title: H3K27me3 blastocyst WT rep1

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by fastp (version 0.21.0) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CATCH-seq and CUT&RUN, mm10 for general CATCH-seq and CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -t -N 1" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.5.1) with the parameters "--binSize 50 --scaleFactor 1 --normalizeUsing RPKM --numberOfProcessors 28 --extendReads 200 --ignoreDuplicates --smoothLength 100".
For allele-specific analysis of CATCH-seq and CUT&RUN in the B6 or BDF1 x PWK F1 hybrid embryos, BDF1 and PWK SNPs were masked as "N" in the reference genome. MACS2 (version 2.2.7.1) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H3K27me2 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Assembly: mm10
Supplementary files format and content: BigWig

value: H3K27me3(Miilipore, #07449)

value: blastocyst


title: Mettl3-4oht-dmso-2

status: Public on Sep 05 2024

type: SRA

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

country: China

institute: Tsinghua University

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Deeptools bamCoverage (CPM normalized and extended reads) was used to generate bigwig files from bam files
MACS2 was used for peak calling and to generate bed files from aligned reads
HOMER annotatePeaks.pl was used to annotate the peaks.
Assembly: mm10
Supplementary files format and content: csv
Supplementary files format and content: bigwig

molecule: total RNA

organism: Mus musculus

source_name: intestine

extract_protocol:
organoids were harvested and collected by centrifugation. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The RNA-seq library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina. For ChIP-seq library, Alive lentivirus-infected organoids overexpressing Atf3 were sorted and collected into 500 uL PBS, cells conducted ChIP-seq following the NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, H259-YH01) and the lysates were incubated with anti-ATF3 antibody (1:100, Abcam, ab207434) at 4 ℃ overnight. DNA extracted using Tagment DNA Extract Beads was used as a templet, and amplification was performed with 2X KAPA HIFI HotStart polymerase (KAPA, KK2601).The library was purified with 1.4X AMPure beads and sequenced with the Illumina Novaseq 6000.

tag: tissue

value: intestine

tag: cell line

tag: cell type

value: cells from intestnial organoids


title: Atf3-ChIP-2

library_source: genomic

molecule: genomic DNA


title: H3K27me2 mESC 500 cells

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

source_name: mouse embryonic stem cell

extract_protocol:
For superovulation, 4- to 10-week-old B6N females were injected with 7.5 IU pregnant mare serum gonadotropin (ASKA Pharmaceutical) or 0.15 ml CARD HyperOva (Kyudo Co., Ltd) followed by 7.5 IU human chorionic gonadotropin (hCG) (ASKA Pharmaceutical) at a 48-h interval. Cumulus-oocyte complexes (COCs) were harvested 15–17 h after human chorionic gonadotropin injection. For in vitro fertilization, COCs were inseminated with activated spermatozoa in Human Tubal Fluid medium supplemented with 10 mg/ml BSA (Merck Millipore; 12657). Spermatozoa were obtained from the caudal epididymis of adult PWK/PhJ mice [RBRC00213 (RIKEN BioResource Research Center) originated from 003715 (The Jackson Laboratory)] and B6D2F1 (BDF1) males (Jackson Laboratory). Spermatozoa were capacitated by 1 h incubation in CARD FERTIUP (Kyudo) for PWK sperm or in Human Tubal Fluid medium for BDF1 sperm. At 6–8 h postinsemination, zygotes with two pronuclei were transferred to KSOM and cultured under a humidified atmosphere with 5% CO2/95% air at 37.8°C. For CATCH-seq and CUT&RUN sample collection, polar bodies were removed as described previously (Hayashi and Inoue 2023). Four-cell, eight-cell, morula and blastocyst embryos, were collected at 46–52, 60, 72 and 120 h post-insemination with 500-1,000 blastomeres for each CATCH-seq experiment.
CATCH-seq is an improved method of the ultra low-input native ChIP-seq (ULI-NChIP) (Brind’Amour et al. 2015), and the original protocol of CATCH-seq was described in (Zhu et al. 2021). We have made some changes in CATCH-seq to improve the usability. Cells were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80°C  until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21 or 37°C  for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021). The forward and reverse strands of the carrier DNA were as follows: /5AmMC6/Gtagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggat aacagggtaat*c/3AmMO/ and /5AmMC6/Gattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatcc cta*c/3AmMO/, respectively, where asterisks represent phosphorothioate bonds. The oligos were synthesized by Integrated DNA Technologies. For each immunoprecipitation reaction, 0.5 µL of rabbit anti-H3K27me2 (Cell Signaling Technologies, 9728), 500 ng of rabbit anti-H3K27me3 (Millipore 07449), or 250 ng of rabbit anti-H3K27ac (Diagenode C15410196) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. The quality of these antibodies was validated in previous studies [H3K27me2 (Ferrari et al. 2014a; Juan et al. 2016; Hojfeldt et al. 2018b; Lavarone et al. 2019; Meng et al. 2020), H3K27me3 (Adli et al. 2010; Kelly et al. 2019; Ren et al. 2019), H3K27ac (Zenk et al. 2021)]. After immunoprecipitation at 4°C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65°C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 13-15 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37°C for 2 hrs followed by heat inactivation at 65°C for 20 min and purified by 0.9x SPRIselect beads. The second amplification was not performed. The libraries were sequenced on Nextseq500 (single-end reads) or Nextseq2000 (paired-end reads) (Illumina). CUT&RUN libraries were prepared as previously described (Hayashi and Inoue 2023). For each CUT&RUN library, 100-180 morula embryos were used per replicate, and the same number of embryos were used to compare between control and mutant embryos. The antibodies used in this study were rabbit anti-JARID2 (1/50; Cell Signaling Technologies, 13594), rabbit anti-SUZ12 (1/50; Cell Signaling Technologies, 3737), and rabbit anti-H3K36me3 (1/500; Abcam 9050) antibodies. The specificity of these antibodies was proven in previous studies (Hojfeldt et al. 2018; Healy et al. 2019; Hojfeldt et al. 2019; Glancy et al. 2023). Protein A-MNase was provided by S. Henikoff ’s laboratory (Skene and Henikoff 2017). For quantitative CUT&RUN, 20 pg of yeast DNA was added to each sample. CUT&RUN libraries were sequenced on a NextSeq 500 with single-end reads (Illumina).

