title: RNA-seq of zea mays: T0h Leaves 3-NN

description:
Library name: zma_T0_leaves_r3
T0h Leaves 3-NN


title: Y2

status: Public on Dec 30 2025

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from normal distal colon mucosa within young adults

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on Clariom D Array(human, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: young adult aged 28 years

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Normal clinical colon mucosa tissue samples from different colorectal cancer patients were collected immediately after surgical resection prior to any other therapeutic intervention

extract_protocol: Total RNA was extracted from tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) and purified with a RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: All tissue samples were stored at -80 °C.

tag: gender

value: male

tag: tissue

value: distal colon mucosa


title: RNA-seq of zea mays: T48h Leaves 2-NR

type: SRA

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

country: USA

institute: Cold Spring Harbor Lab

description:
Library name: zma_T2d_leaves_r2
T48h Leaves 2-NR

library_source: transcriptomic

data_processing:
Adapter trimming and quality filtering were performed using Trimmomatic. Filtered reads were aligned to the Zea mays B73 v5 reference genome using STAR. Transcript assembly and quantification were performed using StringTie. Gene-level count matrices were generated for downstream differential expression. Differential expression analysis was conducted using DESeq2.
Raw reads were trimmed and filtered using Trimmomatic. Clean reads were aligned to the Sorghum bicolor BTx623 v3.1.1 reference genome using STAR. Transcript assembly and abundance estimation were performed using StringTie. Gene-level counts were exported for statistical analysis. Differential expression was performed using DESeq2.
Assembly: reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-62/plants/gff3/zea_mays/)
Supplementary files format and content: Expression_TPM_Leaves-maize.csv
Supplementary files format and content: Expression_TPM_Roots-maize.csv

organism: Zea mays

source_name: leaves

growth_protocol: Maize seeds (Zea mays inbred line B73) were germinated on moist rag dolls and maintained under controlled growth chamber conditions. At 7 days after germination (DAG), seedlings were transferred to hydroponic tanks containing full-strength Hoagland nutrient solution. Plants were grown for 12 days under nitrate-sufficient conditions before treatment. Growth conditions were maintained at ~28°C with a 16-hour light / 8-hour dark photoperiod.

extract_protocol:
Root and leaf tissues were immediately frozen in liquid nitrogen at harvest. Total RNA was extracted using a standard plant RNA isolation protocol based on phenol-chloroform or silica-column purification. RNA quality was assessed using an Agilent Bioanalyzer, and samples with high RNA integrity (RIN > 7) were used for library preparation. Each biological replicate consisted of pooled tissue from five plants.
RNA-seq libraries were constructed using the NEBNext RNA-seq Library Prep Kit following the manufacturer’s guidelines. mRNA was enriched using poly(A) selection, fragmented, and converted to cDNA. Libraries were indexed, PCR-amplified, and quality-checked before sequencing. Sequencing was performed on the Illumina NextSeq 2000 platform.

treatment_protocol: At the 5th leaf stage (15 DAG), plants were transferred to a nitrate-limiting hydroponic solution in which Ca(NO₃)₂ and Mg(NO₃)₂ were replaced with CaCl₂ and MgSO₄. Root and leaf tissues were collected at the following time points under nitrate limitation: 0 min, 30 min, 3 hours, and 24 hours. After 24 hours of nitrate deprivation, nitrate was reintroduced to the nutrient solution. Recovery tissues were harvested at: 24h + 30 min and 24h + 48 h.

tag: genotype

tag: treatment

value: nitrogen recovery

tag: time

value: leaves

tag: replicate


title: RNA-seq of zea mays: T0h Leaves 2-NN

description:
Library name: zma_T0_leaves_r2
T0h Leaves 2-NN

value: normal nitrogen


title: BBN963_4

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

description: Library name: BBN963_4

data_processing:
Paired-end reads were aligned to the mouse genome (mm39) using STAR (v2.7.9a).
RSEM (v1.3.3) was used to quantify read counts and transcripts per million (TPM) for genes annotated in the Ensembl database (v105).
Genes with a TPM ≥1 in at least one sample of a comparison were considered expressed and included in the downstream analyses. Differential expression analysis was computed using DESeq2 software (v1.38.3).
Assembly: mm39
Supplementary files format and content: csv-format text file includes raw counts and TPMs for each sample

organism: Mus musculus

source_name: Urinary bladder

growth_protocol: The BBN963, UPPL1541, and MB49 cell lines, were maintained in tissue culture-treated flasks or dishes using Dulbecco’s modified Eagle medium (DMEM, Corning), supplemented with 10% heat-inactivated fetal bovine serum (FBS, R&D Systems), 1% L-glutamine (Corning), and 1% penicillin-streptomycin (100 U/ml; Corning). All cells were incubated in a humidified environment at 37°C and 5% CO2.

extract_protocol:
RNA was collected using the RNeasy Plus Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality was assessed by a Bioanalyzer RNA Pico (Agilent); samples achieving a RIN ≥ 8.0 proceeded to sequencing.
Admera Health prepared RNA libraries using SMART-seq V4 with NExtera XT kit following manufacturer's protocols.

treatment_protocol: BBN963, UPPL1541, and MB49 cells were cultured in 5 separate tissue-culture flasks, each serving as a biological replicate, and allowed to expand for 1 week.

value: Urinary bladder

tag: cell line

tag: cell type

value: Urothelial cell

value: WT


title: BBN963_2

description: Library name: BBN963_2


title: O4

description: Gene expression data from normal distal colon mucosa within aged adults

source_name: old adult aged 79 years


title: Y3

source_name: young adult aged 36 years


title: UPPL1541_5

description: Library name: UPPL1541_5


title: UPPL1541_3

description: Library name: UPPL1541_3


title: UPPL1541_1

description: Library name: UPPL1541_1


title: BBN963_5

description: Library name: BBN963_5


title: RNA-seq of zea mays: T0h Leaves 1-NN

description:
Library name: zma_T0_leaves_r1
T0h Leaves 1-NN

value: normal nitrogen (NN)


title: BBN963_3

description: Library name: BBN963_3


title: BBN963_1

description: Library name: BBN963_1


title: RNA-seq of zea mays: T24h Leaves 3-ND

description:
Library name: zma_T1d_leaves_r3
T24h Leaves 3-ND

value: nitrogen deprivation


title: UPPL1541_4

description: Library name: UPPL1541_4


title: UPPL1541_2

description: Library name: UPPL1541_2


title: MB49_4

description: Library name: MB49_4

value: Bladder transitional cell carcinoma


title: MB49_5

description: Library name: MB49_5


title: Kuffer cells 5-HT treated, repeat 3

city: Hefei, Anhui

first: Guorong

last: Zhang

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

description: Library name: 5-HT-3

data_processing:
Raw RNA sequencing reads were aligned to the mouse genome (mm10) using hisat2 (v2.2.1). Gene expression levels were analyzed with featureCounts (v2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Kuffer cells

extract_protocol:
Total RNA was extracted using TRIzol (TIANGEN)
Berrygenomics processed the total RNA to construct mRNA libraries, which were then subjectedto standard illumina sequencing on the Novaseq 6,000 system

value: Kuffer cells

value: 5-HT treated


title: Kuffer cells 5-HT treated, repeat 2

description: Library name: 5-HT-2


title: MB49_3

description: Library name: MB49_3


title: MB49_1

description: Library name: MB49_1


title: Kuffer cells untreated, repeat 2

description: Library name: KO-2

value: untreated


title: Kuffer cells untreated, repeat 3

description: Library name: KO-3


title: cDC1, TC-1-iBimS medium, 6 h, rep 2

city: Leiden

first: Jannie

last: Borst

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

description:
Library name: Sample 9
BimS_cDC1_rep2

data_processing:
Seqpurge trimmed reads were aligned to the Mus musculus GRCm39 reference genome (annotation source: Ensembl v112) using STAR (v2.7.10a); key parameters: '--runRNGseed 12031 --quantMode GeneCounts --outSAMattributes NH HI NM MD AS --sjdbOverhang 53 --alignSJDBoverhangMin 1 -sjdbGTFfile ${gtf}', achieving an average mapping rate of 93%. Gene/transcript quantification was performed using gensum (version: 0.2.1).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes normalized counts for each Sample

