title: sows liver (low bile acid group) IP

value: female

value: Anti-H4K12la (PTM1411)


title: ssRNAseq_B_hdp2-1_ARE//AGe_sMf_Rep1

status: Public on Sep 21 2023

type: SRA

city: Kearneysville

first: Zongrang

last: Liu

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

country: USA

institute: USDA-ARS

library_source: transcriptomic

data_processing:
The obtained reads were trimmed and aligned to the reference Arabidopsis genome (TAIR10) using using HISAT2 with default parameters.
Those reads mapped to the sense and antisense starnds of AGe, AGp/M2 regions within a 17.3-kb genomic region were retrieved and counted using htseq-count (version 0.13.5; Anders et al., 2015) for calculation of the value of Normalized Read Per Million mapped reads (NRPM) in each region
Supplementary files format and content: xls file includes the value of NRPM in the AGe and AGp/M2 regions  within the 17.3-kb genomic region for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Young flower

growth_protocol: Arabidopsis plants were grown under a 16/8h light:dark photoperiod at 20-22˚C for approximately 4-5 weeks prior to transformation.

extract_protocol:
Total RNA was extracted from young flowers pooled from five to ten lines with the same phenotype for each replicate using Tri-Reagent (Sigma, MO) followed by two rounds of phenol–chloroform extraction (50:50).
Approximately one µg of total RNA was used for construction of strand-specific RNA-seq (ssRNA-seq) library using the Illumina TruSeq® Stranded Total RNA Library Preparation Kit with Ribo-Zero™ Plant kit and different barcode Index primers. ssRNA-seq libraries for the Group A samples were made using TruSeq RNA CD barcode Index primers, while the Group B samples  using TruSeq Unique Dual Index (UDI) primers.  The total RNA was first treated with Turbo DNA-free (Fisher Scientific) to remove residual genomic DNA followed by Ribosomal RNA depletion, first- and second-strand cDNA synthesis, 3’ end adenylation, adapter ligation, and DNA fragment enrichment (12 cycles) according to the TruSeq stranded total RNA protocol provided. RNA fragmentation (3 minutes) was performed.  Libraries were pooled and sequenced using HiSeq X-Ten platform.

treatment_protocol: Arabidopisis plants were transformed with various transgene cassetts for evaluation of silencing efficiency and mutant flower frequncy.

tag: tissue

value: Young flower

tag: flower phenotype

value: sMf

tag: genotype

tag: treatment

value: Floral structure change


title: Patient_P1396_Pre_Treatment_ATAC-seq

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

country: Canada

institute: University of Calgary

library_source: genomic

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters using cellranger-atac count.
Assembly: Pre-generated human reference GRCh38
Supplementary files format and content: Filtered peak barcode matrix in hdf5 format and a BED-like tabular file where each line represents a unique ATAC-seq fragment captured by the assay from CellRanger-atac count.

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary CD138+ MM cells

growth_protocol: Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions.  CD138+ fractions were subsequently analyzed by flow cytometry in order to confirm the sample’s purity. HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin. All of the listed cells above were cultured at 37°C and 5% CO2.

extract_protocol: For single-cell library preparation for ATAC-seq the desired number of nuclei were targeted and processed according to 10X Genomics Reagent Kits User Guide (CG000168). The Nuclei Isolation was performed ad indicated in the nuclei Isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration primary MM cells were washed, lysed and re-suspended in appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were then immediately used to generate scATAC-seq libraries. ScATAC-seq libraries were prepared according to 10X Genomics Reagent Kits User Guide. Briefly, the desired number of nuclei were combined with ATAC Buffer and master mix to form transposed Nuclei. Single-cell GEMs were then generated, amplified and subjected to bead clean-ups. Indexed sequencing libraries were constructed using Chromium i7 Sample Index and the barcode sequencing libraries subjected to a final bead clean-up prior to quantification.

tag: patient number

tag: time point

value: Pre

tag: cell type

value: Primary CD138+ MM cells

tag: library preparation

value: 10X Genomics Single Cell ATACseq v1 Chemistry


title: MUC21309 CM-OXT-101-1-J

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic single cell

data_processing:
Technical replicates of the samples were merged, and reads were then mapped to rRNA (from Ensembl, GRCm38 release 102) using Bowtie2 (version 2.3.4.3114) and subsequently, unmapped reads were mapped to the mm10 genome (from Ensembl, GRCm38 release 102) using STAR (2.7.0115). Count matrices were generated by counting reads corresponding to gene exons using featureCounts (version 1.6.3116). Counts were transformed to FPKM and TPM using the actual feature length. The single-nuclei transcriptomics analysis of raw count matrix loaded into python and stored as AnnData object was performed using Scanpy version 1.7.1. Filtering of the cells was based on a minimum count number of 250. Filtering was applied to the matrix of 1536 single nuclei and 55579 genes. Nuclei that had >1000 and <4500 detected genes were kept. Genes detected in fewer than 25 cells and with read count below 250 were filtered out. Hence, only the nuclei having less than 4500 genes detected and a library size between 10000 and 200000 reads were kept. Applying this filtering strategy, the final matrix comprises 1202 single nuclei and 13867 genes. Batch effect corrections were performed employing combat using plates as a covariate.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
The single-nucleus RNA-seq2 methodology was used to capture a high number of transcripts from frozen tissues. the reaction volumes were miniaturized with the aid of the Mosquito HV robot. Per well, 2190 nL of Lysis Buffer 2 (LB2) were dispensed. The final volume of the mixture of Lysis Buffer (LB1 and LB2) was 3.125 μL, containing NP40 2%, Triton-X100 1%, 1/300,000 diluted ERCC RNA spike-in, 3′ SMART-seq CDS Primer II A and RNAse-free water. ERCC spike-ins (Thermo Fischer Scientific, Ref. 4456740; Lot no. 00892098) were diluted 1 in 10, with RNAse-free water with 0.4 U/μL Recombinant RNase Inhibitor (Takara Clontech, Ref. 2313A) and a fresh dilution of 1 in 300,000 was prepared before the first strand synthesis. Reverse transcription and Pre-PCR amplification steps were followed as described by the manufacturer with four-times reduced volumes for all steps.
Sequencing libraries were prepared using the Illumina Nextera XT DNA Sample Preparation kit (Illumina, Ref. FC-131-1096) and the combination of 384 Combinatorial Dual Indexes (Illumina- Set A to D, Ref. FC-131-2001 to FC-131-2004). In brief, 500 nL of the undiluted cDNA were transferred to a new 384 well-plate containing 1500 nL of Tagmentation Mix (TD and ATM reagents). Accordingly, all Nextera XT reagents (NT, NPM and i5/i7 indexes) were added stepwise to a final library volume of 5 μL per well. The final PCR amplification was performed through 12 cycles. Once the libraries were prepared, 500 nL from each well were pooled together into a tube (total volume of ~192 μL) to perform a final AMPure XP bead (Beckman Coulter, Ref. A63882) clean-up step. For our single nuclei libraries, two consecutive clean-ups with a ratio of sample to bead 0,9X led to library sizes between 200 and 1000 bp. Each plate, counting with a total of 384 libraries, was pooled together into one final library. A total of 4 final libraries were sequenced using an Illumina NovaSeq 6000 NGS sequencer in an SP XP flowcell, in a paired-end 150 bases length.

value: Oxytocin neurons

value: Brain

tag: strain

value: C57BL/6JRj -OXT-sun1-sfGFP

tag: age

value: 6 months

tag: Sex

value: Male

tag: treatment/diet

value: HFHS diet


title: Patient_P1723_Pre_Treatment_scRNA-seq

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

molecule: polyA RNA

extract_protocol: Single-cell library preparation for RNA-sequencing primary MM cells were processed according to 10X Genomics reagent Kits User Guide (CG00052 v2 Chemistry). Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) using 10X GemCode Technology. Primers containing (i) an Illumina R1 sequence, (ii) a 16 bp 10x barcode, (iii) a 10 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were incubated with partitioned cells resulting in barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents/primers, then cDNA was amplified by PCR. Enzymatic Fragmentation and Size Selection was used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation, whereas P5, P7, a sample index (i7), and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR.

value: 10X Genomics Single Cell RNAseq v2 Chemistry


title: MUC21310 CM-OXT-101-1-K


title: Patient_P1809_Post_Treatment_ATAC-seq

value: Post


title: ssRNAseq_B_hdp2-1_ARE//AGe_rMf_Rep2

value: rMf


title: MUC21306 CM-OXT-101-1-G

value: SC diet


title: MUC21308 CM-OXT-101-1-I


title: MUC21307 CM-OXT-101-1-H


title: ssRNAseq_B_hdp2-1_ARE//AGe_Wt flower_Rep3

value: Wt


title: ssRNAseq_B_hdp2-1_ARE//AGe_rMf_Rep1

value: Young flower


title: Patient_P1680_Pre_Treatment_ATAC-seq


title: Patient_P1751_Pre_Treatment_ATAC-seq


title: MUC21305 CM-OXT-101-1-F


title: MUC21304 CM-OXT-101-1-E


title: ssRNAseq_B_hdp2-1_ARE//AGe_sMf_Rep3

value: sMf


title: ssRNAseq_B_hdp2-1_ARE//AGe_Wt flower_Rep2

value: Floral structure change


title: Patient_P1752_Pre_Treatment_ATAC-seq

value: Pre


title: ssRNAseq_B_hdp2-1_ARE//AGe_Wt flower_Rep1


title: Patient_P1643_Pre_Treatment_ATAC-seq

value: Primary CD138+ MM cells


title: ssRNAseq_B_hdp2-1_Wt flower_Rep3


title: Patient_P1345_Post_Treatment_ATAC-seq

value: 10X Genomics Single Cell ATACseq v1 Chemistry


title: ssRNAseq_B_hdp2-1_Wt flower_Rep2


title: MUC21303 CM-OXT-101-1-D

value: Oxytocin neurons


title: ssRNAseq_B_hdp2-1_ARE//AGe_rMf_Rep3


title: MUC21301 CM-OXT-101-1-B

value: Brain


title: MUC21302 CM-OXT-101-1-C

value: C57BL/6JRj -OXT-sun1-sfGFP


title: Patient_P1675_Post_Treatment_ATAC-seq


title: Patient_P1299_Pre_Treatment_ATAC-seq


title: MUC21300 CM-OXT-101-1-A

value: 6 months


title: ssRNAseq_B_hdp1-1_ARE//AGe/sMf_Rep3


title: Patient_P1608_Pre_Treatment_ATAC-seq


title: ssRNAseq_B_hdp2-1_Wt flower_Rep1


title: Patient_P1388_Pre_Treatment_ATAC-seq


title: ssRNAseq_B_hdp1-1_ARE//AGe/sMf_Rep2


title: B6_F1_GS_ICSI_M1_21

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

description: Germline stem cells of ICSI-derived mice.