tag: chip antibody

tag: developmental stage

value: embryonic stem cell

value: mouse embryonic stem cell

tag: strain

tag: genotype

value: wild-type


title: H3K27me2 mESC 5k cells


title: Input mESC


title: Mettl3-4oht-Nec-1-1


title: H3K36me3 4-cell rep1

source_name: Preimplantation embryo

value: H3K36me3(Active Mitif, #61022)

value: Preimplantation embryo

value: C57BL/6 (B6) x PWK


title: HeLa_mock_rep2_polyA_RNA_seq

city: Chicago

first: Jingyi

last: Fei

state: IL

address: GCIS W142, 929 E 57th Street

country: USA

institute: The University of Chicago

data_processing:
The adaptor sequences were trimmed with Cutadapt using the parameter cutadapt -a CCCAGATCGGAAGAGCACACGTC
The reads were first mapped to the corresponding rRNA sequences to remove rRNA contamination.
The remaining unmapped reads were mapped to the human genome hg38.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file included raw counts on gene level.

molecule: polyA RNA

organism: Homo sapiens

source_name: Cervical cancer cells

growth_protocol: HeLa or HepG2 cells were cultured with DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher). Poly A RNA was isolated using Dynabeads mRNA DIRECT Purification Kit (ThermoFisher). Ribosome RNA was depleted by RiboMinus Eukaryote Kit (ThermoFisher).
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 (Takara) following the manufacturer's instructions.

treatment_protocol: For heat shock treatment, HeLa cells were stressed at 43°C for 2 h. For plab B treatment, cells were treated with Plad B (100 nM) at 37°C for 4 h.

value: HeLa

value: Cervical cancer cells

value: WT

tag: treatment

value: Mock


title: Mettl3-4oht-dmso-1


title: Input morula oocyte

value: morula


title: HeLa_pladB_rep2_polyA_RNA_seq

value: Pladienolide B treated


title: Mettl3-etoh-Nec-1-2


title: HeLa_pladB_rep1_polyA_RNA_seq


title: HepG2_mock_rep1_polyA_RNA_seq

source_name: Liver cancer cells

value: Liver cancer cells


title: H3K27me2 8-cell rep2


title: CUT&RUN JARID2 morula rep1

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by fastp (version 0.21.0) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CATCH-seq and CUT&RUN, mm10 for general CATCH-seq and CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -t -N 1" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.5.1) with the parameters "--binSize 50 --scaleFactor 1 --normalizeUsing RPKM --numberOfProcessors 28 --extendReads 200 --ignoreDuplicates --smoothLength 100".
For allele-specific analysis of CATCH-seq and CUT&RUN in the B6 or BDF1 x PWK F1 hybrid embryos, BDF1 and PWK SNPs were masked as "N" in the reference genome. MACS2 (version 2.2.7.1) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H3K27me2 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&RUN


title: Input 4-cell


title: H3K27me2 4-cell rep2


title: H3K27me2 8-cell rep1-1


title: Mettl3-etoh-Nec-1-1


title: HepG2_mock_SRRM2_rep2_ARTR

data_processing:
The adaptor sequences were trimmed with Cutadapt using the parameter cutadapt -n 3 -a AGATCGGAAGAGCACACGTC -a "G{20}" -a "A{15}"; the 8-nt UMI sequences were removed by UMI-tools.
The reads were first mapped to the corresponding rRNA sequences to remove rRNA contamination.
The remaining unmapped reads were mapped to the human genome hg38.
Uniquely mapped reads were deduplicated to get the final usable reads using UMI-tools.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file included raw counts on gene level (all counts, exonic counts, and intronic counts)
Library strategy: ARTR-seq (an Assay of Reverse Transcription-based RBP binding sites Sequencing)

extract_protocol:
Cells were fixed with 1.5 % paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 min, and permeabilized with 0.5% Triton X-100 on ice for 10min. Samples were blocked with 1 mg/ml BSA, followed by staining with primary antibody, secondary antibody and protein A/G-reverse transcriptase. Then, the in-situ reverse transcription was preformed at 37°C for 30 min. Cells were digested with proteinase K at 37°C for 2 h, and total nucleic acids were extracted with phenol-chloroform extraction and concentrated by ethanol precipitation.
Biotinylated cDNA were enriched by strepavidin beads. 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated by T4 RNA ligase 1 by incubating at 25 °C for 16 h. cDNA was recovered from beads. Then, the library can be obtained by PCR amplification with NGS sequencing primer and gel purification of size between 180bp and 400bp.

treatment_protocol: For heat shock treatment, HeLa cells were stressed at 43°C for 2 h. For plab treatment, cells were treated with Plad B (100 nM) at 37°C for 4 h.

tag: antibody

value: SRRM2 (Sigma Aldrich, #HPA041411)


title: Mettl3-etoh-dmso-2


title: H3K27me2 4-cell rep1


title: Mettl3-etoh-dmso-1


title: H3K27me2 morula rep2


title: H3K27me2 morula rep1


title: RNA-seq, single female morula embryo, Jarid2 KO, rep4

description: RNA-seq single female morula embryo Jarid2 KO rep4

data_processing:
For RNA-seq, all reads after trimming by fastp (version 0.21.0) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.6a) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
About 20 or single mourla embryo(s) per sample were pooled to generate each RNA-seq library. The zona pellucida was removed by brief incubation in acidic Tyrode's solution. All samples for RNA-seq were washed three times in 0.2% BSA/PBS before being transferred into a 0.2-ml tube with ~0.5μl carryover.
RNA-seq libraries were prepared as previously described (Mei et al. 2021). Briefly, complementary DNA was prepared using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara; 634890) according to the manufacturer’s instructions. Library construction was performed on a Nextera XT DNA Library Prep Kit (Illumina; FC-131-1024) with 200 pg complementary DNA, according to the manufacturer’s instructions. All RNA-seq libraries were sequenced on a NextSeq 500 (bcl2fastq version 2.17 and RTA version 2.4.11) with single-end 75-bp reads (Illumina).

