title: LPS/IFNg + FK866 - 3 [X441DS_LI.FK]

city: Tel Aviv

first: Lior

last: Mayo

state: Israel

address: Britannia Bldg. Room 204, Tel Aviv univeristy

country: Israel

institute: Tel Aviv Unoversity

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt; resulting reads shorter than 30bp were discarded
Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the M. musculus, mm10 genome according to Refseq annotations, using STAR] with EndToEnd option and outFilterMismatchNoverLmax was set to 0.05.
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Counts for each gene were quantified using htseq-count, using the gtf above and corrected for UMI saturation
Assembly: M. musculus, mm10 genome
Supplementary files format and content: NOT PROVIDED

organism: Mus

source_name: astrocyte

extract_protocol:
RNA was extracted with a GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, # PLN70)
RNA libraries for RNA-seq were prepared using using the MARS-seq protocol [H. Keren-Shaul, et al., Nat Protoc 14, 1841–1862 (2019)]
Libraries were normalized, pooled, and sequenced on a single lane of an Illumina NovaSeq. Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt and resulting reads shorter than 30 bp were discarded. The remaining reads were mapped onto 3’ UTR regions (1000 bases) of the M. musculus, mm10 genome according to Refseq annotations, using STAR (77) with the EndToEnd option and with outFilterMismatchNoverLmax set to 0.05. Deduplication was accomplished by flagging all reads that were mapped to the same gene and had the same UMI.

value: astrocyte

value: LPS/IFNg + FK868


title: iCCA_36_iCCA

status: Public on Aug 12 2022

type: genomic

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

description: Illumina HumanMethylation450 BeadChip

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing: Methylation data were processed using the R platform for statistical computing.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: supplier protocol (Illumina)

extract_protocol: Genomic DNA was isolated from fresh frozen tissue using the QIAamp DNA micro kit (Qiagen, Hilden, Germany) for whole exome sequencing according to the manufacturer's instructions. From formalin-fixed paraffin-embedded (FFPE) samples, genomic DNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen), as recommended by the manufacturer with the following modifications: After addition of xylene, samples were incubated at 56°C for 2 minutes followed by two ethanol washes. The first proteinase K digestion was performed with 20 µL at 56°C for 30 minutes. The DNA was eluted twice with 30 µL of H2O.

tag: gender

value: male

value: FFPE


title: K562 e1i&e4i rep2 [Trac-looping]

type: SRA

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

country: USA

institute: FRED HUTCHINSON CANCER CENTER

library_source: genomic

data_processing:
  tracPre2.py in cLoops2 package was used to trimmed and mapped raw FASTQ files to hg19, then paired-end tags (PETs) were filtered  and converted to non-redundant BEDPE files for each sample.
Genome_build: hg19
Supplementary_files_format_and_content:  non-redundant BEDPE files: each row is one unique paired-end tag (PET). The columns are: chromosome1, start1, end1, chromosome2, start2, end2, PETID_read1LinkerPos_read2LinkerPos, MAPQ value from Bowtie2, strand1 and strand2.

source_name: dCas9-KRAB expressing K562 cell line

growth_protocol: The K562 (human myelogenous leukemia cells, female, ATCC) cells were cultured in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% Tet-system-approved FBS (Life Technologies), GlutaMAX (Thermo Fisher Scientific), and Penicillin-Streptomycin (Thermo Fisher Scientific). K562-KRAB-dCas9 cell line was a gift from Dr. Luke Gilbert (University of California San Francisco) and cultured in the same condition(Gilbert et al., 2014).

extract_protocol: Modified Trac-looping was performed for mapping chromatin architecture in 4 conditions (wildtype, perturbation of individual e3 or e7, and perturbation of both e3&e7). One million cells were fixed with 1% formaldehyde in the culture medium at room temperature for 10 minutes. Cells were washed with PBS and resuspended with a reaction buffer (50mM Tris acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). The short adapter and biotinylated bridging linker with Tn5, and then incubated at room temperature for 20 minutes to generate Tnp bridging complex. This complex was added to cells and mixed gently. Chromatin interacting regions were bridged at this step. EDTA was added to stop the reaction and reverse crosslinked by incubating at 65°C overnight. Genomic DNA was extracted by Phenol-Chloroform and the purified DNA was digested with restriction enzymes MluCI/NlaIII. Streptavidin beads were used to enrich biotin-labeled DNA fragments, followed by adapter ligation and amplification by PCR with Illumina multiplexing indexed primers. Libraries were purified and submitted for paired-end sequencing (Illumina NovaSeq 6000). The detailed protocol is being prepared for publishing elsewhere.

treatment_protocol: dCas9-KRAB expressing K562 cells were infected with lentiviruses expressing sgRNAs against e1, e4 or e1&e4.

tag: genotype/variation

value: dCas9-KRAB expressing K562 cell line

tag: cell type

value: K562 cell line

tag: treatment

value: e1 and e4 dual inhibition


title: iCCA_34_iCCA

description: Illumina HumanMethylation450 BeadChip


title: K562 WT rep1 [ChIP-seq]

data_processing:
Bowtie2 was used to map raw FASTQ files to hg19, then paired-end reads were filtered  and converted to non-redundant BEDPE files for each sample.
Genome_build: hg19
Supplementary_files_format_and_content:  non-redundant BEDPE files: each row is one unique paired reads. The columns are: chromosome1, start1, end1, chromosome2, start2, end2, PairedReadID, MAPQ value from Bowtie2, strand1 and strand2.

extract_protocol: Cells were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Quench the reaction by adding 250 mM Glycine, then wash cells twice with cold PBS. Three million fixed cells were used for each H3K9me3 ChIP-seq assay. Resuspend cells with 1 x TE buffer plus 1 x protease inhibitor cocktail and 1 mM PMSF. Chromatin was sheared by sonication on a Diagenode Bioruptor Pico device at 4 °C for 18 cycles with 30 seconds on and 30 seconds off. Adjust chromatin solution to 1 x RIPA buffer (1 x TE, 0.1% SDS, 0.1% Sodium Deoxycholate and 1% Triton X-100) plus 500 mM NaCl. After centrifuging at 13, 000 rpm for 10 min at 4 °C, chromatin supernatant was collected and 10% of it was saved at input. Mix 2 mg H3K9me3 antibody (Abcam, Cat. ab8898) with 20 mL Dynabeads Protein A beads (ThermoFischer Scientific, Cat. 10001D), then incubate at room temperature for 1 hour with rotation. Wash beads once with 1 x PBS, then add chromatin solution to beads, and incubate at 4 °C overnight with rotation. Wash beads three times with RIPA buffer plus 500 mM NaCl, then three times with RIPA buffer plus 1 M NaCl, then three times with LiCl buffer (1 x TE, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate), and finally three times with 1 x TE buffer. Elute DNA and reverse crosslinking with protease K digestion and incubating at 65 °C for over 6 hours. DNA was purified with MinElute Reaction Cleanup Kit (QIAGEN, Cat. 28206). Repair DNA ends with End-It DNA End-Repair Kit (Lucigen, Cat. ER0720), then perform A-tailing with Klenow Fragment (3’ -> 5’ exo-) (NEB, Cat. M0212S) provided with dATP, then followed by adapter ligation with T4 DNA ligase (NEB, Cat. M0202S). Finally, the library was indexed and amplified by PCR, and DNA fragments between 200 bp and 600 bp were purified and sequenced.

treatment_protocol: dCas9-KRAB expressing K562 cells were infected with lentiviruses expressing sgRNAs against e3, e7, e3&e7, e1, e4, or e1&e4.

value: WT


title: LPS/IFNg + FK866 - 2 [X428DS_LI.FK]

library_source: transcriptomic

molecule: total RNA

tag: genotype

value: LPS/IFNg + FK867


title: ETiX day 8 fraction 1

city: Cambridge

first: Florian

last: Hollfelder

address: 80 Tennis court road

country: United Kingdom

institute: University of Cambridge

description:
Induced synthetic embryo sample at 8 days of development created with the reported method (Amadei et al. 2021), dissected embryonic compartment
Synthetic ETiX embryo at day 8 (scRNA-seq libraries), embryonic cells

data_processing:
BCL to fastq conversion using bcl2fastq (illumina script)
demultiplexing with Pheniqs from biosails
Filtering,mapping,quantification with zUMIs
Integration, normalisation, scaling of the matrix (containing intronic and exonic de-duplicated reads) with Seurat
Batch effect removal with Harmony
Genome_build: Mus_musculus.GRCm38.99
Supplementary_files_format_and_content: de-duplicated gene expression matrix containing merged intronic and exonic counts

organism: Mus musculus

source_name: Stem cell derived embryo

growth_protocol: AggreWell plates (STEMCELL Technologies 34415) were prepared as described in (Amadei et al., 2021).To generate ETiX-embryos, Doxycycline was added to tetO-Gata4 ES cells for 6 hours. TS cells were trypsinised and were added to a gelatinised plate to deplete the mouse embryonic fibroblasts for 20 minutes at 37°C. ES cells and tetO-Gata4 ES cells were subsequently trypsinised. Cell suspensions with 19,200 TS cells, 6000 ES cell and 6,000 tetO-Gata4 ES cells were mixed and pelleted by centrifugation. The cell pellet was resuspended in 1ml FC medium with 7.5nM ROCK inhibitor (Y27632, STEMCELL Technologies 72304). After adding the cell mixture drop-wise to the AggreWell, the plate was centrifuged at 100g for 3 minutes. On the next day, media change was performed twice by removing 1ml medium from each well and adding 1ml fresh FC medium without ROCK inhibitor. On Day 2, media change was performed once to replace 1ml medium with 1ml fresh FC medium. On Day 3, 1.2ml medium was removed from each well and 1.5ml IVC1 was added, after equilibrating for 20 minutes in the incubator. IVC1 (Bedzhov et al., 2014) is made of advanced DMEM/F12 (Gibco, 21331-020) supplemented with 20% (v/v) FBS, 2 mM GlutaMax, 1% v/v penicillin–streptomycin, 1X ITS-X Thermo Fisher Scientific, 51500-056), 8 nM β-estradiol, 200 ng/ml progesterone and 25 μM N-acetyl-L-cysteine. On Day 4, ETiX-embryos in the AggreWell were transferred to CELLSTAR 6 well multiwell plate for suspension culture (Greiner Bio-One 657185) with 5ml of IVC1 (with FBS at 30% v/v) per well. On Day 5 IVC1 was replaced with ex utero culture medium (EUCM) (Aguilera-Castrejon et al., 2021). EUCM comprises 25% DMEM (GIBCO 11880) supplemented with 1× Glutamax (GIBCO, 35050061), 100 units/ml penicillin and 100 μg/ml streptomycin and 11 mM HEPES (GIBCO 15630056), plus 50% rat serum (rat whole embryo culture serum, Charles River) and 25% human cord serum obtained from the Cambridge Blood Biobank. Human and rat serum were heat-inactivated for 35 minutes (from frozen) at 56 C and sterilised by filtration. Each ETiX was transferred to a single well of 24-well, non-adherent dish (Greiner 662102) with 250 uL of EUCM . On day 6 each ETiX embryos was fed with an additional 250 uL of EUCM. On day 7, EUCM was supplemented with 3.0 mg/ml of D-Glucose (Sigma G8644) and the samples were moved to a rotating bottle culture chamber apparatus10. Each rotating bottle contained 2 ml of EUCM and 3 ETiX embryos. On day 8 EUCM was supplemented with 3.5 mg/ml of D-Glucose; in each rotating bottle 2 ETiX were cultured with 3 ml of EUCM. NAtural embryos were recovered from pregnant females at the approrpaite timepoint.

