title: HAE_BCI_NHBE (HTO)

status: Public on Sep 01 2023

first: Alec

last: Pankow

address: 1 Gustave L. Levy Place, Anbg 17 17-70

description: 10x Genomics

data_processing:
The sequence library alignment, filtering, barcode counting, and UMI counting were performed using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw counts matrices were loaded into the R statistical environment (4.0.3) and sample demultiplexing was performed using Seurat (v4.0) and the HTODemux function with default parameters. Hastag oligo assigments were as follows: primary_1: {HTO_25: 'TCGATAATGCGA'}, primary_2: {HTO_28: 'ACTGTCTAACGG'}, primary_3: {HTO_30: 'CACATAATGACG'}, BCI_1: {HTO_44: 'TAACGACGTGGT'}, BCI_2: {HTO_51: 'CGCCTATATACT'}, BCI_3: {HTO_52: 'GACGTACCGGAT'}
Assembly: GRCh38-2020-A (hg38)
Supplementary files format and content: gene-cell barcode matrices

source_name: Human airway epithelium

growth_protocol: Bci-NS1.1 cells (kind gift of Dr. Ronald Crystal) and NHBE (cat. no. CC-2541, Lonza, lot no. 623950, 626776, and 630564) were seeded into Pneumacult™-Ex Plus Medium (StemCell) and passaged at least two times before plating (7x104 cells/well) on rat-tail collagen type-I coated permeable transwell membrane supports (6.5mm; Corning Inc) to generate HAE. HAE were maintained in Pneumacult™-Ex Plus Medium until confluent, then grown at an air-liquid interface with Pneumacult™-ALI Medium in the basal chamber for approximately 3 weeks to form well differentiated , polarized cultures that resemble pseudostratified mucociliary epithelium in vivo.

extract_protocol:
The apical surface was washed once to remove mucus by adding 100 ul of PBS and incubating for 30 min at 37°C. Cells were dissociated by cutting out the transwell membrane and incubating it in 700 ul TrpLE 10 (cat. no. A1217701; Thermo Fisher) for 30 min with rocking at 37°C. To increase dissociation, cells were pipetted through wide-bore tips every 10 min during the incubation time. When cells were visually dissociated, 700ul of ALI maintenance medium supplemented with 0.1% Pluronic (cat. no. 24040032; Thermo Fisher) was added, and cells were carefully pipetted again using wide-bore tips. The cell suspension was centrifuged through a 10-mm filter at 300 g for 5 min to break up any remaining cell clumps. The cell pellet was washed once with 200 ul ALI maintenance medium supplemented with 0.1% Pluronic before cell number and viability were assed using the Countess II instrument (Thermo Fisher).
Libraries were prepared in accordance with the Chromium Next GEM Single Cell 5' Reagent Kit (v2 Chemistry) protocol.

value: multiple

value: Human airway epithelium


title: HAE_BCI_NHBE (GEX)

type: SRA

city: New York

state: New York

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue


title: LB00197-003_fRNA_IL21_UP1010

status: Public on Aug 31 2023

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

library_source: transcriptomic single cell

data_processing:
For TEA-seq, demultiplexing of raw base call files into FASTQ files was performed using bcl2fastq2 (Illumina v2.20.0.422, parameters: --create-fastq-for-index-reads, --minimum-trimmed-read-length=8, --mask-short-adapter-reads=8, --ignore-missing-positions, -ignore-missing-filter, --ignore-missing-bcls, -r 24 -w 24 -p 80). The --use-bases-mask option was used to adjust the read lengths for each library type as follows: Y28n*,I10,I10n*,Y90n* for RNA, Y50n*,I8n*,n8Y16,Y50n* for ATAC, and Y28n*,I8n*,n*,Y90n* for ADT and cell hashing (HTO).
For TEA-seq, the RNA and ATAC assays were run through cellranger-arc count to align to the genome.  For scRNA-seq, the fastq files were run through cellranger count.
ADT and HTO count matrices were generated using BarCounter v1.0 (Swanson et al. 2022). The RNA count matrix, and ADT count matrix were then combined into a single Seurat object. Cells were filtered based on the following cutoffs: > 250 genes/cell, > 500 RNA UMIs/cell, < 10,000 ADT UMIs/cell, < 35% mitochondrial reads, < 20,000 RNA UMIs/cell. Normalization, feature selection and scaling were performed on the RNA matrix (SCTransform function, default settings), followed by PCA (RunPCA function, default settings). A UMAP projection was generated (RunUMAP, dims = 1:30) and clustering was performed (FindNeighbors, dims = 1:30; FindClusters, resolution = 0.5). We used the Seurat Multimodal Reference Dataset for PBMCs (available from the Satija lab (Hao et al. 2021)) to perform label transfer on the dataset using the functions described in the Seurat V4 Vignettes (FindTransferAnchors; TransferData). Two clusters were identified to be non-T cells and were excluded. Sample specific transcripts, AC105402.3 and MTRNR2L8, were identified and removed prior to further downstream RNA analysis.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: scRNA-seq files have suffix _labeled.h5 and are hdf5 format.  TEA-seq data comes in a few formats: hdf5 for RNA and ADT data, and tsv.gz for ATAC fragment data and csv.gz for ATAC metadata.

source_name: peripheral blood mononuclear cells

extract_protocol:
All samples were collected, processed to PBMCs using a Ficoll-based approach and frozen in FBS with 10% DMSO within 4 hours of blood draw. Cord and peripheral blood samples for follow-up studies were purchased from Bloodworks Northwest (Seattle, WA) through protocols approved by the Bloodworks Northwest and internal Allen Institute IRBs.
TEA-seq library preparation was performed as described previously (Swanson et al. 2021), with the addition of Cell Hashing (Stoeckius et al. 2018) to allow for sample multiplexing and limit well-to-well batch effects. In brief, samples were thawed and processed across three batches, with each batch containing a common PBMC control. Antibody staining for Cell Hashing and cell sorting was performed simultaneously on 2 x 106 cells from each sample. Each sample was incubated with uniquely barcoded TotalSeq-A antibody, anti-CD45 antibody and anti-CD3 antibody, then pooled by T cell proportion previously determined, targeting 800,000 T cells for each donor sample and 200,000 T cells for the control, and sorted on a BD FACSAria Fusion. T cells were sorted as live, single CD45+CD3+ cells. 2 x 106 sorted T cells were then used for the library preparation. A panel of 55 barcoded oligo-conjugated antibodies (BioLegend TotalSeq-A) was used for these studies (Supp Table 4). Individual ATAC, RNA, and ADT libraries were prepared, sequenced and processed as described previously.(Swanson et al. 2021)
Single cell RNA sequencing was performed on PBMCs was previously described. (Genge et al. 2021) In brief, scRNA-seq libraries were generated using a modified 10x genomics chromium 3’ single cell gene expression assay with Cell Hashing. 8 donors were pooled per library, with the addition of a common batch control sample in each library. Libraries were sequenced on a Illuminia Novaseq platform. scRNA-seq Analysis. Count matrices from each sample were merged into age-specific Seurat objects, followed by normalization, feature selection, scaling, PCA, UMAP embedding, and clustering. Label transfer from the T cell subset Seurat reference was performed as previously described on each age specific Seurat Object. Following label transfer, all objects were merged into a single object. Cells identified CD4 Naïve with a prediction score greater than 0.7 were taken into downstream analysis. We then averaged the expression on each cell in each age group (AverageExpression function, group.by = ‘age’) for the DEGs identified in our TEA-seq analysis.

value: peripheral blood mononuclear cells

tag: library type

value: single-cell RNA-seq

tag: birth year

tag: Sex

value: Female

tag: race

value: Caucasian

tag: age


title: LB00197-002_fRNA_PMA_UP1010


title: LB02232_fRNA_Unstim_Pooled_Peds


title: LB00182-003_fRNA_IL21_UP1003


title: LB00182-001_fRNA_TCR_UP1003


title: LB00197-001_fRNA_TCR_UP1010


title: LB00173-003_fRNA_IL21_UP1006


title: LB00173-002_fRNA_PMA_UP1006


title: LB00173-001_fRNA_TCR_UP1006


title: BCBL1_K4me2_2

status: Public on Sep 08 2023

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

library_source: genomic

data_processing:
Base calling and quality scoring were performed using bcl2fastq v2.17 for Novaseq 6000 output.
CUT&RUN reads were processed with fastp and aligned to the GRCh38 (hg38) human reference genome assembly with Bowtie2.
Hypergeometric Optimization of Motif EnRichment (HOMER) v4.11 was used for peak detection were annotated utilizing the defalt parameters described in the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
CPM-normalized  data files in bigWig format were generated. Mapped reads in BAM format were converted and scaled, using CPM (Counts Per Million mapped reads) normalization, to bedGraph using bedtools. BedGraph files were then converted to bigwig files for visualization.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data are in bigWig format.
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: Primary effusion lymphoma cell lines (BCBL-1, BC1, BC3) were cultured in RPMI 1640 medium supplemented with 15% FBS, 2 mM L-glutamine, and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) in a humidified atmosphere with 5% CO2 at 37C. iSLK cells were cultured with DMEM medium with 10% FBS 2 mM L-glutamine, and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed with PBS and wash buffer (20mM HEPES-KOH pH7.5, 150mM NaCl, 0.5mM spermidine (Sigma, S2626) and proteinase inhibitor (Roche). After removing wash buffer, cells were captured on magnetic ConA beads (Polysciences), in presence of CaCl2. Beads/cells complexes were washed with digitonin wash buffer (0.02% digitonin, 20mM HEPES-KOH pH7.5, 150mM NaCl, 0.5mM spermidine and 1x proteinase inhibitor) three times, and incubated with specific antibodies in 250 mL volume. After incubation, unbound antibody was washed by digitonin wash buffer 3 times. Beads were then incubated with the recombinant pAG-MNase, in 250μl digitonin wash buffer (1.0 mg/mL final concentration) for an hour at 4°C with rotation. Unbound pAG-MNase was removed by washing with digitonin wash buffer 3 times. Pre-chilled 2 mM CaCl2 containing digitonin wash buffer (200 mL) was added to beads and incubate on ice for 30 min. The pAG-MNase digestion was halted by the addition of 200μl 2× STOP solution (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml RNase A, 50 mg/ml Glycogens). The beads were incubated/shaked at 37°C for 10min in tube shaker at 500 rpm to release digested DNA fragments from the insoluble nuclear chromatin. The supernatant was collected after centrifuge (16,000 x g for 5 min at 4°C) and place on magnetic stand. DNA was extracted using the NucleoSpin & PCR kit (Takara Bio, Kusatsu, Shiga, Japan).
Sequencing libraries were prepared from 3 ng of CUT&RUN DNA with the Kapa HyperPrep Kit (Roche) according to the manufacturer’s standard protocol. Libraries were multiplex sequenced (2 x 150bp, paired-end) on an Illumina NovaSeq 6000 sequencing system.

