title: CSENaringenin3


title: 33C Macaca fascicularis LT Mock Patient5 Batch1

status: Public on Aug 08 2023

type: SRA

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

country: France

institute: INSERM U1052, UCBL1, ENS de Lyon

library_source: transcriptomic

data_processing:
Raw reads were quantified using the quasi-mapping-based mode of Salmon.
The references used were the Genome Reference Consortium Human Build 38 (hg38, Genbank accession GCA_000001405.15),
for the Human analysis and Macaca_fasicularis_5.0 (Genbank accession GCA_000364345.1) for the Monkey analysis.
Raw counts were processed using package DESeq2 in R/Bioconductor.
Assembly: hg38, GCA_000001405.15 and Macaca_fasicularis_5.0, GCA_000364345.1
Supplementary files format and content: Tab-delimited csv file containing normalized counts for Homo sapiens samples,
Supplementary files format and content: another tab-delimited csv file containg normalized counts for Macaca fascicularis samples.

molecule: total RNA

organism: Macaca fascicularis

source_name: PBMCs

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human donors (n=6) and Mauritius cynomolgus macaques (n=6) using ficoll-plaque PLUS.

extract_protocol:
PBMCs were immediately sorted into pDC, mDC, T and B cell populations by FACS, collected and lysed using Trizol. RNA extraction was performed using Phasemaker Tubes Complete System.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

treatment_protocol: For each condition, 15x10^6 PBMCs were incubated 2 h at 37°C with 5% CO2 in RPMI-1640 culture medium with or without HBV (MOI 100).

tag: tissue

value: PBMCs

tag: cell type

value: LT

tag: treatment

value: Mock

tag: patient

tag: batch


title: W4_ROs_1042_N1

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

data_processing:
Image analysis and base calling is performed using the Illumina Real Time Analysis (3.4.4) software with default parameters.
Pass-filtered reads were mapped using STAR 2.7.3a
Count table of the gene features was obtained using FeatureCounts
Statistics and Differential expression analysis done with EdgeR
Pathways analysis representation done with the package GOPlot
Assembly: Ensembl genome assembly GRCh38 (release 98)
Supplementary files format and content: Tab-delimited text files of the raw counts

organism: Homo sapiens

source_name: Retinal Organoids

extract_protocol:
Total RNAs were extracted using the NucleoSpin RNA XS kit according to the manufacturer’s protocol. RNA yields and quality were determined using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed from 1 µg of total RNAs using the NEB Next Ultra II Directional RNA (New England Biolabs) and paired-end sequencing of 100 bases length was performed on a Novaseq system (Illumina).

value: Retinal Organoids

tag: cell line

value: retinal cells

tag: time

value: Week 4

value: ProNM


title: Usp7IAA_2

city: Hangzhou

first: Chao

last: Liu

state: State...

address: Zhejiang University

country: China

institute: Zhejiang University

data_processing:
The FASTQ data were trimmed with fastp.
mapped to mouse genome mm10 via HISAT2 to generate count files.
Genome_build: mm10
Supplementary_files_format_and_content: count

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cells E14 were cultured on 0.1% gelatin (Yeasen, Shanghai, China)-coated plates in Dulbecco’s Modification of Eagel’s Medium with 4.5g/L glucose(10-013-CVR; USA, Corning), supplemented with 15% fetal bovin serum (FBS, Cat:10099; Gibco, Australia), GlutaMAX (35050-61; Gibco, USA), MEM non-essential amino acids (11140-050, Gibco, USA), penicillin/streptomycin (Gibco), 0.1mM β-mercaptoethanol (M3148; Sigma), and 1000U/ml leukemia inhibitory factor (LIF, Millipore).

extract_protocol:
RNA was extracted by RNAiso Plus (Takara, 9109) following the manufacturer’s instruction.
RNA-seq library preparation and sequencing were performed by Novogene in Tianjin, China

treatment_protocol: The auxin analogue indole-3-acetic acid (IAA, 500μM) was used to induce the degradation of AID-tagged Usp7 protein.

tag: cell strain

tag: cell stype

value: mouse embryonic stem cell

tag: genotype

value: Usp7(-/-),FLAG-AID-Usp7 and HA-Usp7-wildtype overexpressed


title: Usp7IAA_1


title: 1C Macaca fascicularis LT Mock Patient1 Batch1


title: 25C Macaca fascicularis LT Mock Patient4 Batch2


title: 17C Macaca fascicularis LT Mock Patient3 Batch1


title: ControlIAA_3

value: Usp7(-/-),FLAG-AID-Usp7 overexpressed


title: 5C Macaca fascicularis LT HBV Patient1 Batch1

value: HBV


title: CSENaringenin1

city: Guangzhou 510275

first: Weiyang

last: Fan

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCm39 (mmu10)
Supplementary files format and content: excel,expression profiles

source_name: Small RNA of EVs from MH-S cells

growth_protocol: Mouse alveolar macrophage (MH-S, CRL-2019 from ATCC) cell lines were maintained in RPMI 1640, 0.05 mM 2-mercaptoethanol, GlutaMAX™ supplemented base medium. The base media were supplemented with penicillin-streptomycin (100 U/mL and 100 μg/mL, respectively) and 10% EV-depleted fetal bovine serum (i.e., FBS was ultracentrifuged at 100,000 g for 12 h, and then the supernatants were filtered by 0.1 µm sterile membrane to remove particle and EVs) for continuous maintenance of cultures.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: MH-S cells were divided into four groups, depending on the different treatments with or without 2.5% CSE, or 100 μM naringenin (Sigma-Aldrich, Missouri, USA) for 24 h.

value: MH-S cells

value: 24 hours

tag: source

value: extracellular vesicles (EVs)

value: EVs from 2.5% CSE and 100 μM naringenin co-treated MH-S cells


title: CSE5

value: EVs from 2.5% CSE-treated MH-S cells


title: FS, donor2, scRNA-seq

city: Chicago

first: Rui

last: Yi

address: 303 E. Chicago Avenue

country: USA

institute: Northwestern University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing genes by barcode counts matrices

molecule: polyA RNA

source_name: Foreskin

extract_protocol:
Fresh human foreskin specimens were cut into 4 mm x 4 mm pieces. The fat layer was trimmed off from the bottom. Then the skin was floated on 2 mL of dispase in a 6-well plate and incubated at 37 °C for 1 hour. The epidermis was separated from the dermis and trypsinized for 12 minutes at 37 °C to get the epidermal single-cell suspension. For the dermis part, it was further cut into smaller pieces, then incubated with 0.25% collagenase I in 2 mL HBSS for 1 hour at 37 °C. Collagenase-treated pieces were trypsinized for 10 minutes at 37 °C. The tissue was then dissociated by pipetting and single-cell suspension was obtained. Epidermal and dermal cells were combined at a 1:1 ratio for loading onto the 10X Chromium Controller.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Foreskin

tag: Sex

value: Male

tag: age

value: Neonatal


title: FS, donor1, S1, 10X Visium FFPE ST

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation, and spatial localization were made using the Space Ranger software v1.3.1.
Assembly: GRCh38
Supplementary files format and content: H5 files containing genes by barcode counts matrices, JPEG/PNG of all replicate images, barcode file containing spot barcode position information, and Visium tissue position lists per sample
Library strategy: 10X FFPE Visium

extract_protocol:
Fresh human foreskin samples from the donor were cut with 8mm punches. They were then fixed with 4% PFA and embedded with paraffin and stored in sealed bags at room temperature. 5mm sections were cut with the microtome. The cut sections were transferred onto capture area of the Visium FFPE slide in the waterbath following the manufacter's instructions.
Library was performed according to the manufacter’s instructions (Visium Spatial Gene Expression for FFPE v1 protocol, 10x Genomics).


title: FS, donor1, S2, 10X Visium FFPE ST

description: 10x Genomics


title: Suspension, Immune, replicate 3, scRNAseq

city: Leiden

first: Vincent

last: van Unen

state: ZH

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University

description: 10x Genomics

data_processing:
Sequences from scRNA-seq were processed with Cell Ranger (v.6.1.1) software (10X Genomics) with UMI (unique molecular identifier) collapsing and alignment to the GRCh38 human transcriptome. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ALI Distal Lung Organoid

growth_protocol: Human distal lung was washed with PBS, minced finely on ice, and resuspended in Cultrex Rat Collagen I ((R&D). 1mL of tissue-collagen suspension was layered on top of pre- solidified 1 mL collagen gel within a 30 mm, 0.4mm inner transwell. After fully solidifying, the 6 collagen transwells were placed in a standard 6-well tissue culture plate. 1mL of lung ALI culture media (see below) was added into the tissue culture plate, below the bottom surface of the collagen-containing transwell. Media was changed twice a week.

extract_protocol:
Organoids were harvested either from collagen or suspension, digested into single-cell suspensions, and sorted on a BD FACSAria II SORP for singlet discrimination, followed by live/dead gating, then CD45-/+gating, and analyzed using scRNAseq.
Library was performed according to the manufacter’s instructions (single cell 5’ protocol, 10x Genomics). 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 poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains  Ilumina primer sequences, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Immune

value: ALI Distal Lung Organoid

tag: culture

value: Suspension

value: 76 yrs

tag: infection status

value: non-infected


title: ControlIAA_2

value: mouse embryonic stem cell


title: CSE4


title: Tissue, Nonimmune, replicate 2, scRNAseq

description: 10x Genomics

source_name: Distal Lung tissue

value: NonImmune

value: Distal Lung tissue

value: Tissue

value: 66 yrs


title: 45C Macaca fascicularis LT HBV Patient6 Batch2

value: PBMCs

value: LT

value: HBV


title: CSE3

value: MH-S cells

value: 24 hours

value: extracellular vesicles (EVs)

value: EVs from 2.5% CSE-treated MH-S cells


title: Tissue, Immune, replicate 2, scRNAseq

description: 10x Genomics

value: Immune

value: Male


title: ControlIAA_1

value: Usp7(-/-),FLAG-AID-Usp7 overexpressed


title: CSE2


title: Control_3


title: Collagen, Nonimmune, replicate 2, scRNAseq

description: 10x Genomics

value: ALI Distal Lung Organoid

value: Collagen


title: 37C Macaca fascicularis LT HBV Patient5 Batch1


title: 29C Macaca fascicularis LT HBV Patient4 Batch2


title: CSENaringenin2

value: EVs from 2.5% CSE and 100 μM naringenin co-treated MH-S cells


title: Control_2

value: mouse embryonic stem cell


title: CSE1


title: 21C Macaca fascicularis LT HBV Patient3 Batch1


title: C224SIAA_3

value: Usp7(-/-),FLAG-AID-Usp7 and HA-Usp7-C224S overexpressed


title: Suspension, Immune, replicate 1, scRNAseq

description: 10x Genomics

value: Suspension

value: 75 yrs

value: non-infected


title: Normal4

value: EVs from normal cultured MH-S cells


title: Normal3


title: Normal5


title: Collagen, Nonimmune, replicate 1, scRNAseq

description: 10x Genomics

value: NonImmune


title: 42C Macaca fascicularis LB Mock Patient6 Batch4

value: PBMCs

value: LB

value: Mock


title: 34C Macaca fascicularis LB Mock Patient5 Batch3


title: Suspension, Nonimmune, replicate 1, scRNAseq

description: 10x Genomics

value: Female

value: 48 yrs


title: Normal2

value: MH-S cells

value: 24 hours

value: extracellular vesicles (EVs)


title: 2C Macaca fascicularis LB Mock Patient1 Batch3


title: Collagen, Immune, replicate 1, scRNAseq

description: 10x Genomics

value: Immune

value: ALI Distal Lung Organoid

value: Collagen

value: Male


title: Usp7_Rybp

library_source: genomic

data_processing:
library strategy: CUT&Tag
The fastq files were checked by FastQC for quality control
alignment to mm10 and E. coli genome (for spike-in calibration) by Bowtie2 (PMID: 22388286) using parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Mapped reads were filtered and file format conversion were performed by samtools
Read pairs that are on the same chromosome and fragment length less than 1000bp were kept. Spike-in calibration was performed by Bedtools
Peak calling was performed by SEACR
Genome_build: mm10
Supplementary_files_format_and_content: peak csv files
Supplementary_files_format_and_content: bigwig files generated by Bedtools

molecule: genomic DNA

extract_protocol: CUT&Tag libraries were constructed via the Hyperactive In-Situ ChIP Library Prep Kit for Illumina(pG-Tn5) (TD901, Vazyme, Nanjing, China) according to the manufacturer’s instructions.

