title: DNA-NRCAM-FOXA1-Round4-Rep2

description:
Library name: DNA-NRCAM-FOXA1-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 4 rounds, Biological replicate 2

value: synthetic DNA


title: DNA-NRCAM-GATA1-Round1-Rep1

status: Public on May 01 2025

type: SRA

city: Boston

first: Luca

last: Mariani

state: ma

address: 77 Avenue Pasteur

department: Medicine

country: USA

institute: Harvard Medical School

description:
Library name: DNA-NRCAM-GATA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of GATA1 for 1 rounds, Biological replicate 1

library_source: other

data_processing:
The forward (labeled ‘R1’) and reverse complement (labeled ‘R2’) 150-bp paired-end sequencing fastq reads were merged with PEAR in default setting (PMID: 24142950).
PCR duplicates were removed and the reads were trimmed at the 3’ end to remove the 6-bp UMIs. Since PIONEAR-seq libraries by design are 147-bp long, trimmed reads with different lengths were removed.
To extract the DNA sequence and the location of the tiles, the reads were aligned to the associated template  by the  R function pairwiseAlignment (default setting except: type='overlap’,  gapOpening=1000, gapExtension=0). This function furnishes an alignment score and the position of the base mismatches for each read. Given the template is 147-bp long and the random tile is 20-bp long, reads with an alignment score smaller than 127 were considered non-aligned and removed.
The position of the first and last mismatch were compared to assign the random tile position of each read
For each library, the read count of tiles at different position varies. To give the same weight to each tile position, the median read count of the library was used to resample the tiles at each psoition (Isotiling). To calculate motif enrichment the internal 16-bp of all the isotiles of the library were merged and compared to the associated input library by using the SELEX R package.
Assembly: Synthetic DNA
Supplementary files format and content: XXX_kmer_enrichment_table.txt' file is in txt format and contains a table showing:
Supplementary files format and content: the enrichment rank (Column 1: ID), the sequence of the enriched k-mer (column 2: Kmer), the k-mer count observed in the assessed library (column 3: ObservedCount), the expected k-mer count inferred from the associated input library used as background set (Column 4: ExpectedCount), their relative k-mer count increase, which is a measure of k-mer enrichment and is defined as the ration between the expected and observed counts (Column 5: Increase).
Library strategy: SELEX

molecule: other

organism: synthetic construct

source_name: synthetic DNA

extract_protocol:
Amplicon DNA
Sequencing libraries were prepared by adding to the selected libraries (1) 5' end Unique Molecular Identifies (UMIs), (2) llumina adaptors (IAs), (2) TRUseq dual barcodes (BCs) and (2) Illumina sequencing promoters P5 and P7 (P5/P7) by PCR amplification with custom primers.  10 ng of DNA was used as starting material samples. Libraries were with KAPA HiFi HotStart ReadyMix PCR Kit amplified by using 2 consecutive 6-cycle PCR runs (first cycle for UMIs and IAs, second cycle for BCs and P5/P7)  on the thermocycler. Post amplification libraries were size selected at ~3000bp in length by Azenta using AMPure XP beads. Libraries were validated by using both the Tapestation D1000 and  Qubit.

treatment_protocol: DNA Libraries were PCR amplified, assembled on in vitro reconstituted histone octamers to form nucleosome and incubated with GST-tagged transcription factors. TF-bound elements were selected by glutathione beads followed by PCR amplification. The treatment was repetead for 4 rounds.

tag: tissue

tag: treatment

value: Free DNA


title: human embryonic stem cells, no treatment, rep2

city: Beijing

first: Ke

last: Zhang

address: Huayuan North Road

country: China

institute: Peking university

description:
H1_2
gene_expression.xls

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke, afterwards clean reads were obtained and stored in FASTQ format.
Experssion level of gene was calculated by featureCount (v2.14.2).
The raw data was filtered by using Fastp.
The heatmap was drawn by pheatmap (v1.0.8) [19] according to the gene expression difference.
Differential expression analysis was performed using the DESeq2(v1.4.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FLPM values for each samples

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using the Direct-zol RNA MiniPrep Kit from Zymo Research, and checked for integrity using an Agilent Bioanalyzer 2100.
mRNA is enriched by oligo (dT) -attached magnetic beads from total RNA, and strand specific transcriptome library is constructed.
The transcriptome library was sequenced by DNBSEQ high-throughput platform and Illumina Novaseq6000/BGISEQ-500.

tag: cell line

tag: cell type

value: human embryonic stem cell

tag: genotype

value: no treatment


title: cipro_t15_rep1

city: San Diego

first: Yuan

last: Yuan

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description: Library name: Sample 29

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts are generated using featureCounts
Assembly: U00096.3
Supplementary files format and content: Comma-separated text file including raw counts for each gene and sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: K-12 substr. MG1655

growth_protocol: An overnight E. coli MG1655 culture was inoculated from a glycerol stock and grown at 37°C with shaking. The next morning, a fresh culture in MHB-CA was prepared at an initial OD₆₀₀ of 0.05. Once the OD₆₀₀ reached 0.5, cultures were aliquoted into plastic tubes (16 mL per tube) containing stir bars and placed on a 24-well magnetic heat block.

extract_protocol:
Total RNA was extracted using a Luna Nanotech PuroMAG™ Total RNA Purification Kit (NKM051-384) which included a DNaseI treatment and a modification to incorporate bead beating as a means of cell lysis. RNA quality and concentration were assessed using an Agilent TapeStation and a Nanodrop, respectively.
One microgram of total RNA underwent ribosomal RNA removal using RiboRid, and the resulting rRNA-depleted RNA was used to make RNA-Seq libraries with the Kapa Biosystems (Roche) RNA HyperPrep Kit, following the manufacturer’s protocol.

treatment_protocol: Ampicillin (final concentration: 16 µg/mL or 4 µg/mL) or ciprofloxacin (0.016 µg/mL) was immediately added. Samples were collected in duplicate at 0, 1.5, 3.5, 7.5, 15, and 30 minutes post-exposure, treated with RNAprotect Bacteria Reagent, and stored at -80°C for RNA-Seq library preparation.

tag: strain

value: K-12 substr. MG1655

value: WT

value: Exposure to ciprofloxacin


title: DNA-NRCAM-FOXA1-Round4-Rep1

description:
Library name: DNA-NRCAM-FOXA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 4 rounds, Biological replicate 1


title: human embryonic stem cells, no treatment, rep1

description:
H1_1
gene_expression.xls


title: cipro_t1_5_rep2

description: Library name: Sample 28


title: cipro_t1_5_rep1

description: Library name: Sample 27


title: ADRA03_IOF3_5_H [HTO-derived cDNA]

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
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 (v3.0.1) and aligning to the GRCh38-3.0.0  genome build
Assembly: GRCh38-3.0.0
Supplementary files format and content: 10x Genomics output files: h5 format, containing matrix of Gene, ADT and HTO counts

molecule: protein

source_name: PBMC

extract_protocol:
Sample pool was counted and loaded on five lanes of the 10x Genomics NextGem 3’v3.0 assay as per the manufacturer’s protocol with a targeted cell recovery of 30,000 cells per lane. Gene expression and ADT libraries were made as per the 10x Genomics demonstrated protocol (https://assets.ctfassets.net/an68im79xiti/40xc58fJNcCWipI1YIdXoS/a87092c1c1faa0f316c552a97229a268/CG000185_ChromiumSingleCell3_v3_FeatureBarcoding_CellSurfaceProtein_UG_Rev_D.pdf). Hashtag oligonucleotides (HTO) were enriched during cDNA amplification with the addition of 3 pmol of a HTO Additive primer (5’GTGACTGGAGTTCAGACGTGTGCTC). This PCR product was isolated from the mRNA-derived cDNA via SPRISelect size selection, and libraries were made as per the New York Genome Center Hashing protocol. The hashed samples were then pooled and stained together with a cocktail of 73 Biolegend Totalseq-A antibodies. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer and KAPA library quantification kit (Roche Cat# 0796014001.) Gene expression libraries were sequenced at a targeted depth of 25,000 reads per cells. ADT libraries were sequenced at a targeted read depth of 10,000 reads per cell. HTO libraries were sequenced at a targeted read depth of 1,000 reads per cell. Libraries were sequenced on the Illumina NextSeq Hi 500/550 75 cycle kit, NovaSeq 6000 100 cycle kit, or NovaSeq S2 100 cycle kit with run parameters set to 28x8x0x60 (R1xi7xi5xR2).
Hashtag Antibody Staining: Cells were thawed and counted using the Nexcelom Cellaca. An aliquot of 500,000 cells from each sample were centrifuged at 350 RCF for 5 minutes (4°C). The supernatant was discarded and the pellets were resuspended in a combinatorial hashtag antibody solution (see: Table1) and incubated at 4°C for 20 minutes. Hashtag antibodies were conjugated as per New York Genome Center hashing protocol (https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf). Stained cells were washed three times in 1mL wash buffer (PBS + 0.5% BSA) by 4°C centrifugation at 350 RCF to remove unbound antibodies. Washed cells were resuspended in 150ul wash buffer and counted using a Nexcelom Cellaca. Hashed samples were pooled (see: Table2) and centrifuged at 350 RCF for 5 minutes (4°C). Supernatant was removed and pellet was resuspended in 100ul of antibody cocktail (see: Table3) and incubated at 4°C for 30 minutes. Stained cells were washed three times in 1mL PBS + 0.5% BSA by 4°C centrifugation at 350 RCF to remove unbound antibodies. The washed cells were resuspended in wash buffer to achieve a target concentration of 4 million cells/mL.