tag: cell line

value: B-cell

tag: treatment

value: No treatment

tag: cut&run antibody

value: H3K4me2 (CST C64G9)


title: LB00172-003_fRNA_IL21_UP1002


title: BC1_H3K4me1_1

value: H3K4me1 (CST D1A9)


title: PB03223_scRNA-seq_B138

molecule: polyA RNA

value: Male


title: BCBL-1_K4me1_1


title: PB02392_scRNA-seq_B138


title: LB00172-001_fRNA_TCR_UP1002


title: IMM19_463_scRNA-seq_B096-P2

extract_protocol:
All samples were collected, processed to PBMCs using a Ficoll-based approach and frozen in FBS with 10% DMSO within 4 hours of blood draw. Cord and peripheral blood samples for follow-up studies were purchased from Bloodworks Northwest (Seattle, WA) through protocols approved by the Bloodworks Northwest and internal Allen Institute IRBs.
TEA-seq library preparation was performed as described previously (Swanson et al. 2021), with the addition of Cell Hashing (Stoeckius et al. 2018) to allow for sample multiplexing and limit well-to-well batch effects. In brief, samples were thawed and processed across three batches, with each batch containing a common PBMC control. Antibody staining for Cell Hashing and cell sorting was performed simultaneously on 2 x 106 cells from each sample. Each sample was incubated with uniquely barcoded TotalSeq-A antibody, anti-CD45 antibody and anti-CD3 antibody, then pooled by T cell proportion previously determined, targeting 800,000 T cells for each donor sample and 200,000 T cells for the control, and sorted on a BD FACSAria Fusion. T cells were sorted as live, single CD45+CD3+ cells. 2 x 106 sorted T cells were then used for the library preparation. A panel of 55 barcoded oligo-conjugated antibodies (BioLegend TotalSeq-A) was used for these studies (Supp Table 4). Individual ATAC, RNA, and ADT libraries were prepared, sequenced and processed as described previously.(Swanson et al. 2021)     Single cell RNA sequencing was performed on PBMCs was previously described. (Genge et al. 2021) In brief, scRNA-seq libraries were generated using a modified 10x genomics chromium 3’ single cell gene expression assay with Cell Hashing. 8 donors were pooled per library, with the addition of a common batch control sample in each library. Libraries were sequenced on a Illuminia Novaseq platform. scRNA-seq Analysis. Count matrices from each sample were merged into age-specific Seurat objects, followed by normalization, feature selection, scaling, PCA, UMAP embedding, and clustering. Label transfer from the T cell subset Seurat reference was performed as previously described on each age specific Seurat Object. Following label transfer, all objects were merged into a single object. Cells identified CD4 Naïve with a prediction score greater than 0.7 were taken into downstream analysis. We then averaged the expression on each cell in each age group (AverageExpression function, group.by = ‘age’) for the DEGs identified in our TEA-seq analysis.

value: African American

value: Unknown


title: PB02391_scRNA-seq_B138


title: IMM19_185_scRNA-seq_B041-P1


title: PB00927_scRNA-seq_B096


title: LB00182-002_fRNA_PMA_UP1003


title: IMM19_497_scRNA-seq_B138-P1


title: IMM19_461_scRNA-seq_B094-P2


title: IMM19_497_scRNA-seq_B138-P2


title: IMM19_432_scRNA-seq_B063-P2


title: IMM19_447_scRNA-seq_B078-P2


title: IMM19_425_scRNA-seq_B053-P1


title: IMM19_447_scRNA-seq_B078-P1


title: IMM19_420_scRNA-seq_B048-P1


title: IMM19_419_scRNA-seq_B047-P2


title: IMM19_420_scRNA-seq_B048-P2


title: LB00172-002_fRNA_PMA_UP1002


title: IMM19_417_scRNA-seq_B045-P1


title: IMM19_413_scRNA-seq_B040-P2


title: IMM19_389_scRNA-seq_B007-P1


title: IMM19_695_scRNA-seq_B004-P2


title: IMM19_709_scRNA-seq_B001-P1


title: PB00928_scRNA-seq_B096


title: PB00910_scRNA-seq_B094


title: PB00913_scRNA-seq_B096


title: PB00892_scRNA-seq_B094


title: IMM19_427_scRNA-seq_B054-P1


title: PB00833_scRNA-seq_B094


title: PB00031_scRNA-seq_B078


title: GBM_10

status: Public on Sep 14 2023

city: Regensburg

first: Markus

middle: J.

last: Riemenschneider

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg University Hospital

data_processing:
fastq files were aligned to version 102 of Homo_sapiens reference genome GRCh38 using the HiSat2 aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm (v2.0.1).
Batch effects (RNA Seq RUN) were removed with Combat_Seq of the SVA package using a negative binomial regression model
Expression data was normalized using the normalization function of DeSeq2 package or TPM/RPKM values
Differentially expressed genes (logFC±1, padj ≤ 0.05) were identified by negative binomial generalized linear models statistics using the DeSeq2 package
Assembly: version 102 of Homo_sapiens reference genome GRCh38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: CNS brain

extract_protocol:
RNA was isolated using the Maxwell® RSC Simply RNA Tissue kit (AS1340, Promega) and processed as per manufacturer’s instructions.
Illumina Stranded total RNA Prep kit (#20040529, Illumina) and processed as per manufacturer’s instructions.
RNA-seq with 75 cycles single-end read protocol and a NextSeq 500/550 High Output Kit v2.5 (#20024906, Illumina).

value: CNS brain

tag: rna seq_run

tag: tspo expression

value: HIGH

tag: tspo cluster

value: HIGH III

tag: diagnosis

value: IDH-wt WHO grade 4 solid glioblastoma tumor


title: PB00010_scRNA-seq_B078


title: PB00026_scRNA-seq_B078


title: PB00842_scRNA-seq_B063


title: PB00352_scRNA-seq_B078


title: IMM19_418_scRNA-seq_B046-P2


title: PB00841_scRNA-seq_B063


title: PB00811_scRNA-seq_B060


title: BCBL1_SMARCA5_1

value: Invitrogen Cat# PA5-52601


title: PB00193_scRNA-seq_B053


title: PB00023_scRNA-seq_B078


title: PB00561_scRNA-seq_B054


title: PB00809_scRNA-seq_B053


title: PB00582_scRNA-seq_B048


title: PB00539_scRNA-seq_B048


title: PB00568_scRNA-seq_B048


title: PB00914_scRNA-seq_B096


title: PB00569_scRNA-seq_B047


title: PB00566_scRNA-seq_B053


title: PB00537_scRNA-seq_B046


title: PB00356_scRNA-seq_B046


title: PB00530_scRNA-seq_B045


title: PB00510_scRNA-seq_B043


title: PB00386_scRNA-seq_B041


title: PB00507_scRNA-seq_B041


title: PB00552_scRNA-seq_B045


title: PB00363_scRNA-seq_B040


title: PB00388_scRNA-seq_B040


title: PB00030_scRNA-seq_B004


title: PB00002_scRNA-seq_B001


title: PB00342_scRNA-seq_B050


title: PB00384_scRNA-seq_B040


title: IMM19_1852_scRNA-seq_B041-P2


title: IMM19_413_scRNA-seq_B040-P1


title: IMM19_412_scRNA-seq_B039-P1


title: IMM19_425_scRNA-seq_B053-P2


title: IMM19_431_scRNA-seq_B060-P2


title: IMM19_422_scRNA-seq_B050-P1


title: IMM19_415_scRNA-seq_B043-P1


title: IMM19_418_scRNA-seq_B046-P1


title: PB00884_scRNA-seq_B094


title: IMM19_445_TEA-seq_B076

library_source: other

data_processing:
For TEA-seq, demultiplexing of raw base call files into FASTQ files was performed using bcl2fastq2 (Illumina v2.20.0.422, parameters: --create-fastq-for-index-reads, --minimum-trimmed-read-length=8, --mask-short-adapter-reads=8, --ignore-missing-positions, -ignore-missing-filter, --ignore-missing-bcls, -r 24 -w 24 -p 80). The --use-bases-mask option was used to adjust the read lengths for each library type as follows: Y28n*,I10,I10n*,Y90n* for RNA, Y50n*,I8n*,n8Y16,Y50n* for ATAC, and Y28n*,I8n*,n*,Y90n* for ADT and cell hashing (HTO).
For TEA-seq, the RNA and ATAC assays were run through cellranger-arc count to align to the genome.  For scRNA-seq, the fastq files were run through cellranger count.
ADT and HTO count matrices were generated using BarCounter v1.0 (Swanson et al. 2022). The RNA count matrix, and ADT count matrix were then combined into a single Seurat object. Cells were filtered based on the following cutoffs: > 250 genes/cell, > 500 RNA UMIs/cell, < 10,000 ADT UMIs/cell, < 35% mitochondrial reads, < 20,000 RNA UMIs/cell. Normalization, feature selection and scaling were performed on the RNA matrix (SCTransform function, default settings), followed by PCA (RunPCA function, default settings). A UMAP projection was generated (RunUMAP, dims = 1:30) and clustering was performed (FindNeighbors, dims = 1:30; FindClusters, resolution = 0.5). We used the Seurat Multimodal Reference Dataset for PBMCs (available from the Satija lab (Hao et al. 2021)) to perform label transfer on the dataset using the functions described in the Seurat V4 Vignettes (FindTransferAnchors; TransferData). Two clusters were identified to be non-T cells and were excluded. Sample specific transcripts, AC105402.3 and MTRNR2L8, were identified and removed prior to further downstream RNA analysis.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: scRNA-seq files have suffix _labeled.h5 and are hdf5 format.  TEA-seq data comes in a few formats: hdf5 for RNA and ADT data, and tsv.gz for ATAC fragment data and csv.gz for ATAC metadata.
Library strategy: TEA-seq

