title: NCP-W601-GATA4-Round4-Rep2

description:
Library name: NCP-W601-GATA4-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of GATA4 for 4 rounds, Biological replicate 2


title: Syngeneic Placenta Erythroid Cells E12.5 3

status: Public on May 01 2025

type: RNA

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)

hyb_protocol: 200ng of total RNA was hybridized with NanoString Mouse Immunology V1 panel according to the manufacturer's protocols.

scan_protocol: Automated scanning was performed on the NanoString Sprint system

data_processing: We performed QC on the raw data, normalized gene expression using 15 housekeeping genes, performed background thresholding (removed the genes with less expressiom that the mean of POS_D controls in all samples).

molecule: polyA RNA

organism: Mus musculus

source_name: Placenta

growth_protocol: We collected mouse semi-allogeneic and syngeneic placentas at E12.5 at E19.5

extract_protocol: We extracted  Ter-119 Erythroid cells from murine placenta via Ter-119 magnetic separation

tag: day of development

tag: pregnancy type

value: Syngeneic


title: NCP-W601-GATA1-Round4-Rep2

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: NCP-W601-GATA1-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of GATA1 for 4 rounds, Biological replicate 2

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

value: synthetic DNA

tag: treatment

value: DNA assembled onto nucleosomes


title: NCCLu-354

city: Goyang-si

first: namhee

last: yu

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National cancer center

library_source: transcriptomic

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic(Version 0.39) (standard parameters)
Mapping with STAR(version 2.7.0a)
Quantification with RSEM (v1.2.31 )
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Lung cancer patient derived cells

growth_protocol: Pleural effusions, pericardium effusions, ascites and tissues were obtained by lung cancer patients at National Cancer Center. All experiments utilizing human material were approved by NCC IRB. For liquid samples, effusions were transferred to conical tube and centrifuged at 120 x g for 10 min. The cell pellet was resuspended in RPMI and carefully layered onto LSM (Lymphocyte Separation Medium, #091692249 MP Biomedicals, France). After centrifugation at 400 x g for 30 min at room temperature, interphase layer between RPMI and LSM including tumor cells was harvested and washed with RPMI. For tissue sample, tumor tissues were minced finely and washed with RPMI. After washing, cells from effusion or tissue were cultured in AR-5 medium (5% FBS, 1 X GlutaMAX (Thermo Fisher Scientific), 1 X ITS (Insulin-Transferrin-Selenium, Thermo Fisher Scientific), 1% Penicillin/streptomycin, 50 nM hydrocortisone, 1 mM Sodium Pyruvate and 1 ng/ml EGF in RPMI) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was purified from cultured cell using RNeasy® mini kit, and AllPrep DNA/RNA Mini kit (Qiagen, German) and handled by QIAcube automatic instrument (Qiagen, German).
For RNA-seq analysis, we prepared mRNA sequencing libraries as paired-end reads with a length of 100 bases using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturers’ protocols. Briefly, mRNA molecules were purified and fragmented from 2 μg of total RNA. The libraries were sequenced as paired-end reads (2 × 150 bp) using the NovaSeq 6000 (Illumina).

treatment_protocol: non-treatment

value: lung cancer derived cells

tag: disease

value: Lung cancer


title: Syngeneic Placenta Erythroid Cells E12.5 2


title: NCCLu-351


title: NCP-W601-GATA1-Round4-Rep1

description:
Library name: NCP-W601-GATA1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of GATA1 for 4 rounds, Biological replicate 1


title: NCCLu-350


title: NCP-W601-FOXA1-Round4-Rep2

description:
Library name: NCP-W601-FOXA1-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of FOXA1 for 4 rounds, Biological replicate 2


title: NCP-W601-FOXA1-Round4-Rep1

description:
Library name: NCP-W601-FOXA1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of FOXA1 for 4 rounds, Biological replicate 1


title: NCP-W601-CEBPB-Round4-Rep1

description:
Library name: NCP-W601-CEBPB-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of CEBPB for 4 rounds, Biological replicate 1


title: NCCLu-347


title: Syngeneic Placenta Erythroid Cells E12.5 1


title: NCCLu-343


title: NCP-NRCAM-PU1-Round4-Rep1

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


title: NCP-NRCAM-RUNX2-Round4-Rep1

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


title: NCP-NRCAM-RUNX2-Round4-Rep2

description:
Library name: NCP-NRCAM-RUNX2-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence NRCAM for the binding of RUNX2 for 4 rounds, Biological replicate 2


title: Semi-allogeneic Placenta Erythroid Cells E12.5 3

value: Semi-allogeneic


title: Tumor tissue, Lipo-TriTE-treated, rep3

city: Tianjin

first: Helong

last: Kang

state: 选择一个

address: 94 Weijin Road

country: China

institute: Nankai University

description: Library name: Sample 9

data_processing:
Statistical methods were used to compare gene expression differences under two or more conditions, aiming to identify condition-specific genes. These specific genes were then further analyzed to explore their biological significance. The analysis workflow included quality control, read alignment, quantification, differential expression analysis, and functional enrichment.
Assembly: ensembl_107_mus_musculus_c57bl6nj_c57bl_6nj_v1_toplevel
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumour

extract_protocol:
The tumor was removed and frozen in liquid nitrogen.The tissue sample were homogenized the lysated using a rotor-stator homogenizer in Trizol. After DNA removal by AllPrep DNA spin column,the RNA were collected using a RNeasy spin column. After two washes, the RNA was dissolved in RNase-free water.
Fragmented mRNA was used as a template to synthesize the first-strand cDNA using random hexamer primers and M-MuLV reverse transcriptase. The RNA strand was then degraded with RNase H, and the second-strand cDNA was synthesized using DNA polymerase I and dNTPs. The resulting double-stranded cDNA was purified, followed by end repair, A-tailing, and ligation of sequencing adapters. Fragments of approximately 250–300 bp were selected using AMPure XP beads. The selected fragments were PCR-amplified and purified again with AMPure XP beads to obtain the final sequencing library.

value: Tumour

tag: cell line

tag: cell type

value: Mouse bladder cancer cells

tag: genotype

value: overexpression of HER2

value: Tumor and Lipo-TriTE


title: NCP-NRCAM-OCT4-Round4-Rep2

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


title: NCP-NRCAM-PAX7-Round4-Rep1

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


title: NCCLu-338


title: NCP-NRCAM-OCT4-Round4-Rep1

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


title: NCP-NRCAM-KLF4-Round4-Rep1

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


title: Semi-allogeneic Placenta Erythroid Cells E12.5 1


title: Tumor tissue, Lipo-TriTE-treated, rep2

description: Library name: Sample 8


title: NCCLu-335


title: NCP-NRCAM-GST-Round4-Rep2

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


title: Tumor tissue, Lipo-TriTE-treated, rep1

description: Library name: Sample 7


title: NCP-NRCAM-GST-Round4-Rep1

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


title: NCP-NRCAM-GATA4-Round4-Rep2

description:
Library name: NCP-NRCAM-GATA4-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence NRCAM for the binding of GATA4 for 4 rounds, Biological replicate 2


title: NCCLu-334


title: NCP-W601-ASCL1-Round4-Rep1

description:
Library name: NCP-W601-ASCL1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence W601 for the binding of ASCL1 for 4 rounds, Biological replicate 1


title: NCP-NRCAM-GATA4-Round4-Rep1

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


title: Tumor tissue, Lipo-BiTE-treated, rep3

description: Library name: Sample 6

value: Tumor and Lipo-BiTE


title: NCP-NRCAM-ZNF143-Round4-Rep1

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


title: NCCLu-333


title: Tumor tissue, Lipo-BiTE-treated, rep2

description: Library name: Sample 5


title: NCCLu-342


title: NCP-NRCAM-PAX7-Round4-Rep2

description:
Library name: NCP-NRCAM-PAX7-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence NRCAM for the binding of PAX7 for 4 rounds, Biological replicate 2


title: Semi-allogeneic Placenta Erythroid Cells E12.5 2


title: NCP-NRCAM-GATA1-Round4-Rep2

description:
Library name: NCP-NRCAM-GATA1-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence NRCAM for the binding of GATA1 for 4 rounds, Biological replicate 2