extract_protocol:
Samples were dissociated to single cells by cutting with needles and then incubation in TrypLE Express dissociation solution for 15 minutes followed by reaction inactivation with media containing 15% fetal bovine serum, filtration and 2 washes in PBST (0.02% Tween-20.
inDrop v3

treatment_protocol: not applicable

tag: tissue

value: Stem cell derived synthetic embryo

tag: strain

value: Mixed strain:CD1/MF1/C57BL/6

tag: developmental day

tag: ploidy

value: Euploid

tag: stem cells of origin

value: embryonic stem cells transiently expressing Gata4, embryonic and trophoblast stem cells

tag: transgenes

value: Embryonic stem cells:Sox2-Venus/Bry-mCherry/Oct4-Cyan;CAG-GFP/tetO-mCherry; Cerl-GFP ES cells; CD1 WT. Trophoblast stem cells:WT CD1; ES cells transiently expressing Gata4:CD1; CAG-GFP/tetO-mCherry; tetO=Gata4; Cerl-GFP


title: ETiX day 6 fraction 4

description:
Induced synthetic embryo sample at 6 days of development created with the reported method (Amadei et al. 2021)
Synthetic ETiX embryo at day 6 (scRNA-seq libraries)


title: ETiX day 6 fraction 5


title: K562 e1i&e4i rep1 [Trac-looping]


title: Acinar2 (RNA-seq)

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center

description:
single-cell RNA-seq
RNA_readcount_matrix.csv.gz
RNA_UMIcount_matrix.csv.gz

library_source: transcriptomic single cell

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrices (UMI counts and read counts) in csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

source_name: exocrine pancreas

extract_protocol:
Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the scNMT-seq protocol. For more information on the generation of pancreatic organoids, see the following papers (Wollny et al., 2016; Krieger et al., 2021).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set, i.e. transcript UMI counts and read counts assessed with single-cell RNA-seq.
Single-cell RNA-seq (Smart-seq3)

value: exocrine pancreas

value: acinar cell

value: wild type

tag: culture condition

value: 9 days as 3D organoids


title: Acinar21 (RNA-seq)


title: K562 e4i rep2 [Trac-looping]

value: e4 inhibition


title: ETiX day 6 fraction 3


title: ETiX day 6 fraction 2


title: K562 e4i rep1 [Trac-looping]


title: LPS/IFNg + vehicle - 3 [X438DS_LI]

value: astrocyte

value: LPS/IFNg + vehicle


title: LPS/IFNg + vehicle - 2 [X431DS_LI]


title: K562 e1i rep2 [Trac-looping]

value: dCas9-KRAB expressing K562 cell line

value: e1 inhibition


title: K562 e1i rep1 [Trac-looping]

value: K562 cell line


title: iCCA_30_iCCA

description: Illumina HumanMethylation450 BeadChip

value: female

value: FFPE


title: iCCA_29_iCCA

description: Illumina HumanMethylation450 BeadChip


title: LPS/IFNg + vehicle - 1 [X426DS_LI]

value: WT


title: LPS/IFNg + FK866 - 1 [X411DS_LI.FK]

value: LPS/IFNg + FK866


title: ETiX day 5 fraction 3

description:
Induced synthetic embryo sample at 5 days of development created with the reported method (Amadei et al. 2021)
Synthetic ETiX embryo at day 5 (scRNA-seq libraries)

value: Stem cell derived synthetic embryo

value: Mixed strain:CD1/MF1/C57BL/6

value: Euploid


title: ETiX day 5 fraction 2

value: embryonic stem cells transiently expressing Gata4, embryonic and trophoblast stem cells

value: Embryonic stem cells:Sox2-Venus/Bry-mCherry/Oct4-Cyan;CAG-GFP/tetO-mCherry; Cerl-GFP ES cells; CD1 WT. Trophoblast stem cells:WT CD1; ES cells transiently expressing Gata4:CD1; CAG-GFP/tetO-mCherry; tetO=Gata4; Cerl-GFP


title: Con + FK866 - 3 [X439DS_FK]

value: Con + FK868


title: ETiX day 5 fraction 1


title: iCCA_31_iCCA

description: Illumina HumanMethylation450 BeadChip


title: K562 WT rep1 (For e1 and e4 inhibition experiment) [Trac-looping]


title: iCCA_32_iCCA

description: Illumina HumanMethylation450 BeadChip

value: male


title: Con + FK866 - 2 [X427DS_FK]

value: Con + FK867


title: iCCA_27_iCCA

description: Illumina HumanMethylation450 BeadChip


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_minus_rep4

city: Aachen

first: Chao-Chung

last: Kuo

state: NRW

address: Pauwelsstrasse 30

department: IZKF Genomics Facility

institute: RWTH Aachen University Hospital

data_processing:
Illumina RTA 2.0 for basecalling
Alignment is done by STAR_2.5.2b with default parameters
Generating the count table by featureCounts v1.5.1; Command:featureCounts -s 2 -p -t exon
Genome_build: mm9

growth_protocol: For the generation of immoralized fibroblast cultures (iMEF) the cells were infected with a retrovirus encoding an shRNA against p19Arf and a Blasticidin resistance gene used for the initial selection of infected cells (10 µg/ml Blasticidin, Invivogen, ant-bl). MEF cells were cultivated in DMEM (ThermoFisher Scientific, 61965059) supplemented with 10% heat-inactivated fetal bovine serum (FBS, ThermoFisher Scientific, 10270106) and 1% penicillin/streptomycin (ThermoFisher Scientific, 15070063).

extract_protocol:
Total RNA was isolated with the High Pure RNA Isolation Kit (Roche, 11828665001) and cDNA synthesized with the QuantiTect Reverse Transcription Kit (Qiagen, 205314).]
The cell number was used to adjust the amount of ERCC RNA Spike-In Mix (ThermoFisher Scientific, 4456740). Generation of RNA-seq libraries (TruSeq Stranded Total RNA Sample Library Prep, Illumina, 20020596) and next-generation sequencing (NextSeq 500/550 High Output Kit v2.5, 150 cycles, Illumina, 20024907) were performed.

treatment_protocol: At day 0 cells were treated with 5 nM 4-Hydroxytamoxifen (+HOT) (Tocris, 3412) or with vehicle (-HOT, 100% ethanol). Thereafter cells were passaged when needed to maintain subconfluency or solely supplied with new medium with the addition of HOT or vehicle as before.

tag: cell line

tag: chip antibody

value: HOT minus


title: K562 WT rep2 (For e1 and e4 inhibition) [Trac-looping]


title: Con + FK866 - 1 [X405DS_FK]

value: astrocyte

value: Con + FK866


title: Con + vehicle - 3 [X437DS_cont]

value: Con + vehicle


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_minus_rep3


title: ETiX day 6 fraction 1


title: EZHi_Rep2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: CAL51 cells treated with EZH2 inhibitor

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with different concentrations of CARM1 inhibitor or EZH2 inhibitor for 24 hours, with DMSO as negative control

value: breast cancer cell line

tag: passages

value: Low passages (6-10)

value: wild type


title: iCCA_25_iCCA

description: Illumina HumanMethylation450 BeadChip

value: FFPE


title: iCCA_26_iCCA

description: Illumina HumanMethylation450 BeadChip

value: female


title: iCCA_24_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_23_iCCA

description: Illumina HumanMethylation450 BeadChip


title: EZHi_Rep1

description: CAL51 cells treated with EZH2 inhibitor


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_minus_rep2


title: CARM1_EZHi_Rep2

description: CAL51 cells treated with CARM1 inhibitor and EZH2 inhibitor


title: Con + vehicle - 2 [X429DS_cont]

value: WT


title: Con + vehicle - 1 [X425DS_cont]


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_minus_rep1


title: iCCA_20_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_22_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_19_iCCA

description: Illumina HumanMethylation450 BeadChip


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_plus_rep4

value: HOT plus


title: iCCA_21_iCCA

description: Illumina HumanMethylation450 BeadChip


title: CD38KO LPS/IFNg - 3 [X424TM_KO.LI]

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt; resulting reads shorter than 30bp were discarded
Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the M. musculus, mm10 genome according to Refseq annotations, using STAR] with EndToEnd option and outFilterMismatchNoverLmax was set to 0.05.
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Counts for each gene were quantified using htseq-count, using the gtf above and corrected for UMI saturation
Assembly: M. musculus, mm10 genome
Supplementary files format and content: not provided

treatment_protocol: Astrocytes were treated with lipopolysaccharide (100 ng/ml) and Interferon-γ (100 ng/ml) (LPS/IFNγ) or left untreated (Control; Con) for 6H

value: LPS/IFNg


title: CARM1_EZHi_Rep1


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_plus_rep3


title: iCCA_17_iCCA

description: Illumina HumanMethylation450 BeadChip


title: CARM1i_Rep2

description: CAL51 cells treated with CARM1 inhibitor


title: DMSO_Rep1 (CARM1 control)

description: CAL51 cells treated with DMSO


title: DMSO_Rep2 (CARM1 control)

description: CAL51 cells treated with DMSO


title: CD38KO LPS/IFNg - 2 [X420TM_KO.LI]


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_plus_rep2


title: CD38KO LPS/IFNg - 1 [X416TM_KO.LI]


title: iCCA_18_iCCA

description: Illumina HumanMethylation450 BeadChip


title: RNA-Seq_w_spikein_iMEF2_KO_HOT_plus_rep1


title: CARM1i_Rep1


title: iCCA_16_iCCA

description: Illumina HumanMethylation450 BeadChip


title: CD38KO Con - 3 [X423TM_KO.cont]

value: Con


title: CD38KO Con - 2 [X419TM_KO.cont]


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_minus_rep4


title: K562 e3i&e7i rep2

data_processing:
Library strategy: Trac-looping
  tracPre2.py in cLoops2 package was used to trimmed and mapped raw FASTQ files to hg19, then paired-end tags (PETs) were filtered  and converted to non-redundant BEDPE files for each sample.
Genome_build: hg19
Supplementary_files_format_and_content:  non-redundant BEDPE files: each row is one unique paired-end tag (PET). The columns are: chromosome1, start1, end1, chromosome2, start2, end2, PETID_read1LinkerPos_read2LinkerPos, MAPQ value from Bowtie2, strand1 and strand2.

extract_protocol: Fix 1 million cells with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash the cells with PBS. Resuspend with reaction buffer (50mM Tris acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). Mix short adapter, bridging linker with Tn5, and then incubate at room temperature for 20 minutes to produce Tnp complex. Add the complex to cells and  mix gently, then incubate at 37°C for 4 hours with interval shaking. Stop the reaction by adding EDTA, then reverse crosslinking by incubating at 65°C overnight.   Purify genomic DNA, and fill-in gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads, and wash away free adapters. Run PCR with illumina multiplexing indexed primers. Libraires are purified and submitted for paired-end sequencing.

treatment_protocol: dCas9-KRAB expressing K562 cells were infected with lentiviruses expressing sgRNAs against e3, e7 or e3&e7.

