title: MEFs Untreated-1

value: Untreated


title: RMB4186

status: Public on Jun 06 2024

type: SRA

city: Singapore

first: Nirmala

last: Arul Rayan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

library_source: transcriptomic

data_processing:
RNA-seq data were aligned to the Rattus norvegicus rn6 genome (Rn6 UCSC) with the STAR aligner. Read counts were concurrently calculated using Htseq
Any dataset that failed the default Fastqc sequencing parameters and < 75% mapping rate was discarded.
Assembly: rn6
Supplementary files format and content: fastq and read count files

molecule: total RNA

organism: Rattus norvegicus

source_name: brain

growth_protocol: Tissue RNA-seq. Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson

extract_protocol:
Frozen, pooled brain tissue punches for each region were thawed on ice in 1 ml Trizol. Tissue was then homogenized using a manual glass douncer with 7-15 slow strokes on ice. RNA was extracted from each replicate sample using the Qiagen RNA Mini kit (Qiagen, Cat# 74104) as per the manufacturer’s instructions with on-column DNase I treatment. RNA quality was examined using a Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA). RNA Integrity Number (RIN) values ranged from 7.1 to 10, with a median value of 9.5. cDNA libraries were prepared using 300 ng of total RNA, from 27 regions in every replicate, using the Illumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301). Paired-end, 150 bp read length RNA-seq was carried out on the Illumina HiSeq 4000 at a depth of 20M reads per sample.
llumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301)

treatment_protocol: Animals: 60-day old Long Evans uncharacterized male rats ordered from Charles River.  Treatment: Three weeks administration ad libitum in drinking water. There are 6 treatment groups.   Dosages for each treatment group are as follows:  Fluoxetine: 13mg/kg/day (Sigma Aldrich (PHR1394));  Desipramine: 7.5 mg/kg/day;  Bupropion: 15mg/kg/day;  Probiotic: 1.5 x 10 9 CFU/day (1 billion CFU/day);  Maltodextrin control: 10 g/L ;  Water control group

tag: replicate

tag: brain region_name

value: PLC

tag: treatment

value: Bupropion

tag: tissue

value: brain


title: Patient 7 HCC 13

type: RNA

city: Toronto

first: Mamatha

last: Bhat

address: 101 college street

country: Canada

institute: University Health Network

data_processing: To account for background noise and sample variation across multiple runs on the nCounter platform, raw gene expression count data was normalized in NanoString nSolver 4.0 using six positive controls and eight negative controls. A manual calculation of the background threshold was carried out by taking the Mean of negative controls ± 2 standard deviations of negative control probes to exclude lowly expressed targets before conducting gene expression analysis. The nSolver 4.0 software integrated housekeeping gene probes and facilitated data normalization through the GeNorm Algorithm.

label: NanoString

organism: Homo sapiens

source_name: Primary HCC

extract_protocol: Five μm thick scrolls were sectioned from formalin-fixed, paraffin-embedded (FFPE) tumor tissue blocks. Total RNA was extracted using the RNeasy FFPE Kit (QIAGEN) according to the manufacturer’s protocol, using xylene for deparaffinization. The Nanostring nCounter tumor signaling 360 panel was utilized for gene expression analysis, and data was acquired with Nanostring's Digital Analyser (FOV, 555).

value: liver


title: RMB4191

value: dorDG


title: Patient 4 HCC 7


title: KO rep3 (Set8)

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

description: KO rep3

data_processing:
Low quality reads and adapter sequences were trimmed by Trimmomatic
Surviving reads were aligned to mouse reference genome by STAR and gene counts were quantified
Assembly: mm10
Supplementary files format and content: Tab-separated value files for gene count

organism: Mus musculus

source_name: retina

extract_protocol:
Three independent replicates of the developing cerebellum from WT or mouse Atoh7 remote enhancer knockout at P18
Illumina RNA-seq library preparation kit
Bulk RNA-seq

value: retina

tag: age

tag: genotype

value: Atoh7 Remote Enhancer KO


title: MEFs Untreated-2

city: cleveland

first: Lingzi

last: Hong

state: oh

address: 10900 Euclid Avenue

department: biochemistry

institute: Case western reserve university

data_processing:
RNA-seq reads were aligned against the mm10 using STAR(2.7.0e).
The number of reads mapped to mouse genome mm10 was counted using RSEM(1.3.3).
Differential gene expression was determined using the R-package DEseq2
Assembly: mm10
Supplementary files format and content: csv file containing normalized count reads and adjusted p-values

source_name: flag-Act1KO/WT MEF cells

growth_protocol: Act1-/- Mouse Embryonic Fibroblasts transfected with flag-tagged Act1 wild-type (flag-Act1KO/WT) MEFs were maintained and propogated in DMEM supplemented with 10%FBS  and antiboitics at 37 °C under a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer’s instructions followed by isopropanol precipitation. Total RNAs were further purified using Qiagen's miRNeasy micro kit (217084, Qiagen) plus Qiagen’s DNase set (79254, Qiagen) for on-column DNase digestion option.
Sequencing library preparation and RNA-seq were conducted by Novogene. mRNA was purified using PolyA+ selection.

treatment_protocol: flag-Act1KO/WT MEF cells were untreated or treated with IL-17A (50ng/mL) for 1h

tag: cell line

value: flag-Act1KO/WT MEF cells

tag: cell type

value: Mouse Embryonic Fibroblasts

value: WT


title: Patient 4 HCC 8

source_name: Recurrent HCC


title: KO rep1 (Set8)

description: KO rep1


title: Patient 3 HCC 6


title: WT rep3 (Set8)

description: WT rep3


title: RMB4185

value: NACShell


title: RMB4184

value: mPOA


title: Rpe65-KO TMB

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

library_source: transcriptomic single cell

data_processing:
The pre-processing steps such as generation and demultiplexing of FASTQ files from raw sequencing reads (bclfastq, v2.20), aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger (v6.0.1) with default parameters. Cumulus software v1.5.0 was used to combine expression matrices and to remove cell doublets by Scrublet v0.2.1. The pipelines were run in Terra Cloud Platform (https://app.terra.bio/).  Seurat v3.2.2 was used to perform downstream analysis following the standard pipeline using cells with >=500 genes, resulting in 4,135 WT mouse cells, 3,979 vehicle treated RPE65 cells, and 5,901 TMB treated RPE65 cells. Principal Component (PC) analysis was performed on a submatrix of the top 1,000 most variable genes computed using the function FindVariableGenes in Seurat. Batch effect between experimental conditions was minimzed using the Harmony package v0.1.0 to remove non-cell-type-specific factors that may impact clustering. The number of top PCs was assessed by the elbow method. Cells were clustered using a shared nearest neighbor modularity optimization-based algorithm (FindClusters in Seurat).
Assembly: mm10
Supplementary files format and content: ExpressionMatrix.mtx.gz: Expression Matrix is sparse format.
Supplementary files format and content: MetaData.csv.gz: Metadata related to columns (cells) of the Expression Matrix.
Supplementary files format and content: Genes.txt.gz: Gene symbols related to rows of the Expression Matrix.
Supplementary files format and content: CellIDs.txt.gz: Cellular barcodes in the Expression Matrix.

molecule: polyA RNA

growth_protocol: All mice were housed under a standard 12-hour light (≤150 lux)/12-hour dark cycle, fed ad libitum, and maintained using standard procedures.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, the retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions.
Sublibraries were generated and sequenced independently on Illumina NovaSeq6000 at an average sequencing depth of 50,000 reads/cell, for a projected total of 5 billion reads for the entirety of the 100,000 cell barcoded library. Reads from identical cells from each of the sublibraries were consolidated during analysis and processing of raw reads.

treatment_protocol: Dietary vehicle (normal pellets) or TMB treatment was started at P21-P24.

tag: time

value: 2 months

value: TMB pellet


title: Day7 of JGEO reprogramming without BMP4 treatment

city: zhejiang, china

first: jin

last: ming

address: 西湖大学

country: China

institute: Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4)and then mapped to the mm10 reference genome with HISAT2 (v2.2.1), and StringTie (v2.2.1) was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads).
GFOLD (v1.1.4) was used to perform differential expression analysis between conditions. The differentially expressed genes were identified with gfold value > 0.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: reprogramming cells from E13.5 mouse embryonic fibroblast

growth_protocol: BMP4- group cells were cultured in iCD3 medium with TV,Vitamin C,mLIF, bFGF,CHIR99021, SGC0946, LSD1-HCL and Y27632 after transfected by JGES virus for 2 days, BMP4+ group cells were cultured by the same way plus BMP4; WT_SALL4 and delN12_SALL4 groups were also cultured in iCD3. Cells are collected after 0.25% trypsin-EDTA digestion.

extract_protocol:
Total RNAs were extracted by FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01)
In brief, 1 μg total RNAs were used, library strategy are followed by mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611), library DNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411). High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150.

treatment_protocol: BMP4+ group cells were treated with BMP4(10 ng/ml) for 7 days, BMP4- group were not treated by BMP4, so as WT_SALL4 and delN12_SALL4 groups

tag: chip antibody


title: WT rep1 (Set8)

description: WT rep1


title: Patient 3 HCC 5


title: Patient 2 HCC 4


title: WT rep2 (Set8)

description: WT rep2


title: RMB4182

value: ILC


title: KO rep2 (Set7)

description: KO rep2

extract_protocol:
Three independent replicates of the developing cerebellum from WT or mouse Atoh7 large enhancer knockout at P18
Illumina RNA-seq library preparation kit
Bulk RNA-seq

value: Atoh7 Large Enhancer KO


title: KO rep3 (Set7)

description: KO rep3


title: KO rep1 (Set7)

description: KO rep1


title: WT rep1 (Set7)

description: WT rep1


title: WT rep2 (Set7)

description: WT rep2


title: KO rep2 H3K4me2 ChIP (Set6)

description: KO rep2 H3K4me2 ChIP

library_source: genomic

data_processing:
Low quality reads and adapter sequences were trimmed by Trimmomatic
Surviving reads were aligned to mouse reference genome by BWA aligner and filtered by Picard tools
Peak calling was performed by MAC with the subtraction of input samples
Assembly: mm10
Supplementary files format and content: BW peak file

molecule: genomic DNA

extract_protocol:
Mouse cerebellum from P18 pups were collected
Samples were subjected to chromatin prep and ChIP protocol ( Diagenode's iDeal ChIP-seq protocol) using H3K27AC antibody (Abcam ab4729) and H3K4me2  antibody (Abcam ab7766).

value: KO


title: KO rep2 (Set8)

description: KO rep2


title: Patient 2 HCC 3


title: RMB4180

value: CGC


title: RMB4181

value: Bupropion


title: KO rep2 input (Set6)

description: KO rep2 input


title: RMB4179

value: BLA

value: brain


title: Patient 1 HCC 2

value: liver


title: cells of embryonic heart, 72 hpf, line: et33

first: Karim

last: Abu Nahia

address: Księcia Trojdena 4

institute: IIMCB Warsaw

description: single-cell RNA-seq 10x Genomics library

data_processing:
Demultiplexing bcl files by cellranger mkfastq command
Aligning fastq files to the reference genome and getting count matrices by cellranger count command
Downstream data processing in R using Seurat package.
Assembly: GRCz11 (Ensembl release 100)
Supplementary files format and content: Raw counts and associated barcodes and features matrices generated from fastq files by cellranger pipeline

organism: Danio rerio

source_name: heart

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
Whole hearts were extracted from double transgenic individuals [sqet31Et x Tg(myl7:mRFP) and sqet33mi59BEt x Tg(myl7:mRFP)]. Embryos were anesthetized with Tricaine (0.16 mg/ml in egg water) and large-scale extraction was performed according to a previously published protocol. Hearts were manually separated from remaining tissue under a fluorescence stereomicroscope and collected into 0,5 ml of EDM (L-15/10% FBS). Single cell heart suspension was obtained according to Bresciani et al. Ultimately, cells were resuspended by gentle pipetting, loaded on the cell counting chamber, visually inspected under the microscope (Zeiss Apotome), and quantified by Countess automated cell counter (Invitrogen).
After viability and quantity check, dissociated cells derived from embryonic zebrafish hearts at 48 hpf and 72 hpf were loaded on 10x Chromium Controller Chip G (10x Genomics) and processed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1. Final libraries were sequenced on Nextseq 500 (Illumina) in the following mode: (read 1 - 28 cycles, i7 index - 8 cycles, i5 index - 0 cycles,  read 2 - 91 cycles).
scRNA-seq accroding to 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1.