title: NCP-NRCAM-GATA1-Round4-Rep1

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


title: Tumor tissue, Lipo-BiTE-treated, rep1

description: Library name: Sample 4


title: NCP-NRCAM-FOXA1-Round4-Rep2

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


title: NCCLu-339


title: NCCLu-327


title: NCP-NRCAM-FOXA1-Round4-Rep1

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


title: NCP-NRCAM-CEBPB-Round4-Rep1

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


title: NCP-NRCAM-ASCL1-Round4-Rep1

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


title: NCP-CX3-ZNF143-Round4-Rep1

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


title: NCCLu-326


title: NCCLu-324


title: Tumor tissue, PBS-treated, rep3

description: Library name: Sample 3

value: Tumor and PBS


title: Tumor tissue, PBS-treated, rep2

description: Library name: Sample 2


title: Tumor tissue, PBS-treated, rep1

description: Library name: Sample 1


title: NCP-CX3-RUNX2-Round4-Rep1

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


title: NCP-CX3-RUNX2-Round4-Rep2

description:
Library name: NCP-CX3-RUNX2-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence CX3 for the binding of RUNX2 for 4 rounds, Biological replicate 2


title: NCP-CX3-PU1-Round4-Rep1

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


title: NCP-CX3-PAX7-Round4-Rep2

description:
Library name: NCP-CX3-PAX7-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence CX3 for the binding of PAX7 for 4 rounds, Biological replicate 2


title: NCP-CX3-PAX7-Round4-Rep1

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


title: NCP-CX3-OCT4-Round4-Rep2

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


title: NCCLu-318


title: mutant liver, rep3

city: Los Angeles

first: Alexander

last: Nguyen

state: CA

address: 675 Charles E Young Dr S

institute: University of California, Los Angeles

description: Library name: MUT3

data_processing:
Fastq files were uploaded to the Galaxy web platform, and public server at usegalaxy.org was used to analyze the data.
Reads were trimmed using Trimmomatic, assessed for quality using FastQC and aligned to GRCm38/mm10 using RNA STAR.
Aligned reads were counted using FeatureCounts. EdgeR was used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: tab-separate values contain differential expression output from EdgeR

source_name: liver

extract_protocol:
RNA from frozen liver tissue was homogenized and purified using RNeasy Mini Kit (Qiagen)
Stranded poly-A library preparation (Illumina) and paired-end sequencing on NovaSeq X Plus were performed by UCLA Technology Center for Genomics & Bioinformatics

value: liver

tag: strain

tag: Sex

value: male

value: homozygous mutant (A227)


title: mutant liver, rep4

description: Library name: MUT4


title: NCCLu-328


title: NCCLu-317


title: NCP-CX3-OCT4-Round4-Rep1

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


title: mutant liver, rep2

description: Library name: MUT2


title: NCP-CX3-KLF4-Round4-Rep1

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


title: NCP-CX3-GST-Round4-Rep1

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


title: mutant liver, rep1

description: Library name: MUT1


title: NCP-CX3-GATA4-Round4-Rep1

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


title: NCCLu-313


title: NCCLu-311


title: NCP-CX3-GATA1-Round4-Rep2

description:
Library name: NCP-CX3-GATA1-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence CX3 for the binding of GATA1 for 4 rounds, Biological replicate 2


title: wild-type liver, rep4

description: Library name: WT4

value: wildtype


title: wild-type liver, rep3

description: Library name: WT3


title: NCCLu-316


title: NCP-CX3-FOXA1-Round4-Rep2

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


title: NCP-CX3-FOXA1-Round4-Rep1

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


title: NCP-CX3-GATA1-Round4-Rep1

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


title: NCCLu-308


title: NCP-CX3-GATA4-Round4-Rep2

description:
Library name: NCP-CX3-GATA4-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence CX3 for the binding of GATA4 for 4 rounds, Biological replicate 2


title: NCP-CX3-CEBPB-Round4-Rep1

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


title: wild-type liver, rep2

description: Library name: WT2


title: NCCLu-306


title: NCCLu-320


title: NCP-CX3-GST-Round4-Rep2

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


title: NCCLu-304


title: NCP-CX3-ASCL1-Round4-Rep1

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


title: wild-type liver, rep1

description: Library name: WT1


title: NCP-ALB1-RUNX2-Round4-Rep1

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


title: NCP-ALB1-RUNX2-Round4-Rep2

description:
Library name: NCP-ALB1-RUNX2-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of RUNX2 for 4 rounds, Biological replicate 2


title: NCP-ALB1-ZNF143-Round4-Rep1

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


title: tumour-infiltrating immune cells, treated,12h, rep2

city: Lisboa

first: Nuno

middle: Luís

last: Barbosa-Morais

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

library_source: transcriptomic single cell

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: batch

tag: sample id

tag: age

value: 5-15 weeks

value: Treated


title: NCP-ALB1-PU1-Round4-Rep1

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

value: synthetic DNA

value: DNA assembled onto nucleosomes


title: NCCLu-303

value: lung cancer derived cells

value: Lung cancer


title: tumour-infiltrating immune cells, treated,12h, rep1


title: NCCLu-301


title: NCP-ALB1-PAX7-Round4-Rep1

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


title: NCCLu-299


title: NCP-ALB1-PAX7-Round4-Rep2

description:
Library name: NCP-ALB1-PAX7-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of PAX7 for 4 rounds, Biological replicate 2


title: tumour-infiltrating immune cells, not-treated, rep4


title: Cd24a-Pax9+ anti-IgG Cut&Tag_rep2

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

description: Sample 27

library_source: genomic

data_processing:
Sample 1-2  Raw data was processed using the Cell Ranger pipeline (cellranger-7.1.0) to generate gene-barcode matrices. Quality control was performed using Seurat (version 5.1.0) to filter out cells with low gene counts, high mitochondrial gene content, and potential doublets. Sample 3-6  Paired-end reads were aligned to the mm10 reference genome using HISAT2 version 2.2.1.FeatureCounts version 2.0.1 was used to add a gene tag to each alignment. The feature-barcode matrix was processed using Seurat (V5.0.1) package. Sample 7-11  Paired-end reads were aligned to the mm10 reference genome using HISAT2 version 2.2.1. FeatureCounts version 2.0.1 was used to add a gene tag to each alignment.  Sample 12-27  Paired-end reads were aligned to the mm10 reference genome using Bowtie2 version 2.3.5.1.Peak calling was executed using SEACR 1.3.
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz,features tsv.gz,matrix.mtx.gZ gene counts expression matrix file gene expression matrix file .bw
Assembly: bw
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: Cells isolated from primary tissues

