title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-C_dPP_batch1

value: Nsd1 knockout 2; piggyBac NSD1-C_dPP


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-FL_dPP

status: Public on Jul 03 2023

type: SRA

city: New York

first: Zhen

last: Sun

state: NY

address: 408 E 69th street, Z619

department: Human Oncology and Pathogenesis Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Bcl files containing raw sequencing data were converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422, Illumina). Paired-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) using Bowtie2 (v2.3.4.1) with “--local --very-sensitive-local --phred33 --no-unal --no-mixed --no-discordant -I 10 -X 700 -S”. Reads were also aligned to the drosophila (dm6) genome with additional “--no-overlap” to map spike-in reads. Number of mapped reads to each genome was used to generate scaling factors for downstream spike-in normalization. Sam files were converted to bam files, sorted and indexed using samtools (v1.9). Peaks were called using MACS2 (v2.2.6) callpeak program with “-f BAMPE --keep-dup 1 -q 0.05”. Peaks from NSD1 CUT&RUN using NSD1-dTAG mESCs were additionally filtered for q < 0.000001. For peak calling, datasets generated using NSD1 degraded (72h) cells, Nsd1 KO cells or IgG was used as controls. Bigwig pileup files were generated using the bamCoverage program from DeepTools (v3.2.1) with “-bs 10 --extendReads --normalizeUsing RPKM --exactScaling --skipNonCoveredRegions” and filtered for mouseENCODE blacklisted genomic regions (v2). For NSD1/H3K36me2 and SETD2/H3K36me3 CUT&RUN in NSD1-dTAG and SETD2-dTAG cells, respectively, as well as for NSD1 CUT&RUN in rescue cells expressing NSD1 C series, scaling factors calculated using the percentage of spike-in reads were applied to the “--scaleFactor” option for cell number based normalization. In other cases, the spike-in read percentage was very close and a scaling factor of 1 was applied.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14 mESCs were cultured on 0.1% gelatin-coated dishes in 2i/LIF medium (50% DMEM/F12, 50% Neurobasal, 0.5% N2 supplement, 1% B27 supplement, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium Pyruvate, 50 μM b-mercaptoethanol, 1 μM MEKi (PD0325901), 3 μM GSK3i (CHIR99021), and 1x Leukemia Inhibitory Factor (LIF, produced in the Helin lab)). EpiSCs were cultured on 16.7 μg/mL fibronectin-coated dishes in medium containing 50% DMEM/F12, 50% Neurobasal, 0.5% N2 supplement, 1% B27 supplement, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 50 μM b-mercaptoethanol, 12.5 ng/mL recombinant human basic FGF (FGF2), 20 ng/mL Activin A, and 175 nM Wnt inhibitor NVP-TNKS656.

extract_protocol:
Dessociated cells were bound to Concanavalin A beads and permeabilized with Digitonin, followed by binding of antibodies and pAG-MNase to targets on native chromatin in situ. MNase cleavage of target occupied DNA was activated by addition of CaCl2 at 4C. Cleaved DNA was released by incubation at 37C and purified using Monarch DNA Cleanup Kit (NEB).
Libraries were prepared with less than 10 ng CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol with modifications: end prep was performed for 30 min at 20C followed by 1 h at 50C to prevent melting of small fragments, adaptor-ligated DNA was cleaned up without size selection, and the anneal/extension step of PCR amplification was performed for 10s at 65C to favor exponential amplification of the desired CUT&RUN fragments.

treatment_protocol: Cells were treated with 500 nM dTAG-13 for indicated amount of time. For EB differentiation, mESCs were grown in suspension in non-TC-treated culture dishes in medium containing GMEM, 10% heat-inactivated FBS, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium Pyruvate, and 100 μM β-Mercaptoethanol.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Nsd1 knockout 2; piggyBac NSD1-FL_dPP

tag: treatment

value: no treatment

tag: cut&run antibody

value: HA (Cell Signaling, 3724)


title: Neurologically unaffected control Sample 1

city: Gainesville

first: Curtis

middle: A

last: Nutter

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description:
rRNA depleted
CTL_1

library_source: transcriptomic

data_processing:
aligned using STAR
alignment analyzed using rMATS
alignment analyzed using DESEQ2
alignment analyzed using HOMER
Assembly: GRCh38/hg38
Supplementary files format and content: DataFileS2_Nutter_Final is an excel file which contains tabs with paired group comparisons of alternative splicing changes from rMATS or differential expression from DESeq2. There are also tabs with gene counts for all expressed genes for all sample groups.

molecule: total RNA

organism: Homo sapiens

source_name: choroid plexus, lateral

extract_protocol:
Human ChP tissues (Alzheimer’s disease and neurologically unaffected controls) were obtained from the NIH NeuroBioBank. Myotonic dystrophy type 1 ChP tissues were obtained both from the University of Florida (UF) Center for NeuroGenetics and the Stanford University Neuromuscular BioBanks. All human ChP tissues used in this study were pre-existing and deidentified.
For RNA isolation, tissue samples were homogenized in 300 μL TRI Reagent (Zymo R2050-1-200) and incubated at 25C for 10 min. Total RNA was isolated using the Direct-zol RNA miniprep kit (Zymo), following the manufacturer’s instructions, including an on-column DNase I digestion step. RNA concentration was determined using the Qubit 4 Fluorometer with a broad range RNA quantification broad range kit (Invitrogen). RNA quality was checked using a Fragment Analyzer (Agilent) and depleted of rRNA (rRNA Depletion Kit v2 Human/Mouse/Rat, NEB).
cDNA libraries prepared using the Ultra II Directional RNA Library, NEB. Human ChP libraries were generated using 500 ng of total RNA input and sequenced on Illumina NextSeq500 and/or NextSeq2000 platforms.

tag: tissue

value: choroid plexus, lateral

tag: Sex

value: female

tag: disease group

value: Neurologically unaffected control

tag: age of_death

tag: (co-)morbidities

value: Hypertension, Atherosclerosis, Cardiovascular disease


title: SMA patient after six months of  Nusinersen treatment  [15_T6]

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Trimmed reads were aligned through Bluebee Corall platform. Differential expression analysis was performed using R package DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 output

source_name: CSF

extract_protocol:
RNA was extracted using miRNeasy Serum/Plasma (Qiagen)
Libraries were prepared starting from 500 ng of total RNA. RNA was fractioned for rRNA depletion using RiboCop V1.3 (Lexogen) and libraries were prepared with the CORALL Total RNA-Seq Library Prep Kit (Lexogen) following manufacturer's intructions. The quality of libraries was analyzed using 4200 Tape Station with a “DNA High sensitivity” assay (Agilent) and quantified using High Sensitivity dsDNA assay with a Qubit device (Life Technologies). Sequencing was performed using Illumina NextSeq 500.

value: CSF

tag: disease state

value: SMA

tag: treatment/time point


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-C_dPWWP2_batch1

value: Nsd1 knockout 2; piggyBac NSD1-C_dPWWP2


title: SMA patient after six months of  Nusinersen treatment  [16_T6]


title: myotonic dystrophy type 1 Sample 2

description:
rRNA depleted
DM1_2

value: male

value: myotonic dystrophy type 1


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-C_rescue_batch2_bioRep2

value: Nsd1 knockout 2; piggyBac NSD1-C


title: SMA patient after six months of  Nusinersen treatment  [18_T6]


title: SMA patient after six months of  Nusinersen treatment  [14_T6]


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-C_dPHD1-4_batch1

value: Nsd1 knockout 2; piggyBac NSD1-C_dPHD1-4


title: SMA patient after six months of  Nusinersen treatment  [13_T6]


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-C_rescue_batch1_bioRep1


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_batch1

value: Nsd1 knockout 2


title: RNA-seq_mESC_WT_nontreated_bioRep3

data_processing:
Bcl files containing raw sequencing data was converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). Single-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) with default parameters. The number of reads mapped to each gene was counted using STAR with “--quantMode GeneCounts”. Differential gene expression analysis was performed using DESeq2 (v1.30.0) with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing raw read counts at genes

molecule: polyA RNA

growth_protocol: E14 mESCs were cultured on 0.1% gelatin-coated dishes in 2i/LIF medium (50% DMEM/F12, 50% Neurobasal, 0.5% N2 supplement, 1% B27 supplement, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium Pyruvate, 50 μM b-mercaptoethanol, 1 μM MEKi (PD0325901), 3 μM GSK3i (CHIR99021), and 1x Leukemia Inhibitory Factor (LIF, produced in the Helin lab)).

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and ERCC RNA Mix 1 was spiked in. Poly(A) RNA was selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

value: WT


title: RNA-seq_mESC_WT_nontreated_bioRep2

value: mouse embryonic stem cells


title: SMA patient after six months of  Nusinersen treatment  [10_T6]


title: CUT&RUN_H3K36me3_mESC_SETD2-dTAG_dTAG-13_6h

value: SETD2-dTAG knockin

value: dTAG-13 for 6h

value: H3K36me3 (Active Motif, 61022)


title: CUT&RUN_H3K36me3_mESC_SETD2-dTAG_dTAG-13_24h

value: dTAG-13 for 24h


title: SMA patient after six months of  Nusinersen treatment  [11_T6]


title: CUT&RUN_H3K36me3_mESC_SETD2-dTAG_dTAG-13_48h

value: dTAG-13 for 48h


title: SMA patient after six months of  Nusinersen treatment  [9_T6]


title: CUT&RUN_H3K36me3_mESC_SETD2-dTAG_dTAG-13_1h

value: dTAG-13 for 1h


title: SMA patient after six months of  Nusinersen treatment  [4_T6]


title: CUT&RUN_H3K36me3_mESC_SETD2-dTAG_dTAG-13_0h

value: no treatment


title: SMA patient after six months of  Nusinersen treatment  [6_T6]

value: CSF


title: SMA patient after six months of  Nusinersen treatment  [3_T6]

value: SMA


title: SMA patient after six months of  Nusinersen treatment  [5_T6]


title: CUT&RUN_H3K27me3_EB_d6_NSD1-dTAG_dTAG-13

value: NSD1-dTAG knockin

value: EB differentiation for 6 days; dTAG-13 for 6 days

value: H3K27me3 (Cell Signaling, 9733)


title: CUT&RUN_H3K36me2_EB_d6_NSD1-dTAG_nontreated

value: EB differentiation for 6 days

value: H3K36me2 (Thermo Fisher, MA5-14867)


title: CUT&RUN_H3K36me2_EB_d6_NSD1-dTAG_dTAG-13


title: SMA patient after six months of  Nusinersen treatment  [7_T6]


title: CUT&RUN_HA_SETD2_mESC_SETD2-dTAG_dTAG-13_0h

value: HA (Cell Signaling, 3724)


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 9

city: Ithaca

first: Praveen

last: Sethupathy

address: Cornell University, College of Veterinary Medicine Room #T7006, Vet Research Tower 618 Tower Rd.