value: heart

tag: Stage

value: 72 hpf

value: cross of two homozygous zebrafish lines expressing EGFP within the cells marking the atrioventricular canal or sinoatrial region and mRFP in cardiomyocytes

value: cross of sqet33mi59BEt x Tg(myl7:mRFP)


title: KO rep1 H3K27AC ChIP (Set6)

description: KO rep1 H3K27AC ChIP

value: retina


title: RMB4178

value: venDG


title: KO rep1 input (Set6)

description: KO rep1 input


title: RMB4183

value: LConly


title: cells of embryonic heart, 72 hpf, line: et31

value: cross of sqet31Et x Tg(myl7:mRFP)


title: KO rep2 H3K27AC ChIP (Set6)

description: KO rep2 H3K27AC ChIP


title: cells of embryonic heart, 48 hpf, line: et33

value: 48 hpf


title: RMB4177

value: Raphe


title: WT rep2 H3K4me2 ChIP (Set6)

description: WT rep2 H3K4me2 ChIP

value: WT


title: cells of embryonic heart, 48 hpf, line: et31


title: WT rep3 (Set7)

description: WT rep3


title: WT rep2 H3K27AC ChIP (Set6)

description: WT rep2 H3K27AC ChIP


title: Patient 1 HCC 1


title: WT rep2 input (Set6)

description: WT rep2 input


title: OCCEV2

city: Tokyo

first: Takaaki

last: Tamura

address: 6-7-1 Nishishinjuku, Shinjyuku-ku

country: Japan

institute: Tokyo Medical University

description:
D06-OCCexo-2_S7
EV-microRNA

library_source: other

data_processing:
GeneGlobe/Strand NGS v4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: UCSC Mouse mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

molecule: other

source_name: EVs

extract_protocol:
EV-associated miRNA were isolated from cultured cells and purified EVs by QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols.
Small RNA libraries were prepared using QIAseq miRNA library Kit and QIAseq miRNA NGS 96 Index IL for Illumina, and yields were evaluated using Agilent 2100 BioAnalyzer.

value: EVs

value: monocytic cell

value: osteoclastic diffrentiation

tag: cell subtype

value: OCC cells


title: WT rep1 H3K4me2 ChIP (Set6)

description: WT rep1 H3K4me2 ChIP


title: Atoh7 RE KO H3K27me3 E14.5 Retina Chip (Set5)

description: Atoh7 RE KO H3K27me3 E14.5 Retina Chip

extract_protocol:
E14.5 retinae from E14.5 WT or Atoh7 REN ko were collected
Samples were subjected to chromatin prep and ChIP protocol ( Diagenode's iDeal ChIP-seq protocol) using H3K27me3 antibody (Millipore 07-449).

value: Atoh7 RE KO


title: RMB4175

value: NACShell

value: Bupropion

value: brain


title: WT rep1 H3K27AC ChIP (Set6)

description: WT rep1 H3K27AC ChIP


title: OCCEV1

description:
D05-OCCexo-1_S6
EV-microRNA


title: RMB4174

value: mPOA


title: OCPEV1

description:
D04-OCPexo_S5
EV-microRNA

value: OCP cells


title: WT rep1 input (Set6)

description: WT rep1 input

value: retina


title: KO rep1 H3K4me2 ChIP (Set6)

description: KO rep1 H3K4me2 ChIP

value: KO


title: OCNEV2

description:
D03-OCNexo-2_S3
EV-microRNA

value: OCN cells


title: WT H3K27me3 E14.5 Retina ChIP (Set5)

description: WT H3K27me3 E14.5 Retina ChIP


title: WT Input E14.5 Retina ChIP (Set5)

description: WT Input E14.5 Retina ChIP


title: RMB4173

value: LConly


title: Atoh7 RE KO Input E14.55 Retina ChIP (Set5)

description: Atoh7 RE KO Input E14.55 Retina ChIP


title: RMB4171

value: dorDG


title: OCEV1

description:
D02-OCexo-1_S3
EV-microRNA

value: OC cells


title: KO rep1 (Set4)

description: scRNA-seq

data_processing:
Data pre-processing (demultiplexing and gene expression counting) was analyzed by 10X CellRanger software
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

extract_protocol:
Two replicates of E14.5 WT retina and Atoh7 REN ko were dissociated
Libraries were processed for sc-RNA-Seq analysis according to 10X genomics protocol.
single-cell RNA-seq by 10X genomics


title: WT rep1 (Set4)

description: scRNA-seq

value: WT


title: RMB4176

value: PLC


title: RMB4172

value: ILC


title: RMB4169

value: BLA


title: RMB4170

value: CGC


title: KO3, adult, heart

city: Beijing

first: Yang

last: Li

address: Anzhen Road, Chaoyang District

institute: Beijing Anzhen Hospital

description:
b19ko_3
adult.txt

data_processing:
Relative expression (fragments per kilobase per million mapped reads, FPKM) was calculated using uniquely mapped pairs with Cufflinks software (Version 2.2.1).
Down-regulated differentially expressed genes (DEGs) from KO embryonic heart met the following criteria: 1) average FPKM in WT group > 2; 2) p-value < 0.1; 3) fold change (mutant/WT) < 0.8. Up-regulated DEGs met the following criteria: 1) average FPKM in KO group > 2; 2) p-value < 0.1; 3) fold change (mutant/WT) > 1.2.
Down-regulated DEGs from KO adult heart satisfied the following criteria: 1) average FPKM in WT group > 2; 2) p-value < 0.05; 3) fold change (mutant/WT) < 0.9. Up-regulated DEGs from KO adult hearts, satisfied the following criteria: 1) average FPKM in KO group > 2; 2) p-value < 0.05; 3) fold change (mutant/WT) > 1.1.
Gene Ontology (GO) enrichment analysis was performed using Novomagic
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample

extract_protocol:
For embryonic mice, hearts were isolated from E18.5 embryos generated by heterozygous parents and stored in Trizol reagent prior to genotyping. Three hearts per genotype were pooled together and total RNA was extracted. RNA quality was evaluated via the Lab-Chip technique (Agilent Bioanalyzer). For adult mice, we extracted total RNA from hearts using Trizol.
The libraries were constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina®

value: heart

value: C10orf71 KO

value: adult


title: OCNEV1

description:
D02-OCNexo-1_S2
EV-microRNA

value: EVs

value: monocytic cell

value: osteoclastic diffrentiation


title: WT rep2 (Set4)

description: scRNA-seq

value: retina


title: OCCcell1

data_processing:
StrandNGS 4.0/Star 2.7.8a
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: UCSC Mouse mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library prep for Illumina, NEBNext rRNA Depletion Kit and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs), and yields were evaluated using Agilent 2100 BioAnalyzer.


title: KO4, adult, heart

description:
b19ko_4
adult.txt


title: RMB4167

value: Raphe

value: FT

value: brain


title: OCCcell2


title: KO rep2 (Set4)

description: scRNA-seq


title: KO rep2 (Set3)

description: KO rep2

extract_protocol:
Three independent replicates from WT or Atoh7 REN KO retinae at E14.5 were processed for RNA extraction
Illumina RNA-seq library preparation kit
Bulk RNA-seq

value: Atoh7 Remote Enhancer KO


title: OCEV2

description:
D03-OCexo-2_S4
EV-microRNA

value: OC cells


title: KO1, adult, heart

description:
b19ko_1
adult.txt


title: OCPcell2


title: KO rep1 (Set3)

description: KO rep1


title: RMB4166


title: KO2, adult, heart

description:
b19ko_2
adult.txt


title: WT4, adult, heart

description:
WT_4
adult.txt

value: WT


title: WT3, adult, heart

description:
WT_3
adult.txt


title: OCPcell1


title: RMB4165

value: NACShell


title: KO rep3 (Set3)

description: KO rep3


title: RMB4168

value: venDG


title: OCNcell2


title: WT1, adult, heart

description:
WT_1
adult.txt


title: KO4, E18.5, heart

description:
KO4
E18.5.txt


title: WT rep2 (Set3)

description: WT rep2


title: OCNcell1


title: WT2, adult, heart

description:
WT_2
adult.txt


title: KO3, E18.5, heart

description:
KO3
E18.5.txt


title: RMB4161

value: dorDG


title: KO rep4 (Set2)

description: KO rep4

extract_protocol:
Four independent replicates from WT or Atoh7 REN KO retinae at E14.5 were processed for RNA extraction
Illumina RNA-seq library preparation kit
Bulk RNA-seq

value: Atoh7 Large Enhancer KO


title: WT rep1 (Set3)

description: WT rep1


title: WT rep3 (Set3)

description: WT rep3


title: OCcell2


title: HSA_CTRL__S458

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Sample 16

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (version 2.5.2a, Dobin et al., Bioinformatics 2013),  with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (version 1.16.0, Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with EntrezID (1. column), 2. (gene length in bp), and raw counts for each sample

source_name: gastrocnemius muscle

extract_protocol:
Gastrocnemius muscles were powdered in liquid nitrogen, and 1/3 of the muscle was used for RNA extraction. The powder was lysed in the RLT buffer provided in the RNeasy mini kit (Qiagen) and homogenized with a syringe. Total RNAs were extracted with the RNeasy Mini Kit (Qiagen), with proteinase K and DNAse treatment.
mRNA-sequencing stranded libraries were generated using the TruSeq Illumina kit according to the manufacturer’s instructions.

treatment_protocol: AICAR (Toronto Research Chemicals; 500 mg/kg) for 7 days

value: gastrocnemius muscle

tag: mouse id

value: HSA transgene

value: CTRL


title: RMB4159

extract_protocol:
Frozen, pooled brain tissue punches for each region were thawed on ice in 1 ml Trizol. Tissue was then homogenized using a manual glass douncer with 7-15 slow strokes on ice. RNA was extracted from each replicate sample using the Qiagen RNA Mini kit (Qiagen, Cat# 74104) as per the manufacturer’s instructions with on-column DNase I treatment. RNA quality was examined using a Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA). RNA Integrity Number (RIN) values ranged from 7.1 to 10, with a median value of 9.5. cDNA libraries were prepared using 300 ng of total RNA, from 27 regions in every replicate, using the Illumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301). Paired-end, 150 bp read length RNA-seq was carried out on the Illumina HiSeq 4000 at a depth of 20M reads per sample.
llumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301)

value: BLA


title: KO rep3 (Set2)

description: KO rep3


title: RMB4164

value: mPOA


title: KO1, E18.5, heart

description:
KO1
E18.5.txt

value: heart

value: C10orf71 KO


title: WT rep4 (Set2)

description: WT rep4

value: retina


title: RMB4162

value: ILC

value: FT


title: HSA_CTRL__S459

description: Sample 14


title: FVB_AICAR__S448

description: Sample 15

value: FVB/N

value: AICAR


title: KO rep2 (Set2)

description: KO rep2


title: RMB4160

value: CGC

value: brain


title: KO rep1 (Set2)

description: KO rep1


title: KO2, E18.5, heart

description:
KO2
E18.5.txt


title: OCcell1

value: monocytic cell

value: osteoclastic diffrentiation


title: WT4, E18.5, heart

description:
WT4
E18.5.txt

value: WT


title: RMB4158

value: venDG


title: WT rep3 (Set2)

description: WT rep3


title: FVB_CTRL__S450

description: Sample 13

value: gastrocnemius muscle


title: RMB4163

value: LConly


title: RMB4157

value: Raphe


title: WT rep2 (Set2)

description: WT rep2


title: FVB_CTRL__S445

description: Sample 12

value: CTRL


title: RMB4156

value: PLC


title: WT2, E18.5, heart

description:
WT2
E18.5.txt

value: heart


title: RMB4155

value: NACShell


title: HSA_CTRL__S451

description: Sample 9

value: HSA transgene


title: WT1, E18.5, heart

description:
WT1
E18.5.txt


title: KMS27 C5 S2

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
Resistant clone to venetoclax
KMS27_venetoclax_raw_counts_Deseq2.csv

data_processing:
fastq files were processed with SALMON 1.4.0 to get raw read counts
Refseq GTF files were used to generate SALMON index
Assembly: hg38
Supplementary files format and content: tab-delimited raw read counts for each sample

source_name: Bone marrow plasma cell

growth_protocol: All myeloma cell lines were cultured in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (Gibco, Life Technologies, Carlsbad, CA), 1% penicillin/streptomycin and 1% L-glutamine in humidified atmosphere with 5% CO2 at 37℃ .