value: BDF1 x PWK

value: Jarid2 knockout


title: Tumor PIB+PD1, TCR

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: sorted live(DAPI-), CD45+, CD3+

library_source: other

data_processing:
10x Genomics Cell Ranger Single Cell Software v7.1.0 was used for demultiplexing, alignment (mm10), filtering, UMI counting, single-cell 5′ end gene counting, TCR assembly, annotation of paired VDJ and performing quality control using the manufacturer’s parameters.
The resulting expression matrix was used as input to the Seurat library v4.3.0
The resulting TCR repertoire data was used as input to the scRepertoire library v1.8.0
Assembly: mm10
Supplementary files format and content: 10x Gene Expression matrix
Supplementary files format and content: csv, TCR repertoire
Library strategy: scTCR-seq

molecule: other

source_name: Tumor

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
scRNA-seq libraries were prepared with Chromium Next GEM Automated Single Cell 5’ Kit (10x Genomics) according to manufacturer’s instructions. TCR libraries were prepared with Chromium Automated Single Cell Human TCR Amplification & Library Construction Kit(10x Genomics) according to manufacturer’s instructions. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

treatment_protocol: Cells were sorted by FACS.

value: Tumor

tag: tumor establishment

value: Injection of PIB-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.

tag: time

value: T cells were isolated from animals 21 days after tumor establishment

tag: sorted cell_type

value: sorted live(DAPI-), CD45+, CD3+

tag: pd1 treatment

tag: library type

value: TCR enrichment


title: H3K27me2 FGO rep1

source_name: Fully grown oocyte

value: Fully grown oocyte

value: wild-type


title: RNA-seq, single female morula embryo, Jarid2 KO, rep3

description: RNA-seq single female morula embryo Jarid2 KO rep3

value: Preimplantation embryo


title: HepG2_mock_SON_rep1_ARTR

value: SON (Novus Biologicals, #NBP1-88706)


title: Tumor PIB+PD1, GEX

description: sorted live(DAPI-), CD45+, CD3+

library_source: transcriptomic single cell

data_processing:
10x Genomics Cell Ranger Single Cell Software v7.1.0 was used for demultiplexing, alignment (mm10), filtering, UMI counting, single-cell 5′ end gene counting, TCR assembly, annotation of paired VDJ and performing quality control using the manufacturer’s parameters.
The resulting expression matrix was used as input to the Seurat library v4.3.0
The resulting TCR repertoire data was used as input to the scRepertoire library v1.8.0
Assembly: mm10
Supplementary files format and content: 10x Gene Expression matrix
Supplementary files format and content: csv, TCR repertoire

value: mRNA


title: HepG2_mock_Control_rep2_ARTR

value: WT

value: Mock


title: Input FGO


title: H3K27me2 FGO rep2


title: RNA-seq, single female morula embryo, WT, rep3

description: RNA-seq single female morula embryo Jarid2 WT rep3

value: morula


title: RNA-seq, single female morula embryo, Jarid2 KO, rep1

description: RNA-seq single female morula embryo Jarid2 KO rep1


title: RNA-seq, single female morula embryo, WT, rep2

description: RNA-seq single female morula embryo Jarid2 WT rep2


title: HepG2_mock_Control_rep1_ARTR

value: Liver cancer cells


title: RNA-seq, single female morula embryo, WT, rep1

description: RNA-seq single female morula embryo Jarid2 WT rep1


title: Tumor PIB, TCR

description: sorted live(DAPI-), CD45+, CD3+


title: Tumor PIB, GEX

description: sorted live(DAPI-), CD45+, CD3+


title: HepG2_mock_SRRM2_rep1_ARTR

value: SRRM2 (Sigma Aldrich, #HPA041411)


title: Hela_HeatShock_SRRM2_rep2_ARTR

value: HeLa

value: Cervical cancer cells

value: Heat shock


title: Tumor PD1, TCR

description: sorted live(DAPI-), CD45+, CD3+

value: Tumor

value: Injection of eGFP-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.


title: Tumor_HET-6989

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (mem mode; default settings).
Duplicate reads were removed, and only reads mapping as matched pairs and uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option.
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: mm10
Supplementary files format and content: bigWig, fastq

extract_protocol:
Tissues were dissociated into single cells by enzymatic digestion using procedure described previously in Li, et al., Cell Reports. 33, 108566 (2020).
Cell pellets were tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).


title: Tumor_HET-6986


title: Tumor_WT-6992


title: Tumor_HET-6934


title: Tumor PD1, GEX

description: sorted live(DAPI-), CD45+, CD3+

value: T cells were isolated from animals 21 days after tumor establishment

value: sorted live(DAPI-), CD45+, CD3+


title: Hela_HeatShock_SON_rep2_ARTR


title: HepG2_mock_SON_rep2_ARTR


title: Tumor_WT-6982


title: Tumor_WT_6971


title: Tumor GFP, TCR

description: sorted live(DAPI-), CD45+, CD3+

value: TCR enrichment


title: Normal_HET_5425

source_name: AV cells

value: AV cells


title: HeLa_mock_rep1_polyA_RNA_seq


title: Hela_HeatShock_Control_rep2_ARTR


title: Normal_HET_5469


title: Normal_HET_5472


title: tdLN PIB+PD1, TCR

description: sorted live(DAPI-), CD45+, CD3+

source_name: Tumor-draining lymph nodes (tdLN)

value: Tumor-draining lymph nodes (tdLN)

value: Injection of PIB-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.