value: mouse embryonic stem cell

tag: cut&tag antibody


title: MD_75_S60

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

data_processing:
fastq files were aligned to ensembl human reference genome hg38 using HISAT2 (Version 2.1.1, Galaxy).
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1, Galaxy) algorithm
Expression data was normalized using DESEQ2 (Version 2.11.40.6) followed by normalizaton with RUVrseq, k = 4, estimation of variation (Version 1.24.0)
Differentially expressed genes (10% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Assembly: hg38
Supplementary files format and content: DESEQ2 differential expression analysis output

source_name: Bulk OFC tissue

extract_protocol:
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.

value: Bulk OFC tissue

value: male

tag: condition

value: MDD


title: Normal1

value: EVs from normal cultured MH-S cells


title: 26C Macaca fascicularis LB Mock Patient4 Batch4

tag: tissue

value: PBMCs


title: Usp7IAA_3

value: Usp7(-/-),FLAG-AID-Usp7 and HA-Usp7-wildtype overexpressed


title: MD_73_S90


title: 44870_17_Spleen-STAT3ko_to_WT-CD8-2

city: Duarte

first: Defu

last: Zeng

state: CA

address: 1500 E Duarte Rd

department: Immunology & Theranostics

institute: City of Hope National Medical Center

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 RPKM values for each Sample

source_name: Spleen

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

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

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

value: Spleen

tag: cell type

value: CD8 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: 10C Macaca fascicularis LB Mock Patient2 Batch4

value: LB

tag: treatment

value: Mock


title: C224S_Rybp


title: Collagen, Immune, replicate 2, scRNAseq

description: 10x Genomics

value: Immune

value: 66 yrs

value: non-infected


title: Control_1

value: Usp7(-/-),FLAG-AID-Usp7 overexpressed


title: IAA_Rybp

value: mouse embryonic stem cell


title: 44732_5_Spleen-STAT3ko_to_WT-CD8-1


title: 13C Macaca fascicularis LT HBV Patient2 Batch2

value: LT

value: HBV

tag: patient


title: C224SIAA_2

value: Usp7(-/-),FLAG-AID-Usp7 and HA-Usp7-C224S overexpressed


title: 44869_16_Spleen-WT_to_WT-CD8-2

value: WT


title: MD_63_S96

value: Bulk OFC tissue

value: male

value: MDD


title: 22C Macaca fascicularis LB HBV Patient3 Batch3

value: PBMCs

tag: batch


title: IAA_H3K27me3


title: 44867_14_Spleen-STAT3ko_to_WT-CD4-2

value: Spleen

value: CD4 T cell

value: hematopoietic cell transplantation


title: Usp7_H3K27me3


title: C224SIAA_1


title: 44731_4_Spleen-WT_to_WT-CD8-1

value: CD8 T cell

value: Day 6 after HCT


title: 6C Macaca fascicularis LB HBV Patient1 Batch3

value: LB


title: 46C Macaca fascicularis LB HBV Patient6 Batch4


title: Ctrl_Rybp


title: MD_71_S83


title: 38C Macaca fascicularis LB HBV Patient5 Batch3


title: 44866_13_Spleen-WT_to_WT-CD4-2


title: Ctrl_H3K27me3


title: 44729_2_Spleen-STAT3ko_to_WT-CD4-1


title: 14C Macaca fascicularis LB HBV Patient2 Batch4


title: MD_56_S62


title: MD_53_S91


title: MD_58_S63


title: Usp7_H2AK119ub


title: MD_51_S79


title: 44728_1_Spleen-WT_to_WT-CD4-1


title: Inha PND0 KO 4295_3

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

department: Institute for Veterinary Anatomy,  Histology and Embryology

country: Germany

institute: Justus Liebig University Giessen

data_processing:
Raw FASTQ files were analysed using the RNAsik (v1.5.4) pipelineusing STAR aligner.
Reads were quantified using FeatureCountsproducing the raw genes count matrix and various quality control metrics.
Raw counts were then analysed with Degust, a web tool which performs differential expression analysis using limma-voom normalisation, producing counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation(Robinson and Oshlack, 2010)for RNA composition normalisation.
Differentially expressed genes (DEGs) inInhaWT and KO testis at each age were defined as those with a false-discovery rate (FDR) of < 0.05, showing a > 3-fold (absolute log fold-change >1.5) change in expression.
List of DEGs was submitted to DAVID to identify significantly associated functions, and upstream regulators and gene networks were generated using the IPA software using criteria of  p-value ≤0.05 and a Z-score of (inhibition) -3 ≤ Z ≥ 3 (activated).
Assembly: GRCm38 (Ensemble release 84)
Supplementary files format and content: Excel spreadsheet with raw counts for every gene and every sample

source_name: Testis

extract_protocol:
RNA was extracted from testis tissue using the Qiagen RNeasy Mini kit with on-column Dnase treatment, according to manufacturers instructions
Libraries were sequenced on the DNBSEQ-G400 with the PE100 by BGI-Hong Kong Co. Ltd

treatment_protocol: Whole testes were collected from Inha WT and KO mice aged E13.5, E15.5 or PND 0 (day of birth).

value: Testis

value: PND 0

tag: organ

value: Inha KO

tag: strain


title: Inha PND0 KO 4295_4


title: C224S_H2AK119ub

tag: cell strain

value: mouse embryonic stem cell


title: C224S_H3K27me3

tag: cell stype


title: 44877_24_Liver-STAT3ko_PD-1ko_to_WT-CD8-2

source_name: Liver

value: Liver

tag: genotype

value: STAT3ko PD-1ko

tag: time


title: IAA_H2AK119ub


title: FD_78_S84

tag: Sex

value: female


title: 44876_23_Liver-STAT3ko_to_WT-CD8-2


title: FD_77_S68

value: Bulk OFC tissue


title: Inha PND0 KO 4183

tag: age


title: Inha PND0 WT 4296

value: Inha WT


title: 44875_22_Liver-WT_to_WT-CD8-2

value: WT


title: Inha PND0 WT 4183_7


title: Ctrl_H2AK119ub


title: FD_72_S69

value: MDD


title: 44738_11_Liver-STAT3ko_to_WT-CD8-1


title: FD_70_S89


title: Inha PND0 WT 4183_6


title: Usp7 CUT&tag


title: SiEs12_CITE

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description: Single-cell RNA-seq with 10x Genomics 5' v2 CITE

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Genome_build: mm10
Supplementary_files_format_and_content: sc_SiEs12_cd45jaml_annotation.txt.gz metadata for 5976 cells in TAB delimited TXT
Supplementary_files_format_and_content: sc_SiEs12_cd45jaml_feature_barcodes.csv.gz Cell Ranger's feature table to demultiplex TotalSeq C data.
Supplementary_files_format_and_content: sc_SiEs12_cd45jaml_umi.txt.gz UMI counts for 5976 cells and 15416 features in TAB delimited TXT

source_name: Tumor

extract_protocol:
CD45+JAML+ TREG cells were sorted into 1.5ml collection tubes containing 500ul of a 1:1 solution of PBS and FBS and a 1:100 dilution of Rnase inhibitor. Subsequent processing was performed as to manufacturers (10x Genomics) instructions
RNA libraries were constructed following the manufacturers instructions

value: CD45+JAML+ Tcells isolated from tumor


title: 44737_10_Liver-WT_to_WT-CD8-1


title: FD_66_S64


title: Inha E15.5 KO 4138_3


title: FD_64_S66


title: Inha E15.5 KO 589_3


title: FD_61_S67


title: Inha E15.5 KO 4136


title: SiEs12_Gex

description: Single-cell RNA-seq with 10x Genomics 5' v2 GEX


title: 168_antiAMICA1_C4_CD8_Tcell

description: <400 cells bulk, full-transcriptome (Smart-seq2)

data_processing:
FASTQ was merged and filtered using fastp (v0.20.1)
Reads were aligned with the STAR aligner (v2.7.3a)
samtools (v0.1.19-44428cd) was used to index and sort the BAM files from STAR
QC reports was performed with bamCoverage (v3.3.1) and Qualimap (vv.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR's BAM aligned output
Genome_build: mm10
Supplementary_files_format_and_content: bulk_counts.txt.gz raw counts for 202 samples in TAB delimited TXT
Supplementary_files_format_and_content: bulk_metadata.txt.gz metadata for 202 samples in TAB delimited TXT
Supplementary_files_format_and_content: bulk_tpm.txt.gz transcripts per million reads (TPM) for 202 samples in TAB delimited TXT

extract_protocol:
CD4+FOXP3+ or CD8+ T cells from different treatment conditions were sorted into PCR tubes containing 8ul lysis buffer
Bulk RNA-seq libraries were prepared for sequencing using the Smart-seq2 protocol adapted for samples with small cell numbers (Rosales et al, 2018) and following standard Illumina protocols.

