title: D53, RNA-seq

value: proliferative zone of the acetabular cartilage

value: DDH

value: five days after birth


title: HFD-112

status: Public on Apr 03 2024

type: SRA

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

department: Institute of Experimental Genetics (IEG)

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic

data_processing:
Data quality was assessed with MultiQC (version 1.11). Paired-end RNA-seq reads were processed with trim_galore (version 0.6.6) to remove Nextera adaptors. Reads were subsequently mapped to the mouse genome (GRCm38),  using STAR (version  2.7.10a). We then used featurecounts to calculate counts for the total transcripts. Differential expression analysis was performed using DESeq2 package. Uniquely mapped reads were extracted from the BAM files using samtools. These files were used to estimate mtDNA heteroplasmy using MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) a R package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Early 2-cell embryo

extract_protocol:
Early 2 cell embryo have been procsessed according to the SMARTseq2 protocol
Single early 2-cell embryos from the HFD and LFD groups were collected for RNA sequencing. A cDNA library was generated according to the Smart-seq2 protocol (Picelli et al., 2014) without any modifications.

tag: cell type

value: Early 2-cell embryo

tag: genotype

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

tag: treatment

value: High Fat Diet


title: 1377-CD-37

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

country: USA

institute: University of Michigan

data_processing:
STAR alignment
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: read count

organism: Homo sapiens

source_name: Skin

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

tag: tissue

value: Skin

value: Fibroblasts

tag: patient

value: NoStim

tag: disease state

value: Control


title: mixed cells, Parkin_1659_N3

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

data_processing:
Reads were mapped to the mm10 mouse genome merged with eGFP and ERCC spike-in sequences using STAR v2.3.0 with default settings and filtered for uniquely mapping reads.
Read counts and RPKM per gene were computed using rpkmforgenes.py with default settings and Ensembl release 75 gene annotations with addition of the EGFP reporter sequence.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file containing number of mapped reads per gene for all samples.
Supplementary files format and content: A tab-delimited text file containing RPKM per gene for all samples.

source_name: midbrain

extract_protocol:
FACS
smart-seq2

treatment_protocol: Tamoxifen injection

value: midbrain

value: mixed cells

value: Parkin loxP/loxP; +/DatCreERT2

tag: facs population

value: mitoYFP-negative

value: Tamoxifen injection

tag: mouse id

tag: technical replicate

tag: time point

value: 5 weeks after tamoxifen injection

tag: sequencing year


title: D52, RNA-seq

city: Hangzhou

first: Jiahui

last: Liu

state: Zhejiang

address: 3333 Binsheng Rd

country: China

institute: Children's Hospital, Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match were further analyzed and annotated based on the reference genome. HISAT2 soft were used to map with reference genome.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: Rnor_6.0
Supplementary files format and content: TXT files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: proliferative zone of the acetabular cartilage

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
Library preparation for mRNA sequencing: A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library preparation for miRNA sequencing: A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for IlluminaR(NEB, USA) folloing manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: time


title: D51, RNA-seq


title: mixed cells, Parkin_1659_N2


title: HFD-111


title: HFD-110


title: N53, RNA-seq

value: control


title: 1377-CD-33

value: IFNA

value: Lupus


title: HFD-109


title: 1377-CD-32

value: TNF-A


title: N52, RNA-seq

value: proliferative zone of the acetabular cartilage

value: five days after birth


title: mixed cells, Parkin_1659_N1


title: 1377-CD-31

value: TGF-B


title: DA neurons, Parkin_1639_P6

value: DA neurons

value: mitoYFP-positive


title: N51, RNA-seq


title: DA neurons, Parkin_1639_P5


title: 1377-CD-25

value: Skin

value: Fibroblasts

value: NoStim


title: HFD-107

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: HFD-108


title: 1377-CD-21


title: streptozocin-induced diabetic rats 2

city: Fuzhou

first: Jianzhang

last: Hu

state: Fujian

address: No.11 xinquan Road, Gulou District

institute: Fujian Medical University Union Hospital

data_processing:
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used Bowtie2 and Hisat2to map reads to the genome from corneal epithelium of streptozocin-induced diabetic and non-diabetic control rats.
The mapped reads of each sample were assembled using String Tie.
Then, all transcriptomes from corneal epithelium Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: corneal epithlium

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: Male Brown Norway rats weighing 150-200 g from Slaccas, China, were used in this study. Streptozocin (STZ, Sigma-Aldrich, USA) was administered by a single intraperitoneal injection at 50 mg/kg to induce diabetes in rats, while citrate buffer was injected for the control group. Glucose blood readings (Ascencia Contour Glucometer, Bayer Diabetes Care, USA) above 16.67 mmol/l were considered diabetic models in this study.

value: corneal epithlium

tag: cell line

value: Not applicable

value: Diabetic

value: STZ-induced


title: HFD-105


title: 1377-CD-34

value: IFNG

value: Lupus


title: streptozocin-induced diabetic rats 3


title: N52, miRNA-seq

value: proliferative zone of the acetabular cartilage

value: control


title: HFD-106


title: DA neurons, Parkin_1639_P4

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2

value: Tamoxifen injection

value: 5 weeks after tamoxifen injection


title: 1377-CD-20

value: Skin

value: Fibroblasts

value: TNF-A


title: DA neurons, Parkin_1639_P3

value: DA neurons

value: mitoYFP-positive


title: streptozocin-induced diabetic rats 1

value: corneal epithlium


title: HFD-90

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: non-diabetic control rats 3

value: Not applicable

value: Normal

value: Non


title: HFD-89


title: DA neurons, Parkin_1639_P1


title: non-diabetic control rats 2


title: HFD-88


title: DA neurons, Parkin_1639_P2


title: mixed cells, Parkin_1639_N5

value: mixed cells

value: mitoYFP-negative


title: 1377-CD-19

value: TGF-B

value: Lupus


title: HFD-86


title: mixed cells, Parkin_1639_N4

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2

value: Tamoxifen injection

value: 5 weeks after tamoxifen injection


title: non-diabetic control rats 1


title: longissimus dorsi, 44_ULU

city: Lisboa

first: David

middle: Miguel

last: Ribeiro

state: Lisboa

address: Tapada da Ajuda

department: Secção de Produção Animal

country: Portugal

institute: Instituto Superior de Agronomia

data_processing:
Raw data was analyzed using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, accessed 30/03/2023), fastp tool and hisat2 tool (http://daehwankimlab.github.io/hisat2/, accessed 30/03/2023), using the Sus scrofa genome as a reference for read alignment.
Gene expression values were quantified using the FeatureCounts program implemented in Subread software (version 1.5.1). Three comparisons were computed (UL vs control, ULU vs control, and ULU vs UL) using DESeq2 (version 1.34.0) with an adjusted P-value of 0.05 and log2(fold change) threshold of -1 and 1.
Assembly: Sus_scrofa.Sscrofa11.1.dna.toplevel
Supplementary files format and content: comma separated value (.csv) file containing raw reads per sample

organism: Sus scrofa

source_name: longissimus dorsi

extract_protocol:
RNA was isolated from muscle samples of 6 randomly chosen piglets from control, UL and ULU groups. Muscle RNA was extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy mini kit (Qiagen, Hilden, Germany), respectively. Sample DNA was then digested with a treatment of DNAse I (Qiagen, Hilden, Germany), following the manufacturer’s instructions. RNA quantification was done using a spectrophotometer (Nanodrop ND-2000c, NanoDrop, Thermo Fisher Scientific, Willmington, DE, USA). Quality control was carried out on a Fragment Analyser (Agilent Technologies, Santa Clara, CA, USA), using High Sensitivity RNA Analysis Kit (Agilent Technologies, Santa Clara, CA, USA).
cDNA was obtained from 1 µg of RNA samples, using the cDNA Library Construction Kit (Clontech, San Jose, CA, USA), according to the manufacturer’s instructions. RNA libraries were then prepared using adapted protocols. Libraries were sequenced on an Illumina NextSeq500 Sequencer (Illumina, San Diego, CA, USA) using a 75 SE high throughput kit.

value: longissimus dorsi

value: ULU


title: HFD-59


title: 1330-CD-9

value: Skin

value: Fibroblasts

value: IFNA

value: Control


title: mixed cells, Parkin_1639_N3


title: 1377-CD-10

value: IFNG

value: PSLE


title: longissimus dorsi, 43_ULU


title: longissimus dorsi, 42_ULU


title: HFD-31

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: mixed cells, Parkin_1639_N2

value: mixed cells

value: mitoYFP-negative


title: 1330-CD-8

value: TNF-A


title: mixed cells, Parkin_1639_N1

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2


title: 1330-CD-7

value: TGF-B


title: HFD-32


title: 1377-CD-1

value: NoStim


title: longissimus dorsi, 41_ULU

value: longissimus dorsi

value: ULU


title: DA neurons, Parkin_1608_P6

value: DA neurons

value: mitoYFP-positive

value: Tamoxifen injection

value: 5 weeks after tamoxifen injection


title: HFD-30


title: 1330-CD-46

value: Skin

value: Fibroblasts

value: IFNG

value: Lupus


title: HFD-26

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: 1377-CD-13


title: DA neurons, Parkin_1608_P5

value: midbrain


title: longissimus dorsi, 40_ULU


title: longissimus dorsi, 32_UL

value: UL


title: DA neurons, Parkin_1608_P4

value: Parkin loxP/loxP; +/DatCreERT2


title: HFD-25


title: 1330-CD-44

value: TNF-A


title: 1330-CD-45

value: IFNA


title: DA neurons, Parkin_1608_P3


title: longissimus dorsi, 31_UL

value: longissimus dorsi


title: 1330-CD-43

value: TGF-B


title: HFD-20


title: 1330-CD-37

value: NoStim


title: DA neurons, Parkin_1608_P2

value: DA neurons

value: mitoYFP-positive

value: Tamoxifen injection


title: longissimus dorsi, 29_UL


title: longissimus dorsi, 30_UL


title: 1330-CD-34

value: Skin

value: Fibroblasts


title: DA neurons, Parkin_1608_P1

value: 5 weeks after tamoxifen injection


title: HFD-18

value: Early 2-cell embryo


title: 1330-CD-33

value: Lupus


title: HFD-19

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: longissimus dorsi, 27_UL

value: UL


title: longissimus dorsi, 28_UL


title: mixed cells, Parkin_1608_N5

value: midbrain

value: mixed cells

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-negative


title: HFD-17


title: 1330-CD-32

value: TNF-A


title: longissimus dorsi, 26_Control

value: longissimus dorsi

value: Control


title: mixed cells, Parkin_1608_N3


title: mixed cells, Parkin_1608_N4


title: 1330-CD-31

value: TGF-B


title: longissimus dorsi, 25_Control


title: HFD-13


title: HFD-22


title: mixed cells, Parkin_1608_N2

value: Tamoxifen injection


title: longissimus dorsi, 24_Control


title: HFD-8


title: mixed cells, Parkin_1608_N1


title: 1330-CD-22

value: Skin

value: IFNG


title: HFD-7


title: longissimus dorsi, 23_Control


title: 1330-CD-21

value: Fibroblasts

value: IFNA


title: DA neurons, Parkin_1601_P6

value: DA neurons

value: mitoYFP-positive

value: 5 weeks after tamoxifen injection


title: HFD-6

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: High Fat Diet


title: longissimus dorsi, 22_Control


title: DA neurons, Parkin_1601_P5

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2


title: DA neurons, Parkin_1601_P4


title: 1330-CD-1

value: NoStim


title: HFD-16


title: longissimus dorsi, 21_Control

value: longissimus dorsi


title: 1330-CD-20

value: TNF-A

value: Lupus


title: HD; 20 2ary Auditory Anterior (BA21a)