value: PBMC

tag: library type

value: HTO


title: BE31A_mRNA

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

description: Lung biopsy

data_processing:
Basecalling and trimming were performed according to BGI standards
Index for mature miRNAs was built using the reference genome GRCh38 and the salmon tool v1.4.0
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification.
Reads were loaded in R using the tximport library
Assembly: GRCh38
Supplementary files format and content: the txt file was generated based on the txi matrix imported in R.

source_name: human lung ventilated with high tidal volume

extract_protocol:
Lung samples were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries for RNA sequencing were prepared using standard BGI protocols

value: lung

tag: condition

value: VILI


title: DNA-NRCAM-FOXA1-Round3-Rep1

description:
Library name: DNA-NRCAM-FOXA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 3 rounds, Biological replicate 1


title: ADRA03_IOF3_5_G [mRNA-derived cDNA]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

molecule: polyA RNA

value: mRNA


title: cipro_t0_rep2

description: Library name: Sample 26


title: DNA-NRCAM-FOXA1-Round2-Rep2

description:
Library name: DNA-NRCAM-FOXA1-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 2 rounds, Biological replicate 2


title: BE29A_mRNA

description: Lung biopsy

source_name: human lung ventilated with CPAP

value: CPAP


title: BE27A_mRNA

description: Lung biopsy


title: cipro_t0_rep1

description: Library name: Sample 25

value: Exposure to 1/4X MIC ampicillin


title: ADRA03_IOF3_5_A [ADT-derived cDNA]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: ADT

tag: antibodies/tags


title: DNA-NRCAM-FOXA1-Round2-Rep1

description:
Library name: DNA-NRCAM-FOXA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 2 rounds, Biological replicate 1


title: ADRA03_IOF4_3_A [ADT-derived cDNA]


title: amp_1_4_t7_5_rep2

description: Library name: Sample 24


title: BE25A_mRNA

description: Lung biopsy


title: ADRA03_IOF4_2_H [HTO-derived cDNA]


title: ADRA03_IOF3_4_H [HTO-derived cDNA]


title: ADRA03_IOF4_2_G [mRNA-derived cDNA]


title: DNA-NRCAM-FOXA1-Round1-Rep2

description:
Library name: DNA-NRCAM-FOXA1-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 1 rounds, Biological replicate 2


title: BE11A_mRNA

description: Lung biopsy


title: amp_1_4_t7_5_rep1

description: Library name: Sample 23


title: ADRA03_IOF4_2_A [ADT-derived cDNA]


title: DNA-NRCAM-FOXA1-Round1-Rep1

description:
Library name: DNA-NRCAM-FOXA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 1 rounds, Biological replicate 1


title: DNA-NRCAM-CEBPB-Round4-Rep1

description:
Library name: DNA-NRCAM-CEBPB-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of CEBPB for 4 rounds, Biological replicate 1


title: ADRA03_IOF3_4_G [mRNA-derived cDNA]


title: ADRA03_IOF3_4_A [ADT-derived cDNA]


title: BE31A: human lung ventilated with high tidal volume

data_processing:
Basecalling and trimming were performed according to BGI standards
Index for mature miRNAs was built using the miRBase database (release 22.1) and the salmon tool v1.4.0 with the parameters -k 9
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification.
Reads were loaded in R using the tximport library
Genome_build: miRBase 22.1
Supplementary_files_format_and_content: the csv file was generated based on the txi matrix imported in R.

source_name: Lung biopsy

extract_protocol:
Lung samples were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries for miRNA sequencing were prepared using standard BGI protocols


title: DNA-NRCAM-FOXA1-Round3-Rep2

description:
Library name: DNA-NRCAM-FOXA1-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of FOXA1 for 3 rounds, Biological replicate 2


title: DNA-NRCAM-CEBPB-Round3-Rep1

description:
Library name: DNA-NRCAM-CEBPB-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of CEBPB for 3 rounds, Biological replicate 1


title: amp_1_4_t30_rep1

description: Library name: Sample 21


title: BE29A: human lung ventilated with CPAP


title: ADRA03_IOF3_3_H [HTO-derived cDNA]


title: ADRA03_IOF3_3_G [mRNA-derived cDNA]


title: amp_1_4_t3_5_rep2

description: Library name: Sample 20


title: DNA-NRCAM-CEBPB-Round2-Rep1

description:
Library name: DNA-NRCAM-CEBPB-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of CEBPB for 2 rounds, Biological replicate 1


title: BE27A: human lung ventilated with high tidal volume


title: DNA-NRCAM-CEBPB-Round1-Rep1

description:
Library name: DNA-NRCAM-CEBPB-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of CEBPB for 1 rounds, Biological replicate 1


title: ADRA03_IOF3_3_A [ADT-derived cDNA]


title: BE25A: human lung ventilated with high tidal volume


title: amp_1_4_t15_rep2

description: Library name: Sample 18


title: ADRA03_IOF3_2_H [HTO-derived cDNA]


title: DNA-NRCAM-ASCL1-Round4-Rep1

description:
Library name: DNA-NRCAM-ASCL1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of ASCL1 for 4 rounds, Biological replicate 1


title: amp_1_4_t15_rep1

description: Library name: Sample 17


title: BE01A_mRNA

description: Lung biopsy


title: ADRA03_IOF3_2_G [mRNA-derived cDNA]


title: BE11A: human lung ventilated with CPAP


title: amp_1_4_t1_5_rep2

description: Library name: Sample 16


title: BE01A: human lung ventilated with CPAP


title: amp_1_4_t30_rep2

description: Library name: Sample 22


title: ADRA03_IOF3_2_A [ADT-derived cDNA]


title: amp_1_4_t1_5_rep1

description: Library name: Sample 15


title: ADRA03_IOF3_1_H [HTO-derived cDNA]


title: DNA-CX3-ZNF143-Round4-Rep1

description:
Library name: DNA-CX3-ZNF143-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of ZNF143 for 4 rounds, Biological replicate 1


title: DNA-CX3-ZNF143-Round3-Rep1

description:
Library name: DNA-CX3-ZNF143-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of ZNF143 for 3 rounds, Biological replicate 1


title: amp_1_4_t0_rep2

description: Library name: Sample 14


title: DNA-CX3-RUNX2-Round4-Rep1

description:
Library name: DNA-CX3-RUNX2-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of RUNX2 for 4 rounds, Biological replicate 1


title: ADRA03_IOF3_1_G [mRNA-derived cDNA]


title: ABX treated APPPS1-21 cortex 3, snRNA-Seq

city: CHICAGO

first: Sidhanth

last: Chandra

state: IL

address: Tarry Building Room 8-711 300 E Superior

institute: Northwestern University Feinberg School of Medicine

description:
Library name: 3727
10x genomics

library_source: transcriptomic single cell

data_processing:
Libraries were pooled and sequenced on an Illumina Novaseq 6000 and reads were demultiplexed and aligned to the genome using CellRanger. 109,581 nuclei were sequenced at an average post-normalization read depth of 31,674 reads per cell and 1,736 genes per cell. Data then underwent quality control using SoupX and DoubletFinder R packages. Quality controlled data then was then integrated and multidimensional reduction using uniform manifold approximation and projection (UMAP) plots were produced using Seurat. Differential expression analysis between clusters was performed using Seurat’s FindMarkers function. UMAP was manually annotated by using the highly expressed genes in each cluster. Differential expression gene (DEG) analysis between the VHL and abx treated groups was performed using Seurat’s FindMarkers function using the masked augmentation subspace training (MAST) algorithm from the R package MAST. The Benjami-Hochberg (BH) method was used to correct for multiple testing. An FDR corrected p-value of 0.01 with log2FC of 0.25 was the cutoff for significance. Astrocyte clusters were subclustered using the subset function in Seurat. Astrocytes were subclustered using the first 30 principal components at a resolution of 0.1. DEG analysis between astrocyte subclusters was performed using Seurat’s FindMarkers function using the MAST algorithm from the R package MAST (Full results can be found in Table 1). The Benjami-Hochberg (BH) method was used to correct for multiple testing in astrocyte subcluster DEG analysis. An FDR corrected p-value of 0.001 with log2FC of 0.25 was the cutoff for significance for pathway analysis which was performed using Metascape.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain cortex

extract_protocol:
Single nuclei suspensions were generated from the cortices of vehicle and antibiotic treated APPPS1-21 male mice using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). Briefly, frozen brain cortex samples (approximately 40 mg per sample) were transferred to pre-chilled sample dissociation tubes and 500 uL of lysis buffer was used to dissociate tissue for 10 minutes. Dissociated tissue was pipetted onto nuclei isolation columns and centrifuged for 16,000 x g for 20 seconds at 4°C. Flowthrough from the columns were vortexed for 10 seconds to resuspend nuclei and centrifuged at 500 x g for 3 minutes at 4°C. Supernatant was removed and pellets were resuspended with 500 uL of debris removal buffer and centrifuged at 700 x g for 10 minutes at 4°C. The top myelin layer was taken off using a transfer pipette. The rest of the supernatant was then removed, and pellets were resuspended in 1 mL of wash and resuspension buffer and centrifuged at 500 x g for 5 minutes at 4°C. This process was then repeated once. Then samples were resuspended in wash and resuspension buffer and centrifuged at 300 x g for 8 minutes at 4°C Lastly, supernatant was removed, and nuclei pellets were resuspended in 150 uL of wash and resuspension buffer and vortexed for 3 seconds. Final nuclei concentration was determined using the Invitrogen Countess 3 automated cell counter. Further processing of nuclei was completed using 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow
The single nucleus suspension was created using the 10x Genomics Chromium Nuclei Isolation Kit (#PN-1000494). After isolation, nuclei were loaded into the 10x Genomics Chromium Controller with a target of 10,000 nuclei per sample. Gel bead-in emulsions (GEM) generation and library preparation were performed according to the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry workflow. Libraries were pooled and sequenced on an Illumina Novaseq 6000.