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using Bismark (v0.20.0) after trimming adaptor sequences and low-quality bases by Trim galore v0.5.0.
CT conversion in promoter CpG regions were analyzed by methylKit v1.16.0.
Assembly: mm10
Supplementary files format and content: text file. methylBase_count_Matrix.

source_name: Germline stem cell

growth_protocol: Germline stem cells were maintained in IMDM supplemented with 10 ng/ml human FGF2, 15 ng/ml rat GDNF, 25 mg/ml insulin, 100 mg/ml transferrin, 200 mg/ml pyruvic acid, 60 mM putrecine, 30 nM Sodium selenite, 6 mg/ml D-(+)-glucose, 0.1 % DL-lactic acid, 5 mg/ml AlubMAX, 2 mM L-glutamine, 5x10-5 M 2-mercaptoethanol, MEM vitamin solution, non-essential amino acids, 10-4 M ascorbic acid, 10 mg/ml d-biotin, 30 ng/ml b-estradiol, 60 ng/ml progesterone, 1 mg/ml Fetuin, 1 % CD lipid concentrate, 0.2% cholesterol solution, and 5 % knockout serum replacement.

extract_protocol:
Genomic DNA was harvested using DNeasy Blood and Tissue Kit (Qiagen).
Genomic DNA libraries for RRBS were prepared using Zymo-Seq RRBS Library Kit (Zymo Research) following manufacturer's protocols.

value: Germline stem cell

value: WT

value: ICSI


title: ssRNAseq_B_hdp1-1_ARE//AGe/sMf_Rep1


title: Patient_P1723_Pre_Treatment_ATAC-seq


title: B6_F1_GS_Control_C44

description: Germline stem cells of natural mating derived mice.

value: no


title: ssRNAseq_B_hdp1-1_ARE//AGe/rMf_Rep3

value: rMf


title: Day13PC_C (RNA-seq)

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p13 (Gencode release 35) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Assembly: GRCh38.p13 (Gencode release 35)
Supplementary files format and content: tab-delimited text file with DESeq2 VST log2 values for each Sample

source_name: Peripheral blood

extract_protocol:
RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).
Sequencing libraries were generated with a TruSeq stranded total RNA human/mouse/rat kit (Illumina).

treatment_protocol: For day 6 to day 13, at day 6, cells were harvested and seeded at 1 × 10^6/ml in media supplemented with IL-6 (10 ng/ml), IL-21 (10 ng/ml), GSI (100 nM), and multimeric APRIL (100 ng/ml).

value: Peripheral blood

tag: donor

value: C

value: Plasmacell

tag: time


title: Day10PC_C (RNA-seq)


title: Microglia, Vehicle, biol rep 4

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
The fastq sequence files for all RNA-seq samples were filtered for read quality (keeping reads where at least 70% of the cycles had Phred scores ≥ 23), and ribosomal RNA contamination. The remaining reads were aligned to the mouse reference genome (GRCm38) using the GSNAP alignment tool.
These steps, and the downstream processing of the resulting alignments to obtain read counts were implemented in the Bioconductor package HTSeqGenie.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Microglia

growth_protocol: Microglia were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 10 ng/ml recombinant murine CSF-1 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Total RNA was quantified with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies).
RNA-seq libraries were prepared using the Truseq Stranded mRNA Kit (Illumina). Libraries were quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: Microglia were treated with 5 µg/ml LPS (Invitrogen) or vehicle for 24 hours.

value: Microglia

value: Vehicle


title: ssRNAseq_B_hdp1-1_ARE//AGe/Wt flower_Rep3

value: Young flower

value: Wt

value: Floral structure change


title: Microglia, Vehicle, biol rep 3


title: ssRNAseq_B_hdp1-1_ARE//AGe/Wt flower_Rep2


title: B6_F1_GS_Control_C45


title: Microglia, Vehicle, biol rep 2


title: B6_F1_GS_ICSI_M1_20


title: Day6PB_B (RNA-seq)

value: B

value: Plasmablast


title: SITTH6, sample_8

city: Cambridge

first: Stefan

middle: J

last: Marciniak

address: Hills Road

department: CIMR

institute: University of Cambridge

description:
all_cells_metadata.csv
all_counts.txt
all_cells.RDS
stromal_metadata.csv
stromal_counts.txt
stromal_cells.RDS

data_processing:
Raw reads were trimmed with cutadapt (v1.17) for read2, 5’ anchored template switch oligo contamination and read2, 3’ polyA contamination. Trimmed, paired reads with less than 30bp of remaining read2 were discarded.
Trimmed reads were then aligned with the STARsolo implementation of STAR (v2.7.6a) to human genome GRCh38.p13 with Gencode annotation release 38. Cell barcodes from the “filtered” STARsolo outputs were aggregated in R. Cells with more than 20% of transcripts from mitochondrial origin were discarded.
Downstream cell-type annotation analysis was conducted using the package Seurat (v4.0.2). The Seurat package was applied in an iterative process of dimension reduction, graph-embedding, clustering, cell type annotation and subsetting of similar cell types was performed recursively. Significant principal components were determined using JackStraw analysis and visualisation of heatmaps focusing on PCs 1 to 20. PCs 1 to 10 were used for graph-based clustering (at res=0.8) for all samples. These groups were projected onto UMAP analysis run using previously computed principal components 1 to 10. The cluster specific marker genes were identified by running the FindAllMarkers function in Seurat package to the normalised gene expression data. Cell type identities were validated based on expert curation of the distinctiveness and stability of a phenotype across sample replicates; labels were assigned based on concordance with the literature.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated text files with raw counts
Supplementary files format and content: Comma-separated CSV files with detailed metadata
Supplementary files format and content: RDS (R) files with exported seurat objects

source_name: Parietal pleura

growth_protocol: Pleural samples were immersed in cold RPMI supplemented with antibiotics and typically processed within 1 hour.

extract_protocol:
Pleura samples were washed three times in PBS, minced with scalpels and digested in RPMI supplemented with collagenase I (5 mg/ml, Life Technologies) and DNase I (100 µg/ml, Sigma) for 2.5 hrs at 37°C. Digested tissue was filtered through a 100μm cell strainer, washed with PBS and centrifuged at 800g. Cell pellets were resuspended first in red blood cell lysis buffer then in RPMI (2% FBS). Dead cells and cellular debris were removed by sorting 7-AAD negative population with BD FACSMelodyTM Cell Sorter (BD Biosciences). Resulting cells were submitted to library preparation.
Cells were submitted to 10x Genomics and immediately loaded on 10x3’ chip. scRNA-seq libraries were generated using the 10x Chromium platform 3′ v3.1 kit. Library quality was assessed following cDNA synthesis and after completion of the 3’ Gene Expression Libraries on the Agilent TapeStation system employing a DNA High Sensitivity D5000 and D1000 chips, respectively(all Agilent). Single cell libraries were sequenced on Illumina NovaSeq 6000 instrument using read 1: 28bp and read 2: 90bp length sequencing and aiming at 20,000 reads/cell.

value: Parietal pleura

value: male


title: ssRNAseq_B_hdp1-1_ARE//AGe/Wt flower_Rep1


title: Day6PB_A (RNA-seq)

value: A


title: Microglia, Vehicle, biol rep 1

value: WT


title: SITTH5, sample_7


title: Microglia, LPS, biol rep 4

value: LPS


title: ssRNAseq_B_hdp1-1_Wt flower_Rep3


title: Day3PB_C (RNA-seq)

treatment_protocol: For day 3 to day 6, at day 3, cells were detached from the CD40L L cell layer and reseeded at 1 × 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).


title: Day13PC_A (RNA-seq)


title: SITTH10, sample_6


title: ssRNAseq_B_hdp1-1_Wt flower_Rep2


title: ssRNAseq_B_hdp1-1_Wt flower_Rep1


title: ssRNAseq_B_hdp1-1_ARE//AGe/rMf_Rep2


title: Microglia, LPS, biol rep 3


title: Day3PB_B (RNA-seq)


title: Microglia, LPS, biol rep 2


title: SITTG12, sample_5


title: ssRNAseq_B_suvh1-2_ARE//AGe/sMf_Rep3

value: sMf


title: SITTF3, sample_4


title: Day3PB_A (RNA-seq)


title: Day6PB_C (RNA-seq)


title: Microglia, LPS, biol rep 1


title: ssRNAseq_B_suvh1-2_ARE//AGe/sMf_Rep2


title: ssRNAseq_B_suvh1-2_ARE//AGe/sMf_Rep1


title: SITTD11, sample_2

value: female


title: Day1BC_A (RNA-seq)

treatment_protocol: For day 0 to day 3, B cells were cultured in 24-well plates at 2.5 × 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), and F(ab`)2 goat anti-human IgM and IgG (2 mg/ml) on gamma-irradiated CD40L-expressing L cells (6.25 × 10^4/well).

value: Peripheral blood

value: B-cell


title: Day0-12h-BC_B (RNA-seq)


title: beta-glucan supplemented diet, LPS-stimulated BMDM, WD_LPS_2

city: Dublin

first: Aaron

last: Walsh

address: Trinity Translational Medicine Institute

department: Department of Clinical Medicine

country: Ireland

institute: Trinity College Dublin

data_processing:
fastp was used to process reads
STAR was used to align reads to the reference genome
featureCounts was used to count the number of reads aligning to each gene
DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: bone marrow-derived macrophage (BMDM)

extract_protocol:
RNA was isolated from BMDM using the PureLink RNA Mini Kit (Invitrogen)
Sequencing libraries were generated using NEBNext Ultra TM RNA Library Prep Kit for Illumina

value: bone marrow-derived macrophage (BMDM)

tag: animal id

value: 8-12 weeks

tag: diet

value: beta-glucan

value: LPS-stimulated


title: SITTE6, sample_3


title: SITTC3, sample_1


title: ssRNAseq_B_suvh1-2_ARE//AGe/Wt flower_Rep3

value: Young flower

value: Wt


title: beta-glucan supplemented diet, unstimulated BMDM, WD_Ctl_2

value: unstimulated


title: control diet, LPS-stimulated BMDM, CD_LPS_2

value: control


title: Day0-12h-BC_A (RNA-seq)


title: ssRNAseq_B_suvh1-2_ARE//AGe/Wt flower_Rep2

value: Floral structure change


title: control diet, unstimulated BMDM, CD_Ctl_2

value: male


title: ssRNAseq_B_suvh1-2_Wt flower_Rep3


title: Day0-6h-BC_B (RNA-seq)

value: B


title: RUL_Post_2

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0
R packages, Seurat and Harmony are mainly used for normalization, batch correction and data integration.
PCA and Umap are used for dimension reduction and clustering and data visualization
Assembly: hg38

source_name: Endobronchial biopsies

growth_protocol: For scRNAseq, biopsies collceted at baseline and 2 months post iloprsot were proteolytically digested to prepare single cell suspensions and used in the Chromium Single cell 3’ solution capture system from the 10x Genomics platform.

extract_protocol: none provided

value: Airway epithelial and non-epithelial cells

value: Endobronchial biopsies


title: RUL_Post_1

description: 10x Genomics


title: RB6_Post_1

description: 10x Genomics


title: beta-glucan supplemented diet, unstimulated BMDM, WD_Ctl_1


title: Day0-2h30-BC_A (RNA-seq)

value: A


title: beta-glucan supplemented diet, LPS-stimulated BMDM, WD_LPS_1


title: RB6_Post_2

description: 10x Genomics


title: ssRNAseq_B_suvh1-2_Wt flower_Rep2


title: ssRNAseq_B_suvh1-2_Wt flower_Rep1


title: control diet, LPS-stimulated BMDM, CD_LPS_1


title: ssRNAseq_B_Col_Wt flower_Rep3

value: Col


title: Day0-2h30-BC_B (RNA-seq)

value: Peripheral blood


title: LUL_Post_2

description: 10x Genomics


title: Day0-30min-BC_B (RNA-seq)

value: B-cell


title: ssRNAseq_B_Col_Wt flower_Rep2


title: control diet, unstimulated BMDM, CD_Ctl_1

value: bone marrow-derived macrophage (BMDM)


title: LUL_Post_1

description: 10x Genomics


title: Day0BC_C (RNA-seq)

value: C


title: ssRNAseq_B_Col_Wt flower_Rep1


title: RUL_Pre_2

description: 10x Genomics


title: total RNA seq, CM Snord133 KO rep2

city: Tianjin

first: Minjie

last: Zhang

address: No22.Qixiangtai Rd.,Heping Dist

department: Department of Bioinformatics

country: China

institute: Tianjin Medical University

data_processing:
Sequencing data were preprocessed to remove adapters from the 5'end and 3’end using Trimmomatic software (v0.36). PCR duplicates are removed using readCollapse script from the icSHAPE pipeline.
Reads were mapped to the hg38 and mm10 genome using STAR program (v2.7.9).
Bedtools v2.25.0 was used to annotate alignments. Read count extraction and RPM normalization were performed.
P-site offsets of ribosome profiling data was determined using the psite script from plastid package. The parameters used are as follows: psite merlin_orfs_rois.txt outputprefix --min_length 25 --max_length 35 --require_upstream --count_files input.bam --min_counts 100 --figformat pdf --dpi 300.
For nuclear-encoded mRNAs in RNA-seq and ribo-seq from WT and D97 and D133 single KO HEK293 cells, ratios of expression levels were calculated for the top 10% (most up-regulated) and bottom 10% (most down-regulated) mRNAs and weighted by expression levels.
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text file includes RPM values of each sample, and the code usage ratio was calculated for RNA-seq and ribo-seq data.