title: Normal_HET_5428


title: Tumor GFP, GEX

description: sorted live(DAPI-), CD45+, CD3+

value: mRNA


title: tdLN PIB+PD1, GEX

description: sorted live(DAPI-), CD45+, CD3+


title: Normal_HET-5431


title: Normal_HET-5438


title: Normal_HET_5433


title: Hela_pladB_SRRM2_rep2_ARTR

value: WT

value: Pladienolide B treated


title: Hela_HeatShock_Control_rep1_ARTR


title: Hela_HeatShock_SRRM2_rep1_ARTR


title: Normal_WT_5440


title: Hela_pladB_SRRM2_rep1_ARTR


title: tdLN PIB, GEX

description: sorted live(DAPI-), CD45+, CD3+


title: Normal_WT_5468


title: Normal_WT_5434


title: tdLN PIB, TCR

description: sorted live(DAPI-), CD45+, CD3+


title: Hela_pladB_SON_rep2_ARTR

value: SON (Novus Biologicals, #NBP1-88706)


title: Hela_HeatShock_SON_rep1_ARTR


title: 4FM3, replicate5, RNA-seq

city: Tsukuba

first: Koji

last: Nakano

institute: Tsukuba University

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver 10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10).
CLC Main Workbench(Ver 23.0.4, Qiagen) was used for the downstream analysis.
Total counts were normalized by scaling method. Transformed values (log2-converted after adding 1 to the normalized expression value) were used for Heatmap creation.
Low-expression genes (normalized expression value did not exceed 10 in any sample) were excluded before DGE analysis.
Assembly: Differentially expressed genes were identified using metascape of DGE tool.
Supplementary files format and content: Microsoft Excel file  with raw counts, normalized expression values and transformed values for every gene

source_name: Left ventricle

extract_protocol:
Mice were sacrificed by CO2 inhalation, and hearts were immediately cannulated and perfused with cold PBS. After the heart was harvested, the atria and valves and right ventricure were removed, and  RNA was extracted using Trizol reagent.
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420)

value: Left ventricle

value: ICR

tag: Sex

value: male


title: tdLN PD1, GEX

description: sorted live(DAPI-), CD45+, CD3+


title: 4FM3, replicate2, RNA-seq


title: Hela_pladB_SON_rep1_ARTR

value: HeLa

value: Cervical cancer cells


title: 4FM3, replicate3, RNA-seq


title: 4FM3, replicate4, RNA-seq


title: tdLN PD1, TCR

description: sorted live(DAPI-), CD45+, CD3+


title: tdLN GFP, TCR

description: sorted live(DAPI-), CD45+, CD3+


title: Hela_pladB_Control_rep2_ARTR


title: Ctrl, replicate5, RNA-seq

value: MI+PBS


title: tdLN GFP, GEX

description: sorted live(DAPI-), CD45+, CD3+

value: Injection of eGFP-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.


title: Hela_mock_SRRM2_rep2_ARTR

value: Mock

value: SRRM2 (Sigma Aldrich, #HPA041411)


title: Ctrl, replicate2, RNA-seq


title: Ctrl, replicate4, RNA-seq


title: Blood PIB+PD1, TCR

description: sorted live(DAPI-), CD45+, CD3+

source_name: Blood

value: Blood

value: T cells were isolated from animals 21 days after tumor establishment

value: sorted live(DAPI-), CD45+, CD3+

value: TCR enrichment


title: Ctrl, replicate1, RNA-seq


title: Hela_mock_SRRM2_rep1_ARTR


title: 4FM3, replicate1, RNA-seq


title: Blood PIB+PD1, GEX

description: sorted live(DAPI-), CD45+, CD3+

value: Injection of PIB-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.

value: mRNA


title: BC-486

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-gex-GRCh38-2020-A genome assembly using cellranger v8.0.0
Counting data of reference gene expression levels were generated by cellranger v8.0.0 (automatic identification of chemistry properties)
Assembly: GRCh38
Supplementary files format and content: Tab separated values; MatrixMarket

source_name: apheresis

extract_protocol:
Single cells were captured on a 10xGenomics Chromium Controller using a 10X V3 Single Cell 3’ Solution kit (10xGenomics, Chromium Single Cell 3’ Reagent kit V3, Cat. PN-1000092). All protocols were performed following the manufacturer’s instructions.
Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat. 5067-4626). The library concentration was determined with a Qubit High Sensitivity DNA Assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired-end setting of 28 cycles of read (R) 1, 101 cycles of R2, and 8 cycles of index reads on Illumina NextSeq 500 platform, with sequencing depth of ~0.1 million reads per cell.
All protocols were performed following the manufacturer’s instructions.

value: apheresis

value: LMPP


title: Normal_WT_5430

value: AV cells


title: CP-21-191


title: BC-1025

source_name: BM

value: BM


title: Hela_mock_SON_rep2_ARTR

value: WT

value: SON (Novus Biologicals, #NBP1-88706)


title: BC-0171


title: CP-2212


title: Hela_mock_SON_rep1_ARTR

value: HeLa

value: Cervical cancer cells


title: Hela_mock_Control_rep2_ARTR


title: Hela_pladB_Control_rep1_ARTR

value: Pladienolide B treated


title: Ctrl, replicate3, RNA-seq

value: Left ventricle

value: ICR

value: male

value: MI+PBS


title: Blood PIB, GEX

description: sorted live(DAPI-), CD45+, CD3+

value: Blood

value: T cells were isolated from animals 21 days after tumor establishment

value: sorted live(DAPI-), CD45+, CD3+


title: SOD1-A4V/EGLN2-/- TIC DIFF2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: ElementBio AVITI

data_processing:
Sequence reads were trimmed using FastX 0.0.14
Trimmed sequence reads were mapped to reference genome Homo_sapiens.Ensembl.GRCh38.88 using STAR 2.5.2b (parameters: --outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate)
Reads in the alignments that overlap with gene features were counted using featureCounts 1.5.3 (parameters: -Q 0 -s 2 -t exon -g gene id)
Normalization of counts for each sample was performed using EDASeq.
Assembly: Homo_sapiens.Ensembl.GRCh38.88
Supplementary files format and content: tab-delimited .txt file containing raw counts for each sample
Supplementary files format and content: tab-delimited .txt file containing FPKM values for each sample

extract_protocol:
RNA was harvested using RNAeasy mini kit (Qiagen). 1.6ug of total RNA for each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library prep kit using manufacturer's instructions.

value: iPSC-derived Astrocytes

value: ALS + EGLN2-KO

value: TIC


title: Blood PD1, TCR

description: sorted live(DAPI-), CD45+, CD3+

value: Injection of eGFP-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.