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen).
Libraries were prepared using the xGen™ RNA Library Prep (Integrated DNA Technologies) with an "on-bead" poly-A enrichment using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB).

value: Spleen

value: type 1 conventional dendritic cell


title: cDC1, TC-1-iRIPK3 medium, 6 h, rep 1

description:
Library name: Sample 13
RIPK3_cDC1_rep1


title: cDC1, TC-1-iBimS medium, 6 h, rep 3

description:
Library name: Sample 11
BimS_cDC1_rep3


title: Kuffer cells 5-HT treated, repeat 1

description: Library name: 5-HT-1


title: cDC2, TC-1-iRIPK3 medium, 6 h, rep 2

description:
Library name: Sample 16
RIPK3_cDC2_rep2

value: type 2 conventional dendritic cell


title: cDC1, TC-1-iBimS medium, 6 h, rep 1

description:
Library name: Sample 7
BimS_cDC1_rep1


title: Kuffer cells untreated, repeat 1

description: Library name: KO-1


title: cDC2, TC-1-iRIPK3 medium, 6 h, rep 1

description:
Library name: Sample 14
RIPK3_cDC2_rep1


title: cDC2, TC-1 WT medium, 6 h, rep 3

description:
Library name: Sample 6
WT_cDC2_rep3


title: cDC1, TC-1-iRIPK3 medium, 6 h, rep 3

description:
Library name: Sample 17
RIPK3_cDC1_rep3


title: cDC2, TC-1-iBimS medium, 6 h, rep 2

description:
Library name: Sample 10
BimS_cDC2_rep2


title: cDC1, TC-1-iRIPK3 medium, 6 h, rep 2

description:
Library name: Sample 15
RIPK3_cDC1_rep2


title: cDC1, TC-1 WT medium, 6 h, rep 3

description:
Library name: Sample 5
WT_cDC1_rep3


title: cDC2, TC-1-iBimS medium, 6 h, rep 1

description:
Library name: Sample 8
BimS_cDC2_rep1


title: cDC2, TC-1 WT medium, 6 h, rep 2

description:
Library name: Sample 4
WT_cDC2_rep2


title: cDC1, TC-1 WT medium, 6 h, rep 2

description:
Library name: Sample 3
WT_cDC1_rep2


title: cDC1, TC-1 WT medium, 6 h, rep 1

description:
Library name: Sample 1
WT_cDC1_rep1


title: cDC2, TC-1 WT medium, 6 h, rep 1

description:
Library name: Sample 2
WT_cDC2_rep1


title: MB49_2

description: Library name: MB49_2


title: Colon_DSS_WT

city: Chong qing

last: Zhao

address: 30 Main Street, Gao Tanyan

institute: Army Medical University

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw data was processed using the Cell Ranger analysis software from 10x Genomics to perform data filtering. Eventually, the gene expression matrices of each cell were obtained. Subsequently, Seurat was employed for further cell filtering, standardization, classification of cell subgroups, analysis of differentially expressed genes in each subgroup, and screening of marker genes.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
The colon tissues were longitudinally dissected, and cut into 0.5 cm pieces in ice-cold HBSS (w/o) . These tissue pieces were then transferred to 20 mL of pre-digestion solution (5% FBS + HBSS (Ca2+ & Mg2+ free) + 1 mM DTT + 5 mM EDTA + 10 mM HEPES) and shaken horizontally at 37°C for 20 minutes to separate crypts. The digested tissue pieces were collected on a 100 μm MACS filter, fresh pre-digestion solution was added, and the process was repeated twice to further remove intestinal epithelial cells. The tissue pieces were then rinsed with Hanks buffer,and the rinse was followed by digestion in lamina propria digestion solution (RPMI1640, 0.05% type II collagenase, 5% FBS, and DNAase 100 μg/mL) at 37°C for 30 minutes, with the process repeated twice. The digestion solution was filtered through a 70 μm cell filter to obtain the supernatant, which was then centrifuged at 500 g for 8 minutes to obtain cell clumps. Non-cellular debris was removed by Percoll gradient centrifugation, and the single-cell suspension was obtained by filtering through a 40 μm cell filter.
cDNA was enzymatically segmented into approximately 200-300 bp fragments. Following this segmentation, standard library preparation steps were undertaken, including the attachment of sequencing adapters and primers. A final round of PCR amplification was conducted to finalize the DNA library.Library construction and 10× single-cell sequencing were performed according to the standard protocol provided by LC-Bio Technology (Hangzhou, China). Briefly, single cells were captured using the 10× Genomics Chromium Single-Cell 3’ kit (V3) on a 10× Chromium chip, and cDNA amplification and library construction were performed. The libraries were then sequenced on an Illumina NovaSeq6000 sequencing system by LC-Bio Technology (Hangzhou, China).

value: colon

value: Neutrophils

value: DSS


title: WT-LPS-03

description: Library name: Sample9

data_processing:
RNA-seq
The libraries were sequenced on an Illumina Novaseq 6000 platform. Differential gene expression analysis was performed using DESeq2, with fold change > 2 or < 0.5 and p < 0.05 set as the threshold for significantly differentially expressed genes
Based on the hypergeometric distribution, GO and KEGG pathway enrichment analyses of DEGs were conducted to screen for significantly enriched terms
Gene set enrichment analysis (GSEA) was performed using GSEA_4.2.1 software and gene sets were obtained from the Molecular Signatures Database (MSigDB).
Assembly: GRCm39
Supplementary files format and content: text file include FPKM for all samples
Supplementary files format and content: text file include Counts for all samples

source_name: bone marrow

growth_protocol: Bone marrow-derived neutrophils were isolated with the Easy Sep Mouse neutrophil enrichment kit (19762, STEM Cell) according to the manual protocols.

extract_protocol:
Gently aspirate the cell culture medium and add 1 ml Trizol reagent (15596026, Invitrogen).Total RNA was extracted from neutrophil samples using Trizol reagent. The integrity of the obtained RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent, CA, USA).
libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) following the manufacturer's instructions.

treatment_protocol: The neutrophils were added to IMDM medium and seeded in a six-well plate. The neutrophils were stimulated with lipopolysaccharide at a final concentration of 1 μg/ml for 4 hours. 4-OI was dissolved in DMSO  at a final concentration of 125 μM and added to the cells for an additional 2 hours of treatment.