extract_protocol:
RNA was harvested using AllPrep DNA/RNA Mini Kit of Qiagen.200ng of total RNA was used for the construction of sequencing libraries
Roche Kapa mRNA Hyper prep.

treatment_protocol: The DTEP clones were maintained in 100nM Venetoclax.

value: Bone marrow plasma cell

value: cell line

value: Clone C5


title: KMS27 C5 S1


title: FVB_AICAR__S449

description: Sample 8

value: FVB/N

value: AICAR


title: RMB4152

value: ILC

value: FT

value: brain


title: KMS27 C1 S2

value: Clone C1


title: fibroblast reprogramming, JGES-BMP4, Day7, rep1

description: 10x Genomics

data_processing:
Reads mapping and counting were performed using STAR. The cells of low quality were filtered out using scanpy.
Assembly: gencode.vM21
Supplementary files format and content: Gzip of tab-separated matrix files
Supplementary files format and content: Raw_Counts

source_name: fibroblast

growth_protocol: BMP4- group cells were cultured in iCD3 medium with TV,Vitamin C,mLIF, bFGF,CHIR99021, SGC0946, LSD1-HCL and Y27632 for 7 days after transfected by JGES virus for 2 days, BMP4+ group cells were cultured by the same way plus BMP4,cells are collected after 0.25% trypsin-EDTA digestion.

extract_protocol:
Total RNAs were extracted as described below, The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation.
In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

treatment_protocol: BMP4+ group cells were treated with BMP4(10 ng/ml) for 7 days, BMP4- group were not treated by BMP4

value: fibroblast

value: Day 7


title: ALD216A2 (Set1)

description: scATAC-seq

library_source: genomic single cell

data_processing:
Data pre-processing (demultiplexing and ATAC peak counting) was analyzed by 10X CellRanger software
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

extract_protocol:
Two replicates of E14.5 WT retina were dissociated
Libraries were processed for sc-ATAC-Seq analysis according to 10X genomics protocol.
single-cell ATAC-seq by 10X genomics

value: retina

value: WT


title: fibroblast reprogramming, JGES+BMP4, Day7, rep1

description: 10x Genomics


title: RMB4151

value: dorDG


title: RMB4153

value: LConly


title: ALD216A1 (Set1)

description: scATAC-seq


title: KMS27 C1 S1


title: chip.RPE_DrM6

city: Koupio

first: Henri

last: Leinonen

address: Yliopistonranta 1

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

data_processing:
Quality of reads checked using fastqc
Sequence reads were trimmed and low qualaity reads were removed using trimmomatic
Trimmed reads were mapped to GRCm38/mm10 using STAR aligner (Parameters: 1. Maximum alignments per read = 10, 2. Maximum mismatches per alignment = 10, 3.Mismatch ratio = 0.3, 4. Maximum gap between two mates = 0 )
Read count were performed using HTSeq
Read count were normalized and differential expression among different groups were performed using DESeq2
Assembly: GRCm38/mm10
Supplementary files format and content: Seperated tab-delimited text files of raw read counts for genes expressed in mitocondria and nuclear region

source_name: Retina

growth_protocol: Rd10 vehicle and Rd10 TMB and WT mice: dark rearing P0-29 and vivarium P29-36. Complele dark rearing in one group of Rd10 mice through their lifespan P0-P30.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, RNA was extracted using Qiagen RNAeasy Mini-kit following manufacturers instructions. Genomic DNA was removed during RNA extraction.
Polyadenylated RNA was selected from the total RNA samples using Oligo dT conjugated magnetic beads and prepared for single-end sequencing according to the Illumina TruSeq RNA Sample Preparation Kit v2

treatment_protocol: Tamsulosin, metoprolol and bromocriptine drug treatment (´TMB´) in Rd10 mice was administered using dietary self-administration. Rd10 vehicle group received same base chow, similarly as WT and dark reared Rd10 control groups.

value: Retina

value: Male

value: LCA disease

value: Rpe65-/- (C57BL/6J background)

value: TMB diet

tag: condition

value: Rpe65-/- TMB


title: WT3, E18.5, heart

description:
WT3
E18.5.txt

value: heart


title: FVB_CTRL__S446

description: Sample 6

value: gastrocnemius muscle

value: FVB/N

value: CTRL


title: KMS27 B5 S2

value: Bone marrow plasma cell

value: cell line

value: Clone B5


title: WT rep1 (Set2)

description: WT rep1

value: retina


title: RMB4150

data_processing:
RNA-seq data were aligned to the Rattus norvegicus rn6 genome (Rn6 UCSC) with the STAR aligner. Read counts were concurrently calculated using Htseq
Any dataset that failed the default Fastqc sequencing parameters and < 75% mapping rate was discarded.
Assembly: rn6
Supplementary files format and content: fastq and read count files

value: CGC

value: FT

value: brain


title: HSA_CTRL__S453

description: Sample 11

value: HSA transgene


title: HSA_AICAR__S455

description: Sample 5

value: AICAR


title: RMB4154

value: mPOA


title: HSA_AICAR__S462

description: Sample 10


title: KMS27 B5 S1


title: RMB4149

value: BLA


title: HSA_AICAR__S454

description: Sample 7


title: HSA_AICAR__S463

description: Sample 4


title: chip.RPE_DrF4

value: Retina

value: Female

value: LCA disease

value: Rpe65-/- (C57BL/6J background)

value: TMB diet


title: KMS27 WT 2

description:
Sensitive parental cells
KMS27_venetoclax_raw_counts_Deseq2.csv

value: KMS27 WT


title: RMB4148

value: venDG


title: chip.RPE_DrF3

value: Rpe65-/- TMB


title: HSA_AICAR__S460

description: Sample 3

value: gastrocnemius muscle


title: KMS27 WT 1

value: Bone marrow plasma cell

value: cell line


title: chip.RPE_DrF1


title: RMB4147

value: Raphe

value: FT


title: Parental 3

description:
Sensitive parental cells
KMS12PE_venetoclax_raw_counts_Deseq2.csv

value: WT


title: FVB_AICAR__S447

description: Sample 2

value: FVB/N

value: AICAR


title: RMB4146

value: PLC

value: brain


title: HSA_CTRL__S452

description: Sample 1

value: HSA transgene

value: CTRL


title: RMB4145

value: NACShell


title: Parental 1


title: chip.RPE_CtM4

value: Retina

value: Male

value: LCA disease

value: Rpe65-/- (C57BL/6J background)

value: Vehicle/base diet

value: Rpe65-/- vehicle


title: chip.RPE_DrM5

value: TMB diet

value: Rpe65-/- TMB


title: chip.RPE_CtF2

value: Female


title: Act1_CLIP3

data_processing:
Reads with length >15bp were mapped to the mm10 genome using Gencode M25 (GRCm38.p6) with Bowtie2(2.4.4). The uniquely mapped reads were used to identify Act1 CLIP clusters that are present in at least 2 biological replicates. Reads were normalized based on the size of uniquely mapped reads of each library. CLIP clusters were identified using SAMTools(1.14), BEDTools(2.30.0). The gene annotation of CLIP clusters was assessed by intersection with gene regions retrieved from the Gencode M25 (GRCm38.p6).
To define 5’UTR or 3’UTR binding target, we calculated the sum of normalized reads on 5’UTR and 3’UTR regions. Genes with higher sum reads on 5’UTR/3UTR were defined as Act1 5’UTR/3’UTR dominant binding targets. Only genes with max read >1 and sum read >3 were used for further analysis. The length of 5’UTR/3’UTR were extracted using R package GenomicFeatures(1.50.4)(Lawrence et al., 2013). The longest transcript per gene was selected for calculation of UTR density.
genome build: mm10
processed data files format and content bed file: bed

growth_protocol: Act1−/− MEFs reconstituted with FLAG-tagged wild-type Act1 (WT) by retroviral infection were maintained and propogated in DMEM supplemented with 10%FBS  and antiboitics at 37 °C under a humidified atmosphere of 5% CO2.

extract_protocol:
Immunoprecipitated protein-RNA complexes were separated by SDS-PAGE and then transferred to PVDF membrane; RNA-protein complexes were cut out from the membrane corresponding to the size of flag-Act1. Purified RNAs from RNA-Protein complex were subjected to the small RNA library construction
Purified RNAs from RNA-Protein complex were subjected to the small RNA library construction as described previously (Zagore, et al. 2018)

treatment_protocol: Three 15cm plates of flag-Act1KO/WT MEF cells were treated with IL-17A (50ng/mL) for 1h, followed by irradiating with 365 nm UV light to induce crosslinking

value: flag-Act1KO/WT MEF cells

value: Mouse Embryonic Fibroblasts

value: WT

value: IL17 treated


title: RMB4144

value: mPOA

value: FT

value: brain


title: Clone D S3

description:
Resistant clone to venetoclax
KMS12PE_venetoclax_raw_counts_Deseq2.csv

value: Bone marrow plasma cell

value: cell line

value: Clone D


title: Act1_CLIP2


title: Clone D S1


title: Act1_CLIP1


title: RMB4143

value: LConly


title: chip.RPE_CtF1

value: Retina

value: LCA disease

value: Rpe65-/- (C57BL/6J background)


title: RMB4142

value: ILC


title: Clone C S3

value: Clone C


title: chip.WT_F4_y

value: Female

value: Healthy

value: Vehicle/base diet

value: Wild-type


title: chip.RD10_DM5_S20

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, RNA was extracted using Qiagen RNAeasy Mini-kit following manufacturers instructions. Genomic DNA was removed during RNA extraction.
Polyadenylated RNA was selected from the total RNA samples using Oligo dT conjugated magnetic beads and prepared for single-end sequencing according to the Illumina TruSeq RNA Sample Preparation Kit v2 (# RS-122-2001, Illumina)

value: Male

value: Strong disease

value: Rd10 (C57BL/6J background)

value: Rd10 TMB, DR P0-P29 vivarium P29-P36


title: Clone C S1

value: Bone marrow plasma cell


title: chip.WT_F3_y


title: Clone A S3

value: cell line

value: Clone A


title: chip.RD10_DM4_S19


title: RMB4140

value: CGC

value: FT

value: brain


title: chip.RD10_DM3_S18

value: Retina


title: chip.WT_M2_y


title: RMB4139

value: BLA


title: chip.RD9_DM4_S11


title: chip.RPE_CtM5

value: LCA disease

value: Rpe65-/- (C57BL/6J background)

value: Rpe65-/- vehicle


title: RMB4141

value: dorDG


title: Clone A S1


title: chip.WT_M1_y

value: Healthy

value: Vehicle/base diet

value: Wild-type


title: Rd10_Female_TMB

data_processing:
The pre-processing steps such as generation and demultiplexing of FASTQ files from raw sequencing reads (bclfastq, v2.20), aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger (v6.0.1) with default parameters. Cumulus software v1.5.0 was used to combine expression matrices and to remove cell doublets by Scrublet v0.2.1. The pipelines were run in Terra Cloud Platform (https://app.terra.bio/).  Seurat v3.2.2 was used to perform downstream analysis following the standard pipeline using cells with >=500 genes, resulting in 4,478 WT mouse cells, 5,952 vehicle treated Rd10 cells, and 4,812 TMB treated Rd10 cells. Principal Component (PC) analysis was performed on a submatrix of the top 1,000 most variable genes computed using the function FindVariableGenes in Seurat. Batch effect between experimental conditions was minimzed using the Harmony package v0.1.0 to remove non-cell-type-specific factors that may impact clustering. The number of top PCs was assessed by the elbow method, keeping 19 PCs for clustering and data visualization. Cells were clustered using a shared nearest neighbor modularity optimization-based algorithm (FindClusters in Seurat).
Assembly: mm10

growth_protocol: All mice were housed under dark conditions throughout their life but otherwise bred using standard procedures. Dark rearing slows retinal degeneration in Rd10 mice significantly.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, the retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions.
In each experimental group, one retina each from n=4 mice were pooled and used for single cell RNA-seq (scRNA-seq). For each group, freshly dissociated cells (~16,500) were loaded into a 10× Genomics Chromium Single Cell system using v3 chemistry following the manufacturer’s instructions. Libraries were pooled and sequenced on Illumina NovaSeq6000 platform.