value: TCR enrichment


title: Blood PD1, GEX

description: sorted live(DAPI-), CD45+, CD3+

value: mRNA


title: SOD1-A4V/EGLN2-/- VEH DIFF3

description: ElementBio AVITI

value: VEH


title: SOD1-A4V/EGLN2-/- VEH DIFF2

description: ElementBio AVITI


title: Hela_mock_Control_rep1_ARTR

value: HeLa

value: WT

value: Mock


title: SOD1-A4V/EGLN2-/- VEH DIFF1

description: ElementBio AVITI


title: hiPS-CPC, low, biol rep2

city: Madison

first: Aaron

middle: D

last: Simmons

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin

data_processing:
Raw FASTQ files were mapped to the human genome (hg38+decoy) using STAR v2.5.3a
Gene-level transcript abundances were calculated using featureCounts v2.0.3
Assembly: hg38+decoy
Supplementary files format and content: featureCounts_CPC.tsv; tsv file of all the count data (output from featureCounts as specified in data processing step) including Chromosome (Chr), Start, End, Strand, and Length data
Supplementary files format and content: TPM_CPC.csv; .csv file of the TPM values for all 6 samples

growth_protocol: hPSCs were differentiated into cardiac progenitor cells using the GiWi protocol as described previously 1. Briefly, hPSCs were singularized in Accutase (Innovative Cell Technology - AT104) prior to resuspension in mTeSR1 with 5 uM Y-27632 and seeding onto Matrigel-coated 12-well plates. Plates were set at room temperature for 30 min prior to transfer to a cell culture incubator. The following day medium was replaced with fresh mTeSR1. The next day, designated Day 0, differentiation was induced with the addition of CHIR99021 supplemented into RPMI1640 medium with 2% v/v B27 minus insulin (R/B-). 48 hours later (Day 2), medium was replaced with fresh R/B- supplemented with IWP2. Another 48 hours later (Day 4), medium was replaced with fresh R/B-. The following day (Day 5), wells (at the CPC stage of differentiation) were singularized with Accutase, pooled, and cryopreserved in 6:3:1 R/B-:FBS:DMSO in aliquots of 3 well equivalents (~5 million cells) per vial.

extract_protocol:
RNA was extracted from Trizol-collected samples by tri-phasic extraction followed by purification and concentration with Zymo Direct-zol MiniPrep Plus columns (Zymo – R2072) per kit instructions (including on-column DNAse treatment). The concentration of purified RNA was quantified on a NanoDrop spectrophotometer (ThermoFisher – ND2000c) and stored at -80°C.
Quantity and quality of RNA samples were first analyzed for the presence of 18S and 28S ribosomal RNA with A260/A280 ratio around 2.0 and A260/A230 ratios greater than 2.0. RNA was next quantified on an Agilent 2100 Bioanalyzer using Qubit prior to library construction and sequencing. Sequencing libraries were constructed from 500 ng of total RNA per sample using the Takara SMARTer Stranded Total RNA Kit – HI Mammalian.

treatment_protocol: Cryo-preserved CPCs were thawed and plated (in RPMI1640 supplemented with 2% v/v B27 supplement), allowed to adhere overnight, and collected the following day (Day 6) for analysis.

tag: group

value: low

value: induced Pluripotent Stem Cell

value: Cardiac Progenitor Cell (CPC) differentiation


title: SOD1-A4V/EGLN2-/- TIC DIFF3

description: ElementBio AVITI


title: Blood GFP, GEX

description: sorted live(DAPI-), CD45+, CD3+


title: SOD1-A4V TIC DIFF2

description: ElementBio AVITI

value: ALS


title: Blood PIB, TCR

description: sorted live(DAPI-), CD45+, CD3+

value: Blood

value: Injection of PIB-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.


title: SOD1-A4V TIC DIFF1

description: ElementBio AVITI


title: SOD1-A4V/EGLN2-/- TIC DIFF1

description: ElementBio AVITI


title: hiPS-CPC, low, biol rep1


title: OE2ac

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
bcl2fastq conversion software used for basecalling.
TrimGalore was used to clean adapters.
Reads were aligned to mm10 by using Bowtie2.
MACS2 software was used for peak calling. bamCoverage fo deepTools was used for generating bigwig files
Assembly: mm10
Library strategy: CUT&Tag

source_name: Mouse Embryo

extract_protocol:
Tagmentation was performed for 1 hr in Dig-300 buffer and then fragmentated with 300µL tagmentation buffer incubated for 1 hr at TM. Extracted nucleic acid with phenolic chloroform and dissolved in 1xTE solution.
The nucleic acid samples suspension was amplificated 13 cycles with 50µL amplification mix (TAE, TAB and P5, P7 primer) (TD901, Vazyme), and purified using VAHTS DNA Clean Beads (N411, Vazyme)

value: Mouse Embryo

value: Stem Cell

value: Transient

value: Cpt1a Overexpression

value: anti-H3K27ac (Abcam, no. ab4729, 1:50)


title: CP-0729

value: apheresis

value: LMPP


title: hiPS-CPC, high, biol rep3

value: high


title: hiPS-CPC, high, biol rep2


title: SOD1-A4V VEH DIFF1

description: ElementBio AVITI

value: iPSC-derived Astrocytes

value: VEH


title: OE1ac


title: SOD1-A4V VEH DIFF2

description: ElementBio AVITI


title: SOD1-A4A TIC DIFF3

description: ElementBio AVITI

value: isogenic control

value: TIC


title: Conac

value: Control


title: hiPS-CPC, high, biol rep1

value: induced Pluripotent Stem Cell

value: WT

value: Cardiac Progenitor Cell (CPC) differentiation


title: Blood GFP, TCR

description: sorted live(DAPI-), CD45+, CD3+

value: Blood

value: Injection of eGFP-transduced YUMM1.7 melanoma cells mixed at 1:1 ratio with untransduced parental cells.

value: T cells were isolated from animals 21 days after tumor establishment

value: sorted live(DAPI-), CD45+, CD3+

value: TCR enrichment


title: sgA2-D3-2

data_processing:
bcl2fastq conversion software used for basecalling.
TrimGalore was used to clean adapters.
Reads were aligned to mm10 by using STAR aligner.
Counts were extracted with scTE
Assembly: mm10

