title: Negative control non-target siRNA POVPC treated 2

description: LncRNA/mRNA expression profiling of MASMC treated with non-target siRNA for 48h followed by POVPC for 24h, Replicate 2

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, POVPC 24h, Replicate 2


title: heart biopsy: 396

status: Public on Apr 02 2024

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: heart biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: tissue

value: heart biopsy

tag: lowlvef (yes, no)

value: no


title: vascular, AB42

type: SRA

city: New York

first: Caghan

last: Kizil

state: NY

country: USA

institute: Columbia University Irving Medical Center

description:
10x Genomics
CP016

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

organism: Danio rerio

source_name: telencephalon

growth_protocol: Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH 7.5, at 28 °C (±1 °C) in groups of 20 animals per 2.8 L.

extract_protocol:
Cells from zebrafish telencephalon were dissociated, cells were sorted by FACS based on the reporter line. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics

treatment_protocol: Tg(her4.1:dRED) and Tg(fli1a:GFP) lines were injected with Amyloid-beta 42 peptide and PBS as control as descibed (Bhatatrai et al. 2016).

value: telencephalon

tag: genotype

tag: treatment


title: heart biopsy: 400


title: Negative control non-target siRNA POVPC treated 3

city: Cleveland

first: Olga

last: Cherepanova

state: Ohio

address: 9620 Carnegie Avenue

department: Cardiovascular and metabolic sciences

institute: Cleveland Clinic Foundation

description: LncRNA/mRNA expression profiling of MASMC treated with non-target siRNA for 48h followed by POVPC for 24h, Replicate 3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5μl 10 × Blocking Agent and 1μlof 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Mus musculus

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, POVPC 24h, Replicate 3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each RNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured by NanoDrop ND-1000.

extract_protocol: cells were harvested with the Trizol reagent (Invitrogen), and the total RNA was isolated as per the manufacturer-recommended protocol. The total RNA isolated from MASMC was quantified by the Nanodrop ND-1000, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, the Agilent Array platform was employed.

treatment_protocol: Primary mouse aortic smooth muscle cells (MASMC) were isolated and grown as previously described (Cherepanova et al., 2016). For experiments, cells at the 70% confluency were transfected with blocking siOct4 or non-target siRNA (NT siRNA) for 48 hours in serum-free media, followed by the treatment with 10 µg/mL POVPC (Cayman Chem, #10031) or vehicle (DMSO) for 24 hours based on our previous findings (Pidkovka et al., 2007).

value: aortic smooth muscle cells

tag: cell type

value: smooth muscle cells


title: heart biopsy: 397


title: heart biopsy: 395


title: Negative control non-target siRNA POVPC treated 1

description: LncRNA/mRNA expression profiling of MASMC treated with non-target siRNA for 48h followed by POVPC for 24h, Replicate 1

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, POVPC 24h, Replicate 1


title: glia, AB42

description:
10x Genomics
CP015


title: Negative control non-target siRNA DMSO treated 1

description: LncRNA/mRNA expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 1

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, DMSO 24h, Replicate 1


title: Negative control non-target siRNA DMSO treated 2

description: LncRNA/mRNA expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 2

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, DMSO 24h, Replicate 2


title: heart biopsy: 394


title: YAA698

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

library_source: transcriptomic

data_processing:
UMIs were first extracted with UMItools. Read adapters, polyA tails and rRNA sequences were then removed with bbduk.sh, following the Lexogen recommendations. Reads were aligned with Bowtie2 to the mouse reference genome (GRCm39). SAM files were converted to BAM and sorted with samtools 1.9. Sorted BAM files were deduplicated with UMItools and converted to FASTQ format.  Processed reads were finally analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm39) with TopHat-2.0.10 using Bowtie 1.0.0 (--library-type fr-secondstrand in TopHat), allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM26.GRCm39.Ensembl103). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Tabulated text file with DESeq2 normalized counts

source_name: Bone marrow derived Neutrophils

extract_protocol:
RNA was extracted from cells with TRItidy and Picopure RNA Isolation Kit (Arcturus, Applied Biosystems, #12204-01) following manufacturer´s instructions.
Total RNA samples (average 100ng, range 16-180ng) were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) with a UMI Second Strand Synthesis module. Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. While primers from both steps contain Illumina-compatible sequences, random primers additionally feature 6 nt long Unique Molecular Identifier (UMI) tags. Libraries are completed by PCR, and sequenced on anIllumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation.

value: Bone marrow derived Neutrophils

tag: age

value: young ( 2 months old)


title: heart biopsy: 393


title: vascular, PBS

description:
10x Genomics
CP014

value: PBS


title: YAA00466

data_processing:
Read adapters, polyA tails and rRNA sequences were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm39) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM26.GRCm39.Ensembl103). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Tabulated text file with DESeq2 normalized counts

source_name: Kidney

extract_protocol:
Total RNA was extracted from tissues with TRItidy (Panreac Applichem, #A4051,0200) and using RNeasy kit from Qiagen (#74106) according to manufacturer´s instructions
Total RNA samples (500ng; RQS/RIN average 7.1, range 6.5-8.0) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation.

value: Kidney

value: whole tissue

value: RagC S74N (KI/+)

value: young mice (3 months old)


title: heart biopsy: 389


title: glia, PBS

description:
10x Genomics
CP013


title: heart biopsy: 391


title: YAA700

description: Illumina NextSeq 550 (with v2.5 reagent kits)


title: glia, vascular mix_Ab42

description:
10x Genomics
CP004

value: Tg(her4.1:dRED); Tg(kdrl:GFP)


title: heart biopsy: 388


title: YAA00458


title: heart biopsy: 390


title: heart biopsy: 386


title: heart biopsy: 387


title: Negative control non-target siRNA DMSO treated 3

description: LncRNA/mRNA expression profiling of MASMC treated with non-target siRNA for 48h followed by DMSO for 24h, Replicate 3

source_name: Primary mouse aortic smooth muscle cells (MASMC), non-target siRNA 48h, DMSO 24h, Replicate 3


title: unsorted, whole telcenphalon

description:
10x Genomics
CP001

value: WT-AB

value: Control


title: heart biopsy: 384


title: YAA00455


title: YAA00456


title: heart biopsy: 383


title: heart biopsy: 392


title: heart biopsy: 382


title: heart biopsy: 381


title: YAA00453


title: HAVSMC, AGE-BSA, input

city: Jinan

first: Fei

last: Xie

address: 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province

country: China

institute: Qilu Hospital of Shandong University

data_processing:
Use cutadapt program to remove the joint sequence in the original disembarkation data; Use Trimmomatic21 program to remove low-quality sequences to get clean data; Use Fastqc3 program to calculate the amount of clean data and the proportion of g30
Bowtie2 program was used to compare clean data to rRNA sequence and remove rRNA sequence. The non-rRNA sequence was obtained. non-rRNA was compared to the reference genome using the hisat2 program; MarkDuplicates program in picard was used to remove duplicate sequences
Peak-calling on the genome using MACS2; Use BedTools for peak annotation; HOMER was used for motif detection of binding peaks
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: aorta

growth_protocol: HAVSMCs were cultured in smooth muscle cell media (SMCM, 5.5 mM glucose) supplemented with 1% smooth muscle cell growth supplement, 2% fetal bovine serum (FBS), and 1% penicillin/streptomycin solution.Cells were incubated at 37 °C in an incubator with 5% CO2.

extract_protocol:
HAVSMCs were incubated with BSA or AGE-BSA for four days and fixed using 1% methanal for 10 mins. The reaction was stopped using 2.66 M glycine, and then cells were collected and lysed using RIPA lysis buffer. After adding A/G agarose beads and NF90 antibody (Santa cruz, sc-377406) to the lysis buffer, the mixture was incubated for 2 h at 20 ℃. The protein A/G agarose beads were washed several times and digested using 90% proteinase K. Subsequently, the pulled-down RNA was purified.
RNA-seq strand-specific libraries were constructed using the TruSeq® Stranded Total RNA Sample Preparation kit. Qubit® 2.0 Fluorometer was used to quantify purified libraries, and Agilent 2100 bioanalyzer was used to confirm the insert size. A cluster was generated by cBot and sequenced on the HiSeq X Ten.

treatment_protocol: The cultured HAVSMCs were treated in osteogenic medium with BSA (200 µg/ml) or AGE-BSA (200 µg/ml) for 24h.

value: aorta

tag: cell line

value: HAVSMC

value: human aortic vascular smooth muscle cells

value: WT

value: AGE-BSA


title: HAVSMC, AGE-BSA, RIP

tag: antibody

value: NF90 antibody (Santa cruz, sc-377406)


title: YAA00440


title: heart biopsy: 379

value: heart biopsy

value: no


title: YAA00454


title: heart biopsy: 385


title: HAVSMC, BSA, input

value: BSA


title: YAA00457


title: HAVSMC, BSA, RIP


title: heart biopsy: 374


title: heart biopsy: 378


title: YAA00438


title: YAA00439


title: heart biopsy: 376


title: YRN00233

extract_protocol:
Total RNA was extracted from tissues with TRItidy (Panreac Applichem, #A4051,0200) and using RNeasy kit from Qiagen (#74106) according to manufacturer´s instructions
Total RNA samples (300 ng, with an average quality score of 6.7 (range 6.2-7) on labchip analysis) were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation

value: old mice (1.5 yr old)


title: heart biopsy: 375


title: heart biopsy: 377


title: CD3

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
Illumina Novaseq 4000  polyA RNA reads were trimmed using cutadapt and checked  with FASTQC
Illumina reads were aligned to the Drosophila reference genome (dm6 Ensembl release 70) with Hisat2
Read counts were generated for each annotated gene using HTSeq-Count. RPKM (Reads Per Kilobase of exon per Megabase of library size) values were calculated using Cufflinks. Reads normalization, variance estimation and pair-wise differential expression analysis with multiple testing correction were conducted using the R Bioconductor DESeq2 package
Genomic  reads were aligned using bowtie2 on Drosophila genome (dm6 Ensembl realease 70)
The resulting reads were mapped to their respective reference genome using Bowtie2 (v2.4.2), reporting at most one hit for each read .
Assembly: Drosophila genome (dm6 Ensembl realease 70)
Supplementary files format and content: text file with RNA-seq RPKM expression per gene and condition
Supplementary files format and content: BigWig with read coverage per position across the genome.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: central nervous system

extract_protocol:
The central nervous systems from wild type (w11118), Tet null or Tet CD (catalytic dead) mutant third instar Drosophila melanogaster larvae were dissected in PBS. For RNA-seq, total RNA was extracted with Trizol. ChIP-seq were performed as described in Loubiere et al. (Bio Protocol 2017). CUT&RUN were performed as described in Ahmad et al. (PLoS Genet. 2019).
For RNA-seq, libraries were prepared using the Illumina TruSeq RNA Library Prep kit. For ChIP-seq and CUT&RUN, libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: central nervous system

value: Tet CD


title: heart biopsy: 372


title: heart biopsy: 373


title: heart biopsy: 371


title: YRN00230

value: Kidney

value: whole tissue

value: RagC S74N (KI/+)


title: heart biopsy: 380


title: heart biopsy: 370


title: CD2


title: CD1


title: heart biopsy: 369


title: heart biopsy: 368


title: heart biopsy: 367


title: YRN00227


title: CD4


title: heart biopsy: 366


title: TETnull4

value: Tet null


title: heart biopsy: 364


title: TETnull3


title: YRN00183


title: heart biopsy: 361


title: heart biopsy: 365


title: YRN00177


title: heart biopsy: 362


title: YRN00176


title: heart biopsy: 363


title: TETnull2


title: TETnull1


title: heart biopsy: 359


title: YRN00173


title: WT4


title: glia, vascular mix_control

description:
10x Genomics
CP003

value: telencephalon

value: Tg(her4.1:dRED); Tg(kdrl:GFP)

value: PBS


title: YRN00229


title: YRN00170


title: heart biopsy: 358


title: WT3


title: WT2


title: heart biopsy: 357


title: heart biopsy: 353


title: heart biopsy: 356


title: GMSC-EV 3

city: Shanghai

first: Jingrong

last: Chen

address: 768 Zhongshan Middle Road, Shanghai

institute: Shanghai Jiaotong University

data_processing:
CLC Genomics workbench v 11.0.1
Assembly: hg18
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Tissue

growth_protocol: GMSCs or Fibroblasts were maintained in MEM alpha medium containing 10% fetal bovine serum, 100 U/mL penicillin/100 μg/mL streptomycin at 37°C in an incubator with 5% CO2 and 95% O2.