treatment_protocol: B16F10-OVA tumor-bearing mice were treated with 200ug of either isotype control antibody, anti-PD-1 antibody or anti-JAML antibody. 1 day later, the tumors were harvested and the  tumor-infiltrating cells were purified, FACS stained and sorted into lysis buffer

value: anti-JAML


title: 44874_21_Liver-STAT3ko_PD-1ko_to_WT-CD4-2

value: CD4 T cell

value: hematopoietic cell transplantation


title: 44873_20_Liver-STAT3ko_to_WT-CD4-2

value: Day 6 after HCT


title: MD_52_S80

value: male


title: Inha E15.5 WT 4195_5

value: Testis


title: 167_antiAMICA1_C3_CD8_Tcell


title: 44872_19_Liver-WT_to_WT-CD4-2


title: Input


title: FD_57_S82


title: FD_60_S92


title: 44736_9_Liver-STAT3ko_PD-1ko_to_WT-CD4-1


title: Inha E15.5 WT 4138


title: 44739_12_Liver-STAT3ko_PD-1ko_to_WT-CD8-1

value: CD8 T cell


title: 166_antiAMICA1_C2_CD8_Tcell


title: 44735_8_Liver-STAT3ko_to_WT-CD4-1


title: FD_55_S94


title: 165_antiAMICA1_C1_CD8_Tcell


title: Inha E13.5 KO 375_5

value: Inha KO


title: Inha E13.5 KO 467


title: FD_54_S81


title: 44734_7_Liver-WT_to_WT-CD4-1


title: MC_74_S59

value: control


title: ITK-SYK+ CD4+ T cells PD1 KO replicate 4

city: Munich

first: Tim

last: Wartewig

address: Einsteinstrasse 25

department: Clinical Chemistry

institute: TUM

description: TAAGAT

data_processing:
Raw sequencing data was processed with DropSeq-tools (v1.12) using gene annotations from the Ensembl GRCm38.87 database to generate sample- and gene-wise UMI tables.
Downstream analysis was conducted using R v3.4.452 and DESeq2 v1.18.15375
Assembly: mm10
Supplementary files format and content: tab-delimited text file include counts values for each Sample

source_name: ITK-SYK+ CD4+ T cells (primary cells)

extract_protocol:
Five days later, the spleens were harvested and 1,000 eGFP+ ITK-SYK-expressing CD4+ T cells from both genotypes were directly sorted (FACSAria Fusion, BD Biosciences) into a 96-well PCR plate pre-filled with 10 µL of 1× TCL buffer (1070498, Qiagen) containing 1% (v/v) β-mercaptoethanol (M6250, Sigma).
Library preparation for bulk 3-sequencing of poly(A)-RNA was performed as outlined earlier (Parekh et al. Sci Rep 2016).
The library was sequenced on a NextSeq 500 platform (Illumina) with 75 cycles for the cDNA and 16 cycles for the barcodes and UMIs.

treatment_protocol: ITK-SYKCD4-creERT2 or ITK-SYKCD4-creERT2;Pdcd1-/- mice received a single dose of 2 mg tamoxifen.

value: ITK-SYK+ CD4+ T cells (primary cells)

value: PD1 KO

value: Day 5


title: 164_antiPD1_C4_CD8_Tcell


title: ITK-SYK+ CD4+ T cells PD1 KO replicate 3

description: TTAGTT


title: Inha E13.5 WT 486


title: 162_antiPD1_C2_CD8_Tcell


title: ITK-SYK+ CD4+ T cells PD1 KO replicate 2

description: AAGATT


title: MC_49_S78

value: Bulk OFC tissue


title: 161_antiPD1_C1_CD8_Tcell


title: Inha E13.5 WT 4182

value: Inha WT


title: MC_65_S65


title: ITK-SYK+ CD4+ T cells PD1 WT replicate 4

description: TTATTG

value: PD1 WT


title: Inha E15.5 WT 3915_6


title: 163_antiPD1_C3_CD8_Tcell


title: ITK-SYK+ CD4+ T cells PD1 KO replicate 1

description: ATTACT


title: MC_43_S76


title: 159_isotype_C3_CD8_Tcell

value: isotype control


title: Inha E13.5 WT 255_6


title: 160_isotype_C4_CD8_Tcell


title: MC_44_S61


title: MC_68_S88


title: MC_42_S57


title: 158_isotype_C2_CD8_Tcell


title: Col-0, +Fe, biol rep 3 [3-plus_S29]

city: Amherst

first: Elsbeth

last: Walker

state: MA

address: 611 N Pleasant St Morrill Science Center IV South

department: Biology

institute: University of Massachusetts Amherst

data_processing:
Cutadapt was used to remove adapter sequences
Shortstack was used to align, annotate, and quantify small RNAs.
After processing the raw reads, raw read counts were used as input for differential expression analysis with DESeq2
Assembly: TAIR10
Supplementary files format and content: Matrix table of raw counts table with coordinates of each loci, output of ShortStack

organism: Arabidopsis thaliana

source_name: phloem sap

growth_protocol: Wild type Arabidopsis thaliana accession Columbia-0 (Col-0) was used for all experiments. Surface sterilized seeds were plated directly on sterile petri plates containing ½ Murashige and Skoog (MS) medium and placed at 4°C for three days. Following stratification, plates were exposed to light for six hours and again placed in dark at room temperature for three days to encourage longer hypocotyl growth. After dark treatment, plates were positioned vertically in the growth chamber (16h light/8h dark at 22°C) for 10 days until the plants made their second set of true leaves. On day 11, the seedlings were transferred to sterile petri plates containing ½ MS+Fe or ½MS-Fe for three days.

extract_protocol:
Urine Cell-Free Circulating RNA Purification Maxi Kit (Norgen Biotek Corp.) was used according to the manufacturer’s instructions to isolate total RNA from Arabidopsis phloem exudates
Lexogen Small RNA-Seq Library Prep Kit was used according to the manufacturer’s instructions to create small RNA libraries from phloem exudates.

treatment_protocol: for +Fe samples: plants were grown on 1/2XMS+ Fe for 11 days, then were transferred to fresh MS+Fe for 3 days; -Fe samples: plants were grown on 1/2XMS+ Fe for 11 days, then were transferred to MS-Fe for 3 days

value: phloem sap

value: WT

tag: ecotype


title: 157_isotype_C1_CD8_Tcell


title: Col-0, +Fe, biol rep 4 [4-plus_S30]


title: Col-0, -Fe, biol rep 4 [4-minus_S34]

value: Fe deficiency


title: 144_antiAMICA1_C4_CD4_TREG

value: TREG

value: anti-JAML


title: MC_39_S93

value: male


title: Col-0, -Fe, biol rep 3 [3-minus_S33]


title: ITK-SYK+ CD4+ T cells PD1 WT replicate 1

description: GTTCGA


title: MC_38_S58


title: Col-0, +Fe, biol rep 2 [2-plus_S28]


title: 143_antiAMICA1_C3_CD4_TREG


title: 142_antiAMICA1_C2_CD4_TREG


title: Col-0, -Fe, biol rep 2 [2-minus_S32]


title: ITK-SYK+ CD4+ T cells PD1 WT replicate 3

description: CTGCGG


title: MC_25_S72


title: ITK-SYK+ CD4+ T cells PD1 WT replicate 2

description: CCCTGG


title: MC_23_S71


title: 141_antiAMICA1_C1_CD4_TREG


title: Col-0, -Fe, biol rep 1 [1-minus_S31]


title: DT_Spleen_Treg_1

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

data_processing:
Reads from all libraries were mapped to the mouse genome (mm9) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: rpkm.txt.gz - tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq transcripts

source_name: Foxp3Thy1.1+CD4+ Treg cells

extract_protocol:
total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted Foxp3GFP-CD4+ conventional T cells (Tconv), Foxp3Thy1.1+CD4+ regulatory cells (Treg) isolated from indicated mice
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

value: DT-treated

value: Treg cells


title: Col-0, +Fe, biol rep 1 [1-plus_S27]


title: 140_antiPD1_C4_CD4_TREG


title: FC_79_S85

value: female


title: ΔwatR strain after 10 min of acetate treatment, biol rep 2

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using hisat2 v. 2.2.1 with default parameter.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, normalization of retrieved counts and fold change calculation between groups were performed by DESeq2 package.
Assembly: Methylomonas sp. DH-1 (GCF_001644685.1)
Supplementary files format and content: tsv, DESeq2 normalized abundance matrix
Supplementary files format and content: tsv, DESeq2 comparison result

organism: Methylomonas sp. DH-1

source_name: bacterial culture

growth_protocol: All samples were cultivated 12.5 mL of NMS medium in the 125 mL of baffled flask sealed with rubber type screw cap, with the addition of 20% (V/V) methane. The initial OD600 was 0.1 and incubated at 30°C, with shaking of 170 rpm.

extract_protocol:
Total RNA was extracted by RNeasy Mini kit (#74106, Qiagen) according to the manufacturer's instructions.
1 ug of total RNA was proceeded to rRNA depletion using NEBNext rRNA depletion kit (Bacteria) (#7850, NEB). Resulted mRNA was used for sequencing library construction by TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina). All experiments were performed following manufacturer's instructions.

treatment_protocol: Cells were grown at OD600 ~1.0, 1 mL of samples were extracted from the flask with syringe needle. After initial sampling (0 min), 1 mL of pH7 neutralized acetate was added to the final concentration 0.6 g/L. After 10 min of culture in same condition, 1 mL of samples were extracted by syringe needle.

value: bacterial culture

value: <delta>watR (AYM39_21120)

value: final 0.6 g/L of acetate (pH=7 neutralized)

tag: timepoint

value: 10 min


title: 139_antiPD1_C3_CD4_TREG


title: FC_67_S86

value: Bulk OFC tissue

value: control


title: FC_62_S87


title: 138_antiPD1_C2_CD4_TREG


title: 137_antiPD1_C1_CD4_TREG


title: DT_Spleen_Treg_3


title: Wild-type after 10 min of acetate treatment, biol rep 1

value: wild type


title: MC_35_S74


title: FC_59_S95


title: 136_isotype_C4_CD4_TREG

value: isotype control


title: DT_Spleen_Treg_2


title: DT_Lung_Treg_2


title: ΔwatR strain before acetate treatment, biol rep 2

value: 0 min


title: 135_isotype_C3_CD4_TREG


title: DT_Spleen_Tconv_3

source_name: Foxp3GFP-CD4+ Tconv cells

value: Tconv cells


title: FC_37_S75


title: DT_Spleen_Tconv_2


title: 134_isotype_C2_CD4_TREG


title: DT_Lung_Treg_1


title: DT_Lung_Tconv_3


title: ΔwatR strain before acetate treatment, biol rep 1


title: ΔwatR strain after 10 min of acetate treatment, biol rep 1


title: Wild-type before acetate treatment, biol rep 2


title: FC_33_S73


title: DT_Spleen_Tconv_1


title: FC_36_S70


title: 133_isotype_C1_CD4_TREG


title: Wild-type after 10 min of acetate treatment, biol rep 2


title: DT_Lung_Tconv_1


title: DT_Lung_Tconv_2


title: Wild-type before acetate treatment, biol rep 1


title: RH4 cells, si-SCR, biol rep 1

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

data_processing:
Raw sequencing data processing (format conversion and demultiplexing) was performed using Bcl2Fastq version 2.20.0.422.
Due to a laser intensity drop in the last cycles of the sequencing reaction, the last 20 based of reverse reads exhibited low Phred quality scores. Trimmomatic software was employed to cut reverse reads down to 130 nucleotides; a second Trimmomatic run, with parameters ILLUMINACLIP:path/to/adapter:2:30:10:8:true MINLEN:35, allowed to remove adapter sequences (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/).
Alignment to human GRCh38 genome and Ensembl 99 transcriptome was performed using STAR aligner version 2.5.2b with parameters --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMattrIHstart 0 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout –outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04.
Reads mapping to each gene were counted using htseq-count software with parameters -m intersection-strict -f bam -s reverse. Read count files were combined into a count matrix file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene-level raw counts for si-SCR and si-circAFF1 samples.