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

data_processing:
Read trimming (paired-end ): trimmomatic-0.36 PE -phred33 ILLUMINACLIP:all.fa:2:30:10:2:true SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:20
Read trimming (single): trimmomatic-0.36 SE -phred33 ILLUMINACLIP:all.fa:2:30:10:2:true SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:20
Read alignment (paired-end ): hisat2 --no-softclip --max-intronlen 1000000 -k 20 –no-unal -q
Read alignment  (single): hisat2 --no-softclip --max-intronlen 1000000 -k 20 –no-unal -q -U
Abundance estimation: stringtie -e -A -G -b; Python script prepDE.py was used to generate read counts from the files generated by StringTie
Assembly: Ensemble genomes and annotation were used for all species: GRCh38.91
Supplementary files format and content: csv files with counts for all samples

molecule: polyA RNA

source_name: brain

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, California).
Sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit (Illumina) according to manufacturer’s instruction. Briefly, poly-T oligo-attached magnetic beads were used to isolate long polyadenylated RNA from 1 μg of total RNA. After fragmentation, first-strand cDNA was reverse transcribed with random hexamer-primers, followed by second-strand cDNA synthesis, end repair, adenylation of 3′ ends, and ligation of the adapters. Fragments were then enriched by PCR.

value: brain

tag: individual

value: hd

tag: brain region

value: 2ary Auditory Anterior (BA21a)

value: healthy control

tag: sample id


title: LoowFD-66

value: Low Fat Diet


title: HFD-2


title: DA neurons, Parkin_1601_P3

value: DA neurons

value: Tamoxifen injection


title: HD; 19 Temporopolar (BA38)

value: Temporopolar (BA38)


title: 1330-CD-25

value: Skin

value: Fibroblasts


title: 1330-CD-19

value: TGF-B


title: LoowFD-65

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: 1330-CD-13

value: NoStim


title: DA neurons, Parkin_1601_P2

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-positive

value: 5 weeks after tamoxifen injection


title: LoowFD-64


title: 1330-CD-10

value: IFNG

value: Control


title: HC; 19 Temporopolar (BA38)

value: brain

value: hc

value: healthy control


title: DA neurons, Parkin_1601_P1

value: DA neurons

value: Tamoxifen injection


title: HC; 20 2ary Auditory Anterior (BA21a)

value: 2ary Auditory Anterior (BA21a)


title: mixed cells, Parkin_1601_N5

value: mixed cells

value: mitoYFP-negative


title: 1323-CD-55

value: Skin

value: Fibroblasts

value: IFNA


title: LoowFD-59

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: HB; 19 Temporopolar (BA38)

value: hb

value: Temporopolar (BA38)


title: 1323-CD-52

value: IFNG

value: Control


title: mixed cells, Parkin_1601_N4

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2

value: 5 weeks after tamoxifen injection


title: LoowFD-58


title: HA; 20 2ary Auditory Anterior (BA21a)

value: brain

value: ha

value: healthy control


title: mixed cells, Parkin_1601_N2

value: mixed cells

value: mitoYFP-negative

value: Tamoxifen injection


title: LoowFD-56


title: 1323-CD-51

value: Skin

value: Fibroblasts

value: IFNA


title: HA; 19 Temporopolar (BA38)


title: DA neurons, Parkin_1424_P5

value: DA neurons

value: mitoYFP-positive

value: 40 weeks after tamoxifen injection


title: 1323-CD-50

value: TNF-A


title: 1323-CD-49

value: TGF-B

value: Control


title: LoowFD-53

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: astrocyte_1020_vehicle_2

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR 2.6.0a to the reference genome UCSC hg19.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from the UCSC annotation package hg19.
Assembly: hg19
Supplementary files format and content: counts.txt: Tab-delimited text file of gene level counts.

source_name: iPSC-derived astrocyte

growth_protocol: Briefly, iPSCs were cultured on Matrigel-coated plates (BD Biosciences) in mTeSR1 medium (STEMCELL technology, MA, USA). All iPSCs were regularly verified to be free from mycoplasma. All cell lines revealed normal karyotypes, and they all expressed pluripotency markers. AUD patient-derived iPSCs (n=6, S1 Table) were differentiated into astrocytes. Briefly, iPSC colonies were detached from the Matrigel (Corning) with 1 mg ml−1 collagenase treatment for an hour and the cells were suspended in embryoid body (EB) medium, consisting of FGF-2-free iPS cell medium supplemented with 2 μM dorsomorphin (Sigma) and 2 μM A-83 (Sigma), in non-treated polystyrene plates for six days with a daily medium change. After six days, EB medium was replaced by neural induction medium (hNPC medium) consisting of DMEM/F12, N2 supplement, NEAA, 2 μg ml−1 heparin (Tocris Bioscience) and 2 μM cyclopamine (Tocris Bioscience). The floating EBs were then transferred to Matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with hNPC medium change every other day. On day 22, the rosettes were transferred to low attachment plates in hNPC medium containing B27 (Thermo-Fisher). On day 24, for astrocyte differentiation, resuspended neural progenitor spheres were dissociated with Accutase (STEMCELL technology, MA, USA) and placed onto Matrigel-coated plates in astrocyte culture medium (1801, ScienCell). Cells were prepared for subsequent experiments between passage 3-6.

extract_protocol:
Trizol and QIAGEN RNeasy kit.
RNA-seq experiments were conducted by GENEWIZ using an Illumina HiSeq 4000 with eight samples in each lane using 100bp paired end index reads.

treatment_protocol: Cells were seeded in T75 flasks treated with EtOH (25 mM), a concentration that is considered physiologically relevant for EtOH use, with 25 mM EtOH being slightly higher than the 0.08% blood alcohol concentration that is often used as a measure of intoxication. The concentrations of acamprosate (5 µM, Sigma, A6981) and naltrexone (30 nM, Selleckchem, S2103) used to perform those experiments were selected to fall within the range of blood concentrations for these drugs observed during clinical therapy. Cells were cultured with the drugs for seven days and the medium was changed daily.

value: iPSC-derived astrocyte

value: vehicle


title: 1323-CD-46

value: IFNG


title: LoowFD-54


title: LoowFD-63


title: LoowFD-48


title: LoowFD-50


title: astrocyte_1020_vehicle_1


title: astrocyte_1020_naltrexone_2

value: naltrexone


title: DA neurons, Parkin_1424_P2

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2

value: Tamoxifen injection


title: HB; 20 2ary Auditory Anterior (BA21a)

value: brain

value: hb

value: 2ary Auditory Anterior (BA21a)

value: healthy control


title: 1323-CD-45

value: Skin

value: Fibroblasts

value: IFNA


title: DA neurons, Parkin_1424_P3

value: DA neurons

value: mitoYFP-positive

value: 40 weeks after tamoxifen injection


title: LoowFD-45

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: DA neurons, Parkin_1424_P1


title: LoowFD-43


title: astrocyte_1020_ethanol_2

value: iPSC-derived astrocyte

value: ethanol


title: mixed cells, Parkin_1601_N1

value: midbrain

value: mixed cells

value: Parkin loxP/loxP; +/DatCreERT2

value: mitoYFP-negative

value: 5 weeks after tamoxifen injection


title: astrocyte_1020_ethanol_1


title: 1323-CD-37

value: NoStim

value: Control


title: DA neurons, Parkin_1423_P2

value: Tamoxifen injection


title: DA neurons, Parkin_1424_P4


title: DA neurons, Parkin_1423_P1


title: LoowFD-42


title: 1323-CD-34

value: Skin

value: Fibroblasts

value: IFNG


title: astrocyte_1020_acamprosate_2

value: acamprosate


title: astrocyte_1020_acamprosate_1


title: DA neurons, Parkin_1251_P5

value: DA neurons

value: mitoYFP-positive

value: 40 weeks after tamoxifen injection


title: DA neurons, Parkin_1251_P4


title: 1323-CD-32

value: TNF-A


title: LoowFD-39

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)

value: Low Fat Diet


title: LoowFD-38


title: 1323-CD-44


title: 1323-CD-25


title: astrocyte_1019_vehicle_1

value: iPSC-derived astrocyte

value: vehicle


title: LoowFD-31


title: astrocyte_1019_vehicle_2


title: LoowFD-28


title: 1323-CD-31

value: TGF-B


title: astrocyte_1020_naltrexone_1

value: naltrexone


title: 1323-CD-43

value: Control


title: 1323-CD-22


title: DA neurons, Parkin_1251_P2

value: midbrain

value: Parkin loxP/loxP; +/DatCreERT2

value: Tamoxifen injection


title: DA neurons, Parkin_1251_P1


title: LoowFD-25


title: 1323-CD-21

value: Skin

value: Fibroblasts

value: IFNA


title: LoowFD-22


title: astrocyte_1019_naltrexone_1


title: DA neurons, Control_B553_P8

value: DA neurons

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive


title: astrocyte_1019_ethanol_2

value: ethanol


title: LoowFD-20

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: astrocyte_1019_ethanol_1

value: iPSC-derived astrocyte


title: LoowFD-18

value: Low Fat Diet


title: DA neurons, Parkin_1251_P3

value: 40 weeks after tamoxifen injection


title: 1323-CD-1

value: NoStim


title: DA neurons, Control_B553_P6


title: 1323-CD-19

value: TGF-B

value: Control


title: LoowFD-8


title: LoowFD-4


title: astrocyte_1019_acamprosate_1

value: acamprosate


title: DA neurons, Control_B553_P5

value: midbrain

value: Tamoxifen injection


title: astrocyte_1018_vehicle_2

value: vehicle


title: astrocyte_1019_naltrexone_2

value: naltrexone


title: DA neurons, Control_B553_P4

value: DA neurons


title: 1323-CD-13

value: Skin

value: Fibroblasts


title: 1277-CD-9

value: IFNA


title: 1323-CD-20

value: TNF-A


title: LoowFD-1

value: Early 2-cell embryo

value: nuclear DNA:C57BL/6N; mtDNA:Staudach (ST)


title: astrocyte_1018_vehicle_1

value: iPSC-derived astrocyte


title: 1277-CD-8


title: DA neurons, Control_B553_P3

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive

value: 40 weeks after tamoxifen injection


title: 1277-CD-49

value: NoStim

value: Control


title: DA neurons, Control_B553_P7

value: midbrain


title: DA neurons, Control_B553_P1

value: Tamoxifen injection


title: 1277-CD-7

value: TGF-B


title: astrocyte_1018_naltrexone_2

value: naltrexone


title: astrocyte_1019_acamprosate_2

value: acamprosate


title: DA neurons, Control_B548_P7

value: DA neurons


title: astrocyte_1018_ethanol_2

value: ethanol


title: Sperm Mrlp23

data_processing:
All sequencing files were quality checked using MultiQC v1.11. Reads were trimmed using cutadapt 2.8 according to kit manufacturer instructions. Sequencing files were aligned and annotated to the mouse genome (mm10) using the SPORTS1.1 pipeline (1). The total number of mismatch parameters allowed was a maximum of 2, the rest of the parameters were kept default. Reference genome and small RNA annotation databases of mm10 were downloaded from the Sports website (https://github.com/junchaoshi/sports1.1). edgeR was used to identify differentially expressed fragments.
mm10
Table files for annotation information for every unique sequence and reads number of each major smallrna biotype for every samples.