extract_protocol:
Total RNA from EVs was isolated using miRNeasy Serum/Plasma Kit (QIAGEN) according to the protocol. The quantity and quality of total RNA were assessed using the Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA).
The NEBNext Multiplex Small RNA Library Prep Set for Illumina was utilized to prepare a small RNA library. The qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA) was used to determine precise measurement for sequencing purposes.

value: Tissue

value: Mesenchymalstemcell


title: WT1


title: heart biopsy: 355


title: heart biopsy: 360


title: heart biopsy: 352


title: YRN00149


title: heart biopsy: 350


title: IgG_WT2

library_source: genomic

data_processing:
Illumina Novaseq 4000  polyA RNA reads were trimmed using cutadapt and checked  with FASTQC
Illumina reads were aligned to the Drosophila reference genome (dm6 Ensembl release 70) with Hisat2
Read counts were generated for each annotated gene using HTSeq-Count. RPKM (Reads Per Kilobase of exon per Megabase of library size) values were calculated using Cufflinks. Reads normalization, variance estimation and pair-wise differential expression analysis with multiple testing correction were conducted using the R Bioconductor DESeq2 package
Genomic  reads were aligned using bowtie2 on Drosophila genome (dm6 Ensembl realease 70)
The resulting reads were mapped to their respective reference genome using Bowtie2 (v2.4.2), reporting at most one hit for each read .
Assembly: Drosophila genome (dm6 Ensembl realease 70)
Supplementary files format and content: text file with RNA-seq RPKM expression per gene and condition
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: Cut&Run

molecule: genomic DNA


title: GMSC-EV 1


title: GMSC-EV 2


title: heart biopsy: 349


title: heart biopsy: 348


title: Fib-EV 3

value: Fibroblast


title: heart biopsy: 347


title: heart biopsy: 346


title: Fib-EV 2


title: heart biopsy: 345


title: H3K27me3_WT1


title: heart biopsy: 354


title: heart biopsy: 344


title: heart biopsy: 343


title: H3K27me3_TETnull2


title: Fib-EV 1


title: IgG_WT1


title: heart biopsy: 351


title: heart biopsy: 342


title: H3K27me3_TETnull1


title: heart biopsy: 340


title: H3K27ac_WT2


title: heart biopsy: 338


title: HepG2-tLNP/siHBV, replicate2

first: Wenjing

last: Zai

state: 上海

address: Room 306, Fuxing Building, 131 Dongan Road, Shanghai 200032, China

institute: Fudan University

data_processing:
The fastq. files were trimmed by Cutadapt v3.1 and then applied to human or mouse reference genome by Hisat2, sorted by SAMtools and analyzed for expression using featureCounts.
Assembly: mm10/hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cell line

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted by TRIzol.
cDNA libraries were prepared according to manufactures’instructions.

treatment_protocol: HepG2 cells were incubated with tLNP/siNC or tLNP/siHBV at the dose of 50 nM for 16 h. Mice were intravenously injected with tLNP/siNC or tLNP/siHBV at the dose of 1 mg/kg for 72 h.

value: cell line

value: Hepatocellular carcinoma

value: WT

value: tLNP/siHBV, 50nM


title: heart biopsy: 339

value: heart biopsy

value: no


title: heart biopsy: 341


title: HepG2-tLNP/siHBV, replicate3


title: heart biopsy: 334


title: H3K27ac_TETnull2

value: central nervous system


title: H3K27me3_WT2


title: HepG2-tLNP/siHBV, replicate1


title: H3K27ac_WT1


title: heart biopsy: 337


title: HepG2-tLNP/siNC, replicate3

value: tLNP/siNC, 50nM


title: heart biopsy: 336


title: HepG2-tLNP/siNC, replicate2


title: heart biopsy: 333


title: heart biopsy: 332


title: H3K4me3_WT_CD_2


title: H3K27ac_TETnull1


title: heart biopsy: 331


title: HepG2-Mock, replicate3

value: Mock


title: heart biopsy: 330


title: heart biopsy: 329


title: heart biopsy: 328


title: HepG2-Mock, replicate2


title: H3K4me3_WT_CD_1


title: heart biopsy: 335


title: heart biopsy: 326


title: H3K4me3_CD2

value: Tet CD


title: heart biopsy: 324


title: heart biopsy: 325


title: heart biopsy: 322


title: HepG2-Mock, replicate1


title: Tet3_mutant_WGBS

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
For RNA-seq RNA was extracted using Qiagen RNeasy Mini kid (74104). Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.7) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.9a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) (Langmead and Salzberg, 2012) with the parameters: --local --sensitive --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) (Zhang et al., 2008) with options -p 0.00001 -f BAMPE --keep-dup all.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.0% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -adaMR 0.25 -ada_trim -polyX 50 -minReadLen 100 to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Neuroectoderm cells

growth_protocol: ESCs were cultured on gelatin in serum/LIF for 24 hours. LIF was removed and 1uM retinoic acid (RA) was added for 72 hours to generate NE cells, which were harvested for subsequent high-throughput sequencing.

extract_protocol:
For RNA-seq, RNA was extracted from NE cells using Qiagen RNeasy Mini kit. For WGBS, DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/). CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.
RNA-seq, WGBS, CUT&Tag

treatment_protocol: For CUT&Tag, NE cells were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex.

value: Neuroectoderm cells

tag: strain

value: V6.5 Male mixed 129/C57BL/6

value: Tet3 mutant


title: H3K4me3_WT_null2


title: heart biopsy: 320


title: HepG2-tLNP/siNC, replicate1


title: Tet3_knockout_WGBS

value: Tet3 knockout


title: heart biopsy: 318


title: heart biopsy: 321


title: Tet3_wildtype_WGBS

value: Tet3 wildtype


title: H3K4me3_TETnull1

value: Tet null


title: heart biopsy: 317


title: H3K4me3_WT_null1


title: heart biopsy: 327


title: H3K4me3_TETnull2


title: heart biopsy: 316


title: Adipocytes, DMEM, ACI-23 co-culture, replicate 3

city: San Diego

first: Carrie

last: House

state: CA

address: 5500 Campanile Dr

institute: San Diego State University

description:
mAdipCC_3
mAdip_ACI23CC_processed.xslx

data_processing:
Raw data quality control (method: FASTQC)
Alignment of raw data to genome (method: STAR)
Gene or transcript level quantification (method: RSEM or Kallisto)
Quality control of read quantification & outlier detection (method: MDS plot)
Normalization (method: TMM normalization)
Differential expression analysis (method: limma-voom)
Assembly: hg38
Supplementary files format and content: excel files, contains normalized read counts for each biological replicate.

source_name: omental adipose

extract_protocol:
Trizol RNA extraction with Zymo Direct-zol RNA Miniprep Kit
TruSeq RNA Library Prep Kit v2