department: Cell and Molecular Biology

institute: Cornell University

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using STAR/Salmon (RNA-seq)
smRNA- and RNA-seq data was normalized using DESeq2. smRNA-seq data was rlog transformed followed by limma batch correction.
Assembly: mm9 (small RNAseq) or vM10 (RNAseq).
Supplementary files format and content: Normalized counts

source_name: Humanized Female Adipose

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

treatment_protocol: 129S6/SvEvTac (WT and humanized for both sexes) mice expressing exposed to 400ppb of iAs for 4 weeks

tag: strain

value: female

tag: genetic modification

value: expressing the human ortholog of AS3MT

value: exposed to 400ppb of iAs

value: Adipose


title: smRNA 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 11

source_name: WT Male Adipose

value: male

value: expressing the mouse ortholog of AS3MT


title: smRNA 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 12


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 12


title: SMA patient after six months of  Nusinersen treatment  [12_T6]


title: SMA patient after six months of  Nusinersen treatment  [8_T6]


title: SMA patient after six months of  Nusinersen treatment  [2_T6]


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 10

source_name: Humanized Male Adipose


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 13


title: SMA patient after six months of  Nusinersen treatment  [1_T6]


title: CUT&RUN_HA_SETD2_mESC_SETD2-dTAG_dTAG-13_48h

value: mouse embryonic stem cells

value: SETD2-dTAG knockin

value: dTAG-13 for 48h


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 6


title: CUT&RUN_HA_NSD1_EB_d6_NSD1-dTAG_nontreated


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 11


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 11

source_name: WT Female Adipose


title: CUT&RUN_H3K27me3_EB_d6_NSD1-dTAG_nontreated


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 10


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 9


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 7


title: SMA patient before Nusinersen treatment  [17_T0]

value: CSF

value: before Nusinersen treatment


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 8


title: CUT&RUN_H3K27ac_EpiSC_NSD1-dTAG_nontreated

value: mouse epiblast stem cells

value: NSD1-dTAG knockin

value: no treatment

value: H3K27ac (Thermo Fisher, MA5-23516)


title: SMA patient before Nusinersen treatment  [16_T0]

value: SMA


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 6


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 8


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 9


title: CUT&RUN_H3K36me2_EpiSC_NSD1-dTAG_nontreated

value: H3K36me2 (Thermo Fisher, MA5-14867)


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 8

value: female


title: SMA patient before Nusinersen treatment  [15_T0]


title: SMA patient before Nusinersen treatment  [14_T0]


title: CUT&RUN_IgG_mESC_NSD1-dTAG_nontreated

value: IgG (Abcam, ab46540)


title: SMA patient before Nusinersen treatment  [18_T0]


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 6

value: expressing the human ortholog of AS3MT

value: exposed to 400ppb of iAs


title: SMA patient before Nusinersen treatment  [13_T0]


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 7

value: Adipose


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 5

source_name: WT Male Liver

value: male

value: expressing the mouse ortholog of AS3MT

value: Liver


title: CUT&RUN_OCT4_mESC_NSD1-dTAG_nontreated

value: mouse embryonic stem cells

value: OCT4 (Santa Cruz, sc-5279)


title: SMA patient before Nusinersen treatment  [12_T0]

value: CSF

value: before Nusinersen treatment


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 4


title: CUT&RUN_BRG1_mESC_NSD1-dTAG_nontreated

value: NSD1-dTAG knockin

value: BRG1 (Santa Cruz, sc-17796)


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 3


title: SMA patient before Nusinersen treatment  [11_T0]


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 5

source_name: WT Female Liver


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 4


title: SMA patient before Nusinersen treatment  [10_T0]


title: CUT&RUN_H3K4me3_mESC_NSD1-dTAG_nontreated

value: no treatment

value: H3K4me3 (Thermo Fisher, PA5-27029)


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 6

source_name: Humanized Male Liver


title: SMA patient before Nusinersen treatment  [9_T0]

value: SMA


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 3

value: female


title: CUT&RUN_H3K4me1_mESC_NSD1-dTAG_nontreated

value: H3K4me1 (Cell Signaling, 5326)


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 5

value: expressing the human ortholog of AS3MT


title: CUT&RUN_HA_NSD1_EpiSC_NSD1-dTAG_nontreated

value: mouse epiblast stem cells

value: HA (Cell Signaling, 3724)


title: CUT&RUN_BRD4_mESC_NSD1-dTAG_dTAG-13_6h

value: dTAG-13 for 6h

value: BRD4 (Abcam, ab128874)


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 7

value: male

value: exposed to 400ppb of iAs

value: Adipose


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 4

value: Liver


title: CUT&RUN_BRD4_mESC_NSD1-dTAG_dTAG-13_0h

value: mouse embryonic stem cells


title: SMA patient before Nusinersen treatment  [8_T0]

value: CSF

value: before Nusinersen treatment


title: CUT&RUN_MED1_mESC_NSD1-dTAG_dTAG-13_6h

value: NSD1-dTAG knockin

value: MED1 (Abcam, ab64965)


title: SMA patient before Nusinersen treatment  [7_T0]

value: SMA


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 2

value: female

value: expressing the mouse ortholog of AS3MT


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 5

source_name: Humanized Female Liver

value: expressing the human ortholog of AS3MT


title: SMA patient before Nusinersen treatment  [6_T0]


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 4


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 2


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 1


title: CUT&RUN_MED1_mESC_NSD1-dTAG_dTAG-13_24h

value: dTAG-13 for 24h


title: CUT&RUN_HA_NSD1_EB_d6_NSD1-dTAG_dTAG-13

value: EB differentiation for 6 days; dTAG-13 for 6 days

value: HA (Cell Signaling, 3724)


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 3


title: SMA patient before Nusinersen treatment  [4_T0]


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 2


title: smRNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 1


title: CUT&RUN_MED1_mESC_NSD1-dTAG_dTAG-13_1h

value: dTAG-13 for 1h


title: CUT&RUN_MED1_mESC_NSD1-dTAG_dTAG-13_0h

value: no treatment


title: SMA patient before Nusinersen treatment  [2_T0]


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 1

value: male

value: exposed to 400ppb of iAs


title: smRNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 3

value: Liver


title: smRNA 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 2

source_name: Humanized Male liver


title: CUT&RUN_H3K27ac_mESC_NSD1-dTAG_dTAG-13_6h

value: mouse embryonic stem cells

value: dTAG-13 for 6h

value: H3K27ac (Thermo Fisher, MA5-23516)


title: SMA patient before Nusinersen treatment  [5_T0]

value: CSF

value: before Nusinersen treatment


title: smRNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 1


title: SMA patient before Nusinersen treatment  [1_T0]

value: SMA


title: MV4_11_GenomewideCRISPRScreens_C6_Rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
Ribosome Profiling analysis: 1. trim adapters using Cutadapt with  -a AGATCGGAAGAGCACACGTC -g AGATCGGAAGAGCAC; 2. remove UMI and attach to readID ( --extract-method=string --bc-patter  n=NN  & --extract-method=string --bc-pattern=NNNNNXXXXX   --3prime); 3. barcode demultiplexing using sabre; 4. align aginst rRNA using Bowtie2; 5. algin unmapped reads from step4 against transcriptome using STAR; 6. deduplicate using UMI-tools; 7. generate count table to central ORF using bedtools coverage; 8. after batch removal, send RPF count and mRNAseq count to Xtail for differential translation analysis.
Multiplexing Barcodes: DMSO ATCGT; C6 AGCTA; C16 CGTAA
RNAseq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
CRISPR screen data were analyzed using MAGeCK
Assembly: hg19
Supplementary files format and content: Ribosome Profiling: tab-delimited text file include raw counts for each sample
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample
Supplementary files format and content: CRISPR screen: tab-delimited text file include raw counts for each sample
Library strategy: CRISPR Screen

growth_protocol: MV411 cells were grown in RPMI-1640 media supplemented with 10% FBS, 100 IU/mL penicillin, and 100 ug/mL streptomycin at 37°C in the presence of 5% CO2.

extract_protocol:
Genomic DNA was isolated from cells using the Quick-gDNA Midiprep Kit (Zymo Research) per the manufacturer’s instructions.
Illumina-compatible sequencing libraries were generated by PCR amplification of sgRNA sequences from gDNA using adapter-containing primers annealing to regions flanking the sgRNA sequence. PCR reactions were pooled and purified by ZymoSpin V column with Reservoir (Zymo Research).
CRISPR Screen

value: MLL-rearranged leukemia

value: Treated with 2 uM C6


title: MV4_11_GenomewideCRISPRScreens_DMSO_Rep2

value: Treated with 0.1% DMSO


title: CUT&RUN_H3K27me3_mESC_Nsd1_KO2

value: Nsd1 knockout 2

value: H3K27me3 (Cell Signaling, 9733)


title: SMA patient before Nusinersen treatment  [3_T0]


title: CUT&RUN_H3K27me3_mESC_NSD1-dTAG_dTAG-13_24h

value: NSD1-dTAG knockin

value: dTAG-13 for 24h


title: MV4_11_GenomewideCRISPRScreens_C6_Rep1


title: CUT&RUN_H3K27me3_mESC_NSD1-dTAG_dTAG-13_0h

value: no treatment


title: CUT&RUN_H3K27me3_mESC_NSD1-dTAG_dTAG-13_6h


title: Ctrl 3

city: Montreal

first: Hua

last: Gu

state: qc

address: 110 Pine avenue west

country: Canada

institute: The Clinic research Institute of Montreal

data_processing:
Reads were aligned to the reference mouse genome version GRCm38 using STAR version 2.5.1b
Raw counts for each feature from GRCm38 ENSEMBL v84 annotation file were extracted using FeatureCounts v1.4.6
DESeq2 version 1.12.3 was used to normalize gene readcounts and compute differential expression between conditions
Assembly: GRCm38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
FACS sorting of CD4+TCRb+PD1hiCXCR5hiCells
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IP injection of NP-OVA

value: Spleen

value: Tfh

value: wt ctrl

value: NP-OVA


title: CUT&RUN_H3K36ac_mESC_NSD1-dTAG_dTAG-13_24h

value: mouse embryonic stem cells

value: H3K36ac (Thermo Fisher, RM154)


title: Ctrl 1


title: CUT&RUN_H3K27ac_mESC_NSD1-dTAG_dTAG-13_24h

value: H3K27ac (Thermo Fisher, MA5-23516)


title: Cbl-/-Cbl-b-/- 3

value: dko (Cbl-/- Cbl-b-/-)