molecule: other

extract_protocol:
All samples were collected, processed to PBMCs using a Ficoll-based approach and frozen in FBS with 10% DMSO within 4 hours of blood draw. Cord and peripheral blood samples for follow-up studies were purchased from Bloodworks Northwest (Seattle, WA) through protocols approved by the Bloodworks Northwest and internal Allen Institute IRBs.
TEA-seq library preparation was performed as described previously (Swanson et al. 2021), with the addition of Cell Hashing (Stoeckius et al. 2018) to allow for sample multiplexing and limit well-to-well batch effects. In brief, samples were thawed and processed across three batches, with each batch containing a common PBMC control. Antibody staining for Cell Hashing and cell sorting was performed simultaneously on 2 x 10^6 cells from each sample. Each sample was incubated with uniquely barcoded TotalSeq-A antibody, anti-CD45 antibody and anti-CD3 antibody, then pooled by T cell proportion previously determined, targeting 800,000 T cells for each donor sample and 200,000 T cells for the control, and sorted on a BD FACSAria Fusion. T cells were sorted as live, single CD45+CD3+ cells. 2 x 10^6 sorted T cells were then used for the library preparation. A panel of 55 barcoded oligo-conjugated antibodies (BioLegend TotalSeq-A) was used for these studies (Supp Table 4). Individual ATAC, RNA, and ADT libraries were prepared, sequenced and processed as described previously.(Swanson et al. 2021)
Single cell RNA sequencing was performed on PBMCs was previously described. (Genge et al. 2021) In brief, scRNA-seq libraries were generated using a modified 10x genomics chromium 3’ single cell gene expression assay with Cell Hashing. 8 donors were pooled per library, with the addition of a common batch control sample in each library. Libraries were sequenced on a Illuminia Novaseq platform. scRNA-seq Analysis. Count matrices from each sample were merged into age-specific Seurat objects, followed by normalization, feature selection, scaling, PCA, UMAP embedding, and clustering. Label transfer from the T cell subset Seurat reference was performed as previously described on each age specific Seurat Object. Following label transfer, all objects were merged into a single object. Cells identified CD4 Naïve with a prediction score greater than 0.7 were taken into downstream analysis. We then averaged the expression on each cell in each age group (AverageExpression function, group.by = ‘age’) for the DEGs identified in our TEA-seq analysis.
single-cell RNA-seq, single-cell CITE-seq, single-cell ATAC-seq


title: IMM19_438_TEA-seq_B069


title: IMM19_435_TEA-seq_B065


title: PB00197_TEA-seq_B065


title: PB00127_TEA-seq_B076


title: PB00172_TEA-seq_B069


title: PB00182_TEA-seq_B069


title: PB00545_TEA-seq_B076


title: PB00599_TEA-seq_B076

value: Other


title: PB00368_TEA-seq_B076

value: peripheral blood mononuclear cells


title: PB00323_TEA-seq_B069


title: PB00377_TEA-seq_B076


title: PB00353_TEA-seq_B076


title: XEN replicate1 [HiChIP]

status: Public on Aug 21 2023

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

description:
H3k27ac HiChiP seq for mouse XEN replicate 1
xen.bedpe

data_processing:
All sequencing files were processed with HiC-Pro pipeline (version 3.0.0).
Bed files with in silico digestion of the mm10 genome by MboI or Arima restriction enzymes were generated with ‘digest_genome.py’ tool from HiC-Pro and were used for assigning mapped reads to DNA fragments.
Valid deduplicated reads from replicates were merged and were used for loop calling at 5kb resolution with FitHiChIP (release 9.0) and coverage bias regression option active.
Loops with one peak in either of the two interacting regions (IntType = 3: “peak to all” option), sizes between 10-2000kb and FDR <0.01 for ESC, TSC, XEN and <0.05 for EPISC were considered valid.
Assembly: mm10
Supplementary files format and content: valid read pairs and loops in bed format
Library strategy: HiChIP

organism: Mus musculus

source_name: XEN

extract_protocol:
5ng of immunoprecipitated DNA material was used to make libraries using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat #21024) according to manufacturer’s instructions and performing between 8-14 cycles of amplification for all samples.
ESC cells were processed for each HiChIP replicate using the Abcam H3K27ac antibody (ab4729) and following the HiChIP protocol as previously described (Di Giammartino et al., 2019). TSC, XEN and EpiSC cells were used for each HiChIP replicate using the Arima-HiC+ kit (Arima, A101020) and the H3K27ac antibody (active motif H3K27ac 91193) according to manufacturer’s instructions with few modifications.

value: XEN

value: extra embryonic stem cells


title: PB00173_TEA-seq_B065

value: Female

value: Caucasian


title: EPISC replicate1 [HiChIP]

description:
H3k27ac HiChiP seq for mouseEPISC replicate 1
episc.bedpe

source_name: EPISC

value: EPISC

value: Epiblast-like stem cells


title: TSC replicate1 [HiChIP]

description:
H3k27ac HiChiP seq for mouse TSC replicate 1
tsc.bedpe

source_name: TSC

value: TSC

value: trophoblast stem cells


title: PB00192_TEA-seq_B065


title: TSC replicate2 [HiChIP]

description:
H3k27ac HiChiP seq for mouse TSC replicate 2
tsc.bedpe


title: PB00041_scRNA-seq_B007

value: Male


title: PB00807_TEA-seq_B069

value: African American


title: XEN replicate2 [HiChIP]

description:
H3k27ac HiChiP seq for mouse XEN replicate 2
xen.bedpe


title: PB00334_TEA-seq_B076


title: PB00124_TEA-seq_B076


title: SOX17 XEN replicate1

description:
4C seq of SOX17 in XEN, replicate 1
av_xen_sox17.bw

data_processing:
Demultiplexing, trimming of VP and resizing of sequence reads to 35 bp was performed with fastq_trimmer while fastx_clipper (Fastx-toolkit version 0.0.14) was used for selecting reads with RE site next to the VP.
Alignment of sequence reads was performed with Bowtie2 (version 2.3.4.1) (Langmead and Salzberg, 2012) and “--local –very-sensitive-local” option to mouse genome (mm10 genome version).
Both Samtools (version 1.7-2) (Li et al., 2009) and Bedtools (version 2.26.0) (Quinlan and Hall, 2010) were used for filtering low quality reads (MAPQ<20) , chrM and blacklisted regions.
All reads were assigned to an RE site and all reads within 2MB of the VP excluding the first 2 REs in both sides of the VP were used for CPM normalization. BigWig were generated with bedtools genomecov and bedGraphToBigWig (Kent et al., 2010). All regions between RE sites were assigned RE normalized CPM value of the first RE while rolling mean of 21 RE was performed in R (version 4.0.4) with “rollmeanr”.
Assembly: mm10
Supplementary files format and content: bigwig of average normalized interactions from 2/3 independent biological samples
Library strategy: 4C-Seq

extract_protocol:
Briefly, 10 million cultured ESC, TSC and XEN cells were fixed with 12 ml of 1% formaldehyde (Thermo Scientific, 28908) in 10% FBS for 10 min at room temperature (RT) (tumbling).
Quenching of the cross-linking was performed with the addition of 1.8 ml of freshly prepared ice-cold 1 M glycine (Sigma-Aldrich #500046). Tubes were transferred directly on ice and centrifuged for 5 min 500g at 4°C. Cells were washed with 1× PBS and centrifuged for 5 min 500g at 4°C, and pellets were frozen in liquid nitrogen and stored at −80°C. Next, cells were then vigorously resuspended in 1 ml of fresh ice-cold lysis buffer (10 mM tris (pH 8), 10 mM NaCl, 0.2% NP-40, and 1 tablet of complete protease inhibitor (Roche, 04693159001)], transferred to 9 ml of prechilled lysis buffer, and incubated for 20 min on ice. Following centrifugation at 500g for 5 min at 4°C, the pellet was resuspended in 50uL of 0.5% SDS and incubated for 10 min at 65°C. SDS was quenched with 145uL ddH2O and 25uL of 10% Triton X-100 for 15 mins at 37°C. At this point, 5 l of the sample was taken as the “undigested control”. Next, 25ul of CutSmart buffer (NEB, B7204S) was added with 10μl DpnII enzyme (NEB, R0543M) and the samples were incubated overnight at 37°C under agitation (750rpm). Upon first digestion, 5μl of the sample was taken as the “digested control” while the efficiency of chromatin digestion was verified after DNA extraction from 5l of undigested and digested controls and loading in a 1.5% agarose gel. After verification of chromatin digestion (smear between 0.2 and 2 kb), DpnII was deactivated by 20 min incubation at 62°C (under agitation 750 rpm). Ligation of DNA ends between the cross-linked DNA fragments was performed  by diluting the samples in 669 μL ddH2O and adding 120 μL T4 ligation buffer (NEB, B0202), 60 μL 10mM ATP (NEB, P0756S), 120 μL 10% Triton X-100, 6 μL 20mg/ml BSA and 5 μL 400U/μl T4 DNA Ligase (NEB, M0202) overnight at 16oC (tumbling)  followed by 30min at RT. 10μl  of the ligated sample was tested as “ligated control,” on a 1.5% agarose gel. The samples were then treated with proteinase K and reverse crosslinked overnight at 65oC. Following RNase treatment, phenol/chloroform extraction and DNA precipitation, the pellets were dissolved in 100 μL of 10mM Tris pH 8 and incubated for 1 hour at 37°C. Efficiency of extraction and purification were verified on a 1.5% agarose gel. For the second digestion 20 μL of 10x buffer B (Fermentas), 10 μL Csp6I (Fermentas, ER0211), 80 μL ddH2O were added to the DpnII-ligated 3C template and samples were incubated overnight at 37°C under agitation (750rpm). Csp6I was inactivated at 65°C for 20 min, and DNA fragmentation was tested on 1.5% agarose gel. A second ligation was performed by adding 300 μL T4 ligation buffer, 150 μL 10mM ATP, 5μL T4 DNA Ligase, and ddH2O to 3mL and incubating overnight at 16°C. After 30 min of incubation at RT, samples were PCI-extracted, ethanol-precipitated, resuspended in 200 l of sterile water, and purified using the Qiaquick PCR Purification Kit (Qiagen). DNA concentration of each digested sample was calculated using the Qubit brDNA HS assay kit (Invitrogen). For library preparation, primers were designed either around the enhancer or the promoter of lineage specific genes. Library preparation was then performed using the inverse PCR strategy. Briefly, 4x200 ng of 4C-template DNA was used to PCR amplify the libraries using the Roche Expand long template PCR system (Roche, 11681842001) with the following PCR conditions: 94 °C for 2 min, 16 cycles: 94 °C for 10 s; [primer specific]°C for 1 min; 68 °C for 3 min, followed by a final step of 68 °C for 5 min. Amplified material was pooled, and primers were removed using SPRIselect beads (Beckman Coulter, B23317). A second round of PCR with the following conditions: (94 °C for 2 min, 20 cycles: 94 °C for 10 s; 60 °C for 1 min; 68 °C for 3 min and 68 °C for 5 min) was performed using the initial PCR library as a template, with overlapping primers to add the P5/P7 sequencing primers and indexes.