value: bone marrow

value: Bone marrow-derived neutrophils

value: LPS

tag: batch


title: WT-LPS-02

description: Library name: Sample8


title: Colon_NC_WT

description:
Library name: Sample 2
10x Genomics

value: control


title: cDC2, TC-1-iBimS medium, 6 h, rep 3

description:
Library name: Sample 12
BimS_cDC2_rep3


title: WT-Con-02

description: Library name: Sample5

value: WT

value: DMSO


title: WT-Con-03

description: Library name: Sample6


title: WT-Con-01

description: Library name: Sample4


title: WT-4OI-01

description: Library name: Sample1

value: 4-octyl itaconate and LPS


title: heart, chow diet, 12weeks, rep2

city: Taiyuan

first: Xingpeng

last: Bu

address: No. 85, Jiefang South Road

institute: Shanxi Medical University

description:
Library name: Sample 2
Con_02

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample csv files include FPKM
Supplementary files format and content: values for each Sample

source_name: heart

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

value: heart


title: WT-4OI-03

description: Library name: Sample3


title: heart, chow diet, 12weeks, rep1

description:
Library name: Sample 1
Con_01


title: BM monocytes CD300e-/- 4

city: Padova

first: Gaia

last: Codolo

state: Padova

address: via U. Bassi 58/b

department: Department of Biology

country: Italy

institute: University of Padova

description: Library name: BIODIVERSAK10

data_processing:
Reads from RNA-seq data were mapped and quantified with RSEM software (v1.3.1, genome sequence GRCm39, annotations from Ensembl version 109.149, [39]). Transcripts with less than 10 counts in at least 60% of samples per class were filtered out. Differentially Expressed Genes (DEGs) were computed using edgeR (version 3.42.4, q-value <0.05; [39,40]). Gene Ontology pathway enrichment analysis of differentially expressed genes was performed with the R package clusterProfiler (version 4.8.3).
Assembly: GRCm39
Supplementary files format and content: csv files include raw counts for each Sample

extract_protocol:
Total RNA was extracted with TRIzol reagent according to the manufacturer’s protocol. RNA was quantified using a NanoDrop 1000 spectrophotometer. RNA extracted from BM monocytes was analyzed with 2100 Bioanalyzer to assess RNA quality and integrity.
RNA libraries were constructed using Stranded mRNA Prep kit.

treatment_protocol: Bone marrow (BM) cells were obtained by flushing femurs and tibias with RPMI medium supplemented with 10% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were filtered through a 70 μm filter and red blood cells were lysed. Monocytes were purified from bone marrow cells using Monocyte Isolation Kit from mouse BM.

value: primary monocytes


title: heart, high-fat diet and L-NAME, 12weeks, rep2

description:
Library name: Sample 5
HFpEF_02


title: heart, high-fat diet and L-NAME, 12weeks, rep1

description:
Library name: Sample 4
HFpEF_01


title: wildtype biol rep 1

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
Library name: 21163X2
10X Genomics

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1)
Assembly: mm10-2020-A
Supplementary files format and content: brainstem_counts_matrix.csv
Supplementary files format and content: brainstem_metadata.csv

molecule: nuclear RNA

source_name: Brain-brainstem

growth_protocol: Dravet mice were generated by breeding a Scn1a floxed male with a Sox2-Cre female. About ~25% of the litter will be mice with Dravet Syndrome (Scn1aA1783V/WT). Wildtype (WT) mice that have intact, functional copies of the SCN1A gene utilized for the experiment were obtained from littermates. Both Dravet and WT mice are on C57Bl6 background.

extract_protocol:
Dissected mouse brainstem was flash frozen in LN2 and preserved at -80C until processing. The specimens were gently thawed in 2 ml of ice-cold phosphate-buffered saline (PBS, devoid of Ca2+ and Mg2+). This solution was supplemented with various compounds to preserve the quality of the sample: 0.54 μM Nectostatin (Inc. #J65341, ThermoFisher Scientific Chemicals, Waltham, MA), 1 μM HPN-07 (SML2163, Sigma-Aldrich), 0.32 μM sodium hydroxybutyrate (A1161314, ThermoFisher Scientific Chemicals), 78 nM Q-VD-Oph (SML0063, Sigma-Aldrich), and 0.2 U/ml of Ribolock RNase inhibitor (EO0381, Life Technologies Corporation, Carlsbad, CA). The tissue, held over dry ice in a 60-mm Petri dish, was methodically minced into fragments smaller than 2 mm using a razor blade. Subsequently, this tissue was transitioned to a 2 ml Dounce homogenizer containing 1.5 ml of nuclei extraction buffer (130-128-024, Miltenyi Biotec, Bergisch Gladbach, Germany) along with 0.2 U/ml Ribolock RNase inhibitor.  Samples were then centrifuged at 600×g for 5 min, resuspended in 400 μL of PBS enriched with 2% BSA, passed through a 70-μm FLOWMI for clarification, and strained via a 40-μm FLOWMI. Specimens were then entrusted to the Hunstman Cancer Institute High Throughput Genomics Core for 10X Genomics library construction and sequencing.
snRNA-seq libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 with UDI, Next GEM protocol, NovaSeq S4 Reagent Kit v1.5_150x150 bp Sequencing (2500 M read-pairs/lane)

treatment_protocol: No treatments were performed. Scn1a knock-in also termed as Dravet Syndrome (DS, Scn1aA1783V/WT) mice are haploinsufficient for the SCN1A gene which encodes for the voltage-gated sodium channel subunit alpha. They carry a knock-in missense mution in the SCN1A gene that results in loss-of-function of the sodium channel. These mice exhibit hyperthermia-induced and spontaneous seizures, developmental delay, cardio-respiratory issues, and high mortality.

value: Brain-brainstem

tag: age

value: post-natal day 41

tag: Sex

value: Female

value: wildtype


title: heart, high-fat diet and L-NAME, 12weeks, rep3

description:
Library name: Sample 6
HFpEF_03


title: BM monocytes CD300e+/+ 3

description: Library name: BIODIVERSAK04


title: BM monocytes CD300e-/- 3

description: Library name: BIODIVERSAK09


title: CD11b CD300e+/+, CD11b CD300e-/-

description:
Library name: SampleTag01_mm
BD Rhapsody� Single-Cell Analysis System

data_processing:
Raw data was aligned using the BD Rhapsody Sequence Analysis CWL pipeline v2.2.1 using the RhapRef_Mouse_WTA_2023-02 as genome reference. Then, the h5mu to Seurat pipeline v2.2.1 was used for conversion (https://openpipelines.bio/). Data processing and normalization has been performed through the package Seurat (v5.3.0). The single-cell expression matrix was filtered (nFeature_RNA > 700 & nFeature_RNA < 5500, percent.mt < 25% and nCount_RNA > 1000 & nCount_RNA < 100000). PCA was computed using the 2000 highly variable features obtained by the FindVariableFeatures function. Graph-based unsupervised clustering and UMAP were performed by selecting the first top 10 PCs.
Assembly: GRCm39
Supplementary files format and content: .rds file containing Seurat object

source_name: Colon adenoma

extract_protocol:
Colonic adenomas and subcutaneous tumors were isolated and cut into small pieces of 2-4 mm in Petri dishes. The minced tissues were transferred into GentleMACS Tubes containing DMEM with 1 mg/mL collagenase IV (Sigma-Aldrich) and 0.5 mg/mL Dnase I. GentleMACS Tubes were attached onto a GentleMACS Octo Dissociator and tumors were maintained for 40 minutes at 37°C under continuous rotation. The resulting cell suspension was filtered through a 70 µm strainer and incubated with TruStain FcX™ PLUS. CD45+ cells from three CD300e+/+ and three CD300e-/- mice were isolated and independently labeled using Single Cell Labeling with the BD Single-Cell Multiplexing kit (BD Biosciences, #633793); next, the six samples were pooled prior FACS-sorting. CD11b+ myeloid cells were FACS-sorted as L/D-CD3e-CD19-CD11b+ cells.
CD11b+ myeloid cells were processed using Single Cell Capture and cDNA Synthesis with the BD Rhapsody Express Single-Cell Analysis System. The resulting cDNA Libraries were prepared using mRNA Whole Transcriptome Analysis (WTA) and Sample Tag library preparation protocol.