source_name: Sperm

extract_protocol:
Mouse sperm were collected from paired cauda epididymis of C57BL/6J mice by using a swim-up procedure.
Sequencing libraries were prepared using NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA)

value: Sperm

value: C57BL/6 het


title: Sperm Tsfm


title: 1277-CD-46

value: Skin

value: Fibroblasts

value: IFNG


title: Sperm 2+4 smallrna LFD3

value: C57BL/6 wildtype

value: Low Fat Diet


title: Sperm 2+4 smallrna LFD2


title: DA neurons, Control_B548_P6

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive

value: 40 weeks after tamoxifen injection


title: 1277-CD-45

value: IFNA

value: Control


title: 1277-CD-44

value: TNF-A


title: DA neurons, Control_B548_P5

value: midbrain

value: Tamoxifen injection


title: Sperm Ndufb8


title: Sperm 2+4 smallrna LFD1


title: astrocyte_1016_vehicle_2

value: iPSC-derived astrocyte

value: vehicle


title: astrocyte_1018_acamprosate_1

value: acamprosate


title: DA neurons, Control_B548_P3

value: DA neurons


title: DA neurons, Control_B548_P4


title: Sperm 2+4 smallrna HFD3

value: Sperm

value: High Fat Diet


title: astrocyte_1018_ethanol_1

value: ethanol


title: astrocyte_1018_acamprosate_2


title: DA neurons, Control_B553_P2


title: 1277-CD-37

value: Skin

value: Fibroblasts

value: NoStim


title: astrocyte_1018_naltrexone_1

value: naltrexone


title: Sperm 2+4 smallrna HFD2

value: C57BL/6 wildtype


title: astrocyte_1016_vehicle_1


title: DA neurons, Control_B548_P2

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive

value: 40 weeks after tamoxifen injection


title: 1277-CD-34

value: IFNG

value: Control


title: Sperm 2+4 smallrna HFD1


title: DA neurons, Control_B548_P1

value: midbrain

value: Tamoxifen injection


title: 1277-CD-33

value: IFNA


title: astrocyte_1016_naltrexone_2

value: iPSC-derived astrocyte


title: Sperm smallrna LFD4

value: Sperm

value: Low Fat Diet


title: DA neurons, Control_2121_P3

value: DA neurons

value: 5 weeks after tamoxifen injection


title: astrocyte_1016_naltrexone_1


title: 1277-CD-43

value: Skin

value: Fibroblasts

value: TGF-B


title: Sperm smallrna LFD3

value: C57BL/6 wildtype


title: 1277-CD-32

value: TNF-A


title: 1277-CD-31


title: astrocyte_1016_ethanol_2

value: ethanol


title: Sperm smallrna LFD2


title: 1277-CD-25

value: NoStim


title: DA neurons, Control_2113_P2

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive


title: astrocyte_1016_acamprosate_2

value: acamprosate


title: DA neurons, Control_2113_P1

value: midbrain

value: Tamoxifen injection


title: astrocyte_1016_ethanol_1

value: iPSC-derived astrocyte


title: DA neurons, Control_2121_P1


title: 1277-CD-21

value: IFNA

value: Control


title: Sperm smallrna LFD1

value: Sperm

value: Low Fat Diet


title: astrocyte_1016_acamprosate_1


title: Sperm smallrna HFD3

value: High Fat Diet


title: DA neurons, Control_2112_P1

value: DA neurons

value: 5 weeks after tamoxifen injection


title: 1277-CD-20

value: Skin

value: Fibroblasts


title: astrocyte_1015_vehicle_2

value: vehicle


title: Sperm smallrna HFD2

value: C57BL/6 wildtype


title: 1277-CD-19

value: TGF-B


title: Sperm smallrna HFD1


title: DA neurons, Control_2103_P3

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive


title: astrocyte_1015_naltrexone_2

value: naltrexone


title: astrocyte_1015_vehicle_1


title: DA neurons, Control_2121_P2

value: midbrain

value: Tamoxifen injection


title: DA neurons, Control_2103_P2


title: 1277-CD-22

value: IFNG


title: Round Spermatids smallrna LFD4

source_name: Round Spermatids

value: Round Spermatids


title: 1277-CD-13

value: NoStim

value: Control


title: Round Spermatids smallrna LFD3

value: Low Fat Diet


title: 1277-CD-10


title: Sperm smallrna HFD4

value: Sperm

value: High Fat Diet


title: DA neurons, Control_2103_P1

value: DA neurons

value: 5 weeks after tamoxifen injection


title: astrocyte_1015_ethanol_1

value: iPSC-derived astrocyte

value: ethanol


title: DA neurons, Control_1609_P8


title: Round Spermatids smallrna LFD1

value: C57BL/6 wildtype


title: Round Spermatids smallrna LFD2


title: DA neurons, Control_1609_P7

value: Parkin +/+; +/DatCreERT2


title: dESC + euploid EVs, biol rep 5 [27]

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.32)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts. Only reads mapped to exons were considered in the counting procedure for stromal cell samples (samples 1-28), while all the reads mapped somewhere on the transcripts or on the gene bodies were considered in the counting procedure for EVs samples (D3_35a, D3_35b, D3_35x and E1-5, A1-4 respectively).
Genomic features were annotated according to the Gencode basic annotations (Gencode version 28 for samples D3_35a, D3_35b, D3_35x; Gencode version 31 for all the other samples A1-4, E1-5, 1-28)
Assembly: UCSC hg38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: endometrial stromal cells

extract_protocol:
EVs samples (D3_35a, D3_35b, D3_35x, E1-5, A1-4) were lysed directly using lysis buffer from the library preparation kit, RNA extraction from ESCs and dESCs untreated or treated with EVs (sample 1-28) was performed using the RNeasy Plus Micro kit (Qiagen)
cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan) for Evs samples (D3_35a, D3_35b, D3_35x, E1-5, A1-4), and using the Illumina TruSeq Stranded mRNA kit (Illumina, San Diego, CA) for ESCs and dESCs untreated or treated sampes (samples 1-28)

tag: sample source

value: endometrial tissue

value: endometrial stromal cells

value: decidualised and treated with 50 µg/ml of EVs from euploid blastocyst stage embryos, 24h


title: DA neurons, Control_2103_P4

value: midbrain

tag: cell type

value: mitoYFP-positive

value: Tamoxifen injection


title: DA neurons, Control_1609_P6

tag: genotype


title: Round Spermatids smallrna HFD4

value: Round Spermatids

tag: treatment


title: astrocyte_1015_acamprosate_2

value: acamprosate


title: ESC, biol rep 5 [25]

value: undecidualised


title: astrocyte_1015_acamprosate_1


title: dESC + aneuploid EVs, biol rep 4 [22]

value: decidualised and treated with 50 µg/ml of EVs from aneuploid blastocyst stage embryos, 24h


title: DA neurons, Control_1609_P5

tag: tissue


title: astrocyte_1014_vehicle_2

value: vehicle


title: astrocyte_1015_naltrexone_1

value: naltrexone


title: Round Spermatids smallrna HFD3

value: High Fat Diet


title: Round Spermatids smallrna HFD2


title: astrocyte_1014_vehicle_1

value: iPSC-derived astrocyte


title: dESC + euploid EVs, biol rep 4 [21]


title: Round Spermatids smallrna HFD1


title: DA neurons, Control_1609_P4

value: DA neurons

value: 5 weeks after tamoxifen injection


title: astrocyte_1015_ethanol_2

value: ethanol


title: astrocyte_1014_naltrexone_2


title: dESC, biol rep 4 [20]

value: endometrial tissue

value: decidualised and untreated


title: DA neurons, Control_1609_P3

value: Parkin +/+; +/DatCreERT2


title: DA neurons, Control_1609_P2

value: midbrain


title: HFD3, scRNAseq

description: Testis HFD scrna-seq rep 3

library_source: transcriptomic single cell

data_processing:
De-multiplexed reads were processed and mapped to the mouse genome (refdata-gex-mm10-2020-A), filtering and UMI counting was performed to obtain gene transcript counts per cell (gene barcode matrix) using Cell Ranger (version 6.0.1) count function. We filtered raw count matrices by excluding cells expressing fewer than 200 detectably expressed genes and genes expressed in fewer than three cells. Cell with greater then 40000 number of detected features (nFeature_RNA) per cell were excluded.
Assembly: mm10
Supplementary files format and content: TAB separated value files and matrix files with raw gene counts for every gene and every single cell

source_name: Testis

extract_protocol:
Freshly isolated testis were processed to obtain single cell suspension according to 10x genomics protocols and recommendations. Targeted 10000 cells for each sample was loaded into Chromium microfluidic chip used to generate single-cell gel bead emulsions using the 10× Genomics Chromium controller, as per manufacturer’s protocol.
Single cell library were constructed according to the manufactures instructions (Chromium Single Cell 3’ Library Kit v2, 10x Genomics)

value: Testis

value: C57BL/6 wildtype


title: ESC, biol rep 4 [19]

value: endometrial stromal cells


title: DA neurons, Control_1609_P1

value: mitoYFP-positive

value: Tamoxifen injection


title: dESC, biol rep 5 [26]


title: astrocyte_1014_naltrexone_1


title: dESC + aneuploid EVs, biol rep 3 [16]

value: decidualised and treated with 50 µg/ml of EVs from aneuploid blastocyst stage embryos, 24h


title: HFD2, scRNAseq

description: Testis HFD scrna-seq rep 2


title: astrocyte_1014_ethanol_1


title: DA neurons, Control_1602_P6


title: LFD3, scRNAseq

description: Testis LFD scrna-seq rep 3

value: Low Fat Diet


title: DA neurons, Control_1602_P5


title: dESC + aneuploid EVs, biol rep 5 [28]


title: astrocyte_1014_ethanol_2


title: HFD1, scRNAseq

description: Testis HFD scrna-seq rep 1


title: dESC, biol rep 3 [14]


title: astrocyte_1014_acamprosate_1

value: acamprosate


title: LFD2, scRNAseq

description: Testis LFD scrna-seq rep 2


title: ESC, biol rep 3 [13]

value: undecidualised


title: DA neurons, Control_1602_P4


title: DA neurons, Control_1602_P3


title: LFD1, scRNAseq

description: Testis LFD scrna-seq rep 1


title: dESC + aneuploid EVs, biol rep 2 [10]


title: Sample 18_NHBE, 10 ng/ml IL4 + ALOX15 Smartpool siRNA

city: Thousand Oaks

first: Jonathan

last: Phillips

state: CA

address: 1 Amgen center drive

institute: Amgen

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: NHBE – Human Bronchial/Tracheal Epithelial Cells for B-ALITM Culture

growth_protocol: One vial of primary NHBE cells (Lonza) were thawed and grown in a T75 cm2 flask in 15 ml BEGMTM Bronchial Epithelial Cell Growth Medium (Lonza) for 4 days (exchange media after 2 days) to obtain ~4.5 - 5  x 10^6 cells

extract_protocol:
Qiagen RNAeasy mini prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary NHBE cells were seeded in 3 x 6 well plates @ 2.5 x 10^5 cells/well in 2 ml media; treated with +/- 10 ng/ml IL4 and +/- 1 uM Smartpool ALOX15 siRNA (24 hr pretreatment) for 48 hrs before mRNA extraction.