growth_protocol: HEK293 and HEK293-SNORD97/D133-KO cells were maintained in Dulbecco’s modified Eagle’s medium (Gibco) + 10% FBS (Gibco) + 1% Pen Strep (Gibco) in 37°C incubator with 5% CO2. TC1 mESCs were grown under feeder-free 2i+LIF medium, containing DMEM-High Glucose (CORNING) supplemented with 15% FBS (Gibco), 1% Pen Strep (Gibco), 10 mM HEPES (Gibco), 1 mM sodium-pyruvate (Sigma), 55 µM 2-Mercaptoethanol (Gibco), 1x GlutaMax (Gibco), 1x non-essential amino acids (Gibco), 1000 U/mL leukemia inhibitory factor (Sigma-Aldrich), 3 µM CHIR99021 (Stem Cell Technologies) and 2 µM PD0325901 (Stem Cell Technologies).

extract_protocol:
For RNAseq, total RNAs were isolated using TRIzol reagent following the manufacturer’s instructions. Ribosomal RNA was depleted by using rRNA Depletion Kit v2. Small RNA (15-50nt) was excised after running 12% (wt/vol) urea polyacrylamide gel and purified using ZR small-RNA PAGE Recovery Kit.
For Riboseq, cells were lysed on wet ice for 10 minutes. Lysate RNA was digested with RNase A and RNase T1. Following nuclease digestion, monosomes were purified using ultracentrifugation at 55,000 rpm 4°C for 5 hours. Then RNAs were extracted using the TRIzol method and 15% polyacrylamide TBE-Urea gel was used to isolate ribosome-protected fragments (RPFs) (26-34 nt).
The fragmented RNAs were end-repaired by T4PNK at 37 °C for 30 minutes. Adapter (/5rApp/AGATCGGAAGAGCGGTTCAG/3Biotin/) was ligated to end-repaired RNA fragments using high concentration T4 RNA ligase 1. Free adapters were removed by RecJf and 5’ deadenylase. RNA was purified with Zymo RNA clean and Concentrator-5 Kit. An RT-step and PCR amplification were coupled with barcoding.

treatment_protocol:
Oxidative stress treatment was performed by adding 250 μM sodium arsenite (Sigma) for 4 hours.
Cardiomyocyte differentiation was performed in DMEM-High Glucose (CORNING) supplemented with 15% FBS (Gibco), 1% Pen Strep (Gibco), 1x GlutaMax (Gibco), and 1 mM Ascorbic Acid (Sigma-Aldrich, A4544).

tag: cell line

value: mouse embryonic stem cell

value: Snord133 knockout

value: cardiomyocyte differentiation

tag: fraction

value: total RNA


title: total RNA seq, CM Snord133 KO rep3


title: RUL_Pre_1

description: 10x Genomics

tag: tissue


title: ssRNAseq_A_Col_ARE//AGe_Wt flower_Rep3

value: Young flower

tag: flower phenotype

value: Wt

tag: genotype


title: total RNA seq, CM Snord133 KO rep1

tag: treatment


title: Day0BC_B (RNA-seq)


title: ssRNAseq_A_Col_ARE//AGe_Wt flower_Rep2

value: Floral structure change


title: Day0-6h-BC_A (RNA-seq)


title: RB6_Pre

description: 10x Genomics


title: Day0BC_A (RNA-seq)


title: ssRNAseq_A_Col_ARE//AGe_Wt flower_Rep1


title: total RNA seq, CM WT rep3

value: WT


title: LUL_Pre_2

description: 10x Genomics


title: total RNA seq, CM WT rep2


title: LUL_Pre_1

description: 10x Genomics


title: Day13PC_C (ATAC-seq)

data_processing:
ATAC-seq FASTQ files were first quality checked with FastQC. Trim Galore was then used with default settings to remove Illumina sequencing adaptors and low quality reads (Q < 20).  Trimmed, paired ATAC-seq reads were aligned to the human genome (NCBI GRCh38 decoy version) using bowtie2 (--very-sensitive). Post-alignment, low-quality mappings (MAPQ < 20) were filtered out with Samtools and duplicates were removed with Picard tools. Bedtools was used to filter out ENCODE and mitochondrial blacklists, and select fragments <100bp to isolate nucleosome-free regions. Coordinates were shifted with deepTools +4 bp on the positive strand and -5 bp on the negative to centre on the Tn5 cutting site. Narrow peaks were called with Macs2 in paired-end mode with q = 0.05.
Assembly: NCBI GRCh38 decoy version
Supplementary files format and content: MACS2 narrowPeak

extract_protocol:
Immediately following transposition, DNA was purified using a Qiagen MinElute Kit with elution into 10mM Tris buffer, pH 8.
Initial amplification of transposed fragments was performed using customized Nextera PCR Primer 1* and  customized Nextera PCR Primer 2* with  NEBNext High-Fidelity PCR mix (New England Labs Cat #M0541) with 8-14 (median 12) cycles of amplification. Amplification was monitored using qPCR and Bioanalyser (Bioanalyzer High Sensitivity DNA kit). Amplified libraries were cleaned up using Qiagen PCR Cleanup Kit and eluted in 10mM Tris Buffer, pH 8 and quantified using KAPA Library Quant Kit for Illumina Sequencing Platforms (KAPABiosystems). Samples were sequenced on a NextSeq500 with 2x76-bp run paired-end reads.

treatment_protocol:
For day 6 to day 13, at day 6, cells were harvested and seeded at 1 × 10^6/ml in media supplemented with IL-6 (10 ng/ml), IL-21 (10 ng/ml), GSI (100 nM), and multimeric APRIL (100 ng/ml).
ATAC-seq was performed according to the protocol described by Buenrostro et al. Cells were harvested at indicated time points with 50,000 cells used per time point. Cells washed once with 50 μL of cold 1x PBS buffer were resuspend in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition reactions were performed at  37°C for 90 min using Tn5 Transposes (Illumina Cat #FC-121-1030) in 2x TD Buffer (Illumina Cat #FC-121-1030) and nuclease free H2O.

value: Plasmacell


title: total RNA seq, CM WT rep1


title: ssRNAseq_A_Col_Ctr//AGe_Wt flower_Rep2


title: Day13PC_A (ATAC-seq)


title: Placebo_POST_219914_RUL

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2 fastq 2.17 software
After investigating the quality of the raw data, sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using cutadapt program
The trimmed reads were mapped to hg38 using the STAR aligner. BAM files were generated as a result of this step.
The fragments per exon kilobase per million mapped reads (FPKM) values were calculated using RNA-Seq by expectation maximization (RSEM)
Significant differences between groups (pre, post iloprost and placebo) were calculated using moderated t-statistics
Assembly: hg38
tab-delimited text file includes FPKM values for each sample

extract_protocol:
During the initial training visit, a 2.5 µg test dose was administered and participants delivered the full 5 µg doses subsequently. All study participants were to self-administer 5 µg iloprost or placebo QID for 2 months. An initital bronchoscopy (Pre) and 2 monnths (post) treatment were performed.
Frozen airway biopises collceted at pre and post treatment were analyzed. Bronchial biopsies frozen in OCT were used to purify total RNA using an RNA extraction microkit (Qiagen), followed by mRNA library prep (Illumina) and sequencing (NovaSEQ next-gen sequencer).

treatment_protocol: Iloprost or matched placebo was delivered by the FDA approved I-neb Adaptive Aerosol Delivery (AAD) device (Accredo). Each participant was taught to self-administer the experimental agent. Treatments last 4-10 minutes and the device measures compliance and delivered dose.

value: Airway epithelial and non-epithelial cells

value: 2 months placebo treatment


title: Day0-30min-BC_A (RNA-seq)

value: A


title: total RNA seq, EB SnordD133 KO rep3


title: Placebo_POST_219914_LUDB

value: Endobronchial biopsies


title: total RNA seq, EB Snord133 KO rep2


title: Day10PC_A (ATAC-seq)

value: Peripheral blood


title: Placebo_POST_219912_LUL


title: total RNA seq, EB Snord133 KO rep1


title: Day6PB_C (ATAC-seq)

value: Plasmablast


title: ssRNAseq_A_Col_Ctr//AGe_Wt flower_Rep1


title: ssRNAseq_A_Col_AGP//AGe_Wt flower_Rep2


title: Day6PB_A (ATAC-seq)


title: Placebo_POST_219912_RUL


title: ssRNAseq_A_Col_Ctr//AGe_Wt flower_Rep3


title: total RNA seq, EB WT rep3


title: Placebo_PRE_219914_RUL

value: Baseline bronchoscopy


title: ssRNAseq_A_Col_AGP//AGe_Wt flower_Rep1


title: total RNA seq, EB WT rep2


title: ssRNAseq_A_Col_AGP//AGe_rMf_Rep3

value: rMf


title: Placebo_PRE_219914_LUL


title: total RNA seq, EB WT rep1

value: mouse embryonic stem cell


title: Day10PC_C (ATAC-seq)

value: C


title: Placebo_PRE_219912_LUL


title: ssRNAseq_A)_Col_AGP//AGe_rMf_Rep1


title: ssRNAseq_A_Col_AGP//AGe_rMf_Rep2


title: Day1BC_A (ATAC-seq)

treatment_protocol:
For day 0 to day 3, B cells were cultured in 24-well plates at 2.5 × 10^5/ml with IL-2 (20 U/ml), IL-21 (50 ng/ml), and F(ab`)2 goat anti-human IgM and IgG (2 mg/ml) on gamma-irradiated CD40L-expressing L cells (6.25 × 10^4/well).
ATAC-seq was performed according to the protocol described by Buenrostro et al. Cells were harvested at indicated time points with 50,000 cells used per time point. Cells washed once with 50 μL of cold 1x PBS buffer were resuspend in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition reactions were performed at  37°C for 90 min using Tn5 Transposes (Illumina Cat #FC-121-1030) in 2x TD Buffer (Illumina Cat #FC-121-1030) and nuclease free H2O.

value: B-cell


title: total RNA seq, mES Snord133 KO rep3

value: Snord133 knockout

value: no

value: total RNA


title: Placebo_PRE_219912_RUL


title: Day3ABC_A (ATAC-seq)

treatment_protocol:
For day 3 to day 6, at day 3, cells were detached from the CD40L L cell layer and reseeded at 1 × 10^5/ml in media supplemented with IL-2 (20 U/ml) and IL-21 (50 ng/ml).
ATAC-seq was performed according to the protocol described by Buenrostro et al. Cells were harvested at indicated time points with 50,000 cells used per time point. Cells washed once with 50 μL of cold 1x PBS buffer were resuspend in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition reactions were performed at  37°C for 90 min using Tn5 Transposes (Illumina Cat #FC-121-1030) in 2x TD Buffer (Illumina Cat #FC-121-1030) and nuclease free H2O.


title: Day0-12h-BC_B (ATAC-seq)

value: B


title: Iloprost_POST_219901_RUL

value: 2 months inhaled Iloprost treatment


title: ssRNAseq_A_Col_AGP//AGe_Wt flower_Rep3

value: Young flower

value: Wt

value: Floral structure change


title: total RNA seq, mES Snord133 KO rep2


title: ssRNAseq_A_Col_AGP//AGe_sMf_Rep3

value: sMf


title: Iloprost_POST_219901_LUL

value: Endobronchial biopsies

value: Airway epithelial and non-epithelial cells


title: Day3ABC_C.2 (ATAC-seq)

value: Peripheral blood

value: Plasmablast


title: Day3ABC_B (ATAC-seq)


title: total RNA seq, mES WT rep3

value: WT


title: Iloprost_POST_219760_RUL


title: ssRNAseq_A_Col_AGP//AGe_sMf_Rep1


title: ssRNAeq_A_M317_Wt flower_Rep3


title: Day0-2h30-BC_B (ATAC-seq)


title: total RNA seq, mES WT rep2

value: mouse embryonic stem cell


title: total RNA seq, mES Snord133 KO rep1


title: Iloprost_POST_219347_LUL


title: ssRNAeq_A_M317_Wt flower_Rep2


title: Day0-2h30-BC_A (ATAC-seq)

value: A


title: Iloprost_PRE_219901_RUL

value: Baseline bronchoscopy


title: total RNA seq, mES WT rep1


title: ssRNAeq_A_M317_Wt flower_Rep1


title: Day0-30min-BC_B (ATAC-seq)

value: B-cell


title: Iloprost_PRE_219901_LUL


title: Day0-30min-BC_A (ATAC-seq)


title: B6_F1_GS_ICSI_M1_11

source_name: Germline stem cells of ICSI-derived mice

value: Germline stem cell

value: ICSI


title: ssRNAeq_A_M318_Wt flower_Rep2


title: ssRNAseq_A_Col_AGP//AGe_sMf_Rep2


title: Day0-12h-BC_A (ATAC-seq)


