title: TissueCD45-_P2

city: Rozzano, Milan

first: Paolo

last: Marzano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas Research Hospital

description:
Library name: Sample 2_TissueCD45-
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1
Assembly: GRCh38 – hg38
Supplementary files format and content: Matrix files in h5  format

molecule: cytoplasmic RNA

source_name: ovarian cancer

extract_protocol:
Freshly isolated ovarian tissues were processed for scRNA-seq experiments as follows: the tissues were dissociated using enzymatic and mechanical digestion in a gentleMACS Dissociator (Miltenyi, Germany) with RPMI-1640 supplemented with 1%FBS, 2mg/mL collagenase D (Merck, Germany), and 100μg/mL hyaluronidase (Merck). The resulting single-cell suspension was filtered through 100μm and 70μm cell strainers (Corning, USA), washed in HBSS−/− (Euroclone SpA, Italy), and frozen in liquid nitrogen for further analysis. Upon thawing, the cells were stained for live/dead discrimination (Zombie AquaTM Fixable Viability Kit; BioLegend, USA), and with anti-human CD45 monoclonal antibody (mAb) (Clone 5B1; Miltenyi; dilution 1:166). The CD45+ immune cells and tumor-associated CD45- cell counterparts were then sorted by FACS Melody cell sorter (BD Biosciences).PBMCs were isolated using Lympholyte®-H Cell Separation density gradient solution (Cedarlane Laboratories, USA) according to the manufacturer’s instructions and were frozen. Upon thawing, PBMC viability exceeded 95% and the cells were immediately processed for scRNA-seq experiments.
Libraries for scRNA-seq were prepared following the manufacturer's guidelines using the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics). For each sample 10,000 target cells were loaded onto a Chromium single-cell controller (10X Genomics) to generate GEMs. Captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEMs. Complementary (c)DNAs were amplified, and their quality was assessed using an Agilent 4200 Tapestation. The scRNA-seq libraries were sequenced with a paired-end 150-bp (PE150) reading strategy, on the Illumina NextSeq500 sequencer for P1 and the Illumina NextSeq2000 sequencer for P2.

value: ovarian cancer

value: Stromal cells

tag: batch

tag: figo stage

tag: grading

value: High grade

tag: histotype

value: High grade serous carcinoma


title: TissueCD45+_P2

status: Public on Mar 24 2025

type: SRA

description:
Library name: Sample 2_TissueCD45+
10x Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

tag: tissue

tag: cell type

value: TILS

tag: age


title: A549 cells, CIC KO infection rep2

city: Iowa City

first: Priya

middle: D

last: Issuree

state: IA

address: 431 Newton Road

department: Internal Medicine

country: USA

institute: University of Iowa

library_source: genomic

data_processing:
Sequencing adapters were removed from paired‐end reads using Trimmomatic version 0.39. Trimmed reads were aligned to human reference genome GRCh37/hg19 using Bowtie 2 version 2.4.1. Following genome alignment, Picard was used to mark PCR duplicates, and samtools version 1.3.1 was used to remove PCR duplicates, discordant pairs, and alignments to the mitochondrial genome. Peak calling was performed using MACS2 version 2.2.7.1, and differential accessibility analyses of MACS2 peaks were performed using the R package DiffBind version 2.10.0. Differentially accessible peaks were annotated to genome regions of interest using the R package ChIPseeker version 1.18.0.
Assembly: hg19 reference genome
Supplementary files format and content: bigwig files

molecule: genomic DNA

source_name: A549 cells

extract_protocol:
Nuclei for tagmentation was prepared using the ATAC-Seq Kit from Active Motif following the manufacturer's instructions
ATAC-Seq libraries were prepared using the ATAC-Seq Kit from Active Motif following the manufacturer's instructions

tag: cell line

value: A549 cells

value: human epithelial cell line

tag: genotype

value: knock-out

tag: treatment

value: IAV infection


title: mouse 8-AP802;Hp FeMale RNA rep1

city: Pittsburgh

first: Irene

middle: Miriam

last: Kaplow

state: PA

address: 5000 Forbes Avenue, Gates-Hillman 7703

department: Computational Biology

institute: Carnegie Mellon University

library_source: transcriptomic

data_processing:
We used a custom python script to tally the barcode counts per sample.
For each sequence entry, we searched for the common restriction enzyme site present in both the DNA and the RNA.
Using the location of the enzyme, we identified the sequence of the unique barcode.
We noted cases where the restriction enzyme site or the barcode sequence were not found in sequence entry.
Supplementary files format and content: csv file, where each row is for a bar-code, each column is for a tissue or cell line sample, and each entry is the number of reads for the bar-code in the sample

molecule: total RNA

organism: Mus musculus

source_name: brain (hippocampus)

growth_protocol: HMC3 cells (ATCC #CRL-3304) were maintained according to manufacturer's specifications

extract_protocol:
We extracted total RNA using RNeasy Mini Kit (Qiagen, cat#74104) and prepared cDNA with a specific reverse transcription primer
MPRA barcodes were amplified from cDNA using Illumina Nextera amlification primers

treatment_protocol:
HMC3 cells were transfected with 250 ug of the MPRA plasmid library with FuGENE6 and allowed to incubate for 72 hours
C57BL6/J mice were transduced with 7.73x1011 to 2.28x1012 vector genomes (vg) total into the retro-orbital cavity

value: brain (hippocampus)

value: AAV transduction

tag: time

value: 20 days


title: CD8_Temra_SA_3

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
using scZapR. No samples were pooled prior to PCR2 where 12 cycles were completed. Library quantification and assessment was done using a Qubit FLEX fluorometer and an Agilent TapeStation 4150/Fragment Analyzer 5300. Libraries were normalized and pooled to 2nM by calculating the concentration based off the fragment size (base pairs) and the concentration (ng/𝜇l) of the libraries. Sequencing was performed on an Illumina NextSeq 2000, using a P3 200 flow cell.
Assembly: Hg38
Supplementary files format and content: Count_Data.csv

source_name: peripheral blood

extract_protocol:
Up to 100,000 T cells from three populations (CD8+ naïve, CD8+ CD45RO+ memory, and CD8+ TEMRAs) were sorted directly in to 1 mL of RLT buffer (Qiagen).
Libraries were generated with the Takara SMART-Seq Stranded kit using Takara SMARTer RNA Unique Dual Index A and B Kits according to the manufacturer’s instructions. RNA was normalized to 5 ng/𝜇l with water for a total volume of 7 𝜇l of input RNA. RNA fragmentation was carried ou
The pooled library was loaded at 750 pM. Sequencing was carried out 2x101 bp, with a target of 40 million reads per sample. A custom run chemistry was used to incorporate 3 dark cycles at the start of R2 that mask the 3 bp of the Takara adapter present in the read. Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software (v3.10.12).

treatment_protocol: Cryopreserved cell suspensions were thawed as above and resuspended in FACS buffer but instead of stimulation were incubated with optimally diluted labeled monoclonal antibodies for 30 min at 0oC. Cells were washed and then sorted on an Aurora CS cell sorter using SpectroFlo software.

value: peripheral blood

value: sorted TEMRAs


title: CD8_Temra_SA_1


title: PBMCs_P2

description:
Library name: Sample 2_PBMC
10x Genomics

source_name: blood

value: blood

value: PBMC


title: mouse 8-AP802;CTX FeMale RNA rep1

source_name: brain (cortex)

value: brain (cortex)


title: CBC 40 μM, biol rep3

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Library name: CBC24

data_processing:
Concatenated base call files (.cbcl) generated from the sequencing run were converted to a FASTQ file for each sample by the DRAGEN BCL Convert pipeline. The .cbcl files were further analyzed by the DRAGEN RNA pipeline to generate transcript quantification results at the gene level (.quant.genes.sf).
Assembly: Human reference genome hg38-alt-aware
Supplementary files format and content: Files in .sf format containing transcript quantification results at the gene level.

source_name: iPSC-derived hepatocytes

growth_protocol: Commercial iPSC-derived hepatocytes (iCell Hepatocytes 2.0) from FUJIFILM Cellular Dynamics (Madison, WI) were cultured following the manufacturer’s protocols.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.
Sequencing libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (San Diego, CA) following protocols provided by the manufacturer.

treatment_protocol: Cells cultured at day 6 after seeding were exposed to CBC at varying concentrations (0.1-40 µM) in triplicate for 24 h.

value: iPSC-derived hepatocytes

value: CBC 40 μM


title: mouse 8-AP802;STR FeMale RNA rep1

source_name: brain (striatum)

value: brain (striatum)


title: A549 cells, CIC KO infection rep1


title: A549 cells, WT IAV infection rep2

value: wild-type


title: mouse 8-AP802;MC FeMale RNA rep1

source_name: brain (motor cortex)

value: brain (motor cortex)


title: CBC 0.0 μM (control), biol rep3

description: Library name: CBC03

value: CBC 0.0 μM (control)


title: A549 cells, WT IAV infection rep1

value: A549 cells

value: human epithelial cell line


title: CD8_CD45ro_SA_3

value: sorted CD45RO+ Memory T cells


title: CD8_Naive_SA_1

value: sorted naive T cells


title: mouse 8-AP802;Liver FeMale RNA rep1

source_name: liver

value: liver

value: AAV transduction


title: mouse 7-AP796;PFC Male RNA rep1

source_name: brain (pre-frontal cortex)

value: brain (pre-frontal cortex)

value: 20 days


title: A549 cells, CIC KO mock rep2

value: knock-out

value: uninfected (mock)


title: CD8_CD45ro_SA_2

value: peripheral blood


title: mouse 7-AP796:Liver Male RNA rep1


title: A549 cells, CIC KO mock rep1


title: CD8_Temra_SA_2

value: sorted TEMRAs


title: mouse 7-AP796;Hp Male RNA rep1

value: brain (hippocampus)


title: A549 cells, WT mock rep1


title: A549 cells, WT mock rep2


title: mouse 7-AP796;STR Male RNA rep1

value: brain (striatum)


title: KO_clone1_hPSC_rep2

city: Ulm

first: Alexander

last: Kleger

state: Baden-Württemberg

address: Albert-Einstein-Allee 23

department: Institute of Molecular Oncology and Stem Cell Biology (IMOS)

country: Germany

institute: University Hospital Ulm

description: Library name: X598_87_HUES8_EXDPF_KO_day0

data_processing:
RNA-seq reads were aligned to the human genome using STAR Aligner v.2.5.2a with the Ensembl 86 reference genome.
Sequenced read quality was checked with FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and alignment quality metrics were calculated using the RNASeQC v1.18.
Following read alignment, duplication rates of the RNA-seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment. Unique read counts were retrieved from the “featureCounts” software package.
For quality control, total read counts, the rate of ribosomal RNA, the rate of intergenic and intronic reads and distribution of logarithmic RPKM values were assessed for each sample. While all samples except of one were of very good quality with 20-40 million 85bp single end reads and very low ribosomal, intergenic, and intronic rates, one sample (PPDPFWT/WT cl. 1 at DE, replicate 3) was excluded from downstream analysis. This sample information is still listed in the supplementary files (raw count and RPKM values but not in Rlog normalized counts and also no FASTQ file is provided)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample
Supplementary files format and content: tab-delimited text file includes R-log normalized (DESeq2) read counts for each sample

growth_protocol: hPSC differentiation along DE, PE, and PP stage as detailed in the associated publication

extract_protocol:
Total RNA was isolated with GeneJET RNA Purification Kit (Thermo)
Sequencing library preparation has been performed with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122–2002, Illumina Inc, San Diego, CA) producing 275 bp fragments including adapters in average size. Pooled libraries have then been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3—cBot—HS(GD-401–3001, Illumina Inc, San Diego, CA).