value: dCas9-KRAB expressing K562 cell line

value: e3 and e7 dual inhibition


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_minus_rep3


title: iCCA_15_iCCA

description: Illumina HumanMethylation450 BeadChip

value: male


title: CD38KO Con - 1 [X415TM_KO.cont]


title: K562 e3i&e7i rep1


title: WT LPS/IFNg -3 [X422TM_WT.LI]


title: K562 e7i rep2

value: e7 inhibition


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_minus_rep2

value: HOT minus


title: K562 e7i rep1


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_minus_rep1


title: WT LPS/IFNg -2 [X418TM_WT.LI]

value: astrocyte


title: iCCA_28_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_13_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_14_iCCA

description: Illumina HumanMethylation450 BeadChip


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_plus_rep4


title: WT LPS/IFNg -1 [X414TM_WT.LI]


title: iCCA_12_iCCA

description: Illumina HumanMethylation450 BeadChip


title: K562 e3i rep2

value: e3 inhibition


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_plus_rep3


title: WT Con - 3 [X421TM_WT.cont]


title: iCCA_10_iCCA

description: Illumina HumanMethylation450 BeadChip


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_plus_rep2


title: iCCA_11_iCCA

description: Illumina HumanMethylation450 BeadChip


title: K562 WT rep2


title: RNA-Seq_w_spikein_iMEF1_KO_HOT_plus_rep1


title: WT Con - 2 [X417TM_WT.cont]


title: K562 WT rep1


title: K562 e3i rep1


title: WT Con - 1 [X413TM_WT.cont]


title: iCCA_9_iCCA

description: Illumina HumanMethylation450 BeadChip

value: Fresh frozen


title: iCCA_8_iCCA

description: Illumina HumanMethylation450 BeadChip


title: iCCA_7_iCCA

description: Illumina HumanMethylation450 BeadChip


title: Transfer of WT CD8 T cells biol. repl. 4

status: Public on Aug 11 2022

type: RNA

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

description: Gene expression data from bone marrow after transfer of WT CD8 T cells.

hyb_protocol: Following fragmentation, cRNA was hybridized on Clariom_S_Mouse Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G and GeneChip Command Console 3.2 software.

data_processing: Data were normalized according to vsn and imported into Gene Spring GX 7.3.1 and filtered according to a minimum amount of 4 present calls (according to GC-RMA normalization and flagging by MAS5) within at least one condition (cell type) and raw signal above 50. Remaining probe sets were exported, processed with ComBat software to compell batch effects and reimported into Gene Spring for further analysis.

label: biotin

source_name: bone marrow cells from septic mice after transfer of WT CD8 T cells

label_protocol: Two rounded in vitro transcription protocol with Ambion MessageAmpII kit and MessageAmp Biotin Enhanced-Kit according to manufacturer's instructions.

extract_protocol: RNeasy Mini Kit (Qiagen, Düsseldorf, Germany) according to the manufacturer's instructions.

treatment_protocol: Female BALB/c mice (10-14 wks old) received 1 mill. CD8+ T cells from WT or TLR2 ko mice immediately before cecal ligation and puncture. After 24 h, bone marrow cells were isolated for RNA extraction.

value: bone marrow


title: Transfer of TLR2 ko CD8 T cells biol. repl. 3

description: Gene expression data from bone marrow after transfer of TLR2 ko CD8 T cells.

source_name: bone marrow cells from septic mice after transfer of TLR2 CD8 T cells


title: iCCA_6_iCCA

description: Illumina HumanMethylation450 BeadChip


title: Transfer of TLR2 ko CD8 T cells biol. repl. 4


title: Transfer of TLR2 ko CD8 T cells biol. repl. 1


title: 18593X12 14 hr E93 mutant 3

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description:
w1118 fkh>GFP; +/+; E93Δ12/E93Δ13
18593X12

data_processing:
The fruitfly BDGP6.28 genome and gene feature files were downloaded from Ensembl release 102
The reference database was created using STAR version 2.7.6a with splice junctions optimized for 150 base pair reads
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Genome_build: BDGP6.28
Supplementary_files_format_and_content: Raw counts from FeatureCounts combined into a single tab-delimited file

organism: Drosophila melanogaster

source_name: salivary glands

growth_protocol: regular cornmeal molasses diet

extract_protocol:
NucleoSpin RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 14 hrs after pupariation

value: w1118 fkh>GFP; +/+; E93delta12/E93delta13


title: 18593X11 14 hr E93 mutant 2

description:
w1118 fkh>GFP; +/+; E93Δ12/E93Δ13
18593X11


title: 18593X7 14 hr control 1

description:
w1118 fkh>GFP; +/+; +/E93Δ1
18593X7


title: 18593X8 14 hr control 2

description:
w1118 fkh>GFP; +/+; +/E93Δ1
18593X8


title: 18593X10 14 hr E93 mutant 1

description:
w1118 fkh>GFP; +/+; E93Δ12/E93Δ13
18593X10


title: Transfer of TLR2 ko CD8 T cells biol. repl. 2


title: Transfer of WT CD8 T cells biol. repl. 2


title: Transfer of WT CD8 T cells biol. repl. 3


title: Transfer of WT CD8 T cells biol. repl. 1


title: 18593X9 14 hr control 3

description:
w1118 fkh>GFP; +/+; +/E93Δ1
18593X9


title: 18593X6 12 hr E93 mutant 3

description:
w1118 fkh>GFP; +/+; E93Δ12/E93Δ13
18593X6

value: 12 hrs after pupariation


title: 18593X5 12 hr E93 mutant 2

description:
w1118 fkh>GFP; +/+; E93Δ12/E93Δ13
18593X5


title: 18593X4 12 hr E93 mutant 1

description:
w1118 fkh>GFP; +/+; E93Δ12/E93Δ13
18593X4


title: 18593X3 12 hr control 3

description:
w1118 fkh>GFP; +/+; +/E93Δ1
18593X3


title: iCCA_5_iCCA

description: Illumina HumanMethylation450 BeadChip


title: 18593X2 12 hr control 2

description:
w1118 fkh>GFP; +/+; +/E93Δ1
18593X2


title: iCCA_4_iCCA

description: Illumina HumanMethylation450 BeadChip


title: 18593X1 12 hr control 1

description:
w1118 fkh>GFP; +/+; +/E93Δ1
18593X1


title: iCCA_3_iCCA

description: Illumina HumanMethylation450 BeadChip


title: nonNDNF 100 nuclei biological replicate 3

city: Rehovot

first: Daniella

last: Apelblat

address: Hertzl

department: Neuroscience

institute: Weizmann Institute of Science

description: nuclear RNA

data_processing:
Basecall and quality scoring was performed by the RTA software, version 2.11.3.0
Mouse samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the mm10 genome using STAR version 2.5.3a.
Monkey samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the Macaca fascicularis 6.0 genome using STAR version 2.5.3a.
Assembly: mm10, Macaca fascicularis 6.0
Supplementary files format and content: .csv files include raw read values for every gene in the sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Mouse Visual Cortex

extract_protocol:
Freshly dissected visual cortices were snap frozen in liquid nitrogen and stored at -80C. Nuclei were then extracted,  stained with antibodies and Dapi and FACS-sorted  into 0.2ml low-bind tubes containing 2.03 µl lysis buffer.
Libraries were prepared based on the Smart-Seq2 protocol with small modifications. Briefly, 100 nuclei were collected directly into 2.03 microliter lysis buffer (0.2% Triton X-100 in ddW) supplemented with dNTPs (2mM each), SMART-dT30VN primers (1mM), ERCC (1:1.25x107), and RNAse inhibitor. Reverse transcription was performed directly on isolated nuclei, followed by PCR-amplification (17 cycles). After cleanup with Agencourt Ampure XP beads (Beckman Coulter), the amplified cDNA underwent library generation using Nextera XT (Illumina). Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent).

value: visual cortex


title: nonNDNF 100 nuclei biological replicate 2

description: nuclear RNA


title: NDNF 100 nuclei biological replicate 3

description: nuclear RNA


title: nonNDNF 100 nuclei biological replicate 1

description: nuclear RNA


title: NDNF 100 nuclei biological replicate 2

description: nuclear RNA


title: oASC, RNA Rep1

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: aging.csv

data_processing:
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:10:20 MINLEN:30’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 516 -q 10 -b’.
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value table of genes with their corresponding FPKM values as output by Ballgown

molecule: polyA RNA

source_name: 2.5days post-injured old satellite cells

extract_protocol:
RNA was isolated using miRNeasy FFPE Kit (Qiagen).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol and processed for library generation using Tn5-mediated library generation. Sequencing was carried out in 2 × 100 cycle paired-end mode on a DNBSEQ-G400 sequencer (BGI).

treatment_protocol: Mouse hind limb was injured by BaCl2 injection. Mice were perfused with PFA before satellite cell isolation.

value: Skeletal muscle

value: Muscle stem cells

value: BaCl2 injury

tag: time

value: 2.5 dpi


title: NDNF 100 nuclei biological replicate 1

description: nuclear RNA


title: Tsc1-WT, cTag-PABP, pAAV-Camk2a-iCre, Rep2

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score. Filtered reads with the exact sequence were collapsed into one. The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011). Trimmed reads that are at least 25-nt in length are retained for mapping to reference genome (mm10 or hg19).
Mapping was performed using Novoalign without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster. The clusters were filtered by PH before downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the accompanying publication for further information.
Assembly: mm10 (samples 1~4) and hg19 (samples 5~8)
Supplementary files format and content: txt files for unique read counts at gene level (RefSeq)

source_name: Brain cortex

extract_protocol:
Sample preparation, immunoprecipitation, SDS-PAGE and RNA extraction were performed using the PAPERCLIP protocol (Kunisky et al., Cell Rep. 2021) or the cTag-PAPERCLIP protocol (Hwang et al. Neuron, 2017)
The sequencing library was constructed using the PAPERCLIP method (Kunisky et al., Cell Rep. 2021).  The library contains a 11-nt degenerate linker sequence at the 5′ end (3-nt degenerate sequence, 4-nt sample multiplexing index and 7-nt random barcode) as described in (Kunisky et al., Cell Rep. 2021).

value: Brain cortex

value: Tsc1 WT

tag: library

value: cTag-PAPERCLIP


title: Tsc1-KO, cTag-PABP, pAAV-Camk2a-iCre, Rep2

value: Tsc1 KO


title: Tsc1-KO, cTag-PABP, pAAV-Camk2a-iCre, Rep1


title: FISC H3K27ac, ChIP-seq, Rep 1 Input

data_processing:
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
read mapping with bwa_mem
mark and remove duplicates with picard
call relaxed peaks with narrow settings on individual replicates using macs2, make it output treatment and control bedgraph files
create fold change bigWig track using macs2 bedgraph output files with macs2 bdgcmp, use bedGraphToBigWig to convert to bigWig
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files of each replicates; BigWig treatment over control fold change tracks

source_name: Skeletal muscle

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was constructed using ChIPmentation protocol from Schmidl et al., (2015). Briefly, antibody-bound DNA was tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct ChIP-seq library. Library was then sequenced using Illumina Nextseq 500 ( 1 x 75).

value: freshly isolated


title: FISC H3K27ac, ChIP-seq, Rep 2 Input


title: ASC H3K27ac, ChIP-seq, Rep 2


title: ASC H3K27ac, ChIP-seq, Rep 2 Input


title: ASC H3K27ac, ChIP-seq, Rep 1


title: Tsc1-WT, cTag-PABP, pAAV-Camk2a-iCre, Rep1


title: ASC H3K27ac, ChIP-seq, Rep 1 Input


title: oFISC, ATAC Rep2

data_processing:
Adapters were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters‘PE CROP: 50.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with parameters ‘--minins 30 --maxins 2000 --dovetail -k 4 --very-sensitive-local’
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings.
Next, unmapped reads, duplicate reads, non-primary alignments, reads with their mate unmapped and read alignments with a mapping quality below 30 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1804 -f 2 -q 30 -b’.
Peak calling was performed on each individual replicate from the previous section using Genrich (v0.6, available at https://github.com/jsh58/Genrich) with the following parameters: -j -y -r -e chrM -v -f.
Genome_build: mm10
Supplementary_files_format_and_content: NarrowPeak files with blacklisted peaks removed; BigWig files of ATAC-seq signal along mm10 after downsampling step.

source_name: freshly isolated old satellite cells

extract_protocol:
Isolated satellite cells were lysed using ATAC-seq lysis buffer ( (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Library was constructed based on protocols from Buenrostro et al., (2015) and Chen et al., (2016). Briefly, lysates were tagmented with Tn5 (Vazyme), reverse-crosslinked,  and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library was then sequenced using DNBSEQ-G400 sequencer (BGI).