title: Iloprost_PRE_219760_RUL


title: Day0BC_C (ATAC-seq)

value: C


title: B6_F1_GS_Control_C37

source_name: Germline stem cells of natural mating derived mice

value: no


title: ssRNAeq_A_M318_Wt flower_Rep1

value: Young flower


title: B6_F1_GS_Control_C29


title: Day0BC_B (ATAC-seq)

value: B


title: Riboseq, HEK293 SNORD133 KO rep2

data_processing:
Sequencing data were preprocessed to remove adapters from the 5'end and 3’end using Trimmomatic software (v0.36). PCR duplicates are removed using readCollapse script from the icSHAPE pipeline.
Reads were mapped to the hg38 and mm10 genome using STAR program (v2.7.9).
Bedtools v2.25.0 was used to annotate alignments. Read count extraction and RPM normalization were performed.
P-site offsets of ribosome profiling data was determined using the psite script from plastid package. The parameters used are as follows: psite merlin_orfs_rois.txt outputprefix --min_length 25 --max_length 35 --require_upstream --count_files input.bam --min_counts 100 --figformat pdf --dpi 300.
For nuclear-encoded mRNAs in RNA-seq and ribo-seq from WT and D97 and D133 single KO HEK293 cells, ratios of expression levels were calculated for the top 10% (most up-regulated) and bottom 10% (most down-regulated) mRNAs and weighted by expression levels.
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text file includes RPM values of each sample, and the code usage ratio was calculated for RNA-seq and ribo-seq data.
Library strategy: Ribo-Seq

value: human embryonic kidney cells

value: SNORD133 knockout

value: Flash freezin in liquid nitrogen


title: Day0BC_A (ATAC-seq)


title: unaligned_034502_O

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

data_processing:
all data was processed using the default parameters for 10X genomics CellRanger software to align the reads to the mouse genome and create count matrices of genes for each cell
data was normalized using SCT and analyzed using Seurat v3 in R
Assembly: mm10, Grc38m
Supplementary files format and content: all data is in a .rds file that contains @ metadata slot which references the cell barcode number and sample, cell type, and contains the normalized count matricies

source_name: hindlimb skeletal muscle mononuclear cells old mice 7 days post injury

extract_protocol:
mononuclear cells were isolated from muscle at 7 days post injury following a published protocl (Liu et al., 2015). Cells were sorted using a live/dead stain to exclude debris or dead cells and hoescht
libraries were prepared following 10X Genomics protocol for v3 3' single-cell sequencing and samples were prepared for high throughput sequencing following Illumina's specifications. Prior to sequencing all samples were evaluated using an Agilent Bioanalyzer high sensitivity chip

value: hindlimb skeletal muscle

tag: number of samples

value: 22 months

value: male


title: unaligned_034503_Y

source_name: hindlimb skeletal muscle mononuclear cells young mice 7 days post injury

value: 3 months


title: BSseq_C_hdp2-1_Wt flower

data_processing:
Illumina paired-end bisulfite sequences were evaluated for quality using FastQC (version 0.11.9)
FASTQ files were aligned to the Araport11/TAIR10 Arabidopsis reference genome (Cheng et al. 2017) using the Bismark Bisulfite Read Mapper with the Hisat2 alignment algorithm
The methylation status of each cytosine in each context was extracted from the alignments with the bismark methylation extractor. The percent of methylated reads on a nucleotide level was calculated for regions of interest where total read depth was at least 4 reads.
Sequencing data in a 17.3-kb region containing the AG locus were retrieved and exported into xls for analysis of methylation rates and preparation of graphical presentation.
Supplementary files format and content: xls file includes methylation rate in each cytosine position within 17.3-kb genomic region for each sample

extract_protocol:
Genomic DNA was isolated from flowers pooled from five to ten lines with the same flower phenotype for each replicate using the Dneasy® Plant Mini Kit (Qiagen, Hilden, Germany).
Bisulfite treatment, library construction and sequencing were performed by BGI Americas Cooperation (Cambridge, MA).

value: Wt

value: Floral structure change


title: BSseq_C_hdp2-1_ARE//AGe_rMf

value: rMf


title: Riboseq, HEK293 SNORD133 KO rep1

tag: cell type


title: BSseq_C_hdp2-1_ARE//AGe_sMf

value: sMf


title: BSseq_C_hdp1-1_ARE//AGe_sMf


title: Patient_1627_Post_Treatment CNV

data_processing:
Library strategy: CNV-Seq
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from cellranger-dna pipeline

extract_protocol: For single-cell DNA library generation for CNV single-cell suspensions of primary MM cells were processed according to 10X Genomics Reagent Kits User Guide (CG000153). Single cells were partitioned in a hydrogel matrix by combining with a CB polymer to form Cell beads (CBs) using a microfluidic chip. Post a first encapsulation, CBs were treated to lyse the encapsulated cells and denature the genomic DNA (gDNA). The denatured gDNAs in the CB were then accessible to amplification and barcoding. A second microfluidic encapsulation step was then required to partition the CB with 10x barcode Gel Beads (GBs) to generate GEMs. Immediately after barcoding and amplification, 10x barcoded fragments were pooled and attached to standard Illumina adaptors. For all the single cell methods, quality control and quantification was performed using a Kapa Library Quantification qPCR kit (Kapa Biosystems) on a BioRad qPCR instrument prior to preparing a single pool containing equal amounts of each library. This pool was then subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2.5 150 sequencing kit for RNA-seq and ATAC-seq and 300 cycle sequencing kit for CNV-seq as per the standard Illumina protocols. After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger suite v3.0 and downstream analyses were realized with Seurat, Monocle, Signac, and Cicero R packages.

tag: patient number


title: Large intestine, BMT, 3

city: Duarte

first: Anastasia

middle: I

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

data_processing:
Quality control (QC) was performed with FastQC (v0.11.9).
Raw reads were aligned with STAR aligner (v2.7.0e) against the mouse genome assembly.
Aligned reads were in turn assigned to genes using featureCounts (v1.6.3).
The resulting count tables were imported to R for further processing, analysis, and visualization.
Assembly: GRCm38.p5
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: epithelial cell fractions of the large intestine

extract_protocol:
Tissue was harvested on day 7 post-transplant and bulk liver and isolated epithelial cells of the small and large intestine were suspended in TRIzol and homogenized with metal beads. Phase separation in homogenized tissue or in cells lysed in TRIzol was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher catalog # A27828) on the KingFisher Flex Magnetic Particle Processor (Thermo Scientific catalog # 5400630) according to the manufacturer’s protocol. Samples were eluted in 34 µL elution buffer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 7.2-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).  An average of 30 million paired reads was generated per sample. Ribosomal reads represented 0.2-0.9% of the total reads generated and the percent of mRNA bases averaged 93%.

treatment_protocol: Lethally irradiated 6-8 weeks old female BALB/c mice were transplanted with 10x10^6 BM cells alone (BM) or together with 1x10^6 T cells (BMT).

tag: strain

value: BALB/cJ

value: female

value: BMT

value: Day 7


title: B6_F1_GS_ICSI_M1_17

value: Germline stem cell

value: WT

value: ICSI


title: Riboseq, HEK293 SNORD97 KO rep1

value: human embryonic kidney cells

value: SNORD97 knockout


title: Day10PC_A (RNA-seq)

value: Peripheral blood

value: A

value: Plasmacell


title: Riboseq, HEK293 SNORD97/SNORD133 KO rep2

value: SNORD97/133 double knockout

value: Flash freezin in liquid nitrogen


title: Large intestine, BMT, 2

value: epithelial cell fractions of the large intestine


title: BSseq_C_hdp1-1_ARE//AGe_rMf

value: Young flower

value: rMf

value: Floral structure change


title: Iloprost_PRE_219347_LUDB

value: Endobronchial biopsies

value: Airway epithelial and non-epithelial cells

value: Baseline bronchoscopy


title: Large intestine, BMT, 1

value: BALB/cJ

value: female

value: BMT

value: Day 7


title: BSseq_C_hdp1-1_Wt flower

value: Wt


title: BSseq_C_suvh1-2_ARE//AGe_sMf

value: sMf


title: Large intestine, BM, 3

value: BM


title: Riboseq, HEK293 SNORD97/SNORD133 KO rep1

value: human embryonic kidney cells


title: Patient_1479_Post_Treatment CNV


title: Patient_1698_Post_Treatment CNV


title: Riboseq, HEK293 WT rep2

value: WT


title: Riboseq, HEK293 SNORD97 KO rep2

value: SNORD97 knockout

value: Flash freezin in liquid nitrogen


title: Patient_1426_PreTreatment CNV


title: BSseq_C_suvh1-2_Wt flower

value: Young flower


title: Riboseq, HEK293 WT rep1


title: Large intestine, BM, 2

value: epithelial cell fractions of the large intestine


title: Large intestine, BM, 1


title: Patient_1389_Pre_Treatment CNV


title: Patient_1555_Post_Treatment CNV


title: BSseq_C_Col_Wt flower_C

value: Col_Wt flower

value: Floral structure change


title: BSseq_C_Col_ARE//AGe_Wt flower


title: Patient_1498_Pre_Treatment CNV


title: Small intestine, BMT, 3

source_name: epithelial cell fractions of the small intestine


title: Patient_1217_PreTreatment CNV


title: Small intestine, BMT, 2

value: epithelial cell fractions of the small intestine


title: small RNA seq, HEK293 sFBL rep1_2

value: FBL knockdown

value: Oxidative stress

value: small RNA (15-50nt)


title: small RNA seq, HEK293 sFBL rep2_2


title: small RNA seq, HEK293 sFBL rep2_1


title: Small intestine, BMT, 1

value: BALB/cJ

value: female

value: BMT


title: Patient_1479_Post_Treatment RNA-seq


title: small RNA seq, HEK293 sFBL rep1_1


title: Patient_1438_Post_Treatment RNA-seq


title: BSseq_B_Col_AGE_rMf

value: rMf


title: Patient_1555_Post_Treatment RNA-seq


title: BSseq_B_Col_Wt flower_B

value: Wt


title: small RNA seq, HEK293 siCtrl rep2

value: human embryonic kidney cells

value: Ctrl


title: Small intestine, BM, 3

value: BM

value: Day 7


title: BSseq_B_Col_Ctr//AGE_rMf

value: Young flower


title: Small intestine, BM, 2


title: small RNA seq, HEK293 siCtrl rep1


title: Patient_1404_Post_Treatment CNV


title: Small intestine, BM, 1


title: small RNA seq, HEK293 SNORD133 KO rep2

value: SNORD133 knockout


title: Patient_1627_Post_Treatment RNA-seq


title: BSseq_B_ddm1-1_Ctr//AGE_rMf


title: Liver, BMT, 3

source_name: bulk liver

value: bulk liver


title: BSseq_B_ddm1-1_ARE//AGe_rMf

value: Floral structure change


title: small RNA seq, HEK293 SNORD133 KO rep1


title: BSseq_B_ddm1-1_ARE//AGe_sMf

value: sMf


title: small RNA seq, HEK293 SNORD97 KO rep2

value: SNORD97 knockout


title: Liver, BMT, 2


title: Patient_1393_Pre_Treatment RNA-seq


title: Patient_1498_Pre_Treatment RNA-seq


title: Liver, BMT, 1


title: small RNA seq, HEK293 SNORD97 KO rep1

value: Oxidative stress


title: BSseq_B_Met1-1_Ctr//AGe_rMf


title: Liver, BM, 3


title: BSseq_B_Col_Ctr//AGE_Wt flower


title: BSseq_B_ddm1-1_Wt flower


title: BSseq_B_Met1-1_ARE//AGe_sMf


title: BSseq_B_Met1-1_ARE//AGe_rMf


title: Liver, BM, 1


title: Patient_1389_Pre_Treatment RNA-seq


title: Patient_1393_Pre_Treatment ATAC-seq

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters using cellranger-atac count.
Assembly: Pre-generated human reference GRCh38
Supplementary files format and content: Filtered peak barcode matrix in hdf5 format and a BED-like tabular file where each line represents a unique ATAC-seq fragment captured by the assay from CellRanger-atac count.