extract_protocol:
Sample1-2 Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.  Sample3-6 Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.  Sample7-11 Following euthanasia of mice and tooth extraction, PN3 molar tissue was embedded in OCT compound. Laser capture microdissection (LCM) was conducted following an established protocol using Cresyl violet staining (Merck, C5042) for enhanced visualization of cellular morphology on PEN Membrane slides (MMI, 50102). Five regions were dissected: "Center," "Direct Below," "Side," "Pax9 Positive," and "Pax9 Negative." Samples were collected on IsolationCaps (MMI, 50206). Sample12-27 Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.
Sample1-2 Cell counting and viability confirmation were performed using the Countess II Automated Cell Counter (Thermo Fisher, AMQAX1000). Samples were then utilized for single-cell RNA sequencing with the 10x Genomics system.By using laser capture microdissection and odified SMART-seq3 library preparation methods, the relationships between different tissue regions were compared. Sample 3-6 Smart-seq3 was conducted with slight modifications. Single cells were sorted into 96-well plates with lysis buffer, then incubated at 72°C. Reverse transcription was performed with a mix containing RNase inhibitor and Maxima H-minus RT enzyme at 42°C. PCR pre-amplification followed, using KAPA HiFi HotStart buffer and specific primers. Samples were purified using homemade PEG beads and quantified. Tagmentation was done with homemade Tn5 and the libraries were amplified using the TruePrep Index Kit V2. Finally, samples were pooled, purified, and sequenced with 150-bp paired end using NovaSeq6000 Sample 7-11 The LCM samples collected on the IsolationCaps (MMI, 50206) were checked before further lysis with 50µl of 4M Guanidine isothiocyanate (GuSCN) solution (Invitrogen, 15577-018). RNA precipitation was conducted by adding a 771µl buffer composed of 600µl anhydrous ethanol (Fisher Chemical, A995-4), 20µl of 1.5M sodium acetate (Invitrogen, AM9740), 1µl glycogen (Thermo Fisher, AM9516), and 150µl of DNase/RNase-Free Distilled Water (Thermo Fisher, 10977015). The mixture was then incubated at -80°C for 30min, followed by centrifugation at 4°C at 12,000g for 30min to recover RNAs. The obtained RNA was processed for library construction utilizing the smart-Seq3 protocol (2) with slight modifications: The lysis buffer comprised 0.5U/μl of recombinant RNase inhibitor (RRI) (Takara, 2313A), 0.5mM dNTP (Thermo Scientific, R0192), and 0.5μM Smart-seq3 oligo-dT primer (5′-biotin-ACGAGCATCAGCAGCATACGAT30VN-3′; HPLC) (Takara). Following lysis, 10μl of reverse transcription mix was added to each sample, comprising 25mM Tris-HCl, pH 8.0 (Thermo Fisher, AM9855G), 30mM NaCl (Thermo Fisher, AM9760G), 1mM GTP (Thermo Fisher, R1461), 2.5mM MgCl2 (Thermo Fisher, AM9530G), 8mM DTT (Thermo Fisher, 707265ML), 0.5U/μl RRI, 2μM of Smart-seq3 TSOs (5′-biotin-AGAGACAGATTGCGCAATGNNNNNNNNrGrGrG-3′; HPLC) (Takara), and 2U/μl of Maxima H-minus RT enzyme (Thermo Fisher, EP0751). This integrated approach facilitates the detailed transcriptomic profiling of discrete anatomical regions. Sample 12-27 After harvesting, cells were counted and centrifuged for 3 minutes at 600g at room temperature, followed by resuspension in 4ml PBS and another centrifugation. Cells were then resuspended in 2ml ice-cold NE1 buffer with Pierce Protease Inhibitor Tablets (Thermo Fisher, A32965) and left on ice for 10 minutes. After centrifugation at 1,300g for 4 minutes at 4°C, cells were resuspended in 2ml PBS and centrifuged again. Nuclei were resuspended in wash buffer to approximately 1 million cells/ml, frozen in cryogenic vials with 10% DMSO, and stored at -80°C. Upon thawing, nuclei were incubated with Concanavalin A-coated magnetic beads (Bangs Laboratories, BP531), and then with primary antibody (α-H3K4me3 rabbit polyclonal antibody (Diagenode, C15410003)) and negative control (guinea pig α-rabbit IgG antibody (Antibodies online, ABIN101961)) overnight at 4°C. Secondary antibody (guinea pig α-rabbit IgG antibody (Antibodies online, ABIN101961)) was added and incubated for 1 hour. pA-Tn5 transposon was then added, and tagmentation was performed for 1 hour at 37°C. DNA was extracted, amplified by PCR for 17 cycles, purified using VAHTS DNA Clean Beads (Vazyme, N411), and sequenced at 150-bp paired end by Novaseq6000

value: dental mesenchymal stem cells

value: Cells isolated from primary tissues

tag: antibody

value: IgG

value: 9days old


title: NCP-ALB1-OCT4-Round4-Rep2

description:
Library name: NCP-ALB1-OCT4-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of OCT4 for 4 rounds, Biological replicate 2


title: Cd24a+Pax9+anti-IgG Cut&Tag_rep2

description: Sample 26


title: NCP-ALB1-KLF4-Round4-Rep1

description:
Library name: NCP-ALB1-KLF4-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of KLF4 for 4 rounds, Biological replicate 1


title: NCCLu-296


title: NCCLu-298


title: NCP-ALB1-GST-Round4-Rep1

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


title: Cd24a+Pax9- anti-IgG Cut&Tag_rep2

description: Sample 25


title: NCP-ALB1-GATA1-Round4-Rep2

description:
Library name: NCP-ALB1-GATA1-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of GATA1 for 4 rounds, Biological replicate 2


title: NCCLu-295


title: NCP-ALB1-GST-Round4-Rep2

description:
Library name: NCP-ALB1-GST-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of GST for 4 rounds, Biological replicate 2


title: NCP-ALB1-GATA4-Round4-Rep1

description:
Library name: NCP-ALB1-GATA4-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of GATA4 for 4 rounds, Biological replicate 1


title: NCP-ALB1-GATA4-Round4-Rep2

description:
Library name: NCP-ALB1-GATA4-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of GATA4 for 4 rounds, Biological replicate 2


title: Cd24a-Pax9- anti-IgG Cut&Tag_rep2

description: Sample 24


title: NCCLu-292


title: NCCLu-287


title: Cd24a-Pax9+ anti-H3K4me3 Cut&Tag_rep2

description: Sample 23


title: Cd24a+Pax9+ anti-H3K4me3 Cut&Tag_rep2

description: Sample 22


title: NCP-ALB1-CEBPB-Round4-Rep1

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


title: NCP-ALB1-OCT4-Round4-Rep1

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


title: NCCLu-285


title: NCP-ALB1-ASCL1-Round4-Rep1

description:
Library name: NCP-ALB1-ASCL1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of ASCL1 for 4 rounds, Biological replicate 1


title: DNA-W601-ZNF143-Round4-Rep1

description:
Library name: DNA-W601-ZNF143-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of ZNF143 for 4 rounds, Biological replicate 1

value: Free DNA


title: DNA-W601-ZNF143-Round3-Rep1

description:
Library name: DNA-W601-ZNF143-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of ZNF143 for 3 rounds, Biological replicate 1


title: NCCLu-277


title: DNA-W601-RUNX2-Round4-Rep1

description:
Library name: DNA-W601-RUNX2-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of RUNX2 for 4 rounds, Biological replicate 1


title: Cd24a-Pax9- anti-H3K4me3 Cut&Tag_rep2

description: Sample 20


title: NCCLu-261


title: DNA-W601-RUNX2-Round3-Rep1

description:
Library name: DNA-W601-RUNX2-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of RUNX2 for 3 rounds, Biological replicate 1


title: DNA-W601-RUNX2-Round2-Rep1

description:
Library name: DNA-W601-RUNX2-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of RUNX2 for 2 rounds, Biological replicate 1


title: DNA-W601-RUNX2-Round1-Rep1

description:
Library name: DNA-W601-RUNX2-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of RUNX2 for 1 rounds, Biological replicate 1


title: NL_M125_3

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Fastq reads were indexed using Nanopolish (v0.14.0).
Reads were aligned to rn7 assembly using minimap2 (v2.24) and indexed with Samtools (v1.6).
CpG methylation calling was performed using Nanopolish.
Methylation frequency was determined by the "calculate_methylation_frequency.py" script provided by Nanopolish.
Assembly: rn7
Supplementary files format and content: Test file of tab-separated values (.tsv) of called methylation values.
Library strategy: long-read DNA sequencing nanopore

organism: Rattus norvegicus

source_name: Neurohypophysis (Neural Lobe)

extract_protocol:
Rats were anesthetized with isoflurane and euthanized via transcardial perfusion with PBS. Brains were removed from the skull to gain access to the pituitary gland. The neurohypophysis was removed and immediately flash frozen by liquid nitrogen.
Genomic DNA was collected by ethanol precipitation. In brief, frozen tissue was ground under liquid nitrogen, and lysed with buffer ATL (Qiagen). DNA was isolated via phenol:chloroform: isoamyl alcohol and cintrifuged. DNA was washed and precipitated with 70% ethanol and the resuting DNA pellet was resuspended in buffer EB (Qiagen).
DNA was fragmented using a Covaris g-TUBE (Covaris). Libraries were prepared using the Oxford Nanopore Ligation Sequencing Kit (Oxford).