title: PDGFA XEN replicate3

description:
4C seq of PDGFA in XEN, replicate 3
av_xen_pdgfra.bw


title: NANOG ESC replicate2

description:
4C seq of NANOG in ESC, replicate 3
av_esc_nanog.bw

source_name: ESC

value: ESC

value: embryonic stem cells


title: SOX17 XEN replicate2

description:
4C seq of SOX17 in XEN, replicate 2
av_xen_sox17.bw


title: NANOG ESC replicate1

description:
4C seq of NANOG in ESC, replicate 2
av_esc_nanog.bw


title: PB00366_scRNA-seq_B039


title: PB00593_TEA-seq_B065


title: PDGFA XEN replicate1

description:
4C seq of PDGFA in XEN, replicate 1
av_xen_pdgfra.bw


title: PDGFA XEN replicate2

description:
4C seq of PDGFA in XEN, replicate 2
av_xen_pdgfra.bw


title: PB00562_scRNA-seq_B046


title: EPISC replicate2 [HiChIP]

description:
H3k27ac HiChiP seq for mouse EPISC replicate 2
episc.bedpe


title: MYCN ESC replicate1

description:
4C seq of MYCN in ESC, replicate 1
av_esc_mycn.bw


title: MYCN TSC replicate3

description:
4C seq of MYCN in TSC, replicate 3
av_tsc_mycn.bw


title: MYCN TSC replicate2

description:
4C seq of MYCN in TSC, replicate 2
av_tsc_mycn.bw


title: MYCN ESC replicate3

description:
4C seq of MYCN in ESC, replicate 3
av_esc_mycn.bw


title: MYCN ESC replicate2

description:
4C seq of MYCN in ESC, replicate 2
av_esc_mycn.bw


title: GATA6 XEN replicate3

description:
4C seq of Gata6 in XEN, replicate 3
av_xen_gata6.bw


title: XEN replicate2 [ChIP-Exo]

description: CTCF ChiP-Exo for mouse XEN replicate 2

data_processing:
library strategy: ChIP-Exo
ChIP-Exo reads were aligned to the mm10 genome using Bowtie version 2.3.4.1 with ‘--local –very-sensitive-local’ option active.
Filter low quoality reads (MAPQ<20), chrM and blacklisted regions with samtools and bedtools
Filter duplicates with picard tools
MACS2 (version 2.2.7.1) default settings with -broad option
Assembly: mm10
Supplementary files format and content: bigWig for each Chip-seq replicate and merged Peaks from 2 replicates
Supplementary files format and content: .bed files with peak coordinates and bigwig files

growth_protocol: Bruce-4 cells were cultured at 37˚C on gelatinized plate in FBS/LIF + 2i conditions. Cells were collected by trypsinization for 3 mins and were washed with PBS followed by centrifugation (500 g, 5 mins, 4˚C). 10 M cells were used per each replicate of library. Pellet was resuspended to have 1 million cells per mL in PBS (RT). Cells were crosslinked with 1% formaldehyde in RT for 10 mins on platform shaker. Crosslinking was quenched with 125 mM glycine for 5 min at RT on platform shaker. Crosslinked cells were centrifuged (500 g, 5 mins, 4˚C) and was washed twice with ice cold PBS. After the final wash and centrifuge, the pellet was snap frozen before extraction.

extract_protocol:
Frozen cell pellets were processed as described previously in ChIP-exo 5.0 protocol (Rossi et al.). 3 µg of anti-CTCF antibody (Sigma-Aldrich, 07-729) was used for o/n chromatin immunoprecipitation at 4˚C.
Immunoprecipitated material was processed as described previously in ChIP-exo 5.0 protocol (Rossi)

tag: chip antibody

value: CTCF antibody (Sigma-Aldrich, 07-729)


title: MYCN TSC replicate1

description:
4C seq of MYCN in TSC, replicate 1
av_tsc_mycn.bw


title: XEN replicate1 [ChIP-Exo]

description: CTCF ChiP-Exo  mouse XEN replicate 1


title: GATA6 ESC replicate2

description:
4C seq of Gata6 in ESC, replicate 2
av_esc_gata6.bw


title: GATA6 ESC replicate1

description:
4C seq of Gata6 in ESC, replicate 1
av_esc_gata6.bw


title: GATA6 ESC replicate3

description:
4C seq of Gata6 in ESC, replicate 3
av_esc_gata6.bw


title: GATA6 XEN replicate1

description:
4C seq of Gata6 in XEN, replicate 1
av_xen_gata6.bw


title: GATA6 XEN replicate2

description:
4C seq of Gata6 in XEN, replicate 2
av_xen_gata6.bw


title: TSC replicate2 [ChIP-Exo]

description: CTCF ChiP-Exo for mouse TSC replicate 2


title: ESC replicate1 [ChIP-Exo]

description: CTCF ChiP-Exo for mouse ESC replicate 1


title: XEN replicate2 [Hi-C]

description:
H3k27ac ChiP seq for mouse XEN replicate 2
xen_compartment.bedGraph
xen_tad.bed
xen2.reg

data_processing:
Hi-C data were pre-processed using HiC-bench platform
Read pairs with low MAPQ, self-ligated fragments and short-range interaction (<40kb) were filtered out prior to downstream analysis. ICE normalized matrices at various resolutions and .hic files were generated with both Hi-C-bench and juicer tools ‘pre’ option
Compartment analysis was performed at 100kb resolution with the use of CscoreTool (version 1.1) (Zheng and Zheng, 2018) for each experiment and chromosome separately with ‘minDis 1000000’
Topologically associated domains, boundaries and insulation scores were calculated with Hi-C-bench pipeline by using the ‘domain’ operation on the hic matrix at 40kb resolution.
Assembly: mm10
Supplementary files format and content: valid read pairs (.reg files), compartments and Tads in bed format

extract_protocol:
Approximately 500ng of DNA was used for each Hi-C sample to prepare libraries using the KAPA Hyper Prep Kit (KAPA, KK8502) and performing 5 cycles of amplification.
The protocol was performed as previously described (Rao et al., 2014; Di Giammartino et al., 2019). Hi-C was performed starting with 2M cells per replicate and using the Arima-Hi-C kit (Arima, A510008) according to manufacturer’s instructions.


title: TSC replicate2 [Hi-C]

description:
H3k27ac ChiP seq for mouse TSC replicate 2
tsc_compartment.bedGraph
tsc_tad.bed
tsc2.reg


title: XEN replicate1 [Hi-C]

description:
H3k27ac ChiP seq for mouse XEN replicate 1
xen_compartment.bedGraph
xen_tad.bed
xen1.reg


title: GATA4 XEN replicate2

description:
4C seq of Gata4 in XEN, replicate 2
av_xen_gata4.bw


title: GATA4 XEN replicate1

description:
4C seq of Gata4 in XEN, replicate 1
av_xen_gata4.bw


title: GATA4 TSC replicate1

description:
4C seq of Gata4 in TSC, replicate 1
av_tsc_gata4.bw


title: GATA4 TSC replicate2

description:
4C seq of Gata4 in TSC, replicate 2
av_tsc_gata4.bw


title: TSC replicate1 [Hi-C]

description:
H3k27ac ChiP seq for mouse TSC replicate 1
tsc_compartment.bedGraph
tsc_tad.bed
tsc1.reg


title: TSC input  [ChIP-Seq]

description: H3k27ac Input for TSC

data_processing:
ChIP-seq reads were aligned to the mm10 genome using Bowtie version 2.3.4.1 with ‘--local –very-sensitive-local’ option active.
Filter low quoality reads (MAPQ<20), chrM and blacklisted regions with samtools and bedtools
Filter duplicates with picard tools
MACS2 (version 2.1.1) default settings with -broad option
Assembly: mm10
Supplementary files format and content: bigWig for each Chip-seq replicate and merged Peaks from 2 replicates (except for Input sample)
Supplementary files format and content: .bed files with peak coordinates and bigwig files

growth_protocol: Initially cells were crosslinked in 1% formaldehyde at RT for 10 minutes and quenched with 125mM glycine for 5 mins at RT.

extract_protocol:
Cell pellets were washed twice in PBS and resuspended in 300ul lysis buffer (10mM Tris pH8, 1mM EDTA, 0.5% SDS) for at least 15 minutes.  Next, chromatin was sonicated in a Pico bioruptor device for 10 cycles with the length of the intervals being 30sec on/off, in order to produce 300-800 bp chromatin fragments. Sonicated chromatin was then spun down for 15 minutes at 4°C at 22.000g and 10μl of the sheared soluble chromatin solution was used in order to check the shearing efficiency and the rest was kept at 4oC. 5% of each sample was kept as an input while the rest of the supernatants were diluted 5 times with dilution buffer (0.01% SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with 3μg H3K27ac antibody (ab4729) O/N under agitation at 4°C.
25ng of immunoprecipitated material and input were used for ChIP-seq library preparation using the KAPA Hyper prep kit (KK8502) according to manufacturer’s instructions.