title: Patient_1217_Pre_Treatment ATAC-seq


title: small RNA seq, HEK293 SNORD97/133 KO rep2

value: SNORD97/133 double knockout

value: small RNA (15-50nt)


title: Liver, BM, 2

value: BALB/cJ

value: female


title: Patient_1389_Pre_Treatment ATAC-seq


title: PS19_fE4R/S_50

city: San Francisco

first: Ayushi

last: Agrawal

address: 1650 Owens St

institute: Gladstone Institutes

description: 10x Genomics single nucleus RNA sequencing

data_processing:
Demultiplexed fastq files were aligned to a custom reference genome built from mm10 2020-A that includes introns, using the Cellranger v7.0.0 counts function with default parameters, as described in the Cellranger documentation. UMI counts were also determined using the Cellranger counts function.
Assembly: The Homo sapiens microtubule associated protein tau (MAPT) (NCBI Reference Sequence: NM_001123066.4) and the Homo sapiens APOE are genes of interest for this study. Custom mouse reference genome was made using these genes of interest , the reference mouse genome sequence (GRCm38) from Ensembl (release 98) and the mouse gene annotation file from GENCODE (release M23), similar to those used in 10x Genomics Cell Ranger mouse reference package mm10 2020-A.
Supplementary files format and content: feature-barcode matrix in the Hierarchical Data Format (HDF5 or H5) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

source_name: hippocampus

growth_protocol: All protocols and procedures followed the guidelines of the Laboratory Animal Resource Center at the University of California, San Francisco (UCSF). All mice had identical housing conditions from birth through sacrifice (12 h light/dark cycle, housed 5 animals/cage, PicoLab Rodent Diet 20). APOE3-KI and APOE4-KI (Bien-Ly, N et al. 2012) mice were born and aged under normal conditions at the Gladstone Institute/UCSF animal facility. To generate APOE4-KI mice harboring the R136S mutation (E4-S/S or E4-R/S), CRISPR-Cas9-based knock-in strategy was used, as described in Methods. APOE4-KI, APOE3-KI, APOE4-S/S-KI, and APOE4-R/S-KI mice were then cross-bred with Tau-P301S (PS19 line) (Jax #008169) mice to generate PS19-E4, PS19-E3, PS19-E4-S/S, and PS19-E4-R/S mice.

extract_protocol:
The mouse hippocampal homogenate was filtered using a 70 µM Flowmi strainer. Nuclei were pelleted by spinning for 5 min at 4°C at 350 RCF and were resuspended in 400 µL 1X HB. Next, 400 µL of 50% Iodixanol solution was added to the nuclei and then slowly layered with 600 µL of 30% Iodixanol solution under the 25% mixture, then layered with 600 µL of 40% Iodixanol solution under the 30% mixture. The nuclei were then spun for 20 min at 4°C at 3,000RCF in a pre-chilled swinging bucket centrifuge. 200 µL of the nuclei band at the 30%-40% interface was collected and transferred to a fresh tube. Then, 800 µL of 2.5% BSA in PBS plus 0.2 units/µL of RNase inhibitor was added to the nuclei and were then spun for 10 min at 500 RCF at 4C. The nuclei were resuspended with 2% BSA in PBS plus 0.2 units/µL RNase inhibitor to reach at least 500 nuclei/µL. The nuclei were then filtered with a 40 µM Flowmi cell stainer. The nuclei were counted and then ~13,000 nuclei per sample were loaded onto 10x Genomics Next GEM chip G.
snRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.
OTHER: 10X Single-nucleus RNAseq

value: hippocampus


title: BSseq_B_Met1-1_Wt flower

source_name: Young flower

value: Wt


title: Patient_1217_Pre_Treatment RNA-seq

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: Primary CD138+ MM cells


title: small RNA seq, HEK293 WT rep2

value: human embryonic kidney cells

value: WT


title: Patient_1438_Post_Treatment ATAC-seq

extract_protocol: For single-cell library preparation for ATAC-seq the desired number of nuclei were targeted and processed according to 10X Genomics Reagent Kits User Guide (CG000168). The Nuclei Isolation was performed ad indicated in the nuclei Isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration primary MM cells were washed, lysed and re-suspended in appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were then immediately used to generate scATAC-seq libraries. ScATAC-seq libraries were prepared according to 10X Genomics Reagent Kits User Guide. Briefly, the desired number of nuclei were combined with ATAC Buffer and master mix to form transposed Nuclei. Single-cell GEMs were then generated, amplified and subjected to bead clean-ups. Indexed sequencing libraries were constructed using Chromium i7 Sample Index and the barcode sequencing libraries subjected to a final bead clean-up prior to quantification.


title: Patient_1479_Post_Treatment ATAC-seq


title: PS19_fE4R/S_30


title: total RNA seq, HEK293 SNORD133 KO rep2

value: no

value: total RNA


title: total RNA seq, HEK293 SNORD133 KO rep1


title: BSseq_A_Col_ARE//AGe_Wt flower

value: Young flower


title: BSseq_B_Col_Wt flower_A


title: small RNA seq, HEK293 SNORD97/133 KO rep1


title: PS19_fE4R/S_19


title: Patient_1498_Pre_Treatment ATAC-seq


title: BSseq_A_Col_UF4//AGe_sMf

value: rMf


title: PS19_fE4R/S_15


title: PS19_fE4S/S_169


title: total RNA seq, HEK293 SNORD97 KO rep2


title: small RNA seq, HEK293 WT rep1


title: BSseq_A_Col_UF2//AGe_sMf


title: total RNA seq, HEK293 SNORD97 KO rep1


title: PS19_fE4S/S_154


title: total RNA seq, HEK293 SNORD97/133 KO rep2


title: BSseq_A_Col_AGp_Sterile

value: Sterile


title: PS19_fE4S/S_152


title: Patient_1698_Post_Treatment ATAC-seq


title: total RNA seq, HEK293 WT rep2


title: Patient_1555_Post_Treatment ATAC-seq


title: BSseq_A_M318_Wt flower_B

value: Floral structure change


title: MCF10A p53 WTOE control cells - ChIP-Seq - V5

city: Tempe

first: Jin

middle: G

last: Park

state: AZ

address: 727 E. Tyler St., Suite A220C

institute: Arizona State University

data_processing:
Paired-ended reads were mapped to the reference human genome (GRCh38.p92/hg38) end to end using Bowtie2 (Bowtie2 2.1.0) with the default setting
Non-primary alignment, unmapped reads were removed by Samtools (Samtools v1.7)
MACS2 (macs2 2.1.2.20181017) was used for peak calling using BAMPE mode with the q-value cutoff 0.05 by using the genomic DNA sequencing data (input DNA) as the background
Peaks were annotated under Ensembl genome annotation (GRCh38.p92/hg38) using Homer toolkit (Homer v4.9.1)
HOMER (Homer v4.9.1) was used to call known and de-novo motifs  from 300 bp bins centered at the summit of peaks at promoter region. Regions located between -100 and 2500 bp upstream of the nearest TSS were defined as the promoter region.
bed files were generated using macs2, Scores represent the -log10(pvalue) at the summit of peaks

source_name: ectopic expression of wild type p53 protein with V5 tag at C-term

growth_protocol: MCF10A cells were cultured at 37˚C in a 5% CO2 humidified incubator. DMEM/F12 media (ThermoFisher #11320-082) was supplemented with 5% Horse Serum (ThermoFisher #16050-122), hEGF (10ng/ml, ThermoFisher #PHG0311), hydrocortisone (0.5µg/ml, Sigma #H0888), cholera toxin (100ng/ml, Sigma #C8052), and Insulin (10µg/ml, Sigma #I9278). Cell were routinely passaged with trypsin (0.25% in HBSS with 0.2g/ml EDTA, GE Healthcare #SH30042.01) at 80-90% confluence.

extract_protocol:
RNA-Seq: Total RNA extracted from the cells (Qiagen cat no. 74134) were used to prepare cDNA using Nugen’s Ovation RNA-Seq System via single primer isothermal amplification (Catalogue # 7102-A01) automated on the Apollo 324 liquid handler from Wafergen.
RNA-Seq: cDNA was sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using Kapa Biosystem’s library preparation kit (KK8201). Fragments were end-repaired and A-tailed, individual indexes and adapters (Bioo, catalogue #520999) were ligated on each separate sample. The adapter ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883), and amplified with Kapa’s HIFI enzyme.  The library was then analyzed on an Agilent Bioanalyzer, and quantified by qPCR (KAPA Library Quantification Kit, KK4835) before multiplex pooling and sequencing a 2x75 PE flow cell on the NextSeq500 platform (Illumina) at the ASU’s CLAS Genomics Core facility.
RNA-Seq: The library was then analyzed on an Agilent Bioanalyzer, and quantified by qPCR (KAPA Library Quantification Kit, KK4835) before multiplex pooling and sequencing a 2x75 PE flow cell on the NextSeq500 platform (Illumina) at the ASU’s CLAS Genomics Core facility.
chip-seq: All the MCF10A cell lines were fixed with 1% formaldehyde in PBS and incubated for 10 min at RT. Formaldehyde was quenched with glycine (125mM final conc.) for 5 min at RT. Cells were rinsed with ice cold PBS twice and scraped with 2ml of cold PBS with protease inhibitor (Sigma Aldrich Cat no. 04693124001). Cells were washed two more times with cold PBS with protease inhibitor and pellets from 20 million cells were snap frozen and stored at -80oC. 1ml of ChIP lysis buffer (1% SDS,10mM EDTA, 50mM Tris-HCl pH8.1) with protease inhibitors was added and the cells were sonicated in the Covaris M220 ultrasonicator for 8 min. The time and setting for sonication would vary with the cell-line and concentration. The lysates were spun at maximum speed at 4oC for 10 min and the DNA concentration was checked. The supernatant was transferred into fresh tube. 25-50ul of the lysate was incubated at 65oC overnight with 0.1M NaCl and run on a 2% agarose gel to check the sonication efficiency. You should get an average fragmentation of ~500 bp. For IP, 30ul of beads (Thermo Cat no. 11203D) were first washed with 1ml of cold BSA (5mg/ml) in PBS at RT (3 times). Then V5 antibody (CST Cat no. 13202S) was added to the beads in 1ml of PBS+ BSA. The beads with the antibody were incubated for 4 to 6 hrs at 4oC. The IP was performed on 50ug of total DNA and the samples were diluted accordingly in the dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl pH 8.0). The diluted chromatin was precleared with 15ul of washed beads for 1hr at 4oC. 5% of this precleared lysate was kept as input control. PBS/BSA was aspirated from the antibody coated beads and precleared lysate was added to incubate O/N at 4oC on a rotating wheel. Next day beads were collected using the magnetic concentrator and washed 6 times with ChIP RIPA buffer (50mM HEPES, 1mM EDTA, 0.7% Na Deoxycholate, 1% NP-40, 0.5M LiCl pH 7.6) at RT on a rotating platform for 10 min between every wash. Then washed twice with 1X TE (pH7.6) at RT. 100 ul of Elution buffer (1% SDS, 0.1M NaHCO3, 0.1M NaCl) was added to the beads and input samples (make up volume to 100ul). The beads were vortexed in this solution every few minutes for 30 minutes in total at RT and incubated at 65oC O/N for 12-14 hrs. Next day 1ul of proteinase K (10mg/ml) was added and incubated at 42oC for 2 hrs. The IP DNA was purified with QIAquick PCR purification kit.

treatment_protocol: No treatment

value: MCF10A mammary epithelial cells

tag: genotype/variation

value: p53 WTOE control cells

tag: chip antibody

value: V5 tag

value: untreated


title: total RNA seq, HEK293 WT rep1


title: BSseq_A_M317_Wt flower_C


title: BSseq_A_M318_Wt flower_C


title: PS19_fE4S/S_132


title: BSseq_A_M317_Wt flower_B


title: optimized RiboMethSeq, HEK293 SNORD97_133 KO rep4

description:
RMseq_HEK293_D97_133KO_rep4
RMseq_HEK293_D97_133KO_by_5end.txt
RMseq_HEK293_D97_133KO_by_3end.txt

data_processing:
Sequencing data were preprocessed to remove adapters from the 5'end and 3’end using Trimmomatic software (v0.36).
PCR duplicates are removed using readCollapse script from the icSHAPE pipeline.
Reads were mapped to the hg38 genome using STAR program (v2.7.9).
The number of 5’end and 3’end reads were calculated with bedtools genomecov (v2.29.2).
The methylation score in the 2’-O-Me sites was computed with four neighboring nucleotides (±2 nucleotide window) from 5’-end and 3’-end reads at nucleotide resolution.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains the 5'end and 3'end coverage of mapped reads and Nm levels.