value: omental adipose

value: Primary omental differentiated adipocyte

value: co-culture


title: heart biopsy: 314


title: H2Aub_WT2


title: heart biopsy: 323


title: Adipocytes, DMEM, ACI-23 co-culture, replicate 1

description:
mAdipCC_1
mAdip_ACI23CC_processed.xslx


title: H3K4me3_CD1


title: heart biopsy: 313


title: H2Aub_WT1


title: heart biopsy: 312


title: H2Aub_TETnull2


title: heart biopsy: 309


title: Adipocytes, DMEM, monoculture, replicate 2

description:
mAdip_2
mAdip_ACI23CC_processed.xslx

value: monoculture


title: heart biopsy: 311


title: heart biopsy: 310


title: heart biopsy: 319


title: H2Aub_TETnull1


title: heart biopsy: 315


title: heart biopsy: 308


title: heart biopsy: 304


title: Input2


title: heart biopsy: 305


title: heart biopsy: 306


title: Adipocytes, DMEM, ACI-23 co-culture, replicate 2

description:
mAdipCC_2
mAdip_ACI23CC_processed.xslx


title: Preadipocytes, DMEM/OM-PM, ACI-23 co-culture, replicate 4

description:
pAdipCC_4
pAdip_ACI23CC_processed.xslx

value: Primary omental preadipocyte


title: heart biopsy: 302

value: heart biopsy


title: heart biopsy: 303

value: no


title: Preadipocytes, DMEM/OM-PM, ACI-23 co-culture, replicate 3

description:
pAdipCC_3
pAdip_ACI23CC_processed.xslx


title: Input1

value: central nervous system


title: Preadipocytes, DMEM/OM-PM, ACI-23 co-culture, replicate 2

description:
pAdipCC_2
pAdip_ACI23CC_processed.xslx


title: WT2_TET_GFP


title: heart biopsy: 301


title: Adipocytes, DMEM, monoculture, replicate 3

description:
mAdip_3
mAdip_ACI23CC_processed.xslx


title: WT1_TET_GFP


title: Adipocytes, DMEM, monoculture, replicate 1

description:
mAdip_1
mAdip_ACI23CC_processed.xslx


title: heart biopsy: 299


title: Preadipocytes, DMEM/OM-PM, ACI-23 co-culture, replicate 1

description:
pAdipCC_1
pAdip_ACI23CC_processed.xslx


title: heart biopsy: 298


title: heart biopsy: 297


title: Preadipocytes, DMEM/OM-PM, monoculture, replicate 4

description:
pAdip_4
pAdip_ACI23CC_processed.xslx


title: heart biopsy: 300


title: Preadipocytes, DMEM/OM-PM, monoculture, replicate 3

description:
pAdip_3
pAdip_ACI23CC_processed.xslx


title: GFP_TET1

value: Tet GFP


title: heart biopsy: 307


title: GFP_TET2


title: heart biopsy: 296


title: WT2_TET_CD2


title: heart biopsy: 294


title: heart biopsy: 293


title: Preadipocytes, DMEM/OM-PM, monoculture, replicate 2

description:
pAdip_2
pAdip_ACI23CC_processed.xslx


title: WT1_TET_CD1


title: heart biopsy: 295


title: heart biopsy: 292


title: heart biopsy: 290


title: Preadipocytes, DMEM/OM-PM, monoculture, replicate 1

description:
pAdip_1
pAdip_ACI23CC_processed.xslx


title: heart biopsy: 291


title: heart biopsy: 289


title: ACI-23 cells, DMEM, adipocyte co-culture, replicate 3

description:
mAdipAciCC_3
ACI23_mAdipCC_processed.xslx

source_name: primary ovarian serous carcinoma

value: primary ovarian serous carcinoma

value: Cancer cell line


title: heart biopsy: 288


title: GFP_TET_CD1

value: Tet CD


title: heart biopsy: 287


title: GAF_WT2


title: heart biopsy: 286


title: ACI-23 cells, DMEM, adipocyte co-culture, replicate 2

description:
mAdipAciCC_2
ACI23_mAdipCC_processed.xslx


title: heart biopsy: 285


title: heart biopsy: 284


title: ACI-23 cells, DMEM, adipocyte co-culture, replicate 1

description:
mAdipAciCC_1
ACI23_mAdipCC_processed.xslx


title: GAF_WT1


title: heart biopsy: 283


title: heart biopsy: 282


title: ACI-23 cells, DMEM, monoculture, replicate 4

description:
AciCtlDMEM_4
ACI23_mAdipCC_processed.xslx


title: ACI-23 cells, DMEM, monoculture, replicate 3

description:
AciCtlDMEM_3
ACI23_mAdipCC_processed.xslx


title: NSG iPAX7 Replicate 3

city: Minneapolis

first: Sarah

last: Crist

state: Minnesota

address: 2231 6th St SE

institute: University of Minnesota

description:
NSG_TC1133_19174
NSG_TC1133_19174

data_processing:
Reads were trimmed using Trimmomatic (v0.33) and quality control on raw reads was performed with FastQC(v0.11.9) (mean quality score 36) was assessed.
STAR(v2.7.3a) was used to align to human (hg38) and mouse (mm10) reference genomes.
Subtraction of mouse sequences was performed using XenofilteR(v1.6).
Aligned reads were counted for gene associations against the UCSC genes data base with HTSeq(v0.11.0).
Differentially expressed genes were identified using edgeR (v3.42.4, negative binomial)
Assembly: mm10 and hg38
Supplementary files format and content: Comma separated value text files of raw counts for each sample (.CSV) - there is one file for counts mapped to human genome and one file for counts mapped to mouse genome
Supplementary files format and content: Raw sequencing data for each sample (.FASTQ)

organism:
Homo sapiens
Mus musculus

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated from iPAX7 in vitro-differentiated myotubes and homogenized tibialis anterior muscles using TRIzol (Invitrogen) and the PureLink RNA mini kit (Invitrogen, #12183025) with on-column DNaseI treatment following the manufacturer’s recommendations.
500 ng of total RNA was used to for generate unique dual-indexed (UDI) TruSeq stranded mRNA libraries.

treatment_protocol: 6–8-week-old male NSG and NSG-mdx4Cv mice were used for these experiments. One day before intramuscular cell transplantation, target muscles (tibialis anterior) were pre-injured with cardiotoxin (15 μl of 10 μM stock).  Myogenic progenitors were injected at 1.65×106 (resuspended in 15 μl of PBS) using a 26 g Hamilton syringe. As control, contralateral legs were injected with the same volume of PBS. Two months after transplantation muscles were collected for RNA isolation.

value: Skeletal muscle

value: iPSC-derived myogenic progenitor

value: WT

value: CTX + cell therapy


title: heart biopsy: 281

source_name: heart biopsy


title: GFP_TET_CD2


title: heart biopsy: 280


title: NSG iPAX7 Replicate 2

description:
NSG_TC1133_19173
NSG_TC1133_19173


title: ACI-23 cells, DMEM, monoculture, replicate 2

description:
AciCtlDMEM_2
ACI23_mAdipCC_processed.xslx


title: heart biopsy: 278


title: NSG iPAX7 Replicate 1

description:
NSG_TC1133_19172
NSG_TC1133_19172


title: heart biopsy: 279


title: heart biopsy: 276


title: NSG-mdx iPAX7 Replicate 3

description:
MDX_TC1133_19353
MDX_TC1133_19353

value: DMD


title: ACI-23 cells, DMEM/OM-PM, preadipocyte co-culture, replicate 4

description:
pAdipAciCC_4
ACI23_pAdipCC_processed.xslx


title: heart biopsy: 275


title: NSG-mdx iPAX7 Replicate 2

description:
MDX_TC1133_19351
MDX_TC1133_19351


title: heart biopsy: 274


title: ACI-23 cells, DMEM, monoculture, replicate 1

description:
AciCtlDMEM_1
ACI23_mAdipCC_processed.xslx


title: ACI-23 cells, DMEM/OM-PM, preadipocyte co-culture, replicate 3

description:
pAdipAciCC_3
ACI23_pAdipCC_processed.xslx


title: heart biopsy: 273


title: heart biopsy: 271


title: heart biopsy: 272


title: heart biopsy: 270


title: ACI-23 cells, DMEM/OM-PM, preadipocyte co-culture, replicate 2

description:
pAdipAciCC_2
ACI23_pAdipCC_processed.xslx


title: heart biopsy: 269


title: ACI-23 cells, DMEM/OM-PM, preadipocyte co-culture, replicate 1

description:
pAdipAciCC_1
ACI23_pAdipCC_processed.xslx


title: heart biopsy: 268


title: ACI-23 cells, DMEM/OM-PM, monoculture, replicate 4

description:
AciCtlOMPM_4
ACI23_pAdipCC_processed.xslx


title: heart biopsy: 267


title: Tet3_KO_hmeDIP

data_processing:
For RNA-seq, Ladaptors were trimmed using trim galore (v0.6.7) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.9a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) (Langmead and Salzberg, 2012) with the parameters: --local --sensitive --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) (Zhang et al., 2008) with options -p 0.00001 -f BAMPE --keep-dup all.
For WGBS, bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.0% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -adaMR 0.25 -ada_trim -polyX 50 -minReadLen 100 to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
For hmeDIP, cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) (Langmead and Salzberg, 2012) with the parameters: --local --sensitive --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) (Zhang et al., 2008) with options -p 0.0001 -f BAMPE --keep-dup all.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10

extract_protocol:
For RNA-seq, RNA was extracted from NE cells using Qiagen RNeasy Mini kit. For WGBS, DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit. For hmeDIP, DNA was extracted from NE cells using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/). HmeDIP libraries were prepared by NEBNext HiFi 2x PCR Master mix. CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.

value: Neuroectoderm cells

value: V6.5 Male mixed 129/C57BL/6

value: Tet3 knockout


title: Tet3_Mut_hmeDIP

value: Tet3 mutant


title: heart biopsy: 277


title: heart biopsy: 266


title: ACI-23 cells, DMEM/OM-PM, monoculture, replicate 3

description:
AciCtlOMPM_3
ACI23_pAdipCC_processed.xslx

value: monoculture


title: Tet3_WT_hmeDIP

value: Tet3 wildtype


title: heart biopsy: 264

value: heart biopsy

value: no


title: heart biopsy: 261


title: ACI-23 cells, DMEM/OM-PM, monoculture, replicate 2

description:
AciCtlOMPM_2
ACI23_pAdipCC_processed.xslx


title: YRN00229

source_name: kidney

extract_protocol:
Total RNA was extracted from tissues with TRItidy (Panreac Applichem, #A4051,0200) and using RNeasy kit from Qiagen (#74106) according to manufacturer´s instructions. Isolated RNA was treated with DNAse (Qiagen, #79254)
Total RNA samples (500ng; RQS/RIN average 7.5, range 7.4-7.6) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation (the read1 - the only read in single read format) has the sense orientation.

value: kidney

value: wild type

value: 16 month old (old)


title: NSG-mdx iPAX7 Replicate 1

description:
MDX_TC1133_19350
MDX_TC1133_19350


title: heart biopsy: 262


title: heart biopsy: 263


title: heart biopsy: 260


title: YRN00183


title: heart biopsy: 258


title: ACI-23 cells, DMEM/OM-PM, monoculture, replicate 1

description:
AciCtlOMPM_1
ACI23_pAdipCC_processed.xslx

value: primary ovarian serous carcinoma

value: Cancer cell line


title: PT34_IR_InsulinResistant_GTG_IMI_44

city: Lausanne

first: Richard

last: Coward

address: Dorothy Hodgkin Building, Whitson Street, Bristol

department: Bristol Medical School

country: United Kingdom

institute: Bristol Royal hospital for Sick Children & University of Bristol

data_processing:
Sequence reads were mapped to GRCh38.p12 with STAR 2.7.10 and its parameters by default.
Read count were quantified with htseq-count 0.9.1
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

source_name: Proximal tubular cell

extract_protocol:
Cellular RNA was isolated using a RNeasy Mini kit (QIAGEN) as per the manufacturer’s recommendations.
cDNA libraries were prepared using the Clonetech SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

value: Proximal tubular cell


title: IgG_hmeDIP


title: heart biopsy: 257


title: heart biopsy: 256


title: PT34_IR_InsulinResistant_GTG_IMI_40


title: heart biopsy: 259


title: YRN00176


title: PT34_IR_InsulinResistant_GTG_IMI_36


title: heart biopsy: 254


title: PT34_IR_InsulinResistant_GTG_IMI_32


title: heart biopsy: 265


title: YRN00173


title: YAA189

value: 3 month old (young)


title: heart biopsy: 252


title: heart biopsy: 251


title: PT34_IR_InsulinResistant_GTG_IMI_28


title: YRN00227


title: PT34_IR_Basal_GTG_IMI_43


title: heart biopsy: 249


title: YAA170


title: heart biopsy: 247


title: heart biopsy: 248


title: heart biopsy: 255


title: PT34_IR_Basal_GTG_IMI_39


title: heart biopsy: 242


title: YAA160


title: Control (YFP GEMM) Immune cells, 4 weeks after Ad5SPC-Cre

city: Boston

first: Aaron

middle: L.

last: Moye

state: MA

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

data_processing:
10X Genomics Cell Ranger 3.1.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Assembly: mm10-1.2.0
Supplementary files format and content: h5 files for each library

source_name: Immune cells

extract_protocol:
For GEMM experiments, lungs from KRAS(G12D) p53(-/-) R26(YFP) mice 4, 7, 10, and 16 weeks after Ad5SPC-Cre infection were extracted and single-cell suspensions were generated. AT2 epithelial, immune, endothelial, and mesenchymal cells were collected using FACS. For organoid experiments, AT2 organoids and their co-cultured mesenchymal cells were collected using FACS 4, 7, 10, and 14 days after Ad5CMV-Cre infection. All cells were encapsulated, and libraries were generated using the 10X Genomics Single Cell 3' v3 pipeline. Pooled libraries were sequenced using an Illumina NextSeq500.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 3

treatment_protocol: For GEMM experiments, KRAS lsl-G12D; Rosa26 lsl-YFP mice were given 6x10^8 PFU of Ad5SPC-Cre intratracheally to activate oncogenic KRAS G12D, p53 loss, and YFP expression specifically in AT2 cells. For organoid experiments, FACS-sorted AT2 cells from Y and KPY mice were infected with 6x10^7 PFU/ml of Ad5CMV-Cre and co-cultured with lung mesenchymal cells.

value: Immune cells

value: Rosa26 lsl-YFP


title: Control (YFP GEMM) Endothelial cells, 4 weeks after Ad5SPC-Cre

source_name: Endothelial cells

value: Endothelial cells


title: PT34_IR_Basal_GTG_IMI_35


title: heart biopsy: 253

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).