title: oFISC, ATAC Rep1


title: uninjured, ATAC Rep2

source_name: In situ fixed satellite cells


title: uninjured, ATAC Rep1


title: oFISC, RNA Rep2

description: aging.csv


title: iCCA_2_iCCA

description: Illumina HumanMethylation450 BeadChip

tag: gender

value: male


title: FISC H3K27ac, ChIP-seq, Rep 2

tag: cell type


title: AB4253 (123.12.02-CD11b)

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 followed by UMI N8 in read 2.
paired-end (read2 used to read cell and molecule barcodes only)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

growth_protocol: ex vivo experiments: 50,000 iTregs were incubated with 10ug/ml anti-CTLA-4 m2a or m1 versions or kept untreated for 30 min on ice. iTregs+antibody mix was added to the sided BMDM cells (ratio is 10:1 BMDM:Treg) and co-incubated for 12 hours. Cells were removed from the culture using a cell scraper and stained for flow cytometric analysis and single-cell sorting.

extract_protocol:
Tumor bearing mice were sacrificed at the described time points. The tumors underwent mechanical (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 15 min at 37°C. Cells then filtered through 100µm cell strainer, washed with ice cold PBS, centrifuged (5 min, 4°C, 300g), and stained with fluorophore conjugated antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single-cell RNA-sequencing for gene expression quantitation
instrument models: Illumina NextSeq 500/550, NovaSeq 6000

treatment_protocol: 8-10 weeks old female mice were inoculated subcutaneously (s.c.) with 5x105 MCA-205 cells suspended in 100μl PBS on their right flank. Tumor volume was measured using a caliper. Tumor volume was assessed by measuring two diameters and calculated using the formula X2 × Y × 0.52 (where X, smaller diameter and Y, larger diameter).

value: Myeloid

tag: replicate

tag: treatment

tag: day of tumor harvest

tag: sequencing batch

tag: gating

tag: institute

value: WIS

tag: batch

tag: experiment

tag: protocol version

value: new

tag: sorting date

tag: libraries date


title: AB4254 (123.12.03-CD11b)

tag: strain


title: FISC H3K27ac, ChIP-seq, Rep 1

tag: tissue

tag: chip antibody


title: iCCA_1_iCCA

description: Illumina HumanMethylation450 BeadChip

data_processing: Methylation data were processed using the R platform for statistical computing.

value: female

value: Fresh frozen


title: AB4251 (122.12.03-CD11b)


title: AB4249 (122.12.01-CD11b)


title: AB4248 (121.12.03-CD11b)


title: AB4244 (103.12.01-CD11b)


title: AB4247 (121.12.02-CD11b)


title: AB4246 (121.12.01-CD11b)


title: AB3747 (8.07.7-CD45)

value: Broad


title: AB3746 (8.07.7-CD45)


title: AB4240 (101.12.01-CD11b)

value: UT


title: AB4239 (101.12.01-CD11b)


title: AB3745 (8.07.6-TCR)

value: T

value: TCR

tag: empty rows

value: A-E

tag: partial plate

tag: notes

value: A-E sorting speed 3


title: AB4252 (123.12.01-CD11b)

tag: cell type

tag: replicate


title: AB4243 (103.12.01-CD11b)

tag: treatment

tag: day of tumor harvest


title: AB4250 (122.12.02-CD11b)

tag: sequencing batch

tag: gating


title: AB3744 (8.07.6-CD45)

tag: institute


title: AB3742 (8.07.6-CD45)

tag: experiment

value: Low number of cells


title: AB3743 (8.07.6-CD45)

tag: protocol version


title: AB3740 (7.07.7-CD45)

tag: sorting date


title: AB3738 (7.07.7-CD45)

tag: libraries date


title: AB3741 (7.07.7-TCR)

tag: strain


title: AB3739 (7.07.7-CD45)


title: AB4245 (121.12.01-CD11b)

tag: batch


title: AB3736 (7.07.6-CD45)


title: AB3737 (7.07.6-TCR)


title: AB4242 (102.12.01-CD11b)


title: AB4241 (102.12.01-CD11b)


title: AB3735 (7.07.6-CD45)


title: AB3729 (8.07.5-TCR)

value: A-F


title: AB3734 (7.07.6-CD45)


title: AB3731 (7.07.5-CD11b)


title: AB3732 (8.07.5-CD45)

value: First mouse of second batch


title: AB3733 (8.07.5-CD45)


title: AB3730 (7.07.5-TCR)


title: AB3703 (112.12.01-CD11b)


title: AB3723 (7.07.5-CD45)


title: AB3705 (112.12.03-CD11b)


title: AB3702 (111.12.04-CD11b)


title: AB3701 (111.12.03-CD11b)


title: AB3697 (113.12.03-CD11b)


title: AB3695 (113.12.01-CD11b)


title: AB3696 (113.12.02-CD11b)


title: AB3692 (102.12.03-CD11b)


title: AB3698 (113.12.04-CD11b)


title: AB3691 (102.12.02-CD11b)


title: AB3693 (102.12.04-CD11b)


title: AB3694 (102.12.05-CD11b)


title: AB3704 (112.12.02-CD11b)


title: AB3706 (112.12.04-CD11b)


title: AB3724 (7.07.5-CD45)


title: AB3690 (101.12.05-CD11b)


title: AB3689 (101.12.04-CD11b)


title: AB3687 (101.12.02-CD11b)


title: AB3700 (111.12.02-CD11b)


title: AB3686 (103.12.05-CD11b)


title: AB3688 (101.12.03-CD11b)


title: AB3684 (103.12.03-CD11b)


title: AB3699 (111.12.01-CD11b)


title: AB3685 (103.12.04-CD11b)


title: AB3589 (101.12.01-CD11b)


title: AB3587 (102.12.01-CD11b)


title: AB3683 (103.12.02-CD11b)


title: AB3590 (101.12.01-CD11b)


title: AB3583 (103.12.01-CD11b)


title: AB3240 (13.07.04-TCR)


title: AB3241 (11.07.04-CD45)


title: AB3238 (13.07.03-TCR)


title: AB3237 (13.07.03-TCR)


title: AB3584 (103.12.01-CD11b)


title: AB3586 (102.12.01-CD11b)


title: AB3582 (103.12.01-CD11b)


title: AB3585 (102.12.01-CD11b)


title: AB3236 (13.07.02-TCR)


title: AB3252 (13.07.05-TCR)


title: AB3250 (11.07.04-TCR)


title: AB3235 (13.07.02-TCR)


title: AB3239 (13.07.04-TCR)

value: Machine rinsed before this plate.


title: AB3249 (13.07.05-CD45)


title: AB3233 (13.07.01-TCR)


title: AB3588 (101.12.01-CD11b)

value: Left for long time on 4c


title: AB3243 (11.07.04-CD45)


title: AB3223 (11.07.03-TCR)

value: A-M


title: AB3222 (11.07.02-TCR)


title: AB3242 (11.07.04-CD45)


title: AB3234 (13.07.01-TCR)


title: AB3220 (11.07.01-TCR)

value: Left at RT for long time


title: AB3219 (11.07.01-TCR)

value: WIS


title: AB3212 (13.07.02-CD45)

value: new


title: AB3214 (13.07.03-CD45)


title: AB3217 (13.07.04-CD45)


title: AB3216 (13.07.04-CD45)


title: AB3218 (13.07.04-CD45)


title: AB3215 (13.07.03-CD45)


title: AB3210 (13.07.02-CD45)


title: AB3213 (13.07.03-CD45)


title: AB3211 (13.07.02-CD45)


title: AB3224 (11.07.03-TCR)

value: Cloged in the middle of the plate


title: AB3221 (11.07.02-TCR)


title: AB3209 (13.07.01-CD45)


title: AB3208 (13.07.01-CD45)


title: AB3192 (11.07.03-CD45)


title: AB3191 (11.07.02-CD45)


title: AB3190 (11.07.02-CD45)


title: AB3194 (11.07.03-CD45)


title: AB3189 (11.07.02-CD45)


title: AB3193 (11.07.03-CD45)


title: AB3187 (11.07.01-CD45)


title: AB3247 (13.07.05-CD45)


title: AB3248 (13.07.05-CD45)


title: AB3186 (11.07.01-CD45)


title: AB3207 (13.07.01-CD45)


title: AB3157 (1.07.117-CD45)


title: AB3156 (1.07.117-CD45)


title: AB3147 (1.07.116-CD45)


title: AB3146 (1.07.116-CD45)


title: AB3154 (1.07.117-TCR)


title: AB3148 (1.07.116-TCR)


title: AB3149 (1.07.116-TCR)


title: AB3155 (1.07.117-TCR)


title: AB3152 (1.07.117-CD45)


title: AB3153 (1.07.117-CD45)


title: AB3150 (1.07.117-CD45)


title: AB3143 (3.07.135-TCR)


title: AB3188 (11.07.01-CD45)


title: AB3141 (3.07.135-CD45)


title: AB3142 (3.07.135-CD45)


title: AB3139 (3.07.135-CD45)


title: AB3138 (3.07.134-TCR)


title: oFISC, RNA Rep1

description: aging.csv

tag: tissue

value: Skeletal muscle

value: Muscle stem cells

value: BaCl2 injury

tag: time

value: freshly isolated


title: oASC, RNA Rep2

description: aging.csv

value: 2.5 dpi


title: AB3137 (3.07.134-TCR)

value: T

value: TCR

tag: empty rows

tag: partial plate


title: AB3151 (1.07.117-CD45)

tag: cell type

value: Broad

value: UT


title: AB3136 (3.07.134-CD45)

tag: replicate


title: AB3135 (3.07.134-CD45)

tag: treatment


title: AB3134 (3.07.134-CD45)

tag: day of tumor harvest


title: AB3133 (3.07.134-CD45)

tag: sequencing batch


title: AB3144 (1.07.116-CD45)

tag: gating


title: AB3140 (3.07.135-CD45)

tag: institute


title: AB3145 (1.07.116-CD45)

tag: experiment


title: AB3132 (3.07.131-TCR)

tag: protocol version

tag: notes

value: Clog-machine was cleaned


title: AB3131 (3.07.131-TCR)

tag: sorting date

tag: libraries date

value: A-E


title: AB3128 (3.07.131-CD45)

tag: strain

tag: batch


title: AB3129 (3.07.131-CD45)


title: AB3130 (3.07.131-CD45)


title: AB3124 (1.07.112-CD45)


title: AB3120 (1.07.111-TCR)

value: 1/2 plate


title: AB3122 (1.07.112-CD45)


title: AB3125 (1.07.112-TCR)


title: AB3123 (1.07.112-CD45)


title: AB3117 (1.07.111-CD45)


title: AB3126 (1.07.112-TCR)


title: AB3121 (1.07.112-CD45)


title: AB3116 (1.07.111-CD45)


title: AB3118 (1.07.111-CD45)


title: AB3114 (2.07.124-TCR)


title: AB3119 (1.07.111-TCR)


title: AB3111 (2.07.124-CD45)


title: AB3112 (2.07.124-CD45)


title: AB3127 (3.07.131-CD45)


title: AB3113 (2.07.124-TCR)


title: AB3108 (2.07.123-TCR)


title: AB3103 (2.07.123-CD45)


title: AB3107 (2.07.123-TCR)


title: AB3110 (2.07.124-CD45)


title: AB3104 (2.07.123-CD45)


title: AB3106 (2.07.123-CD45)


title: AB3109 (2.07.124-CD45)


title: AB3105 (2.07.123-CD45)


title: AB3115 (1.07.111-CD45)