title: CUT&RUN_H3K36ac_mESC_NSD1-dTAG_dTAG-13_6h

value: dTAG-13 for 6h


title: Cbl-/-Cbl-b-/- 2


title: CUT&RUN_H3K36ac_mESC_NSD1-dTAG_dTAG-13_1h

value: dTAG-13 for 1h


title: Cbl-/-Cbl-b-/- 1


title: CUT&RUN_H3K36ac_mESC_NSD1-dTAG_dTAG-13_0h


title: CUT&RUN_H3K27ac_mESC_NSD1-dTAG_dTAG-13_0h


title: Ube3a_PATHET_12mo_Rep6

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Reads were quality-ﬁltered by requiring at least 90% of bases to have a quality score greater than 20 using fastq_quality_ﬁlter in FASTX-toolkit.
Adapter sequences were removed using cutadapt
Reads were then aligned to the mm9 reference genome using STAR 2.5.2b
Transcript abundance was measured using salmon, and differential expression tests were performed using DESeq2 corrected for library batch
Assembly: mm9
Supplementary files format and content: VST normalized expression values from DESeq2, corrected by library batch

source_name: Cerebral cortex

growth_protocol: Male and female adult C57BL/6J mice (Stock #: 000664) were obtained from Jackson Laboratories (Bar Harbor, ME) and housed in standard polycarbonate cages with cob bedding, shelter, and nesting material. Males were housed singly and females were housed in groups of up to five mice per cage. Mice had ad libitum access to food (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO) and water and were maintained on a 12:12 hr light/dark cycle. Mice were mated in 2 hr sessions and copulation was confirmed by presence of a vaginal plug. The beginning of the mating session when the plug was found was defined as E0.0. All experimental procedures were approved by the Animal Care and Use Committee at UNC-Chapel Hill in accordance with NIH Guidelines

extract_protocol:
Either 2 or 4 hr after the injection, dams were sacrificed via CO2 followed by cervical dislocation. Embryos were dissected from the placenta and stage-matched based on somite number (2 hr: 19-20 somites; 4 hr: 20-21 somites). A maximum of two embryos per litter were used to minimize litter effects. RNA from the rostroventral neural tube (RVNT) from each embryo was isolated using the RNeasy Plus Micro kit (Qiagen, Germantown, Maryland) as previously described (Boschen et al., 2020). RNA from a total of 6 embryos per condition and time point (24 total embryos) were submitted for RNA-seq.
Libraries for RNA sequencing (RNA-seq) were prepared using the SMARTr Ultra Low Input RNA (Clontech, Mountainview, CA) and Nextera XT DNA (Illumina, San Diego, CA) kits by the UNC High Throughput Sequencing Facility. Samples were pooled prior to sequencing, after RNA extraction and library preparation was complete. Six total pools (1 sample/group/pool) and 1 pool per lane were used. Paired-end (50bp) sequencing was performed on an Illumina HiSeq 4000.

treatment_protocol: Pregnant dams were administered a single dose of 2.9 g/kg ethanol (25% vol/vol; Pharmaco-Aaper, Brookfield, CT) in Lactated Ringer’s solution via i.p. injection on E9.0 to target neurulation. Blood alcohol concentrations ± standard error, collected from a separate cohort of dams (n = 6), were 366.8 ± 30.3 mg/dl 30 min after injection and 337.9 ± 18.8 mg/dl 2 hr after injection. Control mice were administered an equal volume of Lactated Ringer’s solution (1.5 ml/100 g body weight).

tag: age

tag: librarybatch


title: Ube3a_MATHET_12mo_Rep6


title: HTMEx TGF-treated sample 7

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

data_processing:
Sequence reads were mapped to the Human genome GRCh38 using the STAR aligner (v2.7.9a) with default parameters. Assembly and gene annotations were collected from Ensembl v106.
Counts extraction was done by STAR with parameter ‘--quantMode GeneCounts’.
Normalization and differential expression values were computed with the Internet-baseD tool for the Visualization and exploration of RNA-Seq data, based on the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: Comma-separated file including raw counts for all Samples
Supplementary files format and content: Comma-separated file containing all Samples metadata

source_name: Human trabecular meshwork explants

growth_protocol: After dissection, HTMEx were divided into equal parts and stimulated with recombinant human TGF-β2 (PeproTech Inc., 100-35B, Thermo Fisher Scientific, MA, USA) at a concentration of 5ng/mL for 48h in complete culture medium [DMEM/F12 (Gibco, 11320) supplemented with 1% penicillin and streptomycin solution (penicillin 10,000 U/mL, streptomycin 10,000 μg/mL) and 0.001% bovine serum albumin (BSA) (Sigma-Aldrich, A2153)]. Vehicle control explants were incubated with equal volumes of complete culture medium.

extract_protocol:
After tissue lysis, total RNA was extracted from the HTMEx using the Nucleo Spin RNA XS kit according to the manufacturer’s specifications.
Amplification and RNA sequencing experiments from 3.5 ng of total RNA were conducted using SmartSeq (Takara), Nextera XT (Illumina), and NovaSeq 6000 SP Reagent Kit (200 cycles) (Illumina) at iGenSeq (Institut du Cerveau (ICM), Paris, France).

treatment_protocol: The HTMEx were stimulated with recombinant human TGF-β2 at a concentration of 5ng/mL for 48h in complete culture medium supplemented with 1% penicillin and streptomycin solution (penicillin 10,000 U/mL, streptomycin 10,000 μg/mL) and 0.001% bovine serum albumin (BSA).

value: Human trabecular meshwork explants

value: TGF


title: CUT&RUN_H3K36me3_mESC_NSD1-dTAG_dTAG-13_0h

value: H3K36me3 (Active Motif, 61022)


title: CUT&RUN_H3K27me3_mESC_NSD1-dTAG_dTAG-13_1h

value: H3K27me3 (Cell Signaling, 9733)


title: HTMEx TGF-treated sample 6


title: HTMEx TGF-treated sample 8


title: MV4_11_GenomewideCRISPRScreens_DMSO_Rep1

value: MLL-rearranged leukemia

value: Treated with 0.1% DMSO


title: CUT&RUN_H3K36me3_mESC_NSD1-dTAG_dTAG-13_72h

value: NSD1-dTAG knockin

value: dTAG-13 for 72h


title: Ctrl 2

value: Spleen

value: Tfh


title: HTMEx TGF-treated sample 5


title: CUT&RUN_H3K36me2_mESC_Nsd1_KO2_batch1

value: Nsd1 knockout 2

value: no treatment

value: H3K36me2 (Thermo Fisher, MA5-14867)


title: HTMEx TGF-treated sample 1


title: HTMEx TGF-treated sample 3


title: HTMEx TGF-treated sample 2


title: HTMEx control sample 8

treatment_protocol: The control HTMEx were incubated with equal volumes of complete culture medium.

value: control


title: Ube3a_HOM_12mo_Rep6


title: Ube3a_WT_12mo_Rep6


title: Ube3a_PATHET_6mo_Rep6


title: HTMEx control sample 7


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_72h_batch1_bioRep1

value: mouse embryonic stem cells


title: HTMEx control sample 6


title: HTMEx control sample 5


title: HTMEx control sample 4


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_48h_batch1

value: dTAG-13 for 48h


title: HTMEx control sample 3


title: Ube3a_HOM_6mo_Rep6


title: Ube3a_MATHET_6mo_Rep6


title: HTMEx control sample 2


title: Ube3a_WT_6mo_Rep6


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_24h_batch1

value: dTAG-13 for 24h


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_6h_batch1

value: dTAG-13 for 6h


title: Ube3a_PATHET_1mo_Rep6


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_1h_batch1

value: dTAG-13 for 1h


title: Loucy H3K27ac (HiChIP)

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

data_processing:
Read alignment: The Hi-C reads were aligned by the BWA aligner (v0.7.17). Params: "-A1 -B4 -E50 -L0".
Filtering: Mapped reads were filtered by the GenomicTools tools-hic filter command integrated in HiC-Bench for known artifacts of the Hi-C protocol. HiC-Bench: https://github.com/NYU-BFX/hic-bench
Valid pairs: We used the accepted intra-chromosomal read-pairs (‘ds.accepted intra’) and filtered out multi-mapped reads (‘multihit’), read-pairs with only one mappable read (‘single sided’), duplicated read-pairs (‘ds.duplicate’), low mapping quality reads (MAPQ < 20), read-pairs resulting from self-ligated fragments.
Normalization: Contact matrices were generated using the HiC-Bench pipeline and ICE correction was performed using the algorithm detailed in Imakaev et al. (2012) publication. For this, we used the matrix-ic functionality built into HiC-bench which uses the ‘mirnylib.numutils’ python library.
Loop calling: We used the HiC valid pairs with the FitHiC tool (v2.0.7) to identify significant interactions. Parameters: resolution=10kb ; q-value <= 0.01; Min. distance=30kb; Max. distance=1Mb.
Virtual4C: HiC-Bench ‘virtual4C’ pipeline was used to compute the interactions of each selected viewpoint in a roll-window fashion. We summed the valid read pairs in a 5 kb area centered at 200 bp bins that covered the area of +-2.5 Mb from the viewpoint (25k bins per viewpoint). The interactions were normalized by the total number of valid pairs of the sample.
Assembly: hg19
Supplementary files format and content: *.reg.txt files contain the HiChIP valid read pairs (both intra and inter-chromosomal).
Library strategy: HiChIP

source_name: Loucy

extract_protocol:
Chromatin was extracted and processed by Arima HiC+ kit following manufacturer's instructions.
HiChIP libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit.

value: Loucy

value: ETP-ALL

tag: chip antibody


title: MV4-11_RNAseq_3_RPL22KO_C16_Rep4

data_processing:
Ribosome Profiling analysis: 1. trim adapters using Cutadapt with  -a AGATCGGAAGAGCACACGTC -g AGATCGGAAGAGCAC; 2. remove UMI and attach to readID ( --extract-method=string --bc-patter  n=NN  & --extract-method=string --bc-pattern=NNNNNXXXXX   --3prime); 3. barcode demultiplexing using sabre; 4. align aginst rRNA using Bowtie2; 5. algin unmapped reads from step4 against transcriptome using STAR; 6. deduplicate using UMI-tools; 7. generate count table to central ORF using bedtools coverage; 8. after batch removal, send RPF count and mRNAseq count to Xtail for differential translation analysis.
Multiplexing Barcodes: DMSO ATCGT; C6 AGCTA; C16 CGTAA
RNAseq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
CRISPR screen data were analyzed using MAGeCK
Assembly: hg19
Supplementary files format and content: Ribosome Profiling: tab-delimited text file include raw counts for each sample
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample
Supplementary files format and content: CRISPR screen: tab-delimited text file include raw counts for each sample

extract_protocol:
Cells were lysed in TRIzol Reagent and RNA isolated using the Zymo Direct-zol RNA MiniPrep Kit with on-column DNAse treatment according to manufacturer’s instructions.
Total RNA was subjected to ribosome RNA depletion and sequencing libraries generated using standard Illumina protocols.
RNA-Seq

tag: cell line

value: Cell Line

value: 48 Hour treatment with 100 nM C16


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_72h_batch4_bioRep2

tag: cell type

value: NSD1-dTAG knockin


title: Ube3a_HOM_1mo_Rep6

tag: genotype


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_0h_batch4_bioRep4

tag: treatment


title: CUTLL3, H3K27ac (HiChIP)