title: XEN input replicate2 [ChIP-Seq]

description: H3k27ac Input for XEN replicate 2


title: TSC replicate1 [ChIP-Exo]

description: CTCF ChiP-Exo for mouse TSC replicate 1


title: EPISC input replicate1 [ChIP-Seq]

description: H3k27ac Input for EPISC replicate 1

value: epiblast-like stem cells


title: ESC input replicate1 [ChIP-Seq]

description: H3k27ac Input for ESC replicate 1


title: XEN input replicate1 [ChIP-Seq]

description: H3k27ac Input for XEN replicate 1


title: EPISC input replicate2 [ChIP-Seq]

description: H3k27ac Input for EPISC replicate 2


title: EPISC replicate2 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse EPISC replicate 2
episc2.bw
episl.bed

value: Abcam H3K27ac antibody (ab4729)


title: ESC input replicate2 [ChIP-Seq]

description: H3k27ac Input for ESC replicate 2


title: XEN replicate1 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse XEN replicate 1
xen1.bw
xen.bed


title: TSC replicate1 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse TSC replicate 1
tsc1.bw
tsc.bed


title: TSC replicate2 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse TSC replicate 2
tsc2.bw
tsc.bed


title: ESC replicate1 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse ESC replicate 1
esc1.bw
esc.bed


title: EPISC replicate3

description:
ATAC-seq for mouse EPISC replicate 3
episl.bed

data_processing:
All paired-end sequenced reads were aligned to mouse genome (mm10) with  Bowtie2 (version 2.3.4.1) and “--local –very-sensitive-local -I 10 X 2000” option.
amtools, “MarkDuplicates” from picard tools and bedtools were used to filter out low quality reads (MAPQ<20), duplicate reads, chrM and blacklisted regions. All filtered reads were corrected for Tn5 insertion at each read end by shifting +4/-5 bp from the positive and negative strand respectively.
Not overlapping peaks from replicates were filtered out and only common peaks were used. Peak center (summit file) generated with MACS2 with ‘--narrow’ option were extended to 100bp (+/-50bp) for motif search and all overlapping summits were merged to form an accessibility atlas which was used as background for motif and chip enrichment with LOLA R package.
Assembly: mm10
Supplementary files format and content: bigWig for each of the three cell lines and common Peaks (summit of peak extended by 50bp) from 2 replicates
Supplementary files format and content: .bed files with peak coordinates extended 50bp around peak summit and bigwig files

growth_protocol: ATAC-seq was carried out as previously described with minor modifications (Buenrostro et al., 2015). For each cell line two replicates were performed and analyzed.

extract_protocol:
A total of 50,000 cells were washed with 50 μL of cold PBS and then nuclei were isolated in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). Nuclei were then centrifuged for 10min at 800g at 4°C, followed by the addition of 50 μL transposition reaction mix (25 μL TD buffer, 2.5 μL Tn5 transposase and 22.5 μL ddH2O) using reagents from the Nextera DNA libraryPreparation Kit (Illumina #FC-121-103). Samples were then incubated at 37°C for 30min. DNA was isolated using a ZYMO Kit (D4014).
ATAC-seq libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541)


title: ESC replicate2 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse ESC replicate 2
esc2.bw
esc.bed


title: GATA4 XEN replicate3

description:
4C seq of Gata4 in XEN, replicate 3
av_xen_gata4.bw


title: XEN replicate2 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse XEN replicate 2
xen2.bw
xen.bed


title: EPISC replicate2

description:
ATAC-seq for mouse EPISC replicate 2
episl.bed


title: GATA4 TSC replicate3

description:
4C seq of Gata4 in TSC, replicate 3
av_tsc_gata4.bw


title: EPISC replicate1 [ChIP-Seq]

description:
H3k27ac ChiP seq for mouse EPISC replicate 1
episc1.bw
episl.bed


title: XEN replicate2

description:
ATAC-seq for mouse XEN replicate 2
xen.bw
xen.bed


title: EPISC replicate2 [RNA-Seq]

description:
mouse epiblast-like stem cell replicate 2
EPISC2

data_processing:
Alignment with Tophat2
Filtering and data format conversion with Samtools
Read mapping to genes was performed with Htseq-count and  ‘-m intersection-nonempty’ option
DESeq was used to identify differential expressed genes between cell lines with fold change 2 and p-adj <0.01 as cut off
Only and protein coding and lincRNA were used from GRCm38.95
Assembly: mm10
Supplementary files format and content: csv-delimited text file with raw counts from HT-seq count

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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 TruSeq RNA Sample Preparation Kit (20020594) according to the manufacturer’s protocol

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: genotype

value: WT


title: EPISC replicate1

description:
ATAC-seq for mouse EPISC replicate 1
episl.bed


title: TSC replicate3

description:
ATAC-seq for mouse TSC replicate 2
tsc.bw
tsc.bed


title: TSC replicate2


title: XEN replicate1

description:
ATAC-seq for mouse XEN replicate 1
xen.bw
xen.bed


title: TSC replicate2 [RNA-Seq]

description:
mouse trophoblast stem cell replicate 2
TSC2


title: TSC replicate1

description:
ATAC-seq for mouse TSC replicate 1
tsc.bw
tsc.bed


title: ESC new replicate1

description:
ATAC-seq for mouse ESC new replicate 1
escnew.bw
esc.bed


title: ESC new replicate2

description:
ATAC-seq for mouse ESC new replicate 2
escnew.bw
esc.bed


title: XEN replicate2 [RNA-Seq]

description:
mouse extraembryonic endoderm stem cells replicate 2
XEN2


title: Set5 3D culture (N/A) and with T cells, 3D triculture (N/A/M), and 3D PiChip (N/A/M/T cells)  in CTRL (G10) and AD (H10)

status: Public on Aug 14 2023

city: Charlestown

first: Joseph

last: Park

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital/Harvard Medical School

description: Set5. 3D culture (Neuron/astrocyte), 3D triculture (Neuron/Astrocyte/Microglia), 3D PiChip (Neuron/Astrocyte/Microglia/T cells), and 3D culture with T cells (Neuron/Astrocyte/T cells) in CTRL (G10) and AD (H10).

data_processing:
Demultiplexing, barcode processing, and gene count matrix files generated.
Assembly: hg38
Supplementary files format and content: gene name and count matrix file

source_name: ReN cells, iPSCs and Human derived blood T cells)

extract_protocol:
Cells treated with Accutase at room termperature for 10mins and then dissociated to disperse into single cells. Shorlty after that Live/cell dead assay performed to count live cells and then loaded into InDrop in-house equipment for the capturing of the single cells.
After generating barcoded cDNA from single cells, the droplets are broken and cDNA is processed for next-gen sequencing (Nature Protocol, ; doi:10.1038/nprot.2016.154). Briefly, purification of the cDNA library and second-strand synthesis, followed by in vitro transcription (IVT) using T7 RNA polymerase. The amplified antisense RNA is fragmented using zinc-ion-mediated cleavage, and converted into a DNA library ready for Illumina sequencing by a second RT reaction and a few cycles of PCR. This library preparation step takes ~2 d and includes two quality control (QC) steps. As detailed in Figure 3, a library index is added during the final PCR to allow pooling of multiple libraries for sequencing in a single run. Our protocol is designed to work with all Illumina sequencing platforms and can possibly be adapted to work with different sequencers.

value: Brain cells (Neuron, astrocyte, microglia and T cells)


title: ESC ad replicate1

description:
ATAC-seq for mouse ESC ad replicate 1
escad.bw
esc.bed


title: ESC ad replicate2

description:
ATAC-seq for mouse ESC ad replicate 2
escad.bw
esc.bed


title: Set3 3D culture (N/A) and with T cells, 3D triculture (N/A/M), and 3D PiChip (N/A/M/T cells)  in CTRL (G10) and AD (H10)

description: Set3. 3D culture (Neuron/astrocyte), 3D triculture (Neuron/Astrocyte/Microglia), 3D PiChip (Neuron/Astrocyte/Microglia/T cells), and 3D culture with T cells (Neuron/Astrocyte/T cells) in CTRL (G10) and AD (H10).

value: ReN cells, iPSCs and Human derived blood T cells)


title: EPISC replicate1 [RNA-Seq]

description:
mouse epiblast-like stem cell replicate 1
EPISC1


title: ESC replicate2 [RNA-Seq]

description:
mouse embryonic stem cell replicate 2
ESC2


title: TSC replicate1 [RNA-Seq]

description:
mouse trophoblast stem cell replicate 1
TSC1


title: Set4 3D culture (N/A) and with T cells, 3D triculture (N/A/M), and 3D PiChip (N/A/M/T cells)  in CTRL (G10) and AD (H10)

description: Set4. 3D culture (Neuron/astrocyte), 3D triculture (Neuron/Astrocyte/Microglia), 3D PiChip (Neuron/Astrocyte/Microglia/T cells), and 3D culture with T cells (Neuron/Astrocyte/T cells) in CTRL (G10) and AD (H10).


title: XEN replicate1 [RNA-Seq]

description:
mouse extraembryonic endoderm stem cells replicate 1
XEN1

value: XEN

value: extra embryonic stem cells


title: ESC replicate1 [RNA-Seq]

description:
mouse embryonic stem cell replicate 1
ESC1


title: Set2 3D culture (N/A) and with T cells, 3D triculture (N/A/M), and 3D PiChip (N/A/M/T cells)  in CTRL (G10) and AD (H10)

description: Set2. 3D culture (Neuron/astrocyte), 3D triculture (Neuron/Astrocyte/Microglia), 3D PiChip (Neuron/Astrocyte/Microglia/T cells), and 3D culture with T cells (Neuron/Astrocyte/T cells) in CTRL (G10) and AD (H10).


title: 5_S27_L006_R1_001

status: Public on Aug 07 2023

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

data_processing:
Raw sequencing reads were aligned to the mouse (mm10) or human (hg38) genome using default settings of HISAT2.
Alignments were filtered to only include uniquely mapped reads using SAMtools v.1.8.
Peak-calling was normalized to respective inputs for each sample and was performed using MACS v.2.1.1 (44) with default settings and filtered for FDR < 0.05 and fold change > 1.5.
Differential analysis was performed using diffReps (45) with a 1 kb? window size.
Peaks and differential sites were further annotated to nearby genes or intergenic regions using the region analysis tool from the diffReps package.
Assembly: mm10, hg38
Supplementary files format and content: Tab-delimited text files containing peaks

source_name: adult (6-wk) dorsal raphe nucleus tissue

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the TruSeq® ChIP Sample Preparation kit. All the DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter??? Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: defeat

tag: gender

value: Female


title: 4_S26_L006_R1_001

value: adult (6-wk) dorsal raphe nucleus tissue


title: 6_S28_L006_R1_001


title: 4-input_S20_L005_R1_001

value: Input


title: Set1 3D culture (N/A) and with T cells, 3D triculture (N/A/M), and 3D PiChip (N/A/M/T cells)  in CTRL (G10) and AD (H10)

description: Set1. 3D culture (Neuron/astrocyte), 3D triculture (Neuron/Astrocyte/Microglia), 3D PiChip (Neuron/Astrocyte/Microglia/T cells), and 3D culture with T cells (Neuron/Astrocyte/T cells) in CTRL (G10) and AD (H10).