title: AB3099 (2.07.122-CD45)


title: AB3102 (2.07.122-TCR)


title: AB3097 (2.07.122-CD45)


title: AB3100 (2.07.122-CD45)


title: AB3101 (2.07.122-TCR)


title: AB3098 (2.07.122-CD45)


title: AB3093 (2.07.121-CD45)


title: AB3080 (7.07.3-CD45)


title: AB3094 (2.07.121-CD45)


title: AB3081 (7.07.3-CD45)


title: AB3092 (2.07.121-CD45)


title: AB3079 (7.07.3-CD45)


title: AB3077 (7.07.3-CD45)


title: AB3078 (7.07.3-CD45)


title: AB3035 (7.07.4-TCR)


title: AB3034 (7.07.4-TCR)


title: AB3033 (7.07.3-TCR)


title: AB3096 (2.07.121-TCR)


title: AB3030 (8.07.4-TCR)


title: AB3026 (8.07.4-CD45)


title: AB3095 (2.07.121-TCR)


title: AB3031 (8.07.4-TCR)


title: AB3023 (8.07.3-CD45)


title: AB3024 (8.07.3-CD45)


title: AB3021 (8.07.3-CD45)

value: poor staining for cd11b (bv650) and TCRb FITC


title: AB3028 (8.07.3-TCR)


title: AB3025 (8.07.4-CD45)


title: AB3017 (7.07.1-TCR)


title: AB3091 (2.07.121-CD45)


title: AB3022 (8.07.3-CD45)


title: AB3016 (8.07.2-TCR)


title: AB3009 (7.07.1-TCR)


title: AB3015 (8.07.2-TCR)


title: AB3012 (7.07.2-TCR)


title: AB3008 (8.07.2-CD45)


title: AB3007 (8.07.2-CD45)


title: AB3006 (8.07.2-CD45)


title: AB3005 (8.07.2-CD45)


title: AB3004 (7.07.2-CD45)


title: AB3032 (7.07.3-TCR)


title: AB3003 (7.07.2-CD45)


title: AB3002 (7.07.2-CD45)


title: AB3029 (8.07.3-TCR)


title: AB3027 (8.07.4-CD45)


title: AB2993 (7.07.1-CD45)


title: AB2995 (7.07.1-CD45)


title: AB3001 (7.07.2-CD45)


title: AB2838 (2.07.20-T)

value: intermediate


title: AB2994 (7.07.1-CD45)

value: WIS


title: AB2992 (7.07.1-CD45)

value: new


title: AB2835 (2.07.20-Innate)

value: Innate


title: AB2837 (2.07.20-T)


title: AB2834 (2.07.20-Innate)


title: AB3011 (7.07.2-TCR)


title: AB2833 (3.07.19-T)


title: AB2836 (2.07.20-Innate)


title: AB2827 (2.07.18-T)


title: AB2826 (2.07.18-Innate)


title: AB2828 (2.07.18-T)


title: AB2829 (3.07.19-Innate)


title: AB2831 (3.07.19-Innate)


title: AB2830 (3.07.19-Innate)


title: AB2825 (2.07.18-Innate)


title: AB2822 (3.07.18-T)


title: AB2832 (3.07.19-T)


title: AB2823 (3.07.18-T)


title: AB2824 (2.07.18-Innate)


title: AB2820 (3.07.18-Innate)


title: AB2819 (3.07.18-Innate)


title: AB2821 (3.07.18-Innate)


title: AB2817 (2.07.17-T)


title: AB2818 (2.07.17-T)


title: AB2814 (2.07.17-Innate)


title: AB2815 (2.07.17-Innate)


title: AB2816 (2.07.17-Innate)


title: AB2811 (3.07.17-T)


title: AB2812 (3.07.17-Innate)


title: AB2813 (3.07.17-T)


title: AB2810 (3.07.17-Innate)


title: AB2809 (3.07.17-Innate)


title: AB2461 (3.7.15-T)


title: AB2462 (3.7.15-T)


title: AB2460 (3.7.15-Innate)


title: AB2456 (3.7.14-T)


title: AB2446 (3.7.11-T)


title: AB2458 (3.7.15-Innate)


title: AB2455 (3.7.14-T)


title: AB2454 (3.7.14-Innate)


title: AB2445 (3.7.11-T)


title: AB2452 (3.7.14-Innate)


title: AB2444 (3.7.11-Innate)


title: AB2442 (3.7.11-Innate)


title: AB2443 (3.7.11-Innate)


title: AB2453 (3.7.14-Innate)


title: AB2437 (2.7.13-Innate)


title: AB2438 (2.7.13-T)

value: A-K


title: AB2439 (2.7.11-T)


title: AB2436 (2.7.13-Innate)


title: AB2435 (2.7.14-T)

value: A-I, J empty


title: AB2433 (2.7.14-Innate)


title: AB2434 (2.7.14-T)


title: AB2432 (2.7.14-Innate)


title: AB2431 (2.7.14-Innate)


title: AB2426 (2.7.11-T)

value: bad accudrop,flow rate 3


title: AB2424 (2.7.11-Innate)


title: AB2423 (2.7.11-Innate)


title: AB2422 (2.7.11-Innate)


title: AB2089 (3.07.4-Innate)

value: UCL

value: old


title: AB2088 (3.07.4-Innate)


title: AB2087 (3.07.4-T)

value: T


title: AB2459 (3.7.15-Innate)


title: AB2082 (3.07.3-T)


title: AB2081 (3.07.2-Innate)


title: AB2080 (3.07.2-Innate)


title: AB2078 (3.07.2-T)


title: AB2079 (3.07.2-T)


title: AB1996 (3.07.1-Innate)


title: AB1995 (3.07.1-T)


title: AB1994 (3.07.1-T)

value: 1st plate blocked - binned


title: AB2425 (2.7.11-T)

value: TCR


title: AB2076 (2.07.3-Innate)


title: AB2077 (2.07.3-Innate)


title: AB2072 (2.07.3-T)


title: AB2073 (2.07.3-T)


title: AB2074 (2.07.3-T)


title: AB2075 (2.07.3-Innate)

value: 2 index files


title: AB2071 (2.07.2-Innate)


title: AB2084 (3.07.3-Innate)


title: AB2085 (3.07.3-Innate)

value: left plate 13 mins in centrifuge


title: AB2068 (2.07.2-T)

value: up to N9 index


title: AB2067 (2.07.2-T)

value: pre-sort piece of foil fell into one of the wells, recovered with tip


title: AB2083 (3.07.3-T)

value: O10 onwards empty


title: AB2070 (2.07.2-Innate)


title: AB2066 (2.07.2-T)


title: AB2086 (3.07.3-Innate)

value: M onwards empty


title: AB2065 (2.07.1-Innate)


title: AB1997 (3.07.1-Innate)


title: AB2063 (2.07.1-Innate)


title: AB2064 (2.07.1-Innate)


title: AB2061 (2.07.1-T)


title: AB2062 (2.07.1-T)


title: AB2060 (2.07.1-T)


title: AB2156 (1.07.3-T)

value: UT

value: New plate


title: AB2155 (1.07.3-T)

value: up to middle , 2 index files


title: AB2154 (1.07.3-T)


title: AB2059 (1.07.2-Innate)

value: Innate


title: AB2057 (1.07.2-T)


title: AB2056 (1.07.2-T)


title: AB2058 (1.07.2-Innate)


title: AB2055 (1.07.1-Innate)


title: AB2069 (2.07.2-Innate)


title: AB2053 (1.07.1-Innate)


title: AB2052 (1.07.1-T)


title: AB2054 (1.07.1-Innate)

value: A1-A15 no index


title: AB2050 (1.07.1-T)

value: O and P empty controls


title: AB1317 (3.14.6-Innate)

value: UCL


title: AB1315 (3.14.4-Innate)

value: old


title: AB1316 (3.14.6-Innate)


title: AB1309 (2.14.4-Innate)


title: AB1310 (1.14.9-T)

value: T

value: UT mouse is day 15, not day 14 as previous


title: AB1312 (3.14.5-T)


title: AB1311 (3.14.4-T)


title: AB1313 (3.14.6-T)

value: P1-16 empty


title: AB1314 (3.14.4-T)

value: mouse 2 leftover sample from plates  81-83, so ran more, J1-7 empty , J8 onwards J full, K down empty


title: AB727 (1.14.5-Innate)


title: AB690 (1.14.5-Innate)

value: Was left at room temp for 10 min


title: AB724 (3.14.2-Innate)


title: AB726 (3.14.3-Innate)


title: AB728 (1.14.5-Innate)


title: AB686 (3.14.2-Innate)


title: AB723 (3.14.2-Innate)


title: AB2051 (1.07.1-T)


title: AB722 (3.14.1-Innate)

value: sorted rows A-J


title: AB683 (3.14.1-Innate)


title: AB679 (1.14.4-T)


title: AB680 (1.14.4-Innate)


title: AB721 (1.14.4-Innate)


title: AB678 (1.14.4-T)


title: AB719 (2.14.2-Innate)


title: AB731 (1.14.4-T)


title: AB677 (2.14.2-Innate)

value: gate of the nk1.1 was expanded to include all nk1.1+ cells (CD11b + and -)


title: AB730 (2.14.2-T)


title: AB675 (2.14.2-T)


title: AB676 (2.14.2-T)


title: AB718 (2.14.1-Innate)


title: AB672 (2.14.1-T)


title: AB674 (2.14.1-Innate)


title: AB673 (2.14.1-T)


title: AB725 (3.14.3-Innate)


title: AB670 (1.14.1-T)


title: AB729 (2.14.1-T)


title: AB716 (1.14.3-Innate)


title: AB671 (1.14.1-T)


title: AB712 (1.14.1-Innate)


title: AB714 (1.14.2-Innate)


title: AB713 (1.14.2-Innate)


title: AB715 (1.14.3-Innate)


title: AB720 (2.14.2-Innate)


title: AB711 (1.14.1-Innate)


title: nonVIP.tp1.biorep3

description: nonVIP 100 nuclei time point 1 biological replicate 3

data_processing:
Basecall and quality scoring was performed by the RTA software, version 2.11.3.0
Mouse samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the mm10 genome using STAR version 2.5.3a.
Monkey samples: Sequenced reads were trimmed for adaptor sequence using Cutadapt and mapped to the Macaca fascicularis 6.0 genome using STAR version 2.5.3a.
Genome_build: mm10, Macaca fascicularis 6.0
Supplementary_files_format_and_content: .csv files include raw read values for every gene in the sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

tag: tissue

value: visual cortex

tag: genotype


title: nonVIP.tp3.biorep2

description: nonVIP 100 nuclei time point 3 biological replicate 2


title: nonVIP.tp3.biorep1

description: nonVIP 100 nuclei time point 3 biological replicate 1


title: nonVIP.tp1.biorep2

description: nonVIP 100 nuclei time point 1 biological replicate 2


title: nonVIP.tp1.biorep1

description: nonVIP 100 nuclei time point 1 biological replicate 1


title: nonVIP.tp0.5.biorep2

description: nonVIP 100 nuclei time point 0.5 biological replicate 2


title: nonVIP.tp0.5.biorep3

description: nonVIP 100 nuclei time point 0.5 biological replicate 3


title: AB717 (2.14.1-Innate)

tag: partial plate


title: nonVIP.tp0.5.biorep1

description: nonVIP 100 nuclei time point 0.5 biological replicate 1


title: nonVIP.tp0.biorep1

description: nonVIP 100 nuclei time point 0 biological replicate 1


title: nonVIP.tp0.biorep3

description: nonVIP 100 nuclei time point 0 biological replicate 3


title: VIP.tp3.biorep3

description: VIP 100 nuclei time point 3 biological replicate 3


title: nonVIP.tp0.biorep2

description: nonVIP 100 nuclei time point 0 biological replicate 2


title: VIP.tp1.biorep3

description: VIP 100 nuclei time point 1 biological replicate 3


title: VIP.tp1.biorep2

description: VIP 100 nuclei time point 1 biological replicate 2


title: VIP.tp1.biorep1

description: VIP 100 nuclei time point 1 biological replicate 1


title: VIP.tp3.biorep2

description: VIP 100 nuclei time point 3 biological replicate 2


title: VIP.tp0.5.biorep3

description: VIP 100 nuclei time point 0.5 biological replicate 3


title: VIP.tp0.5.biorep2

description: VIP 100 nuclei time point 0.5 biological replicate 2


title: VIP.tp0.biorep3

description: VIP 100 nuclei time point 0 biological replicate 3


title: nonVIP.tp3.biorep3

description: nonVIP 100 nuclei time point 3 biological replicate 3


title: Corrected [Taka14]