title: MV4-11_RNAseq_3_RPL22KO_DMSO_Rep4

value: 48 Hour treatment with 0.1% DMSO


title: MV4-11_RNAseq_3_RPL22KO_C16_Rep2


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_0h_batch3_bioRep3

tag: cut&run antibody


title: MV4-11_RNAseq_3_RPL22KO_C16_Rep1


title: MV4-11_RNAseq_3_RPL22KO_DMSO_Rep3


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep2


title: Ube3a_WT_1mo_Rep6


title: MV4-11_RNAseq_3_RPL22KO_DMSO_Rep2


title: MV4-11_RNAseq_3_RPL22KO_DMSO_Rep1


title: Ube3a_PATHET_E14.5_Rep6


title: HTMEx control sample 1

tag: tissue

value: Human trabecular meshwork explants


title: MV4-11_RNAseq_3_C16_Rep3


title: MV4-11_RNAseq_3_C16_Rep4


title: CUT&RUN_H3K36me2_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1


title: MV4-11_RNAseq_3_RPL22KO_C16_Rep3


title: Ube3a_MATHET_1mo_Rep6


title: CUT&RUN_HA_NSD1_mESC_NSD1-dTAG_dTAG-13_72h

value: dTAG-13 for 72h

value: HA (Cell Signaling, 3724)


title: MV4-11_RNAseq_3_C16_Rep1


title: MV4-11_RNAseq_3_C16_Rep2


title: CUT&RUN_HA_NSD1_mESC_NSD1-dTAG_dTAG-13_1h


title: Ube3a_HOM_E14.5_Rep6


title: MV4-11_RNAseq_3_DMSO_Rep4


title: Ube3a_WT_E14.5_Rep6


title: Ube3a_PATHET_12mo_Rep5


title: MV4-11_RNAseq_3_DMSO_Rep3


title: MV4-11_RNAseq_3_DMSO_Rep1


title: MV4-11_RNAseq_3_DMSO_Rep2


title: CUT&RUN_HA_NSD1_mESC_NSD1-dTAG_dTAG-13_0h

value: no treatment


title: GeoMx_Slide_2_3re  004  CD4 contour

city: Krume

first: Koichi

last: Ohshima

state: Fukuoka

address: Asahimachi 67

department: Pathology

country: Japan

institute: Kurume University

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
NovaSeq-derived FASTQ files for each sample were compiled for each compartment using the bcl2fastq program of Illumina, and then demultiplexed and converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline.
DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP Control Center software (version 2.5.1.145) (Nanostring Technologies).
To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers.
Supplementary files format and content: text files include values for each sample

source_name: Lymph node

extract_protocol:
For GeoMx DSP sample collections, entire slides were imaged at 20X magnification. AOIs were segmented using CD30 and CD4 markers. CD30+ large cells were defined as HRS cells (CD30+). CD4+ cells within 20μm from CD30+ HRS cell were defined as “contour”. The remaining CD4+ cells were defined as “remainder”. A total of 24 AOIs from 8 samples were segmented and exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited into a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 10 μl of DEPC-treated water.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences. Unique i5 and i7 sample indexes were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer’s protocol.
GeoMx Seq

treatment_protocol: Slide preparation was followed the GeoMx DSP slide preparation user manual (MAN-10087-04). In summary, FFPE tissue microarray section of 4-µm were mounted on positively charged histology slides. Sections were incubated at 65 °C for 1 hour. Slides were deparaffinized and antigen retrieval was performed in Tris-EDTA pH 9.0 at 100°C for 15 min at low pressure. The RNA probe mix (Whole Transcriptome Atlas (https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-rna-assays/geomx-whole-transcriptome-atlas/), a pool of in situ hybridization probes with UV photocleavable oligonucleotide barcodes) was placeed on each section. Slides were incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced Cell Diagnostics). After hybridization, tissues were stained with CD30 (clone Ber-H2, dilution 1:10, Cell Marque) and CD4 (clone EPR6855, 1:20, Abcam) and located on the GeoMx Digital Spatial Profiler (DSP).

value: Lymph node

tag: slide name

tag: roi number

tag: segment type

tag: patient id

value: patient 9

tag: sample

tag: disease

value: Classic Hodgkin lymphoma


title: ChIP-seq_H3K27ac_EB_d6_NSD1-dTAG_dTAG-13

data_processing:
Bcl files containing raw sequencing data was converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). Paired-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) using Bowtie2 (v2.3.4.1) with “--local --very-sensitive-local --phred33 --no-unal --no-mixed --no-discordant -I 10 -X 700 -S”. Reads were also aligned to the drosophila (dm6) genome with additional “--no-overlap” to map spike-in reads when applicable. Sam files were converted to bam files, sorted and indexed using samtools (v1.9). Peaks were called using MACS2 (v2.2.6) callpeak program with “-f BAMPE --keep-dup 1 -q 0.05” using input as control. Bigwig pileup files were generated using the bamCoverage program from DeepTools (v3.2.1) with “-bs 10 --extendReads --normalizeUsing RPKM --exactScaling --skipNonCoveredRegions” and filtered for mouseENCODE blacklisted genomic regions (v2). The spike-in read percentage was very close and a scaling factor of 1 was applied.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Cells were dissociated and crosslinked with 1% formaldehyde. Nuclei were isolated and chromatin was fragmented using a bioruptor sonicator. Drosophila chromatin was spiked in for Pol II ChIPs. Immunoprecipitation was performed using indicated antibodies and immunocomplexes were further pulled down using Protein G beads. Beads were washed and eluted followed by reverse crosslinking and DNA purification.
Libraries were prepared with 3 ng ChIP or input DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol. Bead based sized selection was performed to enrich for DNA with ~250 bp inserts

value: mouse embryonic stem cells

value: EB differentiation for 6 days; dTAG-13 for 6 days

value: H3K27ac (Thermo Fisher, MA5-23516)


title: GeoMx_Slide_2_3re  004  CD4 remainder


title: Ube3a_MATHET_E14.5_Rep6

tag: strain


title: GeoMx_Slide_2_3re  004  CD30


title: Ube3a_HOM_12mo_Rep5


title: ChIP-seq_H3K27ac_EB_d6_NSD1-dTAG_nontreated

value: EB differentiation for 6 days


title: GeoMx_Slide_2_3re  003  CD4 remainder

value: patient 8


title: GeoMx_Slide_2_3re  003  CD4 contour


title: ChIP-seq_H3K27ac_mESC_NSD1-dTAG_nontreated


title: Ube3a_WT_12mo_Rep5


title: ChIP-seq_PolII_S5P_mESC_NSD1-dTAG_dTAG-13_6h_batch2_bioRep2

value: dTAG-13 for 6h

value: Pol II S5P (Cell Signaling, 13523)


title: GeoMx_Slide_2_3re  002  CD4 remainder

value: patient 7


title: Ube3a_PATHET_6mo_Rep5


title: Ube3a_MATHET_6mo_Rep5


title: ChIP-seq_PolII_S5P_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep1

value: NSD1-dTAG knockin


title: GeoMx_Slide_2_3re  002  CD4 contour


title: Ube3a_HOM_6mo_Rep5


title: GeoMx_Slide_2_3re  002  CD30


title: Ube3a_MATHET_12mo_Rep5


title: GeoMx_Slide_2_3re  001  CD4 remainder

value: patient 6


title: ChIP-seq_PolII_S2P_mESC_NSD1-dTAG_dTAG-13_6h_batch2_bioRep2

value: Pol II S2P (Cell Signaling, 13499)


title: Ube3a_WT_6mo_Rep5


title: ChIP-seq_PolII_S2P_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep1


title: GeoMx_Slide_1_3re  004  CD4 contour

value: patient 5


title: GeoMx_Slide_1_3re  004  CD4 remainder


title: GeoMx_Slide_1_3re  004  CD30


title: Ube3a_PATHET_1mo_Rep5


title: ChIP-seq_PolII_NTD_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep1

value: Pol II NTD (Cell Signaling, 14958)


title: GeoMx_Slide_2_3re  003  CD30


title: GeoMx_Slide_1_3re  003  CD4 remainder

value: patient 3


title: ChIP-seq_PolII_NTD_mESC_NSD1-dTAG_dTAG-13_6h_batch2_bioRep2


title: GeoMx_Slide_1_3re  003  CD4 contour

value: Lymph node


title: Ube3a_MATHET_1mo_Rep5


title: GeoMx_Slide_1_3re  003  CD30


title: Ube3a_HOM_1mo_Rep5


title: ChIP-seq_PolII_S5P_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep2

value: no treatment


title: GeoMx_Slide_2_3re  001  CD4 contour

value: Classic Hodgkin lymphoma


title: GeoMx_Slide_1_3re  002  CD4 contour

value: patient 4


title: ChIP-seq_PolII_S5P_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1

value: mouse embryonic stem cells


title: GeoMx_Slide_1_3re  002  CD30


title: Ube3a_WT_1mo_Rep5


title: GeoMx_Slide_1_3re  001  CD4 contour

value: patient 2


title: GeoMx_Slide_1_3re  001  CD4 remainder


title: ChIP-seq_PolII_S2P_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep2


title: Ube3a_PATHET_E14.5_Rep5


title: GeoMx_Slide_2_3re  001  CD30


title: ChIP-seq_PolII_S2P_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1


title: GeoMx_Slide_1_3re  001  CD30


title: EPB41L5 KO-2 repl.-1

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

description: featureCounts on EPB41L5 KO-2 repl. 1

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19.
Sequenced reads were quality trimmed using Cutadapt v1.16
Reads were mapped to hg38 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differential expression analysis
Supplementary files format and content: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary files format and content: tab-delimited text file includes normalized counts for all Samples

source_name: human immortalized podocyte (AB8/13)

growth_protocol: Podocytes were cultured in RPMI 1640 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #61870036), 10 % FCS (Merck, #S0615), 10 µg/ml ITS (Merck, #11074547001), 5 mM HEPES (Thermo Fisher Scientific, #15630-056), non-essential amino acids (MEM NEAA, Thermo Fisher Scientific, #11140050) 1:1000, 0.1 mM Sodium-Pyruvate (Thermo Fisher Scientific, #11360-039) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 95% air and 5% CO2.