value: Colon adenoma

value: primary CD11b


title: BM monocytes CD300e+/+ 2

description: Library name: BIODIVERSAK01


title: BM monocytes CD300e+/+ 1

description: Library name: BIODIVERSAJ99


title: WT-LPS-01

description: Library name: Sample7


title: WT-4OI-02

description: Library name: Sample2


title: BM monocytes CD300e+/+ 4

description: Library name: BIODIVERSAK05


title: Mouse Lung, dNS1-based virus and STFK subunit mixed immunization, replication 2, V(D)J sequencing for BCR

city: Xiamen

first: junyu

last: chen

state: Fujian

address: No.4221, South Xiang'an Road

department: School of Public Health

institute: Xiamen University

description:
Library name: dNS1-STFK-BCR_2
10x Genomics

data_processing:
10X genomics single cell gene expression analysis pipeline -- Raw sequencing data quality control and mapping CellRanger's pipelines(Version 7.1.0) analyze sequencing data produced from Chromium Single Cell Gene Expression. Cell Ranger's pipelines(Version 6.0.1) analyze sequencing data produced from Chromium Single Cell VDJ.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Excise the lungs into cold PBS. Mince tissue finely, then digest in a pre-warmed enzymatic cocktail at 37°C for 20-45 min with gentle agitation. Quench digestion with cold FBS. Mechanically dissociate further by pipetting and pass the suspension sequentially through 70µm and 40µm cell strainers. Centrifuge, resuspend in ACK lysis buffer for 1-2 min on ice to lyse red blood cells, then immediately quench and centrifuge. Wash the pellet twice in cold PBS buffer . Resuspend in buffer containing RNase inhibitor. Assess cell count and viability (>85%), adjust concentration for the scRNA-seq platform, and keep on ice for immediate processing.
1. Cell Counting & Quality Control: The prepared cell suspension was counted using TC20 Automated Cell Counter (Bio-Rad, USA) to obtain the information of cell size, concentration and viability, and to determine the sample loading volume. 2. GEM Generation and cDNA Amplification: Within the Chromium instrument, barcoded Single Cell 5’ Gel Beads are mixed with cells or nuclei, enzymes, and partitioning oil to form tens of thousands of single cell emulsion droplets called “GEMs” (Gel Bead-in-emulsion). Immediately following GEM generation, the Gel Bead is dissolved and any co-partitioned cell is lysed. Oligonucleotides containing (i) an Illumina Read 1 (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt unique molecular identifier (UMI), and (iv) 13 nt template switch oligo (TSO) are released and mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents and poly(dT) RT primers. Incubation of the GEMs produces 10x Barcoded, full-length cDNA from poly-adenylated mRNA. Then, the first-strand cDNA of 10X Barcoded was purified by silane magnetic beads, and sufficient mass was obtained by PCR amplification. The PCR products were clean up by SPRI beads, and double-stranded cDNA was obtained. For VDJ sequencing A small amount of dsDNA was selected for nest amplification using BCR specific primers. Then quantify and qualify the PCR products by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), so as to confirm the input amount of template and the final PCR cycle number for library construction. 3.Library Construction : 50ng PCR products was then treated with Fragmentation Mix to fragment cDNA, End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Each sample was then amplified by PCR for 9 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform Illumina bridge PCR. And P7 primers are a mixture of four primers, each carrying a eight-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: Lung


title: Mouse Lung, dNS1-based virus and STFK subunit mixed immunization, replication 1, V(D)J sequencing for BCR

description:
Library name: dNS1-STFK-BCR_1
10x Genomics


title: Mouse Lung, STFK subunit vaccine immunization, replication 1, V(D)J sequencing for BCR

description:
Library name: STFK-BCR_1
10x Genomics

value: STFK subunit vaccine immunization


title: Mouse Lung, dNS1-based live-attenuated virus immunization, replication 2, V(D)J sequencing for BCR

description:
Library name: dNS1-BCR_2
10x Genomics


title: Scn1a knock-in biol rep 1

description:
Library name: 21163X4
10X Genomics

value: Scn1a knock-in


title: Mouse Lung, dNS1-based live-attenuated virus immunization, replication 1, V(D)J sequencing for BCR

description:
Library name: dNS1-BCR_1
10x Genomics


title: heart, chow diet, 12weeks, rep3

description:
Library name: Sample 3
Con_03


title: Mouse Lung, dNS1-based live-attenuated virus immunization, replication 3, V(D)J sequencing for BCR

description:
Library name: dNS1-BCR_3
10x Genomics

value: dNS2-based live-attenuated virus immunization


title: Mouse Lung, STFK subunit vaccine immunization, replication 2, V(D)J sequencing for BCR

description:
Library name: STFK-BCR_2
10x Genomics


title: BM monocytes CD300e-/- 2

description: Library name: BIODIVERSAK08

value: bone marrow


title: BM monocytes CD300e-/- 1

description: Library name: BIODIVERSAK06


title: Mouse Lung, Negtive Control,V(D)J sequencing for BCR

description:
Library name: NC-BCR
10x Genomics

value: Negtive


title: Mouse Lung, dNS1-based virus and STFK subunit mixed immunization, replication 3

description:
Library name: dNS1-STFK_3
10x Genomics


title: Mouse Lung, dNS1-based virus and STFK subunit mixed immunization, replication 1

description:
Library name: dNS1-STFK_1
10x Genomics


title: Mouse Lung, STFK subunit vaccine immunization, replication 3

description:
Library name: STFK_3
10x Genomics


title: Mouse Lung, STFK subunit vaccine immunization, replication 2

description:
Library name: STFK_2
10x Genomics


title: Mouse Lung, STFK subunit vaccine immunization, replication 1

description:
Library name: STFK_1
10x Genomics


title: Mouse Lung, dNS1-based live-attenuated virus immunization, replication 3

description:
Library name: dNS1_3
10x Genomics


city: Cambridge

first: Amy

middle: K.

last: Barczak

state: MA

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

description:
Library name: 12 weeks Mtb infected + 8 weeks RIPE treated- biol rep 2
Lungs of Mtb infected - RIPE treated mice

data_processing:
Sequencing reads were aligned to mm10 reference genome using STAR/Salmon (v2.5)
Raw gene counts were generated from STAR/Salmon output
Assembly: GRCm38 (mm10)
Supplementary files format and content: TPM_Mouse_fibrosis_Abx.csv

growth_protocol: The Erdman strain of Mycobaterium tuberculosis was grown to mid-log phase in 7H9 media, then washed and used for aerosol infections of mice.

extract_protocol:
RNA was then isolated using Trizol (Invitrogen) according to the manufacturer’s protocols.
Libraries were prepared using Qiagen Fast Select rRNA removal reagents followed by Kapa RNA Hyper Prep reagent kits from 200ng of purified total RNA according to manufacturers' protocols.

treatment_protocol: C3HeB/FeJ mice were infected with Mycobactertium tuberculosis Erdman via low dose aerosol. After 12 weeks post infection, the mice were treated with either carrier (water) or RIPE regiment for 2, 4 and 8 weeks respectively. Thereafter, mouse lungs were isolated were soaked in RNAlater and frozen at -80 until the completion of the experiment.