treatment_protocol: Tamsulosin, metoprolol and bromocriptine drug treatment (´TMB´) in Rd10 mice was administered using dietary self-administration. Rd10 vehicle group received same base chow, similarly as WT conrol group.

value: 8 weeks

tag: strain

tag: agent

value: Tamsulosin+metoprolol+bromocriptine


title: input-BTZ-S2

city: Rome

first: Francesco

last: Fazi

state: RM

address: Via Antonio Scarpa

department: Department of Anatomical, Histological, Forensic & Orthopaedic Sciences

country: Italy

institute: Sapienza University of Rome

description:
RNA after RNase R treatment
input-BTZ7_S5

data_processing:
Sequence reads were mapped to hg19 by using STAR v2.7.9a58 with parameters --chimJunctionOverhangMin 15, --chimOutType Junctions SeparateSAMold, -- chimScoreMin 15, -- chimScoreSeparation 10, --chimSegmentMin 10
The coordinates of fragments mapping to back-spliced junction sites were extracted using the parse module of CIRCExplorer2 v.2.3.8 with parameter -t STAR. The detected back-spliced junctions were annotated with the annotate module of CIRCExplorer2 v.2.3.8.
The quantification of both control and bortezomib-treated samples of circRNA with m6A modification was performed using the CIRIquant toolkit v.1.1.2 and was corrected based on the total amount of circRNA before and after treatment.
Per-sample m6A circRNA quantification results were merged into a single matrix using the prep_CIRIquant module of CIRIquant v.1.1.2.
Raw counts of identified circRNAs with m6A modification were normalized using a multi-step procedure integrating DGEList, filterByExpr, calcNormFactors, and estimateDisp functions from the EdgeR v. 3.38.4 R package.
Assembly: hg19
Supplementary files format and content: comma-delimited text file includes count per million for each Sample

growth_protocol: MOLM-13 cell lines were cultured with RPMI 1640 (Gibco® Thermo Fisher Scientific, Waltham, MA USA) enriched with pen/strep (50 U/mL) and with 10% heat-inactivated South-American Fetal Bovine Serum (FBS) (Gibco® Thermo Fisher Scientific), at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol RNA Isolation System (Invitrogen) according to manufacturer instructions. The samples were treated with RNAseR, in order to remove all the linear RNA.
Takara - SMARTer Stranded Total RNA Sample Prep Kit -Low Input Mammalian following the manufacturer's protocol but without ribosomal depletion

treatment_protocol: MOLM-13 cells were treated with 5nM Bortezomib (Btz) or DMSO (CTR)

value: acute myeloid leukemia

value: WT

value: 5nM Bortezomib


title: chip.RD10_DF1_S16

value: Female

value: Strong disease

value: Rd10 (C57BL/6J background)

value: Rd10 TMB, DR P0-P29 vivarium P29-P36


title: RMB4137

value: Raphe

value: FT

value: brain


title: input-BTZ-S1

description:
RNA after RNase R treatment
input-BTZ1_S1


title: Rd10_Female_vehicle

value: Vehicle


title: input-CTRL-S2

description:
RNA after RNase R treatment
input-C7_S3

value: control


title: Wild_Type_non_treated

value: wildtype


title: RMB4136

value: PLC


title: input-CTRL-S1

description:
RNA after RNase R treatment
3-C-input-7-21_S9


title: RMB4135

value: NACShell


title: RMB4134

value: mPOA


title: m6A-BTZ-S2

description:
RNA after RNase R treatment and immunoprecipitation with m6A-specific antibody
m6A-BTZ7_S6


title: WT3

city: HeFei

first: hui

last: zhang

state: 请选择省份

address: No. 81 Meishan Road, Shushan District

department: college of life science

institute: anhui medical university

data_processing:
Paired-end sequencing was performed at BGIseq-50 platform (BGI, Shenzhen). An average of ~45 million cleanreadswere generated afterremovinglow-qualityreads, and then mapped to the mouse reference genome (GCF_000001635.26_GRCm38.p6; http://asia.ensembl.org/Mus_musculus/Info/Annotation/) using HISAT and Bowtie2. The StringTie and featureCounts were used to calculate the counts of all annotated genes. Then, differentially expressed genes (DEGs) were identified by the "DESeq2" R package.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts and reliably expressed genes (FPKM) for each sample

source_name: testis

extract_protocol:
The four Tmem232-/- and four Tmem232+/+ mice testis at 2 months old were obtained to isolate total RNA using TRIzol (Cat#15596018, Thermo Fisher, Waltham, MA, USA) according to the manufacturer's instructions.
After assessing the quality of RNA by concentration determination and agarose gel electrophoresis without degradation, 1 μg of total RNA was then used to construct cDNA libraries using the TruSeq RNA Sample Preparation kit (Illumina, Inc, San Diego, California, USA).

value: testis


title: m6A-BTZ-S1

description:
RNA after RNase R treatment and immunoprecipitation with m6A-specific antibody
m6A-BTZ1_S2

value: acute myeloid leukemia


title: chip.RD8_CM1_S5

value: Retina

value: Male

value: Vehicle/base diet

value: Rd10 vehicle, DR P0-P29 vivarium P29-P36


title: RMB4133

value: LConly


title: WT2


title: RMB4138

value: venDG


title: chip.RD9_CM3_S7

value: Strong disease

value: Rd10 (C57BL/6J background)


title: m6A-CTRL-S1

description:
RNA after RNase R treatment and immunoprecipitation with m6A-specific antibody
5-C-m6A-7-21_S10

value: WT


title: WT1


title: RMB4131

value: dorDG

value: FT

value: brain


title: KO4

value: Tmem232 knockout


title: chip.RD10_DF2_S17

value: Female

value: Rd10 TMB, DR P0-P29 vivarium P29-P36


title: chip.RD10_CM5_S15


title: Thyroid – GD3

city: Madrid

first: Rebeca

last: Martinez

address: C/Diego de Leon 62

department: Endocrinology

country: Spain

institute: IIS la Princesa

description: OCT frozen Visium spatial gene expression sequencing

data_processing:
Raw FASTQ data were processed using the 10x Genomics SpaceRanger
Sequences were aligned to GRCh38 genome using SpaceRanger’s default settings
Gene expression level of the coding genes were quantified using SpaceRanger’s default settings
Assembly: Human genome reference GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: Gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducuals.jpg.gz: Aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: Image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: Scale factors in json format
Supplementary files format and content: tissue_hires_image.png.gz: High resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: Low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz : List of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Thyroid

extract_protocol:
Thyroid tissue samples were immediately snap-frozen in liquid nitrogen cooled in isopentane and transferred to a −80 °C freezer. RNA was isolated from 40 fresh-frozen thyroid tissues (21 controls, 11 HT and 8 GD samples). Total RNA was isolated using miRNeasy Mini Kit (Qiagen). The quality and quantity of RNA was assessed in a 2100 Bioanalyzer using a RNA 6000 Nano kit (Agilent Technologies). Eight samples with RIN>7 were selected for Spatial Transcriptomics using the Visium spatial Gene expression Kits from 10X Genomics. Briefly, the Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics) was used to optimize permeabilization conditions for thyroid tissue. Then, they were cryosectioned at 10μm onto 6.5 × 6.5 mm capture areas from Visium spatial slides and processed according to the manufacturer’s instructions (10x Genomics). Briefly, after permeabilization, reverse transcription and second strand synthesis were performed on slides, followed by cDNA amplification and quality control, and the pooled libraries were sequenced on Nova-seq 6000 (Illumina).
Spatial gene expression sequencing libraries were prepared with 10x Genomics Visium Spatial Gene expression Slides and Reagent kit according to manufacturer’s construction

value: Thyroid

tag: disease state

value: Graves' disease


title: KO3

value: testis


title: chip.RD9_CF1_S6

value: Retina


title: chip.RD9_DF2_S10


title: RMB4130

tag: replicate

value: CGC


title: Thyroid – GD2


title: RMB4129

tag: brain region_name

value: BLA


title: KO2


title: chip.RD10_CF1_S12

tag: treatment

value: Vehicle/base diet

value: Rd10 vehicle, DR P0-P29 vivarium P29-P36


title: Thyroid – GD1

tag: tissue


title: chip.RD9_CM4_S8

value: Male

value: Strong disease


title: Thyroid – HT3

value: Hashimoto's thyroiditis


title: chip.RD10_CF2_S13

value: Rd10 (C57BL/6J background)


title: RMB4132

value: ILC

value: FT


title: RMB4128

value: venDG

value: brain


title: m6A-CTRL-S2

description:
RNA after RNase R treatment and immunoprecipitation with m6A-specific antibody
m6A-C7_S4

value: acute myeloid leukemia

value: WT

value: control


title: KO1

value: testis

value: Tmem232 knockout


title: Total RNA, dimt-1 RNAi, biological replicate 4

first: Wayne

last: Mitchell

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
Fastq files were mapped to the WBCel235 genome using STAR v.2.7.2b
Assembly: WBCel235
Supplementary files format and content: excel file containing raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole-worm lysates

extract_protocol:
RNA was purified using the Rneasy Plus Mini Kit (QIAGEN)
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

value: whole-worm lysates

value: dimt-1 RNAi


title: chip.RD10_CF3_S14

value: Retina

value: Female

value: Vehicle/base diet


title: Total RNA, dimt-1 RNAi, biological replicate 3


title: chip.RD10_DR_M2_S23

value: Male

value: Mild disease

value: Rd10, dark-reared, P30


title: RMB4125

value: NACShell


title: chip.RD10_DR_M3_S24

value: Rd10 (C57BL/6J background)


title: Thyroid – C2

value: Thyroid


title: Thyroid – HT1

value: Hashimoto's thyroiditis


title: Total RNA, dimt-1 RNAi, biological replicate 1


title: Total RNA, dimt-1 RNAi, biological replicate 2


title: Thyroid – C1


title: chip.RD10_DR_F1_S21


title: RMB4123

value: LConly

value: FT

value: brain


title: RMB4124

value: mPOA


title: Total RNA, control RNAi, biological replicate 4

value: control RNAi


title: chip.RD10_DR_F4_S22


title: RMB4127

value: Raphe


title: RMB4126

value: PLC


title: F5-XR

city: Shanghai

first: xu

last: wu

address: 83 Fenyang Road

institute: EENT Hospital, Fudan University

data_processing:
All samples were sequenced using Illunima Novaseq 6000.
Software Solexa pipeline version 1.8  is used for image processing and base recognition
Fastq software (version 0.11.7)  was used to assess the sequencing quality of trimmed reads, which are then aligned to a reference genome using Hisat2 (version 2.1.0) software.
StringTie (version 1.3.3) software was employed to estimate transcript abundance by referencing an official database, resulting in the generation of RNA transciptome expression profiles.
Assembly: hg38
Supplementary files format and content: Xlsx data including RPKM value for each sample.

source_name: auricular cartilage

extract_protocol:
The isolated cartilage tissues were rapidly immersed in TRIzol reagent (Invitrogen). RNA was extracted by adding chloroform and then precipitated with isopropyl alcohol. The RNA precipitates were washed twice with 70% ethanol, dried, and resolved in water without RNase. RNA quantity and quality were measured by NanoDrop ND-1000. 1.5ug RNA was used for construction of sequencing libraries.
RNA library for RNA-seq were using KAPA Stranded RNA-Seq Library Prep Kit(Illumina).