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as 10.0 for all samples using an Agilent Fragment Analyzer system.
After polyA selection, RNA libraries were prepared for sequencing using the NEBnext ultra II RNA directional kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

value: human immortalized podocyte (AB8/13)

value: podocyte

value: EPB41L5 KO


title: EPB41L5 KO-1 repl.-2

description: featureCounts on EPB41L5 KO-1 repl. 2


title: ChIP-seq_PolII_NTD_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep2


title: Ube3a_WT_E14.5_Rep5


title: Ube3a_MATHET_E14.5_Rep5


title: GeoMx_Slide_1_3re  002  CD4 remainder


title: EPB41L5 WT-2 repl.-2

description: featureCounts on EPB41L5 WT-2 repl. 2

value: EPB41L5 WT


title: ChIP-seq_input_mESC_NSD1-dTAG_dTAG-13_0h


title: Ube3a_HOM_E14.5_Rep5


title: ATAC-seq_EB_d6_NSD1-dTAG_dTAG-13

data_processing:
Bcl files containing raw sequencing data were converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). Paired-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) using Bowtie2 (v2.3.4.1) with “--local --very-sensitive-local --phred33 --no-unal --no-mixed --no-discordant -I 10 -X 700 -S”. Sam files were converted to bam files, sorted and indexed using samtools (v1.9). Peaks were called using MACS2 (v2.2.6) callpeak program with “-f BAMPE --keep-dup 1 -q 0.05”. Bigwig pileup files were generated using the bamCoverage program from DeepTools (v3.2.1) with “-bs 10 --extendReads --normalizeUsing RPKM --exactScaling --skipNonCoveredRegions” and filtered for mouseENCODE blacklisted genomic regions (v2).
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Nuclei were isolated from dessociated cells and treated with a Tn5 transposition mix followed by purification of transposed genomic DNA.
Libraries were contructed by PCR amplification of transposed genomic DNA using NEBNext High-Fidelity 2x PCR Master Mix with custom Nextera PCR primers. Libraries were double-side size-selected using Agencourt AMPure XP magenetic beads.

value: EB differentiation for 6 days; dTAG-13 for 6 days


title: Ube3a_PATHET_12mo_Rep4


title: EPB41L5 KO-1 repl.-1

description: featureCounts on EPB41L5 KO-1 repl. 1


title: ChIP-seq_PolII_NTD_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1

value: NSD1-dTAG knockin


title: EPB41L5 WT-2 repl.-1

description: featureCounts on EPB41L5 WT-2 repl. 1


title: ATAC-seq_EB_d6_NSD1-dTAG_nontreated

value: EB differentiation for 6 days


title: Ube3a_MATHET_12mo_Rep4


title: Ube3a_HOM_12mo_Rep4


title: TEADi repl.-2

description: featureCounts on TEADi repl.-2: Counts

data_processing:
Demultiplexing was performed with bcl2fastq v2.19.
Sequenced reads were quality and adapter trimmed using fastp v0.23.2
Reads were mapped to hg38 whole genome using HISAT2 v2.2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.6 were applied for differential expression analysis
Supplementary files format and content: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary files format and content: tab-delimited text file includes normalized counts for all Samples

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as 10.0 for all samples using an Agilent Fragment Analyzer system.
After polyA selection, RNA libraries were prepared for sequencing using the NEBnext ultra II RNA kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

treatment_protocol: Cells were differentiated at 37°C for 12 days. Cells were detached, counted, equalized, seeded, supplemented with Doxycycline and cultured for another 24 hours. Cells were 80% to 90% confluent after 24 hours.

value: TEADi

value: Doxycycline for 24 hours


title: TEADi repl.-1

description: featureCounts on TEADi repl.-1: Counts


title: EGFP repl.-2

description: featureCounts on Ctrl. repl.-2: Counts

value: EGFP


title: EGFP repl.-3

description: featureCounts on Ctrl. repl.-3: Counts


title: Ube3a_WT_12mo_Rep4


title: EPB41L5 KO-2 repl.-2

description: featureCounts on EPB41L5 KO-2 repl. 2


title: EGFP repl.-1

description: featureCounts on Ctrl. repl.-1: Counts


title: EPB41L5 WT-1 repl.-1

description: featureCounts on EPB41L5 WT-1 repl. 1


title: ATAC-seq_mESC_NSD1-dTAG_dTAG-13_6h

value: dTAG-13 for 6h


title: CUT&RUN_H3K27ac_mESC_NSD1-dTAG_dTAG-13_1h

value: dTAG-13 for 1h

value: H3K27ac (Thermo Fisher, MA5-23516)


title: Ube3a_PATHET_6mo_Rep4


title: Ube3a_MATHET_6mo_Rep4


title: ATAC-seq_mESC_NSD1-dTAG_dTAG-13_24h


title: ATAC-seq_mESC_NSD1-dTAG_dTAG-13_0h

value: no treatment


title: FFPE1 | 004 | CD4

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 4_CD4_remainder

data_processing:
library strategy: GeoMx-Seq
NovaSeq-derived FASTQ files for each sample were compiled for each compartment using the bcl2fastq program of Illumina, and then demultiplexed and converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline.
DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP Control Center software (version 2.5.1.145) (Nanostring Technologies).
To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers.
Assembly: N/A
Supplementary files format and content: text files include values for each sample

extract_protocol:
For GeoMx DSP sample collections, entire slides were imaged at 20X magnification. ROIs were segmented using CD30 and CD4 markers. CD30+ large cells were defined as HRS cells (CD30+). CD4+ cells within 20μm from CD30+ HRS cell were defined as “contour”. The remaining CD4+ cells were defined as “remainder”. A total of 12 AOIs from 4 ROIs were segmented and exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited into a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 10 μl of DEPC-treated water.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences. Unique i5 and i7 sample indexes were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer’s protocol.

treatment_protocol: Slide preparation was followed the GeoMx DSP slide preparation user manual (MAN-10087-04). In summary, FFPE tissue microarray section of 4-µm were mounted on positively charged histology slides. Sections were incubated at 65 °C for 1 hour. Slides were deparaffinized and antigen retrieval was performed in Tris-EDTA pH 9.0 at 100°C for 15 min at low pressure. The RNA probe mix (Whole Transcriptome Atlas (https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-rna-assays/geomx-whole-transcriptome-atlas/), a pool of in situ hybridization probes with UV photocleavable oligonucleotide barcodes) was placeed on each section. Slides were incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced Cell Diagnostics). After hybridization, tissues were stained with CD30 (clone Ber-H2, 5μg/ml, Cell Marque), CD4 (clone EPR6855, 1:100, Abcam), and CD8a (Clone OTI3H6, 1:100, Origene) and located on the GeoMx Digital Spatial Profiler (DSP).

value: Lymph node

tag: alternative name

value: Classic Hodgkin lymphoma


title: FFPE1 | 003 | CD4

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 3_CD4_remainder


title: FFPE1 | 004 | CD30

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 4_CD30


title: FFPE1 | 003 | CD30

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 3_CD30


title: FFPE1 | 004 | Contour

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 4_CD4_contour


title: Ube3a_HOM_6mo_Rep4

tag: age


title: Ube3a_WT_6mo_Rep4

tag: librarybatch


title: ATAC-seq_mESC_NSD1-dTAG_dTAG-13_1h

value: mouse embryonic stem cells


title: TEADi repl.-3

description: featureCounts on TEADi repl.-3: Counts

value: human immortalized podocyte (AB8/13)


title: EPB41L5 WT-1 repl.-2

description: featureCounts on EPB41L5 WT-1 repl. 2

value: podocyte


title: Ube3a_PATHET_1mo_Rep4


title: FFPE1 | 002 | CD30

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 2_CD30


title: FFPE1 | 002 | Contour

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 2_CD4_contour


title: LC1

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic single cell

data_processing:
Pre-processing
The Cell Ranger pipeline (v7.0) (Zheng et al. 2017) was used to perform sample demultiplexing, barcode processing and single-nuclei gene counting. Briefly, samples were demultiplexed to produce a pair of FASTQ files for each sample. Reads containing sequence information were aligned using  the default Cell Ranger mm10 genome version 2020-A . PCR duplicates were removed by selecting unique combinations of cell barcodes, unique molecular identifiers (UMIs) and gene ids with the final results being a gene expression matrix that was used for further analysis.
Quality control, Further filtering, Clustering
The derived count matrixes were analyzed using a standard Seurat pipeline (for both quality control/filtering and clustering; https://satijalab.org/seurat/articles/pbmc3k_tutorial.html).
Integration
SCTranformed data were used for integration (https://satijalab.org/seurat/articles/sctransform_vignette.html)
Assembly: UCSC mm10 (GRCm38)
Supplementary files format and content: h5Seurat R data files include Seurat 4 object for each Sample

source_name: locus coeruleus

extract_protocol:
Three- to 4-week-old C57Bl/N mice of both sexes were used for cell collection and capturing as described. Briefly, mice were deeply anesthetized and perfused with 40 ml of ice-cold preoxygenated (95% O2/5% CO2) solution containing the following (in mM): 93 N-methyl-d-glucamin-HCl, 30 NaHCO3, 2.5 KCl, 1.2 NaH2PO4, 20 HEPES-NaOH, 5 Na-ascorbate, 3 Na-pyruvate, 0.5 CaCl2, 8 MgSO4, and 25 glucose (pH 7.4). Next, brains were rapidly extracted and immersed in the same solution to cut 250-μm-thick coronal slices spanning the LC on a vibratome (VT1200S, Leica). After manual isolation of the LC under a stereomicroscope, tissue blocks were subjected to cell dissociation using the papain dissociation system (Worthington) according to the manufacturer’s recommendations. Single cells were re-suspended in sterile cutting solution supplemented with 0.1% BSA, fixed in ice-cold methanol for 10 min, and stored at -80 °C until library preparation.
For single-nucleus RNA-seq, nuclei were isolated from snap-frozen tissues by direct dissociation in cold Nuclei EZ Lysis buffer (Sigma # NUC101) using a pestle. The lysate was incubated on ice for 10 min, filtered through 70 µm-strainer meshes, and centrifuged at 500 rcf at 4˚C for 5 min. Pelleted nuclei were washed in ‘nuclei wash and resuspension buffer’ [1% BSA in 1x DPBS plus 0.5 U/µl Protector RNase-Inhibitor (Sigma #3335402001)], followed by centrifugation at 500 rcf at 4˚C for 5 min. Pelleted nuclei were then washed 3x before taking it up in nuclei wash and resuspension buffer supplemented with 7-amino-actinomycin D (7-AAD, BioLegend # 420404). After straining through a 40-µm mesh, single nuclei were sorted using a SONY SH800S cell sorter. Sorted nuclei were processed for single nuclei RNA-seq using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (10x Genomics #PN1000128) according to manufactures instructions.

value: wild type

value: locus coeruleus

tag: batch


title: FFPE1 | 001 | CD4

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 1_CD4_remainder


title: FFPE1 | 001 | Contour

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 1_CD4_contour


title: TNF, replicate 3, RNA-seq

city: JiNan

first: Shiyang

last: Li

address: Wenhua West Road

country: China

institute: Shandong University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo_sapiens.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon organoid

growth_protocol: The  large intestine of C57BL/6J mice were isolated and dissected lengthwise, then the bowel segment was cut into 5 mm pieces. Then, bowel pieces were resuspended in clean PBS and pipetted several times to isolate intestinal crypts. Isolated crypts were embedded in Matrigel Matrix and seeded in plate.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Colon organoids cultured for 2 days and then were incubated alone or with  TNFα  in combination for 24 hours. The Matrigel Matrix was then thawed by using cell recovery solution, and the organoids were harvested by centrifugation and lysed for RNA extraction.