value: Brain cortex

value: ABX

tag: batch


title: ABX treated APPPS1-21 cortex 2, snRNA-Seq

description:
Library name: 3455
10x genomics


title: amp_1_4_t0_rep1

description: Library name: Sample 13


title: amp_1_4_t3_5_rep1

description: Library name: Sample 19


title: DNA-CX3-RUNX2-Round3-Rep1

description:
Library name: DNA-CX3-RUNX2-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of RUNX2 for 3 rounds, Biological replicate 1

value: synthetic DNA


title: ABX treated APPPS1-21 cortex 4, snRNA-Seq

description:
Library name: 3735
10x genomics


title: amp_1_16_t7_5_rep2

description: Library name: Sample 12

value: Exposure to 1/16X MIC ampicillin


title: ADRA03_IOF3_1_A [ADT-derived cDNA]


title: ABX treated APPPS1-21 cortex 1, snRNA-Seq

description:
Library name: 3431
10x genomics


title: DNA-CX3-RUNX2-Round2-Rep1

description:
Library name: DNA-CX3-RUNX2-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of RUNX2 for 2 rounds, Biological replicate 1

value: Free DNA


title: VHL treated APPPS1-21 cortex 4, snRNA-Seq

description:
Library name: 3448
10x genomics

value: Vehicle


title: amp_1_16_t7_5_rep1

description: Library name: Sample 11

value: K-12 substr. MG1655


title: ADRA03_IOF2_5_G [mRNA-derived cDNA]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA


title: DNA-NRCAM-ASCL1-Round3-Rep1

description:
Library name: DNA-NRCAM-ASCL1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence NRCAM for the binding of ASCL1 for 3 rounds, Biological replicate 1


title: DNA-CX3-RUNX2-Round1-Rep1

description:
Library name: DNA-CX3-RUNX2-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of RUNX2 for 1 rounds, Biological replicate 1


title: amp_1_16_t30_rep2

description: Library name: Sample 10

value: WT


title: ADRA03_IOF2_5_A [ADT-derived cDNA]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: amp_1_16_t30_rep1

description: Library name: Sample 9


title: ADRA03_IOF2_5_H [HTO-derived cDNA]

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)


title: VHL treated APPPS1-21 cortex 2, snRNA-Seq

description:
Library name: 3231
10x genomics


title: VHL treated APPPS1-21 cortex 3, snRNA-Seq

description:
Library name: 3411
10x genomics


title: DNA-CX3-PU1-Round3-Rep1

description:
Library name: DNA-CX3-PU1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of PU1 for 3 rounds, Biological replicate 1


title: ADRA03_IOF2_4_H [HTO-derived cDNA]


title: amp_1_16_t3_5_rep2

description: Library name: Sample 8


title: ADRA03_IOF2_4_G [mRNA-derived cDNA]


title: VHL treated APPPS1-21 cortex 1, snRNA-Seq

description:
Library name: 3227
10x genomics


title: amp_1_16_t3_5_rep1

description: Library name: Sample 7


title: DNA-CX3-PAX7-Round3-Rep1

description:
Library name: DNA-CX3-PAX7-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of PAX7 for 3 rounds, Biological replicate 1


title: amp_1_16_t15_rep2

description: Library name: Sample 6


title: ADRA03_IOF2_4_A [ADT-derived cDNA]


title: ADRA03_IOF2_3_H [HTO-derived cDNA]


title: DNA-CX3-PAX7-Round2-Rep1

description:
Library name: DNA-CX3-PAX7-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of PAX7 for 2 rounds, Biological replicate 1


title: Propionate treated APPPS1-21 cortex 4

description: Library name: 538

data_processing:
The quality of reads, in FASTQ format, was evaluated using FastQC.  Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Martin, 2011).  Trimmed reads were aligned to the Mus musculus genome (mm39) using STAR (Dobin et al, 2013).  Read counts for each gene were calculated using htseq-count (Anders et al, 2015) in conjunction with a gene annotation file for mm39 obtained from Ensembl (http://useast.ensembl.org/index.html).  Normalization and differential expression were calculated using DESeq2 that employs the Wald test (Love et al, 2014). The cutoff for determining significant DEGs was an FDR-adjusted p-value less than 0.1 using the Benjami-Hochberg method. Pathway analysis was performed using Metascape.
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample

extract_protocol:
We followed Heiman et al 2014 for extraction of RNA for TRAPSeq. To capture eGFP+ polysomal complexes in astrocytes for TRAPseq, an anti-GFP affinity matrix (AM) was prepared prior to homogenization of cortical tissue using a previously published protocol(27). Streptavidin MyOne T1 Dynabeads were resuspended, and 450 µL/purification was added to the AM tube. Beads were collected by a magnet and were washed with 1X PBS. 180 µL/purification of biotinylated protein L was then added to the beads and the mixture was incubated on a tube rotator for 35 minutes. The protein L coated beads were captured on a magnet and washed 5 times with 1X PBS containing 3% (w/v) IgG and protease free BSA. 75 µg of anti-GFP antibodies (Htz-GFP-19F7 and Htz-GFP-19C819F7 obtained from Memorial Sloan Kettering Cancer Center Antibody & Bioresource Core Facility) in low salt buffer (20 mM HEPES KOH, 150 mM KCl, 10 mM MgCl2, and 1% (vol/vol) NP-40 in RNase-free water) were then added to the bead mixture and was incubated on a tube rotator for 1 hour. After antibody binding, the final AM was washed 3x with low salt buffer. After washing, the AM was resuspended in a volume of low salt buffer such that each IP received an aliquot of 200 μL. Following AM preparation, flash frozen mouse cortices (washed in dissection buffer before freezing) were homogenized in 1.5 mL tissue lysis buffer (20 mM HEPES KOH, 150 mM KCl, 10 mM MgCl2, EDTA-free protease inhibitor tablet, 0.5 mM DTT, 100 µg/ml cycloheximide in RNase-free water) in a glass tube with an electric homogenizer (Glas-Col #099CK5424) at 900 RPM with 15 full strokes. Lysates were transferred into prechilled microcentrifuge tubes on ice. Post-nuclear supernatants were prepared (S2) by centrifugation at 4°C for 10 minutes at 2000g. S2 was transferred to a new, prechilled microcentrifuge tube on ice. 1/9 sample volume of 10% NP-40 to S2 (final concentration 1%) was added and mixed gently by inverting the tube. 1/9 sample volume of 300 mM DHPC was added to S2 (final concentration 30 mM) and mixed gently by inverting the tube and the mixture was incubated on ice for 5 minutes. Post-mitochondrial supernatants (S20) were prepared by centrifugation at 4°C for 10 minutes at 20,000 xg. S20 was transferred to a new, prechilled microcentrifuge tube. 200 uL of freshly resuspended AM was added to each S20 sample. Beads complexes were washed 4x with high salt buffer (20 mM HERPES, 350 mM KCl, 10 mM MgCl, 1% NP-40 in RNase-free water). RNA was isolated from beads using 100 μL of Nanoprep lysis buffer (from Stratagene Absolutely RNA Nanoprep kit). RNA cleanup was performed according to the kit.
Quality of RNA isolated from TRAP purifications was assessed using Agilent Bioanalyzer. All RNA used for downstream sequencing had a RIN score above 7. mRNA libraries were generated from TRAP-purified RNA using the Illumina Stranded mRNA prep kit. Prepared libraries were sequenced on an Illumina HighSeq 4000.

treatment_protocol: APPPS1-21 male were treated with broad-spectrum antibiotics, propionate, or water vehicle (N=5/group). Antibiotic treatment was via oral gavage from postnatal day 14-21. Propionate treatment (150 mM) was given from 1-3 months via drinking water.

value: Propionate


title: ADRA03_IOF2_3_G [mRNA-derived cDNA]

value: PBMC


title: Propionate treated APPPS1-21 cortex 2

description: Library name: 533


title: amp_1_16_t1_5_rep2

description: Library name: Sample 4


title: DNA-CX3-PU1-Round4-Rep1

description:
Library name: DNA-CX3-PU1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of PU1 for 4 rounds, Biological replicate 1


title: ADRA03_IOF2_3_A [ADT-derived cDNA]


title: Propionate treated APPPS1-21 cortex 1

description: Library name: 532


title: DNA-CX3-OCT4-Round4-Rep2

description:
Library name: DNA-CX3-OCT4-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 4 rounds, Biological replicate 2


title: ADRA03_IOF2_2_H [HTO-derived cDNA]

value: HTO


title: amp_1_16_t1_5_rep1

description: Library name: Sample 3


title: DNA-CX3-PAX7-Round4-Rep1

description:
Library name: DNA-CX3-PAX7-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of PAX7 for 4 rounds, Biological replicate 1


title: DNA-CX3-OCT4-Round4-Rep1

description:
Library name: DNA-CX3-OCT4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 4 rounds, Biological replicate 1


title: amp_1_16_t0_rep2

description: Library name: Sample 2


title: Propionate treated APPPS1-21 cortex 5

description: Library name: 3150


title: ADRA03_IOF2_2_G [mRNA-derived cDNA]


title: ABX treated APPPS1-21 cortex 4

description: Library name: 435


title: amp_1_16_t0_rep1

description: Library name: Sample 1


title: DNA-CX3-OCT4-Round3-Rep1

description:
Library name: DNA-CX3-OCT4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 3 rounds, Biological replicate 1


title: ADRA03_IOF2_2_A [ADT-derived cDNA]


title: DNA-CX3-OCT4-Round3-Rep2

description:
Library name: DNA-CX3-OCT4-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 3 rounds, Biological replicate 2