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include gene read counts for each Sample

source_name: Heart

extract_protocol:
iPSC-CMs were homogenized in 1ml of TRizol (Thermo Fisher Scientific). Flash-frozen cardiac samples were homogenized in 1 ml of TRIzol in Precellys Evolution (2 cycles x 30 s at 5000 rpm). RNA as isolated using RNeasy miRNeasy Kit (Qiagen) as per the provider’s instructions.
RNA-seq libraries were prepared using KAPA mRNA HyperPrep (Kapa Biosystems, kk8580) kit following manufacturer’s specifications.

value: Heart

value: Corrected R636Q/R636Q

value: Base editing


title: Corrected [Taka13]


title: Corrected [Taka15]


title: Corrected [Taka16]


title: R636Q_homozygous [Taka12]


title: VIP.tp0.biorep2

description: VIP 100 nuclei time point 0 biological replicate 2


title: VIP.tp0.biorep1

description: VIP 100 nuclei time point 0 biological replicate 1


title: R636Q_homozygous [Taka11]


title: Dapi.pos.100nuc.mouse.techrep2

description: Dapi+ 100 nuclei mouse technical replicate 2


title: R636Q_homozygous [Taka10]


title: R636Q_homozygous [Taka9]


title: VIP.tp3.biorep1

description: VIP 100 nuclei time point 3 biological replicate 1


title: nonVIP.100nuc.Virus.biorep3

description: nonVIP 100 nuclei virus-injected biological replicate 3

value: Vip-Cre


title: R636Q_heterozygous [Taka7]


title: Prox1pos.NeuNpos.100nuc.mouse.techrep2

description: Prox1+ NeuN+ 100 nuclei mouse technical replicate 2


title: R636Q_heterozygous [Taka6]


title: Dapi.pos.100nuc.mouse.techrep1

description: Dapi+ 100 nuclei mouse technical replicate 1


title: R636Q_heterozygous [Taka8]


title: R636Q_heterozygous [Taka5]


title: nonVIP.100nuc.Virus.biorep1

description: nonVIP 100 nuclei virus-injected biological replicate 1


title: VIP.100nuc.Virus.biorep3

description: VIP 100 nuclei virus-injected biological replicate 3


title: Prox1pos.NeuNpos.100nuc.mouse.techrep1

description: Prox1+ NeuN+ 100 nuclei mouse technical replicate 1


title: VIP.tp0.5.biorep1

description: VIP 100 nuclei time point 0.5 biological replicate 1


title: nonVIP.100nuc.biorep2

description: nonVIP 100 nuclei biological replicate 2


title: VIP.100nuc.biorep3

description: VIP 100 nuclei biological replicate 3


title: VIP.100nuc.Virus.biorep2

description: VIP 100 nuclei virus-injected biological replicate 2


title: nonVIP.100nuc.Virus.biorep2

description: nonVIP 100 nuclei virus-injected biological replicate 2


title: nonVIP.100nuc.biorep3

description: nonVIP 100 nuclei biological replicate 3


title: WT [Taka1]

value: Wild type


title: WT [Taka2]


title: VIP.100nuc.biorep2

description: VIP 100 nuclei biological replicate 2


title: nonVIP.500nuc.techrep3

description: nonVIP 500 nuclei technical replicate 3


title: nonVIP.800nuc.techrep2

description: nonVIP 800 nuclei technical replicate 2


title: nonVIP.500nuc.techrep2

description: nonVIP 500 nuclei technical replicate 2


title: nonVIP.800nuc.techrep1

description: nonVIP 800 nuclei technical replicate 1


title: nonVIP.500nuc.techrep1

description: nonVIP 500 nuclei technical replicate 1


title: WT [Taka4]


title: nonVIP.200nuc.techrep3

description: nonVIP 200 nuclei technical replicate 3


title: nonVIP.200nuc.techrep2

description: nonVIP 200 nuclei technical replicate 2


title: LP118_24h_Rep2

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. cerevisiae S288C genome (sequence assembly version: R64-2-1_20150113)  using Bowtie 2 (version 2.2.5)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated
Detailed parameters for reads mapping: bowtie2 -x S288c -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam
Genome_build: S. cerevisiae S288C genome
Supplementary_files_format_and_content: Tab-delimited text files include the raw reads count and the normalized transcripts abundance (FPKM values) for each sample.

organism: Saccharomyces cerevisiae

source_name: LP118_24h_yeast cells

growth_protocol: The cells of the DSG producing strains LP085-Vc, LP104-17, and LP118 were grown overnight and then transferred into a 15mL liquid SD complete medium to reach an initial cell density of OD600= 0.1. After additional flask culture at 30°C and 250 rpm for 6 h and 24 h, the cells were collected by centrifugation for total RNA isolation and Illumina RNA-Seq library construction.

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: growth

value: SD medium, 2%w/v glucose, 24h


title: WT [Taka3]


title: LP118_24h_Rep3


title: nonVIP.200nuc.techrep1

description: nonVIP 200 nuclei technical replicate 1


title: LP118_24h_Rep1


title: LP118_6h_Rep3

source_name: LP118_6h_yeast cells

value: SD medium, 2%w/v glucose, 6h


title: LP118_6h_Rep2


title: nonVIP.100nuc.techrep2

description: nonVIP 100 nuclei technical replicate 2


title: nonVIP.800nuc.techrep3

description: nonVIP 800 nuclei technical replicate 3


title: VIP.100nuc.Virus.biorep1

description: VIP 100 nuclei virus-injected biological replicate 1


title: nonVIP.100nuc.techrep1

description: nonVIP 100 nuclei technical replicate 1


title: LP118_6h_Rep1


title: LP104-17_24h_Rep3

source_name: LP104-17_24h_yeast cells


title: nonVIP.50nuc.techrep2

description: nonVIP 50 nuclei technical replicate 2


title: nonVIP.50nuc.techrep3

description: nonVIP 50 nuclei technical replicate 3


title: nonVIP.50nuc.techrep1

description: nonVIP 50 nuclei technical replicate 1


title: LP104-17_24h_Rep2


title: LP104-17_6h_Rep3

source_name: LP104-17_6h_yeast cells


title: LP104-17_6h_Rep2


title: VIP.800nuc.techrep2

description: VIP 800 nuclei technical replicate 2


title: VIP.800nuc.techrep3

description: VIP 800 nuclei technical replicate 3


title: LP104-17_6h_Rep1


title: LP085-Vc_24h_Rep2

source_name: LP085-Vc_24h_yeast cells


title: LP085-Vc_24h_Rep3


title: VIP.800nuc.techrep1

description: VIP 800 nuclei technical replicate 1


title: VIP.500nuc.techrep3

description: VIP 500 nuclei technical replicate 3


title: VIP.500nuc.techrep2

description: VIP 500 nuclei technical replicate 2


title: LP085-Vc_24h_Rep1


title: nonVIP.100nuc.techrep3

description: nonVIP 100 nuclei technical replicate 3


title: LP085-Vc_6h_Rep3

source_name: LP085-Vc_6h_yeast cells


title: VIP.200nuc.techrep3

description: VIP 200 nuclei technical replicate 3


title: LP085-Vc_6h_Rep2


title: VIP.200nuc.techrep2

description: VIP 200 nuclei technical replicate 2


title: LP104-17_24h_Rep1


title: LP085-Vc_6h_Rep1


title: VIP.100nuc.techrep3

description: VIP 100 nuclei technical replicate 3


title: VIP.200nuc.techrep1

description: VIP 200 nuclei technical replicate 1


title: VIP.100nuc.techrep2

description: VIP 100 nuclei technical replicate 2


title: VIP.100nuc.techrep1

description: VIP 100 nuclei technical replicate 1


title: VIP.50nuc.techrep3

description: VIP 50 nuclei technical replicate 3


title: VIP.50nuc.techrep2

description: VIP 50 nuclei technical replicate 2


title: VIP.50nuc.techrep1

description: VIP 50 nuclei technical replicate 1


title: VIP.500nuc.techrep1

description: VIP 500 nuclei technical replicate 1


title: Day 34 scRNA-seq KO

city: Vancouver

first: Brad

last: Hoffman

state: BC

country: Canada

institute: University of British Columbia

data_processing:
Illumina NextSeq Control Software v2.2.0.4 for base calling
RNA-seq: Reads aligned to GRCm38/mm10; Gencode vM24 using STAR v2.7.3a with default settings
RNA-seq: Transcript abundance measured using Salmon v1.4.0 in alignment mode with seqBias and gcBias settings
RNA-seq: Differential gene expression determined using DESeq2
scRNA-seq: Cellranger v5.0.0 used to demultiplex and convert to fastq
scRNA-seq: barcode detection, read mapping, quality filtering and transcript counting performed with Alevin (Salmon v1.4.0). Processing steps are documented in "scRNAseq_commands.txt"
Genome_build: GRCm38/mm10; Gencode vM24
Supplementary_files_format_and_content: csv file showing KO vs WT differential gene expression metrics for RNA-seq. Output of DESeq2.
Supplementary_files_format_and_content: csv file showing gene counts for each gene in each sample for RNA-seq. Output of DESeq2.
Supplementary_files_format_and_content: matrix file for gene counts per cell for scRNA-seq. Output of Salmon Alevin.

source_name: Mouse islet cells

extract_protocol:
RNA-seq: FACS-enriched beta cells were pooled with a 10% spike-in of S2 cells. RNA was isolated using Trizol.
RNA libraries were prepared from 400ng of total RNA per sample using poly-A capture beads and NEBNext directional RNA-seq library prep kit for Illumina (E7760). scRNA-seq libraries were prepared using Chromium Single Cell 3’ protocol with Reagent Kit v3.1 (10X Genomics)

value: PdxCreER mTmG

tag: cell type

value: Mouse islet cells

tag: genotype/variation


title: Day 45 scRNA-seq WT

value: CTRL


title: Corrected [TN15]

source_name: iPSC-derived cardiomyocytes

value: iPSC-derived cardiomyocytes

tag: cell line

value: Corrected iPSC

value: iPSCs

tag: treatment


title: Corrected [TN14]


title: Corrected [TN13]


title: R634Q_homozygous [TN9]

value: R634Q/R634Q iPSC


title: R634Q_homozygous [TN8]


title: R634Q_homozygous [TN7]


title: R634Q_heterozygous [TN6]

value: R634Q/+ iPSC


title: R634Q_heterozygous [TN5]


title: JIH5_H3K27ac ChIP-Seq

city: Memphis

first: Xujie

last: Zhao

state: TN

address: 246 Danny Thomas Place, MS 313

institute: St. Jude Children's Research Hospital

data_processing:
Paired-end reads of 100bp were mapped human genome hg19(GRCh37-lite)by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by fastp(version 0.20.0, paired-end mode, parameters “--trim_poly_x --cut_by_quality5 --cut_by_quality3 --cut_mean_quality 15 --length_required 20 --low_complexity_filter --complexity_threshold 30 --detect_adapter_for_pe”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2)
Peaks were called by MACS2 (version 2.1.1.20160309 , “--extsize 200 --nomodel --keep-dup all”)
hg38