value: auricular cartilage

value: chondrocyte


title: RMB4122

first: Nirmala

last: Arul Rayan

address: 60 Biopolis Street

institute: Genome Institute of Singapore

value: ILC


title: Total RNA, control RNAi, biological replicate 3

value: whole-worm lysates


title: F5-P5


title: F5-P0


title: chip.B6_M4_S3_x

value: Retina

value: Male

value: Healthy

value: Vehicle/base diet

value: Wild-type


title: chip.B6_M5_S4_x


title: RMB4121

value: dorDG


title: Total RNA, control RNAi, biological replicate 2


title: chip.B6_F2_S2_x

value: Female


title: L4-XR


title: Total RNA, control RNAi, biological replicate 1


title: RMB4119

value: BLA

value: FT


title: Germline ribosome-bound mRNA, dimt-1 RNAi, biological replicate 4

source_name: germline

value: germline

value: dimt-1 RNAi


title: chip.B6_F1_S1_x


title: L4-P5


title: Kras+p53_Sen3

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

data_processing:
FASTQ files were trimmed and filtered with trim_galore (v0.6.1) for adapter sequences, polyA tails and low quality bases.
Trimmed and filtered reads were mapped with salmon quant function (v1.6.0) to the transcriptome.
Normalization and exploration of differentially expressed genes was perfofrmed with Deseq2 (v1.40.1)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file consisting of raw transcript counts for each sample.

source_name: Pancreas

extract_protocol:
Total RNA was extracted and isolated using TRI reagent (Sigma) and RNA isolation kit (Zymo Research).
Libraries for expression profile were prepared using standard CEL-Seq protocol.
CEL-Seq

treatment_protocol: Tumor bearing mouse pancreata were isolated, dissociated, and underwent FACS sorting. CAFs were isolated by FACS with selection for Pdpn+, Epcam–, Cd45–, Cd31– cells.

value: Pancreas

value: Fibroblast

tag: cell state

value: Sen

value: PDAC


title: Sample 2022-625 technical replicate b

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Dermal cell after 18 jours after EHV4 infection and DTB treatment, sample 2022-625, technical replicate b

data_processing:
Illumina BCL Convert 3.9.3 software used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.6.1. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Equus caballus genome (EquCab3.0 fromEnsembl version 108 and EHV4 virus genome from NCBI (KT324740) using the STAR mapper (version 2.7.8a, with --outSAMunmapped Within parameter). Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, Equus caballus GTF genome annotation version 88 from Ensembl database and EHV4 GTF was used. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3.
Assembly: EquCab3.0 from Ensembl version 108 and EHV4 from NCBI (Genbank: KT324740)
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample

organism: Equus caballus

source_name: NBL-6 ATCC

extract_protocol:
Nucleic acids were extracted using RNeasy Plus mini kit (Qiagen)
Messenger (polyA+) RNAs were purified from 200 ng of total RNA using oligo(dT). Libraries were performed using the strand specific RNA-Seq library preparation Stranded mRNA Prep, Ligation kit (Illumina)

value: NBL-6 ATCC

value: Dermal cell


title: L4-P0

value: auricular cartilage

value: chondrocyte


title: Germline ribosome-bound mRNA, dimt-1 RNAi, biological replicate 3

tag: genotype


title: Sample 2022-625 technical replicate a

description: Dermal cell after 18 jours after EHV4 infection and DTB treatment, sample 2022-625, technical replicate a

tag: cell line


title: Germline ribosome-bound mRNA, dimt-1 RNAi, biological replicate 2


title: Kras+p53_Sen2

tag: cell type


title: J3-XR


title: Germline ribosome-bound mRNA, dimt-1 RNAi, biological replicate 1


title: Sample 2022-579 technical replicate b

description: Dermal cell after 18 jours after EHV4 infection and DTB treatment, sample 2022-579, technical replicate b


title: RMB4120

city: Singapore

source_name: brain

value: CGC

value: brain


title: Kras+p53_Sen1


title: Germline ribosome-bound mRNA, control RNAi, biological replicate 4

value: control RNAi


title: Kras+p53_Non-sen3

value: Non-Sen


title: Germline ribosome-bound mRNA, control RNAi, biological replicate 3


title: J3-P0


title: Sample 2022-533 technical replicate b

description: Dermal cell after 18 jours after EHV4 infection and DTB treatment, sample 2022-533, technical replicate b


title: Kras+p53_Non-sen2


title: Z2-XR


title: Sample 2022-615 technical replicate b

description: Dermal cell after 18 jours after DTB treatment, sample 2022-615, technical replicate b

value: 18 jours after DTB treatment


title: Z2-P5


title: Kras+p53_Non-sen1


title: Kras_Sen5


title: Z2-P0


title: Day11 of elN12_SALL4 induced somatic cell transdifferentiation

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4)and then mapped to the mm10 reference genome with HISAT2 (v2.2.1), and StringTie (v2.2.1) was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads).
GFOLD (v1.1.4) was used to perform differential expression analysis between conditions. The differentially expressed genes were identified with gfold value > 0.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

extract_protocol:
Total RNAs were extracted by FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01)
In brief, 1 μg total RNAs were used, library strategy are followed by mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611), library DNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411). High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150.

value: reprogramming cells from E13.5 mouse embryonic fibroblast


title: Sample 2022-615 technical replicate a

description: Dermal cell after 18 jours after DTB treatment, sample 2022-615, technical replicate a


title: D1-XR


title: Kras_Sen4


title: Sample 2022-569 technical replicate b

description: Dermal cell after 18 jours after DTB treatment, sample 2022-569, technical replicate b


title: Day9 of elN12_SALL4 induced somatic cell transdifferentiation


title: J3-P5


title: Kras_Sen3


title: D1-P5


title: Sample 2022-569 technical replicate a

description: Dermal cell after 18 jours after DTB treatment, sample 2022-569, technical replicate a


title: Day5 of elN12_SALL4 induced somatic cell transdifferentiation


title: Kras_Sen2


title: Germline ribosome-bound mRNA, control RNAi, biological replicate 2


title: D1-P0


title: Sample 2022-523 technical replicate b

description: Dermal cell after 18 jours after DTB treatment, sample 2022-523, technical replicate b


title: Day1 of delN12_SALL4 induced somatic cell transdifferentiation


title: Kras_Sen1


title: Day11 of WT_SALL4 induced somatic cell transdifferentiation


title: Germline ribosome-bound mRNA, control RNAi, biological replicate 1


title: Scolex reads 2

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

institute: Adam Mickiewicz University

data_processing:
The sequencing libraries were multiplexed and clustered on a flowcell, then loaded on the Illumina instrument (HiSeq 4000) according to manufacturer’s instructions. The samples were sequencing using a 2x150 bp Pared End configuration. Image analysis and base calling were conducted by the Control software.
Raw sequence data generated were converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
The RNA-Seq reads were subject to quality control with FastQC v0.11.5. Then quality filtering and adapter trimming were performed with BBDUK2 from BBMAP package v37.02, using the following settings: qtrim=w, trimq=20, maq=10, k=23, mink=11, hdist=1, tbo, tpe, minlength=100, removeifeitherbad=t.
After that, genes and transcripts expression values were calculated using RSEM v1.2.30 and Bowtie 2 as reads aligner. The reads were mapped against T. solium transcriptome obtained from WormBase (taenia_solium.PRJNA170813.WBPS16.mRNA_transcripts.fa.gz).
Assembly: Taenia solium (pork tapeworm) Accesion: PRJNA170813 ID: 170813
Supplementary files format and content: Fastq
Supplementary files format and content: Tab-delimited files with genes expression values, as obtained with RSEM

organism: Taenia solium

source_name: Scolex

growth_protocol: Tissue section were preserved in RNAlater at -70°C until use for total RNA isolation

extract_protocol:
Total RNA from each sample was extracted using Qiagen RNeasy Plus Universal mini kit (Qiagen, Hiden, Germany) and treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and the integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA
The samples were prepared for rRNA depletion using the QIAseq FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation employs the NEBNext Ultra II RNA Library Preparation Kit for Illumina and the manufacturer’s recommendations were followed (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 min. at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were then end repaired and the 3’ ends adenylated, and universal adapters ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: No treatments were used

value: Scolex

value: parenchymal cyst


title: Scolex reads 3


title: Sample 2022-605 technical replicate b

description: Dermal cell after 18 hours after EHV4 infection, sample 2022-605, technical replicate b

value: 18 hours after EHV4 infection


title: Kras_Non-sen2

value: Pancreas


title: Day5 of WT_SALL4 induced somatic cell transdifferentiation


title: Sample 2022-605 technical replicate a

description: Dermal cell after 18 hours after EHV4 infection, sample 2022-605, technical replicate a


title: Sample 2022-533 technical replicate a

description: Dermal cell after 18 jours after EHV4 infection and DTB treatment, sample 2022-533, technical replicate a


title: Scolex reads 1


title: Sample 2022-559 technical replicate b

description: Dermal cell after 18 hours after EHV4 infection, sample 2022-559, technical replicate b


title: Day1 of WT_SALL4 induced somatic cell transdifferentiation


title: Vesicular cysts reads 3

source_name: Bladder wall

value: Bladder wall


title: Kras_Non-sen1

value: Fibroblast


title: chip.RD9_DF1_S9

value: Retina

value: Female

value: Strong disease

value: Rd10 (C57BL/6J background)

value: Rd10 TMB, DR P0-P29 vivarium P29-P36


title: Vesicular cysts reads 2


title: Sample 2022-559 technical replicate a

description: Dermal cell after 18 hours after EHV4 infection, sample 2022-559, technical replicate a

value: NBL-6 ATCC

value: Dermal cell


title: Cultured mouse CAFs_Sen4

data_processing:
FASTQ files were trimmed and filtered with trim_galore (v0.6.1) for adapter sequences, polyA tails and low quality bases.
Trimmed and filtered reads were mapped with salmon quant function (v1.6.0) to the transcriptome.
Normalization and exploration of differentially expressed genes was perfofrmed with Deseq2 (v1.40.1)
Assembly: hg38 and mm39
Supplementary files format and content: Tab-delimited text file consisting of raw gene counts for each sample.

treatment_protocol: Human and mouse primary CAFs were grown in culture. Senescence was induced by activating a Cre-ER vector that excised hTERT and SV40-LT-Antigen.

value: Fibroblasts

value: PDAC

value: Sen


title: Vesicular cysts reads 1


title: Day7 of JGES reprogramming with BMP4 treatment

source_name: reprogramming cells from E13.5 mouse embryonic fibroblast


title: Cultured mouse CAFs_Sen3


title: Sample 2022-512 technical replicate b

description: Dermal cell after 18 hours after EHV4 infection, sample 2022-512, technical replicate b


title: Kras_Non-sen3

value: Non-Sen


title: Sample 2022-523 technical replicate a

description: Dermal cell after 18 jours after DTB treatment, sample 2022-523, technical replicate a

value: 18 jours after DTB treatment


title: Racemose cysts reads 3

value: subarachnoid cyst


title: Day3 of JGES reprogramming withBMP4 treatment

value: reprogramming cells from E13.5 mouse embryonic fibroblast


title: Sample 2022-512 technical replicate a

description: Dermal cell after 18 hours after EHV4 infection, sample 2022-512, technical replicate a

value: 18 hours after EHV4 infection


title: Day9 of WT_SALL4 induced somatic cell transdifferentiation


title: Racemose cysts reads 2

value: Bladder wall


title: Cultured mouse CAFs_Non-sen5

value: Pancreas


title: Day1 of JGES reprogramming with BMP4 treatment


title: Racemose cysts reads 1


title: Day7 of JGES reprogramming without BMP4 treatment


title: Sample 2022-585 technical replicate b

description: Dermal cell after 18 hours after no treatment, sample 2022-585, technical replicate b

value: 18 hours after no treatment


title: WT4

value: testis

value: wildtype


title: Day5 of JGES reprogramming without BMP4 treatment


title: Sample 2022-585 technical replicate a

description: Dermal cell after 18 hours after no treatment, sample 2022-585, technical replicate a


title: Posterior2

city: Madison

first: Melanie

last: Issigonis

state: WI

address: 330 N. Orchard Street, Newmark Lab

institute: Morgridge Institute for Research

description: 10X Genomics

data_processing:
Cell Ranger software was then used to perform demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression estimation for each sample according to the 10x Genomics documentation (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The gene expression estimates from each sample were then aggregated using Cellranger (cellranger aggr) to compare experimental groups with normalized sequencing-depth and expression data.
Assembly: Sexual S. mediterranea S2F2 genome version SMESG.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Schmidtea mediterranea

source_name: Posterior

growth_protocol: Sexual strain of Schmidtea mediterranea were maintained in 0.75X Montjuïc salts at 18°C, reared on a calf liver puree diet, and starved for 1 week before cell dissociation.