title: heart biopsy: 245


title: heart biopsy: 246


title: heart biopsy: 244


title: PT34_IR_Basal_GTG_IMI_31


title: PT34_IR_Basal_GTG_IMI_27


title: Control (YFP GEMM) Mesenchymal cells, 4 weeks after Ad5SPC-Cre

source_name: Mesenchymal cells

value: Mesenchymal cells


title: heart biopsy: 243


title: PT34__InsulinResistant_GTG_IMI_42


title: heart biopsy: 240


title: heart biopsy: 241


title: YAA180


title: heart biopsy: 250


title: heart biopsy: 239


title: heart biopsy: 237


title: PT34__InsulinResistant_GTG_IMI_38


title: heart biopsy: 238


title: Control (YFP GEMM) AT2 cells, 4 weeks after Ad5SPC-Cre

source_name: AT2 cells GEMM

value: AT2 cells GEMM


title: PT34__InsulinResistant_GTG_IMI_34


title: Immune cells, 16 weeks after Ad5SPC-Cre

value: Kras lsl-G12D; p53 fl/fl; Rosa26 lsl-YFP


title: heart biopsy: 236


title: heart biopsy: 235


title: heart biopsy: 234


title: heart biopsy: 233


title: PT34__InsulinResistant_GTG_IMI_30


title: Mesenchymal cells, 16 weeks after Ad5SPC-Cre


title: heart biopsy: 231


title: PT34__InsulinResistant_GTG_IMI_26


title: heart biopsy: 232


title: heart biopsy: 229


title: PT34__Basal_GTG_IMI_41


title: AT2 YFP+ cells, 16 weeks after Ad5SPC-Cre


title: heart biopsy: 228


title: Immune cells, 10 weeks after Ad5SPC-Cre


title: heart biopsy: 227


title: Endothelial cells, 10 weeks after Ad5SPC-Cre


title: heart biopsy: 226


title: heart biopsy: 225


title: PT34__Basal_GTG_IMI_29


title: PT34__Basal_GTG_IMI_33


title: heart biopsy: 224


title: Mesenchymal cells, 10 weeks after Ad5SPC-Cre


title: heart biopsy: 222


title: AT2 YFP+ cells, 10 weeks after Ad5SPC-Cre


title: heart biopsy: 223


title: heart biopsy: 221


title: heart biopsy: 220


title: heart biopsy: 219


title: PT34__Basal_GTG_IMI_25


title: Endothelial cells, 16 weeks after Ad5SPC-Cre


title: K29_IR_InsulinResistant_GTG_IMI_64

source_name: Mesangial cell

value: Mesangial cell


title: Immune cells, 7 weeks after Ad5SPC-Cre


title: heart biopsy: 218


title: heart biopsy: 230


title: K29_IR_InsulinResistant_GTG_IMI_60


title: heart biopsy: 216


title: heart biopsy: 217


title: PT34__Basal_GTG_IMI_37


title: Mesenchymal cells, 7 weeks after Ad5SPC-Cre


title: heart biopsy: 215


title: AT2 YFP+ cells, 7 weeks after Ad5SPC-Cre


title: heart biopsy: 213


title: K29_IR_InsulinResistant_GTG_IMI_52


title: heart biopsy: 214


title: heart biopsy: 212


title: Immune cells, 4 weeks after Ad5SPC-Cre


title: heart biopsy: 210


title: K29_IR_InsulinResistant_GTG_IMI_48


title: heart biopsy: 209


title: heart biopsy: 211


title: Endothelial cells, 4 weeks after Ad5SPC-Cre


title: K29_IR_Basal_GTG_IMI_63


title: heart biopsy: 208


title: heart biopsy: 207


title: heart biopsy: 205


title: Mesenchymal cells, 4 weeks after Ad5SPC-Cre


title: AT2 YFP+ cells, 4 weeks after Ad5SPC-Cre


title: K29_IR_InsulinResistant_GTG_IMI_56


title: heart biopsy: 206


title: K29_IR_Basal_GTG_IMI_55


title: Endothelial cells, 7 weeks after Ad5SPC-Cre


title: heart biopsy: 204


title: heart biopsy: 202


title: KPY AT2 organoids, 14 days after Ad5CMV-Cre

source_name: AT2 organoids

value: AT2 organoids


title: K29_IR_Basal_GTG_IMI_51


title: K29_IR_Basal_GTG_IMI_47


title: heart biopsy: 201

value: heart biopsy


title: Mesenchymal cells co-cultured with Y organoids, 14 days

source_name: Mesenchymal co-culture

value: Mesenchymal co-culture

value: Wildtype


title: heart biopsy: 199

value: no


title: heart biopsy: 200


title: Y AT2 organoids, 14 days after Ad5CMV-Cre


title: heart biopsy: 196


title: heart biopsy: 198


title: Mesenchymal cells co-cultured with KPY organoids, 10 days


title: K29__InsulinResistant_GTG_IMI_58


title: K29__InsulinResistant_GTG_IMI_54


title: K29_IR_Basal_GTG_IMI_59


title: heart biopsy: 197


title: KPY AT2 organoids, 10 days after Ad5CMV-Cre


title: heart biopsy: 194


title: heart biopsy: 195


title: heart biopsy: 193


title: Mesenchymal cells co-cultured with KPY organoids, 14 days


title: heart biopsy: 203


title: K29__InsulinResistant_GTG_IMI_50


title: Mesenchymal cells co-cultured with Y organoids, 10 days


title: heart biopsy: 192


title: heart biopsy: 191


title: heart biopsy: 190


title: K29__InsulinResistant_GTG_IMI_46


title: K29__Basal_GTG_IMI_61


title: Y AT2 organoids, 10 days after Ad5CMV-Cre


title: K29__InsulinResistant_GTG_IMI_62


title: heart biopsy: 188


title: K29__Basal_GTG_IMI_57


title: heart biopsy: 186


title: KPY AT2 organoids, 7 days after Ad5CMV-Cre


title: K29__Basal_GTG_IMI_53


title: heart biopsy: 185


title: Mesenchymal cells co-cultured with Y organoids, 7 days


title: heart biopsy: 184


title: heart biopsy: 183


title: heart biopsy: 181


title: K29__Basal_GTG_IMI_49


title: Mesenchymal cells co-cultured with KPY organoids, 4 days


title: heart biopsy: 178


title: Y AT2 organoids, 7 days after Ad5CMV-Cre


title: K29__Basal_GTG_IMI_45


title: heart biopsy: 177


title: heart biopsy: 182


title: GEnC_IR_InsulinResistant_GTG_IMI_116

source_name: Glomerular endothelial cell

value: Glomerular endothelial cell


title: KPY AT2 organoids, 4 days after Ad5CMV-Cre


title: GEnC_IR_InsulinResistant_GTG_IMI_120


title: heart biopsy: 176


title: heart biopsy: 179


title: Mesenchymal cells co-cultured with Y organoids, 4 days


title: GEnC_IR_InsulinResistant_GTG_IMI_112


title: heart biopsy: 189


title: heart biopsy: 180


title: GEnC_IR_InsulinResistant_GTG_IMI_108


title: Y AT2 organoids, 4 days after Ad5CMV-Cre


title: heart biopsy: 187


title: Mesenchymal cells co-cultured with KPY organoids, 7 days


title: heart biopsy: 174


title: heart biopsy: 175


title: heart biopsy: 172


title: heart biopsy: 173


title: heart biopsy: 171


title: GEnC_IR_InsulinResistant_GTG_IMI_104


title: In vitro mesenchymal cells before co-culturing with organoids


title: heart biopsy: 169


title: heart biopsy: 170


title: Freshly sorted Y AT2 cells, no Ad-Cre treatment

source_name: AT2 cells

value: AT2 cells


title: heart biopsy: 168


title: GEnC_IR_Basal_GTG_IMI_115


title: heart biopsy: 165


title: IgG_CUTnTag

description: CUT&Tag with anti IgG antibody

value: Neuroectoderm cells

value: V6.5 Male mixed 129/C57BL/6

value: Anti IgG Antibody (CST, 3900)

value: Tet3 wildtype


title: heart biopsy: 166


title: heart biopsy: 163


title: heart biopsy: 164


title: Tet3_wildtype_CUTnTag

description: CUT&Tag with anti Tet3 antibody

value: Anti Tet3 Antibody (Millipore, ABE290)


title: heart biopsy: 161


title: heart biopsy: 162


title: GEnC_IR_Basal_GTG_IMI_107


title: GEnC_IR_Basal_GTG_IMI_103


title: heart biopsy: 160


title: GEnC__InsulinResistant_GTG_IMI_118


title: heart biopsy: 158


title: Freshly sorted KPY AT2 cells, no Ad-Cre treatment


title: heart biopsy: 159


title: GEnC__InsulinResistant_GTG_IMI_114


title: GEnC_IR_Basal_GTG_IMI_119


title: heart biopsy: 167


title: heart biopsy: 157


title: GEnC_IR_Basal_GTG_IMI_111


title: Erastin_30_n4

city: Dunedin

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE vM5 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample.

source_name: MEF

extract_protocol:
Total RNA was extracted using TRIzol
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

value: mouse embryonic fibroblasts

value: 0.3 microM Erastin


title: heart biopsy: 155

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.


title: heart biopsy: 154


title: GEnC__InsulinResistant_GTG_IMI_110


title: Erastin_30_n2


title: Erastin_30_n3


title: Erastin_15_n4

value: 0.15 microM Erastin


title: GEnC__InsulinResistant_GTG_IMI_106


title: heart biopsy: 152


title: GEnC__InsulinResistant_GTG_IMI_102


title: heart biopsy: 151


title: Erastin_15_n3


title: Erastin_15_n2


title: heart biopsy: 150


title: GEnC__Basal_GTG_IMI_117


title: heart biopsy: 149


title: heart biopsy: 147


title: heart biopsy: 148


title: GEnC__Basal_GTG_IMI_113


title: Erastin_0_n4

value: 0 microM Erastin


title: heart biopsy: 146


title: heart biopsy: 145


title: heart biopsy: 156


title: heart biopsy: 144


title: Erastin_30_n1


title: Erastin_0_n3


title: GEnC__Basal_GTG_IMI_105


title: heart biopsy: 143


title: heart biopsy: 153


title: heart biopsy: 140


title: heart biopsy: 141


title: heart biopsy: 142


title: Erastin_0_n2


title: GEnC__Basal_GTG_IMI_101


title: heart biopsy: 139


title: Erastin_15_n1


title: Erastin_0_n1


title: K3_20_n4

value: 20 microM vitamin K


title: heart biopsy: 138


title: ABN_IR_InsulinResistant_GTG_IMI_80

source_name: Podocytes

value: Podocytes


title: heart biopsy: 137

value: heart biopsy


title: ABN_IR_InsulinResistant_GTG_IMI_84


title: K3_20_n3


title: ABN_IR_InsulinResistant_GTG_IMI_76


title: heart biopsy: 136


title: K3_20_n2


title: GEnC__Basal_GTG_IMI_109


title: ABN_IR_InsulinResistant_GTG_IMI_72


title: heart biopsy: 134


title: heart biopsy: 133


title: K3_20_n1


title: heart biopsy: 132


title: heart biopsy: 131


title: heart biopsy: 135


title: K3_10_n4

value: 10  microM vitamin K


title: heart biopsy: 130


title: ABN_IR_InsulinResistant_GTG_IMI_68


title: ABN_IR_Basal_GTG_IMI_83


title: heart biopsy: 129


title: heart biopsy: 128


title: ABN_IR_Basal_GTG_IMI_79


title: K3_10_n2


title: heart biopsy: 126


title: heart biopsy: 127


title: ABN_IR_Basal_GTG_IMI_75


title: heart biopsy: 125


title: heart biopsy: 123


title: heart biopsy: 122


title: heart biopsy: 124


title: heart biopsy: 121


title: K3_10_n1


title: ABN_IR_Basal_GTG_IMI_71


title: heart biopsy: 120


title: K3_0_n4

value: 0 microM vitamin K


title: ABN_IR_Basal_GTG_IMI_67


title: K3_0_n3


title: heart biopsy: 119

value: no


title: K3_0_n2


title: heart biopsy: 118


title: ABN__InsulinResistant_GTG_IMI_78


title: heart biopsy: 117


title: ABN__InsulinResistant_GTG_IMI_82


title: heart biopsy: 116


title: heart biopsy: 115


title: ABN__InsulinResistant_GTG_IMI_74


title: K3_10_n3


title: K3_0_n1


title: heart biopsy: 114


title: ABN__InsulinResistant_GTG_IMI_70


title: YA014_NC_3_R1

first: Bin

last: Li

address: 1200 Cailun Road, Pudong New Area

institute: Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: HaCaT cells

extract_protocol:
Total mRNA was extracted from HaCaT cells using standard TRIzol protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human immortalized keratinocytes