title: porcine,pol2,GV,rep2

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

library_source: genomic

data_processing:
For paired-end Stacc-seq, alignment to genomes was executed with Bowtie2 v.2.3.4. Aligned reads underwent filtering with a minimum mapping quality of 20, and PCR duplicates were subsequently removed. Estimation of read coverage across the genome was performed utilizing bamCoverage from deepTools v.3.3.1, with parameters -binSize 100, and normalization using RPKM. Visualization was accomplished using UCSC Browser or IGV (2.16.1). To mitigate batch and cell type variations in comparisons, RPKM values of Stacc-seq data were additionally normalized through z-score transformation.
Assembly: susScr11
Supplementary files format and content: BigWig files of each stage

molecule: genomic DNA

organism: Sus scrofa

source_name: GV

extract_protocol:
The collection timings for porcine oocytes and embryos adhered to the schedule outlined in previous studies (Bu, G. et al.,2022;Gao, L. et al.,2018;Berg, D. K. et al. ,2011).  Porcine IVF embryos at each stage were collected at specified time points: 28 hpi (2-cell), 48 hpi (4-cell),  and 150 hpi (blastocyst). GV oocytes were obtained by removing cumulus cells from fresh COCs through vortexing for 5 minutes in 1 mg/mL hyaluronidase. The removal of the zona pellucida and isolation of ICM were carried out as described (Gao, L. et al.,2018). Briefly, the zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma-Aldrich, P8811). Polar bodies of early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA).
For Stacc-seq library preparation, the method described previously was followed (Liu, B. et al. ,2020).Briefly, a mixture of 7 μL buffer 1 (10 mM Tris-HCl pH =7.4, 150 mM NaCl, 0.5 mM spermidine, and 1 × EDTA-free Roche complete protease inhibitor) with 0.05% digitonin (Sigma D141), 0.5 μL pG-Tn5(Vazyme, TD901), and 0.5 μg antibody was prepared in a 200-μL low-binding tube (Axygen, PCR-02D-L-C) and incubated at 4°C for 30 min. Oocytes or embryos without zona pellucida were then transferred into a 0.2-mL low-binding tube with a small volume of DPBS-0.001% BSA and incubated with 6 μL buffer 1 containing 0.05% digitonin on ice for 10 min. Subsequently, samples were mixed with 35 μL of buffer 1 with 0.05% digitonin and 12.5 μL of prewarmed 5 × TTBL and incubated with the antibody-pG-Tn5 complex at 37°C for 30 min on a thermomixer at 400 rpm (10s on and 10s off). The reaction was stopped by adding 65 μL of 1 × TE, and DNA was purified using phenol-chloroform with 40 ng carrier RNA, followed by isopropanol precipitation for 30 min at −80°C or overnight at −20°C. For the sample with spiked-in DNA, 0.2 pg spike in DNA (prepared from Drosophila genomic DNA) was added before the DNA extraction step (Liu, B. etal. ,2020).PCR was performed to amplify the libraries (Vazyme, TD601) with the following conditions after two wash steps with freshly-prepared, ice-cold 80% ethanol: 72°C for 3 min; 98°C for 30 s; thermocycling with 16 cycles at 98°C for 15 s, 60°C for 30 s, and 72°C for 3 min; followed by 72°C for 5 min. Post-PCR,libraries were purified with 1.7 × AMPure beads (Beckman, A63882) and subjected to next-generation sequencing.

value: GV


title: ADRA03_IOF2_1_H [HTO-derived cDNA]


title: ABX treated APPPS1-21 cortex 2

description: Library name: 447


title: DNA-CX3-OCT4-Round2-Rep2

description:
Library name: DNA-CX3-OCT4-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 2 rounds, Biological replicate 2


title: Propionate treated APPPS1-21 cortex 3

description: Library name: 537


title: ADRA03_IOF2_1_G [mRNA-derived cDNA]


title: porcine,pol2,GV,rep1


title: DNA-CX3-PAX7-Round1-Rep1

description:
Library name: DNA-CX3-PAX7-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of PAX7 for 1 rounds, Biological replicate 1


title: DNA-CX3-OCT4-Round2-Rep1

description:
Library name: DNA-CX3-OCT4-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 2 rounds, Biological replicate 1


title: porcine,pol2,Blastocyst,rep2

source_name: Blastocyst

value: Blastocyst


title: ABX treated APPPS1-21 cortex 1

description: Library name: 575


title: ADRA03_IOF2_1_A [ADT-derived cDNA]


title: DNA-CX3-OCT4-Round1-Rep2

description:
Library name: DNA-CX3-OCT4-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 1 rounds, Biological replicate 2


title: ABX treated APPPS1-21 cortex 5

description: Library name: 574


title: porcine,pol2,Blastocyst,rep1


title: porcine,pol2,4cell,rep2


title: VHL treated APPPS1-21 cortex 4

description: Library name: 565


title: ADRA03_IOF1_5_H [HTO-derived cDNA]


title: DNA-CX3-OCT4-Round1-Rep1

description:
Library name: DNA-CX3-OCT4-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of OCT4 for 1 rounds, Biological replicate 1


title: VHL treated APPPS1-21 cortex 5

description: Library name: 567


title: ADRA03_IOF1_5_G [mRNA-derived cDNA]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: VHL treated APPPS1-21 cortex 3

description: Library name: 9050


title: DNA-CX3-KLF4-Round4-Rep1

description:
Library name: DNA-CX3-KLF4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of KLF4 for 4 rounds, Biological replicate 1


title: ABX treated APPPS1-21 cortex 3

description: Library name: 432


title: porcine,pol2,4cell,rep1


title: ADRA03_IOF1_5_A [ADT-derived cDNA]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: porcine,pol2,2cell,rep2


title: VHL treated APPPS1-21 cortex 2

description: Library name: 9042


title: DNA-CX3-KLF4-Round3-Rep1

description:
Library name: DNA-CX3-KLF4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of KLF4 for 3 rounds, Biological replicate 1


title: ADRA03_IOF1_4_H [HTO-derived cDNA]

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)


title: DNA-CX3-GST-Round4-Rep2

description:
Library name: DNA-CX3-GST-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GST for 4 rounds, Biological replicate 2


title: VHL treated APPPS1-21 cortex 1

description: Library name: 9041


title: porcine,pol2,2cell,rep1


title: ADRA03_IOF1_4_G [mRNA-derived cDNA]


title: porcine,H3K27ac,2-cell,rep2

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) with default parameters to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013) was employed to map the filtered reads onto genomes. Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads.
Assembly: susScr11
Supplementary files format and content: BigWig files of each stage

extract_protocol:
The collection timings for porcine embryos adhered to the schedule outlined in previous studies (Bu, G. et al.,2022;Gao, L. et al.,2018;Berg, D. K. et al. ,2011).  Porcine IVF embryos at each stage were collected at specified time points: 28 hpi (2-cell). Polar bodies of early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA).
In the ULI-NChIP-seq method, each reaction utilized 100 porcine 2-cell embryos. All collected cells underwent a thorough washing process with DPBS-0.001% BSA. The ULI-NChIP procedure followed the established protocol (Lismer,2021).For sequencing, the sequence libraries were constructed using the KAPA Hyper Prep Kit for the Illumina platform (Roche, KK8504) following the provided guidelines.


title: DNA-CX3-GST-Round3-Rep2

description:
Library name: DNA-CX3-GST-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GST for 3 rounds, Biological replicate 2


title: ADRA03_IOF1_4_A [ADT-derived cDNA]


title: DNA-CX3-GATA4-Round4-Rep1

description:
Library name: DNA-CX3-GATA4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA4 for 4 rounds, Biological replicate 1


title: porcine,H3K27ac,2-cell,rep1


title: TC_all_LN_2, GEX

first: Chrysothemis

last: Brown

address: 417 East 68th Street

department: Immunology Program, Sloan Kettering Institute

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: TC_all_LN_2_mRNA
GEX (3' mRNA) library for Thetis cells from lymph nodes of 2-week old mice

data_processing:
GEX FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and counted by Cell Ranger v7.1.0 with default parameters. HTO sequencing data were aligned to the HTO barcodes, and UMIs were counted for each cell using CITE-seq-Count. Samples were then demultiplexed using the SHARP pipeline. The singlet barcodes were further filtered based on the number of RNA-seq transcripts (>1,500), the number of detected genes (>500), and the fraction of mitochondrial transcripts (<5%). Finally, any genes detected in <2 cells in the scRNA-seq data were discarded. The filtered count matrix was library-size normalized, log-transformed, and then centered and scaled using Seurat v4.4.0. Principal component analysis was performed on the scaled data (npcs=50). A nearest-neighbor graph was constructed using the first 30 principal components with 30 nearest neighbors. Clustering was performed using Louvain algorithm with resolution 0.6 on the shared nearest-neighbor graph. Cell clustering was visualized using UMAP, computed from the same nearest neighbor graph used for clustering.
Assembly: mm10
Supplementary files format and content: CellRanger output files: gex_barcodes.tsv.gz, gex_features.tsv.gz, gex_matrix.mtx.gz
Supplementary files format and content: Outpus files for hashtag: hto_barcodes.tsv.gz, hto_features.tsv.gz, hto_matrix.mtx.gz
Supplementary files format and content: Analysis results from Seurat including clusters, annotations, and UMAP
Library strategy: CITE-seq