treatment_protocol: no

value: hPSC

value: PPDPF KO/KO

value: no


title: KO_clone2_PP_rep4

description: Library name: X598_76_HUES8_EXDPF_KO_day14

value: PP


title: KO_clone1_PP_rep4

description: Library name: X598_75_HUES8_EXDPF_KO_day14


title: WT_clone1_hPSC_rep2

description: Library name: X598_85_HUES8_Control_day0

value: PPDPF WT WT


title: mouse 7-AP796;CTX Male RNA rep1

value: brain (cortex)


title: WT_clone2_hPSC_rep2

description: Library name: X598_86_HUES8_Control_day0


title: WT_clone1_PP_rep4

description: Library name: X598_73_HUES8_Control_day14


title: WT_clone2_PP_rep4

description: Library name: X598_74_HUES8_Control_day14


title: CD8_Naive_SA_2

value: sorted naive T cells


title: KO_clone2_PE_rep4

description: Library name: X598_72_HUES8_EXDPF_KO_day10

value: PE


title: gastric cancer [G39T]

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

description: GC.PNI.rds

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: gastric cancer

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1 the Chromium Next GEM Single Cell 5′ Kit v2 for Dual Index (10x Genomics). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct the 3’ and 5’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: gastric cancer

tag: pni

tag: organ

value: stomach

tag: Sex

value: Female

tag: chemotherapy


title: CD8_CD45ro_SA_1

value: sorted CD45RO+ Memory T cells


title: gastric cancer [G36T]

description: GC.PNI.rds


title: mouse 6-AP801;PFC FeMale RNA rep1

value: brain (pre-frontal cortex)

value: AAV transduction

value: 19 days


title: KO_clone1_PE_rep4

description: Library name: X598_71_HUES8_EXDPF_KO_day10


title: WT_clone2_PE_rep4

description: Library name: X598_70_HUES8_Control_day10


title: KO_clone2_hPSC_rep2

description: Library name: X598_88_HUES8_EXDPF_KO_day0


title: gastric cancer [G32T]

description: GC.PNI.rds


title: mouse 6-AP801;Hp FeMale RNA rep1

value: brain (hippocampus)


title: KO_clone2_DE_rep4

description: Library name: X598_68_HUES8_EXDPF_KO_day4

value: DE


title: mouse 6-AP801;STR FeMale RNA rep1

value: brain (striatum)


title: KO_clone1_DE_rep4

description: Library name: X598_67_HUES8_EXDPF_KO_day4

value: PPDPF KO/KO


title: scrnaseq_EDN3_control_invivo_2

city: Cambridge

first: Shlomi

middle: B

last: Brielle

state: MA

address: 7 Divinity Ave, Sherman Fairchild 361, Harvard University, HSCRB

department: Harvard Department of Stem Cell and Regenerative Biology

institute: Harvard University

description: 10x genomics

data_processing:
Processing and filtering of scRNA sequencing data To obtain transcript count matrices, we employed Cell Ranger (version 7.1.0) with the default settings. This involved aligning the sequencing reads to the human genome and transcriptome (hg38, as provided by 10x Genomics, GRCh38-2020-A). The scRNA-seq data analysis pipeline utilized Scanpy 70 for dimensionality reduction, clustering, and visualization. Initially, individual sample output files from CellRanger Count were imported into Scanpy to generate a count matrix based on unique molecular identifiers (UMIs). To assess data quality, the percentage of mitochondrial genes was calculated for each sample in the merged dataset. Cells failing to meet the criteria of having at least 500 identified genes, 1000 UMI, or exceeding 25% of reads originating from mitochondrial genes were excluded from further analysis. Low-frequency genes that were detected in < 3 cells were also removed. After the initial filtering steps, the dataset underwent normalization to address library size bias. This involved scaling the expression values to 10,000 counts per cell to account for variations in sequencing depth. Subsequently, the count-normalized expression matrix was log normalized and highly variable genes were identified based on dispersion and carried forward to the subsequent analysis steps. To address the influence of mitochondrial genes and UMI counts per cell, a simple linear regression was performed aimed to remove the effects of mitochondrial genes and UMI counts from the dataset. The data were further scaled to unit variance, and any values exceeding a standard deviation of 10 were clipped. Principal Component Analysis (PCA) was utilized to reduce the dimensionality of the data. In this step, the first 50 principal components, accounting for the majority variance in the dataset, were selected.  A neighbor graph was constructed based on the PCA representation of the data and subsequently visualized using UMAP embedding.
Processing and of multi-omic data  Multi-omic sequenced files were demultiplexing and analyzed using Cell Ranger ARC v2.0. Genes were mapped and referenced using human reference genome GRCh38. RStudio 1.3.1093 (R version 4.0.3) was used to perform analyses. Datasets were analyzed using Seurat 4.01 74 and Signac 1.3.0 75. For ATAC data, peaks were called using MACS2 and the genomic positions were mapped and annotated with reference human genome EnsDb.Hsapeins.v86 and hg38. Subsequently, we generated a consolidated peak set by merging overlapping peaks derived from all the samples. The consolidated peak set was subjected to re-quantification, followed by normalization using term frequency-inverse document frequency (TF-IDF) normalization. Low-quality cells including doublets, dead cells and poor sequencing depth cells were removed by filtering out cells with low RNA counts (UMI < 1,000) and low ATAC counts (nCount_ATAC < 25,000); high RNA counts (> 40,000 - 50,000) and high ATAC counts (> 40,000 - 50,000); nucleosome signal > 1 and transcription start site (TSS) enrichment < 2. Gene expression data was variance stabilized using SCTransform (v2 regularization), and then normalized for each cell by dividing by the total counts for that cell and then natural-log transformed using log1p.
Assembly: GRCh38
Supplementary files format and content: Filtered Feature-Barcodes Matrix (.filtered_feature_bc_matrix.h5), atac_fragments.tsv.gz: Contains information on DNA fragments from an ATAC-seq experiment. atac_fragments.tsv.gz.tbi: Index file facilitating quick retrieval of data from atac_fragments.tsv.gz. atac_peaks.bed: Lists called peaks or open chromatin regions identified in ATAC-seq data. atac_fragments.tsv.gz.tbi: Index file facilitating quick retrieval of data from atac_fragments.tsv.gz. atac_peaks.bed: Lists called peaks or open chromatin regions identified in ATAC-seq data.

molecule: polyA RNA

source_name: SC-islets

extract_protocol:
SC-islet cell clusters were collected and dissociated in single cells as described before, quantified for viability using the Vi-Cell XR (Beckman Coulter), resuspended in PBS with 0.1% BSA at a concentration of ~1000 cells/μl and put on ice. Before proceeding, all samples were ensured to have > 90% viability to minimize dead cells carry over in sequencing. Single cell samples were then processed using the Chromium 10x genomics instrument, with a target cell number of 10,000. The scRNA-seq libraries were created using the Chromium Single Cell 3' V3 Library & Gel Bead Kit, following the manufacturer's protocol. Single-cell encapsulation and library preparation were carried out as per the manufacturer's guidelines. Libraries were then pooled, and sequenced on the Illumina NovaSeq platform.
The single-cell RNA sequencing (scRNA-seq) or multiome libraries were prepared according to the manufacturer's specifications.

value: SC-islets


title: WT_clone2_DE_rep4

description: Library name: X598_66_HUES8_Control_day4

value: no


title: scrnaseq_O21_2W

description: 10x genomics


title: KO_clone2_PP_rep3

description: Library name: X598_56_HUES8_EXDPF_KO_day14

value: PP


title: mouse 6-AP801;CTX FeMale RNA rep1

value: brain (cortex)


title: KO_clone1_PP_rep3

description: Library name: X598_55_HUES8_EXDPF_KO_day14


title: WT_clone1_DE_rep4

description: Library name: X598_65_HUES8_Control_day4

value: PPDPF WT WT


title: mouse 7-AP796;MC Male RNA rep1

value: brain (motor cortex)

value: 20 days


title: WT_clone2_PP_rep3

description: Library name: X598_54_HUES8_Control_day14


title: scrnaseq_O5_2W

description: 10x genomics


title: WT_clone1_PP_rep3

description: Library name: X598_53_HUES8_Control_day14


title: KO_clone2_PE_rep3

description: Library name: X598_52_HUES8_EXDPF_KO_day10

value: PE


title: mouse 5-AP796;PFC Male RNA rep1


title: scrnaseq_EDN3_OE_invivo_2

description: 10x genomics


title: KO_clone1_PE_rep3

description: Library name: X598_51_HUES8_EXDPF_KO_day10


title: mouse 5-AP796;Hp Male RNA rep1


title: WT_clone2_PE_rep3

description: Library name: X598_50_HUES8_Control_day10


title: multiome_O21_D1 DNA

description: 10x genomics

data_processing:
Processing and filtering of scRNA sequencing data To obtain transcript count matrices, we employed Cell Ranger (version 7.1.0) with the default settings. This involved aligning the sequencing reads to the human genome and transcriptome (hg38, as provided by 10x Genomics, GRCh38-2020-A). The scRNA-seq data analysis pipeline utilized Scanpy 70 for dimensionality reduction, clustering, and visualization. Initially, individual sample output files from CellRanger Count were imported into Scanpy to generate a count matrix based on unique molecular identifiers (UMIs). To assess data quality, the percentage of mitochondrial genes was calculated for each sample in the merged dataset. Cells failing to meet the criteria of having at least 500 identified genes, 1000 UMI, or exceeding 25% of reads originating from mitochondrial genes were excluded from further analysis. Low-frequency genes that were detected in < 3 cells were also removed. After the initial filtering steps, the dataset underwent normalization to address library size bias. This involved scaling the expression values to 10,000 counts per cell to account for variations in sequencing depth. Subsequently, the count-normalized expression matrix was log normalized and highly variable genes were identified based on dispersion and carried forward to the subsequent analysis steps. To address the influence of mitochondrial genes and UMI counts per cell, a simple linear regression was performed aimed to remove the effects of mitochondrial genes and UMI counts from the dataset. The data were further scaled to unit variance, and any values exceeding a standard deviation of 10 were clipped. Principal Component Analysis (PCA) was utilized to reduce the dimensionality of the data. In this step, the first 50 principal components, accounting for the majority variance in the dataset, were selected.  A neighbor graph was constructed based on the PCA representation of the data and subsequently visualized using UMAP embedding.
Processing and of multi-omic data  Multi-omic sequenced files were demultiplexing and analyzed using Cell Ranger ARC v2.0. Genes were mapped and referenced using human reference genome GRCh38. RStudio 1.3.1093 (R version 4.0.3) was used to perform analyses. Datasets were analyzed using Seurat 4.01 74 and Signac 1.3.0 75. For ATAC data, peaks were called using MACS2 and the genomic positions were mapped and annotated with reference human genome EnsDb.Hsapeins.v86 and hg38. Subsequently, we generated a consolidated peak set by merging overlapping peaks derived from all the samples. The consolidated peak set was subjected to re-quantification, followed by normalization using term frequency-inverse document frequency (TF-IDF) normalization. Low-quality cells including doublets, dead cells and poor sequencing depth cells were removed by filtering out cells with low RNA counts (UMI < 1,000) and low ATAC counts (nCount_ATAC < 25,000); high RNA counts (> 40,000 - 50,000) and high ATAC counts (> 40,000 - 50,000); nucleosome signal > 1 and transcription start site (TSS) enrichment < 2. Gene expression data was variance stabilized using SCTransform (v2 regularization), and then normalized for each cell by dividing by the total counts for that cell and then natural-log transformed using log1p.
Assembly: GRCh38
Supplementary files format and content: Filtered Feature-Barcodes Matrix (.filtered_feature_bc_matrix.h5), atac_fragments.tsv.gz: Contains information on DNA fragments from an ATAC-seq experiment. atac_fragments.tsv.gz.tbi: Index file facilitating quick retrieval of data from atac_fragments.tsv.gz. atac_peaks.bed: Lists called peaks or open chromatin regions identified in ATAC-seq data. atac_fragments.tsv.gz.tbi: Index file facilitating quick retrieval of data from atac_fragments.tsv.gz. atac_peaks.bed: Lists called peaks or open chromatin regions identified in ATAC-seq data.
Library strategy: Multiome