tag: genotype/variation

value: normal HaCaT cell


title: YA014_NC_2_R1


title: heart biopsy: 112


title: heart biopsy: 111


title: YA014_NC_1_R1


title: heart biopsy: 108


title: ABN__Basal_GTG_IMI_81


title: heart biopsy: 109


title: heart biopsy: 110


title: ABN__Basal_GTG_IMI_77


title: heart biopsy: 107


title: YA014_CD274_OE_3_R1

value: shRNA-mediated PD-L1 overexpressed HaCaT cell


title: heart biopsy: 106


title: heart biopsy: 105


title: YA014_CD274_OE_2_R1


title: heart biopsy: 104


title: heart biopsy: 103


title: ABN__Basal_GTG_IMI_73


title: ABN__Basal_GTG_IMI_69


title: heart biopsy: 102


title: SpG-ABEmax-g9-003

city: Zurich

first: Desiree

last: Boeck

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

data_processing:
CRISPRESSO2 pipeline (https://github.com/pinellolab/CRISPResso2)
Assembly: n/a (targeted deep amplicon sequencing)
Supplementary files format and content: text files containing quantitative alleles frequency anaylses for each sample

source_name: Hepa1-6 (ATCC CRL-1830)

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for Hepa1-6 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for all samples
targeted amplicon sequencing
two step PCR for targeted amplicon sequencing

treatment_protocol: per 96 well plate: 400ng total DNA with 0.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting different exon-intron junctions at the Ptbp1 locus.

value: Hepa1-6 (ATCC CRL-1830)

value: hepatoma cell line from C57L mouse

value: Lipofectamine 2000


title: heart biopsy: 101


title: heart biopsy: 100


title: SpG-ABEmax-g9-002


title: heart biopsy: 113


title: heart biopsy: 99


title: CD8_TEMRA_IL2_EC95_43

city: South San Francisco

first: Manu

last: Kumar

state: California

address: 650 Gateway Blvd Suite 100

institute: Asher Biotherapeutics

data_processing:
Sequencing data was aligned against the human reference genome (Ensembl GrCh38) using the STAR software package and quantified using the featureCounts package.
Differential expression analysis was performed using the DESeq2 Bioconductor package.
Assembly: GrCh38
Supplementary files format and content: Processed count matrix contains Ensembl Gene Id, Gene Name, and column containing counts for each sample

source_name: peripheral blood

growth_protocol: Human PBMCs from 3 donors were sorted into the following subsets based on the expression of CD45RO and CD62L markers: CD8+-naïve T cells (CD62L+CD45RO-), CD8+ central memory T cells (CD62L+CD45RO+), CD8+ effector memory T cells (CD62L-CD45RO+), and CD8+ effector cells (CD62L-CD45RO-). Briefly, cells were stained with antibodies to sort the individual CD8+ T cell subsets, sorted via FACS, and flow sorted cells were collected in AIM V™ medium (Gibco).

extract_protocol:
Cells were pelleted, and RNA isolated per manufacturer’s instructions (Arcturus PicoPure RNA Isolation Kit, Applied Biosystems)
Ultra-low input RNA-sequencing

treatment_protocol: Cells were treated at concentrations corresponding to the EC95 by pSTAT5 for of rhIL-2 (R&D Systems) or AB248 for 24 h

value: peripheral blood

value: TEMRA CD8+ T cell

value: paired-end

tag: donor

tag: time

value: 24 hours

tag: library


title: SpG-ABEmax-g9-001


title: ABN__InsulinResistant_GTG_IMI_66


title: heart biopsy: 98

last: Chang

institute: University of Alberta

source_name: heart biopsy


title: heart biopsy: 97


title: SpG-ABEmax-g7-003


title: heart biopsy: 96


title: heart biopsy: 95


title: heart biopsy: 93


title: SpG-ABEmax-g7-002


title: SpG-ABEmax-g7-001


title: CD8_TEM_IL2_EC95_43

value: TEM CD8+ T cell


title: YA014_CD274_OE_1_R1


title: ABN__Basal_GTG_IMI_65


title: heart biopsy: 92


title: SpG-ABEmax-g6-003


title: heart biopsy: 91


title: CD8_TEM_AB248_EC95_43


title: CD8_TEM_Media_43

value: Media


title: heart biopsy: 88


title: SpG-ABEmax-g6-002


title: heart biopsy: 89


title: heart biopsy: 90


title: SpG-ABEmax-g6-001


title: heart biopsy: 87


title: heart biopsy: 85


title: CD8_TCM_AB248_EC95_43

value: TCM CD8+ T cell


title: CD8_TEMRA_AB248_EC95_43


title: heart biopsy: 86

value: heart biopsy


title: CD8_TCM_Media_43


title: SpG-ABEmax-g3-003


title: CD8_TEMRA_Media_43


title: heart biopsy: 83


title: heart biopsy: 94


title: heart biopsy: 82


title: SpG-ABEmax-g3-002


title: CD8_Naive_IL2_EC95_43

value: Naive CD8+ T cell


title: CD8_Naive_AB248_EC95_43


title: SpG-ABEmax-g3-001


title: heart biopsy: 80


title: heart biopsy: 79


title: heart biopsy: 81


title: CD8_TCM_IL2_EC95_43


title: heart biopsy: 78


title: heart biopsy: 77


title: SpG-ABE8e-g9-003

description: base-editing-experiment_sgRNA9-ABE8e-SpG


title: heart biopsy: 76


title: SpG-ABE8e-g9-002


title: heart biopsy: 75


title: CD8_Naive_Media_43


title: heart biopsy: 74


title: heart biopsy: 84


title: SpG-ABE8e-g9-001


title: heart biopsy: 73


title: CD8_TEMRA_IL2_EC95_23


title: heart biopsy: 72


title: heart biopsy: 71


title: CD8_TEMRA_Media_23


title: CD8_TEMRA_AB248_EC95_23


title: SpG-ABE8e-g7-003

description: base-editing-experiment_sgRNA7-ABE8e-SpG


title: SpG-ABE8e-g7-002


title: heart biopsy: 70


title: CD8_TEM_IL2_EC95_23


title: heart biopsy: 69


title: heart biopsy: 67


title: heart biopsy: 66


title: SpG-ABE8e-g6-003

description: base-editing-experiment_sgRNA6-ABE8e-SpG


title: CD8_TEM_AB248_EC95_23


title: heart biopsy: 64


title: SpG-ABE8e-g6-002


title: CD8_TCM_IL2_EC95_23


title: heart biopsy: 62


title: CD8_TEM_Media_23


title: heart biopsy: 65


title: heart biopsy: 63


title: SpG-ABE8e-g6-001


title: heart biopsy: 60


title: CD8_TCM_AB248_EC95_23


title: heart biopsy: 58


title: CD8_TCM_Media_23


title: heart biopsy: 56


title: SpG-ABE8e-g3-002

description: base-editing-experiment_sgRNA3-ABE8e-SpG


title: heart biopsy: 68


title: SpG-ABE8e-g3-001


title: SpG-ABE8e-g7-001


title: heart biopsy: 55


title: SpG-ABE8e-g3-003


title: CD8_Naive_AB248_EC95_23


title: heart biopsy: 57


title: CD8_Naive_IL2_EC95_23


title: heart biopsy: 54


title: CD8_Naive_Media_23


title: SpCas-ABEmax-g7-003

description: base-editing-experiment_sgRNA7-ABE-SpCas


title: heart biopsy: 53


title: SpCas-ABEmax-g7-002


title: heart biopsy: 52


title: heart biopsy: 51


title: heart biopsy: 59


title: heart biopsy: 50


title: CD8_TEMRA_IL2_EC95_68


title: SpCas-ABEmax-g7-001


title: CD8_TEMRA_AB248_EC95_68


title: heart biopsy: 48


title: SpCas-ABEmax-g6-003

description: base-editing-experiment_sgRNA6-ABE-SpCas


title: heart biopsy: 47


title: heart biopsy: 49


title: CD8_TEMRA_Media_68


title: heart biopsy: 46


title: SpCas-ABEmax-g6-002


title: CD8_TEM_IL2_EC95_68


title: SpCas-ABEmax-g6-001


title: CD8_TEM_AB248_EC95_68


title: heart biopsy: 43


title: heart biopsy: 42


title: SpCas-ABE8e-g7-003

description: base-editing-experiment_sgRNA7-ABE8e-SpCas


title: heart biopsy: 44


title: heart biopsy: 45


title: heart biopsy: 40


title: heart biopsy: 39


title: heart biopsy: 41


title: CD8_TCM_IL2_EC95_68


title: SpCas-ABE8e-g7-002


title: heart biopsy: 38


title: heart biopsy: 37


title: heart biopsy: 61


title: heart biopsy: 36


title: CD8_TCM_AB248_EC95_68


title: SpCas-ABE8e-g6-003

description: base-editing-experiment_sgRNA6-ABE8e-SpCas


title: heart biopsy: 35


title: heart biopsy: 34


title: SpCas-ABE8e-g6-002


title: SpCas-ABE8e-g6-001


title: heart biopsy: 32


title: heart biopsy: 30


title: sgRNA9-r003


title: CD8_Naive_AB248_EC95_68


title: CD8_Naive_IL2_EC95_68


title: heart biopsy: 31


title: CD8_TEM_Media_68


title: heart biopsy: 28


title: heart biopsy: 25


title: Marrow, lckmCherry-cd79aGFP, Population M1, Sample 56

city: Oklahoma City

first: John

middle: Kimble

last: Frazer

state: Oklahoma

address: 941 Stanton L Young Blvd

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description:
geo_submission_raw_counts.txt
geo_submission_processed_counts.txt

data_processing:
Raw read quality was first assessed using FastQC (v.0.11.8). BBDuk from the BBMap suite (v.38.22) was used for adapter trimming per manufacturer recommendations. rRNA-mapping reads were also filtered at this step. Read quality was assessed post-trimming as well.
Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of 3'-tagged RNA-sequencing, the R2 files containg low-quality reads that are not typically used during processing.
Read counts per gene were generated with FeatureCounts (from Rsubread, v.2.12.2) using the D.rerio Ensembl transcriptome (release v.92) with a min. alignment quality threshold of 10.
DESeq2 (v.1.38.3) was used for downstream processing, library normalization and DE testing.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited file containing raw gene counts for each Sample
Supplementary files format and content: Tab-delimited file containing normalized gene counts and variance-stabilized gene counts (separate files) for each Sample

source_name: Marrow

growth_protocol: For procedures, zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media (RPMI + 1% FBS + 1% Pen/Strep). Single-cell suspensions were prepped by dissociating thymic and marrow tissue using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD-FACSJazz Instrument (analysis performed in FlowJo softare).