value: lung

value: Primary normal human bronchial epithelial cells

value: IL4+ALOX15 siRNA


title: severe symptom, replicate2, scRNA

city: wuhan

first: lingen

last: yang

address: Shizishan Street 1

institute: Huazhong Agricultural University

description: 10X Genomics

data_processing:
the demultiplexing,barcoded processing, gene counting and aggregation were made using the cell ranger 5.0.0
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: cortex, striatum and thalamus of brain

extract_protocol:
the brain were removed and placed in a slicing chamber containing CCS,300um thick brain slabs were cut. Slabs containg the regions of cerebral cortex, striatum and thalamus were gently isolate under the sterecscope and transfered  in a 15 mL falcon tube containing 5 mLCCS+ and incubated for 30 minutes at 33℃, then transferred the tissue into  2mL of  Enzyme1 Buffer, digestion was performed at 37℃for 20minutes. The brain tissue was digest in 2mL Enzyme2 Buffer, digestion was performed on a shaker at 25℃for 20 minutes.. Tissue chunks were then carefully titrated with a series of n = 5 fire-polished, Pasteur pipets with successively smaller bores. then centrifuged at 500g for 5 minutes. The pellet was then resuspended in 3.1 mL CCS in a new tube and mixed with 0.9 mL Debris Removal Solution, slowly add 4 mL CCS on the top layer and centrifuged at 3000 g for 10 minutes, The supernatant was discarded, taking care not to disturb the cell pellet. The cell pellet was resuspended in 10 mL CCS
library were performed according to the manufacter's instructions(Single Cell 3' v3 protocol, 10xGenomics).

value: cortex, striatum and thalamus of brain

value: Japanese Encephalitis virus

value: Goblet cell

tag: strain


title: Sample 17_NHBE, 10 ng/ml IL4 + ALOX15 Smartpool siRNA


title: DA neurons, Control_1602_P2

value: DA neurons

value: Parkin +/+; +/DatCreERT2

value: 5 weeks after tamoxifen injection


title: dESC + euploid EVs, biol rep 2 [9]

value: endometrial tissue

value: decidualised and treated with 50 µg/ml of EVs from euploid blastocyst stage embryos, 24h


title: severe symptom, replicate1, scRNA

description: 10X Genomics


title: dESC, biol rep 2 [8]

value: endometrial stromal cells

value: decidualised and untreated


title: DA neurons, Control_1474_P6

value: midbrain

value: mitoYFP-positive

value: Tamoxifen injection

value: 40 weeks after tamoxifen injection


title: Moderate symptom, replicate1, scRNA

description: 10X Genomics


title: Sample 16_NHBE, 10 ng/ml IL4 + ALOX15 Smartpool siRNA

value: lung


title: DA neurons, Control_1474_P5


title: dESC + euploid EVs, biol rep 3 [15]


title: Sample 15_NHBE, 10 ng/ml IL4 + Control Smartpool siRNA

value: Primary normal human bronchial epithelial cells

value: IL4+non-targeting negative control siRNA


title: ESC, biol rep 2 [7]

value: undecidualised


title: Mild symptom, replicate2, scRNA

description: 10X Genomics

value: cortex, striatum and thalamus of brain

value: Japanese Encephalitis virus


title: dESC + aneuploid EVs, biol rep 1 [4]

value: decidualised and treated with 50 µg/ml of EVs from aneuploid blastocyst stage embryos, 24h


title: Mild symptom, replicate1, scRNA

description: 10X Genomics

value: Goblet cell


title: DA neurons, Control_1474_P3

value: DA neurons

value: Parkin +/+; +/DatCreERT2


title: DA neurons, Control_1474_P4


title: astrocyte_1014_acamprosate_2

value: iPSC-derived astrocyte

value: acamprosate


title: Sample 13_NHBE, 10 ng/ml IL4 + Control Smartpool siRNA


title: DA neurons, Control_1474_P2


title: dESC, biol rep 1 [2]

value: endometrial tissue

value: endometrial stromal cells

value: decidualised and untreated


title: Healthy, replicate3, scRNA

description: 10X Genomics

value: DMEM


title: Sample 12_NHBE, 10 ng/ml IL4 + Compound B

value: IL4+Compound treated


title: dESC + euploid EVs, biol rep 1 [3]

value: decidualised and treated with 50 µg/ml of EVs from euploid blastocyst stage embryos, 24h


title: ESC, biol rep 1 [1]


title: Sample 11_NHBE, 10 ng/ml IL4 + Compound B

value: lung

value: Primary normal human bronchial epithelial cells


title: Healthy, replicate2, scRNA

description: 10X Genomics


title: DA neurons, Control_1474_P1

value: midbrain

value: mitoYFP-positive

value: Tamoxifen injection

value: 40 weeks after tamoxifen injection


title: Healthy, replicate1, scRNA

description: 10X Genomics

value: cortex, striatum and thalamus of brain

value: Goblet cell


title: Sample 10_NHBE, 10 ng/ml IL4 + Compound B


title: Oli-Neu cells, shControl, replicate 3

city: Bologna

first: Federico

middle: Manuel

last: Giorgi

state: Bologna

address: Via Irnerio 49

department: Pharmacy and Biotechnology

institute: Unviersity of Bologna

data_processing:
RNA-Seq data were quantified for transcripts’ expression using Salmon v0.12.0 in mapping-based mode, using Mus musculus transcriptome (cDNA from genome build GRCm39) enabling options --validateMappings,  --gcBias, --seqBias.
Assembly: mm39
Supplementary files format and content: tab-delimited text file (quant.sf) includes the estimated number of reads mapping to each transcript that was quantified for each sample
Supplementary files format and content: tab-delimited text file (quant.sf) includes the TPM values for each sample

source_name: Embryonic brain

growth_protocol: Oli-Neu cells were grown at 37°C and 5% CO2 on poly-L-lisine (10 µg/mL) coated Petri dishes in SATO medium (DMEM basal medium, 2 mM glutamine, 10 µg/ml insulin, 5.5 µg/ml transferrin, 38.72 nM sodium selenite, 100 µM putrescine, 520 nM L-thyroxine (T4), 500 nM triiodo-L-thyronine (T3), 200 nM progesterone, 25 µg/ml  gentamycin)

extract_protocol:
1x106 Oli-Neu cells were collected in 1 ml TRI Reagent (TRI Reagent RNA Isolation Reagent; Sigma-Aldrich). Following addition of 200 μl Chloroform (Sigma-Aldrich), cells were incubated 10 min at RT and centrifugated x12000g 15 min at 4 °C. The upper aqueous phase containing RNA was isolated from the lower phenolic phase, and 500 μl of isopropanol (Sigma-Aldrich) were added to induce RNA precipitation. After incubation 20 min at RT, samples were centrifugated x12000g for 10 min at 4 °C, RNA pellet was washed with 1 ml 75% EtOH solution and centrifugated again x12000g 10 min at 4 °C. EtOH was removed, and RNA pellet was allowed to completely dry at RT. The extracted nucleic acid was resuspended in Milli-Q and quantified by NanoDrop 2000 (Thermo-Fisher Scientific)
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand).

value: Embryonic brain

value: Oli-Neu (CVCL_IZ82)

value: Oligodendroglial precursor

value: WT


title: normal control (NC)3

city: Lishui City

first: zhongjiao

last: xu

address: No. 289, Gucang Road, Liandu District

institute: The Fifth Affiliated Hospital of Wenzhou Medical University

data_processing:
Sequencing is based on Novaseq6000SBSKitv3-HS (200cycles). In the sequencing experiment, the IlluminaTruseqTM RNAsample prepKit method is used to construct the library, and stringtie2.15 software is used to spilce and identify new genes and transcripts. After quality control（fastqc_v0.11.8）, the cleandata (reads) was compared to the human reference genome (GRCh38) by HISAT2 software, ,and the quality of the comparison results of the transcriptome sequencing was evaluated, mainly including sequencing saturation, gene coverage, and distribution of Reads in different regions of the reference genome. According to the comparison results of HISAT2 software, the FPKM value of each gene/ transcript in the sample was calculated, which was used as the expression level of each gene/transcript in the sample.
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human Aortic Smooth Muscle

growth_protocol: Smooth muscle cells (SMCs)  stored in DMEM plus 10% FBS ,This step was followed by a period of incubation at 37 °C containing 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit, Ribosomal RNA in the total RNA was digested using a Ribo-Zero kit, 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingIllumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

treatment_protocol: SiRNAs targeting NOTCH3 (si-NOTCH3) were  transfected with the indicated siRNAs (Genentech) by Lipofectamine 2000.

value: Human Aortic Smooth Muscle

value: normal

value: no


title: normal control (NC)2


title: DA neurons, Control_1472_P5

value: DA neurons

value: Parkin +/+; +/DatCreERT2


title: Oli-Neu cells, shControl, replicate 2


title: normal control (NC)1


title: Sample 9_NHBE, 10 ng/ml IL4 + Compound A

value: lung

value: IL4+Compound treated


title: Sample 14_NHBE, 10 ng/ml IL4 + Control Smartpool siRNA

value: Primary normal human bronchial epithelial cells

value: IL4+non-targeting negative control siRNA


title: DA neurons, Control_1472_P4

value: midbrain

value: mitoYFP-positive

value: Tamoxifen injection


title: Oli-Neu cells, shControl, replicate 1


title: DA neurons, Control_1472_P3

value: 40 weeks after tamoxifen injection


title: Sample 7_NHBE, 10 ng/ml IL4 + Compound A


title: si-NOTCH3  3_3

value: NOTCH3 Knockdown


title: Sample 8_NHBE, 10 ng/ml IL4 + Compound A


title: Oli-Neu cells, shAgc1, replicate 3

value: Embryonic brain

value: Oli-Neu (CVCL_IZ82)

value: Agc1 knockdown


title: DA neurons, Control_1472_P2


title: Sample 6_NHBE, 10 ng/ml IL4

value: IL4 treated


title: si-NOTCH3  3_2

value: Human Aortic Smooth Muscle


title: Oli-Neu cells, shAgc1, replicate 2

value: Oligodendroglial precursor


title: si-NOTCH3  3_1


title: DA neurons, Control_1472_P6

value: DA neurons


title: DA neurons, Control_1472_P1

value: Parkin +/+; +/DatCreERT2


title: Sample 5_NHBE, 10 ng/ml IL4

value: lung


title: DA neurons, Control_1471_P3


title: DA neurons, Control_1471_P2


title: Knockout 4

city: Oxford

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Transcript counting was performed using Salmon 1.4.0 with a full mm10 transcript index performed using selective alignment technique, and using the following parameters --useVBOpt --seqBias --validateMappings
Assembly: mm10
Supplementary files format and content: Salmon Quant files

source_name: Speen

extract_protocol:
CD19+GL-7+CD38- B cells were flow sorted into RLT Plus buffer
NEBNext Ultra II mRNA kit was used as per manufacturer's instructions
Polyadenylated transcript enrichment and strand specific library preparation

value: Speen

value: Germinal centre (GC) B cell

value: Cd79a-cre x Asns flox


title: Sample 4_NHBE, 10 ng/ml IL4

value: Primary normal human bronchial epithelial cells


title: Knockout 3


title: Sample 3_NHBE, Control untreated

value: untreated


title: Oli-Neu cells, shAgc1, replicate 1


title: Sample 2_NHBE, Control untreated


title: S3

city: Jinan

first: Ai-yan

last: Xing

address: Wen Hua Xi Road 107

institute: ShanDong University Qilu Hospital

description: Gene Expression Profiling

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to get the raw count.
edgeR was used to perform normalization.
differentially expressed mRNAs were identified by p-value and fold change.
Assembly: h19
Supplementary files format and content: excel format     gene expression profiling

source_name: breast cancer cell

extract_protocol:
RNA was extracted using trizol reagent.
Total RNAwas used for removing the rRNAs.The rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library  Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.