source_name: lymph nodes

extract_protocol:
For single cell RNA seq of TCs, anatomically distinct lymph nodes were pooled from 2 w old (P14) RorcVenus-creERT2 mice with 7 biological replicates per pool of lymph nodes. Lymph nodes were minced were digested in collagenase in RPMI1640 supplemented with 5% fetal calf serum, 1% L-glutamine, 1% penicillin–streptomycin, 10 mM HEPES, 1 mg/ml collagenase A (Sigma, 11088793001) and 1U/mL DNase I (Sigma, 10104159001) for 45 min at 37°C, 250 rpm. Cells were depleted of Lineage (TCRb, TCRgd, CD19, B220, NK1.1)+ cells via staining with biotinylated antibodies followed by magnetic bead negative selection. Cells were incubated with anti-CD16/32 in sorting buffer (2% FBS in PBS) for 10 minutes at 4°C to block binding to Fc receptors. Extracellular antigens were stained for 30 minutes at 4°C in sorting buffer (2% FBS, 2mM EDTA, in PBS). Cells from distinct lymph nodes were “stained” with TotalSeqTM oligo-conjugated antibodies consisting of a pool of antibodies directed against CD45 (30-F11) and H2 MHC Class I alloantigens (clone M1/42; Biolegend). Cells were washed and resuspended in sorting buffer with SYTOX blue (Invitrogen) for exclusion of dead cells. Live, CD45+Lin(Siglec-F, TCRb, TCRgd, CD19)–RORgt(Venus)+CXCR6–MHCII+ cells were then sort purified. Cells were sorted into cRPMI, before being pelleted and resuspended in RPMI-2% FBS to a final concentration of 700–1,300 cells per μl.  Single Cell Gene Expression was performed on Chromium instrument (10X Genomics) following the user guide manual for 3′ v3.1. In brief, viability of cells was confirmed above 80% with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. ~10,000 cells were targeted in total.
Cells from different lymph nodes were multiplexed together on one lane of 10X Chromium using Hash Tag Oligonucleotides - HTO following previously published protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: lymph nodes

value: Thetis cell

tag: age

value: 2 weeks


title: DNA-CX3-GATA4-Round3-Rep1

description:
Library name: DNA-CX3-GATA4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA4 for 3 rounds, Biological replicate 1


title: ADRA03_IOF1_3_G [mRNA-derived cDNA]


title: TC_all_LN_1, GEX

description:
Library name: TC_all_LN_1_mRNA
GEX (3' mRNA) library for Thetis cells from lymph nodes of 2-week old mice


title: porcine,ATAC-seq,Zygote,rep2

data_processing:
For paired-end ATAC-seq reads, alignment to genomes was executed with Bowtie2 v.2.3.4. Aligned reads underwent filtering with a minimum mapping quality of 20, and PCR duplicates were subsequently removed. Estimation of read coverage across the genome was performed utilizing bamCoverage from deepTools v.3.3.1, with parameters -binSize 100, and normalization using RPKM. Visualization was accomplished using UCSC Browser or IGV (2.16.1). To mitigate batch and cell type variations in comparisons, RPKM values of ATAC-seq data were additionally normalized through z-score transformation.
Assembly: susScr11
Supplementary files format and content: BigWig files of each stage

extract_protocol:
The collection timings for porcine oocytes and embryos adhered to the schedule outlined in previous studies (Bu, G. et al.,2022;Gao, L. et al.,2018;Berg, D. K. et al. ,2011).  Porcine IVF embryos at each stage were collected at specified time points: 28 hpi (2-cell), 48 hpi (4-cell), 72-76 hpi (8-cell), 120 hpi (morula), and 150 hpi (blastocyst). GV oocytes were obtained by removing cumulus cells from fresh COCs through vortexing for 5 minutes in 1 mg/mL hyaluronidase. The removal of the zona pellucida and isolation of ICM were carried out as described (Gao, L. et al.,2018). Briefly, the zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma-Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA).
We prepared libraries of oocytes and early embryos utilizing the TruePrep DNA Library Prep Kit V2 from Illumina (Vazyme Biotech, TD502), with slight modifications (Wu, J. et al. ,2018). Briefly, oocytes or embryos without zona pellucida were transferred into a 0.2-mL conventional, low-binding tube (Axygen, PCR-02D-L-C) with a small volume of DPBS-0.001% BSA. After incubation with 6 μL lysis buffer (10 mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL CA-630) on ice for 10-30 min, 4 μL ddH2O, 4 μL 5 × TTBL, and 5 μL TTE mix V5 were added to the sample. The mixture was incubated at 37°C for 30 min, followed by mixing with 5 μL of 5 × TS stop buffer and further incubation at room temperature for 5 min. The sample was then mixed with 103 μL nuclease-free water and 2 μL of 20 ng/μL carrier RNA (Qiagen, 1068337) and transferred to a phase-lock tube (Qiagen,129056), containing 130 μL of phenol: chloroform: isoamyl alcohol (25:24:1). After centrifugation, the supernatant was transferred to a new low-binding 1.5-mL tube containing 1 μL glycogen, 13 μL of 3 M sodium acetate, and 130 μL isopropanol for DNA precipitation at -20°C overnight. Following centrifugation, the precipitated DNA was washed twice with 500 μL ice-cold 80% ethanol and dissolved in 20 μL of nuclease-free H2O. PCR was performed to amplify the libraries, which were then purified with 1.3 × AMPure beads (Beckman, A63882), as described (Wu, J. et al. ,2016). Subsequently, all miniATAC-seq libraries were sequenced using Illumina Novaseq-6000 with paired-ended 150-bp reads.


title: porcine,ATAC-seq,Zygote,rep1


title: DNA-CX3-GATA4-Round2-Rep1

description:
Library name: DNA-CX3-GATA4-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA4 for 2 rounds, Biological replicate 1


title: TC_all_LN, HTO

description:
Library name: TC_all_LN_HTO
HTO library for Thetis cells from lymph nodes of 2-week old mice


title: ADRA03_IOF1_3_H [HTO-derived cDNA]


title: DNA-CX3-GATA4-Round1-Rep1

description:
Library name: DNA-CX3-GATA4-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA4 for 1 rounds, Biological replicate 1


title: porcine,ATAC-seq,Morula,rep4

source_name: Morula

value: Morula


title: TCRTg_HTO

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

description: Library name: Pooled HTO

data_processing:
Multiome reads were mapped to the mm10 reference genome using 10X Genomics cellranger-arc count pipeline (v2.0.0). Downstream processing of CITE-seq and scRNA-seq was done using scanpy (v1.9.8) pipeline. Viable cells were identified based on library size and complexity, whereas cells with <40% of transcripts derived from mitochondria were excluded from analysis. After mitochondrial and doublet clean up (as identified by HTO), CITE-seq count matrix (CD90.1 versus CD90.2) was analyzed to identify correct TCRTg status from the multiome data. Briefly, raw count matrix was normalized using center log ratio (CLR) normalization method adapted from Seurat (Satija et al., 2015). Upon CLR normalization, Euclidean distance was used to construct nearest-neighbor graph and Leiden clustering was performed for further filtering irrelevant/contaminating barcode sequences.
Assembly: mm10
Supplementary files format and content: adataGEX_processed.h5ad
Supplementary files format and content: adataATAC_processed.h5ad
Supplementary files format and content: adataCITE_processed.h5ad
Supplementary files format and content: adataHTO_processed.h5ad
Library strategy: CITE-seq

source_name: Spleen, Liver, Salivary Gland

extract_protocol:
For preparation of transgenic cells for single-cell multiome sequencing, congenically marked naïve TCRTg cells (M45Tg and M38Tg) were transferred into congenically distinct naïve recipient mice prior to infection with MCMV (see Methods), as illustrated in Extended Data Fig. 4A. On the day of cell isolation, each mouse was injected with 50µg of anti-ARTC2 nanobody (i.p.) 30 minutes before sacrifice (BioLegend, Catalog No. 149803, Clone S+16a) and processed as described above (see Tissue processing and preparation of single cell suspension). Intravenous (I.V.) labeling was not performed prior to sorting due to its limited ability to distinguish circulating from bona fide tissue-resident cells in the liver. Notably, I.V. labeling showed minimal signal in the salivary gland, comparable to the lymph nodes, which remain unlabeled (data not shown). Upon cell sorting into 1× PBS + 0.04% BSA, TCRTg cells were stained with mouse TotalSeq-A Hash Tag Oligonucleotides antibodies (BioLegend, tag number A0301-A0310), oligo-tagged anti-rat/mouse CD90.1 (BioLegend, Catalog No. 202547, Clone OX-7), and anti-mouse CD90.2 (BioLegend, Catalog No. 105345, Clone 30-H12). Hash tagged cells were then pooled at approximately equal ratios for multiome sequencing.
Single Cell Multiome ATAC + Gene Expression was performed with 10X Genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (Catalog No. 1000282) and ATAC Kit A (Catalog No. 1000280). We followed Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide with the difference that single cell suspension was prepared as described(Mimitou et al., 2021) (DOGMA-seq protocol with Digitonin buffer). Briefly, cells were treated with a digitonin lysis buffer (20mM Tris-HCl pH 7.4, 150mM NaCl, 3mM MgCl2, 0.01% DIG and 2U/µl of RNase inhibitor) for 5 mins on ice, followed by adding 1ml of chilled DIG wash buffer (20mM Tris-HCl pH 7.4, 150mM NaCl, 3mM MgCl2 and 1U/µl of RNAse inhibitor) and inversion before centrifugation at 500g for 5 mins at 4 °C. The supernatant was discarded, and cells were resuspended in DIG wash buffer, followed by counting using trypan blue and DAPI on a Countess II FL Automated Cell Counter. Cells were processed according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide. In addition, samples were multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO). Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: Spleen, Liver, Salivary Gland