growth_protocol: RH4 cells were cultured in DMEM high-glucose, 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with Direct-zol RNA Miniprep kit (Zymo Research) with a 15-minute DNase-I treatment according to the manufacturer’s protocol
TruSeq Stranded mRNA kit was used for cDNA library preparation

treatment_protocol: Cells were transfected with 20nM siRNAs (Dharmacon) and Dharmafect-1 Transfection Reagent (Dharmacon), according to the manufacturer’s instructions.

tag: cell line

value: Rhabdomyosarcoma cell


title: DT_Lung_Treg_3


title: EE31_pre

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

data_processing:
Basecalling was performed using the default Ion Torrent software
trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15
Counts were calculated using the pseudoalignment tool salmon v1.9 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Transcript counts were imported into R using the packages Annotationhub and tximport to obtain gene counts
Assembly: GRCh38
Supplementary files format and content: transcript counts

source_name: Blood

extract_protocol:
Venous blood samples were extracted in TEMPUS tubes (Thermo Fisher). After centrifugation, pellets were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)
Amplification of known human transcripts

value: Blood

value: Male

tag: outcome

value: Survivor

value: Admission

tag: endotype


title: DT_Gut_Treg_2

value: DT-treated

tag: cell type

value: Treg cells


title: RH4 cells, si-SCR, biol rep 2


title: EE30_pre

tag: tissue


title: 22 (IgAV10) skin

type: RNA

city: Portland

first: Vanderlene

last: Kung

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Department of Pathology & Laboratory Medicine

institute: Oregon Health & Science University

hyb_protocol: nCounter protocol.

scan_protocol: nCounter protocol.

data_processing: nSolver defaults were used to filter based on default quality control measures.

source_name: Skin

label_protocol: nCounter protocol.

extract_protocol: FFPE blocks were cut at 10 microns x 15 sections; kidney samples were collected as curls, while on sections from skin, the superficial dermis and epidermis were enriched by macrodissection away from deep dermis.  Collected tissue was deparaffinized and total nucleic acids were extracted using the Macherey-Nagel NucleoSpin Tissue Kit.  The samples were DNA depleted using the ArcticZymes Heat&Run gDNA Removal Kit.

value: Skin

tag: patient diagnosis

value: IgAV without nephritis


title: 23 (IgAV11) skin


title: EE24_pre


title: DT_Gut_Treg_3

tag: treatment


title: RH4 cells, si-circAFF1, biol rep 2

value: circAFF1 KD


title: EE30_post

value: After surgery


title: EE31_post


title: Panc-1_RARγi-2

city: Kobe

first: Kohei

last: Yamakawa

address: 7-5-1 Kusunoki-Cho, Chuo-Ku

country: Japan

institute: Kobe University Graduate School of Medicine

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) reference sequences using the Strand NGS software program with default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include Gene Symbol, Entrez Gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: human pancreatic cancer cell line

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared for TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.3).

value: RARγi-1 for 24 hours


title: DT_Gut_Treg_1


title: 21 (IgAV9) skin


title: RH4 cells, si-circAFF1, biol rep 1


title: 24 (IgAV12) skin


title: DT_Gut_Tconv_3


title: EE21_pre


title: Panc-1_RARγi-1


title: 19 (IgaV7) skin C

value: IgAV with nephritis


title: RH4 cells, si-SCR, biol rep 3

value: control


title: 20 (IgAV8) skin


title: DT_Gut_Tconv_2


title: EE24_post


title: PK-1_RARγi-2


title: DT_Gut_Tconv_1


title: EE21_post


title: Panc-1_Control


title: Control_Spleen_Treg_2

value: PBS-treated


title: Control_Spleen_Treg_3


title: EE17_pre

value: Female


title: 17 (IgAV5) skin A


title: PK-1_Control


title: 15

first: Gail

middle: B

last: Mahady

state: Il

address: 833 S Wood St

department: Pharmacy Practice

institute: University of Illinois

data_processing:
Raw reads were trimmed to remove adapters sequence using cutadapt (Martin, 2011). Reads with no adapter were discarded. Remaining trimmed reads were reads were aligned to mature known human microRNA database obtained from miRbase using BWA ALN (Li and Durbin, 2010). miRNA expression levels where quantified by counting the number of reads mapped to each miRNA sequence, and normalized to counts-per-million units for direct comparison between samples.    Differential expression statistics were computed using edgeR (McCarthy, Chen, & Smyth, 2012; Robinson, McCarthy, & Smyth, 2010) on raw expression counts with the exactTest function. P-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg (Benjamini & Hochberg, 1995). k-means clustering was performed using R.
Assembly: hg38 (human mature miRNA)
Supplementary files format and content: Table of raw counts per gene – tabular text file

source_name: hFOB 1.19

growth_protocol: The human osteoblast cell line, hFOB 1.19 (ATCC  CRL-11372 ), were purchased from American Type Cell Culture, ATCC (Manassas, VA). The hFOB 1.19 osteoblasts were cultured in Dulbecco’s Modified Eagle Medium F-12, DMEM/F12 (Thermo-Fisher, ) supplemented with 10% fetal bovine serum (FBS), (ATCC, Manassas, VA) and 1% penicillin/streptomycin (Thermo-Fisher,

extract_protocol: Total RNA was isolated from cell samples. Total RNA was used for miRNA library construction with the QIAseq miRNA library prep kit for Illumina (Qiagen, 331505). Isolated total RNA quality was measured using an Agilent 2100 Bioanalyzer and RNA samples had an RNA Integrity Number (RIN) score     9.6-10. Sequencing libraries were prepared using total RNA at 250 nanograms per sample. Library construction steps included ligation of the specially designed 3' and 5' adapters to mature miRNAs. The ligated miRNAs were then reverse transcribed to cDNA using a reverse transcription (RT) primer with a UMI. Cleanup of the cDNA was performed using a magnetic bead-based method. Following cDNA cleanup, library amplification was performed with a universal forward primer and indexing reverse primers where each sample was assigned a unique custom index. Following a final library cleanup using an Agencourt RNAClean XP Bead assay (Beckman Coulter, PN: A63987), each miRNA library was quantified using Qubit 2.0 Fluorometer (Invitrogen) and pooled in equimolar concentrations. Final sequencing pool was analyzed using Tape Station gel analyzer (Agilent) and re-quantified using the qPCR KAPA Library Quantification Kit (KAPA Biosystems). Sequencing was carried out on NovaSeq6000 SP flow cell, 1x100 nt reads, to achieve approximately 20 M reads per sample.

treatment_protocol: Cell were treated with anthocyanins delphinidn-3-glucoside, peonidin-3-glucoside or resveratrol at a concentration of 1 mcg/ml

value: hFOB 1.19

value: osteoblast


title: PK-1_RARγi-1


title: 16 (IgAV7) kidney C

source_name: Kidney

value: Kidney

value: IgAV


title: EE14_pre

value: Blood

value: Male

value: Survivor


title: 14


title: Control_Spleen_Treg_1

value: Treg cells


title: EE14_post


title: Control_Spleen_Tconv_1

value: Tconv cells


title: EE17_post


title: 15 (IgAV6) kidney B


title: EE10_pre

value: Dead

value: Admission


title: Control_Spleen_Tconv_2


title: 12


title: 14 (IgAV5) kidney A


title: Control_Lung_Treg_3


title: 18 (IgAV6) skin B

value: Skin


title: 11


title: EE10_post

value: After surgery


title: EE8_pre


title: 13 (IgAV4)


title: EE8_post


title: 10


title: 9 (IgA-IRGN1)

value: IgA-IRGN


title: EE7_pre


title: 12 (IgA-IRGN4)


title: 13


title: Control_Lung_Tconv_2


title: Control_Lung_Tconv_1


title: EE7_post


title: Control_Lung_Treg_2


title: 10 (IgA-IRGN2)


title: Control_Gut_Treg_2


title: EE5_post


title: EE5_pre


title: Control_Lung_Treg_1


title: Control_Spleen_Tconv_3


title: 4 (IgAN1)

value: IgAN


title: Control_Lung_Tconv_3

value: PBS-treated


title: 8 (IgAN5)


title: 09


title: 04

description: NC

value: negative control (-10% FBS)


title: EE4_post


title: 08

value: hFOB 1.19


title: 7 (IgAN4)


title: 11 (IgA-IRGN3)


title: Control_Gut_Treg_3


title: 6 (IgAN3)


title: 07

value: osteoblast


title: 2 (IgAV2)

value: Kidney


title: EE2_pre


title: 5 (IgAN2)


title: 05

description: NC


title: EE2_post


title: setdb1_H3K9me3_20_06Jan2021

city: Albany

first: Prashanth

last: Rangan

address: 1400 Washington

institute: RNA Institute

data_processing:
Library strategy: CUT&RUN
FASTQ files were aligned to the dm6 reference genome using HISAT2 (10.1038/s41587-019-0201-4) (-X 10 -I 1000 –no-spliced-alignment, --no-discordant)
Alignment files were sorted and indexed using samtools and were subsequently used to create bigwig files
Raw read counts of H3K9me3 enrichment across gene bodies was calculated using the HOMER annotateRepeats function and differential enrichment was calculated using DESeq2 (HOMER PMID:20513432, DESeq2 citation 10.1186/s13059-014-0550-8)
Genome_build: UCSC dm6
Supplementary_files_format_and_content: Paired end DNA seq libraries

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Ovaries dissected in 1x PBS.

extract_protocol:
PBS was removed and the samples were permeabilized in 1mL of Permeabilization Solution (PBST+1% Triton-X) rotating in RT for 1 hour. Samples were then incubated overnight at 4°C in primary antibody dilutions in freshly prepared BBT+ buffer (PBST + 1% BSA + 0.5 mM Spermidine + 2 mM EDTA + 1 large Roche complete EDTA-free tablets). Primary antibody was replaced with BBT+ buffer and quickly washed twice. Samples were then incubated in ~700 ng/ml of pAG-MNase in BBT+ buffer rotating for 4 hours at 25°C. Samples were then quickly washed twice in wash+ buffer (20 mM HEPES pH7.5 + 150 mM NaCl + 0.1% BSA +  0.5 mM Spermidine + 1 large Roche complete EDTA-free tablets in water). Samples were resuspended in 150 μl Wash+C (wash+ + 100 mM CaCl2) and incubated for 45 minutes on nutator at 4°C. The cleavage reaction was terminated by addition of 150 μl StopR (NaCl final 200 mM + EDTA final 20 mM + 100μg/mL RNaseA) and incubating the sample at 37˚C for 30 minutes. Samples were then centrifuged at 16,000 x g for 5 minutes and 300 μl of the supernatant was collected for DNA discovery. To the supernatant, 2 μL 10% SDS and 2.5 μL of 20 mg /mL Proteinase K was added and incubated at 50°C for 2 hours. Half of this was kept as a backup and half was used in bead cleanup. 20 μL AmpureXP bead slurry and 280 μL MXP buffer (20% PEG8000 + 2.5 M NaCl + 10 mM MgCl2 in water) was added to the sample and mixed thoroughly followed by 15 minutes incubation at RT. The beads were separated by magnet and supernatant was discarded. The beads were carefully washed with 80% ethanol for 30 seconds, while on the magnetic stand and air dried for 2 minutes. The beads were then resuspended in 10 μL DNase free water.
The samples from CUT&RUN assay were used for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7645, E7103) and adaptor ligated DNA were prepared without size selection.