treatment_protocol: Rats were grown to the ages of 35 days old or 125 days old prior to tissue collection.

value: Neurohypophysis (Neural Lobe)

value: Male

value: Sprague Dawley

value: Age - 125 days old


title: DNA-W601-PU1-Round4-Rep1

description:
Library name: DNA-W601-PU1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of PU1 for 4 rounds, Biological replicate 1


title: NCCLu-257


title: NL_M125_2


title: DNA-W601-PAX7-Round4-Rep1

description:
Library name: DNA-W601-PAX7-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of PAX7 for 4 rounds, Biological replicate 1


title: NCCLu-250


title: DNA-W601-PU1-Round3-Rep1

description:
Library name: DNA-W601-PU1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of PU1 for 3 rounds, Biological replicate 1


title: NCP-ALB1-GATA1-Round4-Rep1

description:
Library name: NCP-ALB1-GATA1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of GATA1 for 4 rounds, Biological replicate 1


title: NL_M125_1


title: NCP-ALB1-FOXA1-Round4-Rep1

description:
Library name: NCP-ALB1-FOXA1-Round4-Rep1
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of FOXA1 for 4 rounds, Biological replicate 1


title: NCCLu-238


title: NCP-ALB1-FOXA1-Round4-Rep2

description:
Library name: NCP-ALB1-FOXA1-Round4-Rep2
PIONEAR for the binding of seq of the DNA library based on the tiling of the nucleosome positioning sequence ALB1 for the binding of FOXA1 for 4 rounds, Biological replicate 2


title: DNA-W601-PAX7-Round1-Rep1

description:
Library name: DNA-W601-PAX7-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of PAX7 for 1 rounds, Biological replicate 1


title: NL_M35_3

value: Age - 35 days old (Control)


title: NCCLu-237


title: DNA-W601-PAX7-Round3-Rep1

description:
Library name: DNA-W601-PAX7-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of PAX7 for 3 rounds, Biological replicate 1


title: DNA-W601-PAX7-Round2-Rep1

description:
Library name: DNA-W601-PAX7-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of PAX7 for 2 rounds, Biological replicate 1


title: DNA-W601-OCT4-Round4-Rep2

description:
Library name: DNA-W601-OCT4-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 4 rounds, Biological replicate 2


title: Cd24a+Pax9- anti-H3K4me3 Cut&Tag_rep2

description: Sample 21


title: NL_M35_2


title: DNA-W601-OCT4-Round4-Rep1

description:
Library name: DNA-W601-OCT4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 4 rounds, Biological replicate 1


title: NCCLu-231


title: DNA-W601-OCT4-Round3-Rep2

description:
Library name: DNA-W601-OCT4-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 3 rounds, Biological replicate 2


title: NL_M35_1


title: DNA-W601-OCT4-Round3-Rep1

description:
Library name: DNA-W601-OCT4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 3 rounds, Biological replicate 1


title: NCCLu-214


title: genomic DNA from a FFPE H3K27M-mutant diffuse glioma with a non-midline location

type: genomic

city: Bron

first: Marc

last: Barritault

address: 59 boulevard Pinel

country: France

institute: Hospices Civils de Lyon

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPICV2 DNA methylation Beadchip  using standard Illumina protocol

scan_protocol: Scanning was performed on a nextseq 550 plateform

data_processing: no data processing. Raw intensity files

label: Cy5 and Cy3

source_name: male","brain", "H3K27M glioma", "non-midline location

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE sample using Maxwell® RSC RNA FFPE Kit promega

value: glioma

value: male

value: brain


title: DNA-W601-OCT4-Round2-Rep2

description:
Library name: DNA-W601-OCT4-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 2 rounds, Biological replicate 2

value: synthetic DNA


title: DNA-W601-OCT4-Round2-Rep1

description:
Library name: DNA-W601-OCT4-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 2 rounds, Biological replicate 1


title: NCCLu-213


title: DNA-W601-OCT4-Round1-Rep1

description:
Library name: DNA-W601-OCT4-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 1 rounds, Biological replicate 1


title: DNA-W601-KLF4-Round4-Rep1

description:
Library name: DNA-W601-KLF4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of KLF4 for 4 rounds, Biological replicate 1


title: NCCLu-212


title: DNA-W601-KLF4-Round3-Rep1

description:
Library name: DNA-W601-KLF4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of KLF4 for 3 rounds, Biological replicate 1


title: DNA-W601-GST-Round3-Rep2

description:
Library name: DNA-W601-GST-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GST for 3 rounds, Biological replicate 2


title: RIBO_B.s_ppGpp0_Cm_8_2

city: Amsterdam

first: Yaozu

last: Han

address: Science Park 904

country: Netherlands

institute: Unversity Of Amsterdam

description:
Library name: YH013
amylase production
8 h Mutant Ribo-seq replicate 2

data_processing:
After deep sequencing, the raw sequence reads of both RPFs and unprotected mRNA fragments were uploaded into the Galaxy platform (https://usegalaxy.org/).
Using the Cutadapt tool (version 4.0+galaxy0), the 3’ adapter sequences were removed, and 18 to 34 nt-long reads were selected, which on average removes approximately 15% of the total reads.
After checking that the adapter has been removed from reads by using the FastQC tool (Galaxy Version 0.73+galaxy0), the Bowtie2 tool (Galaxy Version 2.4.2+galaxy0) was used to align reads to the B. subtilis genome sequence NC_000964.3 to generate SAM files, which link reads to their genomic position.
Assembly: Bacillus.fasta
Supplementary files format and content: tab-delimited text file includes Ribo-seq raw counts for each sample
Supplementary files format and content: bigwig file includes Ribo-seq RPKM vaules of each sample
Library strategy: Ribo-Seq

organism: Bacillus subtilis

source_name: Gram-positive bacterium cell

growth_protocol: For our experiments we used B. subtilis production strain BY212, which contains a deletion in the sigma factor gene sigF to prevent sporulation, and lacks the main secreted proteases, including NprE, AprE, Epr, Mpr, NprB, Vpr and Bpr. A high-copy expression plasmid was used to overexpress the heterologous α-amylase AmyM from G. stearothermophilus. The amyM gene was placed under control of the aprE promoter, which becomes active during stationary growth. Throughout this study this strain is referred to as the wild type (WT) strain. The stringent response mutant, BYH35, which is based on BY212, is referred to as strain ppGpp0. Fresh transformants of B. subtilis strain BYH35 and BY212 were streaked out on LB plates containing 20 μg/mL kanamycin at 37 °C. The next day cells were scraped from the plate and resuspended in 0.9 % NaCl and subsequently diluted into 40 mL B3 medium, containing 20 μg/mL kanamycin, to an OD600 of 0.25, and grown at 30 °C for 16 h. The cultures were grown under vigorous shaking in 250 mL Erlenmeyer flasks. The B3 medium is a rich medium containing 20 g/L glucose, 1 g/L yeast extract and 12 g/L potassium glutamate as carbon and nitrogen sources.

extract_protocol:
The culture was cryogenically pulverized to release intracellular substances. And the ribosome bound with RNA was pelleted by ultracentrifugation over a sucrose cushion. The ribosome bound with RNA was digested with micrococcal nuclease and then was ultracentrifuged over a 10-50% sucrose gradient. 30%, 40% and 50% sucrose fractions were collected and used for RNA extraction by using phenol/chloroform/isoamyl alcohol. Ribosome protected fragments (RPFs) were isolated form extracted RNA by electrophoresis on a TBE 7M Urea PAGE gel and used for construction of cDNA libraries.
1 µl of RNA fragments were used to measure the RNA concentration using the Qubit RNA HS assay kit (Thermo Fisher). Both for the RPF and the unprotected mRNA fragments sequencing libraries were constructed using the Small RNA Library Prep Set for Illumina (NEB), following the manufacturer's protocol.

treatment_protocol: 40 ml cultures were poured into 2 Falcon tubes (50 ml) containing each 20 ml crushed frozen PBS buffer and 1 mM (323 µg/ml) chloramphenicol.