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using ACTIVE MOTIF ChIP-seq kit
Libraries were made using NEB ultra II DNA library protocol

value: ALL cell line

tag: antibody

value: ZNF384 (Abclonal # A15964)


title: Mouse I MEDIUM

city: Rome

first: Francesca

last: Di Rosa

address: viale Regina Elena 291

country: Italy

institute: Italian National Research Council (CNR)

hyb_protocol: Samples were hybridized using GeneChip Hybridization, Wash and Stain kit (Affymetrix) • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute • Transfer 120μl of hyb solution to each array • Hybridize 20 hours at 48°.

scan_protocol: Affymetrix Gene ChIP Scanner GCS3000.

data_processing: Arrays were preprocessed and expression levels normalized across samples by using the Robust Multichip Average (RMA) method by the Transcriptomics Platform at the Department of Medicine and Surgery, University of Milano-Bicocca (Milan, Italy).

source_name: Wild-type Bone Marrow derived dendritic cells

label_protocol: Samples were fragmented and labelled using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Briefly, 10–15 × 10^6 BM cells from female C57BL/6 mice were cultured in incubator at 37°C under normoxia (21% O2) in complete RPMI medium with 20 ng/ml of GM-CSF in Petri dishes (BD Falcon, BD Biosciences, San Jose, CA, USA). After 3 days, fresh medium with GM-CSF was added. At day 7, we collected non-adherent and slightly adherent cells after detachment with PBS 3 mM EDTA. CD11c+ cells were purified with anti-CD11c magnetic microbeads (Miltenyi Biotec), thus obtaining highly purified CD11c+ (>98%) BMdDCs. (doi: 10.3389/fimmu.2017.00147).  NB=Complete RPMI medium is RPMI Medium 1640 (Sigma-Aldrich, Milan, Italy) supplemented with glutamine, penicillin/streptomycin, 50 μM β-mercaptoethanol, and 10% heat-inactivated fetal calf serum (FCS).

extract_protocol: BMdDCs were harvested and centrifuged. For each condition, 2 x 10^ 6  BMdDCs were resuspended in 1 ml TRI-reagent followed by a Qiagen RNeasy Micro kit clean-up procedure.

treatment_protocol: CD11c+ (98% pure) BMdDCs were placed in incubator at 37°C under hypoxic conditions (2% O2, ~14 mmHg) with GM-CSF at 20 ng/ml for 2 days in complete Opti-MEM medium, and then either treated for 6 hours with SCF at 100 ng/ml (SCF) or left untreated (medium).  (doi: 10.3389/fimmu.2017.00147). NB=Complete Opti-MEM medium is Opti-MEM Medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with glutamine, penicillin/streptomycin, 50 μM β-mercaptoethanol.

tag: Sex

value: female

value: wild-type

value: CD11c+ BMdDCs

tag: condition

value: hypoxia

value: 6 hour in medium


title: Mouse D2 SCF

value: 6 hour treatment with SCF


title: Mouse I SCF


title: Mouse E SCF


title: JIH5_ZNF384 ChIP-Seq


title: Mouse E MEDIUM


title: Mouse BC MEDIUM


title: WT [TN3]

value: WT-iPSC


title: TCZ PDX-RNAPII ChIA-PET

data_processing: ChIA-PET data from raw compressed FASTQ files—either long-read ( or short-read data—that contain bridge linker sequence are processed with ChIA-PET Utilities (CPU; https://github.com/cheehongsg/CPU)

source_name: PDX

extract_protocol:
ChIA-PET was performed using the in situ ChIA-PET protocol
Long read ChIA-PET library was prepared using ChIP-DNA after end-repair, A-tailing and proximity ligation

value: Patient-derived xenograft

value: RNAPII (BioLegend # 664906)

tag: genome build


title: TCZ PDX-ZNF384 ChIA-PET


title: WT [TN1]


title: shCPSF6-BE2C, NoDox, Rep2

value: No treatment

tag: library

value: PAPERCLIP


title: JIH5-CTCF ChIA-PET

value: CTCF (Abclonal # A1133)


title: JIH5_ZNF384 ChIA-PET

data_processing:
ChIA-PET data from raw compressed FASTQ files—either long-read ( or short-read data—that contain bridge linker sequence are processed with ChIA-PET Utilities (CPU; https://github.com/cheehongsg/CPU)
hg38


title: Mouse D2 MEDIUM


title: JIH5_H3K4me3 ChIP-Seq


title: Mouse BC SCF


title: JIH5-RNAPII ChIA-PET


title: shCPSF6-BE2C, PlusDox, Rep2

value: Doxycycline


title: EPZ PDX2-ATAC-seq

data_processing:
Paired-end reads were applied on cutadapt (version 1.18) for adaptor trimming, and then mapped to the human hg19 genome reference by Bowtie2 (version 2.2.9)
Peaks were called by MACS2 (version 2.1.1.20160309 , “--extsize 200 --nomodel --keep-dup all”)

extract_protocol:
ATAC-seq was performed following the Fast-ATAC protocol
Libraries were made using NEB ultra II DNA library protocol


title: shCPSF6-BE2C, PlusDox, Rep1


title: shCPSF6-BE2C, NoDox, Rep1


title: EPZ PDX1-ATAC-seq


title: TCZ PDX-CTCF ChIA-PET


title: TCZ PDX-IgG CUT&TAG

data_processing:
Library strategy: CUT&TAG
Paired-end reads of 100bp were mapped human genome hg19(GRCh37-lite)by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by fastp(version 0.20.0, paired-end mode, parameters “--trim_poly_x --cut_by_quality5 --cut_by_quality3 --cut_mean_quality 15 --length_required 20 --low_complexity_filter --complexity_threshold 30 --detect_adapter_for_pe”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2)
Peaks were called by MACS2 (version 2.1.1.20160309 , “--extsize 200 --nomodel --keep-dup all”)

extract_protocol:
CUT&RUN was performed using the CUT&RUN assay kit
Libraries were made using NEB ultra II DNA library protocol


title: TCF PDX-H3K4me3 CUT&TAG


title: TCZ PDX-H3K27ac CUT&TAG


title: WT [TN2]

value: iPSC-derived cardiomyocytes

value: iPSCs


title: TCZ PDX-ZNF384 CUT&TAG


title: JIH5-IgG CUT&TAG

value: ALL cell line


title: YJJ

city: Beijing

first: Lei

state: Beijing

address: Gongti Nanlu No.8

institute: Beijing Chaoyang Hospital

data_processing:
Solexa pipline v1.8 software was used in image analysis and base calling.
Trimmed reads (trimmed 5', 3'-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
The abundance of tRF & tiRNA and miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). The tRFs & tiRNAs and miRNAs differentially expressed are screened based on the count value with R package edgeR.
Assembly: GRCh37
Supplementary files format and content: excel files included the counts of reads and CPM values of tsRNAs in each samples

source_name: epicardial adipose tissue

extract_protocol:
Total RAN was extracted from frozen EAT with QIAGEN miRNAeasy Mini Kit (Qiagen, Hilden, Germany) followed by instructions of the manufacturer.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

value: epicardial adipose tissue

tag: disease state

value: Control


title: 1626470


title: AGZ [re-analyzed]


title: LJ [re-analyzed]


title: SSF [re-analyzed]

value: Heart Failure


title: JIH5-ZNF384 CUT&TAG

value: ZNF384 (Abclonal # A15964)


title: v3.1.1

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

description: nuclear RNA

data_processing:
Alignment: The raw sequencing reads were aligned to a marmoset genome assembly, ASM275486v1 (GCA_002754865.1). To build a reference package suitable for analyzing both unspliced pre-mRNA and mature mRNA in the nuclei, as well as to include sequences of mito-chondrial genome, marmoset DNA sequence (FASTA) and annotation (GTF) files were acquired from the Ensembl release-95 and modified as follows. The complete mitochondrial sequence (NC_025586.1, GenBank) and its annotation (Wang et al., 2016) were manually added to the FASTA and GTF files. Next, a pre-mRNA GTF was made by replacing “transcript” with “exon” as the feature-type entry in the original GTF before making a reference package with CellRanger software (v3.0.2, 10x Genomics). This custom-built reference package was then used in CellRanger (version 3.1.0, 10x Genomics) to align sequencing reads for all samples. The option to estimate cell number automatically was used for most of the samples, unless otherwise speci-fied (see Table S1 for details). A filtered cell barcode-to-gene feature matrix was generated from the software and used for downstream analysis (Figure S2A).
Preprocessing & general quality control: The matrix was loaded to create an object in Seurat v3 (Butler et al., 2018; Stuart et al., 2019). Cells with <200 genes, >5000 genes, or >5% of counts mapped to mitochondrial genome were excluded. Genes observed in <5 cells were excluded. The filtered raw count matrix was then log normalized (ln(counts*100,000+1)) within each cell and scaled to account for differences in sequencing depth with Seurat. Next, DoubletFinder (McGinnis et al., 2019) was used to esti-mate and remove putative doublets to mitigate technical confounding artifacts in droplet-based sequencing data analysis. The top 3000 variable genes calculated by Seurat were used in linear dimension reduction (principal components analysis, PCA), and the top 30 PCA were used for clustering at low resolution (parameter = 0.4) to define crude cell types. These unsupervised clusters were used to provide a quick cluster annotation for homotypic doublet probability model-ing in DoubletFinder. Doublet rate was estimated by fitting a linear equation over a multiplet rate table provided by 10x Genomics. The rate = (0.0008*cell.number + 0.0527)/100) was used to calculate a Poisson distribution with and without homotypic doublet proportion to generate low confidence (DF.found.1) and high confidence (DF.found.2) doublet annotation. Unless otherwise specified, pN = 0.25, pK = 0.005 and automatic doublet removal based on DF.found.2 annotation were used, as the first line of screening. In parallel, SoupX (Young and Behjati, 2020) was used for ambient RNA background correction. Taken from the output of the 10x pipeline (raw_feature_bc_matrix), the ambient RNA from empty droplets that contained <10 unique mo-lecular identifiers (UMI) were profiled, and the “soup” contamination fraction was calculated for each cluster. Given that the nuclear transcriptome was profiled, genes that mapped to the mito-chondrial genome could be considered as ambient input. Therefore, the top mitochondrial genes (species with >1000 accumulated counts across profiled empty droplets) were used to estimate the global contamination fraction and adjust the raw count matrix. Next, the cell barcode that passed the DoubletFinder was used as an index to subset the SoupX-corrected matrix to gener-ate a new matrix as our downstream input (Figure S2A). For individual samples, a Seurat object was created, and the index labels (IL01_uniqueID, IL02_species, IL03_source, IL04_sex, IL05_ageDays, IL06_tissue.1, IL06_tissue.2, IL06_tissue.3, IL07_location, IL08_condition, IL09_illumina, IL10_chemistry, IL11_batch, IL12_LMinDays, IL13_LMaxDays, IL14_dataset, IL15_annotation) were added to the metadata as cell attributes. For each sample, 90% of nuclei were randomly selected, then all 42 samples were merged together for downstream comparison. The remaining 10% of the nuclei were set aside for classification assessment and validation.
Level 1 quality control & clustering: To divide nuclei into classes and facilitate artifact identification, nuclei were first classified using a set of parameters that does not highlight granular detail. In this round of clustering, only 50 PC for Harmony were computed to perform linear correction over IL01_uniqueID, as the el-bow plot from the preliminary analysis showing the standard deviation stopped visually decreas-ing after top 50 PC. The top 5 Harmony-corrected embeddings (H5) were used for Seurat to learn the UMAP and find cell classes at a low resolution (0.2). Canonical cell-type markers (PTPRC for immune cells, PDGFRA for OPC, MAG for oligodendrocytes, GFAP and SLC1A2 for astrocytes, LEPR and CEMIP for vasculature and meningeal cells, and CNTN5 and NRG1 for neurons) annotated 6 of the classes unambiguously. One cluster in the middle of the H5 UMAP had mixed expression of canonical markers, which suggested artifact. The “low quality” cell bar-codes that were found from the H50 condition (defined above) were overlaid on the H5 UMAP, which exclusively highlighted the putative artifact cluster. These nuclei were removed from fur-ther analysis, although the original UMAP embeddings were maintained for plotting purposes (Figure 1 and S3).
Level2 quality control & clustering: Nuclei that passed Level 1 QC were divided into 5 partitions (MIC, OPC, OLI, VAS/AST, NEU) based on the H5 UMAP result. The astrocytes and vasculature/meningeal cells were pooled into a single class prior to subclustering to facilitate artifact identification. Shared features in this class of cells were potentially explainable by their close association at CNS barriers (blood–CSF interface, blood–brain interface, and the CSF–brain interface). For each class, log-normalization and scaling were repeated from the divided raw count matrix, the top 3000 variable genes were used for 50 PC computation, Harmony correction over IL01_uniqueID, UMAP learn-ing, and clustering, as described above. The clustering resolution was iteratively increased from low to high (0–1.2), and clustering stability was tracked with clustree (v0.4.3) (Zappia and Oshlack, 2018). Aided by the branch visualization provided by the clustree, a tentative resolution that was relatively stable was selected, then differentially expressed gene (DEG) analysis on the clusters found with this parameter set was performed. The expression pattern of the top-expressed genes for each cluster within and across classes were checked, and artifacts clus-ters were manually imputed. Doublets tended to form small distinct clusters on UMAP that branched early in the clustering tree analysis with low splitting resolution, had mixed canonical marker-gene expression, and had similar expression patterns to cells in other partitions; thus, these doublets could be easily spotted and removed. For putative doublets within each class, additional rounds of DEG analysis were performed as necessary. Each time nuclei were re-moved, basic normalization, scaling, Harmony, and UMAP learning were repeated. To control for over-splitting, for clusters that appeared to be a single pile in the 2D UMAP space but were anno-tated into >1 cluster, additional rounds of DEG analysis were performed to see if binary markers could be found to label them. In addition, clustering was projected onto a 3D UMAP space to en-sure effects were not masked due to overcrowding in 2D. This strategy also helped to further elucidate cluster associations, aid decision-making with respect to groups of clusters that should be tested further, and spot potential gradient changes among clusters. If unique and or binary patterns could not be found in the current splitting resolution after these steps were performed, a step lower in resolution on the clustering tree was examined, and the analysis process was re-peated. The following compound naming convention to la