value: colon organoid


title: FFPE1 | 001 | CD30

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 1_CD30


title: Ube3a_MATHET_1mo_Rep4


title: TNF, replicate 2, RNA-seq


title: Ube3a_HOM_1mo_Rep4


title: OH3

city: Yantai

first: Lanlan

last: Liao

state: Shandong Province

address: No. 346, Guanhai Road, Laishan District, Yantai City, Shandong Province; No. 20, Yuhuangding East Road, Zhifu District, Yantai City

department: The Second Clinical Medical College, Department of Cardiovascular Medicine

institute: Binzhou Medical College, Yantai Yuhuangding Hospital

data_processing:
FastQC software was used to evaluate the quality of Raw data.
The fastp software was used for removing adapter sequence and low-quality reads to filter raw data.
The clean reads were aligned with the known reference genome (human GRCh38) using the spliced mapping algorithm of Hisat2 software to obtain mapped reads.
The gene expression was normalized to the fragments Per Kilobase of exon model per Million mapped fragments (FPKM). That is to say, we first use Stringtie software to compare and count the fragments in each gene segment, then use TMM (trimmed mean of M values) algorithm for normalization, and finally calculate the FPKM value of each gene.
Assembly: human GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: visceral adipose tissue

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing was performed at Shanghai Sinomics Corporation.

value: visceral adipose tissue

tag: Sex

value: female

tag: weight (kg)

tag: height (m)

tag: bmi (kg/m2)

tag: blood pressure (mmhg)

tag: pulse (beats/min)

tag: glucose (mmol/l)

tag: alb (g/l)

tag: scr (umol/l)

tag: bun (mmol/l)

tag: ua (umol/l)

tag: alt (u/l)

tag: ast (u/l)

tag: disease state

value: overweight/obese individuals with hypertension


title: FFPE1 | 003 | Contour

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 3_CD4_contour

tag: tissue

tag: roi number

tag: segment type

tag: alternative name

tag: disease


title: OH2

tag: age

tag: Sex

tag: weight (kg)

tag: height (m)


title: FFPE1 | 002 | CD4

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
ROI 2_CD4_remainder


title: OH1

tag: bmi (kg/m2)

tag: blood pressure (mmhg)

tag: pulse (beats/min)

tag: glucose (mmol/l)


title: TNF, replicate 1, RNA-seq


title: Ube3a_WT_1mo_Rep4

tag: strain

tag: genotype

tag: librarybatch


title: LC2

tag: batch


title: O2

tag: tissue

tag: alb (g/l)

tag: scr (umol/l)

tag: bun (mmol/l)

tag: ua (umol/l)

tag: alt (u/l)

tag: ast (u/l)

tag: disease state

value: overweight/obese individuals (non hypertension)


title: O3

tag: age

tag: Sex

tag: weight (kg)

tag: height (m)


title: C3

tag: bmi (kg/m2)

tag: blood pressure (mmhg)

tag: pulse (beats/min)

tag: glucose (mmol/l)

value: normal weight individuals (non hypertension)


title: Ctrl, replicate 3, RNA-seq


title: C2


title: Ctrl, replicate 2, RNA-seq


title: O1


title: Ctrl, replicate 1, RNA-seq


title: C1


title: p0_WT4

data_processing:
Identification of cells and quantification of transcript abundance was performed using Alevin using a hybrid mouse-human reference genome (mm10-hg38), using GENCODE vM22 and v31 annotations
These gene expression matrices (one per genotype, timepoint, and replicate) were then imported into Seurat version 3.1 using tximport and cells were filtered such that they had to contain at least 2,000 UMIs, had between 1,000–6,000 genes detected, and less than 5% contribution by mitochondrial or hemoglobin transcripts
Each biological sample was normalized and scaled using scTransform v1, then integrated together using Seurat with 5,000 anchors. Dimensionality reduction was conducted using the top 100 principal components
Cell types were identified using Louvain-Jaccard clustering with multilevel refinement and resolution=2
Assembly: mm10-hg38
Supplementary files format and content: SCTransform normalized expression values
Supplementary files format and content: Raw counts as reported by alevin, converted to a matrix using tximport

growth_protocol: Mice were maintained on a 12 h:12 h light:dark cycle and given food and water ad libitum. Timed matings were set up in the evening, using one male and two female C57Bl/6J mice (Jackson Labs) per breeding cage. The male mouse was separated from female mice the next morning. 14 days after separation, pregnant female mice were euthanized and embryonic day 14.5 (E14.5) embryos were collected for dissections. For P0 pups, cages were monitored daily from E18.5 to postnatal day 0 (P0) for newborn pups.

extract_protocol:
Single cell RNA sequencing (drop-seq) was performed on cortices from E14.5 and P0 WT and homoT485A mice (WT E14.5 n = 6, homoT485A E14.5 n = 5, WT P0 n = 3, homoT485A P0 n = 5). WT and mutant samples were performed in parallel. Single cell isolation and sequencing were performed as described in our previous publication (Loo 2019), where data from WT samples were previously reported. Each replicate contained cortical cells from male and female littermates
cDNA from an estimated 12,000 E14.5 cells and 8,000 P0 cells were pooled, purified and tagmented with Nextera XT DNA Library Preparation kit (Illumina). Input cDNA (1 ng) from each replicate was amplified with custom primer P5_TSO_Hybrid and Nextera index primers (Supplementary Table). Tagmented samples were purified twice with 0.6× and 1× AMPure XP beads. All replicates were pooled and sequenced on one Illumina HiSeq 4000 flowcell (eight lanes) to avoid sequencing bias. Read 1 was 20 bp; bases 1–12 represent the cell barcode, bases 13–20 represent the UMI. Read 2 was 50 bp and Read 3 (sample index) was 8 bp. Samples were de-multiplexed using bcl2fastq version 2.18.0.12
Drop-seq

treatment_protocol: Cerebral cortices (both halves) from E14.5 and P0 mice were dissected in neurobasal medium and rinsed with Hank's Balanced Salt Solution (HBSS; 14175095 Gibco). All procedures were done at room temperature, unless otherwise stated. Cortices were then incubated for 30 min at 37°C in papain (1 vial diluted with 2.5 mL of HBSS; Pierce 88285) with DNase I (20 mg/mL; D4513 Sigma) in Ca2+ and Mg2+ free HBSS. Next, 1 mL of neurobasal medium containing 5% FBS was added to the cortical mixture and triturated to deactivate the papain. The cells were centrifuged for 2 min at 4,000 rpm, washed twice, and resuspended in Ca2+ and Mg2+ free HBSS with ion channel inhibitors (5 µM TTX ab120054 Abcam, 25 µM DL-AP5 ab120004 Abcam, 5 µM DNQX 2312 Tocris). Cells were kept on ice until the microfluidics run. A total of nine replicates were prepared from two developmental time points (6 replicates for E14.5 embryos and 3 replicates for P0 pups). Each replicate contained cortical cells from male and female littermates.

tag: strain

tag: genotype


title: Ube3a_WT_E14.5_Rep4

tag: librarybatch


title: Ube3a_PATHET_12mo_Rep3


title: Ube3a_HOM_E14.5_Rep4


title: MV4-11_RNAseq_2_C16_Rep3

tag: cell line

tag: cell type

value: Cell Line

tag: treatment

value: 48 Hour treatment with 100 nM C16


title: p0_WT3


title: MV4-11_RNAseq_2_ABBV075_Rep3

value: 48 Hour treatment with 2.5 nM mivebresib (ABBV-075)


title: MV4-11_RNAseq_2_DMSO_Rep3

value: 48 Hour treatment with 0.2% DMSO


title: MV4-11_RNAseq_2_C16+ABBV075_Rep3

value: 48 Hour treatment with 100 nM C16 and 2.5 nM mivebresib (ABBV-075)


title: p0_WT2


title: MV4-11_RNAseq_2_ABBV075_Rep2


title: MV4-11_RNAseq_2_C16+ABBV075_Rep2


title: Ube3a_MATHET_12mo_Rep3


title: MV4-11_RNAseq_2_C16_Rep2


title: MV4-11_RNAseq_2_DMSO_Rep2


title: Ube3a_HOM_12mo_Rep3


title: Ube3a_PATHET_E14.5_Rep4


title: Ube3a_MATHET_E14.5_Rep4


title: MV4-11_RNAseq_2_ABBV075_Rep1


title: p0_T485A5


title: p0_T485A4


title: MV4-11_RNAseq_2_C16+ABBV075_Rep1


title: p0_T485A3


title: MV4-11_RNAseq_2_DMSO_Rep1


title: p0_T485A2


title: MV4_11_TargetedCRISPRScreens_C6_Rep2

value: MLL-rearranged leukemia

value: Treated with 2 uM C6


title: p0_T485A1


title: Ube3a_HOM_6mo_Rep3


title: Ube3a_MATHET_6mo_Rep3


title: e14_WT9_2


title: MV4_11_TargetedCRISPRScreens_DMSO_Rep2

value: Treated with 0.1% DMSO


title: Ube3a_WT_6mo_Rep3


title: e14_WT9_1


title: MV4_11_TargetedCRISPRScreens_C6_Rep1


title: MV4_11_TargetedCRISPRScreens_DMSO_Rep1


title: MV4-11_RNAseq_C6_Rep3

description: RNAseq.proteincoding.count

extract_protocol:
Total RNA was extracted from cells lysed in Lysis Buffer (20 mM Tris, pH 7.4; 150 mM NaCl; 15 mM MgCl2; 1 mM DTT; 100 ug/mL cycloheximide; 1 % Triton X-100; 25 U/mL Turbo DNase I) using the Zymo Direct-zol RNA MiniPrep Kit with on-column DNAse treatment.
Total RNA was subjected to ribosome RNA depletion and sequencing libraries generated using standard Illumina protocols.
RNA-Seq

value: 48 Hour treatment with 2 uM C6


title: MV4-11_RNAseq_C16_Rep3

description: RNAseq.proteincoding.count


title: MV4-11_RNAseq_DMSO_Rep3

description: RNAseq.proteincoding.count

value: 48 Hour treatment with 0.1% DMSO


title: e14_WT8_2


title: MV4-11_RNAseq_2_C16_Rep1


title: Ube3a_MATHET_1mo_Rep3


title: MV4-11_RNAseq_C16_Rep2

description: RNAseq.proteincoding.count


title: MV4_11_TargetedCRISPRScreens_C16_Rep2

extract_protocol:
Genomic DNA was isolated from cells using the Quick-gDNA Midiprep Kit (Zymo Research) per the manufacturer’s instructions.
Illumina-compatible sequencing libraries were generated by PCR amplification of sgRNA sequences from gDNA using adapter-containing primers annealing to regions flanking the sgRNA sequence. PCR reactions were pooled and purified by ZymoSpin V column with Reservoir (Zymo Research).
CRISPR Screen