value: Gram-positive bacterium cell

value: Chloramphenicol

value: 8 hour


title: NCCLu-207

value: lung cancer derived cells

value: Lung cancer


title: RIBO_B.s_ppGpp0_Cm_16_2

description:
Library name: YH017
amylase production
16 h Mutant Ribo-seq replicate 2

value: 16 hour


title: RIBO_B.s_ppGpp0_Cm_16_1

description:
Library name: YH016
amylase production
16 h Mutant Ribo-seq replicate 1


title: DNA-W601-GST-Round4-Rep2

description:
Library name: DNA-W601-GST-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GST for 4 rounds, Biological replicate 2


title: NCCLu-206


title: RIBO_B.s_ppGpp0_Cm_8_1

description:
Library name: YH012
amylase production
8 h Mutant Ribo-seq replicate 1


title: DNA-W601-GATA4-Round4-Rep1

description:
Library name: DNA-W601-GATA4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA4 for 4 rounds, Biological replicate 1


title: NCCLu-200


title: RIBO_B.s_WT_Cm_8_2

description:
Library name: YH009
amylase production
8 h WT Ribo-seq replicate 2

value: WT


title: DNA-W601-GATA4-Round1-Rep1

description:
Library name: DNA-W601-GATA4-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA4 for 1 rounds, Biological replicate 1

value: Free DNA


title: DNA-W601-GATA4-Round3-Rep1

description:
Library name: DNA-W601-GATA4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA4 for 3 rounds, Biological replicate 1


title: DNA-W601-GATA4-Round2-Rep1

description:
Library name: DNA-W601-GATA4-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA4 for 2 rounds, Biological replicate 1


title: DNA-W601-GATA1-Round4-Rep1

description:
Library name: DNA-W601-GATA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA1 for 4 rounds, Biological replicate 1


title: RIBO_B.s_WT_Cm_8_1

description:
Library name: YH008
amylase production
8 h WT Ribo-seq replicate 1


title: NCCLu-191


title: NCCLu-196


title: DNA-W601-GATA1-Round3-Rep1

description:
Library name: DNA-W601-GATA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA1 for 3 rounds, Biological replicate 1


title: DNA-W601-GATA1-Round2-Rep1

description:
Library name: DNA-W601-GATA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA1 for 2 rounds, Biological replicate 1


title: DNA-W601-OCT4-Round1-Rep2

description:
Library name: DNA-W601-OCT4-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of OCT4 for 1 rounds, Biological replicate 2


title: NCCLu-162


title: RNA_B.s_ppGpp0_Cm_16_1

description:
Library name: YH018
amylase production
16 h Mutant RNA-seq replicate 1

data_processing:
After deep sequencing, the raw sequence reads of both RPFs and unprotected mRNA fragments were uploaded into the Galaxy platform (https://usegalaxy.org/).
Using the Cutadapt tool (version 4.0+galaxy0), the 3’ adapter sequences were removed, and 18 to 34 nt-long reads were selected, which on average removes approximately 15% of the total reads.
After checking that the adapter has been removed from reads by using the FastQC tool (Galaxy Version 0.73+galaxy0), the Bowtie2 tool (Galaxy Version 2.4.2+galaxy0) was used to align reads to the B. subtilis genome sequence NC_000964.3 to generate SAM files, which link reads to their genomic position.
Assembly: Bacillus.fasta
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigwig file includes RPKM vaules of each sample

extract_protocol:
RNA was extracted by using phenol/chloroform/isoamyl alcohol. Ribosomal RNA was depleted using MICROBExpress Bacterial mRNA Enrichment Kit (Thermo Fisher), according to the manufacturer’s protocol. purified mRNA was fragmented by Magnesium RNA Fragmentation Module (NEB) following the manufacturer’s protocol and used for construction of cDNA libraries.
1 µl of RNA fragments were used to measure the RNA concentration using the Qubit RNA HS assay kit (Thermo Fisher). Both for the RPF and the unprotected mRNA fragments sequencing libraries were constructed using the Small RNA Library Prep Set for Illumina (NEB), following the manufacturer's protocol.

tag: time point


title: DNA-W601-FOXA1-Round4-Rep2

description:
Library name: DNA-W601-FOXA1-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 4 rounds, Biological replicate 2


title: NCCLu-145


title: DNA-W601-FOXA1-Round3-Rep2

description:
Library name: DNA-W601-FOXA1-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 3 rounds, Biological replicate 2


title: DNA-W601-FOXA1-Round3-Rep1

description:
Library name: DNA-W601-FOXA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 3 rounds, Biological replicate 1


title: RNA_B.s_ppGpp0_Cm_8_2

description:
Library name: YH015
amylase production
8 h Mutant RNA-seq replicate 2


title: DNA-W601-FOXA1-Round2-Rep1

description:
Library name: DNA-W601-FOXA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 2 rounds, Biological replicate 1


title: NCCLu-099


title: DNA-W601-FOXA1-Round2-Rep2

description:
Library name: DNA-W601-FOXA1-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 2 rounds, Biological replicate 2


title: A549 WT PCBP1 biol rep 2 (BR2)  [CUT&RUN]

city: Charleston

first: Philip

middle: H

last: Howe

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
The reads were trimmed with Cutadapt (v1.12) to remove Illumina sequencing adapters and then aligned separately aligned to the human (GRChg38) and yeast (sacCer3) genomes using Bowtie2 (v2.2.25). For alignment, we used parameters set as—end-to-end — very-sensitive --seed 0 --n-ceil L,0.0,0.15 --dpad 15 --gbar 4 --local --ma 2 --np 1 --score-min G,0.0,10.0 --mp 6,2 --rdg 5,3 --rfg 5,3 -I 20 -X 1000 --no-dovetail. Alignment to the yeast genome was performed to normalize epitope abundance between experiments. After alignment, reads mapping to mitochondria and the ENCODE hg38 blacklist were filtered out, and samples were downscaled according to the reads mapped to yeast spike-in DNA. Peaks were called by inputting both PCBP1 biological replicates as treatment files and both IGG biological replicates as input control files using MACS2 for peak calling with the parameters: -f BAMPE--g 2.70e+09—keep-dup—bw 300—q 5.00e-02--down-sample—slocal 1000-. The output files were then filtered for peaks with greater than 5-fold enrichment in PCBP1 against IGG samples. The returned BAM files were converted to Bigwig format, and biological replicates were merged and visualized in Integrated Genome Browser.
hg38
Bigwig
Merged BAM files converted to BigWig
Narrowpeaks file filtered saved as BED
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN
CUT&RUN libraries were prepared using the SimpleChiP™ chIP-seq library prep kit for Illumina (Cell signaling) according to provided instructions and sequenced from both ends using an Illumina NovaSeq 6000 to a total read length of 150 bp from each end.

value: human lung adenocarcinoma


title: DNA-W601-FOXA1-Round1-Rep2

description:
Library name: DNA-W601-FOXA1-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 1 rounds, Biological replicate 2


title: DNA-W601-FOXA1-Round1-Rep1

description:
Library name: DNA-W601-FOXA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 1 rounds, Biological replicate 1


title: A549 WT H3K4me3 biol rep 2 (BR2)  [CUT&RUN]

data_processing:
The reads were trimmed with Cutadapt (v1.12) to remove Illumina sequencing adapters and then aligned separately aligned to the human (GRChg38) and yeast (sacCer3) genomes using Bowtie2 (v2.2.25). For alignment, we used parameters set as—end-to-end — very-sensitive --seed 0 --n-ceil L,0.0,0.15 --dpad 15 --gbar 4 --local --ma 2 --np 1 --score-min G,0.0,10.0 --mp 6,2 --rdg 5,3 --rfg 5,3 -I 20 -X 1000 --no-dovetail. Alignment to the yeast genome was performed to normalize epitope abundance between experiments. After alignment, reads mapping to mitochondria and the ENCODE hg38 blacklist were filtered out, and samples were downscaled according to the reads mapped to yeast spike-in DNA. Peaks were called by inputting both PCBP1 biological replicates as treatment files and both IGG biological replicates as input control files using MACS2 for peak calling with the parameters: -f BAMPE--g 2.70e+09—keep-dup—bw 300—q 5.00e-02--down-sample—slocal 1000-. The output files were then filtered for peaks with greater than 5-fold enrichment in PCBP1 against IGG samples. The returned BAM files were converted to Bigwig format, and biological replicates were merged and visualized in Integrated Genome Browser.
hg38
Bigwig
Library strategy: CUT&RUN