value: dissected 1-3 days post-eclosion

value: SETDB1 GKD

tag: antibody

value: H3K9me3 (Active Motif, AB_2532132)


title: 06

description: NC


title: EE4_pre

value: Blood

value: Male


title: Control_Gut_Treg_1

tag: strain

value: Treg cells


title: 03

description: PC

value: positive control (+10% FBS)


title: nup154_H3K9me3_22_06Jan2021

value: Nup154 GKD


title: 3 (IgAV3)

value: IgAV


title: Control_Gut_Tconv_3

value: Tconv cells


title: Islet-derived exosomes-Control-Sample 14

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

description:
microRNA (miRNA)
Rawcounts_Human islet derived exosomes_miRNAs.xlsx
vsdcounts_Human islet derived exosomes_miRNAs.xlsx

data_processing:
Data analysis was performed using Partek flow software. The raw sequencing files were aligned to human genome (hg19) using STAR aligner v 2.5.3a.
Mature miRNAs were annotated using miRBase v 20.
Paired sample analysis was used for identifying differentially expressed miRNAs using  DESeq2  package in the R statistical program.
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx file format for processed data files - raw counts and variance stabilized normalized (vsd) counts

source_name: Pancreatic islet derived exosomes

extract_protocol:
Untreated and cytokine treated human islets and islet-cell supernatants were harvested for downstream applications. For exosome isolation, supernatants were collected and centrifuged for 30 minutes at 3000g to remove cellular debris. Exosomes were isolated using ExoQuick-TC (SBI Bioscience, USA) as per the manufacturer’s instructions.
Total RNA and miRNA were first evaluated for quantity, quality, and percent miRNA content in total RNA, using the Agilent Bioanalyzer. The starting amount of RNA was 10-20 ng for each miRNA library. For miRNA library preparation, 0.5% of miRNA in total RNA was the cut-off to decide whether the sample should be enriched for miRNA. When needed, enrichment was performed following the small RNA library preparation procedure and the Ion Total RNA-Seq Kit v2 User Guide, Pub. No. 4476286 Rev. E (Life Technologies, USA). Each resulting barcoded library was quantified and assessed for quality using the Agilent Bioanalyzer. Multiple libraries were pooled in equal molarity. Eight microliters of 100 pM pooled libraries were applied to Ion Sphere Particles (ISP) template preparation and amplification using Ion OneTouch 2, followed by ISP loading onto PI chips and sequencing using Ion Proton semiconductor. Each PI chip is capable of generating approximately 50 million usable reads of 21-22bp miRNA fragments. Sequence mapping was performed using Torrent Suite Software v4.6 (TSS 4.6).

treatment_protocol: Upon receipt, islets from human cadaveric donors were placed in exosome-depleted standard Prodo islet media (Prodo Labs, CA), and allowed to recover overnight. To investigate the effect of cytokine treatment on miRNA expression patterns, islets were cultured with or without 50 U/ml IL-1β and 1000 U/ml IFN-γ for 24 hours.

tag: tissue type

value: Human pancreatic islet-derived exosomes

tag: biomaterial provider

value: the integrated islet distribution program

value: Control

tag: batch

tag: ethnicity

value: White

tag: bmi


title: 1 (IgAV1)


title: EE31

tag: Sex

tag: age

value: Survivor

value: diagnosis


title: Control_Gut_Tconv_2

value: PBS-treated


title: MAH052121_014

data_processing:
Raw reads were aligned to human reference genome hg38 using STAR (Dobin et al., 2013). ENSEMBL genes were quantified using FeatureCounts (Liao, Smyth, & Shi, 2014). Differential expression statistics were computed using edgeR (McCarthy, Chen, & Smyth, 2012; Robinson, McCarthy, & Smyth, 2010) on raw expression counts with the exactTest function. P-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg (Benjamini & Hochberg, 1995).
Assembly: hg38
Supplementary files format and content: Table of raw counts per gene – tabular text file

extract_protocol: Briefly, the sequencing libraries for Illumina sequencing were prepared using 250 ng of total RNA per sample as we have described [29]. Library preparation was carried using a Universal Plus mRNA-Seq library preparation kit (Tecan/NuGen, 0520-A01), as described in the product manual (NuGen, M01485 v5). Briefly, RNA underwent poly-A selection, enzymatic fragmentation, and generation of double-stranded cDNA using a mixture of oligo (dT) and random priming. The cDNA underwent end repair, ligation of dual-index adaptors, strand selection, and 12 cycles of PCR amplification. The number of cycles was determined by qPCR on a small aliquot of the un-amplified libraries. All intermediate purification steps, and final library purification was carried out using Agencourt AMPure XP Beads (Beckman Coulter A63881). Final amplified libraries were measured with the Qubit 1X dsDNA HS Assay Kit (Invitrogen, Q33231), and fragment size distribution was confirmed to be approximately 430 bp using a D5000 ScreenTape assay (Agilent, 5067-5588, 5067-5589).   Concentration of the final library pool was confirmed by qPCR and subjected to test sequencing to confirm sequencing efficiencies and adjust accordingly proportions of individual libraries. The pool was purified with the Agencourt AMPure XP Beads (Beckman Coulter A63881), quantified by qPCR using KAPA Library Quantification Kit and sequenced on a NovaSeq 6000 S4 flow cell, 2x150 bp, approximately 30 M clusters per sample, at the University of Illinois Roy J. Carver Biotechnology Center High-Throughput Sequencing and Genotyping Unit.

value: hFOB 1.19

value: osteoblast


title: 02

description: PC


title: Control_Gut_Tconv_1


title: 01

description: PC


title: MAH052121_013


title: EE1_pre

tag: timepoint

value: Admission


title: setdb1_H3K9me3_16_07Jan2021

tag: time

value: dissected 1-3 days post-eclosion

tag: genotype

value: SETDB1 GKD

value: H3K9me3 (Active Motif, AB_2532132)


title: EE30

value: Blood

value: Male

tag: outcome

tag: endotype


title: MAH052121_011

tag: cell line

tag: cell type


title: Islet-derived exosomes-Cytokine-Sample 14

tag: treatment

value: Cytokine


title: EE1_post

tag: tissue

value: After surgery


title: Islet-derived exosomes-Cytokine-Sample 12

value: Human pancreatic islet-derived exosomes

value: Female


title: MAH052121_015


title: EE32


title: Islet-derived exosomes-Cytokine-Sample 13

value: the integrated islet distribution program


title: NG4_IgG_Rabbit_09_06Jan2021

value: control

tag: antibody

value: IgG (Jackson ImmunoResearch, AB_2337118)


title: nup154_H3K9me3_17_07Jan2021

value: Nup154 GKD


title: MAH052121_012


title: NG4_IgG_Rabbit_07_07Jan2021


title: EE29

value: Survivor

value: diagnosis


title: NG4_H3K9me3_06_03Oct2020


title: EE27

value: Dead


title: EE26


title: Islet-derived exosomes-Control-Sample 12

tag: tissue type

value: Control

value: White


title: EE28


title: NG4_H3K9me3_04_06Jan2021

value: dissected 1-3 days post-eclosion


title: Islet-derived exosomes-Cytokine-Sample 11

tag: biomaterial provider


title: NG4_H3K9me3_03_06Jan2021

value: H3K9me3 (Active Motif, AB_2532132)


title: MAH052121_009

value: hFOB 1.19

value: osteoblast


title: MAH052121_008


title: Islet-derived exosomes-Control-Sample 13

tag: batch


title: MAH052121_007


title: NG4_H3K9me3_03_07Jan2021


title: VIRGIN_S16

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
Differential gene expression was assayed by DEseq2 (version 1.24.0), using a false discovery rate of (FDR) of 0.05, and genes with 1.5-fold or higher Fold Change were considered significant.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: RNA-seq libraries

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026) or phenol-chloroform treatment, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads and then following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08)
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

value: Young control


title: EE25

value: Blood

value: Male


title: Islet-derived exosomes-Control-Sample 10

value: Human pancreatic islet-derived exosomes

tag: ethnicity


title: Islet-derived exosomes-Control-Sample 11

value: the integrated islet distribution program

value: Female

tag: bmi


title: MAH052121_006

description: NC

value: negative control (-10% FBS)


title: Islet-derived exosomes-Cytokine-Sample 10

value: Cytokine

tag: Sex


title: DcrVirgin_S4


title: Islet-derived exosomes-Cytokine-Sample 9

tag: age

value: Hispanic/Latino


title: EE24

value: Survivor

tag: timepoint

value: diagnosis


title: MAH052121_005

description: NC


title: EE23

value: Dead


title: DCR2_S4

tag: time

value: Adult control


title: MAH052121_010


title: Islet-derived exosomes-Control-Sample 9

value: Control


title: Islet-derived exosomes-Cytokine-Sample 8

value: White


title: EE22


title: MAH052121_003

description: PC

value: positive control (+10% FBS)

value: hFOB 1.19


title: DCR1_S3

value: dissected 1-3 days post-eclosion

tag: genotype


title: MAH052121_002

description: PC

value: osteoblast


title: EE21

value: Blood

value: Male

tag: outcome


title: 8_EggRNAi_2_S8

value: SETDB1 GKD


title: 6_EggRNAi_1_S6


title: Islet-derived exosomes-Control-Sample 8

value: Human pancreatic islet-derived exosomes

value: the integrated islet distribution program


title: HBEC_PW3_VEH6H

city: Durham

first: Shaun

middle: David

last: McCullough

state: NC

address: 3040 E. Cornwallis Rd., PO Box 12194

department: Exposure & Protection

institute: RTI International

data_processing:
bcl2fastq ver 2.20.0 used for basecalls
Mapping of sequence reads to the human genome (GRCh38) was performed by STAR (version 2.5)
Mapped read counts per gene were collected by Subread feature Counts (version 1.5.0-0-p1). Genes with a minimum average of normalized mapped read counts > 50 in at least one category were selected for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: raw gene counts for each sample and gene

source_name: Bronchial Epithelial Cell

growth_protocol: Cells were seeded on 12mm inserts and differentiated over 24 days.  Media was changed 3x/week

extract_protocol:
RNA was isolated according to standard protocol for the Thermo PureLink RNA Mini Kit.  Purified RNA was stored at -80°C until core submission
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were either left exposed to air or covered in 250 uL of StemCell Pneumacult Medium