growth_protocol: HEK293 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) + 10% fetal bovine serum (FBS, Gibco) + Penicillin-Streptomycin (Gibco) in 37°C incubator with 5% CO2.

extract_protocol:
Total RNAs were isolated using TRIzol following the manufacturer’s instructions. After running 10% (wt/vol) urea polyacrylamide gel, small RNA (70-300nt) was excised and purified using ZR small-RNA PAGE Recovery Kit.
100 ng of small RNA (70-300 nt) was denatured in 95% DMSO solutions for 3 minutes at 98°C. Then, 10 mM sodium bicarbonate buffer was added to each reaction to perform hydrolysis at different pH (9, 10, and 11) for different times (5, 10, and 15 minutes). The fragmented RNAs were end-repaired by T4PNK. Adapter was ligated to end-repaired RNA fragments using high concentration T4 RNA ligase 1. Free adapters were removed by RecJf and 5’ deadenylase. RNA was purified with Zymo RNA clean and Concentrator-5 Kit. An RT-step and PCR amplification were coupled with barcoding.

treatment_protocol: DsiRNAs were used to knock down FBL and CRISPR/Cas9 was used to mediate SNORD97 and SNORD133 genomic deletion.

value: SNORD97, SNORD133 knockout

value: small RNA (70-300nt)


title: PS19_fE3_579S


title: MCF10A p53 Y234C mutant cells - ChIP-Seq - V5

source_name: ectopic expression of p53 Y234C mutant protein with V5 tag at C-term

value: p53 Y234C mutant cells


title: PS19_fE3_524G

value: hippocampus


title: MCF10A p53 WTOE control cells - ChIP-Seq - input DNA


title: optimized RiboMethSeq, HEK293 SNORD97_133 KO rep2

description:
RMseq_HEK293_D97_133KO_rep2
RMseq_HEK293_D97_133KO_by_5end.txt
RMseq_HEK293_D97_133KO_by_3end.txt


title: MCF10A p53 R273H mutant cells - ChIP-Seq - input DNA

source_name: ectopic expression of p53 R273H mutant protein with V5 tag at C-term

value: p53 R273H mutant cells


title: BSseq_A_Col_AGe_rMf_B


title: MCF10A p53 R273H mutant cells - ChIP-Seq - V5


title: total RNA seq, HEK293 SNORD97/133 KO rep1

value: human embryonic kidney cells

value: SNORD97/133 double knockout


title: PS19_fE4_594S


title: optimized RiboMethSeq, HEK293 SNORD97_133 KO rep3

description:
RMseq_HEK293_D97_133KO_rep3
RMseq_HEK293_D97_133KO_by_5end.txt
RMseq_HEK293_D97_133KO_by_3end.txt


title: BSseq_A_M318_AGe_rMf_C


title: PS19_fE4_518G


title: BSseq_A_M318_AGe_rMf_B


title: MCF10A p53 R273C mutant cells - ChIP-Seq - input DNA

source_name: ectopic expression of p53 R273C mutant protein with V5 tag at C-term

value: p53 R273C mutant cells


title: PS19_fE3_585S


title: optimized RiboMethSeq, HEK293 SNORD97_133 KO rep1

description:
RMseq_HEK293_D97_133KO_rep1
RMseq_HEK293_D97_133KO_by_5end.txt
RMseq_HEK293_D97_133KO_by_3end.txt


title: BSseq_A_M317_AGe_rMf_C


title: MCF10A p53 Y234C mutant cells - ChIP-Seq - input DNA


title: MCF10A p53 R273C mutant cells - ChIP-Seq - V5


title: BSseq_A_M317_AGe_rMf_B


title: optimized RiboMethSeq, HEK293 siFBL rep3

description:
RMseq_HEK293_siFBL_rep3
RMseq_HEK293_siFBL_by_5end.txt
RMseq_HEK293_siFBL_by_3end.txt

value: FBL knockdown


title: Brca2KO, JQ1, Input

city: Davis

first: Chang-il

last: Hwang

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California Davis

data_processing:
CUT-and-RUN-seq reads were aligned to mm9 using HISAT2. Only uniquely mapped reads were retained
Mapped reads were normalized to 1x coverage and bigwig files were generated using Bamcoverage
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: pancreas

growth_protocol: DMEM media supplemented with 10% FBS and P/S

extract_protocol:
Enriched chromatins were extracted with Cell Signaling, Cut and Run Assay Kit.
CUT-and-RUN-seq libraries were prepared and sequenced on a Hiseq-PE150 sequencing system

treatment_protocol: Cells were treated with 1 µM JQ1 for 72 hrs.

value: pancreas

value: mT3-2D KPC

value: mouse pancreatic cancer

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: JQ1 1 µM


title: BSseq_A_M318_AGe_sMf_C

value: Young flower

value: sMf

value: Floral structure change


title: optimized RiboMethSeq, HEK293 siFBL rep4

description:
RMseq_HEK293_siFBL_rep4
RMseq_HEK293_siFBL_by_5end.txt
RMseq_HEK293_siFBL_by_3end.txt


title: MCF10A p53 Y220C mutant cells - ChIP-Seq - input DNA

source_name: ectopic expression of p53 Y220C mutant protein with V5 tag at C-term

value: MCF10A mammary epithelial cells

value: p53 Y220C mutant cells

value: untreated


title: PS19_fE4_461G

value: hippocampus


title: MCF10A p53 WT control cells - RNA-seq

data_processing:
STAR (V020201) (Dobin 2013) was used to align reads to the human genome (GRCh38.p92/hg38) to counts with the following configuration: outSAMmultNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.2 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Mitochondrial reads were removed before gene counts log2 TPM (transcripts per million reads) normalization. Transcript length used in TPM normalization was calculated using the longest transcript of each gene
GRCh38.p92/hg38
csv file of gene expression from individual cell lines. Score represent the gene expression level in log2(TPM+1)

source_name: Endogenous wild type p53 protein without any V5 tag

value: p53 WT control cells


title: optimized RiboMethSeq, HEK293 siFBL rep2

description:
RMseq_HEK293_siFBL_rep2
RMseq_HEK293_siFBL_by_5end.txt
RMseq_HEK293_siFBL_by_3end.txt

value: human embryonic kidney cells

value: small RNA (70-300nt)


title: Brca2KO, DMSO, Input

value: DMSO


title: BSseq_A_M318_AGe_sMf_B


title: BSseq_A_M317_AGe_sMf_B


title: optimized RiboMethSeq, HEK293 siFBL rep1

description:
RMseq_HEK293_siFBL_rep1
RMseq_HEK293_siFBL_by_5end.txt
RMseq_HEK293_siFBL_by_3end.txt

value: FBL knockdown


title: MCF10A p53 WTKD control cells - RNA-seq

source_name: Shutdown of endogenous p53 using shRNA

value: p53 WTKD control cells


title: PS19_fE4_437G


title: Control, DMSO, Input

value: pancreas

value: mT3-2D KPC

value: Control


title: Control, JQ1, Input

value: mouse pancreatic cancer

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: JQ1 1 µM


title: optimized RiboMethSeq, HEK293 siCtrl rep3

description:
RMseq_HEK293_siCtrl_rep3
RMseq_HEK293_siCtrl_by_5end.txt
RMseq_HEK293_siCtrl_by_3end.txt

value: Ctrl


title: optimized RiboMethSeq, HEK293 siCtrl rep4

description:
RMseq_HEK293_siCtrl_rep4
RMseq_HEK293_siCtrl_by_5end.txt
RMseq_HEK293_siCtrl_by_3end.txt


title: BSseq_A_Col_Wt flower_A

value: Young flower

value: Wt

value: Col

value: Floral structure change


title: Brca2KO, JQ1, H3K27ac


title: MCF10A p53 Y220C mutant cells - ChIP-Seq - V5

value: MCF10A mammary epithelial cells

value: p53 Y220C mutant cells

value: V5 tag

value: untreated


title: optimized RiboMethSeq, HEK293 siCtrl rep2

description:
RMseq_HEK293_siCtrl_rep2
RMseq_HEK293_siCtrl_by_5end.txt
RMseq_HEK293_siCtrl_by_3end.txt

value: human embryonic kidney cells

value: small RNA (70-300nt)


title: MCF10A p53 R273C mutant cells - RNA-seq

value: p53 R273C mutant cells


title: BSseq_A_M317_AGe_rMf_A

value: rMf


title: MCF10A p53 Y220C mutant cells - RNA-seq


title: MCF10A p53 WTOE control cells - RNA-seq

value: p53 WTOE control cells


title: Control, JQ1, H3K27ac

value: pancreas

value: mT3-2D KPC

value: mouse pancreatic cancer

value: Control


title: Bsseq_A_Col_AGp_Sterile

value: Young flower

value: Sterile


title: MCF10A p53 R248W mutant cells - RNA-seq

source_name: ectopic expression of p53 R248W mutant protein with V5 tag at C-term

value: p53 R248W mutant cells


title: Brca2KO, DMSO, H3K27ac

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: DMSO


title: chromatin associated RNA, Neuron, PARIS2-seq

data_processing:
Sequencing data were preprocessed to remove adapters from the 5'end and 3’end using Trimmomatic software (v0.36).
PCR duplicates are removed using readCollapse script from the icSHAPE pipeline.
Reads were mapped to the hg38 genome using STAR program (v2.7.9).
The primary mapping alignments were filtered to remove low-confidence segments, rearranged and classified into six different types using gaptypes.py (https://github.com/zhipenglu/CRSSANT).
Gapped alignments were first assembled into duplex groups using CRSSANT software.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file contains disjoint RNA structures and interaction.

source_name: Neuron

growth_protocol: HEK293 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) + 10% fetal bovine serum (FBS, Gibco) + Penicillin-Streptomycin (Gibco) in 37°C incubator with 5% CO2. SHSY5Y was maintained in 1:1 mixture of Eagle’s Minimum Essential Medium and F12 Medium (ATCC, 30-2003) + 10% FBS + Penicillin–Streptomycin. Dr. Jian-fu Chen from University of Southern California help to prepare the human ES cells, human iPS cells and hiPSC derived cell lines, including Neural progenitor cells (NPC), Astrocyte and Neuron cells.

extract_protocol:
Total RNAs were isolated using TNA method. snoRNAs were enriched using antisense oligos (ASOs). Chromatin associated RNAs were extracted by standard cell fractionation procedure, nuclei are isolated and sedimentation is used to separate nuclear particles from the nucleoplasmic fraction.
The fragmented RNAs were end-repaired by T4PNK at 37 °C for 30 minutes. Adapter (/5rApp/AGATCGGAAGAGCGGTTCAG/3Biotin/) was ligated to end-repaired RNA fragments using high concentration T4 RNA ligase 1. Free adapters were removed by RecJf and 5’ deadenylase. RNA was purified with Zymo RNA clean and Concentrator-5 Kit. An RT-step and PCR amplification were coupled with barcoding.

treatment_protocol: Cells were in vivo crosslinked with 2.0 mg/ml amotosalen under UV365 nm.

value: Neuron

value: hiPSC derived neuron

value: WT

value: chromatin associated RNA


title: optimized RiboMethSeq, HEK293 siCtrl rep1

description:
RMseq_HEK293_siCtrl_rep1
RMseq_HEK293_siCtrl_by_5end.txt
RMseq_HEK293_siCtrl_by_3end.txt

value: human embryonic kidney cells

value: Ctrl

value: small RNA (70-300nt)


title: MCF10A p53 R248Q mutant cells - RNA-seq

source_name: ectopic expression of p53 R248Q mutant protein with V5 tag at C-term

value: MCF10A mammary epithelial cells

value: p53 R248Q mutant cells

value: untreated


title: Control, DMSO, H3K27ac

value: pancreas

value: mT3-2D KPC

value: mouse pancreatic cancer


title: BSseq_A_M318_AGe_rMf_A

value: Young flower

value: rMf

value: Floral structure change


title: chromatin associated RNA, NPC, PARIS2-seq

source_name: Neural progenitor cells (NPC)

value: Neural progenitor cells (NPC)

value: hiPSC derived NPC


title: chromatin associated RNA, Astrocyte, PARIS2-seq

source_name: Astrocyte

value: Astrocyte

value: hiPSC derived astrocyte


title: BSseq_A_Col_AGp//AGe_rMf


title: MCF10A p53 R273H mutant cells - RNA-seq

value: p53 R273H mutant cells


title: Bub1bKO1, JQ1

data_processing:
Raw data were aligned to mm10 genome using HISAT2
Read counts and normalized read counts were generated using the featureCounts
the differentially expressed genes were identified using DESeq2
Supplementary files format and content: DESeq2 normalized read count table

extract_protocol:
RNA was harvested using Cells were lysed with 1 mL of TRIzol (Thermo Fisher Scientific, 15596026) and 200 µL of Chloroform following the manufacturer’s instructions. The collected RNA was purified with PureLink RNA Mini Kit (Invitrogen, 12183018A) following the manufacturer’s protocol. mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
mRNA was enriched using oligo(dT) beads, and rRNA was removed using the Ribo-Zero kit. The mRNA was fragmented, and cDNA was synthesized by using an mRNA template and random hexamers primer, after which a second-strand synthesis buffer (Illumina), dNTPs, RNase H, and DNA polymerase I were added for the second-strand synthesis, followed by adaptor ligation and size selection. The library was sequenced by the Illumina Novaseq platform.