title: DNA-W601-CEBPB-Round3-Rep1

description:
Library name: DNA-W601-CEBPB-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of CEBPB for 3 rounds, Biological replicate 1


title: DNA-W601-CEBPB-Round4-Rep1

description:
Library name: DNA-W601-CEBPB-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of CEBPB for 4 rounds, Biological replicate 1


title: A549 WT IGG biol rep 2 (BR2)  [CUT&RUN]

value: IGG


title: RNA_B.s_WT_Cm_8_1

description:
Library name: YH010
amylase production
8 h WT RNA-seq replicate 1


title: RNA_B.s_WT_Cm_8_2

description:
Library name: YH011
amylase production
8 h WT RNA-seq replicate 2


title: RNA_B.s_WT_Cm_16_2

description:
Library name: YH007
amylase production
16 h WT RNA-seq replicate 2


title: DNA-W601-GATA1-Round1-Rep1

description:
Library name: DNA-W601-GATA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of GATA1 for 1 rounds, Biological replicate 1


title: DNA-W601-CEBPB-Round1-Rep1

description:
Library name: DNA-W601-CEBPB-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of CEBPB for 1 rounds, Biological replicate 1


title: RNA_B.s_ppGpp0_Cm_16_2

description:
Library name: YH019
amylase production
16 h Mutant RNA-seq replicate 2


title: A549 WT PCBP1 biol rep 1 (BR1)  [CUT&RUN]


title: DNA-W601-CEBPB-Round2-Rep1

description:
Library name: DNA-W601-CEBPB-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of CEBPB for 2 rounds, Biological replicate 1


title: pH8.0-3

city: Shenzhen

first: Yuping

last: Shang

address: Dapeng district

institute: Chinese Agricultral Academay

data_processing:
Quality assessment of sequencing data using FastQC software (QC)
Trimmomatic was used to filter the reads to remove low-quality reads. All clean reads are mapped onto the reference genome of Fusarium graminearum using HISAT2
Use the featureCounts software to count reads
FPKM ≥1 was used as the expression threshold, and DESeq2 was used to analyze the differential expression of gene transcription levels in three pH-treated samples
p-values < 0.05 and |log2 (fold change)|≥1 are designated as DEGs. The GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations were performed on DEGs using clusterProfiler, and the pathways with pvalue<0.05 were defined as significantly enriched pathways
Assembly: Genome-of-PH-1-version-YL1
Supplementary files format and content: .csv files include the log2(fold_change) of normalized read counts and P value to figure out the differentially expressed genes

organism: Fusarium graminearum

source_name: mycelium

growth_protocol: Fusarium graminearum was placed on PDA medium and incubated at 28°C for 7 days, punched with a sterile pipette head, and 5 bacterial cakes were put into PDB medium with different pH values for 2 days

extract_protocol:
Rinse the mycelium with sterile water to no medium color, quickly cryopreserve in liquid nitrogen, after which the samples are ground in liquid nitrogen with a mortar to powder, and the total RNA is extracted using RNAprep Pur Plant Prosquisite
Libraries were prepared following the manufacturer’s instructions with the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Fusarium graminearum was cultured in PDB (potato dextrose broth) medium with initial pH of 4.5, 6.5 and 8.0 for 48 h, and the total RNA of the strain was extracted to construct a cDNA library.

value: mycelium

value: pH8.0 treatment for 48 h


title: DNA-W601-ASCL1-Round3-Rep1

description:
Library name: DNA-W601-ASCL1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of ASCL1 for 3 rounds, Biological replicate 1


title: DNA-NRCAM-ZNF143-Round4-Rep1

description:
Library name: DNA-NRCAM-ZNF143-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 ZNF143 for 4 rounds, Biological replicate 1


title: pH8.0-2


title: DNA-W601-FOXA1-Round4-Rep1

description:
Library name: DNA-W601-FOXA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of FOXA1 for 4 rounds, Biological replicate 1


title: A549 WT H3K4me3 biol rep 1 (BR1)  [CUT&RUN]


title: RNA_B.s_ppGpp0_Cm_8_1

description:
Library name: YH014
amylase production
8 h Mutant RNA-seq replicate 1


title: A549 WT IGG biol rep 1 (BR1) [CUT&RUN]


title: Yeast cells, npl3∆

city: Göttingen

first: Heike

last: Krebber

address: Grisebachstraße 8

department: Molecular Genetics

country: Germany

institute: Georg-August Universität Göttingen

description:
Count_table_npl3delta.txt
Coverage_35S_rRNA.txt

data_processing:
Fastq files were mapped to the S. cerevisiae genome sacCer3 with Hisat2
Hisat2 was run trice to generate strand specific bam files for downstream applications, once skipping the reverse strand, once the forward strand and once mapping reads to both strands.
Fragment coverage of genomic regions was calculated with deeptools2 and a bin size of 1.
For abundance measurement of reads overlapping with exons featureCounts was applied.
Assembly: Saccharomyces_cerevisiae.R64-1-1.112
Supplementary files format and content: Count_table_npl3∆: tab delimated text file of counts per gene.
Supplementary files format and content: Coverage_35S_rRNA: tab delimated text file of read coverage per nucleotide of 35S rRNA.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Dilution to 1*10^7 cell/ml and growth at 25°C

extract_protocol:
Cells were harvested at 2*10^7 cells/ml, total RNA was extracted with Macherey-Nagel nucleospin RNA extraction Kit
A modified TruSeq Stranded Total RNA Library Prep (Cat. N°20020596) was used starting with 200 ng of total RNA and without rRNA depletion.

value: yeast cell


title: Yeast cells, Wild type

value: Wild type


title: A549 PCBP1 KO2 biol rep 2 (BR2) [RNA-seq]

data_processing:
For RNA-seq analysis, the reads were aligned to the GRChg38 human genome assembly with Bowtie2 and were quantified to the reference genome using Partek (E/M). Differential expression analysis was performed in Partek Flow using the DEseq2.
hg38
TXT file containing DeSeq Output from Partek

extract_protocol:
RNA was harvested using Trizol extraction.
850 µg of total RNA was used to construct libraries with the New England Biolabs NEBNext® rRNA Depletion Kit (Cat# E6310X) and Ultra II Directional RNA Library Prep Kit for Illumina (Cat# 7760L) according to the manufacturer’s instructions. Dual-indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 50 million paired-end 150 bp reads per library.

value: PCBP1 KO

value: sgRNA


title: DNA-NRCAM-RUNX2-Round4-Rep1

description:
Library name: DNA-NRCAM-RUNX2-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 RUNX2 for 4 rounds, Biological replicate 1

value: synthetic DNA


title: DNA-NRCAM-RUNX2-Round3-Rep1

description:
Library name: DNA-NRCAM-RUNX2-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 RUNX2 for 3 rounds, Biological replicate 1


title: pH6.5-2

description: 4.5vs6.5.csv, 8.0vs6.5.csv

value: pH6.5 treatment for 48 h


title: Nip_H3K36me3

city: Nanjing

first: Zhaoguo

state: Jiangsu

address: No.1 Weigang

institute: Nanjing Agricultural University

description: Library name: Sample11

data_processing:
adapters and low-quality reads were removed by using TrimGalore and all clean reads were aligned to the rice reference genome by using bowtie2.
Aligned reads were then filtered using SAMtools with mapping quality (MAPQ) as 30 and PCR duplicated reads were removed using Picard, all clean reads with high quality were analyzed using MACS2.
For normalization and visualization, the filtered, sorted bam files were converted into bigwig format and normalized by RPKM (Reads Per Kilobase per Million mapped reads) using bamCoverage of deepTools.
Assembly: MSU v7.0
Supplementary files format and content: bigWig

organism: Oryza sativa

source_name: seedling

extract_protocol:
After in situ labelling, nuclei aliquot was incubated at 65 °C overnight for reverse crosslinking followed by recovery of biotin labelled DNA by using phenol:chloroform extraction and cold ethanol precipitation. Biotin labelled DNA was enriched by using Dynabeads M-280 Streptavidin (11205D, ThermoFisher Scientific).
The sequencing library was prepared by using scale DNA Lib Prep Kit for Illumina V2 and sequenced on the Illumina NovaSeq platform.

