-C04
GeoMx WTA, CLAD, cd31, slide Clad 2_11.7.24


title: CLAD lung, CD45 segment, ROI C7L2

description:
Library name: DSP-1001660018221-A-C06
GeoMx WTA, CLAD, CD45, slide Clad 2_11.7.24


title: BIR_Discovery_35


title: PCHi-C_PA2_E11.5_Ezh2cKO_2BioRep

description:
Library name: Sample 18
PA2 , E11.5, Ezh2cKO, PCHiC, BioRep 2


title: Control, R23816

description: Library name: R23816

value: Control


title: BIR_Discovery_31


title: PCHi-C_Md_E11.5_Ezh2cKO_1BioRep

description:
Library name: Sample 15
Md , E11.5, Ezh2cKO, PCHiC, BioRep 1


title: Control, R23818

description: Library name: R23818


title: BIS_Discovery_29


title: Control, R18814

description: Library name: R18814


title: CLAD lung, cd31 segment, ROI C7E2

description:
Library name: DSP-1001660018221-A-C03
GeoMx WTA, CLAD, cd31, slide Clad 2_11.7.24

value: CLAD


title: BIS_Discovery_30


title: PCHi-C_FNP_E11.5_Ezh2cKO_2BioRep

description:
Library name: Sample 12
FNP , E11.5, Ezh2cKO, PCHiC, BioRep 2

source_name: FNP

value: FNP


title: PCHi-C_FNP_E11.5_Ezh2cKO_1BioRep

description:
Library name: Sample 11
FNP , E11.5, Ezh2cKO, PCHiC, BioRep 1


title: PCHi-C_Md_E11.5_Ezh2cKO_2BioRep

description:
Library name: Sample 16
Md , E11.5, Ezh2cKO, PCHiC, BioRep 2


title: CLAD lung, Full ROI segment, ROI C3R3

description:
Library name: DSP-1001660018221-A-C01
GeoMx WTA, CLAD, Full ROI, slide Clad 1_11.7.24

value: Full ROI


title: Control, R23814

description: Library name: R23814

value: DLPFC


title: PCHi-C_Mx_E11.5_Ezh2cKO_2BioRep

description:
Library name: Sample 14
Mx , E11.5, Ezh2cKO, PCHiC, BioRep 2

source_name: Mx

value: Mx


title: PCHi-C_Mx_E11.5_Ezh2cKO_1BioRep

description:
Library name: Sample 13
Mx , E11.5, Ezh2cKO, PCHiC, BioRep 1


title: CLAD lung, Full ROI segment, ROI C3R1

description:
Library name: DSP-1001660018221-A-B11
GeoMx WTA, CLAD, Full ROI, slide Clad 1_11.7.24


title: CLAD lung, Tumor segment, ROI C3P3

description:
Library name: DSP-1001660018221-A-B10
GeoMx WTA, CLAD, Tumor, slide Clad 1_11.7.24


title: BIS_Discovery_28


title: T21, R18809

description: Library name: R18809

value: F


title: CLAD lung, cd31 segment, ROI C7E1

description:
Library name: DSP-1001660018221-A-C02
GeoMx WTA, CLAD, cd31, slide Clad 2_11.7.24


title: Control, R18821

description: Library name: R18821


title: Control, R23813

description: Library name: R23813


title: CLAD lung, Full ROI segment, ROI C3R2

description:
Library name: DSP-1001660018221-A-B12
GeoMx WTA, CLAD, Full ROI, slide Clad 1_11.7.24


title: BIS_Discovery_27


title: BIR_Discovery_32


title: PCHi-C_PA2_E11.5_WT_2BioRep

description:
Library name: Sample 10
PA2 , E11.5, WT, PCHiC, BioRep 2

value: WT


title: BIS_Discovery_26


title: CLAD lung, cd45 segment, ROI C3L3

description:
Library name: DSP-1001660018221-A-B07
GeoMx WTA, CLAD, cd45, slide Clad 1_11.7.24