value: Treated with 100 nM C16


title: Ube3a_HOM_1mo_Rep3


title: e14_WT11


title: MV4-11_RNAseq_C6_Rep2

description: RNAseq.proteincoding.count


title: Ube3a_WT_12mo_Rep3


title: MV4_11_TargetedCRISPRScreens_C16_Rep1


title: e14_WT8_1


title: Ube3a_WT_1mo_Rep3


title: MV4-11_RNAseq_C6_Rep1

description: RNAseq.proteincoding.count


title: MV4-11_RNAseq_DMSO_Rep1

description: RNAseq.proteincoding.count


title: Ube3a_PATHET_1mo_Rep3


title: MV4-11_RNAseq_DMSO_Rep2

description: RNAseq.proteincoding.count


title: MV4-11_RNAseq_C16_Rep1

description: RNAseq.proteincoding.count


title: e14_WT10


title: MV4-11_RiboProfile_C16_Rep3

description: RPF.count

library_source: other

data_processing:
Ribosome Profiling analysis: 1. trim adapters using Cutadapt with  -a AGATCGGAAGAGCACACGTC -g AGATCGGAAGAGCAC; 2. remove UMI and attach to readID ( --extract-method=string --bc-patter  n=NN  & --extract-method=string --bc-pattern=NNNNNXXXXX   --3prime); 3. barcode demultiplexing using sabre; 4. align aginst rRNA using Bowtie2; 5. algin unmapped reads from step4 against transcriptome using STAR; 6. deduplicate using UMI-tools; 7. generate count table to central ORF using bedtools coverage; 8. after batch removal, send RPF count and mRNAseq count to Xtail for differential translation analysis.
Multiplexing Barcodes: DMSO ATCGT; C6 AGCTA; C16 CGTAA
RNAseq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
CRISPR screen data were analyzed using MAGeCK
Assembly: hg19
Supplementary files format and content: Ribosome Profiling: tab-delimited text file include raw counts for each sample
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample
Supplementary files format and content: CRISPR screen: tab-delimited text file include raw counts for each sample
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
Cells were washed with ice-cold PBS and lysed in 400 µL Lysis Buffer (20 mM Tris, pH 7.4; 150 mM NaCl; 15 mM MgCl2; 1 mM DTT; 100 ug/mL cycloheximide; 1 % Triton X-100; 25 U/mL Turbo DNase I) by incubation on ice for 10 minutes followed by homogenization by syringe. Lysates were cleared by centrifugation for 10 minutes at 4ºC and RNA quantified by Qubit RNA HS Assay. 30 ug RNA was diluted in 200 uL Polysome Buffer (20 mM Tris, pH 7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 ug/mL cycloheximide) and incubated with 1.5 uL RNase I (10 U/L; Epicentre) for 45 minutes while rotating at room temperature. RNA digestion was quenched with 10 uL SUPERaseIN RNase Inhibitor and samples transferred to 13 mm X 51 mm ultracentrifuge tubes, underlaid with 900 uL 1 M sucrose in polysome buffer supplement with 20 U/mL SUPERaseIn RNase Inhibitor, and centrifuged at 4ºC for one hour at 540,628 x g. RNA was extracted from RNA pellet by Zymo Direct-zol RNA MiniPrep Kit, eluted in water. RNA along with carrier glycogen was precipitated with 1.5 volumes 100% isopropanol supplemented with 0.12 M NaOAc, pH 5.5, by incubation on dry-ice for 30 minutes then centrifugation for 30 minutes at 4C. RNA was resuspended in 5 uL 10 mM Tris, pH 8.0 and 1X Denaturing Sample Loading Buffer (98% Formamide; 10 mM EDTA; 300 ug/mL bromophenol blue) and subjected to electrophoresis on 15% polyacrylamide TBE-Urea gels. Gels were stained briefly with 1X SYBR Gold and 17-34 nucleotide fragments excised using reference oligos run in parallel (NI-800 and NI-800). RNA fragments were extracted by mechanical disruption followed by suspension in 500 uL RNA Gel Extraction Buffer (300 mM NaOAc, pH 5.5; 1 mM EDTA; 0.25% SDS), freezing for 30 minutes on dry-ice, and rotating over-night at room temperature. Polyacrylamide was removed by centrifugation with Spin-X columns and RNA precipitated with isopropanol as described above.
RNA was dephosphorylated by incubation with 5 U T4 PNK in 1X T4 PNK Buffer supplemented with SUPERaseIn RNase Inhibitor for 1 hour at 37C and ligated to pre-adenylated bar-coded linkers with 100 U of T4 Rnl2(tr) K227Q in 1X T4 RNA Ligase Buffer (NEB) supplemented with 35% w/v PEG-8000 incubated at 37ºC for 3 hours. Ligation to bar-coded linkers was verified by electrophoresis, samples combined, and linker-ligated RNA precipitated as described above. Ribosome RNA was depleted with the Lexogen RiboCop rRNA Depletion Kit and rRNA-depleted RNA precipitated as described above. Linker-ligated RNA was reverse transcribed with 200 U Superscript III in 1X First Strand Buffer, dNTPs, DTT, 10 U SUPERaseIn RNase Inhibitor and the primer NI-802. RNA template was hydrolyzed for 15 minutes at 98C in the presence of 0.1M NaOH and cDNA precipitated with isopropanol as described previously. Reverse-transcribed DNA was subjected to electrophoresis using 15% polyacrylamide TBE-Urea gels and reverse-transcription product corresponding to 105 nucleotides excised and extracted from polyacrylamide as described above except with DNA Gel Extraction Buffer (300 mM NaCl; 10 mM Tris, pH 8.0; 1 mM EDTA). cDNA was circularized with 100 U CircLigase in the presence of 1X CircLigase Buffer, ATP, and MnCl2 at 60C for one hour followed by 80C for 10 minutes. Circularized cDNA was quantified by qPCR and amplified with Phusion Polymerase with unique dual indexed primers.
Ribo-Seq


title: Ube3a_PATHET_E14.5_Rep3

extract_protocol:
Either 2 or 4 hr after the injection, dams were sacrificed via CO2 followed by cervical dislocation. Embryos were dissected from the placenta and stage-matched based on somite number (2 hr: 19-20 somites; 4 hr: 20-21 somites). A maximum of two embryos per litter were used to minimize litter effects. RNA from the rostroventral neural tube (RVNT) from each embryo was isolated using the RNeasy Plus Micro kit (Qiagen, Germantown, Maryland) as previously described (Boschen et al., 2020). RNA from a total of 6 embryos per condition and time point (24 total embryos) were submitted for RNA-seq.
Libraries for RNA sequencing (RNA-seq) were prepared using the SMARTr Ultra Low Input RNA (Clontech, Mountainview, CA) and Nextera XT DNA (Illumina, San Diego, CA) kits by the UNC High Throughput Sequencing Facility. Samples were pooled prior to sequencing, after RNA extraction and library preparation was complete. Six total pools (1 sample/group/pool) and 1 pool per lane were used. Paired-end (50bp) sequencing was performed on an Illumina HiSeq 4000.


title: MV4-11_RiboProfile_C16_Rep2

description: RPF.count


title: MV4-11_RiboProfile_C16_Rep1

description: RPF.count


title: MV4-11_RiboProfile_C6_Rep3

description: RPF.count


title: Ube3a_HOM_E14.5_Rep3


title: e14_T485A3


title: MV4-11_RiboProfile_C6_Rep2

description: RPF.count


title: Ube3a_PATHET_12mo_Rep2


title: Ube3a_MATHET_E14.5_Rep3


title: Ube3a_PATHET_6mo_Rep3


title: e14_T485A2


title: SMAD4_siRNA_12dynes/cm2_rep2

city: Mannheim

first: Roxana

last: Ola

state: Baden-Württemberg

address: Ludolf-Krehl-Str. 13 - 17

institute: Medical Faculty Mannheim, Heidelberg University

data_processing:
Quality of RNA seq reads was assessed with the MultiQC tool (v1.13) and trimmed of adapters using Trimmomatic (v0.39).
Reads were mapped by STAR (v2.7.10a) with the following settings: -alignIntronMin 20 and -alignIntronMax 500000 to the hg38 reference genome.
Tag directories were created with makeTagDirectory and reads were counted by the analyzeRepeats.pl function (hg38 -strand both -count exons -noadj) both from HOMER (v4.7.2).
Differential expression was quantified and normalized using DESeq2. Rpkm.default from EdgeR was used to determine average reads per millions mapped (RPKM).
Assembly: hg38
Supplementary files format and content: Excel differential expression data

source_name: HUVEC

growth_protocol: HUVECS were cultured in Endothelial Cell Growth Medium MV 2 (Promocell)  medium supplemented with  penicillin/streptomycin.

extract_protocol:
RNA was isolated with the Quick-RNA Miniprep Kit (Zymo Reasearch).
dnbseq stranded mrna library

treatment_protocol: HUVECS were transfected either with Control or SMAD4 siRNA and 48h after transfection the cells were subjected to 12dynes/cm2 fluid shear stress or kept under static conditions.

value: HUVEC

value: endothelial cells

value: SMAD4 siRNA + 12dynes/cm2


title: e14_T485A1


title: SMAD4_siRNA_12dynes/cm2_rep1


title: Ube3a_MATHET_12mo_Rep2


title: MV4-11_RiboProfile_C6_Rep1

description: RPF.count


title: e14_T485A1_1


title: SMAD4_siRNA_static_rep3

value: SMAD4 siRNA


title: MV4-11_RiboProfile_DMSO_Rep3

description: RPF.count

value: 48 Hour treatment with either 0.1% DMSO


title: MV4-11_RiboProfile_DMSO_Rep2

description: RPF.count


title: SMAD4_siRNA_static_rep1


title: SMAD4_siRNA_static_rep2


title: MV4-11_RiboProfile_DMSO_Rep1

description: RPF.count


title: Ube3a_WT_12mo_Rep2


title: SMAD4_siRNA_12dynes/cm2_rep3


title: Ube3a_HOM_12mo_Rep2


title: e14_T485A4


title: 48hrVSV rep3

city: Davis

first: Qizhi

last: Gong

state: CA

address: One Shields Avenue

department: Cell Biology and Human Anatomy

institute: University of California Davis, School of Medicine

data_processing:
Raw reads were processed with HTStream v.1.0 (https://s4hts.github.io/HTStream/) to perform raw sequence data QA/QC, remove adapter contamination and low-quality bases/sequences.
Trimmed reads were aligned to the Mus musculus genome, using the aligner STAR v. 2.6.0c (Dobin, et al. 2013) to generate raw counts per gene.
RNA data analyzed with limma-voom Bioconductor pipeline
Genome_build: GRCm38 primary assembly genome with GENCODE v.M15 annotation
Supplementary_files_format_and_content: tab-delimited text files with raw counts of reads aligned to each gene.