value: differentiated primary human bronchial epithelial cell

value: Lung bronchial

value: Media applied 6H


title: HBEC_PW3_VEH24H

value: Media applied 24H


title: 4_Wde_2_S4

value: wde GKD


title: Islet-derived exosomes-Cytokine-Sample 7

value: Cytokine

value: Female


title: HBEC_PW3_PRE

value: ALI


title: Islet-derived exosomes-Cytokine-Sample 6

value: Hispanic/Latino


title: EE19

value: Dead

value: diagnosis

tag: endotype


title: EE17

value: Survivor


title: Islet-derived exosomes-Control-Sample 6

value: Control


title: Islet-derived exosomes-Control-Sample 7

value: White


title: HBEC_PW2_VEH24H


title: 2_NGVP16_2_S2

value: dissected 1-3 days post-eclosion

value: Young control


title: EE15

value: Blood

value: Male


title: EE16


title: 3_Wde_1_S3


title: Islet-derived exosomes-Cytokine-Sample 5

value: Human pancreatic islet-derived exosomes

value: the integrated islet distribution program


title: HBEC_PW2_PRE

value: differentiated primary human bronchial epithelial cell

value: Lung bronchial


title: 21_Nup154RNAi_1_S21

value: Nup154 GKD


title: EE14


title: Islet-derived exosomes-Control-Sample 5

value: Female


title: 1_NGVP16_1_S1


title: EE20


title: HBEC_PW1_VEH24H

value: Media applied 24H


title: HBEC_PW1_VEH6H

value: Media applied 6H


title: EE18

value: Dead


title: EE13

value: diagnosis


title: Islet-derived exosomes-Control-Sample 4


title: Islet-derived exosomes-Cytokine-Sample 4

value: Cytokine


title: EE12

value: Survivor


title: HBEC_PW2_VEH6H


title: Islet-derived exosomes-Cytokine-Sample 3

value: White


title: 22_Nup154RNAi_2_S22

value: dissected 1-3 days post-eclosion


title: D3-T4_S12

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

institute: University of Milan

data_processing:
Read were mapped on the genome with bowtie2 in “very sensitive” mode allowing a maximum insert size of 1000 bps.
Expression quantification was performed with respect to the latest gene annotation retrieved from NCBI (GCF_000005845.2_ASM584v2).  Transcript levels of each gene were defined as the number of reads overlapping its transcribed region, computed with bedtools
Assembly: E. coli K12 MG1655 (NC_000913.3)
Supplementary files format and content: counts.txt Tab separated count table with raw read counts per gene

organism: Escherichia coli

source_name: C-6019, grown at 37 C, exponential phase (OD600=0.8) (T=4 min after rifampicin addition)

growth_protocol: Growth in LD broth with aeration up to OD600= 0.8 (samples 1, 3  5 and 7); addition of 0.4 mg/ml rifampicin and 4 min incubation as before (samples 2, 4, 6 and 8)

extract_protocol:
Phenol-based extraction
Library prepared with TruSeq Stranded Total RNA with Illumina Ribo-Zero Plus Sample Prep kit following manufacturer's protocols.

tag: strain


title: EE11


title: D1-T4_S10


title: D2-T4_S11


title: Islet-derived exosomes-Control-Sample 3

value: Control


title: EE10

value: Blood


title: KO_NT_2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description:
RNA from PC3 METTL1 KO cells, non treated with NaBH4 and aniline
CRIPSR Cas9 METTL1 KO clon

data_processing:
tRNA genomic coordinates for the hg38 genome were obtained from the GtRNAdb database (gtrnadb.ucsc.edu). Reads on tRNA coordinates were processed using ‘htseq-count’ from the Python package HTSeq (htseq.readthedocs.io) with the ‘-samout’ option, and counts for individual readc representing tRNA fragments and thcir multiple sequence alignments on tRNAs were extracted from the resulting sam files using custom PERL scrips. Fragments with less than 10 counts over all samples were removed and a pseudo-count of 1 was added. Count data of tRNA fragments, which were shorter than 0.7 of the full tRNA length, was normalized, and differential abundance of tRNA fragments was evaluated for 3 replicates per condition or treatment using the R package ‘DESeq2’
Genome_build: hg38
Supplementary_files_format_and_content: The data matrix contains the sequence and raw counts for each tRNA fragment.

source_name: Prostate cancer cell line PC3

growth_protocol: PC3, DU145, VCap and HEK293FT were cultured in DMEM with L-Glutamine and pyruvate (Gibco) supplemented with 10% FBS (Gibco) and 1% Penicillin/streptomycin, a humidified atmosphere at 37°C and 5% CO2. Cell cultures were tested for mycoplasma monthly and maintained mycoplasma-free.

extract_protocol:
Total RNA was extracted using Trizol and isopropanol (Honeywell, 33539) precipitation, followed by DNAse I Turbo (Invitrogen) treatment for DNA removal. Then, further acidic phenol (Ambion) purification and ethanol precipitation was performed. Briefly, small RNAs (<200 bp) were selected using mirVana miRNA isolation kit (Invitrogen) following the manufacturer’s instructions.
tRNA libraries were generated using TruSeq Small RNA Preparation Kit (Illumina). Briefly, 3’adenylated and 5’phosphorylated adapters suitable for Illumina RNA sequencing were ligated to the small RNA fraction. RNA was reverse-transcribed at 50ºC for 1 h (SuperScript III cDNA synthesis kit, Invitrogen), followed by PCR amplification with Phusion DNA polymerase (Thermo scientific) and size-selected before sequencing. All samples were multiplexed and sequenced in HiSeq platform (Illumina). Empty vector clone 4 was used as control cell line, and clone 1 as METTL1-KO cell line.
Borohydride RNA Sequencing (Bo-Seq)

treatment_protocol: tRNAs were de-aminoacylated with a solution containing 1mM EDTA and 0.1M Tris-HCl pH 9.0 for 30 min at 37°C. For identifying the m7G deposition position, 1-2 mg of tRNAs from WT and KO cell lines were treated with Buffer A (0.2 M Tris-HCl pH, 0.01 M MgCl2, 0.2 M KCl) supplemented with 10 μg of m7GTP (NEB) per 10 μg of tRNAs for 5 min at 85ºC. Freshly prepared NaBH4 was added to a final concentration of 0.5 M and samples were incubated for 30 min on ice. Treated tRNAs were desalted with Micro Bio-Spin 6 columns (Biorad) and ethanol precipitated. To induce complete ꞵ-elimination and cleavage of RNA at methylated guanines, reduced RNAs were treated with aniline/acetate/water solution (1:3:7) (Sigma). All small RNAs were treated with T4 PNK (NEB) to ensure phosphorylated 5’ ends and 3’OH ends, followed by heat inactivation and ethanol precipitation.

tag: culture condition

value: DMEM + 10% FBS + Pen/Strep. 5% CO2. 37ºC.

tag: passage

tag: sequencing platform

value: Illumina NovaSeq6000


title: KO_NT_3


title: KO_NT_1


title: EE8

tag: tissue

value: Male


title: Islet-derived exosomes-Control-Sample 2

tag: tissue type

value: Human pancreatic islet-derived exosomes

value: the integrated islet distribution program

tag: treatment

value: Hispanic


title: EE9

value: Female


title: KO_3

description:
RNA from PC3 METTL1 KO cells, treated with NaBH4 and aniline
CRIPSR Cas9 METTL1 KO clon


title: D3-Tzero_S9

source_name: C-6019, grown at 37 C, exponential phase (OD600=0.8) (T=0)


title: D1-Tzero_S7


title: Islet-derived exosomes-Cytokine-Sample 2

tag: biomaterial provider

tag: batch


title: D2-Tzero_S8


title: HBEC_PW1_PRE

tag: cell type

value: differentiated primary human bronchial epithelial cell

value: Lung bronchial

value: ALI


title: EE7

tag: Sex

value: Dead

value: diagnosis


title: C3-T4_S6

source_name: C-6001, grown at 37 C, exponential phase (OD600=0.8) (T=4 min after rifampicin addition)


title: KO_1


title: C2-T4_S5


title: EE6

tag: age

value: Survivor


title: Islet-derived exosomes-Cytokine-Sample 1

value: Cytokine

tag: ethnicity

value: Black/African American

tag: bmi


title: KO_2


title: Islets-Cytokine-Sample 10

description:
microRNA (miRNA)
Rawcounts_Human islets_miRNAs.xlsx
vsdcounts_Human islets_miRNAs.xlsx

source_name: Pancreatic islet

value: Human pancreatic islets

value: White


title: Islet-derived exosomes-Control-Sample 1

value: Control


title: C1-T4_S4


title: CTRL_NT_2

description:
RNA from PC3 control (WT) cells, non treated with NaBH4 and aniline
CRIPSR Cas9 control clon

value: DMEM + 10% FBS + Pen/Strep. 5% CO2. 37ºC.

value: Illumina NovaSeq6000


title: EE5

value: Blood

value: Male

tag: timepoint


title: Islets-Control-Sample 10

value: the integrated islet distribution program


title: Islets-Cytokine-Sample 9

value: Female


title: CTRL_NT_3


title: EE4

tag: outcome


title: C3-Tzero_S3

source_name: C-6001, grown at 37 C, exponential phase (OD600=0.8) (T=0)


title: CTRL_NT_1


title: EE1

tag: endotype


title: Islets-Control-Sample 9


title: Islets-Cytokine-Sample 8


title: CTRL_1

description:
RNA from PC3 control (WT) cells, treated with NaBH4 and aniline
CRIPSR Cas9 control clon


title: CTRL_3


title: EE2


title: EE3


title: Islets-Control-Sample 8


title: B3-T4_S12

source_name: C-5691, grown at 37 C, exponential phase (OD600=0.8) (T=4 min after rifampicin addition)

tag: strain


title: B2-T4_S11


title: C1-Tzero_S1


title: Islets-Cytokine-Sample 7


title: CTRL_2

tag: culture condition


title: B1-T4_S10


title: SW620+shMETTL17#5 1

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GCF_000001405.38_GRCh38.p12 for Homo sapiens
Supplementary files format and content: csv files include TPM values  for each Sample

source_name: colon

growth_protocol: After lentivirus infection for 48 hours, cells were screened by puromycin selection for another 24 hours to construct stable cell lines. Then, the cells were seeded into 6 well plates and cultured overnight, followed by RNA extraction.

extract_protocol: The RNA of Scramble and shMETTL17 RKO or SW620 cells was extracted using an RNA extraction reagent kit(TIANGEN, Cat#DP419). Two independent samples (biological replicates) were established for each group. The RNA sequencing library was prepared and sequenced.

treatment_protocol: RKO or SW620 cells were infected with pLKO lentivirus containing shRNA for 48 hours.