tag: cell type


title: 1_S23_L006_R1_001

value: ctl

tag: tissue


title: 65364_IFNY

status: Public on Aug 09 2023

type: RNA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Gene expression data from in vitro differentiated mouse bone marrow-derived macrophages (IFNg)

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Mouse array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using TAC software with default parameters (SST-RMA algorithm and then LIMMA to calculate significant differential expression between samples)

label: Biotin

source_name: Total RNA from in vitro differentiated mouse bone marrow-derived macrophages

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted following GenElute RNA MiniPrep Kit (Sigma) Instructions.

tag: condition

value: IFNY


title: 6-input_S22_L005_R1_001


title: 65366_CM_CAF_CT

description: Gene expression data from in vitro differentiated mouse bone marrow-derived macrophages (Wild-type)

value: CM


title: 2-input_S18_L005_R1_001


title: 3_S25_L006_R1_001


title: 65366_IFNY

value: in vitro differentiated mouse bone marrow-derived macrophages


title: 5-input_S21_L005_R1_001


title: 65366_IL4

description: Gene expression data from in vitro differentiated mouse bone marrow-derived macrophages (IL4)


title: 65366_DMEM

description: Gene expression data from in vitro differentiated mouse bone marrow-derived macrophages (DMEM)

value: DMEM


title: 65364_DMEM


title: 65366_CM_CAF_KO

description: Gene expression data from in vitro differentiated mouse bone marrow-derived macrophages (Snai1 knockout)


title: 65364_CM_CAF_KO


title: 65364_IL4


title: 5_S3_L007_R1_001

value: ss

value: Male

value: H3K4me3 (Abcam #ab8580)


title: 65364_CM_CAF_CT


title: 6_S4_L006_R1_001

value: res

value: H3K4me3Q5ser (MilliporeSigma #ABE2580)


title: 4_S2_L005_R1_001


title: 1-input_S17_L005_R1_001


title: 4_S2_L006_R1_001


title: PB00003_scRNA-seq_B001

value: peripheral blood mononuclear cells

tag: birth year

value: Caucasian


title: 2_S1_L007_R1_001


title: 7_S5_L006_R1_001


title: 3-input_S19_L005_R1_001


title: 2_S1_L005_R1_001


title: 7_S5_L005_R1_001


title: 7_S5_L007_R1_001


title: 6_S4_L007_R1_001


title: 6_S4_L005_R1_001


title: 2_S24_L006_R1_001


title: 5_S3_L005_R1_001


title: 2_S1_L006_R1_001


title: 5_S3_L006_R1_001


title: 19_S7_L007_R1_001


title: 19_S7_L005_R1_001


title: 19_S7_L006_R1_001


title: 16_S6_L006_R1_001


title: 15_S9_L007_R1_001


title: 12_S8_L007_R1_001


title: 16_S6_L005_R1_001


title: 4_S2_L007_R1_001


title: 15_S9_L006_R1_001


title: 15_S9_L005_R1_001


title: 12_S8_L005_R1_001


title: WT_P0-3

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Raw sequence reads were processed using lcdb-wf v1.9rc (lcdb.github.io/lcdb-wf/) according to the following steps. Raw sequence reads were trimmed with cutadapt v3.4  to remove any adapters while performing light quality trimming with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length = 25.’
Sequencing library quality was assessed with fastqc v0.11.9 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters ‘–subset 100000 –aligner bowtie2.’ Trimmed reads were mapped to the Mus musculus reference genome (Gencode m18) using HISAT2 v2.2.1 .
Multimapping reads were filtered using samtools v1.12 .
Uniquely aligned reads were then counted in genes with the featureCounts program of the subread package v2.0.1 using Mus musculus reference (Gencode m18) annotations .
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes featureCounts raw counts.

source_name: Palate

extract_protocol:
Dissected palatal shelves from E13.5, E14.5, E15.5, E16.5, and P0 were used for bulk RNA-sequencing. Secondary palate organs from 3 embryos were pooled into 1.5 mL tubes and placed immediately on dry ice and stored in -80°C. Tissues were homogenized using biomasher II. mRNA was extracted and purified using Macherey Nagel™ NucleoSpin™ mini kit.
Samples were processed according to the Illumina RNA library preparation.

tag: developmental stage

value: Post-natal

value: Palate

value: WT


title: embryonic wt mouse palate e15.5 scRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 with default parameters.
Assembly: mm10
Supplementary files format and content: tab-separated gene features (zipped)
Supplementary files format and content: tab-separated cell barcodes (zipped)
Supplementary files format and content: expression matrix (zipped)

source_name: palate

extract_protocol:
Embryonic palatal shelves were collected from the stages of E13.5, E14.5, and E15.5. Tissues from 3 embryos were pooled in 500 µL PBS in 0.04% BSA in a 1.5 mL tubes on ice. Centrifuged the tubes with tissue using mini centrifuge for few seconds. Removed the supernatant and cut the tissues into small fragments using a small surgical scissor. Added 1mL of PBS in 0.04% BSA, spin the tissue down using mini centrifuge and removed supernatant. Enzymatic digestion of the tissues was done using TrypLE express enzyme at 37°C with shaking at 600 rpm for 20 minutes. Occasional pipetting was done with a wide bore pipette tip. Added 4mL DMEM medium to stop enzymatic digestion and mixed well by gentle pipetting. Filtered the cells using a 70 µM cell strainer and centrifuged at 1500 rpm for 5 minutes. Removed supernatant and added 5mL of PBS in 0.04% BSA into the cell pellet and centrifuged at 1500 rpm for 5 minutes. Removed the supernatant and single cell suspension was fixed in methanol according to 10X Genomics protocol and stored in -80°C.
Libraries were prepared according to Illumina Single cell RNA seq preparation procotol

value: palate

value: C57BL/6J (wt)


title: embryonic wt mouse palate e14.5 scRNA-seq


title: embryonic wt mouse palate e13.5 scRNA-seq


title: WT_E16_5-1


title: WT_P0-1


title: WT_E16_5-3


title: WT_E16_5-2


title: WT_E15_5-2


title: 16_S6_L007_R1_001

value: ctl

value: adult (6-wk) dorsal raphe nucleus tissue


title: WT_E14_5-3


title: WT_E15_5-3


title: WT_E14_5-2


title: WT_E14_5-1


title: WT_E13_5-3


title: WT_E13_5-2


title: WT_E15_5-1


title: WT_E13_5-1


title: P40

status: Public on Aug 01 2023

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

country: China

institute: Sichuan university

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 42 months within a one-year follow-up, this defined as:recurrent erosion group

data_processing:
The data was processed by Trimmomatic v0.036, RseQC v2.6.4, fastqc v0.11.5 and hisat v2.2.1.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: oral mucosal cell

extract_protocol:
RNA was extracted by Cetyl Trimethyl Ammonium Bromide (CTAB) method. And the extracted RNA was then tested for purity, concentration, and integrity. A number of library construction procedures, including end repair, end addition of A, ligation adapter addition, and fragment security screening, were carried out once mRNA is recovered. It was sequenced on the device following PCR amplification and purification.
RNA libraries for RNA-seq were prepared using High Sensitivity DNA assay Kit（Agilent Technologies, 5067-4626） following manufacturer's protocols.

value: oral mucosal cell

tag: clinical type (oral mucosa at time of biopsy)

value: EOLP

tag: clinical type (oral mucosa at one-year follow-up)

value: REOLP


title: P37

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 39 months within a one-year follow-up, this defined as:recurrent erosion group


title: 12_S8_L006_R1_001


title: P36

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 38 months within a one-year follow-up, this defined as:persistent non-erosion group

value: SOLP


title: P32

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 34 months within a one-year follow-up, this defined as:recurrent erosion group


title: P35

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 37 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P34

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 36 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P33

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 35 months within a one-year follow-up, this defined as:persistent non-erosion group


title: WT_P0-2


title: P31

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 33 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P30

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 32 months within a one-year follow-up, this defined as:recurrent erosion group


title: P29

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 31 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P25

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 27 months within a one-year follow-up, this defined as:persistent non-erosion group

value: NEOLP


title: P19

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 21 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P27

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 29 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P18

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 20 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P23

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 25 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P22

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 24 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P26

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 28 months within a one-year follow-up, this defined as:recurrent erosion group


title: P21

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 23 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P14

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 16 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P17

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 19 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P20

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 22 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P10

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 12 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P4

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 6 months within a one-year follow-up, this defined as:recurrent erosion group


title: P3

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 5 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P11

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 13 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P6

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 8 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P24

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 26 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P16

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 18 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P39

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 41 months within a one-year follow-up, this defined as:recurrent erosion group


title: P38

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 40 months within a one-year follow-up, this defined as:recurrent erosion group


title: P15

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 17 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P13

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 15 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P9

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 11 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P5

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 7 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P12

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 14 months within a one-year follow-up, this defined as:recurrent erosion group


title: P8

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 10 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P28

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 30 months within a one-year follow-up, this defined as:recurrent erosion group


title: ESCC1-responder (PART2)

status: Public on Jul 07 2023

city: chengdu

first: hong

last: wu

address: 55 renmin south road

institute: sichuan cancer hospital

description:
Responder ESC1-1-2
CCAGGGCA

data_processing:
Basecalls performed using CASAVA version 1.8
Read alignment and count summarization were performed using CellRanger(v3.1.0)
Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38_Ensembl91
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Esophageal cancer

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 5’ Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 5’ Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: ESCC patients underwent Toripalimab plus paclitaxel and carboplatin as neoadjuvant therapy.