source_name: olfactory mucosa

extract_protocol:
Trizol extraction with Zymo RNA clean and concentrator
3'Tag RNA-seq library constructed according to Illumina protocol

tag: tissue

value: olfactory mucosa

value: VSV

tag: time point


title: 48hrVSV rep1


title: 48hrVSV rep2


title: Ube3a_MATHET_6mo_Rep2

data_processing:
Reads were quality-ﬁltered by requiring at least 90% of bases to have a quality score greater than 20 using fastq_quality_ﬁlter in FASTX-toolkit.
Adapter sequences were removed using cutadapt
Reads were then aligned to the mm9 reference genome using STAR 2.5.2b
Transcript abundance was measured using salmon, and differential expression tests were performed using DESeq2 corrected for library batch
Assembly: mm9
Supplementary files format and content: VST normalized expression values from DESeq2, corrected by library batch


title: Ctr_siRNA_12dynes/cm2_rep2

value: Ctr siRNA + 12dynes/cm2


title: 48hrPBS rep3

value: PBS


title: Ctr_siRNA_12dynes/cm2_rep1


title: Patient 02 single-nuclei RNA-seq of whole-liver collected during autopsy

city: NEW YORK

first: Robert

middle: F

last: Schwabe

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description: Processed data file contain raw and CellRanger filtered gene counts

data_processing:
Raw 3′ snRNA-seq data were demultiplexed using CellRanger (v.3.1.0) ‘mkfastq’ followed by ‘count’ to align the sequencing reads to the GRCh38_premrna_SARSCoV2 reference and generate a counts matrix.
For use with single-nuclei data the reference had been customized to include each gene transcript locus as an exon creating a pre-mRNA reference that includes intronic reads in the UMI counts for each gene and barcode.
SARS-CoV-2 genome (severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome, GenBank MN908947.3) was added as an additional ‘gene’ to the GTF file to enable detection of viral reads
Genome_build: GRCh38_premrna_SARSCoV2
Supplementary_files_format_and_content: .h5 file containing CellRanger filtered nuclei gene expression raw counts

source_name: liver

extract_protocol:
Liver samples were processed in a biosafety cabinet equipped for COVID-19 specimens. Tween with salts and tris (TST) buffer was used for tissue dissociation and salt and tris (ST) buffer was used for all wash steps. To dissociate the tissue, a fraction of the OCT embedded tissue was broken off and put in a 50 ml tube (Corning, NY) filled with ice-cold phosphate buffered saline (PBS) and inverted until OCT was fully dissolve. Tissue was collected using centrifugation at 300 x g for 2 min at. PBS was replaced by 2 ml cold dissociation buffer (TST) and the sample was mechanically dissociated using fine scissors and pipettes with decreasing orifice size. After 10 minutes incubation on ice, 8 ml of ST buffer were added, and the sample was filtered through a 70 µM cell strainer (Corning, NY) to remove large debris. The dissociated nuclei were centrifuged for 5 min at 500 x g After decanting the supernatant the nuclei were resuspended in 100-1000 µL ST buffer and filtered again using a 40 µM cell strainer (Corning, NY). After counting, nuclei were immediately processed for droplet-based singe nuclei RNA sequencing.
Single-nuclei RNA sequencing (snRNA-seq) libraries were prepared as previously described (PMID 33915568). 10,000 nuclei were loaded per channel on a Chromium controller using Chromium Next GEM Single Cell 3ʹ v3.1 reagents (10x genomics, Pleasanton, CA) placed inside the bio-safety cabinet. The cDNA was then amplified as by manufacturer instructions while adding one additional cycle to account for lower input amounts from nuclei compared to whole cells. Final sequencing libraries were prepared as by manufacturer instructions. Single-nuclei RNA libraries were quantified using Tapestation D1000 screening tapes (Agilent, Santa Clara, CA) and Qbit HS DNA quantification kit (Thermo Fisher Scientific). Libraries were pooled equimolarly and quantified using quantitative PCR. Libraries were sequenced on a NovaSeq 6000 with S4 flow cell (Illumina, San Diego, CA) using paired end, single index sequencing with 28 cycles read 1, 8 cycles i7 index, and 91 cycles read 2.

treatment_protocol: All samples were obtained during autopsy of individuals with lethal COVID-19 and the post-mortem incision time for autopsy was less than 4.5 h. Tissue samples of ~1 cm3 were snap-frozen embedded in Tissue-Tek optimal cutting temperature (OCT) compound (Sakura Finetek USA Inc., Torrance, CA) and stored at −80 °C until processing.

value: liver

tag: disease state

value: lethal COVID-19

value: M

tag: pmi (post-mortem interval-hours)

tag: molecule subtype

value: nuclear polyA RNA


title: Patient 08 single-nuclei RNA-seq of whole-liver collected during autopsy

tag: Sex

tag: age


title: 48hrPBS rep2


title: Patient 12 single-nuclei RNA-seq of whole-liver collected during autopsy

value: F


title: Ube3a_WT_6mo_Rep2


title: 48hrPBS rep1


title: Patient 01 single-nuclei RNA-seq of whole-liver collected during autopsy


title: Ube3a_HOM_6mo_Rep2


title: Ctr_siRNA_static_rep3

value: Ctr siRNA


title: Ube3a_PATHET_1mo_Rep2


title: Mesothelial cells-HG+Melatonin(MT)_12H

city: Dalian

first: Feng

last: Zheng

state: Liaoning

address: West 9 Lvshun South Boulevard

institute: Second Hospital; Advanced Institute for Medical Sciences, Dalian Medical University.

data_processing:
The RNA-seq reads were aligned to the human reference genome hg38 using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini &Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the 2 threshold for significantly differential expression.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mesothelial cell Line

extract_protocol:
Mesothelial cells were treated with normal or 236mM glucose in the presence or absence of 200mM melatonin and cells were collected after 6 and 12 hours. For melatonin intervention, the indicated concentration of melatonin was added to cells 12 hours prior to exposure to high glucose.RNA was extracted from the cells and mRNAs were enriched via poly A. Illumina NEBNext® Ultra™ RNA Library Prep Kit (Cat#E7530L) was used to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Immortalized human mesothelial cell line HMrSV10

value: treated with 236mM glucose for 12 hours under 200mM melatonin intervention


title: Ctr_siRNA_static_rep2

value: HUVEC


title: 24hrVSV rep3


title: Ube3a_PATHET_6mo_Rep2


title: Ube3a_MATHET_1mo_Rep2


title: Mesothelial cells-HG_12H

value: Immortalized human mesothelial cell line HMrSV9

value: treated with 236mM glucose for 12 hours


title: Ctr_siRNA_12dynes/cm2_rep3

value: endothelial cells


title: Ube3a_HOM_1mo_Rep2


title: 24hrVSV rep2


title: Ctr_siRNA_static_rep1


title: 24hrVSV rep1


title: Mesothelial cells-NG_12H

value: Immortalized human mesothelial cell line HMrSV8

value: untreated


title: 24hrPBS rep3

value: olfactory mucosa


title: Mesothelial cells-HG_6H

value: Immortalized human mesothelial cell line HMrSV6

value: treated with 236mM glucose for 6 hours


title: Ube3a_WT_1mo_Rep2


title: 24hrPBS rep2

value: PBS


title: Ube3a_PATHET_E14.5_Rep2


title: Ube3a_MATHET_E14.5_Rep2


title: Mesothelial cells-NG_6H

value: Immortalized human mesothelial cell line HMrSV5


title: 24hrPBS rep1


title: 9hrVSV rep3

value: VSV


title: Ube3a_HOM_E14.5_Rep2


title: prt6-1erfvii, 7-d-old continuous light grown seedlings, Biological replicate 4

city: Nottingham

first: Michael

last: Holdsworth

address: University of Nottingham, University Park

country: United Kingdom

institute: University of Nottingham

data_processing:
Sequence reads were trimmed for adaptor sequences and low quality sequences using default parameters of skewer v0.2.2
Trimmed sequenes were mapped to Arabidopsis thaliana genome (TAIR10) using  default parameters of hisat2 v2.1.0
Only uniquely mapped were used for further downstream analysis.
Read counts for each gene are calculated using featureCounts v1.6.0.
Supplementary files format and content: rawcounts.txt

organism: Arabidopsis thaliana

source_name: 7-d-old total seedlings

growth_protocol: Seeds were sterilised and grown on 1/2 MS agar plates without sucrose for 7 days in continuous light conditions

extract_protocol: Total RNA was extracted using RNAeasy minikit and sent for RNA sequencing

treatment_protocol: 7 days old seedlings of WT and mutant lines were harvested untreated

value: 7-d-old total seedlings


title: prt6-1erfvii, 7-d-old continuous light grown seedlings, Biological replicate 3


title: 9hrVSV rep2


title: Ube3a_PATHET_12mo_Rep1


title: 9hrVSV rep1


title: hNSC mantained in differentiation medium_rep2

type: RNA

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

description: Gene expression data from human neural stem cells maintained in differentiation medium for 24 hours

hyb_protocol: Purified and fragmented aRNA was hybridized using the GeneChip MG-430 PM microarray (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Scanning was performed with the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
Data analysis was performed using the Partek Express software (Partek Inc., St. Louis, MO, USA) provided by Affymetrix as part of their GeneAtlas system. Compared with the non-treated cells, fold change in expression in the TCQA-treated group was calculated and converted to log 2 data.
RMA

label: biotin

source_name: Human neural stem cells maintained in differentiation medium for 24 hours

label_protocol: Biotin-labeled amplified RNA (aRNA) was synthesized by in vitro transcription using the GeneChip 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: The hNSCs derived from H9 hNSCs were purchased from Gibco, Japan. The hNSCs were cultured in 60 mm Petri dishes (BD Falcon) with a growth medium Knock OutTM:1:1 (v/v) mixture of Dulbecco’s minimum essential medium (Sigma, U.S.A.) and Ham’s F-12 nutrient mixture (Sigma, U.S.A.) supplemented with 2% StemPro neural supplement, 20 ng/mL of fibroblast growth factor (FGF) basic recombinant human, 20 ng/mL epidermal growth factor (EGF) recombinant human and 2 mM GlutaMAX-I supplement. For adhesion, 60-mm Petri dish  coated with CELLStart were used. The hNSCs were cultured at 37ºC in a 95% air / 5% CO2 humidified incubator. The medium was changed every two days to keep cells undifferentiated.

extract_protocol: The total RNA was extracted from the cells using ISOGEN kit (Nippon Gene Co. Ltd., Toyama, Japan) following manufacturer’s instructions.

treatment_protocol: The hNSCs were seeded in 60-mm Petri dishes at the density of 2.5×104 cells/cm2 and were incubated at 37ºC for 48 h. After that, cells were treated with differentiation medium with or without 10 μM of TCQA and were incubated at 37ºC for 24 h.

tag: cell

value: Human Neural Stem Cell


title: Mesothelial cells-HG+Melatonin(MT)_6H

value: Immortalized human mesothelial cell line HMrSV7

value: treated with 236mM glucose for 6 hours under 200mM melatonin intervention


title: prt6-1erfvii, 7-d-old continuous light grown seedlings, Biological replicate 2


title: prt6-1erfvii, 7-d-old continuous light grown seedlings, Biological replicate 1


title: Ube3a_MATHET_12mo_Rep1