value: C3HeB/FeJ mouse - Mtb infected + RIPE treated


title: Mouse Lung, dNS1-based live-attenuated virus immunization, replication 2

description:
Library name: dNS1_2
10x Genomics


description:
Library name: 12 weeks Mtb infected + 8 weeks carrier treated- biol rep 2
Lungs of Mtb infected - carrier treated mice

value: C3HeB/FeJ mouse - Mtb infected + carrier treated


description:
Library name: 12 weeks Mtb infected + 8 weeks RIPE treated- biol rep 1
Lungs of Mtb infected - RIPE treated mice


description:
Library name: 12 weeks Mtb infected + 8 weeks RIPE treated- biol rep 3
Lungs of Mtb infected - RIPE treated mice


title: Mouse Lung, Negtive Control

description:
Library name: NC
10x Genomics


title: Mouse Lung, STFK subunit vaccine immunization, replication 3, V(D)J sequencing for BCR

description:
Library name: STFK-BCR_3
10x Genomics


description:
Library name: 12 weeks Mtb infected + 8 weeks carrier treated- biol rep 3
Lungs of Mtb infected - carrier treated mice


description:
Library name: 12 weeks Mtb infected + 4 weeks carrier treated- biol rep 1
Lungs of Mtb infected - carrier treated mice


title: Mouse Lung, dNS1-based virus and STFK subunit mixed immunization, replication 2

description:
Library name: dNS1-STFK_2
10x Genomics


description:
Library name: 12 weeks Mtb infected + 8 weeks carrier treated- biol rep 1
Lungs of Mtb infected - carrier treated mice


description:
Library name: 12 weeks Mtb infected + 2 weeks RIPE treated- biol rep 2
Lungs of Mtb infected - RIPE treated mice


description:
Library name: 12 weeks Mtb infected + 4 weeks carrier treated- biol rep 2
Lungs of Mtb infected - carrier treated mice


description:
Library name: 12 weeks Mtb infected + 2 weeks RIPE treated- biol rep 3
Lungs of Mtb infected - RIPE treated mice


description:
Library name: 12 weeks Mtb infected + 4 weeks carrier treated- biol rep 3
Lungs of Mtb infected - carrier treated mice


description:
Library name: 12 weeks Mtb infected + 4 weeks RIPE treated- biol rep 1
Lungs of Mtb infected - RIPE treated mice


title: Uninfected - biol rep 2

description:
Library name: Uninfected - biol rep 2
Lungs of uninfected mice

value: C3HeB/FeJ mouse - uninfected


description:
Library name: 12 weeks Mtb infected + 2 weeks carrier treated- biol rep 1
Lungs of Mtb infected - carrier treated mice


title: Mouse Lung, dNS1-based live-attenuated virus immunization, replication 1

description:
Library name: dNS1_1
10x Genomics


description:
Library name: 12 weeks Mtb infected + 2 weeks RIPE treated- biol rep 1
Lungs of Mtb infected - RIPE treated mice


title: Uninfected - biol rep 3

description:
Library name: Uninfected - biol rep 3
Lungs of uninfected mice


description:
Library name: 12 weeks Mtb infected + 2 weeks carrier treated- biol rep 2
Lungs of Mtb infected - carrier treated mice


title: Uninfected - biol rep 1

description:
Library name: Uninfected - biol rep 1
Lungs of uninfected mice


description:
Library name: 12 weeks Mtb infected + 4 weeks RIPE treated- biol rep 2
Lungs of Mtb infected - RIPE treated mice


description:
Library name: 12 weeks Mtb infected + 2 weeks carrier treated- biol rep 3
Lungs of Mtb infected - carrier treated mice


title: ko_CD3_28_6h_16

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

description:
Library name: Sample8
Coloum name in raw_counts_All_Samples.txt

data_processing:
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR and assigned count estimates to genes.
Variance stabilizing transformation and differential gene expression analysis were performed in succession on the filtered genes using R packages DESeq2 and Limma, respectively.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was isolated using the  RNA isolation kit from Qiagen (#74134, Valencia, CA, USA). Total RNA was used for the construction of sequencing libraries.
A Kapa Biosystems (Wilmington, MA, USA) KAPA Hyper mRNA-Seq kit for whole transcriptome libraries was used to primarily target all polyA RNA following manufacturer's protocols.

treatment_protocol: Purified CD4 T cells were stimulated with plate bound anti-CD3/28 antibodies in 10% FBS containing RPMI for 6h.

value: Spleen

value: CD4 T cells

value: CBX7 KO


title: ko_CD3_28_6h_13

description:
Library name: Sample5
Coloum name in raw_counts_All_Samples.txt


title: wt_CD3_28_6h_8

description:
Library name: Sample4
Coloum name in raw_counts_All_Samples.txt

value: WT


title: wt_CD3_28_6h_7

description:
Library name: Sample3
Coloum name in raw_counts_All_Samples.txt


title: wt_CD3_28_6h_5

description:
Library name: Sample1
Coloum name in raw_counts_All_Samples.txt


title: wt_CD3_28_6h_6

description:
Library name: Sample2
Coloum name in raw_counts_All_Samples.txt


title: H3K27me3_ESCs

city: Hangzhou

first: Zheting

state: Zhejiang

address: Dunyu load

department: school of life science

institute: Westlake University

description: Library name: H3K27me3_ESCs

library_source: genomic

data_processing:
The raw reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5). The alignment results were further filtered by removing the low mapping quality records (MAPQ<30), the read pairs from mitochondrial DNA, and the duplicated reads from PCR using Picard. The 5bp resolution histone modification and chromatin accessibility signal are saved as bigwig files generated from the filtered BAM files using the bamCoverage command of deeptools (version 3.3.2) , and the values were normalized by the RPKM method.
Assembly: mm10
Supplementary files format and content: .bw, binary files that store normalized histone modification signals from CUT&Tag experiments
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: mESC

extract_protocol:
DNA was harvested using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901), 100000 cells per sample was used for sequencing libraries construction
CUT&Tag library construction was performed using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202). In brief, around 10000 living cells per sample were obtained and mixed with activated Concanavalin A beads, followed by sequentially incubated with primary and secondary antibodies. The beads were then washed and resuspended in pA(G)-Tn5 buffer supplemented with 10 mM MgCl2 for DNA tagmentation. Next, DNA fragments were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and PCR amplified. After purified by VAHTS DNA Clean Beads (Vazyme, N411), libraries were subjected to Illumina Novaseq instruments for sequencing. Antibodies against Nanog (Abcam, ab214549, 1:50), H3K4me (Abcam, ab313500, 1:50), H3K27ac (Abcam, ab4729, 1:50), flag (Sigma, F1804, 1:50), and Smarca4 (Cell Signaling Technology, 52251, 1:50) were used in this study.

value: mESC

value: 2iL treated


title: H3K9me3_ESCs

description: Library name: H3K9me3_ESCs


title: H3K27ac_ESCs

description: Library name: H3K27ac_ESCs


title: CTCF_ESCs

description: Library name: CTCF_ESCs


title: H3K4me3_ESCs

description: Library name: H3K4me3_ESCs


title: H3K9me3_ciTotiSCs

description: Library name: H3K9me3_ciTotiSCs

value: TAW treated


title: H3K27ac_ciTotiSCs

description: Library name: H3K27ac_ciTotiSCs


title: H3K27me3_ciTotiSCs

description: Library name: H3K27me3_ciTotiSCs


title: H3K9me3_TBLCs

description: Library name: H3K9me3_TBLCs

value: SLP treated


title: H3K27me3_TBLCs

description: Library name: H3K27me3_TBLCs


title: H3K4me3_ciTotiSCs

description: Library name: H3K4me3_ciTotiSCs


title: H3K4me3_TBLCs

description: Library name: H3K4me3_TBLCs


title: CTCF_TBLCs

description: Library name: CTCF_TBLCs


title: H3K27ac_TBLCs

description: Library name: H3K27ac_TBLCs


title: ko_CD3_28_6h_14

description:
Library name: Sample6
Coloum name in raw_counts_All_Samples.txt


title: ESCs_RNAseq_rep2

description: Library name: ESCs_RNAseq_2

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4) and then mapped to the mm10 reference genome with HISAT2 (v2.2.1), and the count table of coding genes was generated by featureCounts (version 2.0.6)
Assembly: mm10
Supplementary files format and content: featureCounts.txt, a data table containing the read counts of the coding genes in all samples

source_name: ESCs

extract_protocol:
RNA was harvested using FreeZol reagent (Vazyme),1 µg of RNA was used for sequencing libraries construction
Liarbries were constructed by VAHTS mRNA-seq v3 Library Prep Kit for Illumina (NR611, Vazyme)