title: mouse 5-AP796;STR Male RNA rep1


title: WT_clone1_PE_rep3

description: Library name: X598_49_HUES8_Control_day10


title: KO_clone1_DE_rep3

description: Library name: X598_47_HUES8_EXDPF_KO_day4


title: multiome_O21_D1 RNA

description: 10x genomics


title: mouse 5-AP796;MC Male RNA rep1


title: WT_clone1_DE_rep3

description: Library name: X598_45_HUES8_Control_day4


title: scrnaseq_O2_D1

description: 10x genomics


title: scrnaseq_EDN3_control_invivo_1

description: 10x genomics


title: WT_clone1_PE_rep4

description: Library name: X598_69_HUES8_Control_day10


title: KO_clone2_PP_rep2

description: Library name: X598_36_HUES8_EXDPF_KO_day14


title: mouse 6-AP801;MC FeMale RNA rep1


title: mouse 2-AP683;Hp FeMale RNA rep1


title: mouse 2-AP683;STR FeMale RNA rep1


title: multiome_O2_D1 DNA

description: 10x genomics


title: WT_clone1_PP_rep2

description: Library name: X598_33_HUES8_Control_day14


title: KO_clone1_PP_rep2

description: Library name: X598_35_HUES8_EXDPF_KO_day14


title: WT_clone2_PP_rep2

description: Library name: X598_34_HUES8_Control_day14


title: multiome_O2_D1 RNA

description: 10x genomics


title: mouse 2-AP683;CTX FeMale RNA rep1


title: multiome_O2_D5 DNA

description: 10x genomics


title: KO_clone1_PE_rep2

description: Library name: X598_31_HUES8_EXDPF_KO_day10


title: KO_clone2_PE_rep2

description: Library name: X598_32_HUES8_EXDPF_KO_day10


title: OpticNerve, NMOSD, 7d, rep3

city: Guangzhou

first: Siqi

last: Chen

state: Guangdong

address: No.54 Xianlie South Road

department: Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-sen University

description: Library name: NMO7d3

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

organism: Rattus norvegicus

source_name: Optic nerve

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: Optic nerve

tag: time point

value: NMOSD


title: OpticNerve, NMOSD, 7d, rep2

description: Library name: NMO7d2


title: mouse 1-AP669;Hp Male RNA rep1


title: WT_clone2_PE_rep2

description: Library name: X598_30_HUES8_Control_day10


title: scrnaseq_O21_4W

description: 10x genomics


title: multiome_O2_D5 RNA

description: 10x genomics


title: mouse 1-AP669;STR Male RNA rep1


title: OpticNerve, NMOSD, 24h, rep3

description: Library name: NMO24h3


title: WT_clone1_PE_rep2

description: Library name: X598_29_HUES8_Control_day10


title: OpticNerve, NMOSD, 7d, rep1

description: Library name: NMO7d1


title: scrnaseq_EDN3_OE_Invitro_O2

description: 10x genomics


title: scrnaseq_O21_D1

description: 10x genomics


title: OpticNerve, NMOSD, 24h, rep2

description: Library name: NMO24h2


title: mouse 1-AP669;CTX Male RNA rep1


title: OpticNerve, NMOSD, 24h, rep1

description: Library name: NMO24h1


title: KO_clone2_DE_rep2

description: Library name: X598_28_HUES8_EXDPF_KO_day4


title: mouse 1-AP669;MC Male RNA rep1


title: KO_clone1_DE_rep2

description: Library name: X598_27_HUES8_EXDPF_KO_day4


title: scrnaseq_O2_D5

description: 10x genomics


title: OpticNerve, Control, rep3

description: Library name: CON3

value: Control


title: WT_clone2_DE_rep2

description: Library name: X598_26_HUES8_Control_day4


title: scrnaseq_O2_2W

description: 10x genomics


title: mouse 2-AP683;MC FeMale RNA rep1

value: AAV transduction


title: OpticNerve, Control, rep2

description: Library name: CON2


title: mouse 9-AP806;Testes Male DNA rep2

source_name: testes

extract_protocol:
We extracted genomic DNA using DNeasy Blood & Tissue Kit (Qiagen, Cat #69504)
MPRA barcodes were aplified from genomic DNA using Illumina Nextera amlification primers

value: testes

value: 21 days


title: mouse 9-AP806;Heart Male DNA rep2

source_name: heart

value: heart


title: WT_clone1_DE_rep2

description: Library name: X598_25_HUES8_Control_day4

value: DE


title: KO_clone2_PP_rep1

description: Library name: X598_16_HUES8_EXDPF_KO_day14

value: PPDPF KO/KO


title: scrnaseq_O5_4W

description: 10x genomics

value: SC-islets


title: T55.H3K27ac

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Reads were aligned to the human genome build GRCh37 using BWA 0.5.9-r26-dev.
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis.
Enrichment over input control was determined using both MACS2 and DFilter. Only peaks identified by both methods, and not overlapping with the ENCODE GRCh37/Hg19 blacklisted regions, were retained.
Deeptools bamCoverage was used to egnerate Reads-Per-Genomic-Contact (RPGC) normalized bigwig files.
Raw data vailable at EGA: EGAS00001007240
Assembly: GRCh37/Hg19
Supplementary files format and content: bigwig
Supplementary files format and content: bed

source_name: Endometrium

extract_protocol:
Chromatin Immunoprecipitation of ERα (SantaCruz #sc-543, 5μg/IP) and H3K27ac (ActiveMotif #39133, 5μg/IP) were performed as previously described in A.A. Singh et al. (Life Sci. Alliance, 2019, 10.26508/lsa.201800115)
Illumina TrueSeq single indexing

value: Endometrium

tag: antibody

tag: disease

value: Endometrial Cancer


title: OpticNerve, Control, rep1

description: Library name: CON1


title: KO_clone1_PP_rep1

description: Library name: X598_15_HUES8_EXDPF_KO_day14

value: PP

value: no


title: mouse 9-AP806;Hypothalamus Male DNA rep2

source_name: hypothalamus

value: hypothalamus


title: T55.ER


title: T5.H3K27ac


title: mouse 10-AP804;Lung Female DNA rep2

source_name: lung

value: lung


title: WT_clone1_PP_rep1

description: Library name: X598_13_HUES8_Control_day14

value: PPDPF WT WT


title: mouse 9-AP806:Kidney Male DNA rep2

source_name: kidney

value: kidney


title: T5.ER


title: WT_clone2_PP_rep1

description: Library name: X598_14_HUES8_Control_day14


title: scrnaseq_EDN3_OE_invivo_1

description: 10x genomics


title: KO_clone2_PE_rep1

description: Library name: X598_12_HUES8_EXDPF_KO_day10

value: PE


title: mouse 9-AP806;Liver Male DNA rep2

value: liver


title: scrnaseq_O2_4W

description: 10x genomics


title: KO_clone1_PE_rep1

description: Library name: X598_11_HUES8_EXDPF_KO_day10


title: scrnaseq_EDN3_OE_Invitro_O21

description: 10x genomics


title: mouse 10-AP804;Ovaries Female DNA rep2

source_name: ovaries

value: ovaries

value: AAV transduction


title: WT_clone2_PE_rep1

description: Library name: X598_10_HUES8_Control_day10


title: mouse 10-AP804:Liver Female DNA rep2

value: 21 days


title: CRPseq,IP,500ng

city: Nanjing

first: Tao

last: Shentong

address: Wei Gang Number1

institute: Nanjing Agricultural Unversity

data_processing:
The raw RNA-seq reads were trimmed using Trim Galore
Clean reads were mapped to reference genome using hisat2
bam files were processed using samtools
Expression levels (FPKM) were calculated using stringtie
Assembly: hg38
Supplementary files format and content: tab-delimited files containg FPKM value for each sample

source_name: helo

growth_protocol: Hela (ATCC CCL-2) cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS, 100 μg/mL streptomycin and 100 U/mL penicillin-streptomycin (37℃, 5% CO2, and 20% O2).

extract_protocol:
Hela cells were scraped and resuspended in TRIZOL and were then sonicated using a Covaris m220 Ultrasonicator using default settings at 10% duty for 5 min. Then fragmented RNA was extracted using Phenol/Chloroform/isoamyl alcohol and isopropanol method. The purified RNA was kept in -20℃ fridge or directly using for library construction.
The 2 μg total RNA sample was then divided into two parts for 150 mM Li+, and 150 mM K+ in Caco buffer in 60 ℃ within 5 min. Five percent of the incubated sample was collected as input control. Next, samples were incubated with 100 μM COL in 5 min after diluted in 10 mM of Li+ or K+. COL-containing samples were centrifuged for 5 min (4℃, 10000 r.p.m.) and supernatant was removed. The precipitate was resuspended with tris-HCl buffer (pH 8.8, 100 mM LiCl) and then was extracted using Qiagen RNeasy Plus Mini Kit following the manufacturer’s protocol. Samples were ribo-depleted using the Ribo-off® rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme). RNA library preparation was performed using the Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen) by following the manufacturer’s instructions.

value: helo


title: T33.ER


title: CRPseq,Input,500ng


title: scrnaseq_O2_D3

description: 10x genomics


title: T33.H3K27ac


title: mouse 10-AP804;Hypothalamus Female DNA rep2


title: WT_clone1_PE_rep1

description: Library name: X598_9_HUES8_Control_day10


title: T119.H3K27ac


title: T119.ER


title: mouse 8-AP802;PFC Female DNA rep1

value: brain (pre-frontal cortex)

value: 20 days


title: CRPseq.Li, R1


title: mouse 10-AP804:Kidney Female DNA rep2


title: T102.H3K27ac


title: KO_clone1_DE_rep1

description: Library name: X598_7_HUES8_EXDPF_KO_day4

value: DE

value: PPDPF KO/KO


title: KO_clone2_DE_rep1

description: Library name: X598_8_HUES8_EXDPF_KO_day4


title: CRPseq,IP, R2


title: T102.ER

value: Endometrium

value: Endometrial Cancer


title: CRPseq,IP, R1


title: WT_clone1_DE_rep1

description: Library name: X598_5_HUES8_Control_day4

value: no


title: mouse 8-AP802;Liver Female DNA rep1


title: H2.B.H3K27ac

value: Healthy


title: WT_clone2_DE_rep1

description: Library name: X598_6_HUES8_Control_day4


title: CD8_Naive_SA_3

source_name: peripheral blood

value: peripheral blood

value: sorted naive T cells


title: H2.A.K27ac


title: H2.B.ER


title: KO_clone2_hPSC_rep1

description: Library name: X598_4_HUES8_EXDPF_KO_day0

value: hPSC


title: CRPseq,Input, R2


title: mouse 8-AP802;Hp Female DNA rep1

source_name: brain (hippocampus)

value: brain (hippocampus)


title: CRPseq,Input, R1


title: mouse 8-AP802;STR Female DNA rep1

source_name: brain (striatum)

value: brain (striatum)


title: mouse 10-AP804;Muscle Female DNA rep2

source_name: muscle

value: muscle


title: KO_clone1_hPSC_rep1

description: Library name: X598_3_HUES8_EXDPF_KO_day0


title: mouse 8-AP802;CTX Female DNA rep1

source_name: brain (cortex)

value: brain (cortex)

value: AAV transduction


title: CRPseq,Li, R2

value: helo


title: H2.A.ER


title: CRPseq,CMScontrol, R1


title: mouse 8-AP802;MC Female DNA rep1

source_name: brain (motor cortex)

value: brain (motor cortex)


title: WT_clone2_hPSC_rep1

description: Library name: X598_2_HUES8_Control_day0

value: PPDPF WT WT


title: mouse 7-AP796;PFC Male DNA rep1

source_name: brain (pre-frontal cortex)

value: brain (pre-frontal cortex)

value: 20 days


title: BG4,Input, R2


title: WT_clone1_hPSC_rep1

description: Library name: X598_1_HUES8_Control_day0


title: mouse 7-AP796:Liver Male DNA rep1

source_name: liver

value: liver


title: BG4,Input, R1


title: CRPseq,CMScontrol, R2


title: H1.12.ER

value: Endometrium


title: H1.147.ER


title: Patient derived day 14 neurons compared to parent (control) day 14 neurons