value: breast cancer cell

value: triple negative

value: SNHG14 knockdown

value: non


title: si-NOTCH3  2_3

value: NOTCH3 Knockdown


title: Knockout 1


title: Sample 1_NHBE, Control untreated


title: Knockout 2


title: DA neurons, Control_1463_P4

value: midbrain

value: mitoYFP-positive

value: Tamoxifen injection

value: 40 weeks after tamoxifen injection


title: DA neurons, Control_1463_P3

value: DA neurons


title: S2

description: Gene Expression Profiling


title: Wild type 3

value: WT


title: A549, 10 ng/ml IL4 + ALOX15 Smartpool siRNA_3

description:
ALOX15_siRNA_3
SE6999_SA81575_S23_L008

source_name: A549_IL4+ALOX15 siRNA

growth_protocol: A549 cells were grown in F12 (Ham's) media containing 10% HI FBS supplemented with 1x non-essential amino acids (Invitrogen) and 1x Pen/Strep glutamine (Invitrogen)

treatment_protocol: A549 cells were seeded in 6 well plates @ 4 x 10^5 cells/well in 2 ml media; treated with +/- 10 ng/ml IL4 and +/- 1 uM Smartpool ALOX15 siRNA for 48 hrs before mRNA extraction.

value: Lung epithelial Adenocarcinoma (Alveolar Type II like)

value: IL4+ALOX15 siRNA


title: DA neurons, Control_1471_P1

source_name: midbrain

value: Parkin +/+; +/DatCreERT2


title: S1

description: Gene Expression Profiling


title: DA neurons, Control_1463_P2


title: si-NOTCH3  2_1

value: Human Aortic Smooth Muscle


title: DA neurons, Control_1463_P1


title: Wild type 1

value: Speen

value: Germinal centre (GC) B cell


title: si-NOTCH3  2_2


title: A549, 10 ng/ml IL4 + ALOX15 Smartpool siRNA_1

description:
ALOX15_siRNA_1
SE6999_SA81565_S13_L008


title: Wild type 2


title: N2

description: Gene Expression Profiling

value: breast cancer cell


title: DA neurons, Control_1281_P5


title: DA neurons, Control_1281_P4


title: Foxp1/2-cKO_P56 #3

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: 10x Genomics

data_processing:
cellranger mkfastq
cellranger count
cellbender
doubletfinder
seurat
Assembly: mm10 (GRCm38p6)
Supplementary files format and content: barcodes.tsv' a tab-delimited text files include list of cell-barcodes and 'features.tsv' a tab-delimited text file include list of genes and 'matrix.mtx' file in a sparse matrix format containing raw counts per gene per cell-barcode.

source_name: Dorsal Striatum

extract_protocol:
P56 mice were sacrificed by rapid dissection and brains were quickly removed and placed in ice-cold 1X PBS. Using a brain matrix with 1mm markings, striatal sections were obtained, as determined by visual cues indicating the presence of  the striatum. Using forceps, the striatum was separated from the cortex, flash frozen, and stored in -80C. Nuclei isolation for snRNA-Seq was done as follows: tissue was homogenized in a glass Dounce tissue grinder (25 times with pestle A, 25 times with pestle B; Sigma, Cat#D8938) in 2mL ice-cold EZ Nuclei Lysis Buffer (Sigma, Cat #NUC-101). Samples were incubated on ice for 5 minutes with an additional 2mL ice-cold EZ lysis buffer and then centrifuged at 500 X g for 5 minutes at 4C, washed with 2mL ice-cold EZ lysis buffer, and incubated on ice for another 5 minutes before being spun again. Nuclei were then washed in 500uL Nuclei Suspension Buffer (NSB; 1X PBS, 0.01% UltraPure BSA, and 0.1% RNase inhibitor) and mixed with 900uL nuclei sucrose cushion buffer (Sigma, Cat #NUC-201). This mixture was layered on top of another 500uL of sucrose cushion buffer and spun at 13,000 X g for 45 minutes at 4C. The supernatant was then discarded, the pellet was resuspended in 60uL NSB, and filtered through FLOWMI tip strainer (Bel-Art Products, Cat# H13680-0040); more NSB was added as needed to help samples go through the FLOWMI tip. An aliquot was stained with Trypan Blue and counted under a microscope to determine concentration (targeting 700-1,200 nuclei/uL). Striatal tissue for P9 mice was collected following rapid decapitation and brains were removed and placed in ice-cold artificial cerebrospinal fluid (ACSF; 126 mM NaCl, 20 mM NaHCO3, 20 mM D-Glucose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM MgCl2) bubbled with 95% O2 and 5% CO2. 500uM coronal sections were made in ACSF using a VF-200 Compresstome (Precisionary Instruments) and transferred to another chamber filled with ACSF. From 3 striatal sections, 6 punches of striatal tissue were collected (2 per hemisphere), flash frozen, and stored in -80C. Nuclei were then isolated in a similar fashion as adults, with only one 5 minute centrifugation in EZ Nuclei Lysis buffer.  No sucrose cushion was used. Again, samples were filtered through the FLOWMI tip strainer, stained with Trypan Blue, counted under a microscope, and stored on ice until library generation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 and v3.1 protocol, 10x Genomics). Isolated nuclei were mixed with the 10X  master mix and loaded with partitioning oil and gel beads onto the provided chip. This results in generation of gel bead-in-emulsion (GEMs).  GEMs were then retrotranscripted to cDNA; these contained  Ilumina R1 primer sequence, Unique Molecular Identifier (UMIs) and the 10x Barcode. Silane DynaBeads were used to purify cDNA which were then amplified by PCR. SPRIselect beads were used to select proper sized fragments. Samples were cleaned with 80% ethanol after every amplification step as well. Finally, libraries were constructed and an Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during these final steps.

tag: Sex

value: F

value: Dorsal Striatum

tag: age

tag: prep batch

tag: sequencing batch


title: N1

description: Gene Expression Profiling

value: triple negative

value: non


title: DA neurons, Control_1281_P3

value: midbrain

tag: facs population

tag: mouse id

tag: technical replicate

tag: time point


title: A549, 10 ng/ml IL4 + Control Smartpool siRNA_3

description:
Control_siRNA_3
SE6999_SA81574_S22_L008

source_name: A549_IL4+non-targeting negative control siRNA

tag: cell line


title: A549, 10 ng/ml IL4 + Control Smartpool siRNA_2

description:
Control_siRNA_2
SE6999_SA81569_S17_L008

value: IL4+non-targeting negative control siRNA


title: Foxp1/2-cKO_P56 #2

description: 10x Genomics


title: A549, 10 ng/ml IL4 + Control Smartpool siRNA_1

description:
Control_siRNA_1
SE6999_SA81564_S12_L008


title: U2OS cells, VEGFA site 2 gDNA

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

library_source: genomic

data_processing:
library strategy: BreakTag
NGSpipe2go Breaktag pipeline (https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/master/pipelines/breaktag)
Reads without breaktag adaptor were filtered out
Reads with breaktag adaptor were mapped using BWA v0.7.15 with “bwa mem” on genome assembly hg38 and filtered out reads with mapping quality below 60
Deduplication of mapped reads based on unique molecular identifiers (UMIs)
Mapped read ends are summed up and reported in BED format
Assembly: UCSC Human Genome version hg38 (timestamp 2014-01-15 21:14) downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
Supplementary files format and content: Breaktag signal as a proxy of double strand breaks counts, a a standard 6-columns BED containing the “chromosome | start | end | name | breaktag_signal | strand”

molecule: genomic DNA

source_name: derived from sarcoma of the tibia

extract_protocol:
gDNA was extracted with DNeasy® Blood & Tissue kit
DNA DSB ends of nuclease-digested gDNA were repaired and 3’ adenylated using the NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB E7546) as described by the manufacturer with the following modification: Reaction volume was halved by adding half volume of the reagents. Labeling of DSB ends with BreakTag linker ligation was performed using the NEBNext® Ultra™ II Ligation Module (NEB E7595) according to manufacturer’s recommendation with the following modifications: Reaction volume was halved by adding half volume of reagents, and USER enzyme digestion step was omitted. BreakTag linker was used at a final concentration of 50 nM per sample. Labeled DNA was size-selected using DNA AMpure XP beads (0.7x volumes) in order to remove unligated linkers and eluted in nuclease-free H2O.  Tagmentation with in-house Tn5 was performed in 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 25% dimethylformamide (DMF, Sigma Aldrich 227056). Tagmentation reactions were assembled using 100-200 ng of DNA as input. Hyperactive Tn5 was used at a final concentration of 1.25 ng/µL per reaction. The tagmentation mix was then incubated at 55ᵒC for 5 minutes in a preheated thermocycler followed by termination with 0.2% SDS at room temperature for 5 minutes. Libraries were amplified with the NEBNext® Ultra™ II Q5® Master Mix (M0544). Amplified and barcoded samples were size-selected in order to remove PCR byproducts by performing two consecutive 0.5x volume right-tail + 0.35x volume left-tail size selection using DNA AMpure XP beads. Final libraries were quantified using Qubit dsDNA High Sensitivity Assay kit and fragment size distribution was assessed in a BioAnalyzer High Sensitivity DNA chip

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with VEGFA site 2 sgRNA


title: Foxp1/2-cKO_P56 #1

description: 10x Genomics

value: M


title: U2OS cells, VEGFA site 1 gDNA

value: WT

value: digested with VEGFA site 1 sgRNA


title: DA neurons, Control_1281_P2

data_processing:
Reads were mapped to the mm10 mouse genome merged with eGFP and ERCC spike-in sequences using STAR v2.3.0 with default settings and filtered for uniquely mapping reads.
Read counts and RPKM per gene were computed using rpkmforgenes.py with default settings and Ensembl release 75 gene annotations with addition of the EGFP reporter sequence.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file containing number of mapped reads per gene for all samples.
Supplementary files format and content: A tab-delimited text file containing RPKM per gene for all samples.

extract_protocol:
FACS
smart-seq2

value: DA neurons

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive

value: Tamoxifen injection

value: 40 weeks after tamoxifen injection

tag: sequencing year


title: Foxp2-cKO_P56 #3

description: 10x Genomics


title: A549, 10 ng/ml IL4 + ALOX15 Smartpool siRNA_2

description:
ALOX15_siRNA_2
SE6999_SA81570_S18_L008

value: Lung epithelial Adenocarcinoma (Alveolar Type II like)

value: IL4+ALOX15 siRNA


title: A549, 10 ng/ml IL4 + Compound A_2

description:
CMPD_2
SE6999_SA81568_S16_L008

source_name: A549_IL4+Compound treated

value: IL4+Compound treated


title: A549, 10 ng/ml IL4 + Compound A_3

description:
CMPD_3
SE6999_SA81573_S21_L008


title: Mettl3 ed/ed

city: Guangzhou

first: Ji-Long

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
Clean reads were mapped to mouse genome (UCSC mm9) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Female mice aged 6-8 weeks were mated with fertile males to induce pregnancy. The appearance of the vaginal plug was designated as gestation day (GD) 1. Pregnant females were sacrificed on GD4.