value: ESCs


title: ko_CD3_28_6h_15

description:
Library name: Sample7
Coloum name in raw_counts_All_Samples.txt


title: ciTotiSCs_RNAseq_rep2

description: Library name: ciTotiSCs_RNAseq_2


title: TBLCs_RNAseq_rep2

description: Library name: TBLCs_RNAseq_2


title: TBLCs_RNAseq_rep1

description: Library name: TBLCs_RNAseq_1


title: ciTotiSCs, rep1

description: Library name: ciTotiSC-1

data_processing:
Pair-ended Hi-C reads were trimmed by Trim Galore with default parameter and aligned to the mm10 mouse genome by bwa-mem (version 0.7.17) with parameters -SP5M. The mapped reads are secondly parsed into the pair format and sorted using pairtools (version 1.0.3). PCR duplication reads and multi-mapped reads were further removed. The multi-resolution raw contact Hi-C matrices were generated by the cooler package  (version 0.7.1). The cool format matrix files were then normalized and transformed into .hic format using juicer_tools (version 1.22.01).
Assembly: mm10
Supplementary files format and content: .hic,binary files that store chromatin interaction data from Hi-C experiments.

extract_protocol:
mouse embryonic stem cells, including wild type, Sall4-KO, and SiTotiSCs of Sall4-KO, were crosslinked with 2% formaldehyde (Sigma, 47608) for 10 min at room temperature, followed with 2 mM ethylene glycol-bis (Thermo, 21565) for 45 min at room temperature twice. Each sample had two replicate libraries. For each individual library, 50,000 crosslinked cells were lysed for 1 h on ice in lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and 1× protease inhibitor cocktail). Then, the supernatant was removed and cell pellets were resuspended in 0.01% SDS to incubate for 25 min at room temperature, then quenched with 3% Triton X-100.
The chromatin was digested with AluI (NEB, R0137L) and HpyCH4V (NEB, R0620L) at 37 °C overnight. A-tailing of the digestion ends was achieved by dATP (NEB, N0440S), Klenow Large fragment (3'→5' exo-) (NEB, M0212L), and BSA (NEB, B9000S) for 1 h at 37 °C. The reaction was deactivated by incubating for 20 min at 65 °C. Proximity fragments were ligated at 16 °C overnight by adding Quick ligation buffer (NEB, B6058S), T4 DNA ligase (NEB, M0202L), bridge linker (Forward strand: 5'-/5Phos/TAGGCGCTGG/iBIOdT/TGCGTTGT-3', reverse strand: 5'-/5Phos/CAACGCAACCAGCGCCTAT-3'), and ddH2O. The supernatant was discarded, then pellets were resuspended in proteinase K (Thermo, AM2548) and SDS for reverse-crosslinking by shaking for 2 h at 65 °C. The DNAs were extracted using DNA Clean & Concentrator-5 (Zymo, 4013), then sonicated so that all fragments were below 500 bp. DNA products were purified using 1.6× SPRIselect beads (Beckman Coulter, B23318) and eluted with 50 μL Buffer EB (Qiagen, 19086). 50 μL previously blocked Dynabeads M-280 Streptavidin (Invitrogen, 11206D) were added to the elution, and the mixture was incubated for 45 min at room temperature. Beads were washed and resuspended with 50 μL Buffer EB. Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L). Briefly, the fragments enriched on M-280 beads went through end repair, dA-tailing, adaptor ligation, then amplification with 8 cycles using VAHTS Multiplex Oligos set 4 for Illumina (Vazyme, N321). The supernatant of PCR products was transferred with the help of magnetic rack, and purified with 1× SPRIselect beads. The final libraries were sequenced on a BGI T7 platform with 150 bp paired-end reads (PE150).


title: ciTotiSCs, rep2

description: Library name: ciTotiSC-2


title: ESCs, rep1

description: Library name: ESC-1


title: ESCs, rep2

description: Library name: ESC-2


title: TBLCs, rep1

description: Library name: TBLC-1


title: CTCF_ciTotiSCs

description: Library name: CTCF_ciTotiSCs


title: ESCs_ATAC

description: Library name: ESCs_ATAC

data_processing:
The raw reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5). The alignment results were further filtered by removing the low mapping quality records (MAPQ<30), the read pairs from mitochondrial DNA, and the duplicated reads from PCR using Picard. The 5bp resolution histone modification and chromatin accessibility signal are saved as bigwig files generated from the filtered BAM files using the bamCoverage command of deeptools (version 3.3.2) , and the values were normalized by the RPKM method.
Assembly: mm10
Supplementary files format and content: .bw, binary files that store normalized chromatin accessibility signals from ATAC-seq experiments

extract_protocol:
50000 cells per sample was used for sequencing libraries construction
ATAC library construction was performed using Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).


title: ciTotiSCs_ATAC

description: Library name: ciTotiSCs_ATAC


title: TBLCs, rep2

description: Library name: TBLC-2


title: TBLCs_ATAC

description: Library name: TBLCs_ATAC


title: M3

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

description: Library name: Sample 6

data_processing:
Base Calling and Demultiplexing:Raw sequencing data (BCL files) were converted to FASTQ format using Illumina's bcl2fastq v2.20 (Illumina Inc.).
Raw Data Quality Control:FastQC v0.11.9 was used to assess per-base sequence quality, adapter contamination, GC content, and sequence duplication levels. Summary reports were aggregated with MultiQC v1.11.
Adapter Trimming and Quality Filtering:cutadapt v4.0 was employed to Trim Illumina TruSeq adapters,Remove low-quality bases、Discard reads shorter than 20 bp after trimming and use paired-end mode with default error tolerance.
Alignment to Reference Genome:Filtered reads were aligned to the mm10 (GRCm38) mouse genome using bowtie2 v2.4.5.Post-Alignment Processing:SAM files were converted to sorted BAM files using samtools v1.12.Duplicate reads were marked and removed with Picard MarkDuplicates v2.26.10.BAM files were indexed using samtools v1.12.
Broad histone marks (H3K27me3) were identified using MACS2 v2.2.7.1 with parameters.Normalized genome coverage tracks (bigWig files) were generated with deepTools bamCoverage v3.5.1.Fraction of Reads in Peaks (FRiP) was calculated using MACS2 output.Normalized Strand Cross-Correlation (NSC) and Relative Strand Correlation (RSC) were assessed via phantompeakqualtools v1.2.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: brain

growth_protocol: CD-1 mice (7–8 weeks old) were provided by Beijing Vital River laboratory Animal Technology Co., Ltd, China (no: 110011200105514958, 16-25g). Female CD-1 mice were fed on low folate diet for more than 8 weeks. Sexually matured individuals were mated overnight; vaginal plug was detected at 8:00 am in the following morning and was designated as E0.5 day. NTDs mouse models were induced by intraperitoneal injection with 1.5 mg/kg of MTX (Sigma-Aldrich, USA) on E7.5. On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope. All samples with NTDs clinical manifestations were collected for experiments. No specific randomization method was used. All procedures involving animal handling were performed according to the institutional guidelines approved by the Animal Ethics Committee of the Shanxi medical university.

extract_protocol:
On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope and the brain were used for experiments.The brain tissue was digested into a single-cell suspension, and 100,000 cells were used for experiments according to Vazyme #TD903 (Hyperactive Universal CUT&Tag Kit).H3K27me3 (CST #9733) was used for experiments.
Amplified libraries using Vazyme HiFi PCR Master Mix (Catalog #TD903),Index primers (Vazyme kit-provided).PCR program:72°C, 5 min; 98°C, 30 sec;12–15 cycles: 98°C 10 sec, 63°C 30 sec, 72°C 30 sec;72°C, 5 min final extension.Library QC:Quantified with Qubit dsDNA HS Assay.Size distribution verified via Bioanalyzer (peak: 200–700 bp).Pooled equimolar libraries for 150-bp paired-end sequencing on Illumina NovaSeq.