extract_protocol:
Tissue sections from 15-20 planarians were finely diced into small fragments (<1 mm) and transferred to a 15 ml conical with CMFB (Calcium-Magnesium Free solution; 400 mg/L NaH2PO4, 800 mg/L NaCl, 1200 mg/L KCl, 800 mg/L NaHCO3, 1.33 mM glucose, 15 mM HEPES pH 7.3, 1% BSA) supplemented with 10 μg/ml collagenase. Cell dissociations were assisted by mechanical agitation on a nutator with intermittent pipetting. Cells were dissociated for ~10 minutes, passed through a 40-μm filter, and pelleted by centrifugation for 5 minutes at 310 x g. After supernatant removal, the cell pellet was resuspended in 4 ml of CMFB. Cells were incubated in Hoechst 33342 (10 mg/mL) for 45 minutes and then stained with propidium iodide (PI; 10 µg/µL) immediately before sorting on a FACSAria (BD Biosciences).
Library was performed according to the manufacturer’s instructions - 10X Genomics 3’ Single Cell RNA-Seq v3.1 protocol

value: Posterior

value: reproductive organs


title: Cultured mouse CAFs_Sen2


title: Posterior1

description: 10X Genomics


title: Sample 2022-539 technical replicate b

description: Dermal cell after 18 hours after no treatment, sample 2022-539, technical replicate b

value: NBL-6 ATCC


title: Anterior2

description: 10X Genomics

source_name: Anterior

value: Anterior


title: Cultured mouse CAFs_Non-sen3

value: Fibroblasts


title: Sample 2022-539 technical replicate a

description: Dermal cell after 18 hours after no treatment, sample 2022-539, technical replicate a

value: Dermal cell


title: Day5 of JGES reprogramming with BMP4 treatment

first: jin

last: ming

address: 西湖大学

institute: Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.


title: Sample 2022-493 technical replicate b

description: Dermal cell after 18 hours after no treatment, sample 2022-493, technical replicate b


title: Cultured mouse CAFs_Sen1

value: PDAC

value: Sen


title: Day3 of JGES reprogramming without BMP4 treatment


title: Day1 of JGES reprogramming without BMP4 treatment


title: Cultured mouse CAFs_Non-sen1

value: Non-Sen


title: Day0 of JGES reprogramming without BMP4 treatment


title: Huh7 Cells, Pla B (Pla B, + 4sU), REP4

status: Public on Jun 05 2024

city: Nottingham

first: Angela

last: Downie Ruiz Velasco

address: School of Pharmacy, Science Road

country: United Kingdom

institute: University of Nottingham

data_processing:
RNAseq data was processed via the nf-core workflow SLAM-seq (v1.0.0)42 with GRCh38 (GCA 000001405.15) as the reference genome. However, coordinates for 3’UTR features were substituted with those of mature has miRNAs obtained from miRbase (v22)43.
To remove randomized adapters included in the library preparation and to ensure that only mature miRNA sequences were analyzed, reads were trimmed by an additional 4bp at the 3’ ends (--three prime clip R1 4)
Reads were filtered to discard those longer than 30bp (--max length 30) during adapter removal via Trim Galore!, with a further 4bp trimmed from 4’ ends when mapped by SLAM-DUNK (--trim5 4).
Alignment filtering by SLAM-DUNK was also altered to remove the mapping quality threshold (-mq 0) but limit the number of mismatches within a read to three (-nm 3), as was SNP masking for which the minimum alternate allele frequency was reduced to 0.4 (--var fraction 0.4). Otherwise, default SLAM-seq settings were used throughout.
Assembly: GRCh38 (GCA 000001405.15)
Supplementary files format and content: Files provided are comma-separated values (.csv) files include read counts per million (readCPM) and T>C conversion rates (conversionRate) which were the main parameters for analysis. The files also include T content, coverage on T's, conversion on T's, total read count, tc read count and multimap count.

growth_protocol: Huh7 cells were grown in high-glucose DMEM media supplemented with 10% Fetal Bovine Serum (FBS) and non-essential amino acids (NEAA). They were grown in humidity at 37C and 5%CO2.

extract_protocol:
Total RNA was extracted using TRI reagent. 8μg of RNA were then used in an IAA-alkylation reaction, and re-precipitated before library precipitation.
Libraries were prepared with the NEXTflex Small RNA-seq kit, according to manufacturers protocol. Libraries were pooled and size selected by excision from a 3% agarose gel.

treatment_protocol: Huh7 cells grown in 10 cm plates were incubated with either DMSO (Ctrl, DMSO) or 500 μM PlaB (PlaB) for 4 hours. Cells in 'DMSO' and 'PlaB' treatment groups were simultaneously incubated with 500μM 4SU.

value: Hepatocyte cell line

value: Pla B (PlaB, 4SU)


title: Anterior1

description: 10X Genomics


title: Huh7 Cells, Pla B (Pla B, + 4sU), REP3


title: Huh7 Cells, Pla B (Pla B, + 4sU), REP1


title: Cultured mouse CAFs_Non-sen4


title: Huh7 Cells, DMSO (DMSO, + 4sU), REP1

description: Insufficient reads were obtained. Library was re-amplified and new library prepped. Three sequencing runs combined for analysis.

value: DMSO (DMSO, 4SU)


title: Huh7 Cells, Ctrl (DMSO, No 4sU), REP2

value: Control (DMSO, No 4SU)


title: Huh7 Cells, Pla B (Pla B, + 4sU), REP2


title: Huh7 Cells, DMSO (DMSO, + 4sU), REP3


title: Huh7 Cells, Ctrl (DMSO, No 4sU), REP4


title: Huh7 Cells, DMSO (DMSO, + 4sU), REP4


title: Huh7 Cells, Ctrl (DMSO, No 4sU), REP3


title: Huh7 Cells, Ctrl (DMSO, No 4sU), REP1


title: 090352_0121201

city: Madiaon

last: Esnault

state: Wisconsin

address: 600 HIGHLAND AVE

department: Medicine

institute: University of Wisconsin

data_processing:
RNA-seq Analysis and Quality Control FASTQ files were generated by CASAVA (v1.8.2). (Langmead et al., 2009) allowing 2-mismatches and a maximum of 20 multiple hits.
Sequences were filtered and trimmed to remove low quality reads, adaptors, and other sequencing artificats.
Reads were mapped to the human transcriptome (RefGene v1.2.3) using Bowtie (v0.12.8).
The gene expression values TPMs (Transcript per Million Reads) were calculated by RSEM (v1.2.3) (Li and Dewey, 2011).
Assembly: hg19 RefSeq reference “NM_” designated genes and mitochondrial genes.
Supplementary files format and content: Processed data files are both in tab-seperated value format and contain expected counts (ec.tsv) and transcripts per million (tpm.tsv)

source_name: human embryonic stem-cell-derived arterial endothelial cells

growth_protocol: Growth or differentiation medium as described in the assocaited study.

extract_protocol:
The AECs were lysed and harvested using the buffer RLT from a Qiagen RNeasy Kit (Qiagen, Valencia, CA, USA) with β-mercaptoethanol.
The ligation-mediated sequencing protocol was used to prepare and index cDNA libraries (Hou et al 2015).
Sequenced on Illumina NextSeq 2000.

treatment_protocol: On day eight of the differentiation protocol, AECs were exposed for 6 hours to 50% (1 ml) human sera from the pre- and post- product challenge conditions.

tag: sample group

value: Post

value: H9 CPTC C13

value: arterial endothelial


title: 090364_0121213

value: human embryonic stem-cell-derived arterial endothelial cells


title: Huh7 Cells, DMSO (DMSO, + 4sU), REP2


title: 090363_0121212

value: Pre


title: Cultured mouse CAFs_Non-sen2

value: Pancreas


title: 090349_0121198


title: 090347_0121196


title: 090332_0121181


title: 090351_0121200


title: 090328_0121177


title: Sample 2022-493 technical replicate a

description: Dermal cell after 18 hours after no treatment, sample 2022-493, technical replicate a

value: NBL-6 ATCC

value: 18 hours after no treatment


title: 090350_0121199


title: 090333_0121182


title: 090342_0121191


title: 090327_0121176


title: 090346_0121195


title: 090319_0121168


title: 090321_0121170


title: PCLD8, scTCRseq

city: London

first: Gillian

middle: S

last: Tomlinson

address: Gower Street

department: Infection and Immunity

institute: University College London

description: 10x Genomics

data_processing:
library strategy: TCR-seq
Raw sequencing files were demultiplexed using BCL Convert v3.7.5 (Illumina) or Cell Ranger version 6.1.1 using the “mkfastq” script. Transcript alignment and quantitation against the GRCh38 human genome assembly was performed using Cell Ranger “multi” for samples with gene expression and T cell VDJ data or Cell Ranger “count” for samples with gene expression data only.
Assembly: GRCh38
Supplementary files format and content: .h5 files are raw count matrices generated by Cell Ranger count or multi, rows are features and columns are cells; .csv files are TCR contig and clonotype annotations generated by Cell Ranger multi.

source_name: Bronchoalveolar cells

extract_protocol:
Flexible fibreoptic bronchoscopy was used to obtain bronchoalveolar lavage (BAL) samples by instillation of up to 240 ml of warmed normal saline into a lung segment affected by the predominant radiological abnormality. Aspirated BAL fluid was cooled to 4°C and filtered through a cell strainer to remove particulate debris before centrifugation. After removal of the supernatant, cells were resuspended in PBS. Cell count and viability were determined by Trypan blue staining and erythrocytes removed where indicated, using red cell lysis buffer. Cells were resuspended at 2 x10^6 per ml for downstream processing. 20,000 cells per sample were loaded on to the Chromium controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs).
Single-cell partitioning, reverse transcription, cDNA amplification and library construction were performed using the Chromium Single-cell 5’ Reagent kits v1.1 and v2 (10x Genomics) according to the manufacturer’s instructions. T cell receptor (TCR) V(D)J segments were enriched from amplified cDNA using Chromium Single-Cell V(D)J Enrichment kits v1.1 and v2 (10x Genomics) per the manufacturer’s protocol.

value: Bronchoalveolar cells

value: Post-COVID-19 lung disease

tag: radiology

value: Fibrotic


title: PCLD12, scTCRseq

description: 10x Genomics

value: Inflammatory


title: PCLD13, scTCRseq

description: 10x Genomics


title: PCLD9, scTCRseq

description: 10x Genomics


title: PCLD6, scTCRseq

description: 10x Genomics


title: PCLD13, scRNAseq

description: 10x Genomics

data_processing:
Raw sequencing files were demultiplexed using BCL Convert v3.7.5 (Illumina) or Cell Ranger version 6.1.1 using the “mkfastq” script. Transcript alignment and quantitation against the GRCh38 human genome assembly was performed using Cell Ranger “multi” for samples with gene expression and T cell VDJ data or Cell Ranger “count” for samples with gene expression data only.
Assembly: GRCh38
Supplementary files format and content: .h5 files are raw count matrices generated by Cell Ranger count or multi, rows are features and columns are cells; .csv files are TCR contig and clonotype annotations generated by Cell Ranger multi.