value: Esophageal cancer

value: Neoadjuvant immunotherapy


title: ESCC3-responder (PART3)

description:
Responder ESC3-1-3
CGTCCTAG


title: ESCC3-responder (PART1)

description:
Responder ESC3-1-1
ACCGGCTC


title: ESCC3-responder (PART2)

description:
Responder ESC3-1-2
GAGTTAGT


title: P7

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 9 months within a one-year follow-up, this defined as:persistent non-erosion group


title: P2

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  EOLP
According to whether the interval of erosions in oral mucosa more than 4 months within a one-year follow-up, this defined as:persistent non-erosion group


title: mouse olfactory bulb, ISS, rep3 [MOB-ISS-3]

status: Public on Jul 11 2023

city: shanghai

first: di

last: sun

address: pujian road 160

department: institute of molecular medicine

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
*library strategy: Spatial transcriptomic sequencing
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: mouse olfactory bulb

extract_protocol:
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Dendrimeric DNA coordinate barcoding arrays capture spatial mRNAs of tissues with high efficiency"
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Amplification, library construction, and sequencing"

value: mouse olfactory bulb


title: mouse olfactory bulb, ISS, rep2 [MOB-ISS-2]


title: ESCC2-Non-responder (PART1)

description:
Non-responder ESC2-1-1
AAGCGCTG


title: ESCC2-Non-responder (PART2)

description:
Non-responder ESC2-1-2
CGTTTGAT


title: ESCC1-responder (PART1)

description:
Responder ESC1-1-1
AATAATGG


title: mouse olfactory bulb, ISS, rep1 [MOB-ISS-1]


title: ESCC1-responder (PART3)

description:
Responder ESC1-1-3
TGCCTCAT


title: CD16 low Vd2 T cells from healthy donor PBMC [Number9]

status: Public on Jun 29 2023

city: Los Angeles

first: Wenbin

last: Guo

address: 610 Charles E. Young Drive, TLSB 5000

institute: UCLA

data_processing:
The raw sequencing data underwent quality check using FastQC software (version 0.11.9), and fastp (version 0.23.2) was employed to remove sequencing adapters and low-quality bases
The trimmed reads were mapped to the human reference genome (hg38) along with and annotation file gencode v32 using software STAR (version 2.7.9a)
gene count matrixes were obtained using featureCounts from Subread package (version 2.0.3)
Batch effect removal was carried out using Combat-Seq, which was implemented in the sva package (version 3.44.0)
Downstream data analysis was performed using R (version 4.2), processing details can be found in the manuscript, code can be requested from the corresponding author
Assembly: hg38
Supplementary files format and content: raw_counts.txt: tab-delimited text file includes gene expression raw counts for each sample
Supplementary files format and content: raw_counts_batch_adjusted.txt: tab-delimited text file includes gene expresson counts for each sample after batch effects correction
Supplementary files format and content: sample_attr.txt: tab-delimited text file includes sample attributes for all of the samples in the dataset, including the reanalyzed samples
Supplementary files format and content: DESeq2_diff_expr_results.tsv: tab-delimited text file includes the differential expression analysis results

extract_protocol:
RNAs were isolated from each cell sample using a miRNeasy Mini Kit (QIAGEN).
Libraries were constructed using an Illumina TruSeq Stranded Total RNA Sample Prep kit.

value: gd T cells

tag: batch


title: ESCC2-Non-responder (PART3)

description:
Non-responder ESC2-1-3
GTAGCACA

tag: treatment


title: ESCC2-Non-responder (PART4)

description:
Non-responder ESC2-1-4
TCCAATGC


title: P1

description:
According to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this grouped as:  NEOLP
According to whether the interval of erosions in oral mucosa more than 3 months within a one-year follow-up, this defined as: persistent non-erosion group


title: CD16 low Vd2 T cells from healthy donor PBMC [PBMC-gdT-2]


title: ESCC3-responder (PART4)

description:
Responder ESC3-1-4
TTAAAGCA


title: CD16 high Vd2 T cells from healthy donor PBMC [Number20]


title: CD16 low Vd2 T cells from healthy donor PBMC [Number17]


title: NK cells from healthy donor PBMC [PBMC-NK-2]

source_name: NK cells from healthy donor PBMC

value: NK cells


title: CD16 low Vd2 T cells from healthy donor PBMC [Number13]


title: CD16 low Vd2 T cells from healthy donor PBMC [Number16]


title: pUbi-OsNAR2.1 transgenic line miRNA sequence

status: Public on Jun 23 2023

city: Nanjing

first: Yong

last: Zhang

address: street of Zhongling 50

institute: Jiangsu Acdemy of Agricultural Sciences

data_processing:
The clean reads that passed the quality filter as raw file, which were processed to remove the adaptor sequence as the trimmed reads. Trimmed reads were alignment to the miRBase pre-miRNAs as processed data file.
miRNA sequencing in this study done by KangChen Bio-tech, Shanghai, China. Sequencing library preparation and data analysis was described as before (Ding et al 2015 ).
Assembly: IRGSP1

organism: Oryza sativa

source_name: leaves, flowers and stems

growth_protocol: WT-N, OsNAR2.1 RNAi and  Ov199 lines for miRNA seq were  grown in plots at Nanjing Agricultural University in Nanjing, Jiangsu, 2014. Nanjing, Jiangsu is in a subtropical monsoon climate zone. Chemical properties of the soils in the plots included organic matter, 11.56 g/kg; total N content, 0.91 g/kg; available P content, 18.91 mg/kg; exchangeable K, 185.67 mg/kg; and pH 6.5. Basal applications of 30 kg P/ha (Ca(H2PO4)2) and 60 kg K/ha (KCl) were made to all plots 3 days before transplanting. N fertilizer as urea accounted for 40%, 30% and 40% of the total N fertilizer was applied prior to transplanting, at tillering, just before the heading stage, respectively.

extract_protocol: Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 36 cycles on Illumina HiSeq per the manufacturer’s instructions.

value: leaves, flowers and stems

tag: line


title: NK cells from healthy donor PBMC [Number6]


title: ESCC1-responder (PART4)

description:
Responder ESC1-1-4
GTGTCATC


title: CD16 high Vd2 T cells from healthy donor PBMC [PBMC-gdT-1]


title: OsNAR2.1RNAi miRNA sequence

treatment_protocol: Chemical properties of the soils in the plots included organic matter, 11.56 g/kg; total N content, 0.91 g/kg; available P content, 18.91 mg/kg; exchangeable K, 185.67 mg/kg; and pH 6.5. Basal applications of 30 kg P/ha (Ca(H2PO4)2) and 60 kg K/ha (KCl) were made to all plots 3 days before transplanting. N fertilizer as urea accounted for 40%, 30% and 40% of the total N fertilizer was applied prior to transplanting, at tillering, just before the heading stage, respectively.

value: Ni


title: NK cells from healthy donor PBMC [PBMC-NK-1]


title: Vehicle (saline) treatment in PFC_D2R-KO mouse 2

status: Public on Jun 17 2023

city: Toronto

first: Martin

last: Beaulieu

state: Ontario

address: 1 king's college circle room 4336

department: Pharmacology and Toxicology

country: Canada

institute: University of Toronto

description:
V_V_7
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA

data_processing:
RNA quality control and alignment were conducted at TCAG at the Hospital for Sick Children. Read quality was assessed by FastQC v.0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter trimming and removal of lower quality ends was performed using Trim Galore v. 0.5.0. All raw FASTQC files were aligned to the Mus musculus GENCODE reference genome (GRCm39) using the STAR aligner, v.2.6.0c software. The STAR alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2 (HTSeq). Differential expression analysis was performed using DESeq2 v.1.26.0s, using R v.3.6.1. Initial minimal filtering of 10 reads per gene for all samples was applied to the datasets. Normalized read counts were converted into the log-read counts which were then used for identifying differential expressed genes (DEGs).
Differential expression testing was carried out for: PFC_D2R-KO Saline versus Control Saline; Control Amph vs. Control Saline; PFC_D2R-KO Amph vs. PFC_D2R-KO Saline.
Assembly: Genome reference sequence: GRCm39, Gencode M27 gene models.
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts.
Supplementary files format and content: VV-KO_vs_VV-Control_DifExp_FPKMs_DESeq2.tsv file is the Reference-based count-based differential gene expression comparison of : Vehicle treatment in PFC D2R-KO mice versus Vehicle in control mice.
Supplementary files format and content: VA-KO_vs_VV-KO_woVA7_DifExp_FPKMs_DESeq2.tsv file is the Reference-based count-based differential gene expression comparison of : Amphetamine treatment in PFC D2R-KO mice versus Vehicle in PFC D2R-KO mice.
Supplementary files format and content: VA-Control_vs_VV-Control_DifExp_FPKMs_DESeq2.tsv file is the Reference-based count-based differential gene expression comparison of : Amphetamine treatment in control mice versus Vehicle in control mice.

source_name: Striatum

extract_protocol:
Mice were killed by rapid cervical dislocation. Heads of animals were immediately cooled by immersion in liquid nitrogen for 3 seconds. Striatum tissues were dissected rapidly (within 30 s) on an ice-cold surface and frozen in liquid nitrogen using microsurgical knife (KF Technology) and stored in -80°C. For RNA preparation, brain tissues were rapidly homogenized in Trizol (ThermoFisher) and proceeded for RNA isolation following the manufacturer’s protocol (Zymo Research). RNA was resuspended in water. Total RNA was monitored for quality control using the Nanodrop absorbance ratios for 260/280nm.
Library construction was performed according to the Illumina NovaSeq – S4 flowcell guide.

treatment_protocol: For striatal RNA sequencing analysis to acute amphetamine treatment, AVV5 D2R-sgRNA/mCherry or AAV5 syn-mCherry (control) was stereotaxically injected into PFC of D2Cre_floxCas9-EGFP mice. Three weeks after surgery, mice were administered saline daily for 5 days followed by a last challenging injection of amphetamine at the day 9 of the experiment. The motor activity was recorded for 30 min everyday after injection. Mice was sacrificed 90 min after the last injection of amphetamine (day9).