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Ste #201

institute: Transcripta Bio

description:
Library name: patient_d14_neuron_vs_parent_d14_neuron
TPMs and fold changes were calculated using Sleuth post alignment of raw data using Kallisto version 0.46.1

data_processing:
Alignment with Kallisto 0.46.1 with bootstraps=100
Fold change and TPM calculation with Sleuth
Assembly: GRCh38
Supplementary files format and content: *_tpm.csv files contain TPMS for each gene for each replicate in the comparison
Supplementary files format and content: *_fold_change.csv is a comma-separated csv file that contains log2(Fold Change) and significance values per gene from sleuth.

source_name: patient-derived

growth_protocol: NPCs were differentiated into neurons using BrainPhys™ Neuronal Medium (StemCell Technologies)

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Plus Mini Kit (Qiagen, Cat: 74134)
Bulk RNA libraries were prepared from 200ng of RNA input using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit.

value: patient-derived

value: neurons

value: 19q12 ASD

tag: differentiation state

value: day 14


title: mouse 7-AP796;STR Male DNA rep1


title: BG4,1ug,IP, R1


title: mouse 7-AP796;Hp Male DNA rep1


title: Patient derived day 7 neurons compared to parent (control) day 7 neurons

description:
Library name: patient_d7_neuron_vs_parent_d7_neuron
TPMs and fold changes were calculated using Sleuth post alignment of raw data using Kallisto version 0.46.1

value: day 7


title: BG4,10ug, IP, R2


title: Patient derived day 20 neurons compared to parent (control) day 20 neurons

description:
Library name: patient_d20_neuron_vs_parent_d20_neuron
TPMs and fold changes were calculated using Sleuth post alignment of raw data using Kallisto version 0.46.1

value: day 20


title: BG4,1ug,IP, R2


title: Patient derived NPCs compared to parent (control) NPCs

description:
Library name: patient_npc_vs_parent_npc
TPMs and fold changes were calculated using Sleuth post alignment of raw data using Kallisto version 0.46.1

value: neural projenitor cells

value: NPC


title: BG4,10ug, IP, R1


title: mouse 7-AP796;CTX Male DNA rep1

value: brain (cortex)


title: mouse 7-AP796;MC Male DNA rep1

value: AAV transduction


title: N87_S23

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

data_processing:
RNA-seq fastq reads were mapped using TopHat version 2.0.13
FPKMs were calculated by Cufflinks version 2.2.1
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab delimited text file includes FPKM values for all samples

source_name: HSC1L cell line

growth_protocol: Passaged in Eagles Minimum Essential Medium (ATTC) + 10% FBS + 1 % penicillin- streptomycin

extract_protocol:
High Pure RNA Isolation Kit (Roche Indianapolis, IN).
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

treatment_protocol: Media replaced with media lacking FBS 72 hours prior to RNA isolation

tag: knock-out (ko)

value: WT CRISPR control


title: N5_S29

value: CRISPR KO


title: Patient derived iPSCs compared to parent (control) iPSCs

description:
Library name: patient_ipsc_vs_parent_ipsc
TPMs and fold changes were calculated using Sleuth post alignment of raw data using Kallisto version 0.46.1

value: induced pluripotent stem cells

value: iPSC


title: N3_S26


title: H1.147.H3K27ac

value: Healthy


title: BG4,10ug,Flag, R2

value: helo


title: BG4,10ug,Flag, R1


title: H1.12.H3K27ac

value: Endometrium


title: N33_S28


title: TissueCD45-_P1

description:
Library name: Sample 1_TissueCD45-
10x Genomics

source_name: ovarian cancer

value: ovarian cancer

value: Stromal cells

tag: batch

tag: figo stage

tag: grading

value: High grade

tag: histotype

value: High grade serous carcinoma


title: RNAseq_H.081.A2

data_processing:
Fastq files have been demultiplexed by Cutadapt
Read were mapped on Hg38/GRCh38 genome assembly using HISAT2 (v2.1.0) using the following parameters: --wrapper basic-0 --min-intronlen 20 --max-intronlen 500000 --rna-strandness FR -k 5 --minins 0 --maxins 500 --fr --new-summary
HISAT2 (v2.1.0) was used to generate raw gene counts
Raw data are available at EGA: EGAS00001007240
Assembly: Hg38/GRCh38
Supplementary files format and content: raw gene counts (.txt) for all samples

source_name: Healthy Endometrium

extract_protocol:
RNA from around 30mg of endometrial healthy or tumor tissue was extracted using the RNeasy mini kit (Qiagen) following manufacture instructions. Quality of the RNA extraction was assessed using the 2100 Bioanalzer (Agilent, RNA 6000 Nano Kit) and selecting samples with a RNA Integrity Number (RIN) above 9.
PolyA+ stranded RNA library was prepared using the Illumina Stranded mRNA Prep kit and quality was assessed by using the 2100 Bioanalyzer (Agilent, DNA 7500 kit). RNA-seq libraries have been pooled equimolarly and sequenced using NovaSeq6000 (Illumina) sequencer with a 51bp Paired-End reads setup.

tag: tissue

value: Healthy Endometrium

tag: cell type

value: Normal


title: N32_S32

tag: cell line


title: PBMCs_P1

description:
Library name: Sample 1_PBMC
10x Genomics

source_name: blood

value: blood

value: PBMC

tag: age


title: mouse 6-AP801;CTX Female DNA rep1

value: brain (cortex)

tag: genotype

tag: treatment

tag: time

value: 19 days


title: mouse 6-AP801;STR Female DNA rep1

value: brain (striatum)

value: AAV transduction


title: TissueCD45+_P1

description:
Library name: Sample 1_TissueCD45+
10x Genomics

value: TILS


title: N15_S30

value: WT CRISPR control


title: mouse 6-AP801;PFC Female DNA rep1

value: brain (pre-frontal cortex)


title: RNAseq_T.001.A1

source_name: Endometrial cancer

value: Endometrial cancer

value: Tumor


title: mouse 6-AP801;MC Female DNA rep1

value: brain (motor cortex)


title: Hi-C_T.039.II1

data_processing:
Raw fastq data were analyzed at 10kb resolution using the snHiC pipeline (v0.2.0) [Gregoricchio, S. and W. Zwart, snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis. Bioinformatics Advances, 2023. 3(1)] applying default parameters.
.mcool files at 2,10,40,100,500kb resolution have been generated using HiCExplorer hicConvertFormat from individual .cool files.
Raw data are available at EGA: EGAS00001007240
Assembly: Hg19/GRCh37
Supplementary files format and content: .mcool

growth_protocol: 3x10 50um-thick slices of flash frozen tissue derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients were used

extract_protocol:
Hi-C single-index library preparation of MCF7 cells was performed as previously described [Donaldson-Collier, M.C., et al., EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains. Nature Genetics, 2019. 51(3): p. 517-528.] using MboI (New England Biolabs) restriction enzyme.
Single-indexing 75bp Paired-end (illumina)


title: KO_clone2_DE_rep3

description: Library name: X598_48_HUES8_EXDPF_KO_day4

value: DE

value: PPDPF KO/KO

value: no


title: Hi-C_T.081.A1


title: RNAseq_T.081.A1


title: N13_S31

value: CRISPR KO


title: RNAseq_H.069.C2

value: Healthy Endometrium

value: N ormal


title: mouse 5-AP796;PFC Male DNA rep1


title: RNAseq_T.039.II1


title: N10_S25


title: N23_S24


title: mouse 5-AP796;Hp Male DNA rep1

value: brain (hippocampus)


title: Hi-C_T.001.A1


title: Hi-C_H.081.A2

value: Normal


title: RNAseq_H.005.A2


title: mouse 6-AP801;Hp Female DNA rep1

value: 19 days


title: Hi-C_H.069.C2


title: mouse 5-AP796;STR Male DNA rep1

value: brain (striatum)


title: Ishikawa_G9a_6h_10nM.E2_rep2

data_processing:
Reads were aligned to the human genome build GRCh37 using BWA 0.5.9-r26-dev
Duplicates have been marked using GATK markdupoplicates
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis
bamCoverage tools was used to generate RPGC normalized bigwigs
bigwigCompare was used to merge bigwigs of the replicates for each condition.
Assembly: Hg19/GRCh37
Supplementary files format and content: RPGC normalized bigWig (.bw) files

growth_protocol: Ishikawa (Merck Sigma Aldrich) and AN3CA endometrial cancer cell lines have been cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) and DMEM Mixture F-12 (DMEM/F-12, Gibco), respectively, supplemented with 10% Fetal Bovine Serum (FBS-12A, Capricorn Scientific) and penicillin/streptomycin (100μg/mL, Gibco).

extract_protocol:
Chromatin Immunoprecipitation of G9a/EHMT2 (Abcam #ab133482, lot # GR154986-1; 5µg/IP) were performed as previously described (A.A. Singh, et al., Life Sci. Alliance; 2019) employing the 1% formaldehyde to perform the crosslinking. Two biological replicates are provided.
Illimina kit, Paired-End 51bp, Novaseq6000

treatment_protocol: For hormone stimulation, cells were pre-cultured for 3 days in phenol red-free DMEM (Gibco) supplied with 5% dextran-coated charcoal (DCC) stripped FBS, 2mM L-glutamine (Gibco), and penicillin/streptomycin (100μg/mL, Gibco), then stimulated with 10nM DMSO-solubilized 17β-estradiol (MedChemExpress, #HY-B0141) for 6 hours.