value: TCRTg CD8 T cells

value: mixed

value: MCMV


title: TCRTg_Multiome

description: Library name: Pooled Multiome

data_processing:
Multiome reads were mapped to the mm10 reference genome using 10X Genomics cellranger-arc count pipeline (v2.0.0). Downstream processing of CITE-seq and scRNA-seq was done using scanpy (v1.9.8) pipeline. Viable cells were identified based on library size and complexity, whereas cells with <40% of transcripts derived from mitochondria were excluded from analysis. After mitochondrial and doublet clean up (as identified by HTO), CITE-seq count matrix (CD90.1 versus CD90.2) was analyzed to identify correct TCRTg status from the multiome data. Briefly, raw count matrix was normalized using center log ratio (CLR) normalization method adapted from Seurat (Satija et al., 2015). Upon CLR normalization, Euclidean distance was used to construct nearest-neighbor graph and Leiden clustering was performed for further filtering irrelevant/contaminating barcode sequences.
Assembly: mm10
Supplementary files format and content: adataGEX_processed.h5ad
Supplementary files format and content: adataATAC_processed.h5ad
Supplementary files format and content: adataCITE_processed.h5ad
Supplementary files format and content: adataHTO_processed.h5ad


title: ADRA03_IOF1_2_H [HTO-derived cDNA]


title: porcine,ATAC-seq,Morula,rep3


title: DNA-CX3-GATA1-Round4-Rep1

description:
Library name: DNA-CX3-GATA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA1 for 4 rounds, Biological replicate 1

value: synthetic DNA

value: Free DNA


title: TCRTg_CITE

description: Library name: Pooled CITE


title: porcine,ATAC-seq,Morula,rep2


title: DNA-CX3-GATA1-Round2-Rep1

description:
Library name: DNA-CX3-GATA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA1 for 2 rounds, Biological replicate 1


title: ADRA03_IOF1_2_A [ADT-derived cDNA]

value: ADT


title: Syngeneic Placenta 3

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

description:
Library name: S3
Visium CytAssist Fresh Frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Visium Mouse Transcriptome Probe Set v1.0 genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5:  matrix, containing filtered spatial barcodes, gene names, and UMI counts
Supplementary files format and content: aligned_fiducials.jpg:  aligned fiducials of the tissue image
Supplementary files format and content: cytassist_image.tiff:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:  low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv:  list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Placenta

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared according to manufacturer's prtocol "10X Genomics Visium CytAssist Spatial Gene Expression (CG000495, rev F)"

treatment_protocol: We collected mouse semi-allogeneic and syngeneic placentas at E12.5

value: Placenta

tag: day of_development

tag: pregnancy type

value: Syngeneic


title: DNA-CX3-GATA1-Round3-Rep1

description:
Library name: DNA-CX3-GATA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA1 for 3 rounds, Biological replicate 1


title: ADRA03_IOF1_1_H [HTO-derived cDNA]

value: PBMC

value: HTO


title: DNA-CX3-GATA1-Round1-Rep1

description:
Library name: DNA-CX3-GATA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of GATA1 for 1 rounds, Biological replicate 1


title: porcine,ATAC-seq,Later_Blastocyst,rep2

source_name: Later-Blastocyst

value: Later-Blastocyst


title: Syngeneic Placenta 1

description:
Library name: S1
Visium CytAssist Fresh Frozen Spatial transcriptome sequencing


title: ADRA03_IOF1_3_A [ADT-derived cDNA]

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: ADRA03_IOF1_1_G [mRNA-derived cDNA]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: Syngeneic Placenta 2

description:
Library name: S2
Visium CytAssist Fresh Frozen Spatial transcriptome sequencing


title: DNA-CX3-FOXA1-Round4-Rep2

description:
Library name: DNA-CX3-FOXA1-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 4 rounds, Biological replicate 2


title: porcine,ATAC-seq,GV,rep3

value: GV


title: Semi-allogeneic Placenta 2

description:
Library name: A2
Visium CytAssist Fresh Frozen Spatial transcriptome sequencing

value: Semi-allogeneic


title: Semi-allogeneic Placenta 3

description:
Library name: A3
Visium CytAssist Fresh Frozen Spatial transcriptome sequencing


title: porcine,ATAC-seq,Later_Blastocyst,rep1


title: MDA-MB-231 cells, siIGF2BP3-rep 3

city: xi'an

first: tongtong

last: jiang

address: changle western load

institute: Fourth Military Medical University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads, remove the contaminated reads for adapters, remove the low quality reads, Remove the reads whose N base more than 5% for total bases.
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast

growth_protocol: MDA-MB-231 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 RNAiso Plus kit (Takara). 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: MDA-MB-231 cells transfected with siIGF2BP3 or siNC for 48 hours

value: breast

value: breast cancer cell

value: IGF2BP3 knockdown

value: tumor metastasis


title: DNA-CX3-FOXA1-Round4-Rep1

description:
Library name: DNA-CX3-FOXA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 4 rounds, Biological replicate 1


title: DNA-CX3-FOXA1-Round3-Rep1

description:
Library name: DNA-CX3-FOXA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 3 rounds, Biological replicate 1


title: porcine,ATAC-seq,GV,rep1


title: porcine,ATAC-seq,GV,rep2


title: Micropilalr implants

city: Evanston

first: Xinlong

last: Wang

address: 2145 Sheridan Road

institute: Northwestern University

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone

extract_protocol:
FFPE slides were collected using microtome in an RNase free environment.
Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per manufacturer’s instructions.

value: Bone

value: nude mice

value: micropillar implant


title: DNA-CX3-FOXA1-Round3-Rep2

description:
Library name: DNA-CX3-FOXA1-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 3 rounds, Biological replicate 2

data_processing:
The forward (labeled ‘R1’) and reverse complement (labeled ‘R2’) 150-bp paired-end sequencing fastq reads were merged with PEAR in default setting (PMID: 24142950).
PCR duplicates were removed and the reads were trimmed at the 3’ end to remove the 6-bp UMIs. Since PIONEAR-seq libraries by design are 147-bp long, trimmed reads with different lengths were removed.
To extract the DNA sequence and the location of the tiles, the reads were aligned to the associated template  by the  R function pairwiseAlignment (default setting except: type='overlap’,  gapOpening=1000, gapExtension=0). This function furnishes an alignment score and the position of the base mismatches for each read. Given the template is 147-bp long and the random tile is 20-bp long, reads with an alignment score smaller than 127 were considered non-aligned and removed.
The position of the first and last mismatch were compared to assign the random tile position of each read
For each library, the read count of tiles at different position varies. To give the same weight to each tile position, the median read count of the library was used to resample the tiles at each psoition (Isotiling). To calculate motif enrichment the internal 16-bp of all the isotiles of the library were merged and compared to the associated input library by using the SELEX R package.
Assembly: Synthetic DNA
Supplementary files format and content: XXX_kmer_enrichment_table.txt' file is in txt format and contains a table showing:
Supplementary files format and content: the enrichment rank (Column 1: ID), the sequence of the enriched k-mer (column 2: Kmer), the k-mer count observed in the assessed library (column 3: ObservedCount), the expected k-mer count inferred from the associated input library used as background set (Column 4: ExpectedCount), their relative k-mer count increase, which is a measure of k-mer enrichment and is defined as the ration between the expected and observed counts (Column 5: Increase).
Library strategy: SELEX

value: synthetic DNA

value: Free DNA


title: ADRA03_IOF1_2_G [mRNA-derived cDNA]


title: porcine,ATAC-seq,Morula,rep1

value: Morula


title: DNA-CX3-FOXA1-Round2-Rep2

description:
Library name: DNA-CX3-FOXA1-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 2 rounds, Biological replicate 2


title: Flat implants

description:
Library name: Sample 1
10x Genomics

value: flat implant


title: MDA-MB-231 cells, siIGF2BP3-rep 2


title: porcine,ATAC-seq,Early_Blastocyst,rep2

source_name: Early-Blastocyst

value: Early-Blastocyst


title: ADRA03_IOF1_1_A [ADT-derived cDNA]

value: PBMC

value: ADT


title: porcine,ATAC-seq,8cell,rep2


title: DNA-CX3-FOXA1-Round1-Rep2

description:
Library name: DNA-CX3-FOXA1-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 1 rounds, Biological replicate 2

source_name: synthetic DNA


title: DNA-CX3-FOXA1-Round2-Rep1

description:
Library name: DNA-CX3-FOXA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 2 rounds, Biological replicate 1


title: MDA-MB-231 cells, siNC-rep 1

value: WT


title: kidney, IgAN, GQYS, rep3

city: Hangzhou

first: Cao

last: Jiawei

address: No. 1630 Huan Ding Road, Shangcheng District

institute: Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University

description: Library name: H6

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 6 G raw reads for each sample were generated. Raw reads of fastq form at were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Fold change > 2 or fold change < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar. Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: kidney

value: gavage with GQYS


title: kidney, IgAN, GQYS, rep2

description: Library name: H4


title: kidney, IgAN, GQYS, rep1

description: Library name: H3


title: porcine,ATAC-seq,Early_Blastocyst,rep1


title: ESC2CM-scRNA_7

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
The Cell Ranger RNA Software Suite (version 3.0.0) was used for processing sequencing information and single cell barcodes
Matrix was filtered for mitochondrial RNA.
Cells were filtered unique molecular identifies greater than 3000 and number of genes greater than 1500.
Seurat was used for further analysis including dimensionality reduction, cell clustring and differential expression.
Genome_build: genome build: hg19/Grhc37
Supplementary_files_format_and_content: scRNA-seq counts sparse matrix

source_name: hESC-dreived cardiomyocyte

growth_protocol: Human ESC lines (H1) were maintained on 1% Matrigel coated plates in Essential 8 Medium, and grown to ~100% confluence(d0). The medium was then replaced with differentiation medium comprising RPMI 1640 medium and B27 supplement minus insulin. On day 0, CHIR99021 was added to the differentiation medium (8 μM final). On day 2, 2 uM Wnt-C59 was added to the differentiation medium. On day 4, B27 supplement minus insulin was added to the differentiation medium. The medium was changed every 2 days for a desired time of culture.