value: lung


title: Control, R18820

description: Library name: R18820


title: PCHi-C_PA2_E11.5_WT_1BioRep

description:
Library name: Sample 9
PA2 , E11.5, WT, PCHiC, BioRep 1

value: Cranial neural crest cells


title: PCHi-C_Md_E11.5_WT_1BioRep

description:
Library name: Sample 7
Md , E11.5, WT, PCHiC, BioRep 1


title: Control, R23811

description: Library name: R23811

value: M


title: Control, R23812

description: Library name: R23812

value: Caucasian


title: PCHi-C_Md_E11.5_WT_2BioRep

description:
Library name: Sample 8
Md , E11.5, WT, PCHiC, BioRep 2


title: BIR_Discovery_23


title: BIR_Discovery_25


title: Control, R23815

description: Library name: R23815


title: CLAD lung, Tumor segment, ROI C3P1

description:
Library name: DSP-1001660018221-A-B08
GeoMx WTA, CLAD, Tumor, slide Clad 1_11.7.24


title: BIS_Discovery_22

value: BIS


title: CLAD lung, cd45 segment, ROI C3L1

description:
Library name: DSP-1001660018221-A-B05
GeoMx WTA, CLAD, cd45, slide Clad 1_11.7.24


title: PCHi-C_Mx_E11.5_WT_2BioRep

description:
Library name: Sample 6
Mx , E11.5, WT, PCHiC, BioRep 2


title: CLAD lung, Tumor segment, ROI C3P2

description:
Library name: DSP-1001660018221-A-B09
GeoMx WTA, CLAD, Tumor, slide Clad 1_11.7.24


title: T21, R23810

description: Library name: R23810


title: CLAD lung, cd45 segment, ROI C3L2

description:
Library name: DSP-1001660018221-A-B06
GeoMx WTA, CLAD, cd45, slide Clad 1_11.7.24


title: T21, R18807

description: Library name: R18807


title: BIR_Discovery_24

value: Blood cells


title: Control, R18817

description: Library name: R18817


title: Control, R23808

description: Library name: R23808


title: Control, R23806

description: Library name: R23806


title: CLAD lung, CD31 segment, ROI C3E3

description:
Library name: DSP-1001660018221-A-B04
GeoMx WTA, CLAD, CD31, slide Clad 1_11.7.24


title: BIS_Discovery_21


title: BIS_Discovery_20


title: PCHi-C_FNP_E11.5_WT_2BioRep

description:
Library name: Sample 4
FNP , E11.5, WT, PCHiC, BioRep 2


title: PCHi-C_Progenitors_E8.5_WT_2BioRep

description:
Library name: Sample 2
NCCprogenitors , E8.5, WT, PCHiC, BioRep 2

source_name: NCCprogenitors

value: NCCprogenitors


title: CLAD lung, CD31 segment, ROI C3E2

description:
Library name: DSP-1001660018221-A-B03
GeoMx WTA, CLAD, CD31, slide Clad 1_11.7.24


title: BIR_Discovery_18

value: BIR


title: CLAD lung, Full ROI segment, ROI C1R2

description:
Library name: DSP-1001660018221-A-A12
GeoMx WTA, CLAD, Full ROI, slide CLAD 1_11.6.24


title: CLAD lung, Full ROI segment, ROI C1R3

description:
Library name: DSP-1001660018221-A-B01
GeoMx WTA, CLAD, Full ROI, slide CLAD 1_11.6.24


title: PCHi-C_FNP_E11.5_WT_1BioRep

description:
Library name: Sample 3
FNP , E11.5, WT, PCHiC, BioRep 1


title: HiC_PA2_E11.5_Hoxa2-PTE-36kb-del

description:
Library name: Sample 7
PA2, E11.5, Hoxa2-PTE-36kb-del, HiC


title: CLAD lung, cd45 segment, ROI C6L3

description:
Library name: DSP-1001660018221-A-E06
GeoMx WTA, CLAD, cd45, slide Clad 2_11.12.24