value: whole uterus

tag: time

value: gestational day 4

value: mixed

value: ed/ed


title: U2OS cells, TRAC site 4 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with TRAC site 4 sgRNA


title: N3

description: Gene Expression Profiling

value: breast cancer cell

value: triple negative

value: WT

value: non


title: U2OS cells, TRAC site 5 gDNA

value: digested with TRAC site 5 sgRNA


title: Foxp2-cKO_P56 #4

description: 10x Genomics

value: M

value: Dorsal Striatum


title: DA neurons, Control_1281_P1

value: midbrain

value: DA neurons

value: Parkin +/+; +/DatCreERT2

value: mitoYFP-positive

value: Tamoxifen injection

value: 40 weeks after tamoxifen injection


title: A549, 10 ng/ml IL4 + Compound A_1

description:
CMPD_1
SE6999_SA81563_S11_L008

value: Lung epithelial Adenocarcinoma (Alveolar Type II like)

value: IL4+Compound treated


title: A549, 10 ng/ml IL4_3

description:
IL4_3
SE6999_SA81572_S20_L008

source_name: A549_IL4 treated

value: IL4 treated


title: U2OS cells, TRAC site 3 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with TRAC site 3 sgRNA


title: Foxp2-cKO_P56 #1

description: 10x Genomics


title: Mettl3 f/f

value: whole uterus

value: gestational day 4

value: mixed

value: f/f


title: U2OS cells, TRAC site 2 gDNA

value: WT

value: digested with TRAC site 2 sgRNA


title: VitDconB

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
Adaptors were trimmed from raw reads with trim_galore.
Reads were mapped to the mm10 genome with hisat2
FeatureCounts was then used to counts mapped reads for genomic features using GENCODE mouse gene annotation v21 (-s 0 -Q 50).
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each sample

source_name: spleen

growth_protocol: gBT-I homozygote murine splenic CD8 T cells are ex vivo engineered with nanowires coated in oligonucleotide constructs then cultured in vitro for 2-4 days at 37oC

extract_protocol:
Trizol based RNA extraction (phenol and guanidinium isothiocyanate solubilization followed by chloroform phase separation)
Directional RNA-seq libraries were prepared from 300ng total RNA using the NEBNext Directional Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Murine CD8 T cells are treated with functionalized nanowires that perform dual insertion of miR-29 ASO and miR-29 mimic

value: spleen

value: CD8+ T cells

value: gBT-I TCR transgenic

value: T cell incubated with Nanowire coated with inert ASO and inert mimic


title: Foxp1-cKO_P56 #3

description: 10x Genomics

value: M

value: Dorsal Striatum


title: U2OS cells, TRAC site 1 gDNA

value: digested with TRAC site 1 sgRNA


title: A549, 10 ng/ml IL4_1

description:
IL4_1
SE6999_SA81562_S10_L008

value: Lung epithelial Adenocarcinoma (Alveolar Type II like)

value: IL4 treated


title: VitDconA


title: A549, Control untreated_3

description:
Control_3
SE6999_SA81571_S19_L008

value: untreated


title: VitDdefB

value: T cell incubated with Nanowire coated with miR-29 ASO and miR-29 mimic


title: U2OS cells, PTPN6 site 4 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with PTPN6 site 4 sgRNA


title: Foxp1-cKO_P56 #2

description: 10x Genomics


title: Foxp1-cKO_P56 #1

description: 10x Genomics


title: U2OS cells, PTPN6 site 3 gDNA

value: digested with PTPN6 site 3 sgRNA


title: VitDdefA


title: Foxp2-cKO_P56 #2

description: 10x Genomics

value: F


title: U2OS cells, PTPN6 site 2 gDNA

value: WT

value: digested with PTPN6 site 2 sgRNA


title: A549, Control untreated_2

description:
Control_2
SE6999_SA81566_S14_L008


title: Control_P56 #1

description: 10x Genomics

value: Control


title: Gas HFDi-3

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

description: GAS HFD intolerant rep 3

data_processing:
Read mapping and differential expression analysis was performed using the A.I.R (Artificial Intelligence RNA-Seq) software from Sequentia Biotech.
GRCm38
tab-delimited text files include count values for each sample

source_name: Gastrocnemius

extract_protocol:
Total RNA was prepared from liver, GAS, and eWAT using the TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA purity, integrity and quality was examined by Bioanalyzer (Agilent Technologies) and Qubit (Thermo Fisher Scientific).
Sequencing libraries were prepared by using the QuantSeq 3′ mRNA-Seq mRNA Library Prep Kit FWD for Illumina (Lexogen) with i7 indexes (Lexogen) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq 2500.

value: Gastrocnemius

value: C57BL/6 wildtype

value: High Fat Diet


title: Control_P56 #3

description: 10x Genomics

value: Dorsal Striatum


title: Kabuki syndrome type 1 replicate 3 (replication cohort)

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

institute: Johns Hopkins University

data_processing:
Reads were mapped to the mm10 mouse assembly.
Duplicates were removed with the MarkDuplicates function from Picard, and mitochondrial reads were removed with samtools
Samples from the same genotype were merged, and peaks were called on these merged meta-samples using MACS2
The peaks from each meta-sample were unionized to yield a final set of genomic intervals. The number of reads from each sample that map onto each of these intervals were counted using the featureCounts function from the Rsubread package.
The processed data file is a matrix (in csv format), with rows corresponding to the genomic intervals obtained after unionizing the peaks called from the individual meta-samples (each interval has its unique coordinates), and columns to samples (each sample name contains information about genotype). The entries in the matrix are counts, as obtained using the featureCounts function from the Rsubread R package.
Assembly: mm10
Supplementary files format and content: atac_peaks_by_samples_matrix_neurons_replication_KS1.csv

source_name: dentate gyrus

extract_protocol:
Hippocampal neurons were isolated using a protocol adapted from the INTACT (Mo et al., 2015) and Omni-ATAC (Corces et al., 2017) protocols. Dentate gyrus was microdissected as previously described (Carosso et al., 2019) and placed into ice cold 1xHBS (1x HBS-B, 1M sucrose, 500mM EDTA, 10\% IGEPAL; 1x HBS-B was initially prepared as 6xHBS with 1MCaCl2, 1MMgAc, 1M Tris pH7.8, 1mM BME). Samples were homogenized in a 2mL glass dounce, pestle A until resistance went away (approximately 15 strokes) and pestle B until the tissue looked homogenized (approximately 8 strokes). Samples were then spun through a discontinuous iodixanol gradient. Gradients were made by diluting homogenized sample 1:1 with 50% iodixanol solution for a final concentration of 25% iodixanol (60% iodixanol solution + HBS), and overlayed on a 30%-35%  iodixanol gradient in 15 mL conical tubes (30% iodixanol solution: 1xHBS, 30% iodixanol solution, 160mM sucrose; 35% iodixanol solution: 1xHBS, 35% iodixanol solution, 160mM sucrose). Gradients were spun for 5000g 20min 4’ with no break in swinging bucket centrifuge. Nuclei were collected at the 30-35% interface, transferred to a new tube and diluted with 1xHBS. Samples were spun for 10min 4’ 1000g, aspirated, then resuspended in 200uL 1xHBS. Nuclei were then stained for NeuN (NeuN-488, EMD Millipore MAB377X) and incubated 30min in dark. DNA was counterstained with Hoechest 33342 and sorted on NeuN+ to collect neurons (to avoid glia). 5000 nuclei were collected for most samples, though some variation was present.
Samples were resuspended in tagmentation reaction mix for 30 min (2.5uL TD1, 1X TD Buffer, Illumina Nextera DNA, FC-121-1030; .25uL 1% digitonin, Promega G9441; 1xPBS) gently shaking (300rpm on Eppendorf thermomixer) at 37’. We purified reactions using Zymo DNA Clean and Concentrator-5 kit (Zymo D4013) following manufacturer protocols and eluted with 10.5uL water to recover 10uL. Each reaction was then amplified and indexed per standard ATAC-seq protocol. After indexing and amplification, we purified samples using Select-A-Size purification columns (Zymo D4080) with a cutoff of 150bp to remove adapter dimers to allow for efficient sequencing on patterned flow cells, checked library size on BioAnalyzer using DNA High Sensitivity reagents (Agilent 5067-4626) and determined concentration using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851).

value: dentate gyrus

value: NeuN+ hippocampal neurons


title: Control_P56 #2

description: 10x Genomics


title: U2OS cells, PTPN6 site 1 gDNA

value: digested with PTPN6 site 1 sgRNA


title: Gas HFDi-2

description: GAS HFD intolerant rep 2


title: Kabuki syndrome type 1 replicate 2 (replication cohort)


title: Gas HFDi-1

description: GAS HFD intolerant rep 1


title: A549, 10 ng/ml IL4_2

description:
IL4_2
SE6999_SA81567_S15_L008

value: Lung epithelial Adenocarcinoma (Alveolar Type II like)

value: IL4 treated


title: Gas HFDt-3

description: GAS HFD tolerant rep 3


title: U2OS cells, PDCD1 site 1 gDNA

value: derived from sarcoma of the tibia

value: digested with PDCD1 site 1 sgRNA


title: Foxp1/2-cKO_P9 #3

description: 10x Genomics


title: U2OS cells, PDCD1 site 12 gDNA

value: sarcoma of the tibia

value: digested with PDCD1 site 12 sgRNA


title: Foxp1/2-cKO_P9 #2

description: 10x Genomics

value: M


title: Kabuki syndrome type 1 replicate 1 (replication cohort)


title: A549, Control untreated_1

description:
Control_1
SE6999_SA81561_S9_L008

value: untreated


title: U2OS cells, PDCD1 site 11 gDNA

value: WT

value: digested with PDCD1 site 11 sgRNA


title: Foxp1/2-cKO_P9 #1

description: 10x Genomics

value: F


title: Kabuki syndrome type 1 replicate 5

data_processing:
Reads were pseudo-aligned to a fasta file containing all mouse cDNA sequences obtained from ENSEMBL (http://uswest.ensembl.org/Mus_musculus/Info/Index, version 91, downloaded January 2018), using Salmon (v0.10)
Transcript quantifications were imported into R with the tximport R package, to obtain gene-level counts
The processed data files are expression matrices (in csv format), with rows corresponding to genes (each gene is associated with its unique ENSEMBL id), and columns to samples (each sample name contains information about genotype). The entries in the matrices are counts, as obtained using the "tximport" function from the tximport R package.
Assembly: mm10
Supplementary files format and content: rna_genes_by_samples_matrix_T_cells.csv

source_name: CD19+ B cells

extract_protocol:
T cells were isolated at exactly the same time as B cells. Specifically, flow through from binding and washing of CD19+ cells on Miltenyi separation columns was collected on ice. These CD19+ depleted samples were then spun and the supernatant was aspirated, resuspended and incubated with 2x (20uL) CD90.2+ microbeads (Miltenyi Biotec 130-121-278). CD90.2+ T cells were bound, washed and eluted per manufacturer protocol, then counted and aliquoted on ice for subsequent processing. Further processing of the T cell samples and RNA sequencing was done in parallel with B cells. Specifically, 100–500k cells were spun at 300–500 g for 5 min at 4’, were homogenized in Trizol (Invitrogen 15596018) and subsequently stored at –80°C until RNA was extracted. We extracted and isolated RNA by phase separation with standard protocols, with purification using the Direct-zol RNA microprep kit (Zymo R2060) with an on-column DNAse step as per manufacturer’s directions. Following purification, RNA was quantified with the Quant-iT RiboGreen RNA Assay Kit (ThermoFisher R11490) or Qubit RNA HS Assay Kit (ThermoFisher Q32852). We assessed the quality of the RNA using Bioanalyzer with the RNA 6000 Pico Kit (Agilent 5067–1513). We used 20 ng RNA per sample were used as input to capture mRNA (NEBNext Poly(A) mRNA Magnetic Isolation Module; NEB #E7490), and subsequently libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760/E7765) as per manufacturer’s protocols. Library size and quality were then evaluated with BioAnalyzer with DNA High Sensitivity reagents (Agilent 5067–4626), and concentration was assessed using the Qubit dsDNA HS Assay Kit (ThermoFisher Q32851) and KAPA Library Quantification Kit for qPCR (KAPA KK4824). Finally, samples were pooled and sequenced on Illumina HiSeq4000 using PE flow cells with 100-8-8-100 read length as per standard manufacturer’s protocols.
Libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760/E7765) per manufacturer protocols. Library size and quality were determined using BioAnalyzer with DNA High Sensitivity reagents (Agilent 5067-4626), and concentration was determined using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851) and KAPA Library Quantification Kit for qPCR (KAPA KK4824).