title: PCLD5, scTCRseq

description: 10x Genomics


title: PCLD7, scTCRseq

description: 10x Genomics


title: PCLD4, scTCRseq

description: 10x Genomics


title: PCLD6, scRNAseq

description: 10x Genomics


title: PCLD5, scRNAseq

description: 10x Genomics


title: PCLD4, scRNAseq

description: 10x Genomics


title: 090343_0121192


title: PCLD3, scRNAseq

description: 10x Genomics


title: PCLD1, scRNAseq

description: 10x Genomics


title: CWR-22Rv1_CSS_siARV7_rep3

first: Maryam

last: Labaf

address: 100 William T Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

description:
22Rv1_5CSS_siV7_rep3
22RV1_count.txt

data_processing:
Raw reads were processed for quality control using fastqc (v.0.11.5)
Raw reads were aligned to Ensembl, GRCh37 using STAR (v2.5.3a)
Gene level read counts was produced by featureCounts from Subread (v1.6.2) package
Assembly: Ensembl GRCH37
Supplementary files format and content: tab-deliminated text files include raw gene counts

growth_protocol: LN-tet-ARV7, LN-tet-ARV7-S81A and AR-Cu-ARV567es cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
TruSeq® Strnd Total RNA LT (Illumina) was used for RNA-Seq library construction.

treatment_protocol: LN-tet-ARV7, LN-tet-ARV7-S81A and AR-Cu-ARV567es cells were grown in 5%CSS and treated with or without doxycycline for 2 days for AR-V7 transcriptome analyses or cumate for 2 days for AR-V567es transcriptome analyses. CWR-22RV1 cells were transfected with siRNAs agaisnt NTC or AR-V7 for 3 days.

value: Prostate Cancer Cell Line


title: CWR-22Rv1_CSS_siARV7_rep2

description:
22Rv1_5CSS_siV7_rep2
22RV1_count.txt


title: 090320_0121169


title: CWR-22Rv1_CSS_siARV7_rep1

description:
22Rv1_5CSS_siV7_rep1
22RV1_count.txt


title: CWR-22Rv1_CSS_siNTC_rep2

description:
22Rv1_5CSS_siNTC_rep2
22RV1_count.txt

value: siNTC


title: CWR-22Rv1_CSS_siNTC_rep1

description:
22Rv1_5CSS_siNTC_rep1
22RV1_count.txt


title: 090318_0121167


title: LN-tet-ARV7-S81A_CSS_Dox_rep3

description:
LN-tet-ARV7-S81_Dox_rep3
LN-tet-ARV7-S81A_count.txt

value: Prostate Cancer Cell Line (generated from LNCaP)

value: Doxycycline


title: LN-tet-ARV7-S81A_CSS_Dox_rep2

description:
LN-tet-ARV7-S81_Dox_rep2
LN-tet-ARV7-S81A_count.txt


title: LN-tet-ARV7-S81A_CSS_Dox_rep1

description:
LN-tet-ARV7-S81_Dox_rep1
LN-tet-ARV7-S81A_count.txt


title: PCLD12, scRNAseq

description: 10x Genomics


title: Thyroid – HT2

description: OCT frozen Visium spatial gene expression sequencing

value: Thyroid

value: Hashimoto's thyroiditis


title: LN-tet-ARV7-S81A_CSS_Veh_rep2

description:
LN-tet-ARV7-S81_Veh_rep2
LN-tet-ARV7-S81A_count.txt

value: Vehicle


title: CWR-22Rv1_CSS_siNTC_rep3

description:
22Rv1_5CSS_siNTC_rep3
22RV1_count.txt


title: LN-tet-ARV7_CSS_Dox_rep1

description:
LN-tet-ARV7_Dox_rep1
LN-tet-ARV7_count.txt


title: LN-tet-ARV7_CSS_Veh_rep1

description:
LN-tet-ARV7_Veh_rep1
LN-tet-ARV7_count.txt


title: LN-tet-ARV7_CSS_Dox_rep2

description:
LN-tet-ARV7_Dox_rep2
LN-tet-ARV7_count.txt


title: ChIP-H3K27ac_LN-tet-ARV7_CSS_Dox_rep2

description:
ChIP-H3K27ac_LN-tet-ARV7_CSS_Dox.narrowPeak
ChIP-H3K27ac_LN-tet-ARV7_CSS_Dox.bw

data_processing:
The sequence quality of raw reads was checked by FastQC (v.0.11.5).
The replicate of raw reads of each sample merged and mapped to the hg19 human genome using bwa (v0.7.5a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS3 (v3.0.0a6) was used to call peak on the bam files.
The bedGraph files from MACS were converted into bigwig files using UCSC tools (version 372)
Assembly: Human hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: LN-tet-ARV7, LN-tet-ARFL and LN-tet-ARV7-S81A cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days

extract_protocol:
Cells were crosslinked with formaldehyde and then sonicated. DNA were immunoprecipitatted with V5, FOXA1, H3K27ac or AR-C antibody and protein A beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
ChIP DNA Library were prepared with NEBNext ChIP-Seq Library Prep Reagent set for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1)

treatment_protocol: LN-tet-ARV7, LN-tet-ARFL and LN-tet-ARV7-S81A cells were grown in 5%CSS (hormone-depelted) and treated with doxycycline for 2 days for ChIP V5, FOXA1 and H3K27ac, and stimulated with DHT for 4 hours for AR-C ChIP.

tag: antibody

value: doxycycline in 5 percent CSS


title: ChIP-H3K27ac_LN-tet-ARV7_CSS_Veh_rep2

description:
ChIP-H3K27ac_LN-tet-ARV7_CSS_Veh.narrowPeak
ChIP-H3K27ac_LN-tet-ARV7_CSS_Veh.bw

value: vehicle in 5 percent CSS


title: ChIP-FOXA1_LN-tet-ARV7_CSS_Dox_rep2

description:
ChIP-FOXA1_LN-tet-ARV7_CSS_Dox.narrowPeak
ChIP-FOXA1_LN-tet-ARV7_CSS_Dox.bw


title: ChIP-H3K27ac_LN-tet-ARV7_CSS_Veh_rep1


title: ChIP-FOXA1_LN-tet-ARV7_CSS_Dox_rep1


title: LN-tet-ARV7_CSS_Veh_rep2

description:
LN-tet-ARV7_Veh_rep2
LN-tet-ARV7_count.txt


title: ChIP-ARC_LN-tet-ARV7_CSS_DHT+Dox_rep2

description:
ChIP-ARC_LN-tet-ARV7_CSS_Dox_DHT.narrowPeak
ChIP-ARC_LN-tet-ARV7_CSS_Dox_DHT.bw

value: ARC

value: doxycycline, 10nM DHT in 5 percent CSS


title: ChIP-FOXA1_LN-tet-ARV7_CSS_Veh_rep2

description:
ChIP-FOXA1_LN-tet-ARV7_CSS_Veh.narrowPeak
ChIP-FOXA1_LN-tet-ARV7_CSS_Veh.bw


title: ChIP-FOXA1_LN-tet-ARV7_CSS_Veh_rep1


title: ChIP-ARC_LN-tet-ARV7_CSS_DHT_rep1

description:
ChIP-ARC_LN-tet-ARV7_CSS_DHT.narrowPeak
ChIP-ARC_LN-tet-ARV7_CSS_DHT.bw

value: 10nM DHT in 5 percent CSS


title: ChIP-ARC_LN-tet-ARV7_CSS_DHT_rep2


title: ChIP-ARC_LN-tet-ARV7_CSS_Dox_rep2

description:
ChIP-ARC_LN-tet-ARV7_CSS_Dox.narrowPeak
ChIP-ARC_LN-tet-ARV7_CSS_Dox.bw


title: ChIP-ARC_LN-tet-ARV7_CSS_Dox_rep1


title: ChIP-ARC_LN-tet-ARV7_CSS_DHT+Dox_rep1


title: ChIP-ARC_LN-tet-ARV7_CSS_Veh_rep1

description:
ChIP-ARC_LN-tet-ARV7_CSS_Veh.narrowPeak
ChIP-ARC_LN-tet-ARV7_CSS_Veh.bw


title: ChIP-V5_LN-tet-ARV7-S81A_CSS_Dox_rep2

description:
ChIP-V5_LN-tet-ARV7-S81A_CSS_Dox.narrowPeak
ChIP-V5_LN-tet-ARV7-S81A_CSS_Dox.bw


title: LN-tet-ARV7_CSS_Dox_rep3

description:
LN-tet-ARV7_Dox_rep3
LN-tet-ARV7_count.txt


title: LN-tet-ARV7-S81A_CSS_Veh_rep3

description:
LN-tet-ARV7-S81_Veh_rep3
LN-tet-ARV7-S81A_count.txt


title: LN-tet-ARV7-S81A_CSS_Veh_rep1

description:
LN-tet-ARV7-S81_Veh_rep1
LN-tet-ARV7-S81A_count.txt


title: LN-tet-ARV7_CSS_Veh_rep3

description:
LN-tet-ARV7_Veh_rep3
LN-tet-ARV7_count.txt


title: ChIP-V5_LN-tet-ARV7-S81A_CSS_Dox_rep1


title: ChIP-V5_LN-tet-ARV7-S81A_CSS_Veh_rep2

description:
ChIP-V5_LN-tet-ARV7-S81A_CSS_Veh.narrowPeak
ChIP-V5_LN-tet-ARV7-S81A_CSS_Veh.bw


title: ChIP-V5_LN-tet-ARV7-S81A_CSS_Veh_rep1


title: ChIP-V5_LN-tet-ARV7_CSS_Dox_rep1

description:
ChIP-V5_LN-tet-ARV7_CSS_Dox.narrowPeak
ChIP-V5_LN-tet-ARV7_CSS_Dox.bw


title: ChIP-H3K27ac_LN-tet-ARV7_CSS_Dox_rep1


title: ChIP-V5_LN-tet-ARV7_CSS_Dox_rep2


title: ChIP-V5_LN-tet-ARV7_CSS_Veh_rep1

description:
ChIP-V5_LN-tet-ARV7_CSS_Veh.narrowPeak
ChIP-V5_LN-tet-ARV7_CSS_Veh.bw


title: ChIP-V5_LN-tet-ARV7_CSS_Veh_rep2


title: ATAC_LN-tet-ARV7_CSS_DHT+Dox_rep2

description:
ATAC_LN-tet-ARV7_CSS_DHT_Dox.narrowPeak
ATAC_LN-tet-ARV7_CSS_DHT_Dox.bw

growth_protocol: LN-tet-ARV7 cells are cultured routinely in 10% tetracycline-free FBS containing RPMI1640 and passed every 5-6 days

extract_protocol:
Around 50,000 LN-tet-ARV7 cells treated with or without doxycycline or DHT were collected and lysed. Nuclei were collected and treated with transposase using Illumina Tagment DNA TDE1 Enzyme and Buffer Kit. DNA samples were then cleaned immediately with a Qiagen QIAquick Purification Kit and PCR preamplified by NEBNext High-Fidelity 2× PCR Master Mix. qPCR amplification was used to determine the additional cycles to prevent overamplification. The final PCR product was purified by Qiagen QIAquick Purification Kit.
ATAC-seq DNA Library were prepared with NEBNext ChIP-Seq Library Prep Reagent set for Illumina

treatment_protocol: LN-tet-ARV7 cells were grown in 5%CSS and treated with or without doxycycline for 2 days and stimulated with or without DHT.


title: ATAC_LN-tet-ARV7_CSS_DHT_rep2

description:
ATAC_LN-tet-ARV7_CSS_DHT.narrowPeak
ATAC_LN-tet-ARV7_CSS_DHT.bw


title: ATAC_LN-tet-ARV7_CSS_DHT_rep1


title: ATAC_LN-tet-ARV7_CSS_DHT+Dox_rep1


title: ATAC_LN-tet-ARV7_CSS_Dox_rep2

description:
ATAC_LN-tet-ARV7_CSS_Dox.narrowPeak
ATAC_LN-tet-ARV7_CSS_Dox.bw


title: ATAC_LN-tet-ARV7_CSS_Dox_rep1


title: ATAC_LN-tet-ARV7_CSS_Veh_rep2

description:
ATAC_LN-tet-ARV7_CSS_Veh.narrowPeak
ATAC_LN-tet-ARV7_CSS_Veh.bw


title: ChIP-ARC_LN-tet-ARV7_CSS_Veh_rep2


title: Apoe-/-Lmna+/+_pool 4 (wild-type control)

city: Oviedo

first: Magda

middle: Rita

last: Hamczyk

state: Asturias

address: C/ Fernando Bongera S/N, Edificio Santiago Gascon

department: Biochemistry and Molecular Biology

institute: Universidad de Oviedo

data_processing:
Library adaptors were removed from sequencing reads using Trim Galore (v0.6.10) with Cutadapt (v4.1)
Trimmed reads were aligned to the GRCm38 version (gene build 102) of the mouse genome using STAR (v2.7.10b). A filtered reference gene set was created with protein-coding and lncRNA genes only. Gene metadata were obtained from the corresponding Ensembl BioMart archive.
With the aligned reads and the filtered reference set, we obtained expected counts per gene using RSEM (v1.2.28).
Expected counts were log2 transformed (pseudocount = 0.5) using Voom and normalized by the trimmed mean of M-value method.
Assembly: GRCm38
Supplementary files format and content: Expected counts per gene (using RSEM) for each sample.
Supplementary files format and content: Expected counts per gene, log2 transformed and normalized using Voom, for each sample.