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

value: Mouse Embryo

value: Stem Cell

value: Transient

value: Cpt1a Knocking Out

value: Primed-To-Naïve transition


title: hiPS-CPC, low, biol rep3

value: low


title: SOD1-A4A TIC DIFF1

description: ElementBio AVITI

value: iPSC-derived Astrocytes

value: isogenic control


title: SOD1-A4A TIC DIFF2

description: ElementBio AVITI

value: TIC


title: SOD1-A4A VEH DIFF3

description: ElementBio AVITI

value: VEH


title: SOD1-A4A VEH DIFF2

description: ElementBio AVITI


title: DRG_GW15_sample2_S7-4_S28

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Barcode filtering and sequence alignment were performed with software Cell Ranger (http://10xgenomics.com). Reads were aligned to the human reference genome (hg19)
raw counts extraction, normalization, dimensional reduction analysis and further downstream analysis were mainly performed with the R package Seurat
Assembly: hg19
Supplementary files format and content: a gzip tab-delimited txt file include raw gene expression counts for each sample

source_name: dorsal root ganglion

extract_protocol:
Human fetal DRG samples across GW7-21 were collected in ice-cold oxygenated artificial cerebrospinal fluid at PH 7.4. DRG samples were transferred into 2 ml ice-cold EZ PREP and were homogenized by grinding with a glass Dounce tissue grinder . Transfer the tissue homogenate into a 15 ml tube, add 2 ml of EZ PREP, incubate on ice for 5 minutes and centrifuge at 500 g at 4℃ for 5 minutes. The supernatant was removed and the nuclei were resuspended in 4 ml ice-cold EZ PREP, and the incubation and centrifugation were repeated once. Then, the nuclei were washed in Nuclei Suspension Buffer and centrifuge at 500 g at 4℃ for 5 minutes. Nuclei were resuspended and filtered through a 70 μm cell strainer, and the nuclei concentration was adjusted to 1,000 nuclei/μl.
The libraries were generated by using the Chromium Next GEM Single Cell 3' Kit v3 according to the 10x GENOMICS official instructions, and processed on the Illumina platform for sequencing with 150 bp paired-end reads

value: dorsal root ganglion


title: sgA2-D3-1


title: DRG_GW15_sample2_S7-3_S27


title: hiPS-CPC ATAC, low, biol rep2

data_processing:
Reads were then aligned and mapped to the GRCh38-hg38 human genome using the BWA (Burrows-Wheeler aligner) algorithm with default settings. Quality requirements included reads passing Illumina’s purity filter, aligning with no more than two mismatches, and mapping uniquely to the genome. Duplicate reads were also removed before subsequent analyses.
The MACS2 peak calling algorithm was then used to determine genomic regions with high levels of transposition and tagging events and differentially enriched regions were identified using DESeq2 in GUAVA. Regions with P values < 0.05 and an absolute fold change > 2 were considered significant differentially enriched peaks.
Peaks within 5,000 bp upstream and 3,000 bp downstream of transcription start sites (TSS) were annotated to the nearest genes in GUAVA’s peak annotation algorithm.
Assembly: hg38
Supplementary files format and content: xls excel file with the chromatin accessibility profile data of all all peaks from four libraries

extract_protocol:
Genome-wide chromatin accessibility was mapped by ATAC-seq using hyperactive Tn5 transposase and insertion of sequencing adapters into accessible regions of chromatin in two biological replicates. 50,000 to 100,000 cardiac precursor cells per high and low potency sample, respectively, were harvested on d6 of differentiation and subjected to ATAC-seq according to standard procedures.
Sequencing was conducted with Illumina NextSeq 500 to produce paired-end 42 bp sequencing reads (PE42).

value: induced Pluripotent Stem Cell

value: WT

value: Cardiac Progenitor Cell (CPC) differentiation


title: WT-D3-2

value: Wild type


title: SOD1-A4V VEH DIFF3

description: ElementBio AVITI

value: ALS


title: hiPS-CPC ATAC, low, biol rep1


title: DRG_GW15_sample2_S7-2_S26


title: hiPS-CPC ATAC, high, biol rep2

value: high


title: hiPS-CPC ATAC, high, biol rep1


title: D3-Cpt1aOE-A485-2

value: Mouse Embryo

value: Inhibiting acetylation


title: WT-D3-1

value: Stem Cell

value: Transient


title: H3K4me3,UNC2400,Day6,Rep3

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
CUT&RUN Raw reads were trimmed using fastp to remove adapters and low quality bases. Reads were aligned to the human genome hg38 using bowtie2 tool. Alignment files were sorted using samtools. Genome track bigwig files were calculated using bamCoverage tool form deepTools package.
Assembly: hg38
Library strategy: CUT&RUN

growth_protocol: BT16 cells were cultured in RPMI-1640 supplemented with 10% FBS.

extract_protocol:
BT16 samples treated with UNC1999 or UNC2400 at 5 μM were harvested at day 4 and day 6. For CUT&RUN samples, the histone-DNA complexes were processed using QIAGEN MinElute Kit to extract DNA.
For CUT&RUN samples, NEBNext Ultra II DNA Library Prep Kit was used.

treatment_protocol: cells were seeded at 50,000 cells/mL for 6–12 h, followed by UNC1999 (5 μM) or UNC2400 (5 μM) treatment.