value: Ishikawa


title: 143B_KO_20_WT

data_processing:
Basecalling: Real Time Analysis 1.18.61 on the HiSeq 2500 HO with bcl2fastq v2.17.1.14 demultiplexing package
RNA-seq reads were mapped using TopHat version 2.0.13.
FPKMs were calculated by Cufflinks version 2.2.1
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab delimited text file includes FPKM values for all samples

source_name: 143B_WT CRISPR control

value: TK-derivative of the human osteosarcoma (HOS) cell line

tag: genotype/variation


title: mouse 5-AP796;MC Male DNA rep1

value: AAV transduction


title: 143B_KO_15

source_name: 143B_CRISPR KO


title: mouse 2-AP683;Hp Female DNA rep1


title: Hi-C_H.005.A2


title: mouse 2-AP683;CTX Female DNA rep1

value: brain (cortex)


title: Ishikawa_G9a_6h_10nM.E2_rep1

value: Endometrial cancer


title: 143B_KO_8_WT

value: WT CRISPR control


title: mouse 2-AP683;STR Female DNA rep1


title: ACHN-CRISPRi Clone 6, D12

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Galaxy: Clip adapter GTTTTAGA and CGGTGTTTC
Galaxy: Collapse sequences
Galaxy: FASTA-to-tabular
MAGeCK sgRNA enrichment
Assembly: GRCh38
Supplementary files format and content: Table of normalized read counts of sgRNAs
Library strategy: CRISPR screen custom DNA library

source_name: Kidney

growth_protocol: ACHN cells were cultured in Minimum Essential Medium Eagle (Sigma-Aldrich, M4655) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco).

extract_protocol:
Genomic DNA was isolated using the MasterPure Complete DNA Purification kit (Lucigen).
Sequencing libraries were generated through two sequential rounds of PCR using Herculase II Fusion DNA polymerase (Agilent). For the first round of PCR, 6.6 µg of genomic DNA was used in each 100 µl reaction. A total of 12 first-round PCR reactions were performed per replicate, with 18 cycles of amplification. For the second round of PCR, 5 µl of the pooled first-round PCR product and primers containing barcodes and Illumina sequencing adaptors were used, with 6 to 8 cycles of amplification.

treatment_protocol: Transduced cells were selected with 2 µg/mL puromycin (Thermo Fisher Scientific).

value: Kidney

value: ACHN

value: Epithelial

tag: clone

value: ACHN-CRISPRi Clone 6


title: Ishikawa_INPUT_6h_10nM.E2_rep1-2


title: 143B_Parent_no_dox

source_name: 143B cell line


title: mouse 1-AP669;Hp Male DNA rep1

data_processing:
We used a custom python script to tally the barcode counts per sample.
For each sequence entry, we searched for the common restriction enzyme site present in both the DNA and the RNA.
Using the location of the enzyme, we identified the sequence of the unique barcode.
We noted cases where the restriction enzyme site or the barcode sequence were not found in sequence entry.
Supplementary files format and content: csv file, where each row is for a bar-code, each column is for a tissue or cell line sample, and each entry is the number of reads for the bar-code in the sample

source_name: brain (hippocampus)


title: 143B_Luciferase_no_dox


title: 143B_KO_7

value: CRISPR KO


title: ACHN-CRISPRi Clone 6, D0


title: mouse 1-AP669;STR Male DNA rep1

source_name: brain (striatum)


title: ACHN-CRISPRi Clone 1, D12

value: ACHN-CRISPRi Clone 1


title: C4-2B_ENZR_H3K27ac

first: Qinwei

last: Liu

address: kangda road 1

institute: First Affiliated Hospital Of Guangzhou Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. The clean reads were then aligned to hg38 reference genome using BWA program.
After reads mapping, MACS2 were used to perform peak calling process with peak cutoff qvalue < 0.05. After peak calling, ROSE software were used to perform enhancer calling process.
The H3K4me1 peaks file identified by MACS2 and the H3K27ac BAM file were used as input for the algorithm. Basically, intergenic and intronic H3K4me1 peaks within 12.5 kb were stitched together to define a single entity spanning a genomic region as enhancers. The stitched and individual enhancers without neighboring peaks within 12.5 kb were ranked by the level of H3K27ac signal in the genomic region. The stitched or individual enhancers with an H3K27ac intensity above a cutoff where the slope of the distribution plot of H3K27ac intensity is 1 were defined as SEs and the remaining enhancers were considered TEs. Integrative Genomics Viewer (IGV) were used to visualize the singal of H3K27ac and H3K4me1 intensity.
Assembly: hg38
Supplementary files format and content: Macs2 narrowPeak file
Library strategy: CUT＆Tag

source_name: Prostate

growth_protocol: C4-2B EnzR cells were generated by cultivating C4-2B cells for at least 6 months in a medium supplemented with 50M Enz. Cells were cultured in RPMI-1640 10% FBS in a 37℃ and 5% CO2 environment. Enz (MD3100) was obtained from Selleckchem.

extract_protocol:
100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 10μL Concanavalin A coated magnetic beads (Bangs Laboratories, Cat #:BP531) were added per sample and incubated at RT for 10min. Remove unbound supernatant and resuspended bead-bound cells with dig wash buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2mM EDTA) and a 1:50 dilution of primary antibody（H3K4me1: abcam,ab8895，H3K27ac: abcam, abcam，ab4729）incubated on a roating platform overnight at 4℃. The primary antibody was removed using magnet stand. Sencondary antibody （Rabbit Anti-Mouse IgG H&L：abcam，ab611709）was diluted 1:100 in dig wash buffer and cells were incubated at RT for 60 min. cells were washed using the magnet stand 2-3 times in dig wash buffer . A 1:100dilution of pA-Tn5 adapter complex was prepared in digmed buffer (0.01% Digitonin; 20mM HEPES pH 7.5; 300mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) and incubated with cells at RT for 1h. Cells were washed 2–3× for 5 min in 1 mL Dig-med buffer. Then cells were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter, a63881).  The size distribution of libraries was determined by Agilent 4200 TapeStation analysis, and libraries were mixed to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer. Sequencing was performed in the Illumina Novaseq 6000 sequencer using 150bp paired-end following the manufacturer’s instructions.

value: prostate

value: prostate cancer

tag: phenotype

value: enzalutamide-resistant prostate cancer cell

tag: antibody


title: HSC1L_S27


title: C4-2B_ENZR_H3K4me1


title: mouse 2-AP683;MC Female DNA rep1

value: brain (motor cortex)

value: 19 days


title: mouse 1-AP669;CTX Male DNA rep1

source_name: brain (cortex)


title: Ishikawa_INPUT_6h_DMSO_rep1-2

value: Ishikawa


title: Top1/2-AID + TIR1  6h, R2

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: sample 12

data_processing:
Read processing was performed using an adapted nf-core/clipseq pipeline with Nextflow. Read demultiplexing was performed using Ultraplex with parameters “--phredquality 15--min_length0” . Adaptor trimming was performed using Cutadapt with parameters “--minimum-length 20”. Bowtie2 was used for premapping to ribosomal and small RNAs. Genome mapping was performed using STAR with the SK1-MvO-V1 annotation. UMI-tools was used for deduplication. BedTools was used to identify the 5’-most nucleotide (tag) and for genome-wide comparative analyses.
Assembly: SK1-MvO-V1
Supplementary files format and content: bedgraph

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: Cells were arrested in early meiosis as described previously 9. Briefly, yeast cells were inoculated in yeast extract peptone dextrose (YPD) media [1% weight/volume (w/v) yeast extract, 2% w/v bacto peptone, 2% w/v glucose, uracil (24 mg/l) and adenine (12 mg/l)] for approximately 24 hours, before being diluted to OD600 0.4 in buffered, yeast extract, tryptone, acetate (BYTA, (1.0% w/v yeast extract, 2.0% w/v peptone, 1% potassium acetate, 50 mM potassium phthalate monobasic) and incubated for 16-18 hours. OD600 1.8 of yeast cells were then washed and transferred to SPO (0.3% Potassium acetate, Acetic acid to pH 7.0, 0.02% D-(+)-Raffinose pentahydrate). 2 hours after transfer to sporulation medium, copper (II) sulphate (CuSO4, 50 μM) and indole-3-acetic acid (IAA, 500 μM) were added to induce synchronous meiotic entry and auxin-induced protein depletion. In all steps yeast were grown at 30°C at 300 rpm, and a 1:10 culture volume to flask total volume ratio was maintained.

extract_protocol:
24 OD units were collected by centrifugation, and snap frozen in liquid nitrogen. Per 10 OD units, RNA was extracted with Tris-EDTA-SDS (TES) buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and Acid Phenol:Chloroform:Isoamyl alcohol (125:24:1, Ambion) at 65°C for 45 minutes. Precipitation was carried out. rDNase (Machery-Nagel) treatment was carried out, before spin column purification (Machery-Nagel).
The TSS-seq protocol: total RNA was dephosphorylated with quickCIP (NEB, 1.2 U/µg RNA) 37°C, with RNasin Plus before heat inactivation. RNA was extracted using phenol/chloroform/isoamyl alcohol as before. RNA was treated with mRNA decapping enzyme (NEB, 0.7 U/µg RNA) at 37°C with RNasin Plus. RNA was extracted using phenol/chloroform/isoamyl alcohol as before. RNA and the 5’ adaptor (10 µM) were denatured for 2 minutes at 70°C, then cooled on ice for 2 minutes. Ligation was performed, 16°C using and T4 RNA ligase I (30 U), with RNasin Plus. RNAClean XP (1.8X ratio, Beckman Coulter) was used to remove unligated adaptors, according to the manufacturer’s instructions. The concentration of the samples was measured using Qubit RNA BR assay, and samples were multiplexed. polyA+ RNA was enriched using Dynabeads Oligo(dT)25 (Thermo Fisher). Yeast RNA was fragmented with alkaline fragmentation reagent (Ambion). RNeasy MinElute Clean-up columns, with 1.5x volume of Ethanol, were used to purify the samples. The 3’ ends were fixed by CIP treatment (NEB,30 U).  Ligation was carried out by T4 Rnl2tr (NEB,200 U) for 2 hours, 25°C then 16 hours, 16°C. RNAClean XP (1.8X ratio) was used to remove unligated adaptors. RNA, RT oligo (0.5 pmol) and dNTP (10 mM each) were denatured at 65°C, then cooled on. Reverse transcription was carried out by SuperScript III (2 µl), with RNasin Plus with the following conditions: 25°C for 5 minutes, 42°C for 20 minutes, 50°C for 40 minutes, 80°C for 5 minutes. Template RNA was removed by RNase H (10 U) for 37°C, 30 minutes. AMPure XP beads (Agencourt, Beckman Coulter) were used to clean up the cDNA. 3X beads and 1.7x isopropanol added to the reverse transcription reaction, and incubated for 5 minutes. Beads were washed twice with 85% ethanol, dried, and eluted twice in nuclease-free water. cDNA pre-amplification was performed with i5_s and i7_s (300 nM each) primers and Phusion HF PCR Mastermix (Thermo Fisher). 6 PCR cycles were carried out (98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, with 3 minutes at 72°C final extension). ProNex beads (Promega) with a 1:2.95 ratio to sample were used to remove sequences less than 55 nt (including primer dimers). Final amplification was carried out with NEBNext i50 and i70 primers (500 nM each) and Phusion HF PCR Mastermix, for 8 cycles. Amplification was checked by using Novex 6% TBE (Tris/Borate/EDTA) gel and staining with SYBR green. ProNex beads (Promega) with a 1:2.3 ratio to sample were used for purification. Library concentration was measured using Qubit High Sensitivity D1000. Libraries were sequenced with Illumina NovaSeq 6000.

value: cells

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, his3::pCUP-OsTIR:His3mx, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX10


title: A-498-CRISPRi Clone 4, D19

growth_protocol: A-498  cells were cultured in Minimum Essential Medium Eagle (Sigma-Aldrich, M4655) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco).