extract_protocol:
Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of ~2.5 ug/sample.
RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.

value: Marrow

value: Early T-committed


title: heart biopsy: 29

first: Jessica

address: 250 Heritage Medical Research Centre

value: no


title: sgRNA9-r002


title: CD8_Naive_Media_68


title: heart biopsy: 27


title: heart biopsy: 26


title: CD8_TCM_Media_68


title: heart biopsy: 24


title: sgRNA9-r001


title: sgRNA6-r001


title: heart biopsy: 22


title: Marrow, lckmCherry-cd79aGFP, Population M1, Sample 54


title: heart biopsy: 33


title: Thymus, lckmCherry-cd79aGFP, Population T4, Sample 53

source_name: Thymus

value: Thymus

value: Thymic B


title: heart biopsy: 23


title: sgRNA5-r003

value: Hepa1-6 (ATCC CRL-1830)


title: heart biopsy: 20


title: heart biopsy: 17


title: heart biopsy: 19


title: Marrow, lckmCherry-cd79aGFP, Population M1, Sample 55


title: heart biopsy: 18


title: Thymus, lckmCherry-cd79aGFP, Population T4, Sample 51


title: heart biopsy: 16


title: Thymus, lckmCherry-cd79aGFP, Population T2, Sample 50

value: T Stage IV


title: sgRNA5-r002

value: hepatoma cell line from C57L mouse

value: Lipofectamine 2000


title: sgRNA5-r001


title: heart biopsy: 15


title: heart biopsy: 14


title: sgRNA5-ABE8e-SpG-r003

description: base-editing-experiment_sgRNA5-ABE8e-SpG


title: heart biopsy: 13


title: sgRNA5-ABE8e-SpG-r002


title: sgRNA6-r003


title: heart biopsy: 12


title: heart biopsy: 11


title: Thymus, lckmCherry-cd79aGFP, Population T2, Sample 49


title: Thymus, lckmCherry-cd79aGFP, Population T2, Sample 48


title: sgRNA5-ABE8e-SpG-r001


title: heart biopsy: 21


title: heart biopsy: 9


title: heart biopsy: 8


title: heart biopsy: 10


title: Thymus, lckmCherry-cd79aGFP, Population T1, Sample 47

value: T State III


title: Thymus, lckmCherry-cd79aGFP, Population T4, Sample 52


title: heart biopsy: 7


title: heart biopsy: 6


title: sgRNA5-ABE-SpG-r003


title: Thymus, lckmCherry-cd79aGFP, Population T1, Sample 45


title: SpCas-ABE8e-g7-001


title: heart biopsy: 5


title: sgRNA5-ABE-SpG-r002


title: sgRNA3-r003


title: Marrow, rag2RFP-cd79aGFP, Population M3B, Sample 44

value: B Stage II


title: heart biopsy: 3


title: heart biopsy: 4


title: heart biopsy: 2


title: heart biopsy: 1


title: Marrow, rag2RFP-cd79aGFP, Population M3A, Sample 41

value: B Stage I


title: sgRNA3-r002


title: Marrow, rag2RFP-cd79aGFP, Population M3B, Sample 42


title: sgRNA3-r001


title: heart biopsy: 3230


title: HepG2, cells, ASO-E5

city: Beijing

first: Gangqiao

last: Zhou

address: 27 Taiping Road, Beijing

institute: Beijing Institute of Radiation Medicine

data_processing:
The quality of raw sequencing reads was evaluated using FastQC. Adaptor sequences and low-quality score bases were trimmed using Trim Galore (v.0.6.7, https://github.com/FelixKrueger/TrimGalore).
These reads were then mapped to the human genome reference GRCh38 from Ensembl release 105 using Bowtie2 (v.2.2.5).
The fragments per kilobase of exon per million mapped reads (FPKM) values and gene count values were computed using RSEM (v.1.2.8) and differentially expressed genes (DEGs) were analyzed using the DESeq2 (v.1.37) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: HepG2, cells, ASO-E5

extract_protocol:
RNA was extracted using RNeasy Mini Kit_QIAGEN . 2ug total RNA was used for construction of sequencing libraries
RNA-seq libraries were constructed using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme, China) according to the manufacturer’s protocol.

value: cell line

value: HCC cells


title: HepG2, cells, ASO-E15

source_name: HepG2, cells, ASO-E15


title: Marrow, rag2RFP-cd79aGFP, Population M3B, Sample 43


title: HepG2, cells, ASO-Ctrl

source_name: HepG2, cells, ASO-Ctrl


title: sgRNA2-r002


title: heart biopsy: 3228


title: sgRNA2-r003


title: heart biopsy: 3227

value: yes


title: Marrow, rag2RFP-cd79aGFP, Population M1, Sample 36

value: Early B-committed


title: sgRNA2-r001


title: Rad50-sKO-Z_END-seq_rep1

first: yuefang

last: liu

address: 320 Yueyang Road

institute: Center of Excellence in Molecular and Cellular Science, Chinese Academy of Sciences

description: germ cell

data_processing:
Basecalls were performed using bcl2fastq v2.17 for HiSeq output.
END-seq reads were trimmed from 3′ end until the final base had a quality score >30, using Trimmomatic v0.33, discarding reads left with <20 bp.
END-seq reads were aligned to the UCSC mm10 genome using B0wtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To creat END-seq coverage polts, the locations of the mapped END-seq reads were extended to 150 bp to represent sequence fragments, renormalized  (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01.
bigWig files were generated using the genomic Radges R package. Score represents the normalized coverage of DNA fragments at a givengenomic coordinate. narrowPeak files were generated using MACS v2 with defaut settings.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: END-seq

source_name: testis

extract_protocol:
Spermatocyte-enrichment testicular cells were embedded into a final concentration of 0.75% agarose and then lysed and digested with proteinase K and RNase.
The plugs that contained  3′ ssDNAs at the end of DSBs were then digested with Exonuclease VII (NEB) and Exonuclease T (NEB) to blunt DNA ends. After blunted, A-tailing were added to the free 3′- OH of blunted ends, then ligated with END-seq hairpin adaptor 1. Subsequently, agarose plugs were melted and dialyzed, the released DNA was sonicated to a shear DNA fragment at the length of about 170 bp. Shear DNA fragment were collected and purified, then the DNA pellet was dissolved in TE buffer. Biotinylated adaptor 1-DNA fragment was further isolated by using MyOne Streptavidin Beads. The second end was repaired and added with A-tail, then ligated with END-seq hairpin adaptor 2. Both sides of hairpin were digested by using USER (NEB) and the resulting DNA fragments amplified by PCR for 16 cycles. Post amplication libraries were selected at 200-400 bp in length by QIAquick Gel Extraction Kit.

treatment_protocol: 2-dpp Rad50-control and Rad50-sKO mice were pipette fed with WIN 18 446 (Sigma, suspended in 1% gum tragacanth, 100 μg/g body weight) for consecutive 7 days. The next day of consecutive WIN 18 446 treatments, these mice received an i.p. injection of retinoic acid (Sigma; 30 μg/g body  weight,  suspended in DMSO) for enrichment of zygotene spermatocytes.

value: testis

value: spermatocytes

value: germ cell specific Rad50 knockout

value: synchronized testis


title: sgRNA5-ABE-SpG-r001


title: heart biopsy: 3226

value: heart biopsy

value: no


title: Thymus, lckmCherry-cd79aGFP, Population T1, Sample 46

value: Thymus


title: Rad50-sKO-Z_END-seq_rep2

description: germ cell


title: Control-Z_END-seq_rep3

description: germ cell

value: wild type


title: sgRNA2-ABE8e-SpG-r002

description: base-editing-experiment_sgRNA2-ABE8e-SpG

value: Hepa1-6 (ATCC CRL-1830)

value: hepatoma cell line from C57L mouse


title: Marrow, rag2RFP-cd79aGFP, Population M3A, Sample 39

value: Marrow


title: Thymus, rag2RFP-cd79aGFP, Population T4, Sample 35

value: Thymic B


title: heart biopsy: 3229


title: Tumor

source_name: Tumor

value: tissue


title: Marrow, rag2RFP-cd79aGFP, Population M3A, Sample 40

value: B Stage I


title: heart biopsy: 3225


title: heart biopsy: 3224


title: Control-Z_END-seq_rep1

description: germ cell


title: Control-Z_END-seq_rep2

description: germ cell


title: Thymus, rag2RFP-cd79aGFP, Population T4, Sample 34


title: sgRNA2-ABE-SpG-r003

value: Lipofectamine 2000


title: sgRNA2-ABE8e-SpG-r001


title: sgRNA2-ABE8e-SpG-r003


title: heart biopsy: 3223


title: heart biopsy: 3222


title: Thymus, rag2RFP-cd79aGFP, Population T3, Sample 31

value: T Stage I


title: sgRNA2-ABE-SpG-r001


title: 01_LXR-WT_LPS_24h

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang etal,2014) for removing the low-quality reads and trimming the Illumina adapter.
Mapping of the reads were obtained using the STAR program against mouse genome (mm10) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
Assembly: mm10
Supplementary files format and content: Excel file includes Entrez Gene ID, read counts, TPM data, Log2 Fold Change values for differential expression of case vs control.