value: Striatum

tag: Sex

value: Male

tag: age

value: 4 months

value: Saline


title: Vehicle (saline) treatment in PFC_D2R-KO mouse 1

description:
V_V_6
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: NK cells from healthy donor PBMC [Number5]


title: Nipponbare miRNA sequence

value: WT-N


title: Vehicle (saline) treatment in control mouse 3

description:
V_V_3
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry

value: Control


title: Vehicle (saline) treatment in control mouse 4

description:
V_V_4
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: Amphetamine treatment in control mouse 3

description:
V_A_3
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry

value: Amphetamine 3mg/kg


title: Vehicle (saline) treatment in control mouse 2

description:
V_V_2
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: Amphetamine treatment in PFC_D2R-KO mouse 2

description:
V_A_8
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: Vehicle (saline) treatment in control mouse 1

description:
V_V_1
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: Amphetamine treatment in PFC_D2R-KO mouse 1

description:
V_A_6
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: Amphetamine treatment in control mouse 2

description:
V_A_2
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: Amphetamine treatment in PFC_D2R-KO mouse 3

description:
V_A_9
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: Amphetamine treatment in PFC_D2R-KO mouse 4

description:
V_A_10
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: Amphetamine treatment in control mouse 1

description:
V_A_1
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: Amphetamine treatment in control mouse 5

description:
V_A_5
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: mRNA-derived cDNA R1041_5-G

status: Public on Jun 16 2023

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
mRNA-derived cDNA
polyA RNA
paired-end
Illumina NovaSeq 6000
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Tumor, Normal, Lymph Node and PBMC

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the hg19 1.2.0 genome build and Ensembl 82 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg19 1.2.0
Supplementary files format and content: Processed counts from CellRanger in an R object, data_SingleCellExperiment_object.Rda; Additional metadata in “sample_annots.csv” and “full_HCC_cluster_annotation.csv”

source_name: Liver

extract_protocol:
Human tumor lesions and non-involved adjacent tissues were digested as described in the material and method. Briefly, samples received mechanical and enzymatic digestion, filtration and the cell suspension was enriched in immune cells using a Percoll gradient, followed by a RBC lysis. Lymph nodes were digested mechanically and enzymatically followed by RBC lysis. Blood samples were processed by Ficoll followed by RBC lysis.
Library was prepared using Chromium Single Cell 3ʹ v2 protocol/3ʹ  protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell associated protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell associated protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

tag: library type

value: mRNA

tag: antibodies/tags


title: mRNA-derived cDNA R1041_4-G


title: Vehicle (saline) treatment in PFC_D2R-KO mouse 4

description:
V_V_9
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: Vehicle (saline) treatment in PFC_D2R-KO mouse 5

description:
V_V_10
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: mRNA-derived cDNA R1041_2-G


title: Vehicle (saline) treatment in PFC_D2R-KO mouse 3

description:
V_V_8
PFC_D2R-KO mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 D2R-sgRNA


title: mRNA-derived cDNA R1041_1-G


title: mRNA-derived cDNA R1040_5-G


title: Vehicle (saline) treatment in control mouse 5

description:
V_V_5
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: mRNA-derived cDNA R1040_6-G


title: mRNA-derived cDNA R1040_3-G


title: mRNA-derived cDNA R1040_1-G


title: mRNA-derived cDNA R1039_6-G


title: mRNA-derived cDNA R1039_5-G


title: Amphetamine treatment in control mouse 4

description:
V_A_4
Control mice = D2RCre_floxCas9-EGFP mice received virus injection in mPFC of AAV5 syn-mCherry


title: mRNA-derived cDNA R1040_2-G


title: mRNA-derived cDNA R1039_4-G


title: mRNA-derived cDNA R1039_2-G


title: mRNA-derived cDNA R1039_3-G


title: mRNA-derived cDNA R1038_5-G


title: mRNA-derived cDNA R1041_3-G


title: mRNA-derived cDNA R1038_4-G


title: mRNA-derived cDNA R1037_5-G


title: mRNA-derived cDNA R1039_1-G


title: mRNA-derived cDNA R1032_6-G


title: mRNA-derived cDNA R1037_2-G


title: mRNA-derived cDNA R1037_3-G


title: mRNA-derived cDNA R1037_6-G


title: mRNA-derived cDNA R1037_1-G


title: mRNA-derived cDNA R1038_3-G


title: mRNA-derived cDNA R1037_8-G


title: mRNA-derived cDNA R1038_1-G


title: mRNA-derived cDNA R1037_4-G


title: mRNA-derived cDNA R1037_7-G


title: mRNA-derived cDNA R1032_5-G


title: mRNA-derived cDNA R1040_4-G


title: mRNA-derived cDNA R1031_6-G


title: mRNA-derived cDNA R1032_3-G


title: mRNA-derived cDNA R1032_1-G


title: mRNA-derived cDNA R1031_5-G


title: mRNA-derived cDNA R1032_4-G


title: mRNA-derived cDNA R1031_4-G


title: mRNA-derived cDNA R1031_3-G


title: mRNA-derived cDNA R1032_2-G


title: mRNA-derived cDNA R1031_1-G


title: mRNA-derived cDNA R1031_2-G


title: mRNA-derived cDNA R1030_6-G


title: mRNA-derived cDNA R1030_5-G


title: mRNA-derived cDNA R1038_2-G


title: mRNA-derived cDNA R1030_3-G


title: mRNA-derived cDNA R1030_4-G


title: mRNA-derived cDNA R1030_1-G


title: mRNA-derived cDNA R1030_2-G


title: mRNA-derived cDNA R1029_6-G


title: mRNA-derived cDNA R1029_5-G


title: mRNA-derived cDNA R1029_2-G


title: mRNA-derived cDNA R1027_4-G


title: mRNA-derived cDNA R1027_5-G


title: mRNA-derived cDNA R1029_4-G


title: mRNA-derived cDNA R1029_3-G


title: mRNA-derived cDNA R1027_1-G


title: mRNA-derived cDNA R1027_3-G


title: mRNA-derived cDNA R1029_1-G


title: mRNA-derived cDNA R1026_1-G


title: mRNA-derived cDNA R1025_5-G


title: mRNA-derived cDNA R1027_2-G


title: mRNA-derived cDNA R1026_4-G


title: mRNA-derived cDNA R1025_6-G


title: mRNA-derived cDNA R1026_2-G


title: mRNA-derived cDNA R1025_4-G


title: mRNA-derived cDNA R1025_3-G


title: mRNA-derived cDNA R1025_2-G


title: mRNA-derived cDNA R1023_6-G


title: mRNA-derived cDNA R1023_5-G


title: mRNA-derived cDNA R1023_3-G


title: mRNA-derived cDNA R1023_2-G


title: mRNA-derived cDNA R1023_1-G


title: mRNA-derived cDNA R1021_6-G


title: mRNA-derived cDNA R1021_4-G


title: mRNA-derived cDNA R1026_5-G


title: mRNA-derived cDNA R1021_5-G


title: mRNA-derived cDNA R1021_3-G


title: mRNA-derived cDNA R1021_2-G


title: mRNA-derived cDNA R1017_6-G


title: mRNA-derived cDNA R1017_5-G


title: mRNA-derived cDNA R1017_3-G


title: mRNA-derived cDNA R1026_3-G


title: mRNA-derived cDNA R1017_2-G


title: mRNA-derived cDNA R1014_3-G


title: mRNA-derived cDNA R1014_2-G


title: mRNA-derived cDNA R1025_1-G


title: mRNA-derived cDNA R1012_6-G


title: mRNA-derived cDNA R1014_1-G


title: mRNA-derived cDNA R1012_4-G


title: mRNA-derived cDNA R1017_4-G


title: mRNA-derived cDNA R1017_1-G


title: mRNA-derived cDNA R1012_1-G


title: mRNA-derived cDNA R1023_4-G


title: mRNA-derived cDNA R1012_2-G


title: mRNA-derived cDNA R1012_3-G


title: mRNA-derived cDNA R1006_5-G


title: mRNA-derived cDNA R1014_4-G


title: mRNA-derived cDNA R1021_1-G


title: mRNA-derived cDNA R1006_3-G


title: mRNA-derived cDNA R1006_1-G


title: mRNA-derived cDNA R1012_5-G


title: mRNA-derived cDNA R1005_4-G


title: mRNA-derived cDNA R1006_4-G


title: mRNA-derived cDNA R1005_6-G


title: mRNA-derived cDNA R1005_5-G


title: mRNA-derived cDNA R1006_6-G


title: mRNA-derived cDNA R1004_6-G


title: mRNA-derived cDNA R1014_6-G


title: mRNA-derived cDNA R1005_2-G


title: mRNA-derived cDNA R1006_2-G


title: mRNA-derived cDNA R1014_5-G


title: mRNA-derived cDNA R1005_1-G


title: mRNA-derived cDNA R1005_3-G


title: mRNA-derived cDNA R1004_5-G


title: mRNA-derived cDNA R1004_2-G


title: mRNA-derived cDNA R1004_4-G


title: mRNA-derived cDNA R1004_3-G


title: mRNA-derived cDNA R1003_4-G


title: mRNA-derived cDNA R1004_1-G


title: mRNA-derived cDNA R1003_6-G


title: mRNA-derived cDNA R1003_3-G


title: mRNA-derived cDNA R1003_5-G


title: mRNA-derived cDNA R1003_1-G


title: mRNA-derived cDNA R1003_2-G


title: mRNA-derived cDNA R1001_6-G


title: mRNA-derived cDNA R1001_4-G


title: mRNA-derived cDNA R1001_5-G


title: mRNA-derived cDNA R1001_3-G


title: mRNA-derived cDNA Li124T-G


title: mRNA-derived cDNA Li121T-G


title: mRNA-derived cDNA Li124P-G


title: mRNA-derived cDNA Li121LN-G


title: mRNA-derived cDNA Li121P-G


title: mRNA-derived cDNA Li121N-G


title: mRNA-derived cDNA Li98T-G


title: mRNA-derived cDNA Li104T-G


title: mRNA-derived cDNA Li104Ppost-G


title: mRNA-derived cDNA Li98N-G


title: mRNA-derived cDNA Li71T-G


title: mRNA-derived cDNA Li98LN-G


title: mRNA-derived cDNA Li63T-G


title: mRNA-derived cDNA Li63post-G


title: mRNA-derived cDNA Li63N-G


title: mRNA-derived cDNA Li71N-G


title: mRNA-derived cDNA Li104N-G


title: mRNA-derived cDNA Li57T-G


title: mRNA-derived cDNA Li57_2-G


title: mRNA-derived cDNA Li57N-G


title: mRNA-derived cDNA Li57_1-G


title: mRNA-derived cDNA Li15_2-G


title: mRNA-derived cDNA R1001_2-G