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: JQ1 1µM


title: Bub1bKO2, JQ1


title: MCF10A p53 Y163C mutant cells - RNA-seq

source_name: ectopic expression of p53 Y163C mutant protein with V5 tag at C-term

value: p53 Y163C mutant cells


title: chromatin associated RNA, iPS, PARIS2-seq

source_name: human iPSC line (clone inventory code: R138363028)

value: human iPSC line (clone inventory code:R138363028)

value: human iPSC line

value: WT

value: chromatin associated RNA


title: MCF10A p53 R175H mutant cells - RNA-seq

source_name: ectopic expression of p53 R175H mutant protein with V5 tag at C-term

value: MCF10A mammary epithelial cells

value: p53 R175H mutant cells

value: untreated


title: Bub1bKO3, DMSO

value: pancreas

value: mT3-2D KPC

value: mouse pancreatic cancer

value: DMSO


title: BSseq_A_M317_AGe_sMf_A

source_name: Young flower

value: Young flower

value: sMf

value: Floral structure change


title: BSseq_A_Col_AGp//AGe_sMf


title: chromatin associated RNA, ECs, PARIS2-seq

value: human embryonic stem cell


title: BSseq_A_M317_Wt flower_A

value: Wt


title: MCF10A p53 G245S mutant cells - RNA-seq

source_name: ectopic expression of p53 G245S mutant protein with V5 tag at C-term

value: p53 G245S mutant cells


title: Bub1bKO3, JQ1

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: JQ1 1µM


title: chromatin associated RNA, HEK293, PARIS2-seq

value: human embryonic kidney cells

value: WT


title: Bub1bKO2, DMSO


title: BSseq_A_M318_AGe_sMf_A


title: MCF10A p53 H179R mutant cells - RNA-seq

source_name: ectopic expression of p53 H179R mutant protein with V5 tag at C-term

value: MCF10A mammary epithelial cells

value: p53 H179R mutant cells


title: enriched snoRNA, SHSY5Y, PARIS2-seq

value: neuroblastoma cells

value: enriched snoRNA


title: BSseq_A_M318_Wt flower_A


title: MCF10A p53 Y234C mutant cells - RNA-seq

source_name: ectopic expression of p53 Y234C mutant protein with V5 tag at C-term

value: p53 Y234C mutant cells

value: untreated


title: Bub1bKO1, DMSO

value: pancreas

value: mT3-2D KPC

value: mouse pancreatic cancer

value: DMSO


title: BSseq_A_Col_AGe/rMf_A

value: Young flower

value: rMf

value: Floral structure change


title: enriched snoRNA, HEK293, PARIS2-seq


title: BSseq_A_Col_Wt flower_C

value: Wt

value: Col


title: AtmKO3, JQ1

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre

value: JQ1 1µM


title: CD8+ T cells, TVA, 2

city: Chicago

first: fan

last: hao

state: IL

address: 5801 S Ellis Ave

institute: University of Chicago

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNA-seq reads were aligned to the mm10 genome assembly using STAR
The aligned reads were then assigned to genes using RSEM
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: CD8+ T cells

growth_protocol: Mouse CD8+ T cells were maintained in Click's medium supplemented with 10% fetal bovine serum (FBS), 1% glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After activation with anti-CD3/28, mouse CD8+ T cells were treated with DMSO or 20 uM TVA for 24 hours

value: CD8+ T cells

value: Primary T cell

value: WT

value: TVA

value: 24 hours


title: AtmKO2, JQ1

source_name: pancreas


title: ssRNAseq_A_Col_35Se//AGe_rMf_Rep3

data_processing:
The obtained reads were trimmed and aligned to the reference Arabidopsis genome (TAIR10) using using HISAT2 with default parameters.
Those reads mapped to the sense and antisense starnds of AGe, AGp/M2 regions within a 17.3-kb genomic region were retrieved and counted using htseq-count (version 0.13.5; Anders et al., 2015) for calculation of the value of Normalized Read Per Million mapped reads (NRPM) in each region
Supplementary files format and content: xls file includes the value of NRPM in the AGe and AGp/M2 regions  within the 17.3-kb genomic region for each sample

extract_protocol:
Total RNA was extracted from young flowers pooled from five to ten lines with the same phenotype for each replicate using Tri-Reagent (Sigma, MO) followed by two rounds of phenol–chloroform extraction (50:50).
Approximately one µg of total RNA was used for construction of strand-specific RNA-seq (ssRNA-seq) library using the Illumina TruSeq® Stranded Total RNA Library Preparation Kit with Ribo-Zero™ Plant kit and TruSeq RNA CD barcode Index primers.  The total RNA was first treated with Turbo DNA-free (Fisher Scientific) to remove residual genomic DNA followed by Ribosomal RNA depletion, first- and second-strand cDNA synthesis, 3’ end adenylation, adapter ligation, and DNA fragment enrichment (12 cycles) according to the TruSeq stranded total RNA protocol provided. RNA fragmentation (3 minutes) was performed for each sample.  Libraries were pooled and sequenced using HiSeq X-Ten platform.


title: total RNA, HEK293, PARIS2-seq

value: human embryonic kidney cells

value: total RNA


title: CD8+ T cells, TVA, 3


title: CD8+ T cells, TVA, 1


title: AtmKO1, JQ1

value: pancreas

value: mT3-2D KPC


title: CD8+ T cells, DMSO, 3

value: DMSO


title: AtmKO3, DMSO

value: mouse pancreatic cancer


title: ssRNAseq_A_Col_35Se//AGe_rMf_Rep2

value: Young flower

value: rMf


title: ssRNAseq_A_Col_Ctr//AGe_rMf_Rep3

value: Floral structure change


title: AtmKO2, DMSO


title: CD8+ T cells, DMSO, 2


title: EndoCbH2 cells, shMAFB 3

city: Nashville

first: Xin

last: Tong

state: TN

address: 2213 Garland Ave.

institute: Vanderbilt University

data_processing:
Genialis Expression software
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
FastQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool
Aligned reads are summarized to gene-level counts by the featureCounts tool.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

growth_protocol: EndoCbH2 cells were maintained by methods described in PMID: 21865645

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using Ultra™ II RNA Library Prep (NEB) standard procedures.
Paired-End 150 bp

treatment_protocol: Lentivirus carrying shScramble (control) or shMAFB were used to infect EndoCbH2 cells. Puromycin was added 3 day post infection and cells were harvested 3 days after puromycin selection

value: Human beta cell

value: MAFB knockdown

value: shMAFB


title: EndoCbH2 cells, shMAFB 1


title: CD8+ T cells, DMSO, 1

value: CD8+ T cells


title: EndoCbH2 cells, shMAFB 2


title: ssRNAseq_A_Col_Ctr//AGe_rMf_Rep2

city: Kearneysville

first: Zongrang

last: Liu

address: 2217 Wiltshire Road

institute: USDA-ARS

treatment_protocol: Arabidopisis plants were transformed with various transgene cassetts for evaluation of silencing efficiency and mutant flower frequncy.


title: ssRNAseq_A_Col_Ctr//AGe_rMf_Rep1


title: AtmKO1, DMSO

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre


title: EndoCbH2 cells, shControl 2

value: WT

value: shControl


title: Brca2KO3, JQ1

value: JQ1 1µM


title: CD8+ T cells, siCreb1, TVA, 3

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

value: Primary T cell

value: Creb1 KD

value: TVA

value: 24 hours


title: EndoCbH2 cells, shControl 3


title: ssRNAseq_A_Col_Leaf_Rep3

source_name: Leaf

value: Leaf

value: Wt

value: Col


title: ssRNAseq_A_Col_Leaf_Rep2


title: Brca2KO2, JQ1

value: pancreas

value: mT3-2D KPC

value: mouse pancreatic cancer


title: Brca2KO1, JQ1


title: CD8+ T cells, siCreb1, DMSO, 3

value: DMSO


title: ssRNAseq_A_Col_Wt flower_ Rep3

value: Young flower

value: Floral structure change


title: ssRNAseq_A_Col_Leaf_Rep1


title: CD8+ T cells, siCreb1, TVA, 2

value: CD8+ T cells


title: D13_CD19def

data_processing:
The fastq files were assessed for initial quality using FastQC, trimmed for adapter sequences using TrimGalore  and aligned to GRCh38.p13 (Gencode release 35) with STAR aligner using twopassMode.
Transcript abundance was estimated using RSEM and imported into R using txImport and then processed using DESeq2, generating VST transformed data.
Assembly: GRCh38.p13 (Gencode release 35)
Supplementary files format and content: tab-delimited text files with DESeq2 VST log2 values for each Sample

source_name: Peripheral blood

extract_protocol:
Peripheral blood was obtained from healthy donors and the affected patient after informed consent. Mononuclear cells were obtained following lymphoprep density centrifugation. B-cell selection was carried out with a Miltenyi memory B-cell isolation kit, selecting for untouched total B cells using the first step of the manufacturer’s protocol which depletes non-B cells. Alternatively, naïve B cells were enriched by depletion of memory cells using anti-CD27 MACs beads (Mitenyi). B-cells were cultured in 24-well plates at 1x10^5 cells/ml in IMDM + 10% FBS with MEM amino acid solution (1:50) and Lipid Mixture 1, chemically defined (1:200) (all Thermo Fisher Scientific) and the addition of 20 U/ml human IL-2 (Roche), 50 ng/ml human IL-21 (Peprotech) and 10 μg/ml F(ab′)2 goat anti-human IgM/IgG (Jackson Immunoresearch) on previously irradiated CD40L-expressing fibroblasts. After 3 days, B cells were removed from the CD40L-cells by gentle pipette mixing. B cells were reseeded at in media containing 20 U/ml human IL-2  and 50 ng/ml human IL-21. On day 6, cells were seeded in media containing human IL-6 (10 ng/ml), human IL-21 (50 ng/ml), 100 U/ml multimeric APRIL (Adipogen) and 100nM gamma secretase inhibitor (GSI) inhibitor (L-685458; Sigma) and re-fed at day 10
RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).