source_name: Peritoneum

extract_protocol:
Sorted cells were directly lysed into RLT lysis buffer from RNeasy micro kit (qiagen). Total RNA was obtained through column purification following the RNeasy micro kit instructions (Qiagen).
Library preparation, quality controls, sequencing with the DNBSEQTMtechnology and generation of raw data were performed at the Beijing Genomics Institute (BGI genomics) according to the standard operating procedure for low-input RNA-seq

treatment_protocol: Peritoneal cells were collected from mice after injection into the peritoneal cavity of 5 ml of HBSS containing 2 mM EDTA and 1% FBS.Total peritoneal cells, were counted using an automated cell counter (Bio-Rad). In order to remove dead or damaged cells before cell sorting, cells were stained with propidium iodide and were excluded during cell sorting on a MoFlo Astrios Sorter (Beckman instrument at IIBM CSIC-UAM). For peritoneal macrophage identification, peritoneal cells were stained with CD11b (clone M1/70), CD115 (AFS98), MHCII (clone (I-A/I-E), and F4/80 (clone BM-8)

value: Peritoneum

value: Peritoneal LPS-elicited macrophages

value: Lxra-fl/fl

value: Lipopolysaccharide 4 mg/Kg 24 hours


title: heart biopsy: 3220


title: heart biopsy: 3219


title: sgRNA1-r003


title: Thymus, rag2RFP-cd79aGFP, Population T2, Sample 29


title: 02_LXR-aKO_LPS_24h

value: Lxra-fl/fl-ivav-Cre+


title: Thymus, rag2RFP-cd79aGFP, Population T3, Sample 30


title: Thymus, rag2RFP-cd79aGFP, Population T2, Sample 28


title: sgRNA1-r002


title: Healthy, 3, Control

city: Seoul

first: Byeongsoo

last: Eom

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v6.1.2 (10x Genomics, USA).
Raw BCL files from Illumina HiSeq X were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
Raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the human reference genome (GRCh38), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (MEX Format)

source_name: gingival

extract_protocol:
Gingival tissues subjected for single-cell RNA sequencing were first dissociated using multi tissue dissociation kit 2 according to the manufacturer’s instruction (#130-110-203, Miltenyi Biotec, Germany)
Library preparation was carried out following the guidelines of the 10X Chromium Next GEM Single Cell Library kit v3.1 (#1000121, 10X Genomics, USA)

value: gingival

tag: disease state

value: Healthy


title: Healthy, 2, Control


title: Healthy, 1, Control


title: sgRNA1-r001


title: heart biopsy: 3218

city: Edmonton

value: heart biopsy

value: no


title: 03_LXR-bKO_LPS_24h

value: LXR-bKO


title: heart biopsy: 3217


title: Thymus, rag2RFP-cd79aGFP, Population T4, Sample 33

value: Thymus


title: Chronic Periodontitis, 3, Patients

value: Chronic Periodontitis


title: Thymus, rag2RFP-cd79aGFP, Population T2, Sample 27


title: heart biopsy: 3216


title: sgRNA2-ABE-SpG-r002

value: Hepa1-6 (ATCC CRL-1830)

value: hepatoma cell line from C57L mouse


title: sgRNA1-ABE8e-SpG-r003

description: base-editing-experiment_sgRNA1-ABE8e-SpG


title: sgRNA1-ABE8e-SpG-r002


title: heart biopsy: 3215


title: sgRNA1-ABE8e-SpG-r001


title: Aggressive Periodontitis, 2, Patients

value: Aggressive Periodontitis


title: heart biopsy: 3214

value: yes


title: Thymus, rag2RFP-cd79aGFP, Population T1, Sample 25

value: T Stage II


title: Aggressive Periodontitis, 1, Patients


title: Thymus, rag2RFP-cd79aGFP, Population T1, Sample 24


title: Marrow, lckmCherry-cd79bGFP, Population M1, Sample 23

value: Marrow

value: Early T-committed


title: heart biopsy: 3213


title: sgRNA1-ABE8e-SpCas-r002

description: base-editing-experiment_sgRNA1-ABE8e-SpCas

value: Lipofectamine 2000


title: MHCC97H, cells, Flag_SRSF7_3

source_name: MHCC97H, cells, Flag_SRSF7_3

value: cell line

value: HCC cells


title: sgRNA1-ABE8e-SpCas-r003


title: MHCC97H, cells, Flag_SRSF7_2

source_name: MHCC97H, cells, Flag_SRSF7_2


title: Thymus, rag2RFP-cd79aGFP, Population T1, Sample 26


title: MHCC97H, cells, Flag_SRSF7_1

source_name: MHCC97H, cells, Flag_SRSF7_1


title: heart biopsy: 3212


title: Marrow, lckmCherry-cd79bGFP, Population M1, Sample 21


title: sgRNA1-ABE8e-SpCas-r001


title: heart biopsy: 3211


title: Thymus, rag2RFP-cd79aGFP, Population T3, Sample 32

value: T Stage I


title: sgRNA1-ABE-SpG-r003


title: heart biopsy: 3210


title: Thymus, lckmCherry-cd79bGFP, Population T4, Sample 20

value: Thymic B


title: sgRNA1-ABE-SpG-r002


title: MHCC97H, cells, Flag_2

source_name: MHCC97H, cells, Flag_2


title: heart biopsy: 3209

value: heart biopsy


title: Thymus, lckmCherry-cd79bGFP, Population T4, Sample 19


title: sgRNA1-ABE-SpG-r001


title: MHCC97H, cells, Flag_3

source_name: MHCC97H, cells, Flag_3


title: Marrow, rag2RFP-cd79bGFP, Population M4, Sample 18

value: B Stage III


title: Marrow, rag2RFP-cd79bGFP, Population M4, Sample 17


title: heart biopsy: 3207

value: no


title: heart biopsy: 3208


title: Marrow, lckmCherry-cd79bGFP, Population M1, Sample 22


title: sgRNA1-ABE-SpCas-r003

description: base-editing-experiment_sgRNA1-ABE-SpCas

source_name: Hepa1-6 (ATCC CRL-1830)


title: HeG2, cells, ASO_E15_3

source_name: HeG2, cells, ASO_E15_3


title: MHCC97H, cells, Flag_1

source_name: MHCC97H, cells, Flag_1


title: sgRNA1-ABE-SpCas-r002


title: Marrow, rag2RFP-cd79bGFP, Population M4, Sample 16

source_name: Marrow


title: heart biopsy: 3206

source_name: heart biopsy


title: HeG2, cells, ASO_E15_2

source_name: HeG2, cells, ASO_E15_2


title: HeG2, cells, ASO_E15_1

source_name: HeG2, cells, ASO_E15_1


title: Marrow, rag2RFP-cd79bGFP, Population M3B, Sample 15

value: B Stage II


title: sgRNA7-r003


title: sgRNA1-ABE-SpCas-r001


title: heart biopsy: 3205


title: Marrow, rag2RFP-cd79bGFP, Population M3B, Sample 14


title: HeG2, cells, ASO_E5_3

source_name: HeG2, cells, ASO_E5_3


title: heart biopsy: 3204


title: HeG2, cells, ASO_E5_2

source_name: HeG2, cells, ASO_E5_2


title: sgRNA7-r002


title: IP_eft-3p, IAA, rep3

city: Québec

first: Pierre-Marc

last: Frédérick

state: Québec

address: 9 Rue McMahon

institute: Centre de recherche du CHU de Québec - Université Laval

description: small RNA analysis

data_processing:
The samples or debarcoded
The adaptors are removed and only >16nt are kept
Small RNAs are mapped to the genome and cDNA using Bowtie 0.12.7 (maximum of 3 seed mismatches)
The samples were normalized to total gene expression (geex) reads excluding structural RNA (struc) and transformed in RPM (read per million).
Assembly: C. elegans WS215
Supplementary files format and content: (PMF1-18) The raw reads were individually normalized on the total gene expression reads (geex) minus the structural reads (struct) and converted to RPM. (PMF19-PMF24) The raw reads were individually normalized on the level of ALG-1 protein immunoprecipitated.

organism: Caenorhabditis elegans

source_name: Ubiquitous

growth_protocol: Worms were grown on NGM plates supplemented with EtOH 0.4% or IAA 4mM at 20°C.

extract_protocol:
TRIzol extraction.
Total RNA was used with NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® (E7560S) and size selected on a gel (approximatively 140bp)

treatment_protocol: 2mL of IAA 1M  (or EtOH 100%) was added to 500mL of cooling NGM (between 40°C and 45°C).

value: Ubiquitous

tag: developmental stage

value: Young adults

value: IAA 4mM


title: HeG2, cells, ASO_E5_1

source_name: HeG2, cells, ASO_E5_1


title: Marrow, rag2RFP-cd79bGFP, Population M3A, Sample 12

value: B Stage I


title: sgRNA7-r001

value: Hepa1-6 (ATCC CRL-1830)

value: hepatoma cell line from C57L mouse


title: HeG2, cells, ASO_Ctrl3

source_name: HeG2, cells, ASO_Ctrl3


title: IP_eft-3p, IAA, rep2

description: small RNA analysis


title: HeG2, cells, ASO_Ctrl2

source_name: HeG2, cells, ASO_Ctrl2


title: IP_eft-3p, IAA, rep1

description: small RNA analysis


title: IP_eft-3p, EtOH, rep3

description: small RNA analysis

value: EtOH 0.4%


title: Marrow, rag2RFP-cd79bGFP, Population M3A, Sample 11

value: Marrow


title: Marrow, rag2RFP-cd79bGFP, Population M3A, Sample 10


title: Marrow, rag2RFP-cd79bGFP, Population M1, Sample 8

value: Early B-committed


title: IP_eft-3p, EtOH, rep2

description: small RNA analysis


title: RNA-Seq of Mouse Embryonic Fibroblast: Transduced with control short-hairpin replicate 3

city: Barcelona

first: Gerard

last: Romero

state: Catalonia

address: Doctor Aiguader, 88

department: Dpt of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS/UPF)

institute: Universitat Pompeu Fabra

description: Raw count matrix containing the raw counts for the different samples with the ensembl_id as rownames

data_processing:
We performed a quality control on the 9 raw single-end reads samples using the nf-core/rnaseq (v. 3.10.1)
Raw FASTQ files were aligned to the GRCm38.p6 version of the reference mouse genome using STAR (v. 2.7.6a) with default parameters except for --sjdbOverhang 49, producing a set of 9 BAM files.
Genes were annotated using the GENCODE vM25 GTF file. We filtered out lowly expressed genes by discarding those that did not show a minimum reliable level of expression of 20 counts per million reads of the smallest library size, in at least all the samples of the smallest group, which was 3.
The DESeq2 package (v. 1.40.0) was used for the differential expression analysis. Surrogate variables were calculated with SVA.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files incudes raw counts for each sample

source_name: Mouse embryonic fibroblasts

extract_protocol:
cells were washed with PBS, scrapped with 6M Urea and 200 mM Ammonium Bicarbonate and sonicated at 4ºC. 10 μl of each sample at 1 mg/ml was submitted for analysis. The samples were digested with Trypsin and LysC and 2 μg were analyzed by LC-MS/MS using a 90 min gradient in the Orbitrap Eclipse
2 μg were analyzed by LC-MS/MS using a 90 min gradient in the Orbitrap Eclipse. Raw MS files were processed in Proteome Discoverer version 2.3.0.523 (Thermo Scientific, Waltham, MA,) [44]. Samples have been searched against SP_Mouse database (June 2020), using the search algorithm Mascot v2.6 (http://www.matrixscience.com/). Peptides have been filtered based on FDR and only peptides showing an FDR lower than 5% have been retained.

value: Mouse embryonic fibroblasts

value: wildtype


title: Biowire, cardiomyocytes from CM+FB+MF, replicate 4

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St.

institute: University Health Network

description:
CM+FB+MF4_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx

data_processing:
RNA sequencing was executed on a NovaSeq 6000 (Illumina) using a paired-end 2x100bp protocol and multiplexing to obtain a sequencing depth of 30-35 million paired-end reads per sample.
Reads were filtered for quality control and mapped to the human genome (hg19) using STAR aligner (version 2.7.9a).
Count files containing uniquely mapped reads were generated using htseq-count (version 0.11.0), retaining protein-coding genes with non-zero counts. Data were pre-filtered to include only genes expressed by at least one sample.
The DESeq2 package was used in R Studio (R version 4.3.2) to normalize counts and compute differentially expressed genes
Assembly: hg19
Supplementary files format and content: Excel file contains raw counts for each sample
Supplementary files format and content: Excel file contains normalized counts (DESeq2) for each sample

source_name: Human cardiac microtissues

growth_protocol: Biowires were cultured in StemPro-34 SFM (1X) medium (ThermoFisher) containing 2-phospho-L-ascorbic acid (64mg/mL; Sigma), 2% v/v HEPES (1M; ThermoFisher), 1% v/v GlutaMax (100X; ThermoFisher), 1% v/v Penicillin-Streptomycin (10,000U/mL; ThermoFisher), Transferrin (30mg/mL; ROCHE).