value: seedling


title: DNA-W601-ASCL1-Round4-Rep1

description:
Library name: DNA-W601-ASCL1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence W601 for the binding of ASCL1 for 4 rounds, Biological replicate 1


title: pH6.5-3

description: 4.5vs6.5.csv, 8.0vs6.5.csv


title: pH8.0-1


title: A549 PCBP1 KO1 biol rep 2 (BR2)[RNA-seq]


title: A549 PCBP1 KO1 biol rep 1 (BR1) [RNA-seq]


title: pH6.5-1

description: 4.5vs6.5.csv, 8.0vs6.5.csv


title: pH4.5-3

value: pH4.5 treatment for 48 h


title: Nip_H3K27me3

description: Library name: Sample10


title: Nip_H3K4me3

description: Library name: Sample8


title: DNA-NRCAM-RUNX2-Round1-Rep1

description:
Library name: DNA-NRCAM-RUNX2-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 RUNX2 for 1 rounds, Biological replicate 1


title: DNA-NRCAM-PU1-Round4-Rep1

description:
Library name: DNA-NRCAM-PU1-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 PU1 for 4 rounds, Biological replicate 1


title: pH4.5-2


title: A549 WT  biol rep 2 (BR2) [RNA-seq]


title: DNA-NRCAM-RUNX2-Round2-Rep1

description:
Library name: DNA-NRCAM-RUNX2-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 RUNX2 for 2 rounds, Biological replicate 1


title: DNA-NRCAM-PU1-Round3-Rep1

description:
Library name: DNA-NRCAM-PU1-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 PU1 for 3 rounds, Biological replicate 1


title: DNA-NRCAM-ZNF143-Round3-Rep1

description:
Library name: DNA-NRCAM-ZNF143-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 ZNF143 for 3 rounds, Biological replicate 1


title: ATAC-seq_Rep2

description: Library name: Sample6


title: A549 PCBP1 KO2 biol rep 1 (BR1) [RNA-seq]


title: DNA-NRCAM-PAX7-Round4-Rep1

description:
Library name: DNA-NRCAM-PAX7-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 PAX7 for 4 rounds, Biological replicate 1


title: SH-SY5Y cells, NC_3

city: Shanghai

first: xiaohua

last: dong

address: 1111 XianXia Road

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

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCh38.p13 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: nervous tissue

growth_protocol: SH-SY5Y cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: SH-SY5Y cells were transfected with LINC00938 lentivirus for 12hpf

value: nervous tissue

value: human neuroblastoma cell

value: LINC00938 knockdown


title: ATAC-seq_Rep1

description: Library name: Sample5

value: WT


title: SH-SY5Y cells, NC_2


title: DNA-NRCAM-PAX7-Round3-Rep1

description:
Library name: DNA-NRCAM-PAX7-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 PAX7 for 3 rounds, Biological replicate 1

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: Free DNA


title: IMR-32 cells, NeuroD1 (ChIP)

city: Suzhou

first: Gen

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

description: Library name: IMR-32, ChIP

data_processing:
Raw Data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using BWA-MEM (v0.7.17)
Peaks were identified using MACS2 (v2.2.7)
Assembly: hg38
Supplementary files format and content: BigWig, narrowPeak (except for input sample)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Neuroblastoma cell line

tag: chip antibody

value: NeuroD1 (CST, #7019)


title: Nip_H3K9ac

description: Library name: Sample9


title: DNase-seq_Rep2

description: Library name: Sample4


title: SH-SY5Y cells, NC_1


title: SH-SY5Y cells, LINC00938KD_3


title: ISDH-seq_Rep2

description: Library name: Sample2

data_processing:
library strategy: ISDH-seq
adapters and low-quality reads were removed by using TrimGalore and all clean reads were aligned to the rice reference genome by using bowtie2.
Aligned reads were then filtered using SAMtools with mapping quality (MAPQ) as 30 and PCR duplicated reads were removed using Picard, all clean reads with high quality were analyzed using MACS2.
For normalization and visualization, the filtered, sorted bam files were converted into bigwig format and normalized by RPKM (Reads Per Kilobase per Million mapped reads) using bamCoverage of deepTools.
Assembly: MSU v7.0
Supplementary files format and content: bigWig


title: human chemically induced pluripotent stem cells, C40 cell line, rep3

city: Beijing

first: Ke

last: Zhang

address: Huayuan North Road

institute: Peking university

description:
hCiPSCs_C40_3
gene_expression.xls

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

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.

value: no treatment


title: DNA-NRCAM-PAX7-Round1-Rep1

description:
Library name: DNA-NRCAM-PAX7-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 PAX7 for 1 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: human chemically induced pluripotent stem cells, C40 cell line, rep2

description:
hCiPSCs_C40_2
gene_expression.xls


title: SH-SY5Y cells, LINC00938KD_2


title: DNA-NRCAM-PAX7-Round2-Rep1

description:
Library name: DNA-NRCAM-PAX7-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 PAX7 for 2 rounds, Biological replicate 1


title: DNase-seq_Rep1

description: Library name: Sample3


title: A549 WT biol rep 1 (BR1) [RNA-seq]

value: human lung adenocarcinoma


title: human chemically induced pluripotent stem cells, C40 cell line, rep1

description:
hCiPSCs_C40_1
gene_expression.xls


title: pH4.5-1

value: mycelium


title: DNA-NRCAM-OCT4-Round4-Rep2

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 4 rounds, Biological replicate 2


title: SH-SY5Y cells, LINC00938KD_1


title: Nip_Input

description: Library name: Sample7


title: ISDH-seq_Rep1

description: Library name: Sample1


title: human chemically induced pluripotent stem cells, C17 cell line, rep3

description:
hCiPSCs_C17_3
gene_expression.xls


title: DNA-NRCAM-OCT4-Round4-Rep1

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 4 rounds, Biological replicate 1


title: con3

city: Singapore

first: Xianglong

last: Liu

address: College of Design and Engineering, National University of Singapore, 5A Engineering Drive 1, T-Lab 03-01

country: Singapore

institute: National University of Singapore

description: Library name: con3

data_processing:
Differential expression analysis was performed using R package DESeq2 (v 1.44.0), fitting a negative binomial model for each gene.
Assembly: GCF_015219905.1
Supplementary files format and content: Xlsx files include count values for each sample.

organism: Staphylococcus aureus

growth_protocol: MRSA was cultured overnight in LB culture medium at 37°C with shaking at 220 rpm.

extract_protocol:
Total RNA of each sample was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA-seq libraries were generated using Illumina Novaseq 6000.