value: A-498-CRISPRi Clone 4


title: Top1/2-AID + TIR1  6h, R1

description: Library name: sample 11

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, his3::pCUP-OsTIR:His3mx, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX9


title: Top1/2-AID + TIR1 0h, R2

description: Library name: sample 10

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, his3::pCUP-OsTIR:His3mx, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX7


title: Ishikawa_G9a_6h_DMSO_rep1

value: Endometrial cancer


title: A-498-CRISPRi Clone 2, D0

value: Kidney

value: A-498-CRISPRi Clone 2


title: Ishikawa_G9a_6h_DMSO_rep2


title: A-498-CRISPRi Clone 4, D0

value: Epithelial


title: mouse 1-AP669;MC Male DNA rep1

source_name: brain (motor cortex)

value: AAV transduction


title: A-498-CRISPRi Clone 2, D19


title: ACHN-CRISPRi Clone 1, D0

value: ACHN

value: ACHN-CRISPRi Clone 1


title: 786-O-CRISPRi Clone 6, D0

growth_protocol: 786-O cells were cultured in RPMI (Invitrogen) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco).

value: 786-O-CRISPRi Clone 6


title: aortic dissection,scRNAseq 3

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

description: 10x Genomics

data_processing:
5000 cells were isolated and library prepared using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 on 10X genomics platform and sequenced on NovaSeqTM 6000 (Illumina) with a coverage of 50,000 reads/ cell.   Alignment and count matrix generation was performed using Cell Ranger v6.0.1 on hg38. Downstream analysis was conducted using the R package Seurat v4.1.0   In brief, cells nFeature_RNA > 200 and nFeature_RNA < 7000 & percent.mt < 5 were retained, then the datasets were normalized with SCT v2 method and merged, and clusterization was performed.   FindMarkers function with “MAST” test was used to characterize specific markers of each cluster. Markers with a logFC > |0.5| were used to perform Ingenuity Pathway Analysis. Pathways and functions with an absolute z-score of >2 were considered significant.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: aorta

extract_protocol:
The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of  700~1200 cells/ul for 10x Genomics Chromium
The 3'Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation,sample index PCR, etc., the library is finally quantitatively examined
The final library pool was sequenced on the Illumina Nova6000 instrument using 150-base-pair paired-end reads

value: aorta

tag: group

value: aortic dissection

value: no


title: DSE4-lung.RNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

data_processing:
IsoSeq (v4.1.1) was used to perform primer removal, polyA tail removal, chimeric reads removal, and reads clustering on the long reads (LRs).
The clustered LRs were aligned to the susScr11 reference genome using pbmm2 (version 1.13.1, parameters --preset ISOSEQ --sort). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The short reads (SRs) were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.10.1), and TPM values were summaized in the processed data table.
Assembly: susScr11.1
Supplementary files format and content: Long reads numbers mapped to each transcript have been summarized into eachSample.FLcount.txt.gz. Genes TPM values were summarized into Genes.exp.TPM.txt.gz. Transcript TPM values were summarized into Transcripts.exp.TPM.txt.gz.
Supplementary files format and content: PacBio's assembly GTF file was tab-delimited. PacBio's assembly sequences were fasta format.

organism: Sus scrofa

source_name: lung

growth_protocol: All samples were acquired from 12-month adult male pigs.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina paired-end sequencing uses standard RNAseq library construction protocol.

value: lung


title: Top1/2-AID + TIR1 0h, R1

description: Library name: sample 9

value: cells

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, his3::pCUP-OsTIR:His3mx, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX6


title: DSE4-spleen.RNAseq

source_name: spleen

value: spleen


title: aortic dissection,scRNAseq 2

description: 10x Genomics


title: DSE4-liver.RNAseq

source_name: liver

value: liver


title: 786-O-CRISPRi Clone 6, D15


title: 786-O-CRISPRi Clone 2, D15

value: 786-O-CRISPRi Clone 2


title: Top1/2-AID 6h, R2

description: Library name: sample 8

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX10


title: aortic dissection,scRNAseq 1

description: 10x Genomics


title: Top1/2-AID 0h, R2

description: Library name: sample 6

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX7


title: abdominal aortic aneurysm,scRNAseq 2

description: 10x Genomics

value: abdominal aortic aneurysm


title: DSE4-heart.RNAseq

source_name: heart

value: heart


title: DSE3-spleen.RNAseq


title: DSE3-lung.RNAseq


title: marfan syndrome,scRNAseq

description: 10x Genomics

value: marfan syndrome


title: nondiseased  aortic wall,scRNAseq 2

description: 10x Genomics

value: nondiseased


title: DSE4-kidney.RNAseq

source_name: kidney

value: kidney


title: Top1/2-AID 0h, R1

description: Library name: sample 5

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX6


title: S-EGFP-Ad4BP-2

city: Bunkyo-ku

first: Shogo

last: Yanai

state: Tokyo

institute: TMDU

description: Library name: Sample2

data_processing:
Sequence reads were trimmed for adaptor sequence using TrimGalore version 0.6.4.
Trimmed sequence reads were mapped to GrCM38/mm10 using Bowtie2 version 2.2.5.
BAM and bigwig files were generated using SAMTools version 0.3.3 and bamCoverage, respectively.
Reads mapped to the Blacklist regions were eliminated.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: testis

extract_protocol:
Fetal Leydig cells (S-EGFP cells) and testicular interstitial cells (W-EGFP cells) were isolated from E16.5 testis of FLE-EGFP mice. 50,000 S-EGFP cells or W-EGFP cells bound to Concanavalin A beads (Polyscience) were permeabilized with 0.02% digitonin at room temperature for 10-min. The permeabilized cells were then incubated with an anti-Ad4BP/SF-1 antiserum (1:200) in 100 mL of antibody buffer (20 mM HEPES (pH7.5), 150 mM NaCl, 0.5 mM spermidine, 0.02% Digitonin, protease inhibitor (Nacalai Tesque)) overnight at 4 °C on a rotator. Next, 150 mL of pAG/MNase (700 ng/mL) was added, and digestion was carried out for 30-min at 4 °C. After the digestion, the samples were incubated for 10-min at 37 °C to release the CUT&RUN DNA fragments.
CUT&RUN libraries were constructed using NEBNext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, New England Biolabs).

value: testis


title: S-EGFP-Ad4BP-1

description: Library name: Sample1


title: abdominal aortic aneurysm,scRNAseq 1

description: 10x Genomics

value: aorta


title: DSE3-kidney.RNAseq


title: W-EGFP-Ad4BP-2

description: Library name: Sample4


title: TIR1 6h, R2

description: Library name: sample 4

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, his3::pCUP-OsTIR:His3mx


title: nondiseased  aortic wall,scRNAseq 1

description: 10x Genomics

value: no


title: HMC3; RNA transfection #5

first: Irene

last: Kaplow

institute: Carnegie Mellon University

extract_protocol:
We extracted total RNA using RNeasy Mini Kit (Qiagen, cat#74104) and prepared cDNA with a specific reverse transcription primer
MPRA barcodes were amplified from cDNA using Illumina Nextera amlification primers

value: AAV transfection

value: 72 hours


title: W-EGFP-Ad4BP-1

description: Library name: Sample3


title: TIR1 0h, R1

description: Library name: sample 1

value: cells


title: TIR1 6h, R1

description: Library name: sample 3


title: nondiseased  aortic wall,scRNAseq 3

description: 10x Genomics


title: HMC3; RNA transfection #3


title: Hpc AD RACE NPAM 067

city: Los Angeles

first: Warren

last: Tourtellotte

state: California

address: 8700 Beverly Blvd

department: Pathology and Laboratory Medicine

institute: Cedars-Sinai

description: Library name: 067

data_processing:
Illumina NextSeq 500
GeoMx_NGS_Pipeline_2.2.0.2
Assembly: mm10
Supplementary files format and content: Segments.jpg: images of segments on each tissue that correspond to the sequencing data
Supplementary files format and content: .dcc- contain raw read counts and probe barcodes
Library strategy: Spatial Transcriptomics

source_name: Hippocampus

extract_protocol:
FFPE tissues were cut at 4um with a cryostat
Spatial Transcriptome sequencing libraries were prepared using Nanostring GeoMx WTA (Ms) according to the manufacturers protocol

value: Hippocampus

value: Iba1+ microglia

value: AD RACE


title: abdominal aortic aneurysm,scRNAseq 3

description: 10x Genomics


title: TIR1 0h, R2

description: Library name: sample 2


title: AD Hippocampus 3

type: RNA

city: Bengaluru

first: Thimmaiah

last: Govindaraju

state: India

address: Jakkur

department: New Chemistry Unit

country: India

institute: JNCASR

hyb_protocol: Ligated product was diluted with 15 µl of nuclease free water and denatured at 85 °C for 5 minutes. 5 µl of this was hybridized overnight at 65 °C with reporter and capture probes. Protocol followed as per nCounter miRNA expression assay user manual (MAN-C0009-07).

scan_protocol: Post hybridization, samples were analysed on nanoString nCounter SPRINT machine.

data_processing: Analysis was performed on all samples using the nCounter Analysis System (NanoString Technologies) and the nCounter Mouse v1 miRNA Panel (NS_M_miR_v1.5) having 599 unique miRNA barcodes for endogenous miRNA. The housekeeping genes used in the panel includes, beta-actin (Actb), beta-2-microglobulin (B2m), glyceraldehyde 3-phosphate dehydrogenase (Gapdh) and ribosomal protein L19 (Rpl19). The panel also includes the SpikeIn mIRNAs, Arabidopsis thaliana miR159a (ath-miR159a), Caenorhabditis elegans (cel)-miR-248 and miR254, and Oryza sativa (osa)-miR 414 along with the positive and negative controls for assessing overall assay efficiency as well as for monitoring the ligation efficiency. The raw miRNA data in.RCC (Reporter Code Count) format was further analyzed using nSolver analysis software (NanoString technologies) version 4.0. QC metrics of imaging, binding density, positive control, limit of detection and ligation were checked before proceeding with further analysis. Normalization of the raw data was performed using the geometric mean of positive controls and top 100 highly expressed miRNAs. The differential expression between the groups were calculated using the build ratio utility present within the nSolver (foldchange), which uses Student’s unpaired t-test for the p value calculation. The thresholds considered for a significant differentially expressed miRNA were, foldchange ≥ 1.2 or ≤ -1.2, P-value ≤ 0.05 and either of the two groups (test/control) should have their geometric mean expression ≥ average count for negative control probes in the panel. Unsupervised hierarchical clustering analysis followed by heatmap visualization and principal component analysis (PCA) was performed with the normalized and log2 transformed data using ClustVis (https://biit.cs.ut.ee/clust vis/).

label_protocol: With NanoString Mouse v1.5 -miRNA assay kit (CSO-MMIR15-12), miRNA (3μl) was ligated to mir-Tag with ligation buffer and ligase supplied with the kit.

extract_protocol: Total RNA including miRNA was isolated from mouse brain tissue using Qiagen miRNAeasy mini kit (Cat#217004). Tissue was homogenized in TOMY homogenizer in presence of liquid nitrogen, for three cycles. 700 µl of QIAzol Lysis reagent was added to the tissue powder and mixed well. Lysate was incubated at room temperature for 5 minutes and 140 µl of chloroform was added for phase separation. Rest of the protocol was followed as per manufacturer’s guidelines. RNA was eluted in 25µl of nuclease free water (Ambion, Cat # AM9932). Quantitation was performed using Qubit RNA HS assay (Invitrogen, Cat # Q32855) kit and also qualitatively analysed on Agilent 2100 bioanalyzer nano chip (Agilent, Cat # 5067-1511).