value: colon

tag: cell line

value: Colorectal cancer cell line

tag: genotype

value: Konckdown of METTL17 with sh#5


title: B3-Tzero_S9

source_name: C-5691, grown at 37 C, exponential phase (OD600=0.8) (T=0)


title: Islets-Control-Sample 7


title: SW620+shMETTL17#3 2

tag: tissue

value: Konckdown of METTL17 with sh#3


title: 8R

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422, Illumina), allowing no mismatches in the index read. Primary read mapping and UMI analysis were conducted via the GeneGlobe Data Analysis Center (Qiagen).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts are provided in a csv ifle

source_name: Small RNA from extracellular vesicles

growth_protocol: Cryopreserved BMSCs at less than passage 3 which were previously isolated from healthy donors using density centrifugation and expanded in Dulbecco’s modified Eagle’s medium (DMEM; Corning) culture medium supplemented with 10% fetal bovine serum (FBS; Gemini Bio-Products) were thawed and expanded again on a CellBIND culture dish (Corning) in the DMEM culture medium. When the cultures attained approximately 80-90% confluency, the cells were harvested by treating with 0.25% trypsin solution for 5 min at 37°C and split into three dishes. After 24 hrs incubation in the DMEM culture medium, the medium in these 3 dishes was replaced with either the DMEM culture medium or the high-performance culture medium (HPM; RoosterNourish-MSC; KT-001, RoosterBio). Once reached 80-90% confluency, the cells were harvested and plated onto 3 dishes at a density of 3,000-4,000 cells/cm2. At 80-90% confluency,  the dishes were washed with phosphate-buffered saline (PBS) three times and replaced the media with basal media. After 24 hrs incubation, the conditioned media were collected and centrifuged at 500 g for 5 min to get rid of cellular debris. The supernatant was then filtrated with a 0.22 µm filter (MilliporeSigma). The filtrated conditioned medium was stored in a -80°C freezer.

extract_protocol:
The filtrated conditioned medium stored at -80°C was thawed and ultracentrifuged at 110,000 g, 4°C for 2.5 hrs to obtain EV pellet using Sorvall Discovery 90SE centrifuge (Hitachi) with AH-629 swinging bucket rotor (ThermoFisher Scientific). The EV pellet was washed with PBS at the same speed for 0.5 hrs. RNA was isolated using mirVana miRNA Isolation Kit (ThermoFisher Scientific) following the manufacturer’s instruction. Specifically, EV pellets isolated from the ultracentrifugation were disrupted with the Lysis Solution. Following organic extraction using acid-phenol: chloroform, total RNA was isolated and eluted in nuclease-free water. RNA quantity and quality isolated from EVs were evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies).
SmRNA-sequencing libraries were prepared from 1.2 to 10 ng of total RNA using the QIAseq miRNA Library Kit (Qiagen, Germantown, MD) as per the manufacturer's instructions. This system offers a built-in Unique Molecular Identifier (UMI) application, which is used to eliminate possible PCR duplicates in sequencing datasets and therefore facilitate unbiased gene expression profiling. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol.
The denatured libraries were loaded onto an SP flow cell on an Illumina NovaSeq 6000 and run for 71 cycles using a single-read recipe according to the manufacturer's instructions.

tag: culture medium

value: cultured in high performance medium

tag: donor

value: healthy donor

tag: cell source

value: bone marrow stromal cells

value: M


title: Islets-Cytokine-Sample 6

tag: tissue type

value: Human pancreatic islets

tag: biomaterial provider

tag: treatment

value: Cytokine

tag: batch

value: Hispanic/Latino


title: 8D

value: cultured in DMEM+10%FBS

tag: Sex


title: SW620+shMETTL17#3 1

tag: cell type


title: 7R

value: F


title: Islets-Control-Sample 6

value: Control

tag: age

tag: ethnicity

tag: bmi


title: SW620+Control 2

value: Scramble


title: C2-Tzero_S2

tag: strain


title: SW620+shMETTL17#5 2


title: B1-Tzero_S7


title: SW620+Control 1


title: Islets-Cytokine-Sample 5

value: the integrated islet distribution program

value: Male

value: White


title: A3-T4_S6

source_name: C-1a, grown at 37 C, exponential phase (OD600=0.8) (T=4 min after rifampicin addition)


title: 6R


title: 6D


title: RKO+shMETTL17#5 2

value: colon

value: RKO

value: Colorectal cancer cell line


title: 5R

value: cultured in high performance medium


title: RKO+shMETTL17#5 1

value: Konckdown of METTL17 with sh#5


title: Islets-Control-Sample 5


title: A1-T4_S4


title: Islets-Cytokine-Sample 4

value: Female


title: Islets-Control-Sample 4


title: B2-Tzero_S8


title: RKO+shMETTL17#3 2

value: Konckdown of METTL17 with sh#3


title: 7D

value: healthy donor

value: bone marrow stromal cells


title: 5D


title: 4R


title: Islets-Cytokine-Sample 3

value: Human pancreatic islets

value: Cytokine

value: Hispanic/Latino


title: RKO+shMETTL17#3 1


title: 4D

value: cultured in DMEM+10%FBS

value: F


title: A3-Tzero_S3

source_name: C-1a, grown at 37 C, exponential phase (OD600=0.8) (T=0)


title: A1-Tzero_S1


title: A2-Tzero_S2


title: RKO+Control 2

value: Scramble

value: Control


title: Islets-Control-Sample 3

value: the integrated islet distribution program

value: Male


title: Islets-Cytokine-Sample 2

value: White


title: RKO+Control 1

value: colon

value: RKO

value: Colorectal cancer cell line


title: 3R

value: cultured in high performance medium

value: M


title: C-6001, grown at 37 C, exponential phase (OD600=0.8), 3

value: substitution of the bacterial ORF with the human


title: A2-T4_S5


title: Islets-Control-Sample 2


title: C-6001, grown at 37 C, exponential phase (OD600=0.8), 2


title: Islets-Cytokine-Sample 1

value: Female

value: Black/African American


title: C-5691, grown at 37 C, exponential phase (OD600=0.8), 3

value: pnp ORF deletion


title: WatR-FLAG strain, biol rep 2

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using bowtie2 with default parameter.
Peak calling was performed by findpeaks command in homer v. 4.10.3 using "-style factor" parameter.
Resulted peaks were annotated by annotatePeaks.pl in homer package.
Peaks was transformed to bed file using pos2bed.pl in homer package for detailed analysis.
Assembly: Methylomonas sp. DH-1 (GCF_001644685.1)
Supplementary files format and content: bigWig, the graph represents normalized reads per million of mapped reads

source_name: bacterial culture

growth_protocol: All samples were cultivated 50 mL of NMS medium in the 500 mL of baffled flask sealed with rubber type screw cap, with the addition of 20% (V/V) methane. The initial OD600 was 0.1 and incubated at 30℃ with shaking of 170 rpm.

extract_protocol:
Cells were lysed with lysozyme treatment, and the lysate were sonicated, immunoprecipitated with anti-DDDDK antibody. RNase I and proteinase K were treated to eliminate RNA and proteins, and DNA was reverse crosslinked by NaCl with heat treatment. Final DNA eluent were precipitated by phenol-chloroform-isoamylalcohol method. For input, the lysate was directly precipitated.
1 ng of prepared DNA was proceeded to sequencing library construction by using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645, NEB) following manufacturer's instructions.

treatment_protocol: When the sample reached OD600 ~1.0, final 2.7% concentration of formaldehyde was treated in order to crosslink the protein and DNA for 25 min, and 250 mM of glycin was added to quench the reaction.

value: bacterial culture

value: WatR-FLAG

tag: antibody

value: anti-DDDDK-tag mAb, MBL (M185-3L)


title: Islets-Control-Sample 1

value: Human pancreatic islets


title: C-5691, grown at 37 C, exponential phase (OD600=0.8), 2

tag: cell line


title: WatR-FLAG strain, input

description:
WatR-IP
No antibody used for input.

tag: genotype


title: K11Q2, IP

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

data_processing:
The obtained DNA library  was  sequenced on Illumina sequencing platform.
Low quality bases were trimmed by using Trimmomatic(version: 0.36). Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. It works with FASTQ or gzipp'ed FASTQ. With 'simple' trimming, each adapter sequence is tested against the reads, and if a sufficiently accurate match is detected, the read is clipped appropriately.
Clean reads were mapped to Arabidopsis thaliana(ENSEMBLE) using Bowtie2 (version:2.3.4.3) with default parameters. The alignment file(SAM) was transformed to BAM file and was filtered by the following criteria: (1) only keep unique aligned reads; (2) remove reads with low MAPQ(<30).
The MACS2 (version: 2.1.2) was used to identify transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity.
The peaks were annotated by ChIPseeker (version: 2.16.0), an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes. Comparison of ChIP peak profiles and annotation are also supported.
Assembly: Saccharopolyspora erythraea NRRL 2338(NCBI,ASM6288v1)
Supplementary files format and content: bigWig, Peak

organism: Saccharopolyspora erythraea

source_name: whole cell

growth_protocol: TSB medium

extract_protocol:
Collected the cultured cells in centrifuge tube and then washed with 1X PBS buffer. After centrifugation and removing the supernatant, 1% formaldehyde in PBS buffer was used to cross-link DNA and proteins for about 10min at 37 ℃.
After that, 0.125 M of glycine was used to stop the crosslinking reaction. the cells were washed with precooled PBS with 0.5% bovine serum and by PBS supplemented with protease inhibitor compound (PIC). The cells were collected by centrifugation at 850 rpm for 3 min after each wash. The cells were resuspended in 200 μl ice-cold lyses buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.5 plus PIC) and then thawed on ice for 10 min to allow cell lyses. The cell lysate was sonicated using Bioruptor Pico to generate chromatin fragments of size range from 100 to 800 bp. One-tenth of the sonicated chromatin sample was separated for input control. The remaining chromatin was immunoprecipitated in ChIP dilution buffer (1% Triton, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 7.5) with 4 μg of antibody that has been pre-incubated with protein A/G magnetic beads (Invitrogen; 10003D). The immunoprecipitation reaction was incubated overnight at 4 °C and the beads were washed twice with each of the following buffers at 4 °C: RIPA buffer (10 mM Tris, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.1% Triton X-100); RIPA buffer plus 0.3 M NaCl; LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and TE buffer. The captured DNA and input control sample were reverse cross-linked by eluting the beads with elution buffer (1% SDS, 0.1 M NaHCO3) at 65 °C for 2 h, respectively. The eluted DNA was purified by phenol-chloroform extraction and precipitated with ethanol and glycogen. The obtained DNA was subjected to library preparation and sequenced on Illumina sequencing platform.