value: CD90.2+ T cells

tag: disease state

value: Kabuki syndrome type 1


title: Gas HFDt-1

description: GAS HFD tolerant rep 1

value: Gastrocnemius

value: C57BL/6 wildtype

value: High Fat Diet


title: U2OS cells, PDCD1 site 10 gDNA

tag: cell type

value: digested with PDCD1 site 10 sgRNA


title: U2OS cells, Non target bfp gDNA

tag: genotype

value: digested with Non target bfp sgRNA


title: eWAT HFDi-3

description: eWAT HFD intolerant rep 3

source_name: eWAT

value: eWAT

tag: treatment


title: Kabuki syndrome type 1 replicate 3


title: Foxp2-cKO_P9 #1

description: 10x Genomics

tag: tissue

value: Dorsal Striatum


title: eWAT HFDi-2

description: eWAT HFD intolerant rep 2


title: eWAT HFDi-1

description: eWAT HFD intolerant rep 1


title: Kabuki syndrome type 2 replicate 5

tag: strain

value: Kabuki syndrome type 2


title: U2OS cells, LAG3 site 1 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with LAG3 site 1 sgRNA


title: Wild-type replicate 5

value: Wild-type


title: Foxp1-cKO_P9 #3

description: 10x Genomics

tag: Sex


title: Foxp2-cKO_P9 #2

description: 10x Genomics

value: M

tag: age


title: U2OS cells, LAG3 site 10 gDNA

value: WT

value: digested with LAG3 site 10 sgRNA


title: eWAT HFDt-3

description: eWAT HFD tolerant rep 3


title: U2OS cells, LAG3 site 3 gDNA

value: digested with LAG3 site 3 sgRNA


title: Wild-type replicate 4

value: CD90.2+ T cells


title: eWAT HFDt-2

description: eWAT HFD tolerant rep 2


title: eWAT HFDt-1

description: eWAT HFD tolerant rep 1


title: Wild-type replicate 3


title: Foxp1-cKO_P9 #2

description: 10x Genomics

value: F

tag: prep batch


title: U2OS cells, FAS site 4 gDNA

value: digested with FAS site 4 sgRNA


title: Foxp1-cKO_P9 #1

description: 10x Genomics

tag: sequencing batch


title: Gas HFDt-2

description: GAS HFD tolerant rep 2

value: Gastrocnemius

value: C57BL/6 wildtype

value: High Fat Diet


title: Control_P9 #3

description: 10x Genomics

value: Control


title: U2OS cells, FAS site 3 gDNA

value: digested with FAS site 3 sgRNA


title: Kabuki syndrome type 1 replicate 4

value: Kabuki syndrome type 1


title: Foxp2-cKO_P9 #3

description: 10x Genomics

value: Dorsal Striatum


title: Kabuki syndrome type 1 replicate 2


title: Kabuki syndrome type 1 replicate 1


title: U2OS cells, LAG3 site 2 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with LAG3 site 2 sgRNA


title: Control_P9 #2

description: 10x Genomics


title: U2OS cells, FAS site 2 gDNA

value: digested with FAS site 2 sgRNA


title: Control_P9 #1

description: 10x Genomics

value: M


title: Liver HFDt-3

description: Liver HFD tolerant rep 3

source_name: Liver

value: Liver


title: Wild-type replicate 2

value: Wild-type


title: Kabuki syndrome type 2 replicate 4

value: CD90.2+ T cells

value: Kabuki syndrome type 2


title: Kabuki syndrome type 2 replicate 3


title: U2OS cells, CXCR4 site 2 gDNA

value: WT

value: digested with CXCR4 site 2 sgRNA


title: U2OS cells, FAS site 1 gDNA

value: digested with FAS site 1 sgRNA


title: Liver HFDi-3

description: Liver HFD intolerant rep 3

value: C57BL/6 wildtype

value: High Fat Diet


title: Kabuki syndrome type 2 replicate 2


title: Foxp1/2-cKO #2

description: 10x Genomics

data_processing:
cellranger-atac mkfastq
cellranger-atac count
macs2
seurat
signac
Assembly: mm10 (GRCm38p6)
Supplementary files format and content: barcodes.tsv' a tab-delimited text files include list of cell-barcodes and 'features.tsv' a tab-delimited text file include list of peaks and 'matrix.mtx' file in a sparse matrix format containing raw counts per peak per cell-barcode.

extract_protocol:
Striatal tissue for P9 mice was collected following rapid decapitation and brains were removed and placed in ice-cold artificial cerebrospinal fluid (ACSF; 126 mM NaCl, 20 mM NaHCO3, 20 mM D-Glucose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM MgCl2) bubbled with 95% O2 and 5% CO2. 500uM coronal sections were made in ACSF using a VF-200 Compresstome (Precisionary Instruments) and transferred to another chamber filled with ACSF. From 3 striatal sections, 6 punches of striatal tissue were collected (2 per hemisphere), flash frozen, and stored in -80C. Nuclei isolation for snATAC-Seq was done as follows: tissue was homogenized in a glass Dounce tissue grinder (25 times with pestle A, 25 times with pestle B; Sigma, Cat#D8938) in 1mL ice-cold EZ Nuclei Lysis Buffer (Sigma, Cat #NUC-101). Samples were incubated on ice for 3 minutes with an additional 1mL ice-cold EZ lysis buffer and then centrifuged at 500 X g for 5 minutes at 4C. Nuclei were then washed in 500uL Nuclei Wash Buffer (20uL of 1M Tris pH 7.4, 4uL of 5M NaCl, 6uL 1M MgCl2, 0.01% BSA, 20uL of 10% Tween-20 + 1.75mL H2O) and spun at 500 X g for 5 minutes again. The supernatant was then discarded, the pellet was resuspended in 150uL nuclei wash buffer, and filtered through FLOWMI tip strainer (Bel-Art Products, Cat# H13680-0040); more wash bufer was added as needed to help samples go through the FLOWMI tip. An aliquot was stained with Trypan Blue and counted under a microscope to determine concentration (targeting 4,000 nuclei/uL). Nuclei were then diluted to desired concentration, using 20X Nuclei buffer provided by 10X.
Library was performed according to the manufacter’s instructions (single cell ATAC v1.1 and v2 protocol, 10x Genomics). Isolated nuclei were mixed with the transposition mix which was followed by transposition. Then, 10X  master mix was and samples were loaded onto chip alongside  partitioning oil and gel beads. This results in generation of gel bead-in-emulsion (GEMs).  GEMs were then cleaned with Silane DynaBeads  followed by size-sleion using SPRIselect beads. Samples were cleaned with 80% ethanol  as well. Finally, libraries were constructed and  paired-end constructs with P5 and P7 sequences and a sample index were added during these final steps.


title: Liver HFDi-1

description: Liver HFD intolerant rep 1


title: U2OS cells, CXCR4 site 1 gDNA

value: digested with CXCR4 site 1 sgRNA


title: Liver HFDt-1

description: Liver HFD tolerant rep 1


title: Round Spermatids LFD3

description: Round Spermatids LFD rep 3

source_name: Round Spermatids

extract_protocol:
Total RNA was prepared from Morula, Sperm and Round spermatids using the RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. RNA purity, integrity and quality was examined by Bioanalyzer (Agilent Technologies) and Qubit (Thermo Fisher Scientific).
Transcript Libraries were constructed using the Nextera Library Prep Kit (Illumina) according to the manufacturer’s instructions and sequenced on an Illumina HiSeq 2500.

value: Round Spermatids

value: Low Fat Diet


title: Foxp1/2-cKO #1

description: 10x Genomics

value: Dorsal Striatum


title: Foxp2-cKO #3

description: 10x Genomics


title: Wild-type replicate 1


title: Foxp2-cKO #2

description: 10x Genomics

value: F


title: Liver HFDt-2

description: Liver HFD tolerant rep 2


title: Kabuki syndrome type 2 replicate 1


title: U2OS cells, CXCR4 site 10 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with CXCR4 site 10 sgRNA


title: Round Spermatids LFD2

description: Round Spermatids LFD rep 2


title: U2OS cells, CTLA4 site 1 gDNA

value: digested with CTLA4 site 1 sgRNA


title: Foxp2-cKO #1

description: 10x Genomics


title: Liver HFDi-2

description: Liver HFD intolerant rep 2

value: Liver


title: C2C12 WT D5 Sample 3

city: Columbus

first: Dominic

last: Kolonay

state: OH

address: 460 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

data_processing:
The R package DESeq2 (v 1.6.3) was used for differential gene expression analysis (Love et al. 2014). Read counts obtained from featureCounts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size (Liao et al. 2014). The average normalized expression values of the samples were used to calculate fold change and P values.
Assembly: mm10
Supplementary files format and content: BAM files include sequencing reads mapped to reference genome and quality scores

extract_protocol:
Total RNA was isolated from n=3 cultured C2C12 myoblasts at D0 and D5 using Tri-Reagent according to the manufacturer’s instructions (Sigma Aldrich).
RNA quality was accessed using a 2100 Bioanalyzer System (Agilent), and samples with RNA Integrity Number (RIN) greater than 8.0 were sequenced. Illumina RNA-Seq was performed by the Genomics Services Laboratory (GSL) at Nationwide Children’s Hospital (Columbus, OH). Quality assessment of the RNA-Seq data was performed using NGS-QC-Toolkit (v 2.3.3) with default settings (Patel & Jain 2012). Quality filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0) aligner with default settings (Kim et al. 2013).

value: Mouse Muscle Myoblasts


title: Round Spermatids LFD1

description: Round Spermatids LFD rep 1


title: Foxp1/2-cKO #3

description: 10x Genomics

value: M


title: U2OS cells, CTLA4 site 12 gDNA

value: WT

value: digested with CTLA4 site 12 sgRNA


title: Foxp1-cKO #3

description: 10x Genomics


title: C2C12 WT D5 Sample 2


title: U2OS cells, CXCR4 site 11 gDNA

value: digested with CXCR4 site 11 sgRNA


title: Foxp1-cKO #1

description: 10x Genomics


title: Foxp1-cKO #2

description: 10x Genomics


title: C2C12 WT D5 Sample 1


title: U2OS cells, CTLA4 site 11 gDNA

value: digested with CTLA4 site 11 sgRNA


title: Control #3

description: 10x Genomics

value: Control


title: C2C12 WT D0 Sample 3


title: Control #2

description: 10x Genomics


title: C2C12 WT D0 Sample 1


title: U2OS cells, CCR5 site 14 gDNA

value: digested with CCR5 site 14 sgRNA


title: U2OS cells, CCR5 site 15 gDNA

value: digested with CCR5 site 15 sgRNA


title: U2OS cells, CTLA4 site 10 gDNA

value: digested with CTLA4 site 10 sgRNA


title: C2C12 WT D0 Sample 2


title: Control #1

description: 10x Genomics

value: Dorsal Striatum


title: G2

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

library_source: other

data_processing:
Cellranger v6.0.1 count and aggr functions to aggregate reads across sequncing lanes into a single set of barcodes.tsv.gz, features.tsv gz and matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files
Library strategy: ECCITE-seq