value: Peripheral blood

value: Plasmacell


title: Brca2KO3, DMSO

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre


title: CD8+ T cells, siCreb1, DMSO, 2

value: Primary T cell


title: D6_CD19def

value: Plasmablast


title: D10_CD19def


title: Brca2KO2, DMSO


title: ssRNAseq_A_Col_Wt flower_Rep2


title: D3_CD19def


title: CD8+ T cells, siCreb1, TVA, 1

value: Creb1 KD

value: TVA


title: Brca2KO1, DMSO


title: ssRNAseq_A_Col_Wt flower_Rep1


title: EndoCbH2 cells, shControl 1

value: Human beta cell

value: WT

value: shControl


title: D0_CD19def

value: B-cell


title: Control3, JQ1

value: pancreas

value: mT3-2D KPC

value: JQ1 1µM


title: BSseg_A_Col_SALK_137982_rMf

data_processing:
Illumina paired-end bisulfite sequences were evaluated for quality using FastQC (version 0.11.9)
FASTQ files were aligned to the Araport11/TAIR10 Arabidopsis reference genome (Cheng et al. 2017) using the Bismark Bisulfite Read Mapper with the Hisat2 alignment algorithm
The methylation status of each cytosine in each context was extracted from the alignments with the bismark methylation extractor. The percent of methylated reads on a nucleotide level was calculated for regions of interest where total read depth was at least 4 reads.
Sequencing data in a 17.3-kb region containing the AG locus were retrieved and exported into xls for analysis of methylation rates and preparation of graphical presentation.
Supplementary files format and content: xls file includes methylation rate in each cytosine position within 17.3-kb genomic region for each sample

value: Young flower

value: rMf


title: Control2, JQ1

value: mouse pancreatic cancer


title: AOOs , scRNAseq

city: New Haven

first: Mario

last: Strazzabosco

state: CT

address: 300 Cedar street

department: Internal Medicine

institute: Yale School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 .
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Biliary organoids

extract_protocol:
Biliary organoids  were spun down and resuspended in 0.25% trypsin and incubated for 30 minutes at 37 °C. At the end of the incubation, organoids were mechanically dissociated by pipetting. Trypsin digestion was blocked by addition of ice-cold resuspension buffer (2% FBS, 1.25 mM CaCl2, 4 mM MgCl2, 10mM HEPES, 5 mM glucose in 1X HBSS) and cells were recovered by centrifugation (1200 rpm for 4 minutes). Cells were resuspended in resuspension buffer, filtered through a 35 µm filter (Corning), counted and checked for viability using Countess II automatic cell counter (Thermo Fisher Scientific). Cells were recovered by centrifugation (1500 rpm for 5 minutes) and resuspended at the desired concentration in PBS containing 0.04% bovine serum albumin.
For 10X Genomics, single cell RNA sequencing 10,000 cells were loaded onto 10X Genomics Single Cell 3' Chips along with maaster mix as per manufacturer's instructions. Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The resulting libraries were sequenced on a NovaSeq6000.

value: Biliary organoids

value: AOOs


title: CD8+ T cells, siNTC, TVA, 3

value: CD8+ T cells

value: 24 hours


title: BSseq_A_Col_SALK_049844_rMf

value: Floral structure change


title: CD8+ T cells, siNTC, TVA, 2

value: Primary T cell


title: CD8+ T cells, siNTC, TVA, 1

value: TVA


title: BME 10%, scRNAseq

description: 10x Genomics

value: BME 10%


title: Control1, JQ1

value: Kras +/LSL-G12D; Trp53 +/LSL-R172H; Pdx1-Cre


title: EMB, scRNAseq

description: 10x Genomics

value: EMB


title: BSseq_A_Col_35Se//AGe_rMf


title: CD8+ T cells, siNTC, DMSO, 3

value: WT

value: DMSO


title: Control3, DMSO

value: pancreas

value: mT3-2D KPC


title: CD8+ T cells, siNTC, DMSO, 2


title: ASF-4-6

city: Kita-ku

first: Eji

last: Naru

state: Tokyo

address: 48-18 Sakae-cho

department: Dermatology and Cosmeceutical Research Laboratories

institute: KOSÉ Corporation

data_processing:
UMI quantifying performed using Cellranger 3.1.0 (10x Genomics)
Assembly: hg38.p13
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

growth_protocol: The ASF-4 cell line was established from the dermis of the inner forearm of the same male donor at different ages. ASF-4 cells were cultured in MEM3 containing 10% FBS.

extract_protocol: Single cell RNA libraries were generated using  Chromium Next GEM Chip G Single Cell Kit (cat no PN-1000120), Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1, 16 (cat no PN-1000121)   and Dual Index Kit TT (cat no PN-1000215)

value: Dermal fibroblast

tag: Sex

value: male

tag: donor age

tag: pdl


title: CD8+ T cells, siCreb1, DMSO, 1

value: Creb1 KD

tag: time


title: Control2, DMSO

value: mouse pancreatic cancer


title: Control1, DMSO


title: CD8+ T cells, siNTC, DMSO, 1


title: BSseq_A_Col_Wt flower_B

value: Young flower

value: Wt

value: Col


title: ASF-4-1


title: Vitrified0 hour (VF_plate1_H07_S35)

status: Public on Sep 20 2023

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

data_processing:
Sequenced reads were uploaded into Partek Flow software for data analyses. We first filtered out potential rDNA and mtDNA contaminants using Bowtie 2. Filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner. Raw read counts were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm. Raw read counts were then normalized based on the Transcripts Per Million (TPM) method, and differential expression analysis was performed by using the DESeq2(R).
Assembly: Ensembl Transcripts release 99
Supplementary files format and content: Raw_counts.txt contains the raw read counts that were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm.
Supplementary files format and content: Log2(TPM+1).txt contains the log2 transformed normalized counts  based on the Transcripts Per Million (TPM) method

source_name: Ovarian follicle

growth_protocol: Vitrified and fresh follicles with intact morphology were encapsulated in 0.5% (w/v) alginate and cultured in 96-well plates, with each well containing one bead and 100 μl growth media. The growth media consisted of 50% αMEM Glutamax (Thermo Fisher Scientific) and 50% F-12 Glutamax (Thermo Fisher Scientific) supplemented with 3 mg/ml bovine serum albumin (BSA; Sigma-Aldrich), 10 mIU/ml recombinant follicle stimulating hormone (rFSH; gifted by Organon, Jersey City, NJ, USA), 1 mg/ml bovine fetuin (Sigma-Aldrich), and 5 μg/ml insulin-transferrin-selenium (ITS, Sigma-Aldrich). Follicles were cultured for 8 days at 37 °C in a humidified environment of 5% CO2 .in air.

extract_protocol:
RNA was extracted using the RNEasy Plus Micro Kit (Qiagen) according to the manufacturers recommendations.
Smart-Seq2 cDNA synthesis was performed on isolated follicle RNA with Maxima H Minus reverse transcriptase (ThermoFisher). Whole transcriptome amplified (WTA) product was purified with AMPure XP beads (Beckman Coulter), quantified with Quanit-iT PicoGreen dsDNA Assay (ThermoFisher), normalized and used for preparing paired-end sequencing libraries with Nextera XT (Illumina, #FC-131) according to the manufacturer’s instructions.
Illumina NextSeq500/550

treatment_protocol: On day 8 of eIVFG, mature follicles with diameter at 300-350 μm were removed from alginate beads by incubation in L15 media containing 1% FBS and 10 IU/ml alginate lyase from Flavobacterium multivorum (Sigma-Aldrich) at 37 °C for 20 minutes. Follicles were then transferred to the maturation media and ovulation was induced by incubation in the maturation media containing 50% αMEM Glutamax and 50% F-12 Glutamax supplemented with 10%FBS, 1.5 IU/ml hCG (Sigma-Aldrich], 10 ng/ml epidermal growth factor (EGF; BD Biosciences), and 10 mIU/ml rFSH. At 0, 1, 4, and 8 hours post-hCG treatment,  follicles were collected and washed in 1X phosphate buffered saline (PBS; Invitrogen) three times .

value: Ovarian follicle

value: Vitrified

value: hCG

value: 0 hour


title: Vitrified0 hour (VF_plate1_H05_S33)


title: Vitrified0 hour (VF_plate1_H02_S30)


title: Vitrified0 hour (VF_plate1_G10_S28)


title: Vitrified0 hour (VF_plate1_G06_S24)


title: Vitrified0 hour (VF_plate1_G08_S26)


title: Vitrified0 hour (VF_plate1_H01_S29)


title: Vitrified0 hour (VF_plate1_G07_S25)


title: Vitrified0 hour (VF_plate1_G05_S23)


title: Vitrified0 hour (VF_plate1_G04_S22)


title: Vitrified0 hour (VF_plate1_G02_S20)


title: Fresh0 hour (VF_plate1_F08_S18)

value: Fresh


title: Vitrified0 hour (VF_plate1_G01_S19)


title: BSseq_A_Col_AGe_rMf_C

extract_protocol:
Genomic DNA was isolated from flowers pooled from five to ten lines with the same flower phenotype for each replicate using the Dneasy® Plant Mini Kit (Qiagen, Hilden, Germany).
Bisulfite treatment, library construction and sequencing were performed by BGI Americas Cooperation (Cambridge, MA).

value: rMf

value: Floral structure change


title: Fresh0 hour (VF_plate1_F07_S17)

value: WT


title: Fresh0 hour (VF_plate1_F05_S15)


title: Fresh0 hour (VF_plate1_F06_S16)


title: Fresh0 hour (VF_plate1_F02_S12)


title: Fresh0 hour (VF_plate1_F03_S13)


title: Fresh0 hour (VF_plate1_E10_S10)


title: Fresh0 hour (VF_plate1_F01_S11)


title: Fresh0 hour (VF_plate1_F04_S14)


title: Vitrified0 hour (VF_plate1_H03_S31)


title: Fresh0 hour (VF_plate1_E09_S9)


title: Vitrified0 hour (VF_plate1_G03_S21)


title: Vitrified0 hour (VF_plate1_G09_S27)


title: Fresh0 hour (VF_plate1_E08_S8)


title: Fresh0 hour (VF_plate1_E05_S5)


title: Fresh0 hour (VF_plate1_E07_S7)


title: Fresh0 hour (VF_plate1_E04_S4)


title: Fresh0 hour (VF_plate1_E06_S6)


title: Fresh0 hour (VF_plate1_E02_S2)


title: Fresh0 hour (VF_plate1_E03_S3)


title: Vitrified8 hours (12xx20YW_X_D10_S37)

value: 8 hours


title: Vitrified8 hours (12xx20YW_X_D09_S36)


title: Vitrified8 hours (12xx20YW_X_D08_S35)


title: Vitrified8 hours (12xx20YW_X_D07_S34)


title: Vitrified8 hours (12xx20YW_X_D06_S33)


title: Fresh0 hour (VF_plate1_E01_S1)


title: Vitrified8 hours (12xx20YW_X_D04_S31)


title: Vitrified8 hours (12xx20YW_X_D01_S28)


title: Vitrified8 hours (12xx20YW_X_D03_S30)


title: Vitrified1 hour (12xx20YW_X_B09_S21)

value: 1 hour


title: Vitrified1 hour (12xx20YW_X_B07_S19)


title: Vitrified1 hour (12xx20YW_X_B08_S20)


title: Vitrified1 hour (12xx20YW_X_B05_S17)


title: Vitrified1 hour (12xx20YW_X_B03_S15)


title: Vitrified1 hour (10xx21YW_X_F09_S18)


title: Vitrified1 hour (12xx20YW_X_B06_S18)


title: Vitrified1 hour (12xx20YW_X_B04_S16)


title: Vitrified1 hour (10xx21YW_X_F04_S13)


title: Vitrified1 hour (12xx20YW_X_B02_S14)


title: Vitrified1 hour (10xx21YW_X_F03_S12)


title: Vitrified1 hour (10xx21YW_X_F01_S10)


title: Vitrified1 hour (10xx21YW_X_F02_S11)


title: Vitrified4 hours (10xx21YW_X_D09_S28)

value: 4 hours


title: Vitrified8 hours (10xx21YW_X_E09_S38)


title: Vitrified4 hours (10xx21YW_X_D07_S26)


title: Vitrified8 hours (10xx21YW_X_E05_S34)


title: Vitrified8 hours (12xx20YW_X_D05_S32)


title: Vitrified4 hours (10xx21YW_X_D04_S23)


title: Vitrified4 hours (10xx21YW_X_D05_S24)


title: Vitrified4 hours (10xx21YW_X_D03_S22)


title: Vitrified1 hour (12xx20YW_X_B01_S13)


title: Fresh1 hour (10xx21YW_X_C05_S14)


title: Vitrified4 hours (10xx21YW_X_D01_S20)


title: Fresh1 hour (10xx21YW_X_C07_S16)


title: Vitrified4 hours (10xx21YW_X_D02_S21)


title: Fresh1 hour (10xx21YW_X_C02_S11)


title: Fresh1 hour (10xx21YW_X_C04_S13)


title: Vitrified8 hours (10xx21YW_X_E10_S39)


title: Fresh1 hour (10xx21YW_X_C01_S10)


title: Fresh8 hours (10xx21YW_X_B03_S3)


title: Fresh8 hours (10xx21YW_X_B07_S7)


title: Fresh8 hours (10xx21YW_X_B01_S1)


title: Fresh4 hours (10xx21YW_X_A04_S4)


title: Fresh4 hours (10xx21YW_X_A05_S5)


title: Fresh4 hours (10xx21YW_X_A01_S1)


title: Fresh4 hours (10xx21YW_X_A07_S7)


title: Fresh4 hours (10xx21YW_X_A02_S2)