organism: Callithrix jacchus

extract_protocol:
Tissue dissection: On the day of tissue harvest, marmosets were deeply anesthetized with 5% isoflurane until all visible signs of breathing were no longer detected. Animals were transcardially perfused with ice-cold artificial cerebrospinal fluid (aCSF) for 5 min with a pump. Brains were removed from the skull and submerged into ice-cold aCSF, and after removal of meninges within the solu-tion, were positioned in a custom-designed brain holder within 10 min post-perfusion. The brain was sectioned at 3 mm into 12–13 slabs in one step with a homemade blade-separator set in the solution. Each brain slab was transferred into a 6-well plate, submerged into RNAlater (RNAlater™ Stabilization Solution, AM7021, Invitrogen) with a homemade brain trap, and stored at 4°C overnight. The following day, brain slabs were positioned in 25 x 20 x 5 mm molds (Tis-sue-Tek® Cryomold®, 4557, Sakura Finetek) on ice to facilitate target sampling. Slabs were matched to MRI for each animal, and tissue annotation for gray (Liu et al., 2018a) and white matter (Liu et al., 2020) was informed by marmoset 3D MRI atlases V1 and V2. A cylinder of tissue 2 mm in diameter and 3 mm in height for each region (Figure 1B and S1) was collected with a tissue punch (EMS-core sampling tool, 69039-20, EMS). There were 5 white matter sam-ples from temporal and parietal lobes that did not exactly match in the two animals, however they were paired in lobes of the brain and showed no significant differences in later analysis (Figure 1B, SS05, SS06, and SS08). The cylinders were ejected into PCR tubes filled with 100 µL of RNAlater and stored at −80°C. Single-nucleus dissociation: Nuclei preparation was carried out as described (Matson et al., 2018), with minor modifi-cations. Briefly, on the day of dissociation, tissue samples were thawed on ice, removed from solution, dabbed with Kimwipes to remove residual RNAlater, and placed in a 1 mL douncer tube (Dounce Tissue Grinder, 357538, Wheaton). Each tissue was homogenized in 500 μL of lysis buffer containing 0.1% Triton-X100 in low sucrose buffer (0.32 M sucrose, 10 mM HEPES, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, and 1 mM DTT in ddH2O, pH8) with loose pestle 25 times and tight pestle 10 times. The homogenate was filtered through a 40-μm mesh (Falcon® 40 µm Cell Strainer, 352340, Corning) to a 50-mL Falcon tube on ice. An additional 5 mL of low sucrose buffer was used to rinse the douncer tube and cell strainer. The filtered homogenate was further mixed with a handheld homogenizer (VWR® 200 Homogenizer) at a speed of ~1000 rpm to brake nuclei clumps for 5 sec. After homogenization, a serological pipet filled with 12 mL of high sucrose buffer (1 M sucrose, 10 mM HEPES, 3 mM MgAc, and 1 mM DTT in ddH2O, pH8) was placed underneath the lysate and disconnected from the pipettor, and the buffer was released from the serological pipette by gravity and set on ice. When most of high sucrose buffer was re-leased to form a density layer underneath the homogenate, the serological pipet was retrieved along the wall of the Falcon tube gently, without disturbing the low-high sucrose interface. The Falcon tube was capped and placed in a swing bucket to be centrifuged at 3,200 rcf for 30 min at 4°C. At the end of spin, the supernatant was decanted quickly without tabbing, and 1 mL of re-suspension buffer (0.02% BSA in 1X PBS, pH7.4) was added to the Falcon tube. Slow pipetting was employed to resuspend nuclei along the Falcon tube wall below the 5-mL mark to preserve nuclei integrity. Specifically, nuclei were rinsed off the wall in courses of 2 sec per trituration for 20 times total per tube. The Falcon tube was then capped and spun at 3,200 rcf for 10 min at 4°C. At the end of spin, the supernatant was removed by gently tabbing the tube until no visible liquid drop was left behind, and 200 μL of resuspension buffer was added to each sample to collect the nuclei. The nuclei suspension was filtered through a 35-μm mesh (Cell Strainer Snap Cap, 352235, Corning) twice and counted on a hemocytometer by trypan blue staining. During count-ing, the size and quantity of myelin and other debris were visually inspected under the scope, and the suspension was filtered 1–3 more times through the 35-μm mesh if necessary. Only round and dark-blue stained nuclei were considered of good quality and included in the final count.
10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v2 and v3

value: F

value: WM

value: Telencephalon

value: fWM

value: NaiveCtrl


title: v3.1.4

description: nuclear RNA

value: M

value: aCC


title: v3.1.2

description: nuclear RNA


title: ZYQ [re-analyzed]


title: SYL [re-analyzed]


title: v3.1.3

description: nuclear RNA


title: REH-MEF2C

data_processing:
Paired-end reads of 100bp were mapped human genome hg38(GRCh38-lite) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by fastp (version 0.20.0, paired-end mode, parameters “--trim_poly_x --cut_by_quality5 --cut_by_quality3 --cut_mean_quality 15 --length_required 20 --low_complexity_filter --complexity_threshold 30 --detect_adapter_for_pe”), duplicated reads were then marked with biobambam2 (version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). We then generated bigwig files using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments.
Peaks were called by MACS2 (version 2.1.1.20160309 , “--extsize 200 --nomodel --keep-dup all”)
Genome_build: hg38

source_name: REH

extract_protocol:
ChIP-seq was performed using the ActiveMotif ChIP-IT Express kit
Libraries were made using NEB ultra II DNA library protocol

value: REH


title: BYP [re-analyzed]


title: XJQ [re-analyzed]


title: Nalm6-IgG

value: IgG


title: ZSX


title: Nalm6-MEF2C


title: REH-IgG


title: GM12878-IgG


title: GM12878-MEF2C


title: R634Q_heterozygous [TN4]

value: R634Q/+ iPSC


title: THY

tag: subject status

value: patient with sinus rhythm

value: Atrial fibrillation


title: XJQ

value: patient with persistent non-valvular AF


title: ZYQ

value: epicardial adipose tissue


title: XXX


title: SYL

value: Control


title: OB/OB 2

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

data_processing:
Sequencing data of mice heads were aligned and mapped to the mouse genome GRCm38.p6 using Genetiles server
Image analysis and base calling were done by the Illumina HCS version 1.15.1. At least 15 million reads were obtained that could be mapped to the mouse genome version GRCm38.
DESeq is used to normalise the reads using a DESeq scaling factor, computed as the median of the ratio, for each gene, of its read count over the geometric mean across samples. Then variance and average of the measurement compared to the control is expressed as a P value, by calculating the dispersion per gene using DESeq.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include normalized read values per million for each Sample

source_name: head

growth_protocol: Mice were kept on a standard-chow diet with ad libitum access to food and water.

extract_protocol:
Frozen ob/ob and C57BL/6 mouse heads (n=4) were thawed in 30 ml of TRIzol Reagent (Life Technologies) and manually crushed in a mortar
Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made: In the adapter ligation step 1 μl instead of 2.5 μl adaptor was used; In the library size selection step, the library fragments were isolated using a double Ampure XP purification with a 0.7x beads to library ratio.

treatment_protocol: No treatment

value: male

tag: strain

value: head

value: OB/OB

tag: time

value: week 14


title: OB/OB 3

tag: tissue

tag: genotype


title: H5

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through Partek GS ANOVA statistic and ToppCluster.

organism: Rattus norvegicus

source_name: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat5

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo (Madison, WI) and were acclimated to our animal facility for 7 days. The use of animals was approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee and conformed to the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol: Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. Two or four pregnant rats were used for each experiment, according to the study design. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity.

value: Sprague-Dawley

value: Lung

tag: age

value: 10 days old


title: 5mo_organoid iPSC 2242 14468X1

first: Yueqi

last: Wang

state: Utah

address: 20 South 2030 East

data_processing:
Reads were processed using the 10X Genomics Cell Ranger 2.0 pipeline and aligned to the human GRCh38 reference assembly (Ensembl v84)
Gene-barcode matrices were constructed for each sample by counting unique molecular identifiers (UMIs).
The four individual samples of the 1-month-old organoids were then aggregated into a single gene-barcode matrix using the Cell Ranger aggr command line function.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files containing the UMI count matrix

extract_protocol:
Cortical organoids were dissociated into single cell suspension. Single cells were isolated and lysed using the 10X Genomics Chromium platform.
Reverse transcription and library construction were performed using the 10X Chromium Single Cell 3' Reagent Kit

value: telencephalic organoid


title: 1mo_organoid iPSC 2242 #2 14741X4


title: H4

source_name: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat4


title: OB/OB 1


title: H6

source_name: The dam was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat6


title: N5

source_name: The pup cared for in room air (NOX) from postnatal day 1 to day 10 (P1-P10), rat5


title: WT control 4

value: WT