tag: strain

value: Brain

value: 12 months


title: Hpc AD RACE NPAM 066

description: Library name: 066


title: DSE3-liver.RNAseq

value: liver


title: DSE3-heart.RNAseq

value: heart


title: DSE2-spleen.RNAseq

value: spleen


title: Hpc AD NORACE NPAM 068

description: Library name: 068

value: AD NORACE


title: 786-O-CRISPRi Clone 2, D0

value: Kidney

value: Epithelial

value: 786-O-CRISPRi Clone 2


title: HMC3; RNA transfection #1

address: 5000 Forbes Avenue, Gates-Hillman 7703


title: DSE2-liver.RNAseq


title: Hpc AD RACE NPAM 065

description: Library name: 065


title: Hpc AD RACE NPAM 063

description: Library name: 063


title: WT Hippocampus 3

value: WT


title: Hpc AD RACE NPAM 062

description: Library name: 062


title: HMC3; RNA transfection #2


title: AD Hippocampus 2


title: DSE2-lung.RNAseq

value: lung


title: WT Hippocampus 1


title: AD Hippocampus 1


title: HMC3; transfection #5

extract_protocol:
We extracted genomic DNA using DNeasy Blood & Tissue Kit (Qiagen, Cat #69504)
MPRA barcodes were aplified from genomic DNA using Illumina Nextera amlification primers

value: AAV transfection


title: DSE2-kidney.RNAseq

value: kidney


title: AD Cortex 3

source_name: Cortex


title: DSE2-heart.RNAseq


title: HMC3; transfection #4

value: 72 hours


title: Top1/2-AID 6h, R1

description: Library name: sample 7

value: cells

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, Top1::Top1-3V5-IAA7::KanMX6, Top2::Top2-3V5-IAA7::KanMX9


title: WT Hippocampus 2


title: DSE1-liver.RNAseq


title: Hpc AD RACE NPAM 059

description: Library name: 059

value: Hippocampus

value: Iba1+ microglia

value: AD RACE


title: Hpc AD RACE NPAM 064

description: Library name: 064


title: DSE1-spleen.RNAseq


title: DSE1-lung.RNAseq


title: Hpc AD RACE NPAM 061

description: Library name: 061


title: COPD-2, Siglec-1- FSClow AM

city: Sendai

first: Takuya

last: Saito

state: Miyagi

address: 1-1 Seiryomachi, Aobaku

department: Department of Respiratory Medicine

institute: Tohoku University Graduate School of Medicine

data_processing:
The FASTQ reads of each sample were aligned to the GENCODE human reference genome GRCh38, and the expression levels for each gene were calculated.
The calculated gene expression data were incorporated into Subio Platform (Subio inc., Japan) and analyzed with Basic and Advanced Plug-ins.
Assembly: hg38
Supplementary files format and content: Text files include normalized processed signals for each Sample

source_name: alveolar macrophages obtained from lung tissue

extract_protocol:
total RNA was extracted with RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
After quality control on an Agilent TapeStation, total RNA with RNA integrity number of 7.0-9.3 was subjected to amplification with the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (CloneTech). cDNA library was prepared with the Nextera XT DNA Library Prep Kit (illumina). Samples were analyzed on NovaSeq 6000 (illumina) in 2 × 150-bp paired-end mode, which generated 40 million paired reads per sample.

value: alveolar macrophages

value: COPD

tag: gender

value: M

tag: ethnicity

value: Japanese


title: COPD-3, Siglec-1- FSChi AM


title: WT Cortex 3

value: Brain

value: 12 months


title: AD Cortex 2


title: Hpc AD RACE NPAM 060

description: Library name: 060


title: AD Cortex 1


title: Hpc AD NORACE PAM 057

description: Library name: 057

value: AD NORACE


title: DT4-spleen.RNAseq

value: spleen


title: COPD-1, Siglec-1- FSClow AM


title: COPD-1, Siglec-1- FSChi AM


title: HMC3; transfection #3

city: Pittsburgh


title: Hpc AD NORACE PAM 056

description: Library name: 056


title: Hpc AD NORACE PAM 055

description: Library name: 055


title: DSE1-kidney.RNAseq


title: Hpc AD NORACE PAM 054

description: Library name: 054


title: DT4-liver.RNAseq

value: liver


title: COPD-2, Siglec-1+ FSChi AM


title: Gcn4-Mnase, crm1(T539C), SDC, Replicate 3

city: Evanston

first: Tiffany

last: Ge

state: IL

address: 2205 Tech Drive

institute: Northwestern University

description: Library name: B57-TG17

data_processing:
ChEC-seq2 mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn). Repetitive regions are masked.
Assembly: S288C, R64.3.1
Supplementary files format and content: bigwig files contain CPMn normalized coverage counts that are not trimmed. Trimming the bams to the first bp of each read as described in VanBelzen et al. 2024 is recommended for processing samples.
Library strategy: ChEC-seq

growth_protocol: Yeast strains were grown in SDC overnight, diluted to ~0.1 OD and placed at 30°C shaking at 200 rpm for > 4 hours.

extract_protocol:
ChEC was performed as described by Zentner et al., 2015 with modifications according to VanBelzen et al., 2024. SDC was removed from the cells after pelleting and replaced with BufferA+SDC (at 1X final concentration of each). Cells were washed twice more with BufferA+SDC, then added to tubes containing 5 ul digitonin for a final concentration of 0.1% digitonin. Tubes were incubated at 30°C for 5' before 10 ul 20mM calcium was added. After cleaving for the factor-specific cleavage time at 30°C, cells were briefly pelleted at 3000 rpm for 20", the supernatant was aspirated, then the pellet was resuspended in 100 ul of BufferA (no SDC), 100 ul 2x Stop Buffer, and 8 ul proteinase K (20 ug/ul). gDNA was isolated using phenol-chloroform extraction.
Libraries were made using partial MNase digestion optimized for each fusion protein, tagmentation with Tn5 loaded with  Illumina Nextera XT index adapters, and amplifying with the KAPA library amplification kit

treatment_protocol: Leptomycin B (LMB; Cayman Chemical Company, cat#10004976) was used to inhibit Crm1 by covalently modifying Cys539. LMB-sensitive strains, which have the crm1-T539C mutation, were treated with 185 nM LMB for 30 min at 30°C prior to harvesting cells for ChEC-seq2.

value: MATa his3delta1 met15delta0 ura3delta0 crm1-T539C-GFP:LEU2:crm1deltaN Gcn4-3FLAG-Mnase::KanMX


title: COPD-2, Siglec-1- FSChi AM


title: WT Cortex 2

value: WT


title: DT4-kidney.RNAseq

value: kidney


title: DSE1-heart.RNAseq

value: heart


title: WT Cortex 1


title: Hpc AD NORACE PAM 053

description: Library name: 053


title: Gcn4-Mnase, crm1(T539C), SDC LMB, Replicate 4

description: Library name: B57-TG14


title: COPD-3, Siglec-1+ FSChi AM


title: DT4-lung.RNAseq

value: lung


title: COPD-3, Siglec-1- FSClow AM


title: CES-3, Siglec-1+ FSChi AM

value: CES


title: Gcn4-Mnase, crm1(T539C), SDC, Replicate 2

description: Library name: B57-TG15


title: DT3-lung.RNAseq


title: Hpc AD NORACE PAM 050

description: Library name: 050

value: Hippocampus

value: Iba1+ microglia


title: Gcn4-Mnase, crm1(T539C), SDC LMB, Replicate 1

description: Library name: B57-TG12


title: Gcn4-Mnase, crm1(T539C), SDC LMB, Replicate 3

description: Library name: B57-TG18


title: DT3-liver.RNAseq


title: Hpc AD NORACE PAM 049

description: Library name: 049


title: Crm1-Mnase, crm1(T539C), SDC LMB, Replicate 5

description: Library name: B57-TG10

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1-T539C-MNase:LEU2:crm1deltaN


title: CNS-3, Siglec-1+ FSChi AM

value: alveolar macrophages

value: CNS

value: F


title: CNS-2, Siglec-1+ FSChi AM

value: M

value: Japanese


title: Hpc AD RACE NPAM 058

description: Library name: 058

value: AD RACE


title: CNS-1, Siglec-1+ FSChi AM


title: Hpc AD NORACE PAM 046

description: Library name: 046

value: AD NORACE


title: COPD-3, monocyte

source_name: monocytes obtained from lung tissue

value: monocytes

value: COPD


title: Hpc AD NORACE PAM 052

description: Library name: 052


title: DT4-heart.RNAseq


title: DT2-lung.RNAseq


title: DT3-spleen.RNAseq

value: spleen


title: Hpc AD NORACE PAM 051

description: Library name: 051


title: Hpc AD NORACE PAM 045

description: Library name: 045


title: CES-2, Siglec-1+ FSChi AM


title: CES-1, Siglec-1+ FSChi AM


title: COPD-1, Siglec-1+ FSChi AM


title: Gcn4-Mnase, crm1(T539C), SDC LMB, Replicate 2

description: Library name: B57-TG16

value: MATa his3delta1 met15delta0 ura3delta0 crm1-T539C-GFP:LEU2:crm1deltaN Gcn4-3FLAG-Mnase::KanMX


title: DT3-kidney.RNAseq

value: kidney


title: DT3-heart.RNAseq

value: heart


title: Crm1-Mnase, crm1(T539C), SDC, Replicate 5

description: Library name: B57-TG09


title: Hpc AD NORACE PAM 048

description: Library name: 048


title: Hpc AD NORACE PAM 047

description: Library name: 047


title: Hpc AD NORACE PAM 044

description: Library name: 044


title: Crm1-Mnase, crm1(T539C), SDC, Replicate 3

description: Library name: B57-TG05


title: Crm1-Mnase, crm1(T539C), SDC, Replicate 4

description: Library name: B57-TG07


title: Gcn4-Mnase, crm1(T539C), SDC, Replicate 1

description: Library name: B57-TG11


title: Crm1-Mnase, crm1(T539C), SDC LMB, Replicate 2

description: Library name: B57-TG04


title: DT2-liver.RNAseq

value: liver


title: COPD-1, monocyte


title: Crm1-Mnase, crm1(T539C), SDC LMB, Replicate 3

description: Library name: B57-TG06


title: COPD-2, monocyte


title: Crm1-Mnase, crm1(T539C), SDC LMB, Replicate 4

description: Library name: B57-TG08


title: Hpc AD RACE PAM 041

description: Library name: 041

value: Hippocampus


title: DT2-kidney.RNAseq


title: Hpc AD RACE PAM 043

description: Library name: 043

value: Iba1+ microglia


title: Crm1-Mnase, crm1(T539C), SDC LMB, Replicate 1

description: Library name: B57-TG02

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1-T539C-MNase:LEU2:crm1deltaN


title: CES-3, monocyte

value: CES


title: DT2-spleen.RNAseq


title: DT2-heart.RNAseq


title: Hpc AD RACE PAM 040

description: Library name: 040


title: CNS-2, monocyte

value: CNS


title: spleen, PHZ treated 35 day, N3

city: Omaha

first: Venkatasai Rahul

last: Dogiparthi

state: NE

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

data_processing:
Bcl2fastq for basecalls, ChIPseeker and UROPA for peak annotation
Assembly: hg38
Supplementary files format and content: Bigwig

growth_protocol: Mouse spleen at various times post-PHZ injection were isolated and lineage-depleted, prior to FACS purification if Kit+Ter119lowCD71+ cells.

extract_protocol:
50,000 sorted cells in each sample were resuspended in cell lysis buffer (containing 10% NP-40, 10% Tween-20, and 1% Digitonin).
DNA fragments were purified using the Qiagen MinElute Reaction Cleanup Kit. During library prep, unique adapters were added to transposed samples using NEBNext Ultra II Q5 2× Master Mix (NEB).  PCR cycles for library amplification were determined by qPCR using NEBNext Library Quant Kit (NEB), and after amplification and purification, the quantity and library quality were determined by QuantiFluor ONE dsDNA System and High Sensitivity DNA ScreenTape Analysis, respectively.