extract_protocol:
Cells were digested into a single-cell suspension and then filtered through a 70-μm cell strainer into 15-ml tubes.
10X Genomics Single Cell RNA version 2

tag: cell type/time point

value: hESC-dreived cardiomyocyte on day 0, 2, 4, 6, 8 and 15


title: MDA-MB-231 cells, siNC-rep 2

value: breast

value: breast cancer cell


title: kidney, IgAN, untreated, rep3

description: Library name: M6

value: gavage with saline


title: porcine,ATAC-seq,8cell,rep1


title: DNA-CX3-CEBPB-Round4-Rep1

description:
Library name: DNA-CX3-CEBPB-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of CEBPB for 4 rounds, Biological replicate 1

extract_protocol:
Amplicon DNA
Sequencing libraries were prepared by adding to the selected libraries (1) 5' end Unique Molecular Identifies (UMIs), (2) llumina adaptors (IAs), (2) TRUseq dual barcodes (BCs) and (2) Illumina sequencing promoters P5 and P7 (P5/P7) by PCR amplification with custom primers.  10 ng of DNA was used as starting material samples. Libraries were with KAPA HiFi HotStart ReadyMix PCR Kit amplified by using 2 consecutive 6-cycle PCR runs (first cycle for UMIs and IAs, second cycle for BCs and P5/P7)  on the thermocycler. Post amplification libraries were size selected at ~3000bp in length by Azenta using AMPure XP beads. Libraries were validated by using both the Tapestation D1000 and  Qubit.


title: kidney, IgAN, untreated, rep2

description: Library name: M5


title: DNA-CX3-CEBPB-Round3-Rep1

description:
Library name: DNA-CX3-CEBPB-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of CEBPB for 3 rounds, Biological replicate 1


title: Semi-allogeneic Placenta 1

description:
Library name: A1
Visium CytAssist Fresh Frozen Spatial transcriptome sequencing

value: Placenta

value: Semi-allogeneic


title: porcine,ATAC-seq,4cell,rep1


title: ESC2CM-scRNA_5


title: kidney, IgAN, untreated, rep1

description: Library name: M2


title: DNA-CX3-CEBPB-Round2-Rep1

description:
Library name: DNA-CX3-CEBPB-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of CEBPB for 2 rounds, Biological replicate 1


title: porcine,ATAC-seq,2cell,rep2


title: ESC2CM-MicroC-d15-2

description: processed data files: ESC2CM-d15.hic,ESC2CM.d15.pairs.gz

data_processing:
library strategy: MicroC
BWA was used mapping DNA sequences against reference genome
pairtools was used to detect ligation junctions, remove PCR duplicates and generate ValidPairs files
mcool files were converted from ValidPairs by Cooler package
hic file were converted from ValidPairs by Juicer tools
Genome_build: hg19/Grhc37
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with mutiple resolutions
Supplementary_files_format_and_content: valid paris file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) chromosome of second locus, 5) read position of second locus,6) strand of first locus,  7) strand of second locus, 8) pair reads type

extract_protocol:
Cells were digested into a single-cell suspension and then filtered through a 70-μm cell strainer into 15-ml tubes.
Dovetail Micro-C v1.0

value: hESC-dreived cardiomyocyte on day 15


title: MDA-MB-231 cells, siNC-rep 3

value: tumor metastasis


title: DNA-CX3-FOXA1-Round1-Rep1

description:
Library name: DNA-CX3-FOXA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of FOXA1 for 1 rounds, Biological replicate 1

value: synthetic DNA

value: Free DNA


title: MDA-MB-231 cells, siIGF2BP3-rep 1

value: IGF2BP3 knockdown


title: DNA-CX3-CEBPB-Round1-Rep1

description:
Library name: DNA-CX3-CEBPB-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of CEBPB for 1 rounds, Biological replicate 1


title: ESC2CM-MicroC-d15-1


title: kidney, control, untreated, rep3

description: Library name: C5


title: porcine,ATAC-seq,2cell,rep1


title: ESC2CM-MicroC-d0-4

description: processed data files: ESC2CM-d0.hic,ESC2CM.d0.pairs.gz

value: hESC-dreived cardiomyocyte on day 0


title: kidney, control, untreated, rep1

description: Library name: C2


title: ESC2CM-scRNA_6


title: kidney, control, untreated, rep2

description: Library name: C3


title: DNA-ALB1-ZNF143-Round4-Rep1

description:
Library name: DNA-ALB1-ZNF143-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of ZNF143 for 4 rounds, Biological replicate 1


title: ESC2CM-MicroC-d0-3


title: ESC2CM-MicroC-d0-2


title: porcine,ATAC-seq,4cell,rep2


title: Katnal2 Mut cortex

city: Shanghai

first: Yao

last: Xue

address: 3663 North Zhongshan Rd

institute: East China Normal University

data_processing:
The quality of each sample was evaluated by using 10x genomics official software Cell Ranger, which integrates STAR software to align reads to the reference genome and obtain high-quality cell number, gene number and genome alignment rate in the raw data.
Single-cell transcriptome sequencing uses the measured transcript sequence in combination with UMI and Cell Barcode to obtain the absolute number of each transcript molecule within a single cell.
Dimensionality reduction and cluster analysis
The bimod test was used to test for differences between the specified cell population and all other cell populations to screen for the specific Marker gene for each cell population.
The Wilcox-test method was used to test the differential genes of the cell population from two groups/two samples in the specified cell population, so as to screen the differential genes between different groups/different samples of each cell population.
Assembly: database=ensembl,version=release-98,refer_name=GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: cortex

extract_protocol:
P5 cortical tissues were treated first by 0.25% Trypsin-EDTA at 37℃ for 30 min, then by 0.2% type-II collagenase for 4 h to dissociate the cells. After removing cell clumps using a 70 μm sterile nylon mesh cell strainer, single cells were isolated using fluorescence-activated cell sorting and encapsulated in droplets along with barcoded beads and reverse transcription reagents using the 10x Genomics Chromium Controller.
The 10x Genomics platform uses microfluidic technology to encapsulate beads and cells with Cell Barcode in droplets, collect the droplets containing the cells, and then lyse the cells in the droplets so that the mRNA in the cells binds to the Cell Barcode on the beads to form Single Cell GEMs, in which reverse transcription reactions are performed to construct cDNA libraries, which are sampled on the library sequences Distinguish the sample source of the target sequence.

value: cortex

value: Mut

value: Dissection under physiological conditions and store at -80 °C


title: DNA-ALB1-ZNF143-Round3-Rep1

description:
Library name: DNA-ALB1-ZNF143-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of ZNF143 for 3 rounds, Biological replicate 1


title: Katnal2 WT cortex

value: WT


title: ESC2CM-MicroC-d0-1


title: DNA-ALB1-RUNX2-Round4-Rep1

description:
Library name: DNA-ALB1-RUNX2-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of RUNX2 for 4 rounds, Biological replicate 1


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; WT, rep 4

city: Charlottesville

first: Audrey

state: Virginia

address: 345 Crispell Dr.

institute: The University of Virginia

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
198

data_processing:
Raw reads were checked for quality using FASTQC v0.11.5
Reads were trimmed to remove adapters using bbmap v39.01.
Salmon v.1.10.1 was used for ‘quasi-mapping’ and quantification
Assembly: mm10
Supplementary files format and content: CSV file with samples in columns and genes in rows. Contains normalized gene counts from Salmon

source_name: Cecum

growth_protocol: Adult mice were challenege with E. histolytica by intra-cecal infection 72h prior to tissue collection.

extract_protocol:
Total RNA was extracted from cecal tissue snips using a Qiagen RNeasy Mini Kit followed by Invitrogen Turbo DNA-Free Kit DNase treatment according the manufacturer's instruction
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: At harvest, cecal tissue was collected and immediately placed in RNAlater at ambient temperature for 1 hour followed by storage in 4C until RNA extraction.

value: Cecum

value: E. histolytica challenge 72h prior


title: ESC2CM-scATAC_2

data_processing:
The Cell Ranger ATAC Software Suite (version 1.0.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the Tn5 transposase made cuts
Barcodes likely associated with whole cells were identified by analyzing the number of fragments (1000) mapped near TSS regions (4).
ArchR was used for further analysis including dimensionality reduction and cell clustring.
Genome_build: genome build: hg19/Grhc37
Supplementary_files_format_and_content: fragments-tsv files contain aligned scATAC-seq fragments

extract_protocol:
Cells were digested into a single-cell suspension and then filtered through a 70-μm cell strainer into 15-ml tubes.
10X Genomics Single Cell ATAC Kit version 1

value: hESC-dreived cardiomyocyte on day 0, 2, 4, 6, 8 and 15


title: DNA-ALB1-RUNX2-Round3-Rep1

description:
Library name: DNA-ALB1-RUNX2-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of RUNX2 for 3 rounds, Biological replicate 1


title: DNA-CX3-ASCL1-Round4-Rep1

description:
Library name: DNA-CX3-ASCL1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of ASCL1 for 4 rounds, Biological replicate 1


title: DNA-CX3-ASCL1-Round3-Rep1

description:
Library name: DNA-CX3-ASCL1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence CX3 for the binding of ASCL1 for 3 rounds, Biological replicate 1


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; WT, rep 3

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
179


title: ESC2CM-scATAC_1


title: DNA-ALB1-RUNX2-Round2-Rep1

description:
Library name: DNA-ALB1-RUNX2-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of RUNX2 for 2 rounds, Biological replicate 1