value: brain

value: neural tube defects


title: ESCs_RNAseq_rep1

description: Library name: ESCs_RNAseq_1


title: M2

description: Library name: Sample 5

treatment_protocol: Female CD-1 mice were fed on low folate diet for more than 8 weeks. Sexually matured individuals were mated overnight; vaginal plug was detected at 8:00 am in the following morning and was designated as E0.5 day. NTDs mouse models were induced by intraperitoneal injection with 1.5 mg/kg of MTX (Sigma-Aldrich, USA) on E7.5.


title: con_3

description: Library name: Sample 3

value: control


title: NTDsB

description: Library name: Sample 4

data_processing:
Raw BCL files converted to FASTQ using Illumina bcl2fastq v2.20.FastQC v0.11.9: Assessed per-base quality, GC content, and adapter contamination.Trimmomatic v0.39: Removed TruSeq adapters,Trimmed low-quality bases (Phred < 20, sliding window 4 bp) Discarded reads < 36 bp.
Aligned to mm10 genome using Bowtie2 v2.4.5. Sorted BAM files: samtools v1.12.Duplicate removal: Picard MarkDuplicates v2.26.10.MACS2 v2.2.7.1 with ATAC-seq mode for peak calling.TSS enrichment score calculated with deepTools v3.5.1.HINT-ATAC v0.13.6 for TF footprint identification.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
On E9.5, pregnant mice were euthanized by cervical dislocation, and the phenotypes of the fetuses were observed under a microscope and the brain were used for experiments.The brain tissue was digested into a single-cell suspension, and 100,000 cells were used for experiments according to Hyperactive ATAC-Seq Library Prep Kit for Illumina(TD711-01).
Purified transposed DNA using Vazyme DNA Clean Beads (Catalog #TD903)，PCR Amplification：72°C for 5 min (gap repair) ；98°C for 30 sec ；12 cycles: 98°C 10 sec, 63°C 30 sec, 72°C 30 sec ；72°C for 5 min (final extension) .Library Purification & QC:Purified with Vazyme DNA Clean Beads (1.0× ratio).Quantified with Qubit dsDNA HS Assay.


title: con_1

description: Library name: Sample 1


title: ControlB

description: Library name: Sample 2


title: ciTotiSCs_RNAseq_rep1

description: Library name: ciTotiSCs_RNAseq_1


title: ControlA

description: Library name: Sample 1


title: Dorsal root ganglia,Saline,Male 7

city: Aurora

first: SATHISH KUMAR

last: YESUPATHAM

state: CO

address: Rm 6440 D, 12700 E 19th Ave., Mail Stop 317

institute: Univerity Of Colorado

description: Library name: B6768_S26

data_processing:
Partek Flow genomics workbench version 12.5.0
Filter contaminants rDNA, tRNA, mtrDNA using  Bowtie 2 - 2.2.5
Trimmed bases (Parameter Phred score >35, 3-prime end minimum read length 25)
Trimmed sequences were aligned to reference index mm39 using STAR - 2.7.8a
Singletons and unaligned reads were filtered
Gene quatification was performed by HTSeq - 0.11.0
Assembly: mm39
Supplementary files format and content: Counts were normalised Counts per million on Partek Flow
Supplementary files format and content: csv file includes CPM for each  samples

extract_protocol:
Total RNA was extracted from lumbosacral DRGs using a RNAeasy miniprep kit (Qiagen, CA, USA), following manufacturer’s instructions.
The universal mRNA Poly-A tail prep kit was used for library preparation following manufacturer instructions

value: Saline


title: Dorsal root ganglia,Saline,Female 7

description: Library name: B6757_S23


title: Dorsal root ganglia,VEGF,Female 6

description: Library name: B6756_S22

value: VEGFA


title: Dorsal root ganglia,Saline,Male 8

description: Library name: B6769_S27


title: Dorsal root ganglia,VEGF,Female 5

description: Library name: B6755_S21


title: Dorsal root ganglia,VEGF,Male 6

description: Library name: B6754_S20


title: Dorsal root ganglia,VEGF,Male 5

description: Library name: B6753_S19


title: Dorsal root ganglia,Saline,Female 4

description: Library name: B5778_S17


title: M1

description: Library name: Sample 4


title: Dorsal root ganglia,Saline,Female 3

description: Library name: B5777_S16


title: Dorsal root ganglia,Saline,Female 8

description: Library name: B6758_S24


title: Dorsal root ganglia,VEGF,Male 2

description: Library name: B5771_S15


title: NTDsA

description: Library name: Sample 3


title: Dorsal root ganglia,VEGF,Male 1

description: Library name: B5770_S14


title: con_2

description: Library name: Sample 2


title: Aa-cko-3

city: guangzhou

first: xiaogang

last: zhang

address: Sha Tai nan Lu 1023hao, Baiyun District

department: School of Basic Medical Sciences

institute: Southern Medical University

description: Library name: sample_6

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

source_name: Lung tissue

value: Lung tissue


title: Dorsal root ganglia,Saline,Male 3

description: Library name: B5772_S110


title: Aa-cko-2

description: Library name: sample_5


title: Dorsal root ganglia,Saline,Male 4

description: Library name: B5773_S111


title: Dorsal root ganglia,VEGF,Female 1

description: Library name: B5775_S112


title: Aa-flox-3

description: Library name: sample_3


title: Aa-flox-2

description: Library name: sample_2


title: Aa-cko-1

description: Library name: sample_4


title: Aa-flox-1

description: Library name: sample_1


title: VE-3

description: Library name: sample_6

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


title: VE-2

description: Library name: sample_5


title: VE-1

description: Library name: sample_4


title: Aalter-1

description: Library name: sample_1


title: Dorsal root ganglia,VEGF,Female 2

description: Library name: B5776_S113


title: Aalter-3

description: Library name: sample_3


title: Aalter-2

description: Library name: sample_2


title: CD38-/- astrocyte rep6

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4). After trimming, only reads with lengths greater than 30bp were mapped to mm10 by STAR (v 2.7.1a).
Raw counts and normalized counts for each gene were outputted by RSEM (v1.2.28). Batch effects were removed with the package sva (v3.46.0). The raw counts were used to identify differentially expressed genes (DEG) by DESeq2 (v 1.36.0). Only genes with qvalue less than 0.05 and at least 1.2-fold change were considered as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: comma-separated values file include TPM values for each Sample

source_name: midbrain

extract_protocol:
RNA was isolated from cells with Direct-zol RNA Microprep kit (Zymo Research, #R2060) following the manufacturer’s instructions
Collected RNA was then converted to cDNA samples by using the Takara SMART-Seq v4Ultra low Input RNA kit. Generated cDNA was checked for quality utilizing Quibit and tapestation measures, whereby libraries with marginal pass and higher quality for were used for pair-ended sequencing on the NovaSeq 6000 platform.