value: Drug-resistant bacterium

value: untreated


title: IMR-32 cells (Input)

description: Library name: IMR-32, Input

value: none (input)


title: 4Gy-CD47-2

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
cell_metadata.csv

data_processing:
FASTQ files were processed with cellranger (v. 5.0.1) to produce UMI count matrices for each sample.
The Seurat R package was used to conduct quality filtering, dimensionality reduction, and clustering of the single cell datasets.
Assembly: GRCh38
Supplementary files format and content: csv file containing a gene by cell matrix of UMI counts
Supplementary files format and content: text file containing cell level metadata with cluster assignments for each cell

source_name: peripheral blood

extract_protocol:
Macrophages that either phagocytose-or not were sorted using flow cytometry
10x Genomics 3' end single cell RNA-seq

treatment_protocol: BT245 cells were exposed to fractionated RT (4gy X 3) and co-incubated with the PBMC-derived macrophages in the presence of anti-CD47 mAb

value: peripheral blood

value: Macrophages + Glioma cells

tag: cell source

value: Macrophages derived from human peripheral blood mononuclear cells

tag: macrophage population

value: Eater

value: 4 Gray IR + Anti-CD47


title: DNA-NRCAM-OCT4-Round3-Rep2

city: Boston

first: Luca

address: 77 Avenue Pasteur

institute: Harvard Medical School

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 3 rounds, Biological replicate 2

value: synthetic DNA


title: human chemically induced pluripotent stem cells, C17 cell line, rep2

description:
hCiPSCs_C17_2
gene_expression.xls


title: con2

description: Library name: con2


title: Control-CD47-2


title: DNA-NRCAM-OCT4-Round3-Rep1

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 3 rounds, Biological replicate 1


title: human chemically induced pluripotent stem cells, C17 cell line, rep1

description:
hCiPSCs_C17_1
gene_expression.xls


title: con1

description: Library name: con1


title: 4Gy-2

value: 4 Gray IR


title: DNA-NRCAM-OCT4-Round2-Rep2

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 2 rounds, Biological replicate 2


title: human chemically induced pluripotent stem cells, C7 cell line, rep3

description:
hCiPSCs_C7_3
gene_expression.xls


title: Control-2


title: T_3

description: Library name: T_3

value: MRSA was incubated in LB culture medium containing 0.5 μM TPA2PyPh (1/2 × MIC) at 37 °C for 24 hours


title: 4Gy-CD47-1

value: Non-eater


title: human chemically induced pluripotent stem cells, C7 cell line, rep2

description:
hCiPSCs_C7_2
gene_expression.xls


title: DNA-NRCAM-OCT4-Round1-Rep2

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 1 rounds, Biological replicate 2

value: Free DNA


title: T_1

description: Library name: T_1


title: human chemically induced pluripotent stem cells, C7 cell line, rep1

description:
hCiPSCs_C7_1
gene_expression.xls


title: T_2

description: Library name: T_2


title: DNA-NRCAM-OCT4-Round1-Rep1

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 1 rounds, Biological replicate 1


title: 4Gy-1


title: cipro_vayr_t3_5_rep2

city: San Diego

first: Yuan

last: Yuan

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description:
Library name: Sample 42
Processed with testing kit different from the rest of the samples

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.

value: K-12 substr. MG1655

value: WT

value: Exposure to ciprofloxacin


title: cipro_vayr_t3_5_rep1

description:
Library name: Sample 41
Processed with testing kit different from the rest of the samples


title: human chemically induced pluripotent stem cells, C6 cell line, rep3

description:
hCiPSCs_C6_3
gene_expression.xls

value: no treatment


title: DNA-NRCAM-KLF4-Round4-Rep1

last: Mariani

description:
Library name: DNA-NRCAM-KLF4-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 KLF4 for 4 rounds, Biological replicate 1


title: Control-1


title: human chemically induced pluripotent stem cells, C6 cell line, rep2

description:
hCiPSCs_C6_2
gene_expression.xls


title: DNA-NRCAM-KLF4-Round3-Rep1

description:
Library name: DNA-NRCAM-KLF4-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 KLF4 for 3 rounds, Biological replicate 1


title: human chemically induced pluripotent stem cells, C6 cell line, rep1

description:
hCiPSCs_C6_1
gene_expression.xls


title: cipro_vayr_t1_5_rep2

description:
Library name: Sample 40
Processed with testing kit different from the rest of the samples


title: DNA-NRCAM-GST-Round4-Rep2

description:
Library name: DNA-NRCAM-GST-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 GST for 4 rounds, Biological replicate 2


title: cipro_vayr_t1_5_rep1

description:
Library name: Sample 39
Processed with testing kit different from the rest of the samples


title: human chemically induced pluripotent stem cells, C4 cell line, rep3

description:
hCiPSCs_C4_3
gene_expression.xls


title: cipro_vayr_t0_rep2

description:
Library name: Sample 38
Processed with testing kit different from the rest of the samples


title: human chemically induced pluripotent stem cells, C4 cell line, rep2

description:
hCiPSCs_C4_2
gene_expression.xls


title: DNA-NRCAM-OCT4-Round2-Rep1

description:
Library name: DNA-NRCAM-OCT4-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 OCT4 for 2 rounds, Biological replicate 1


title: ADRA03_IOF4_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: ADRA03_IOF4_5_G [mRNA-derived cDNA]

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

tag: tissue

value: mRNA


title: DNA-NRCAM-GST-Round3-Rep2

description:
Library name: DNA-NRCAM-GST-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 GST for 3 rounds, Biological replicate 2

tag: treatment


title: Control-CD47-1

description:
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
cell_metadata.csv

value: peripheral blood


title: human chemically induced pluripotent stem cells, C4 cell line, rep1

description:
hCiPSCs_C4_1
gene_expression.xls


title: DNA-NRCAM-GATA4-Round4-Rep1

description:
Library name: DNA-NRCAM-GATA4-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 GATA4 for 4 rounds, Biological replicate 1


title: cipro_vayr_t0_rep1

description:
Library name: Sample 37
Processed with testing kit different from the rest of the samples


title: human chemically induced pluripotent stem cells, C3 cell line, rep3

description:
hCiPSCs_C3_3
gene_expression.xls


title: DNA-NRCAM-GATA4-Round3-Rep1

description:
Library name: DNA-NRCAM-GATA4-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 GATA4 for 3 rounds, Biological replicate 1


title: ADRA03_IOF4_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: cipro_t7_5_rep2

description:
Library name: Sample 36
Processed with testing kit different from the rest of the samples


title: ADRA03_IOF4_4_H [HTO-derived cDNA]


title: DNA-NRCAM-GATA4-Round2-Rep1

description:
Library name: DNA-NRCAM-GATA4-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 GATA4 for 2 rounds, Biological replicate 1


title: human chemically induced pluripotent stem cells, C3 cell line, rep2

description:
hCiPSCs_C3_2
gene_expression.xls

tag: cell line


title: DNA-NRCAM-GATA4-Round1-Rep1

description:
Library name: DNA-NRCAM-GATA4-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 GATA4 for 1 rounds, Biological replicate 1


title: cipro_t7_5_rep1

description: Library name: Sample 35


title: Macs

tag: cell type

value: Macrophages

value: Macrophages derived from human peripheral blood mononuclear cells


title: ADRA03_IOF4_4_G [mRNA-derived cDNA]


title: cipro_t30_rep2

description: Library name: Sample 34

tag: genotype


title: ADRA03_IOF4_4_A [ADT-derived cDNA]


title: DNA-NRCAM-GATA1-Round4-Rep1

description:
Library name: DNA-NRCAM-GATA1-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 GATA1 for 4 rounds, Biological replicate 1


title: Human adult adipose tissue-derived stromal cells, no treatment, rep3

description:
hADSCs_3
gene_expression.xls


title: human chemically induced pluripotent stem cells, C3 cell line, rep1

description:
hCiPSCs_C3_1
gene_expression.xls


title: cipro_t30_rep1

description: Library name: Sample 33

tag: strain


title: ADRA03_IOF4_3_H [HTO-derived cDNA]


title: Human adult adipose tissue-derived stromal cells, no treatment, rep2

description:
hADSCs_2
gene_expression.xls


title: DNA-NRCAM-GATA1-Round3-Rep1

description:
Library name: DNA-NRCAM-GATA1-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 GATA1 for 3 rounds, Biological replicate 1


title: cipro_t3_5_rep2

description: Library name: Sample 32


title: ADRA03_IOF4_3_G [mRNA-derived cDNA]


title: DNA-NRCAM-GATA1-Round2-Rep1

description:
Library name: DNA-NRCAM-GATA1-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 GATA1 for 2 rounds, Biological replicate 1


title: cipro_t3_5_rep1

description: Library name: Sample 31


title: Human adult adipose tissue-derived stromal cells, no treatment, rep1

description:
hADSCs_1
gene_expression.xls


title: human embryonic stem cells, no treatment, rep3

description:
H1_3
gene_expression.xls

value: human embryonic stem cell


title: cipro_t15_rep2

description: Library name: Sample 30