value: whole cell


title: C-1a, grown at 37 C, exponential phase (OD600=0.8), 3

value: wt pnp+


title: K11Q2,Input


title: C-1a, grown at 37 C, exponential phase (OD600=0.8), 2


title: 3D

value: cultured in DMEM+10%FBS

value: healthy donor

value: bone marrow stromal cells


title: Sample_15-05316_MCK_mut2

city: Flora Hill

first: M Cristina

last: Keightley

state: VIC

address: Edwards Rd

department: Rural Clinical Sciences

country: Australia

institute: La Trobe University

data_processing:
Data were QC’d using FastQC, ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome (GRCz10) using STAR.
Counts were derived using HTseq-count and differentially expressed genes determined using limma + voom using Degust v0.21 (David R. Powell, Victorian Bioinformatics Consortium, Australia).
Assembly: genome GRCz10
Supplementary files format and content: Excel spreadsheet includes HT-Seq counts for each sample

organism: Danio rerio

source_name: lyz+, mpx+ granulocytes

extract_protocol:
RNA was extracted from sorted cells using RNeasy Micro (Qiagen).
Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA-Seq system V2 for amplification and cDNA generation, followed by Ovation Ultralow System V2 for library preparation.

value: lyz+, mpx+ granulocytes

value: zbtb11 mutant (mne)

value: 48 hpf


title: Sample_15-05316_MCK_mut3


title: Sample_15-05315_MCK_WT3

value: wild-type


title: Sample_15-05314_MCK_WT2


title: Sample_15-05316_MCK_mut1


title: control1,Input


title: WatR-FLAG strain, biol rep 1


title: Control2

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

institute: Pusan National University Yangsan Hospital

description: Gene expression data from Control

hyb_protocol: Approximately 5.5 μg of the labeled cDNAs were hybridized onto the Affymetrix GeneChip Array at 45℃ for 16 hours.

scan_protocol: After washing, the arrays were stained on a GeneChip Fluidics Station 450 and scanned on the GeneChip Scanner 3000.

data_processing:
Raw data were analyzed using Affymetrix GeneChip Command Console Software (AGCC). The raw data were summarized and normalized with Robust Multi-array Average (RMA) module implemented in Affymetrix Power Tools.
The differentially expressed genes (DEGs) between BPPV and normal control samples were screened by fold-change (fc) filtering combined with student’s t-test. False discovery rate (FDR) was controlled by adjusted p-value using Benjamini-Hochberg algorithm. Genes were considered differentially expressed at |fold changes| > 2 and p-value < 0.05.

label: biotin

source_name: peripheral whole blood

label_protocol: Purified RNA sample was transcribed to double-strand cDNA using the GeneChip Whole Transcript (WT) Amplication kit. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: The samples were incubated for a minimum of 2 hours at room temperature (15-25℃) to achieve complete lysis of blood cells. And then, the samples were centrifuged for 10 minutes at 5000 x g using a swing-out rotor. The supernatant was decanted, and 4 mL of RNase-free water was added to the pellet. The samples were vortexed until the pellet was visibly dissolved, and centrifuged for 10 minutes at 5000 x g. After the entire supernatant was removed, the remaining pellet was resuspended in 350 μL of buffer BR1 and transferred to microcentrifuge tube, followed by automated RNA purification using QIAcube. The purity and quantity of RNA were measured using a NanoDrop ND-1000 (Thermo Fisher Scientiﬁc, Wilmington, DE, USA). The quality of RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an RNA Integrity Number.

treatment_protocol: Peripheral whole blood (2.5 ml) was collected from the patients and ten healthy normal controls. The samples immediately placed into PAXgene Blood RNA Tubes (QIAGEN), and were stored under refrigerated conditions (2-8℃) before RNA extraction.

tag: tissue

value: Whole blood

tag: disease

value: Control


title: C-6001, grown at 37 C, exponential phase (OD600=0.8), 1

value: substitution of the bacterial ORF with the human


title: Control4

description: Gene expression data from Control


title: C-1a, grown at 37 C, exponential phase (OD600=0.8), 1


title: Sample_15-05313_MCK_WT1


title: Control1

description: Gene expression data from Control


title: C-5691, grown at 37 C, exponential phase (OD600=0.8), 1

value: pnp ORF deletion


title: Control3

description: Gene expression data from Control


title: Input_40R_rep2

status: Public on Aug 07 2023

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Low-quality reads and Illumina adaptor sequences from the read ends were removed using Trimmomatic (Bolger et al., 2014).    Quality trimmed reads were aligned to the P. falciparum genome (plasmodb.org, v3, release v32) using HiSat2.  Duplicate reads were removed using samtools (markdup) (Li et al., 2009). GC bias was corrected using deeptool’s correctGCBias tool (Ramirez et al., 2014). For coverage plots of Api2EI 40 h.p.i. and 20 h.p.i. ChIP-seq experiments, deeptool’s bamCompare tool was used to normalize the read coverage per base of the genome position ( option  ‘-bs 1’) in the respective input and ChIP samples to the total number of reads in each library (-- nomarmalizeUsing RPKM). Normalized input coverage  per bin was subtracted from the ChIP values (option – operation subtract). Coverage plots were visualized using IGV genome browser (Thorvaldsdottir et al., 2013).
ChIP-Peaks  (q-value cutoff < 0.05) were identified using macs2 (Zhang et al., 2008) by comparing the input with ChIP  with default settings but without prior peak modelling (option ‘-nomodel’), the fragment size set to 200 bp (option ‘-extsize 200’) and the genome size  (option ‘-g’) set to 233332839. Robust common peaks between replicates were identified using bedtools ‘intersect’ (option –f 0.30 –r) (Quinlan and Hall, 2010). Peak annotation was carried out using Homer’s annotatePeaks.pl that assigned each peak with the nearest downstream gene. Enrichment heatmaps and profile plots were generated using the deepTools computeMatrix and plotHeatmap tools.
Assembly: Plasmodium falciparum build version 3
Supplementary files format and content: Bam files were converted to bigwig files using bamCoverage from the deeptools suite

organism: Plasmodium falciparum

source_name: P. falciparum

growth_protocol: Parasites were maintained in human A+ erythrocytes at 37 °C in RPMI 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM L-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using 70% (v/v) isotonic Percoll (GE Healthcare Life Sciences) before allowing reinvasion to occur, followed by sorbitol treatment.

extract_protocol:
The ChIP assay was performed as described (Pandey et al., 2020) with a few modifications. Parasite culture (50 ml) containing synchronized late-stage schizonts (~ 40 h.p.i.) at ~5% parasitemia was centrifuged at 900 g for 4 min and the cells washed once with PBS. To the cell pellet, 25 ml of 0.15% saponin in PBS was added and incubated on ice for 10 min followed by washing twice with cold PBS. Parasites were crosslinked for 10 min by adding methanol-free formaldehyde at 1% final concentration and incubated for 10 min at 37 °C with occasional shaking. The crosslinking reaction was quenched by adding 1.25 M glycine to achieve a final concentration of 0.125 M and incubated at 37 °C for another 5 min. Parasites were centrifuged for 10 min at 3250 g at 4 °C, washed three times with DPBS, snap frozen in liquid nitrogen and stored at -80 °C until further use. Frozen formaldehyde fixed parasites were thawed on ice for chromatin immunoprecipitation. One ml of nuclear extraction buffer (10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1mM DTT, 1x EDTA-free protease inhibitor cocktail [Roche]) was added to the tubes containing thawed parasites and incubated on ice for 30 min. After the incubation, 10% NP-40 was added to reach a final concentration of 0.25% and the parasites were lysed by passing through a 261/2 G needle seven times. Parasite nuclei were collected by centrifuging at 2500g for 10 min at 4 °C. Shearing of chromatin was carried out using the Covaris Ultra Sonicator (E220) for 14 min with the following settings; 5% duty cycle, 140 intensity peak incident power, 200 cycle per burst to obtain fragment size of 200 to 600 bp. Insoluble materials were removed by centrifuging the sheared chromatin for 10 min at 13500 g at 4 °C. 30 µl of fragmented chromatin were stored as input at -80°C.    Fragmented chromatin was diluted 1:1 in ChIP dilution buffer (30 mM Tris-HCl pH 8.0, 0.1% SDS, 3 mM EDTA, 300 mM NaCl, 1% Triton X-100, EDTA-free protease inhibitor cocktail).  Chromatin was incubated overnight with 6 µg of mentioned antibodies. The antibody-protein complex was recovered with protein A coupled to magnetic beads (Dynabeads, Invitrogen, Cat No. 10002D), followed by extensive washes with low salt immune complex wash buffer, high salt immune complex wash buffer (washes done at 4 °C) and TE buffer (washes done at RT). Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3) at 45 °C for 30 min with shaking. Immunoprecipitated chromatin and input were reverse crosslinked overnight at 45 °C by adding 5 M NaCl to a final concentration of 0.5 M. Samples were treated with RNaseA for 30 min at 37 °C followed by a 2 h incubation at 45 °C with proteinase K (final concentration 66 µg/ml). DNA was purified using ChIP DNA clean & concentrator (Zymo Research, Cat. No. D5205).
Libraries were prepared using NEBNext Ultra II DNA library kit following the manufacturer’s instructions until the step of adapter ligation (Adapters were diluted at 1: 20 ratio). Adapter ligated libraries were purified using AmpureXP beads. The libraries were amplified for a total of 6 PCR cycles (2 min at 98 °C initial denaturation; 6 cycles of 30 s at 98 °C, 50 s at 62 °C, final extension 5 min at 62 °C) using the KAPA HiFi HotStart Ready Mix (Kapa Biosystems).  Amplified libraries were purified and size selected for 350 bp inserts using AmpureXP beads and sequenced on the Illumina HiSeqX platform with 150 bp paired-end read layouts.

tag: chip antibody

value: input


title: BPPV3

description: Gene expression data from AUV

value: AUV


title: BPPV1

description: Gene expression data from AUV


title: BPPV2

description: Gene expression data from AUV


title: BPPV4

description: Gene expression data from AUV


title: control1,IP


title: 40D_H3K9ac_rep1

value: rabbit polyclonal anti H3K9ac (RRID:AB_310544)


title: 40D_H3K9ME3_rep2

value: rabbit polyclonal anti H3K9me3 (RRID:AB_310620)


title: 40D_H3K9ME3_rep1


title: 40D_H3K9ac_rep2


title: Input_20D_rep1


title: 40R_H3K4ME3-rep2

value: Rabbit polyclonal anti H3K4me3 antibody (Cat no. ab8580, Abcam, RRID:AB_306649)


title: 40R_H3K9ME3-rep1


title: 40R_H3K9ac_rep1


title: 40R_H3K9ME3_rep2


title: 40D_H3K4ME3_rep1


title: 40R_H3K4ME3_rep1


title: 20R_H3K9ME3_rep3


title: 40R_H3K9ac_rep2


title: Input_40D_rep1


title: 40D_H3K4ME3_rep2


title: 20R_H3K9ME3_rep2


title: 20R_H3K9ac_rep2


title: Input_20R_rep2


title: 20R_H3K4ME3_rep2


title: 20R_H3K4ME3_rep3


title: 20R_H3K9ac_rep1


title: Input_20R_rep1


title: 20D_H3K9ac_rep2


title: Input_20D_rep2


title: 20D_H3K9ME3-rep2


title: 20D_H3K9ME3_rep1


title: 20R_H3K9ME3_rep1


title: 20D_H3K9ac_rep1


title: 20D_H3K4ME3_rep1


title: 20D_H3K4ME3_rep2