source_name: aortic intima

extract_protocol:
The aorta was excised from each mouse immediately after sacrifice and transcardiac perfusion with sterile PBS. After the removal of fatty tissue, the aortic arch was removed, and QIAzol reagent (79306, Qiagen) was slowly passed through the lumen of the thoracic aorta to lyse the intima. The tissue lysate was collected in an RNase-free 1.5 mL tube placed beneath the aorta. The intima lysate was frozen and stored at −80°C until RNA extraction. Intima samples were pooled from 12–14 animals of the same genotype. Total RNA was extracted using the miRNeasy Micro kit (217084, Qiagen). To avoid DNA contamination, an on-column digestion step using DNase I (79254, Qiagen) was added to the protocol.
Total RNA (100 ng) from mouse intima samples was used to generate barcoded libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, New England Biolabs). Polyadenylated RNA was first obtained using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) and then fragmented. Following first and second cDNA strand synthesis, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated, followed by second strand removal, uracil excision from the adaptor, and PCR amplification.

value: aortic intima

value: Apoe-/-Lmna+/+


title: Apoe-/-LmnaG609G/G609G_pool 1 (ubiquitous progerin expression)


title: Apoe-/-Lmna+/+_pool 2 (wild-type control)


title: Apoe-/-Lmna+/+_pool 1 (wild-type control)


title: Apoe-/-Lmna+/+_pool 3 (wild-type control)


title: Apoe-/-LmnaG609G/G609G_pool 3 (ubiquitous progerin expression)


title: Apoe-/-LmnaG609G/G609G_pool 2 (ubiquitous progerin expression)


title: Sample 2022-579 technical replicate a

description: Dermal cell after 18 jours after EHV4 infection and DTB treatment, sample 2022-579, technical replicate a

value: NBL-6 ATCC

value: Dermal cell


title: Apoe-/-LmnaLCS/LCS SM22Cre_pool 3 (VSMC-specific progerin expression)

value: Apoe-/-LmnaLCS/LCS SM22Cre


title: ATAC_LN-tet-ARV7_CSS_Veh_rep1


title: Apoe-/-LmnaLCS/LCS SM22Cre_pool 2 (VSMC-specific progerin expression)


title: Apoe-/-LmnaLCS/LCS_pool 4 (lamin C only control)

value: Apoe-/-LmnaLCS/LCS


title: Apoe-/-LmnaLCS/LCS_pool 3 (lamin C only control)


title: Apoe-/-LmnaLCS/LCS SM22Cre_pool 1 (VSMC-specific progerin expression)


title: Apoe-/-LmnaLCS/LCS_pool 2 (lamin C only control)


title: input_HA1_R

city: Bethesda

first: Joana

middle: A

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

data_processing:
Processed reads were mapped to the mm10 genome with STAR v2.7.9a with the parameters ‘STAR –readFilesIn Processed_sample.fastq.gz –genomeDir mm10 –runThreadN 12 –genomeLoad LoadAndRemove –limitBAMsortRAM 20000000000 –readFilesCommand zcat –outSAMtype BAM SortedByCoordinate –outReadsUnmapped Fastx –outFilterMismatchNmax 1 –outFilterMismatchNoverLmax 1 –outFilterMismatchNoverReadLmax 1 –outFilterMatchNmin 16 –outFilterMatchNminOverLread 0 –outFilterScoreMinOverLread 0 –outFilterMultimapNmax 5000 –winAnchorMultimapNmax 5000 –seedSearchStartLmax 30 –alignTranscriptsPerReadNmax 30000 –alignWindowsPerReadNmax 30000 –alignTranscriptsPerWindowNmax 300 –seedPerReadNmax 3000 –seedPerWindowNmax 300 –seedNoneLociPerWindow 1000 –outFilterMultimapScoreRange 0 –alignIntronMax 1 –alignSJDBoverhangMin 999999999999,’ as previously described for transposons119. Duplicates of mapped reads were removed on the basis of the UMI sequence using umitools, and fastq files were generated from deduplicated mapped reads using samtools v1.15 (ref.120). Subsequently, fastq files from deduplicated reads were re-mapped. Initially, they were mapped to known noncoding RNA sequences annotated in Ensemble (including miRNAs, rRNAs, small nucleolar RNAs, small nuclear RNAs, and tRNAs). Reads that did not map to these elements were then re-mapped against the consensus sequence of mouse retrotransposon elements, as described above. These consensus sequences were downloaded from the SalmonTE github repository
Assembly: mm10
Supplementary files format and content: count table

source_name: Spleen

extract_protocol:
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Cells were activated in vitro to induce proliferation. AGO2 was immunopercipitated using an antibody against its HA epitope after which RNA was extracted and small RNA libraries prepared. The experiment was also performed in cells from animals not expressing the HA epitope, but no RNA was recovered. Therefore, libraries from those experiments were not prepared.
8 microRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using QIAseq miRNA Library Prep and single-end sequencing
small RNA seq

value: Spleen

value: Resting B cells


title: input_HA2_R


title: Apoe-/-LmnaLCS/LCS_pool 1 (lamin C only control)


title: input_HA2_P

value: Proliferating B cells


title: IP_HA1_R


title: IP_HA2_R


title: input_HA1_P


title: IP_HA1_P


title: IP_HA2_P


title: Batch4_SST_HC_rep3

city: La Jolla

first: Anton

last: Maximov

state: CA

address: 10550 North Torrey OPines Rd

department: Neuroscince

institute: Scripps Research

description:
6
Batch4_RawGeneCounts.txt

data_processing:
The reads were trimmed from adapter sequences using cutadapt 1.18 with Python 3.6.3. The trimmed reads were mapped to the reference genome using the STAR aligner 2.5.2a and gene abundance was estimated with python 2.7.11, and HTSeq 0.11.0. Differential expression analysis was performed in the R package DESeq2. DESeq2 first adjusts read counts based on a normalization factor that accounts for sample size. This was followed by dispersion estimates based on a negative binomial model which accounts for genes with very few counts. Finally, the Wald test was performed to test for statistical significance. Genes with adjusted p-values (padj) of <0.05 were identified as differentially expressed. To remove genes with high fold changes due to low expression, a minimum normalized expression level (basemean) filter of 50 was added. The filtered data were used to generate volcano plots and heatmaps.
Assembly: mm10 for Batch1 and 2,  GRCm39 for Batch3, 4 and 5.
Supplementary files format and content: Tab-delimited TXT files includes raw counts for each sample

source_name: Cortex and hippocampus

extract_protocol:
Isolation of mRNA with RiboTag:
Cortices of p60 PvalbCre/RiboTag and SstCre/RiboTag mice were dissected in ice-cold PBS and homogenized in the buffer containing 100 mM KCl, 50 mM Tris-HCl pH 7.4, 12 mM MgCl2, 100 g/ml cycloheximide (Sigma), 1 mg/ml heparin (Sigma), 1x complete mini, EDTA-free protease inhibitor cocktail (Roche), 200 units/ml RNasin© plus inhibitor (Promega) and 1 mM DTT (Sigma) (500 µl ~3% w/v). The lysate was centrifuged at 2,000g for 10 minutes at 4°C. Igepal-CA380 was then added to the supernatant at the final concentration of 1%. The lysate was briefly incubated on ice and then centrifuged at 12,000g for 10 minutes at 4°C. 25 µl of the supernatant was collected as input sample. 30 µl/ml of anti-HA coupled magnetic beads (Pierce) were then added to the remaining supernatant. Incubation was performed on a rotator for 3 hours at 4°C. The beads were washed four times in the high salt buffer containing 350 mM KCl, 1% Igepal-CA380, 50 mM Tris-HCl, pH7.4, 12 mM MgCl2, 100 µg/ml Cycloheximide (Sigma) and 1 mM DTT (Sigma). Ribosomes were eluted in 350 µl of RLT plus buffer (Qiagen). RNA purification was performed using RNeasy Plus Mini kit (Qiagen) following the manufacturers’ instructions. For qPCR, 20 ng of total RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). qPCR quality controls were performed with the following primers:                                                                                Fos
Forward: 5′- GGGACAGCCTTTCCTACTACC-3′
Reverse: 5′- AGATCTGCGCAAAAGTCCTG-3′
Nr4a1
Forward: 5′- TTGAGTTCGGCAAGCCTACC-3′
Reverse: 5′- GTGTACCCGTCCATGAAGGTG-3′
Gapdh
Forward: 5′- TCAACGGGAAGCCCATCA-3′
Reverse: 5′- CTCGTGGTTCACACCCATCA-3′
Syt2
Forward: 5′- AGAACCTGGGCAAATTGCAGT-3′
Reverse: 5′- CCTAACTCCTGGTATGGCACC-3′
Pvalb
Forward: 5′- CATTGAGGAGGATGAGCTG-3′
Reverse: 5′- AGTGGAGAATTCTTCAACCC-3′
Lhx6
Forward: 5′- CTACTTCAGCCGATTTGGAACC-3′
Reverse: 5′- GCAAAGCACTTTCTCCTCAACG-3′
RNA-seq was performed at the TSRI Next Generation Sequencing Core on the Illumina HiSeq platform. The libraries were generated, barcoded, and sequenced according to the manufacturers’ recommendations.
Sequencing libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

value: Cortex and hippocampus

value: C57/BL6 mouse

value: SST+ neuron

value: Homecage


title: Batch5_SSTN_HC_rep2

description:
92
Batch5_RawGeneCounts.txt


title: Batch4_SST_CFC_rep3

description:
5
Batch4_RawGeneCounts.txt

value: CFC


title: Batch5_SSTN_HC_rep3

description:
93
Batch5_RawGeneCounts.txt


title: Batch5_SSTN_HC_rep1

description:
91
Batch5_RawGeneCounts.txt


title: Batch4_SST_HC_rep2

description:
4
Batch4_RawGeneCounts.txt


title: Batch4_SST_CFC_rep2

description:
3
Batch4_RawGeneCounts.txt


title: Batch4_SST_CFC_rep1

description:
2
Batch4_RawGeneCounts.txt


title: Batch4_SST_HC_rep1

description:
1
Batch4_RawGeneCounts.txt


title: Batch3_PVNR_Rep3

description:
12
Batch3_RawGeneCounts.txt

value: PV+ neuron


title: Batch3_PVNR_Rep1

description:
7
Batch3_RawGeneCounts.txt


title: Batch3_PVR_HC_Rep3

description:
5
Batch3_RawGeneCounts.txt


title: Batch3_PVR_HC_Rep2

description:
4
Batch3_RawGeneCounts.txt


title: Batch3_PVR_HC_Rep1

description:
2
Batch3_RawGeneCounts.txt


title: Batch3_PVR_CFC_Rep2

description:
3
Batch3_RawGeneCounts.txt


title: Batch3_PVNR_Rep2

description:
9
Batch3_RawGeneCounts.txt


title: Batch3_PVR_CFC_Rep1

description:
1
Batch3_RawGeneCounts.txt


title: Batch3_PVR_CFC_Rep3

description:
6
Batch3_RawGeneCounts.txt


title: Batch2_PVR_Saline_Rep1

description:
NS68_M9
Max_NS68_raw.txt

value: Saline