value: ATRT


title: DRG_GW15_sample2_S7-1_S25


title: H3K4me3,UNC2400,Day6,Rep2


title: D3-Cpt1aOE-A485-1

value: Primed-To-Naïve transition


title: DRG_GW15_sample1_S6-4_S24


title: H3K4me3,UNC2400,Day6,Rep1


title: DRG_GW15_sample1_S6-3_S23


title: D3-Cpt1aOE-2

value: Cpt1a Overexpression


title: H3K4me3,UNC1999,Day6,Rep3


title: DRG_GW15_sample1_S6-2_S22


title: DRG_GW15_sample1_S6-1_S21


title: D3-Cpt1aOE-1


title: H3K4me3,UNC2400,Day4,Rep1


title: SOD1-A4A VEH DIFF1

description: ElementBio AVITI

value: iPSC-derived Astrocytes

value: isogenic control


title: H3K4me3,UNC1999,Day6,Rep2


title: H3K4me3,UNC1999,Day4,Rep3


title: DRG_GW12_sample2_S5-4_S20


title: H3K4me3,UNC1999,Day4,Rep2


title: H3K4me3,UNC1999,Day4,Rep1


title: D3-Control-2

value: Control


title: D3-Control-1


title: H3K4me3,UNC2400,Day4,Rep2


title: DRG_GW12_sample2_S5-3_S19

value: dorsal root ganglion


title: H3K4me3,UNC2400,Day4,Rep3


title: H3K27me3,UNC2400,Day6,Rep2


title: H3K27me3,UNC2400,Day6,Rep1


title: H3K27me3,UNC2400,Day4,Rep2


title: D8_1

data_processing:
bcl2fastq conversion software used for basecalling.
TrimGalore was used to clean adapters.
Reads were aligned to mm10 by using HiSAT2.
Counts were extracted with PreDE.py
Assembly: mm10
Supplementary files format and content: MZY_GeneSymbol_counts.txt


title: D8_3


title: H3K27me3,UNC2400,Day4,Rep1


title: H3K4me3,UNC1999,Day6,Rep1


title: H3K27me3,UNC2400,Day6,Rep3


title: H3K27me3,UNC1999,Day6,Rep3


title: H3K27me3,UNC1999,Day6,Rep2


title: DRG_GW12_sample1_S4-3_S15


title: D5_3


title: D5_2


title: H3K27me3,UNC1999,Day4,Rep3


title: H3K27me3,UNC1999,Day6,Rep1


title: D8_2


title: DRG_GW12_sample1_S4-2_S14


title: H3K27me3,UNC2400,Day4,Rep3


title: H3K27me3,UNC1999,Day4,Rep2


title: D5_1


title: DRG_GW12_sample1_S4-1_S13


title: D3_3


title: DRG_GW12_sample2_S5-2_S18


title: DRG_GW12_sample2_S5-1_S17


title: DRG_GW12_sample1_S4-4_S16


title: DRG_GW9_lane3_S3-4


title: D3_2


title: Bd21, root, ammonium, rep1

city: Leioa

first: Daniel

last: Marino

address: Barrio Sarriena s/n

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Paired-end clean reads were mapped to the reference genome using HISAT2 software. Htseq was used to count the read numbers mapped to each gene.
Assembly: v3.1
Supplementary files format and content: comma-separated values file includes raw counts for each sample

organism: Brachypodium distachyon

source_name: Whole root

growth_protocol: Each sample represents a pool of 12 seedlings of B. distachyon Bd21 grown in a hydroponic tank of 4.5 L  with ammonium or nitrate as source of nitrogen. Plants were grown during 19 days with 2.5 mM N supplied  as 1.25 mM (NH4)2SO4 or 1.25 mM Ca(NO3)2 for ammonium and nitrate nutrition, respectively.

extract_protocol:
Total RNA was extracted using the Nucleospin RNA plant kit (Macherey-Nagel)
One μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Whole root

value: ammonium nutrition


title: Bd21, root, ammonium, rep2


title: Bd21, root, nitrate, rep2

value: nitrate nutrition


title: DRG_GW9_lane3_S3-2


title: Bd21, root, nitrate, rep3


title: DRG_GW9_lane3_S3-1


title: DRG_GW9_lane3_S3-3


title: rES_3

value: Naive Stem Cell


title: Bd21, root, nitrate, rep1


title: D3_1


title: CL155_6

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

country: France

institute: oncovirology and Biotherapies, UMR5239, LBMC

data_processing:
RNAseq data were quality tested using fastqc, quality trimmed then quantified using Kallisto. Processed data correspond to raw read counts.
Assembly: hg19
Supplementary files format and content: raw read counts

source_name: dendritic cell

growth_protocol:
MDDCs were derived from purified monocytes from healthy blood donors collected at Etablissement Français du Sang (EFS) from anonymous healthy blood donors according to the institutional Standard Operating Procedures for blood donation, including a signed informed consent. Blood was diluted in PBS 1X (Gibco) and peripheral blood mononuclear PBMCs were isolated using a density gradient separation using Ficoll-Paque. Monocytes were then isolated from PBMCs using a density gradient separation using Percoll Centrifugation Medium.Freshly or frozen monocytes were cultured in six-well plates at 3.106 cells/mL in complete MDDC medium: RPMI1640 GlutaMAX (Gibco) supplemented with 10% FCS, penicillin-streptomycin (100 U/mL and 100 µg/mL respectively), Hepes buffer (Gibco, 15630080; 10 mM), MEM non-essential amino acids (2,5mM, Gibco, 11140050), sodium pyruvate (Gibco, 11360070; 1 mM), and beta-mercaptoethanol (Gibco, 31350-010; 0.05 mM). MDDC medium was supplemented with IL-4 and GM-CSF (Miltenyi Biotec, 130-093-922 and 130-093-866; 100 ng/mL each) for differentiation. On day 3, the culture medium was refreshed by discarding half of the medium and adding the same volume of new MDDC medium and twice concentrated IL-4 and GM-CSF to all cell cultures. Immature MDDCs were harvested on day 5 or 6.
HTLV-1 infected T-cell lines (C91-PL from Cellosaurus ref CVCL_0197, and C8166 ref ECACC 8805160) or control uninfected T-cell lines (Jurkat from ATCC ref ACC 282) were maintained at a cell density of 0.5.106 cells/mL in complete RPMI medium: RPMI1640 GlutaMAX supplemented with 10% fetal calf serum (FCS) and penicillin-streptomycin (100 U/mL and 100 µg/mL respectively).