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; Deletion, rep 4

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
178

value: Deletion


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; WT, rep 2

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
177


title: DNA-ALB1-RUNX2-Round1-Rep1

description:
Library name: DNA-ALB1-RUNX2-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of RUNX2 for 1 rounds, Biological replicate 1


title: amp_1_16_t15_rep1

description: Library name: Sample 5

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts are generated using featureCounts
Assembly: U00096.3
Supplementary files format and content: Comma-separated text file including raw counts for each gene and sample

source_name: K-12 substr. MG1655

extract_protocol:
Total RNA was extracted using a Luna Nanotech PuroMAG™ Total RNA Purification Kit (NKM051-384) which included a DNaseI treatment and a modification to incorporate bead beating as a means of cell lysis. RNA quality and concentration were assessed using an Agilent TapeStation and a Nanodrop, respectively.
One microgram of total RNA underwent ribosomal RNA removal using RiboRid, and the resulting rRNA-depleted RNA was used to make RNA-Seq libraries with the Kapa Biosystems (Roche) RNA HyperPrep Kit, following the manufacturer’s protocol.

value: K-12 substr. MG1655

value: Exposure to 1/16X MIC ampicillin


title: ESC2CM-scRNA_8


title: ESC2CM-scRNA_4


title: Cancer associated fibroblast from NSCLC patient 20150930

type: RNA

city: Taipei

first: Chao-Chi

last: Ho

address: 1 Jen Ai Road, Section 1

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital and National Taiwan University College of Medicine

description: Gene expression data of Cancer-associated fibroblast from NSCLC patient

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA normalization was utilized by the package affy in R.

label: biotin

source_name: Cancer-associated fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 800 cells per well were seeded to ultra-low adherent 24-wel plates (Corning) with MCDB201 medium (Invitrogen), and exposed to condition medium from cultured NFs and CAFs.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The medium was supplemented with epidermal growth factor (20ng/ml, Sigma) and bFGF (20ng/ml, Invitrogen).

value: Cancer-associated fibroblast

tag: smoking

value: Never

tag: gender

value: Female

tag: histology

value: LUAD

tag: Stage

value: Late


title: Cancer associated fibroblast from NSCLC patient 20150826


title: DNA-ALB1-PU1-Round4-Rep1

first: Luca

address: 77 Avenue Pasteur

description:
Library name: DNA-ALB1-PU1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of PU1 for 4 rounds, Biological replicate 1

tag: tissue

value: synthetic DNA

tag: treatment

value: Free DNA


title: Cancer associated fibroblast from NSCLC patient 0304

tag: cell type

value: Early


title: DNA-ALB1-PU1-Round3-Rep1

description:
Library name: DNA-ALB1-PU1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of PU1 for 3 rounds, Biological replicate 1


title: Cancer associated fibroblast from NSCLC patient 20151006


title: ESC2CM-scRNA_2


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; Deletion, rep 2

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
170

tag: genotype


title: DNA-ALB1-PAX7-Round4-Rep1

description:
Library name: DNA-ALB1-PAX7-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of PAX7 for 4 rounds, Biological replicate 1


title: ESC2CM-scRNA_3


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; WT, rep 1

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
169


title: Cancer associated fibroblast from NSCLC patient 20150812


title: Cancer associated fibroblast from NSCLC patient 20150707

value: Ever

value: Male


title: DNA-ALB1-PAX7-Round3-Rep1

description:
Library name: DNA-ALB1-PAX7-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of PAX7 for 3 rounds, Biological replicate 1


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; Deletion, rep 1

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
162


title: 1709_E2-4

city: Montreal

first: Daniel

last: Levesque

state: Qc

address: CP 6128, Succ. Centre-ville

department: Pharmacy

country: Canada

institute: University of Montreal

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the indexes.
Sequenced reads were trimmed for sequencing adapters and low quality extremities using Trimmomatic and mapped to the reference genome using STAR version 2.5.1b.
Readcounts were computed by STAR during sequence alignment based on gene annotations from Ensembl release 84
Assembly: Rnor_6.0
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
Chloroform/isopropanol extraction and purification on RNeasy columns
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: Striatum

value: FHH-Nr4a1m1Mcwi (Nur77-deficient rats)

value: Haloperidol


title: DNA-ALB1-PAX7-Round2-Rep1

last: Mariani

institute: Harvard Medical School

description:
Library name: DNA-ALB1-PAX7-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of PAX7 for 2 rounds, Biological replicate 1


title: Cancer associated fibroblast from NSCLC patient 1213


title: CREM fl/fl and CREM fl/fl CRE-ER same sex littermates; Deletion, rep 3

description:
Sequencing Batch 2
CREM_CRE_ER_WT_v_Deletion.csv
176

value: Cecum

value: E. histolytica challenge 72h prior


title: ESC2CM-scRNA_1

value: hESC-dreived cardiomyocyte on day 0, 2, 4, 6, 8 and 15


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates; Deletion, rep 5

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
488

value: Deletion


title: Cancer associated fibroblast from NSCLC patient 20150818

value: Cancer-associated fibroblast


title: 1699_C1-5

value: Wild type Fawn-Hooded hypertensive (FHH) rats

value: Saline


title: DNA-ALB1-PAX7-Round1-Rep1

description:
Library name: DNA-ALB1-PAX7-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of PAX7 for 1 rounds, Biological replicate 1


title: Cancer associated fibroblast from NSCLC patient 20150902

value: Never

value: Female

value: LUAD


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates: WT, rep 4

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
474

value: WT


title: Cancer associated fibroblast from NSCLC patient 20100510

value: LUSC

value: Late


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates: WT, rep 5

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
487


title: 1691_C2-4


title: Cancer associated fibroblast from NSCLC patient 0330


title: DNA-ALB1-OCT4-Round4-Rep1

description:
Library name: DNA-ALB1-OCT4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 4 rounds, Biological replicate 1

value: synthetic DNA

value: Free DNA


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates; Deletion, rep 4

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
473


title: Cancer associated fibroblast from NSCLC patient 20150519

value: Male

value: Early


title: Cancer associated fibroblast from NSCLC patient 20150505

value: Ever


title: DNA-ALB1-OCT4-Round3-Rep2

description:
Library name: DNA-ALB1-OCT4-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 3 rounds, Biological replicate 2


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates; Deletion, rep 3

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
393

value: Cecum

value: E. histolytica challenge 72h prior


title: 1681_E2-2

value: Striatum

value: FHH-Nr4a1m1Mcwi (Nur77-deficient rats)

value: Haloperidol


title: 1682_C2-3

value: Saline


title: Cancer associated fibroblast from NSCLC patient 20150303

description: Gene expression data of Cancer-associated fibroblast from NSCLC patient

value: Cancer-associated fibroblast

value: Never

value: Other


title: DNA-ALB1-OCT4-Round3-Rep1

description:
Library name: DNA-ALB1-OCT4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 3 rounds, Biological replicate 1


title: Cancer associated fibroblast from NSCLC patient 20150428


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates; Deletion, rep 2

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
337

value: Deletion


title: 1680_C2-2


title: 1677_C1-4

value: Wild type Fawn-Hooded hypertensive (FHH) rats


title: DNA-ALB1-OCT4-Round2-Rep2

description:
Library name: DNA-ALB1-OCT4-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 2 rounds, Biological replicate 2


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates: WT, rep 2

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
336

value: WT


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates: WT, rep 3

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
392


title: 1690_E2-3


title: DNA-ALB1-OCT4-Round1-Rep2

description:
Library name: DNA-ALB1-OCT4-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 1 rounds, Biological replicate 2

value: synthetic DNA


title: 1676_E1-3


title: Cancer associated fibroblast from NSCLC patient 20150318

value: Female

value: LUAD


title: Cancer associated fibroblast from NSCLC patient 20150331_1

value: Male

value: Early


title: Cancer associated fibroblast from NSCLC patient 20100426_1


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates: WT, rep 1

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
247

value: Cecum


title: 1675_C1-3


title: DNA-ALB1-OCT4-Round1-Rep1

description:
Library name: DNA-ALB1-OCT4-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 1 rounds, Biological replicate 1

value: Free DNA


title: tumour-infiltrating immune cells, treated,72h, rep3

city: Lisboa

first: Nuno

middle: Luís

last: Barbosa-Morais

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 and v7.0.1.
Assembly: mm10
Supplementary files format and content: TSV files containing detected cellular barcodes (barcodes.tsv) and corresponding features (features.tsv) as returned by Cell Ranger.MTX sparse matrix containing counts as returned by Cell Ranger.
Supplementary files format and content: Tab-delimited text files containing count matrices in log2(counts+1) corrected for batch effect.

source_name: tumor-infiltrating immune cells

extract_protocol:
Tumors resected from mice were cut in small pieces and digested with 1mg/mL collagenase Type I (Worthington), 0.4 mg/mL collagenase Type IV (Worthington) and 10μg/mL DNase I (Sigma-Aldrich) for 30 min at 37°C, in Eppendorf tubes. Cell suspensions were then filtered through a 100μm nylon cell strainer (Corning). Red blood cells were lysed using RBC Lysis Buffer (Biolegend) for 10 min at RT in the dark. Cells were centrifuged and resuspended in cRPMI (RPMI + Sodium Pyruvate (100x) + Non Essential Acids Amines (100x) + Hepes (100x) + Peni-Strep (100x) + bMercaptoethanol (1000x) + FCS 10%) and immediately processed for the specific readout.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10X Genomics).

value: tumor-infiltrating immune cells

value: immune

tag: strain

tag: sample id

value: 5-15 weeks

value: Treated


title: 1661_E1-1

value: Striatum

value: Haloperidol


title: DNA-ALB1-OCT4-Round2-Rep1

description:
Library name: DNA-ALB1-OCT4-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 2 rounds, Biological replicate 1


title: tumour-infiltrating immune cells, not-treated, rep3