value: midbrain

value: astrocyte

tag: developmental stage

value: 12-14 months


title: CD38-/- astrocyte rep4


title: CD38-/- astrocyte rep3


title: CD38-/- astrocyte rep2


title: CD38-/- astrocyte rep1


title: CD38+/- astrocyte rep3


title: CD38+/- astrocyte rep2


title: CD38+/- astrocyte rep1


title: CD38+/+ astrocyte rep2


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 6

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Raw fastq files were quality trimmed using the cutadapt package
Trimmed reads were aligned using GSNAP (command line parameters -B 5 -A sam -N 1 -t 8 -s splicesites --quality-protocol=sanger --gunzip --sam-multiple-primaries --maxsearch=1000 -- npaths=100)
Read counts were quantified using a custom Perl script and summarized at the gene level
Assembly: GRCm38
Supplementary files format and content: tab-delimited .txt file contains raw counts for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated from ~500 mg aliquots of frozen liver tissue, homogenized for 1-2 min at 4°C in 1 mL Qiazol using Lysing Matrix D (MP Biomedicals #116913500). Total mRNA was prepared using the miRNeasy Mini Kit (Qiagen #1038703).
KAPA mRNA Hyperprep kit was used according to the manufacturer's directions

value: Liver

value: 4 d, 22 h post-injection


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 8


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 7


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 4


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 3


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 2


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 1


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 7

value: 4 d, 4 h post-injection


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 4


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 8


title: DIO, 4 d IUB288 treatment, 22 h after last injection, replicate 5


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 6


title: CD38-/- astrocyte rep5


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 3


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 5


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 1


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 8

value: vehicle


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 6


title: DIO, 4 d IUB288 treatment, 4 h after last injection, replicate 2


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 5


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 7


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 4


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 3


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 2


title: CD38+/+ astrocyte rep3


title: CD38+/+ astrocyte rep1


title: Thymus_TECs_Aire_KO_exp_4

city: San Francisco

first: James

last: Gardner

state: CA

address: 505 Parnassus Ave

institute: UCSF

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, and genomic alignment was performed using kallisto-bustools (v0.27.3) to the prebuilt ensembl v96 mouse transcriptome index for kallisto
Downstream analysis (quality control filtering, read count normalization, dimensionality reduction, and unsupervised clustering) was performed in Python (v3.10.13) using scanpy (v1.9.3), and scvi-tools (v1.0.4)
Doublet detection was performed in Python (v3.10.13) using scrublet (v0.2.3)
Assembly: mm10
Supplementary files format and content: mtx files containing raw feature matrix output from kallisto-bustools, along with single-column txt files with feature and barcode labels
Supplementary files format and content: h5ad file containing an AnnData object with processed count data and pt file containing the processed data scVI model. Library size normalized and log-transformed counts are stored in the AnnData '.raw' attribute, raw and scVI normalized counts are stored as layers. Cell and gene metadata are stored in the '.obs' and '.var' attributes. UMAP coordinates are stored in the '.obsm' attribute.

source_name: Thymus

extract_protocol:
Mouse thymi were isolated, cleaned of fat and transferred to 10 ml of DMEM with 2% Heat-Inactivated HyClone FBS on ice. Thymi were minced with a razor blade and tissue chunks were collected into 15-ml Falcon tubes, vortexed gently for 10 seconds and briefly spun down at 1250 RPM. Tissue fragments were resuspended in 4ml of DMEM digestion medium containing 2% FBS, 100ug/ml DNase I and 100ug/ml liberase TM . Tubes were incubated in a 37 °C water bath and tissue fragments were further digested with mechanical aid by pipetting through a glass Pasteur pipette every 4 min. At 8 min, tubes were spun briefly at 1250 RPM to pellet undigested fragments and the supernatant was transferred to 20 ml of magnetic-activated cell sorting (MACS) buffer containing 0.5% BSA, 2 mM EDTA in PBS on ice to stop the enzymatic digestion. This procedure was repeated twice with 4 ml of fresh digestion medium each time, or until no visible tissue fragments remain. The single-cell suspension was then pelleted and washed once in MACS buffer and passed through a 70 μm filter. To enrich for mTEC subsets, density-gradient centrifugation using a three-layer Percoll gradient with specific gravities of 1.115, 1.065 and 1.0 was applied. Cells isolated from the Percoll-light fraction, between the 1.065 and 1.0 layers, were then resuspended in MACS buffer before counting and flow staining. CD45- EpCAM+ cells were FACS sorted for 10X scRNA-seq library preparation.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells 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). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Thymus

value: TECs

value: Aire KO

tag: strain

value: 4-6 weeks


title: Thymus_TECs_Aire_WT_exp_4

description: 10x Genomics

value: WT


title: Thymus_TECs_Fezf2_KO_exp_3

description: 10x Genomics

value: Fezf2 KO


title: Thymus_TECs_Fezf2_KO_exp_1

description: 10x Genomics


title: Thymus_TECs_Aire_KO_exp_2

description: 10x Genomics


title: Thymus_TECs_Fezf2_WT_exp_1

description: 10x Genomics


title: Thymus_TECs_Fezf2_WT_exp_3

description: 10x Genomics


title: alveolar epithelial cell, PBS2, 24h

city: Nanjing

first: Chen

last: Jing

state: Jiangsu

address: No.87, Dingjiaqiao, Gulou District

department: Department of Critical Care Medicine,

institute: Zhongda Hospital, School of Medicine, Southeast University

data_processing:
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Assembly: HISAT2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: lung

extract_protocol:
RNA was harvested using TRIzol regent (Invitrogen, CA, USA). 1.3μg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were  constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: lung

value: primary

value: alveolar epithelial cell

value: PBS


title: Thymus_TECs_Aire_WT_exp_2

description: 10x Genomics


title: alveolar epithelial cell,OMVs1, 24h

value: OMVs


title: alveolar epithelial cell,OMVs3, 24h


title: alveolar epithelial cell,OMVs2, 24h


title: alveolar epithelial cell, PBS1, 24h


title: Mouse Lung, dNS1-based virus and STFK subunit mixed immunization, replication 3, V(D)J sequencing for BCR

description:
Library name: dNS1-STFK-BCR_3
10x Genomics

value: Lung


title: alveolar epithelial cell, PBS3, 24h


title: DIO, 4 d vehicle treatment, 22 h after last injection, replicate 1


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-P23

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: FC

value: M

value: 9 months


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-O11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-O12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-O23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-N12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-N24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-O24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-P24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-P11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-N11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-P12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-M24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-M23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-M12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-M11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-L12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-L23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-L11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-K24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-K23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-K12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-N23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-K11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-J24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-J12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-J11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-I23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-I11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-H12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-G24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-I12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-G23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-G12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-G11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-F23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-H23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-F24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-L24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-E24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-I24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-E23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-J23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-D11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-D24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-D23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-D12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-F12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-H24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-E11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-C24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-C23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-B24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-C11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-B23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-A24


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-A12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-B11


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-P22


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-F11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-H11


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-P9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-P21


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-A23


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-A11


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-E12


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-C12


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-O9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-O22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-P10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-O21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-O10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-N9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-N10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-N22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-M21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-L9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-M10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-L22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-M22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-L10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-M9


title: AMB_200702_9mo_2A_3A_2_P7-6-N17-B12


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-K9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-L21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-K22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-K10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-J21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-J22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-J9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-I9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-J10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-K21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-I22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-I10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-H21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-H22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-I21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-N21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-H10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-H9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-G9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-G22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-G21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-G10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-F22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-F9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-F10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-F21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-E21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-E22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-E10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-D22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-D9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-D10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-D21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-C22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-C9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-C21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-B21


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-C10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-B9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-B22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-A22


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-A9


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-A10


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-A21


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-P7


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-P8


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-P20


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-P19


title: AMB_200702_9mo_2A_3A_2_P7-5-M24-E9


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-O8


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-N8


title: AMB_200702_9mo_2A_3A_2_P7-4-L15-N20


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title: AMB_200702_9mo_2A_3A_2_P6-2-L17-M15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-L3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-L15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-K4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-K3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-K16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-K15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-J3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-J4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-J15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-I4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-I3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-H3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-I15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-J16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-H4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-I16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-H16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-H15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-F3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-E4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-L16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-G3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-G4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-G16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-D3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-D16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-G15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-C4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-E3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-F4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-F15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-E16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-C15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-B3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-C16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-E15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-D4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-B15


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-A4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-A16


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-A3


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-B16


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-P2


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-F16