molecule: other

source_name: lung

extract_protocol:
CD45+ and tumors (GFP+) were sorted from lungs digested into a singlce cell suspension.  Single cells were encapsulated in gel-beads=in emulsion using the 10x controller with a chromium single cell 5'GEM library and gel bead kit
ECCITE-seq and hashing protocol  described by Stoeckius et al, Mimitou et al, Buus et al  was used to generate an antibody-derived tag(ADT/hashtag oligo (HTO) library, a 5' gene expression library, and a VDJ-TCR library

treatment_protocol: 2 mice (G1 vs G2) per treatment arm: Isotype + Vehicle (HT4), DRP-104  + Isotype (HT2), anti-PD1 + Vehicle (HT3), and DRP-104 + anti-PD1 (HT1). Mice were treated for 5 days then lungs were collected for analysis

value: lung

value: Kras G12D p53-/- Keap1 R470C

value: CD45+ and lung tumor

value: DRP-104 +/- Anti-PD1


title: U2OS cells, CCR5 site 13 gDNA

value: derived from sarcoma of the tibia

value: sarcoma of the tibia

value: digested with CCR5 site 13 sgRNA


title: Sperm LFD-2

description: Cauda Spematozoa rna-seq LFD rep 2

source_name: Cauda Spermatozoa

value: Cauda Spermatozoa

value: C57BL/6 wildtype

value: Low Fat Diet


title: U2OS cells, CCR5 site 11 gDNA

value: WT

value: digested with CCR5 site 11 sgRNA


title: G1


title: Ptch1CKO_cochlear

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

address: 608A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: 10X Chromium Next GEM Single Cell 3' Reagent Kits v3.2

data_processing:
cellranger-6.0.0
Assembly: mm10

source_name: Cochlear

extract_protocol:
Cochleae from E16.5 WT and Emx2Cre;Ptch1f/f (8 cochleae for each genotype) were dissected out from inner ear in cold DEPC treated PBS and incubated in 150µL HBSS supplemented with 1mg/mL collagenase/dispase for 30min at 37°C with shaking at 900rpm. Samples were pipette up and down every 10mins. Following the incubation, 150µL HBSS with 20% FBS was added to stop the digestion and dissociated samples were passed through 40μm cell strainer. Filtered cells was pelleted at 300Xg for 5min and resuspended in HBSS with 10% FBS to around 1000 cells/μL.
Single cell libraries were prepared by single cell omics core of the Chinese University of Hong Kong using the 10X Chromium Next GEM Single Cell 3' Reagent Kits v3.1 according to the manufacturer’s protocols.

value: Cochlear

value: Mixed (129/SvEv, C57BL/6N)


title: Sperm LFD-1

description: Cauda Spematozoa rna-seq LFD rep 1


title: Sperm HFD-3

description: Cauda Spematozoa rna-seq HFD rep 3

value: High Fat Diet


title: U2OS cells, CBLB site 8 gDNA

value: digested with CBLB site 8 sgRNA


title: Round Spermatids HFD3

description: Round Spermatids HFD rep 3

value: Round Spermatids


title: PD #3

city: Ames

first: Minhong

middle: Neenah

last: Huang

state: Iowa

address: 1800 Christensen Dr

department: Deparment of Biomedical Sciences

institute: Iowa State University

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Mouse brain tissue

growth_protocol: All mice used for this study were bred and maintained under a 12-h light cycle in a climate-controlled mouse facility (22±1°C) with food and water available ad libitum.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: None of them were treated.

tag: sample type

value: PD brain cells

value: Transgenic mice from C57BL/6


title: Round Spermatids HFD2

description: Round Spermatids HFD rep 2


title: Round Spermatids HFD1

description: Round Spermatids HFD rep 1


title: WT_E16.5_cochlear

description: 10X Chromium Next GEM Single Cell 3' Reagent Kits v3.1

value: Wildtype


title: Sperm HFD-2

description: Cauda Spematozoa rna-seq HFD rep 2


title: PD #2


title: Sperm LFD-3

description: Cauda Spematozoa rna-seq LFD rep 3


title: Ch25h.none.LPS.18.3

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

data_processing:
Performed initial quality assessment using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.9
Read ends consisting of 50 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome using GSNAP version 2018-07-04 (http://research-pub.gene.com/gmap/) called with args: gsnap.avx2 -N 1 -t 23 -D /gmapdb -d mm10ex_MTb -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --format=sam
Feature counts were extracted from gsnap outputs using the featureCounts software (http://bioinf.wehi.edu.au/featureCounts/) part of Subread package v1.5.2
Differential expression of genes was calculated using edgeR (http://bioconductor.org/packages/edgeR/) version 3.26.8
Assembly: mm10
Supplementary files format and content: A .tsv file with raw counts for all genes

source_name: BMDM

growth_protocol: Bone marrow derived macrophages were prepared as described in Gold, E. S. et al. ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation. J. Exp. Med. 209, 807–817 (2012) and Olson, G. S. et al. Type I interferon decreases macrophage energy metabolism during mycobacterial infection. Cell Rep. 35, 109195 (2021)

extract_protocol:
Cells were harvested for total RNA extraction using SV 96 total isolation RNA kit (Promega Z3500).
Illumina TruSeq stranded

treatment_protocol: Cells were treated for 18 hours with either 25-hydroxycholesterol (5 uM), itraconazole (1 uM), or OSW-1 (0.3 uM) and then stimulated with lipopolysaccharide (10 ng/mL).

value: BMDM

tag: mouse

tag: stimulus

value: LPS

tag: stimtime


title: Sperm HFD-1

description: Cauda Spematozoa rna-seq HFD rep 1


title: PD #1


title: U2OS cells, CBLB site 6 gDNA

value: derived from sarcoma of the tibia

tag: cell line

value: sarcoma of the tibia

value: digested with CBLB site 6 sgRNA


title: Ch25h.none.LPS.18.1


title: U2OS cells, CBLB site 5 gDNA

value: digested with CBLB site 5 sgRNA


title: Morula HFD-2

description: Morula rna-seq HFD rep 2

source_name: Morula

value: Morula

value: C57BL/6 wildtype


title: Morula HFD-3

description: Morula rna-seq LFD rep 5


title: Control #2

value: Littermate control brain cells


title: U2OS cells, CBLB site 4 gDNA

source_name: derived from sarcoma of the tibia

value: WT

value: digested with CBLB site 4 sgRNA


title: Control #1


title: Ch25h.none.none.0.2 (OSBP control)


title: U2OS cells, B2M site 2 gDNA

value: digested with B2M site 2 sgRNA


title: Ch25h.none.LPS.18.2


title: C-40

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: SARS-COV2 infected, hospitalized, not assisted with respirator, replicate 6

data_processing:
The small RNA sequencing data analysis was performed with the XICRA pipeline and XICRA.stats, the R companion package (Sanchez Herrero, Pluvinet, Luna de Haro and Sumoy, 2021). See additional details in https://xicra.readthedocs.io/en/latest/ or https://github.com/HCGB-IGTP/XICRA.
We checked raw data quality before and after trimming the reads to discard sequencing adapters using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and cutadapt (Martín, 2011), respectively.
For the mapping and the biotype feature assignment of all reads we used STAR mapping software (Dobin et al., 2013) and featureCounts (Liao et al., 2014) using as a reference GRCh38
For miRNA identification, we used miraligner (within the SeqBuster software, which can resolve canonical and other isomiR variants (Pantano et al., 2010) and a miRBase (Kozomara et al., 2019) (v22) as the reference database. Then, using miRTop, we formatted results into standardized files and generated expression count matrices.
The analysis of differential expression of small RNA we employed XICRA.stats, running DESeq2 (Love et al., 2014, Zhu et al., 2019) and other packages under the R software environment.
Assembly: hg38 (Ensembl release 78, Homo_sapiens.GRCh38.dna.primary_assembly), and mature miRBase v22
Supplementary files format and content: Supplementary excel file includes DESeq2 normalized read counts for miRNAs

source_name: blood

growth_protocol: This cross-sectional study included plasma samples from 40 hospitalized patients with acute SARS-CoV-2 from the KING observational study at the Hospital Universitari Germans Trias i Pujol (Badalona, Spain), which aimed to characterize virological and immunological features of SARS-CoV-2 infection (49). The study was approved by the Hospital Universitari Germans Trias i Pujol Ethics Committee Board (reference PI-20-122). Participants were enrolled after a positive test for SARS-CoV-2 infection (either a virological test performed by RT-qPCR analysis of nasopharyngeal swabs in routine clinical screenings or a serological test performed by in-house ELISA of plasma samples). Plasma samples from a previously described (14) cohort of 21 healthy, uninfected volunteers were also analyzed as a control group. Patient and healthy donor samples were obtained with written informed consent, as required by the Ethics Committee Board. Blood was collected by venipuncture in EDTA vacutainer tubes (BD Bioscience). Plasma was obtained by centrifugation of blood at 1200 g for 10 min and stored at –80 °C until use.

extract_protocol:
Total RNA was extracted with a miRCURY Isolation kit- Biofluids (Exiqon) following manufacturer indications with modifications that included using glycogen as carrier and a 1:50 dilution of spike in RNA.. Tests of the robustness of the plasma RNA isolation procedure and the detection of hemolysis were performed with the Exiqon serum qPCR panel with all samples entering the experiment having deltaCq (miR‐ 23a‐miR‐451)<5.
Small RNA sequencing libraries were prepared according to the TruSeq Small RNA Sample Preparation Guide (Illumina) using as input all the RNA extracted from 200 ul pf plasma and 15 cycles of PCR amplification. Prior to pooling and size selection, individual library yields and molarities were determined, based on an integration of the 135–160-bp size range, with the DNA 1000 Kit on a Bioanalyzer 2100 (Agilent Technologies). Libraries exhibited visible size patterns and yields according to specifications (with major peaks expected around 142 bp for miRNAs and 152 for piwiRNAs). All libraries were indexed on the basis of barcoded adapter ligation. Libraries were combined to form independent pools. Next, an automated pooled library size selection was carried out. Each individual pool was size selected for products between 115 and 165 bp with the Pippin Prep automated gel system and 3% agarose dye-free gel cassettes with internal standards (Sage Science). Library pools were cleaned and concentrated by performing column centrifugation, prior to and after size selection, with the QIAquick PCR purification kit (Qiagen). Size-selected library pool quality was reassessed with the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). The final concentration was derived with qPCR, performed with the KAPA library quantification Kit for Illumina (Kapa Biosystems) on a 7900-HT PCR system (Applied Biosystems, Thermo Fisher). For each of the two pools, sequencing was performed on three independent HiSeq-2500 lanes (Illumina). Sequencing was performed on cBot and HiSeq-2500 instruments (Illumina), with the HiSeq single-read cluster generation, version 4, designed for the cBot-HiSeq, and the HiSeq sequencing-by-synthesis 50-cycle kit, according to manufacturer protocols. Per-sample raw data files were generated in fastq format with bcl2fastq conversion software (Illumina). A quality control step to select samples with minimal signs of hemolysis was also performed. None of the miRNA sequences that were DE between cases and controls overlapped with miRNA sequences that originated in platelets or erythrocytes.

value: blood

tag: biofluid

value: plasma

value: COVID 19 with acute infection

tag: gender

value: Male

tag: oxygen flow

value: No oxygen

tag: hemolysis score


title: U2OS cells, B2M site 4 gDNA

tag: cell type

tag: genotype

value: digested with B2M site 4 sgRNA


title: U2OS cells, B2M site 3 gDNA

tag: tissue

tag: treatment

value: digested with B2M site 3 sgRNA


title: Morula LFD-2

description: Morula rna-seq LFD rep 2

value: Low Fat Diet