title: BIR_Discovery_16


title: T21, R18806

description: Library name: R18806


title: CLAD lung, CD31 segment, ROI C3E1

description:
Library name: DSP-1001660018221-A-B02
GeoMx WTA, CLAD, CD31, slide Clad 1_11.7.24


title: CLAD lung, Full ROI segment, ROI C1R1

description:
Library name: DSP-1001660018221-A-A11
GeoMx WTA, CLAD, Full ROI, slide CLAD 1_11.6.24


title: Control, R23807

description: Library name: R23807


title: BIR_Discovery_19


title: PCHi-C_Progenitors_E8.5_WT_1BioRep

description:
Library name: Sample 1
NCCprogenitors , E8.5, WT, PCHiC, BioRep 1


title: BIR_Discovery_15


title: HiC_Md_E11.5_Hoxa2-PTE-36kb-del

description:
Library name: Sample 6
Md, E11.5, Hoxa2-PTE-36kb-del, HiC

value: Md


title: PCHi-C_Mx_E11.5_WT_1BioRep

description:
Library name: Sample 5
Mx , E11.5, WT, PCHiC, BioRep 1


title: CLAD lung, Tumor segment, ROI C1P3

description:
Library name: DSP-1001660018221-A-A10
GeoMx WTA, CLAD, Tumor, slide CLAD 1_11.6.24

value: Tumor


title: BIR_Discovery_14


title: BIR_Discovery_13


title: CLAD lung, CD45 segment, ROI C1L3

description:
Library name: DSP-1001660018221-A-A07
GeoMx WTA, CLAD, CD45, slide CLAD 1_11.6.24

value: CLAD


title: BIR_Discovery_11


title: CLAD lung, Tumor segment, ROI C1P2

description:
Library name: DSP-1001660018221-A-A09
GeoMx WTA, CLAD, Tumor, slide CLAD 1_11.6.24


title: BIS_Discovery_10


title: Control, R23809

description: Library name: R23809

value: Control


title: T21, R18805

description: Library name: R18805


title: BIR_Discovery_12


title: Control, R23805

description: Library name: R23805


title: Hi-C_Md_E11.5_Ezh2cKO

description:
Library name: Sample 4
Md, E11.5, Ezh2cKO, HiC


title: Hi-C_PA2_E11.5_WT

description:
Library name: Sample 3
PA2, E11.5, WT, HiC


title: BIR_Discovery_17


title: Hi-C_PA2_E11.5_Ezh2cKO

description:
Library name: Sample 5
PA2, E11.5, Ezh2cKO, HiC


title: Hi-C_Md_E11.5_WT

description:
Library name: Sample 2
Md, E11.5, WT, HiC


title: T21, R18803

description: Library name: R18803


title: Hi-C_CNCC_E10.5_WT

description:
Library name: Sample 1
CNCC (FNP,Mx,Md) , E10.5, WT, HiC

source_name: FNP,Mx,Md

value: FNP,Mx,Md


title: CLAD lung, Tumor segment, ROI C1P1

description:
Library name: DSP-1001660018221-A-A08
GeoMx WTA, CLAD, Tumor, slide CLAD 1_11.6.24


title: CLAD lung, CD45 segment, ROI C1L2

description:
Library name: DSP-1001660018221-A-A06
GeoMx WTA, CLAD, CD45, slide CLAD 1_11.6.24


title: Control, R23803

description: Library name: R23803

value: DLPFC


title: T21, R18804

description: Library name: R18804


title: CLAD lung, CD45 segment, ROI C1L1

description:
Library name: DSP-1001660018221-A-A05
GeoMx WTA, CLAD, CD45, slide CLAD 1_11.6.24


title: BIR_Discovery_9


title: CLAD lung, CD31 segment, ROI C1E3

description:
Library name: DSP-1001660018221-A-A04
GeoMx WTA, CLAD, CD31, slide CLAD 1_11.6.24