extract_protocol:
Biowires were digested in collagenase type I (1370U/mL), hyaluronidase (122U/mL), DNase I (146U/mL), Dispase (1U/mL) , ROCK inhibitor (1uM) and 1uM of Flavopiridol for 40 minutes at 37°C with gentle shaking. After 40 minutes, the digestion mix was pipetted 10 times to physically dissociate cells and was washed in 1mL media. Cells were pelleted (300g for 5 minutes at 4°C) and stained with cell surface antibodies. Cells were stained in FACS buffer (2% heat-inactivated bovine serum in PBS containing 1mM EDTA) with mouse anti-human CD14 (clone M5E2; 1:100) and mouse anti-human CD45 (clone 2D1; 1:100) for 20 minutes at 4°C. Cells were washed once in FACS buffer (2% heat-inactivated bovine serum in PBS containing 1mM EDTA) and spun down 300xg for 5 minutes at 4°C. Finally, cells were resuspended in BD FACS Pre-Sort Buffer with 1:100 DAPI and sorted on Aria Fusion (BD Biosciences) under low pressure (100um nozzle) directly into 350uL of RLT lysis buffer in DNA lobind tubes. Total RNA from sorted hESC-macrophages or hESC-cardiomyocytes was prepared using the Qiagen RNeasy Micro kit with on-column treatment with RNAase-free DNAase.
Sample library preparation using the Takara SMARTer Stranded Total RNA-seq Kit v3

value: Human cardiac microtissues

value: ESI17 hESC-cardiomyocytes

value: hESC-cardiomyocytes

value: ESI17 (WT)

tag: timepoint

value: Day 3


title: IP_eft-3p, EtOH, rep1

description: small RNA analysis


title: RNA-Seq of Mouse Embryonic Fibroblast: Transduced with shor-hairpin to KD RNF144b replicate 1

value: RNF144B KD


title: Biowire, cardiomyocytes from CM+FB+MF, replicate 3

description:
CM+FB+MF3_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx


title: Thymus, rag2RFP-cd79bGFP, Population T4, Sample 6

source_name: Thymus

value: Thymus

value: Thymic B


title: Marrow, rag2RFP-cd79bGFP, Population M3B, Sample 13

value: B Stage II


title: RNA-Seq of Mouse Embryonic Fibroblast: Transduced with control short-hairpin replicate 2


title: RNA-Seq of Mouse Embryonic Fibroblast: Transduced with control short-hairpin replicate 1


title: Biowire, cardiomyocytes from CM+FB+MF, replicate 2

description:
CM+FB+MF2_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx


title: eft-3p, IAA, rep2

description: small RNA analysis

value: Ubiquitous

value: Young adults

value: IAA 4mM


title: RNA-Seq of Mouse Embryonic Fibroblast: Transduced with shor-hairpin to KD RNF144b replicate 3


title: Thymus, rag2RFP-cd79bGFP, Population T4, Sample 5


title: eft-3p, IAA rep3

description: small RNA analysis


title: eft-3p, IAA, rep1

description: small RNA analysis


title: RNA-Seq of Mouse Embryonic Fibroblast: Transduced with shor-hairpin to KD RNF144b replicate 2


title: mouse-siHBV-2.5mg/kg, replicate3

first: Wenjing

last: Zai

address: Room 306, Fuxing Building, 131 Dongan Road, Shanghai 200032, China

institute: Fudan University

data_processing:
The fastq. files were trimmed by Cutadapt v3.1 and then applied to human or mouse reference genome by Hisat2, sorted by SAMtools and analyzed for expression using featureCounts.
Assembly: mm10/hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: tissue

extract_protocol:
RNA was extracted by TRIzol.
cDNA libraries were prepared according to manufactures’instructions.

value: tissue

value: liver

value: tLNP/siHBV, 2.5mg/kg


title: Biowire, cardiomyocytes from CM+FB, replicate 4

description:
CM+FB4_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx


title: Thymus, rag2RFP-cd79bGFP, Population T4, Sample 4


title: HeG2, cells, ASO_Ctrl1

source_name: HeG2, cells, ASO_Ctrl1

value: cell line

value: HCC cells


title: Thymus, rag2RFP-cd79bGFP, Population T1, Sample 3

value: T Stage II


title: mouse-siHBV-2.5mg/kg, replicate1


title: eft-3p, EtOH, rep3

description: small RNA analysis

value: EtOH 0.4%


title: Marrow, rag2RFP-cd79bGFP, Population M1, Sample 7

value: Marrow

value: Early B-committed


title: Biowire, cardiomyocytes from CM+FB, replicate 3

description:
CM+FB3_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx

value: Human cardiac microtissues

value: ESI17 hESC-cardiomyocytes

value: hESC-cardiomyocytes

value: ESI17 (WT)

value: Day 3


title: eft-3p, EtOH, rep2

description: small RNA analysis

value: Ubiquitous


title: Thymus, rag2RFP-cd79bGFP, Population T1, Sample 2

value: Thymus


title: mouse-siHBV-1mg/kg, replicate3

value: tLNP/siHBV, 1mg/kg


title: Biowire, cardiomyocytes from CM+FB, replicate 2

description:
CM+FB2_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx


title: mouse-siHBV-1mg/kg, replicate2

value: tissue


title: Thymus, rag2RFP-cd79bGFP, Population T1, Sample 1


title: Biowire, cardiomyocytes from CM+FB, replicate 1

description:
CM+FB1_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx


title: eft-3p, EtOH, rep1

description: small RNA analysis

value: Young adults


title: D39 CEP:rr14, OD 0.4, Rep3 [RR14-3]

city: Odense M

first: Jens

middle: Sivkær

last: Pettersen

state: Danmark

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

data_processing:
Raw reads from the fastq files were mapped to the genome with bowtie2 using local alignment. Samtools was used for SAM-to-BAM conversion and sorting.
Raw reads were counted at a feature level with featureCounts. Multimapping reads were counted and fractionally assigned to their features. Reads overlapping several features were assigned by largest overlap.
Parameters used with featureCounts (example): featureCounts -p -M --fraction -O --largestOverlap -t gene -f -g  Name  --extraAttributes locus_tag,gene_biotype -a CP027540.1.gff3 -s 2 -o featureCounts_report FILENAMES
Assembly: CP027540.1 (several sRNA features identified in D39W were manually added to the General Feature Format (GFF)-file)
Supplementary files format and content: File contains read counts for all features of S. pneumoniae D39V in all samples (file format: csv). In addition to feature coordinates, the file also contains locus_tags, names, gene_biotypes.

organism: Streptococcus pneumoniae

source_name: Bacterial cell

growth_protocol: Streptococcus pneumoniae D39V and overexpression mutant derivatives were grown in the rich C+Y medium in triplicate cultures at 37°C with 5% CO2 to an OD600 0.4.

extract_protocol:
RNA was extracted from Streptococcus pneumoniae by a phenol-chloroform extraction.
1 µg RNA was depleted for ribosomal RNA using the NEBNext® rRNA Depletion Kit (Bacteria). RNA libraries were then prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit.

value: Bacterial cell

value: C+Y media, 37°C, OD 0.4


title: myo-2p, IAA, rep3

description: small RNA analysis

source_name: Pharynx

value: Pharynx

value: IAA 4mM


title: mouse-siHBV-1mg/kg, replicate1

value: liver


title: mouse-siHBV-2.5mg/kg, replicate2

value: tLNP/siHBV, 2.5mg/kg


title: Digested control cells, macrophages alone, replicate 3

description:
MF3_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx

source_name: Digested cells

value: Digested cells

value: hES2 hESC-macrophages

value: hESC-macrophages

value: hES2 (WT)

value: 40 min digestion


title: mouse-siNC-1mg/kg, replicate3

value: tLNP/siNC, 1mg/kg


title: Digested control cells, macrophages alone, replicate 2

description:
MF2_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx


title: D39 CEP:rr14, OD 0.4, Rep2 [RR14-2]


title: Biowire, cardiomyocytes from CM+FB+MF, replicate 1

description:
CM+FB+MF1_CM
RawCounts_CM.xlsx
NormalizedCounts_CM.xlsx

value: Human cardiac microtissues

value: ESI17 hESC-cardiomyocytes

value: hESC-cardiomyocytes

value: ESI17 (WT)

value: Day 3


title: myo-2p, IAA, rep1

description: small RNA analysis

value: Young adults


title: Digested control cells, macrophages alone, replicate 1

description:
MF1_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx


title: mouse-siNC-1mg/kg, replicate2

value: tissue


title: mouse-siNC-1mg/kg, replicate1


title: D39 CEP:rr13, OD 0.4, Rep3 [RR13-3]

value: Bacterial cell

value: C+Y media, 37°C, OD 0.4


title: Digested control cells, macrophages from FBMF, replicate 3

description:
FB+MF3_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx


title: D39 CEP:rr13, OD 0.4, Rep2 [RR13-2]


title: myo-2p, EtOH, rep2

description: small RNA analysis

value: Pharynx

value: EtOH 0.4%


title: myo-2p, EtOH, rep3

description: small RNA analysis


title: Digested control cells, macrophages from FBMF, replicate 2

description:
FB+MF2_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx

value: Digested cells


title: D39 CEP:rr13, OD 0.4, Rep1  [RR13-1]


title: myo-2p, EtOH, rep1

description: small RNA analysis


title: mouse-PBS, replicate3

value: liver

value: PBS


title: mouse-PBS, replicate2


title: mouse-PBS, replicate1


title: D39 CEP:rr11, OD 0.4, Rep3 [RR11-3]


title: Digested control cells, macrophages from CMFBMF, replicate 3

description:
CM+FB+MF3_controls
RawCounts_ControlCells.xlsx
NormalizedCounts_ControlCells.xlsx

value: hES2 hESC-macrophages

value: hESC-macrophages

value: hES2 (WT)


title: D39 CEP:rr11, OD 0.4, Rep2 [RR11-2]


title: D39 CEP:rr14, OD 0.4, Rep1  [RR14-1]


title: SCMp, IAA, rep2

description: small RNA analysis

source_name: Seam cells

value: Seam cells

value: IAA 4mM


title: myo-2p, IAA, rep2

description: small RNA analysis


title: Replicate 2 Ig control WT marrow B cells stimulated for 48 hours with IL7

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
Data was aligned using Bowtie2. Bigwig files were produced using bedtools genomecov, and WigToBigWig scripts.
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for CUT&RUN data.
Library strategy: CUT&RUN

source_name: Primary marrow B Cells

growth_protocol: Primary B cells were grown in RPMI supplemented with 10% FBS, and either IL7 or LPS, and harvested 48 hours after stimulation.

extract_protocol:
CUT&RUN was performed according to published methods using pA-MNase as secondary reagent. Yeast DNA was spiked into the samples after DNA extraction to normalize signal between samples. Cells were processed on an automated system at the Fred Hutch Cancer Center to carry out MNase cleavage, DNA extraction, and library construction.
Processed on a previously published, automated system at the Fred Hutch Cancer Center that uses KAPA DNA polymerase method for library preparation optimized for recovery of small DNA fragments.

treatment_protocol: Cells were stimulated for 48 hours with IL7 or LPS prior to extraction.

value: Primary marrow B Cells

value: WT

value: IL7 stimulation, 48 hours