treatment_protocol: Subcutaneous injection of PHZ at 100 mg/kg

value: Linneg, CD71pos, Ter119neg

value: erythroid

value: wildtype

value: untreated

value: 35 day


title: DT1-kidney.RNAseq


title: CES-1, monocyte

value: monocytes

value: M

value: Japanese


title: Crm1-Mnase, crm1(T539C), SDC, Replicate 2

description: Library name: B57-TG03


title: Hpc AD RACE PAM 042

description: Library name: 042

value: AD RACE


title: DT1-lung.RNAseq

value: lung


title: CES-2, monocyte

value: F


title: DT1-spleen.RNAseq

value: spleen


title: CNS-1, monocyte


title: Hpc AD RACE PAM 037

description: Library name: 037

value: Hippocampus


title: CNS-3, monocyte


title: spleen, PHZ treated 35 day, N1

value: Phenylhydrazine


title: gastric cancer [G71N]

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

description: GC.PNI.rds

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: Adjacent normal gastric mucosa

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1 the Chromium Next GEM Single Cell 5′ Kit v2 for Dual Index (10x Genomics). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct the 3’ and 5’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: Adjacent normal gastric mucosa

tag: pni

tag: organ

value: stomach

tag: Sex

value: Male

tag: chemotherapy


title: DT1-liver.RNAseq

tag: tissue

value: liver


title: spleen, PHZ treated 21 day, N2

tag: cell line

value: Linneg, CD71pos, Ter119neg

tag: cell type

value: erythroid

value: 21 day


title: Hpc AD RACE PAM 039

description: Library name: 039

value: Iba1+ microglia

tag: genotype


title: Crm1-Mnase, crm1(T539C), SDC, Replicate 1

description: Library name: B57-TG01

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 crm1-T539C-MNase:LEU2:crm1deltaN


title: Hpc AD RACE PAM 038

description: Library name: 038


title: gastric cancer [G69N]

description: GC.PNI.rds

tag: age

value: Female


title: DT1-heart.RNAseq

value: heart


title: gastric cancer [G75N]

description: GC.PNI.rds


title: gastric cancer [G74N]

description: GC.PNI.rds


title: Hpc AD RACE PAM 036

description: Library name: 036

value: AD RACE


title: spleen, PHZ treated 35 day, N2

value: wildtype

tag: treatment

tag: time

value: 35 day


title: spleen, PHZ treated 21 day, N1

value: spleen

value: untreated


title: BS4-kidney.RNAseq

value: kidney


title: BS4-lung.RNAseq

value: lung


title: Hpc AD RACE PAM 032

description: Library name: 032

value: Hippocampus


title: gastric cancer [G66N]

description: GC.PNI.rds

value: Adjacent normal gastric mucosa

value: stomach

value: Male


title: BS4-spleen.RNAseq


title: spleen, PHZ treated 21 day, N3

value: Linneg, CD71pos, Ter119neg

value: erythroid


title: Hpc AD RACE PAM 035

description: Library name: 035

value: Iba1+ microglia


title: Hpc AD RACE PAM 034

description: Library name: 034


title: gastric cancer [G67N]

description: GC.PNI.rds


title: BS4-liver.RNAseq

value: liver


title: spleen, PHZ treated 14 day, N2

value: Phenylhydrazine

value: 14 day


title: spleen, PHZ treated 14 day, N3


title: BS3-spleen.RNAseq


title: gastric cancer [G80T]

description: GC.PNI.rds

source_name: gastric cancer

value: gastric cancer


title: Hpc AD RACE PAM 031

description: Library name: 031

value: AD RACE


title: spleen, PHZ treated 7 day, N3

value: wildtype

value: 7 day


title: gastric cancer [G47N]

description: GC.PNI.rds


title: BS3-liver.RNAseq


title: BS3-lung.RNAseq


title: spleen, PHZ treated 14 day, N1

value: spleen

value: untreated


title: gastric cancer [G77T]

description: GC.PNI.rds


title: BS3-kidney.RNAseq

value: kidney


title: BS3-heart.RNAseq

value: heart


title: spleen, PHZ treated 7 day, N1


title: BS4-heart.RNAseq


title: Hpc AD RACE PAM 027

description: Library name: 027

value: Hippocampus


title: gastric cancer [G79T]

description: GC.PNI.rds

value: stomach


title: Hpc AD RACE PAM 029

description: Library name: 029


title: Hpc AD RACE PAM 033

description: Library name: 033


title: spleen, PHZ treated 3 day, N3

value: 3 day


title: Hpc AD RACE PAM 028

description: Library name: 028


title: BS2-spleen.RNAseq


title: spleen, PHZ treated 7 day, N2

value: Linneg, CD71pos, Ter119neg


title: Hpc AD RACE PAM 030

description: Library name: 030


title: spleen, PHZ treated 3 day, N2

value: erythroid


title: BS2-lung.RNAseq

value: lung


title: Hpc AD RACE PAM 026

description: Library name: 026

value: Iba1+ microglia


title: gastric cancer [G63T]

description: GC.PNI.rds

value: Male


title: Hpc AD RACE PAM 025

description: Library name: 025


title: gastric cancer [G56T]

description: GC.PNI.rds


title: spleen, PHZ treated 1 day, N3

value: 1 day


title: Hpc AD RACE PAM 023

description: Library name: 023


title: BS2-liver.RNAseq

value: liver


title: spleen, PHZ treated 1 day, N2

value: Phenylhydrazine


title: Hpc AD RACE PAM 024

description: Library name: 024

value: AD RACE


title: gastric cancer [G73T]

description: GC.PNI.rds

value: gastric cancer


title: ΔsrrAB-1

city: Dali

first: chunjing

last: Zhao

state: Yunnan

address: wang hua street 22

department: Basic Medicine

institute: Dali University

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome using Bowtie2. The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.Differential expression analysis for mRNA/lncRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis.We performed a Gene Ontology (GO) analysis for biological processes, cellular components and molecular function and a KEGG pathway analysis (Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg) via enrich R package.
Assembly: NZ_CP020463.1
Supplementary files format and content: The count value and FPKM of each sample are shown in table form

organism: Staphylococcus epidermidis RP62A

source_name: bacteria

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing. One micrograms of RNA were used as input material for the RNA sample preparations
RNA-seq strand-specific libraries were constructed using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit (Vazyme, China) according to the manufacturer’s instructions. Briefly, RNA was purified by magnetic beads after removal of rRNA. Then RNA was fragmented into small pieces using divalent cations for 8 min at 94℃. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. These cDNA fragments then go through the end repair process, addition of a single ‘A’ base, and ligation of the adapters. The products were purified and enriched by PCR to create the final cDNA library. Purified libraries were quantified and validated by Qubit® 3.0 Fluorometer and Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot after the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA).

value: bacteria

value: antibiotic


title: Hpc AD RACE PAM 022

description: Library name: 022


title: spleen, PHZ treated 1 day, N1

value: spleen

value: wildtype


title: Hpc AD RACE PAM 021

description: Library name: 021

value: Hippocampus


title: BS1-spleen.RNAseq


title: BS2-heart.RNAseq

value: heart


title: spleen, untreated, N3

value: untreated


title: Hpc AD RACE PAM 020

description: Library name: 020


title: BS1-lung.RNAseq


title: Nup1-AID, SDC 16h, Replicate 5

description: Library name: B56-TG23

data_processing:
single-end sequencing reads were processed using the slamdunk all program from SLAM-DUNK (v0.4.3) with default parameters and reference genome SacCer3 v64.4.1 and a BED-file containing coordinates for 3’ UTRs. This bed file was generated using standard genomic coordinates with a 325bp 3’UTR.
For differential gene expression analysis, we used DESeq2 (v1.46.0) with reads that contain more than one T>C conversions (nascent RNA reads). Size factors were calculated using respective total RNA reads for normalization.
Assembly: SacCer3 v64.4.1
Supplementary files format and content: tab-delimited text files containing raw read counts (total read counts and T>C conversion read counts) at 3' UTR of genes

extract_protocol:
Cells were spun down and snap frozen. Total RNA was extracted using Phenol:Chloroform:IAA (25:24:1) extraction. 5 ug total RNA was treated with 10 mM iodoacetamide (Sigma-Aldrich, cat# I1149), for 15 min at 50˚C. RNA was isolated using phenol-chloroform extraction.
Alkylated RNA was used for 3' mRNA-seq libraries prepared using the QuantSeq 3'mRNA-seq Library Prep Kit for Illumina (FWD; Lexogen) following manufacturer's recommendations

treatment_protocol: Crm1 was inhibited by treating the cultures with 185 nM Leptomycin B (LMB; Cayman Chemical Company, cat#10004976) in ethanol for 30 min at 30˚C. Nup1 or Nup2 was degraded by treating cultures with 500 µM Indole-3-Acetic Acid (3-IAA; Gold Biotechnology, cat#I-110-100) in ethanol for 16 hours at 30˚C. Following treatment with 3-IAA or LMB, cultures were treated with 0.2 mM 4- thiouracil (4sU; Fisher Scientific, cat#AAH6191903), for 6 min at 30˚C.

value: ethanol for 16h

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 URA3:Tir1-3XMyc NUP1:AID-Myc-HygR


title: Nup1-AID, SDC 16h 3-IAA, Replicate 4

description: Library name: B56-TG24

value: 500 uM 3-IAA for 16h


title: spleen, untreated, N2

value: Linneg, CD71pos, Ter119neg

value: erythroid


title: spleen, PHZ treated 3 day, N1

value: 3 day


title: gastric cancer [G68T]

description: GC.PNI.rds

value: stomach

value: Female


title: Nup1-AID, SDC 16h 3-IAA, Replicate 3

description: Library name: B56-TG22


title: Hpc AD RACE PAM 019

description: Library name: 019

value: Iba1+ microglia

value: AD RACE


title: spleen, untreated, N1


title: BS1-kidney.RNAseq

value: kidney


title: Nup1-AID, SDC 16h, Replicate 4

description: Library name: B56-TG21


title: BS1-heart.RNAseq


title: BS2-kidney.RNAseq


title: LTP15 gene silenced strain, Biological replicate 3

city: Tokyo

first: Sota

middle: ミズカミソウタ

last: Mizukami

institute: The university of Tokyo

description: Library name: SAMPLE 6

data_processing:
Illumina NovaSeq 6000
Sequence reads were trimmed, mapped, and assembled to the reference genome assembly (JCVI-ESG2-1.0).
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: JCVI-ESG2-1.0
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Entamoeba histolytica

source_name: strain

growth_protocol: Trophozoites of the E. histolytica clonal strain HM1: IMSS  G3 strain were maintained axenically in Diamond’s BI-S-33 medium at 35.5°C

extract_protocol:
Total RNA was purified using TRIZOL reagent (Thermo Fisher, Waltham, MA, USA) according to manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The trophozoites of G3 strain were transformed with either empty vector or silencing plasmid by liposome-mediated transfection. Transformants were initially selected in the presence of 1 μg/ml geneticin, and the geneticin concentrations were gradually increased during next two weeks prior to subjecting the transformants to analyses.

value: strain

value: trophozoite

value: EhLTP15 gene silenced


title: Hpc No AD NORACE Surveillant 017

description: Library name: 017

value: Hippocampus

value: No AD NORACE