extract_protocol:
MDDCs present in the flowtrough  were lysed and total RNA was extracted using the NucleoSpin RNA Mini kit for RNA purification (Macherey-Nagel, 740955) according to the manufacturer’s instructions
Ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries have been pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol: Immature MDDCs (1.106 cells) were plated in 48-well plates and cocultured with HTLV-1-infected or control uninfected T-cells (2.105 cells) in 300µL complete MDDC medium supplemented with IL-4 and GM-CSF for 24h. After 24h, cells were harvested, or stimulated with LPS or medium for an additional 24h. Cells from MDDC / T-cell lines coculture  were harvested and stained using biotin-coupled anti-CADM1 followed by AlexaFluor647-coupled streptavidin diluted in PBS 1X-1% BSA for 20 min at 4°C. After several washes in PBS, cells were then incubated with anti-AlexaFluor647 MicroBeads (Miltenyi Biotec, 130-091-395) and separated on MACS Separation LD Columns (Miltenyi Biotec, 130-042-901) according to the manufacturer’s instructions.

value: dendritic cell

tag: blood donor

value: MDDCs cultured with HTLV-1 infected cells and restimulated for additional 24h with LPS


title: rES_2

tag: tissue

value: Mouse Embryo


title: CL118_6


title: PBS-BMDMs-ATAC

city: Jinan

first: zhang

last: shi

address: handong First Medical University

institute: handong First Medical University

description: BMDM-ATAC.bed

data_processing:
chip-seq reads were trimmed Trimmomatic V 0.33
chip-seq reads were aligned to hg38 or mm10 by Bowtie V1.1.2
Peaks were calling by MACS V 2.1.0
Assembly: hg38 and mm10
Supplementary files format and content: bed
Supplementary files format and content: bdg

source_name: BMDM

extract_protocol:
Crude nuclear pellets from macrophages were collected by centrifugation, resuspended in lysis buffer, and incubated on ice for 10 minutes. The chromatin was sheared by sonication at 4°C using a Bioruptor 300 at the highest setting for fifteen 1-minute cycles of 30 seconds on and 30 seconds off to generate chromatin fragments of approximately 200-400 bp in length. The soluble chromatin was diluted 1:10 with dilution buffer and precleared with protein A agarose beads. The precleared supernatant was incubated overnight at 4°C with antibodies against H3K27ac.
After washing, the immunoprecipitated material was eluted by adding 100 mM NaCl and incubating at 65°C for 12 hours. After removing protein and RNA, the enriched genomic DNA was extracted with phenol:chloroform:isoamyl alcohol followed by ethanol precipitation. The immunoprecipitated DNA was dissolved in water and analysed by ChIP-seq.

tag: age

value: 8 weeks

value: Male

tag: agent

value: PBS

value: BMDM


title: C156_3

value: MDDCs cultured with HTLV-1 infected cells


title: H3K27me3,UNC1999,Day4,Rep1

tag: cell line

tag: cell type

value: ATRT


title: DRG_GW9_lane2_S3-4


title: rES_1

value: Stem Cell


title: C155_3


title: input-BMDMs

tag: strain


title: CL156_6


title: C118_3


title: DRG_GW9_lane2_S3-2


title: EpiSC_2

value: Primed Stem Cell


title: DRG_GW9_lane2_S3-1


title: BL156_5


title: EpiSC_1


title: BL155_5


title: DRG_GW9_lane1_S3-4_S12_L001_R1_002


title: ESC_3

value: mESC


title: DRG_GW9_lane1_S3-3_S11_L001_R1_002

value: dorsal root ganglion


title: LPS-BMDMs-ChIP

value: LPS


title: BL118_5


title: PBS-BMDMs-ChIP


title: ESC_2


title: LPS-BMDMs-ATAC

description: BMDM-ATAC.bed


title: B156_2


title: EpiSC_3


title: DRG_GW9_lane1_S3-2_S10_L001_R1_001


title: DRG_GW9_lane2_S3-3


title: input-MDMs

source_name: Peripheral blood monocyte

extract_protocol: ATAC-seq was carried out following the process described by Daniel with minor modifications. Macrophages were isolated and counted to obtain 50 cells /ml in PBS. The nuclei of macrophages were isolated with ATAC-LB. After DNA fragmentation and purification, the DNA was amplified using 14 cycles. The fragment distribution of the libraries was assessed with an Agilent Bioanalyzer and libraries were sequenced on a HiSeq 2500 platform.

value: Peripheral blood monocyte


title: LPS-MDMs-ATAC

description: MDM-ATAC.bed


title: ESC_1


title: B155_2


title: PBS-ChIP-MDM


title: DRG10_GW21_S1_L001_R1_004


title: DRG_GW9_lane1_S3-1_S9_L001_R1_001


title: Tumor_HET_d

data_processing:
Paired-end reads were processed and mapped to the mm10 mouse genome using Cell Ranger v6.
Filtering eliminated genes detected in < 20 cells, and discard cells with (1) UMI counts < 1,000 or > 100,000, (2) gene counts < 500 or > 8,000, and (3) mitochondrial gene ratio > 10%.
Assembly: mm10
Supplementary files format and content: Li_Brugge_10XscRNAseq_GeneCellMatrix_RNAcounts.csv: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample
Supplementary files format and content: Li_Brugge_10XscRNAseq_Metadata_GEO.csv: Metadata table containing meta data information for each cell, including sample of origin and designated cell type

extract_protocol:
Tissues were dissociated into single cells by enzymatic digestion using procedure described previously in Li, et al., Cell Reports. 33, 108566 (2020).
Single cell capturing and cDNA library generation were performed using the 10X Chromium 3’ library construction kit v2 (normal samples) or v3 (tumor samples) following the manufacturer’s instruction.

value: Tumor


title: B118_2


title: LPS-ChIP-MDM


title: Tumor_HET_c


title: AL156_4

value: MDDCs cultured with control jurkat cells for 24h and restimulated for additional 24h with LPS


title: PBS-MDMs-ATAC

description: MDM-ATAC.bed


title: DRG10_GW21_S1_L001_R1_003


title: Input2

data_processing:
clc genomics workbench v 11.0.1
Step 1.1: Quality check
Step 1.2: Adaptor and Quality trimming + Removal of very short reads
Step 1.3: Quality recheck
Step 2.1: Generation of gene/transcript-level counts
Assembly: mm39
Supplementary files format and content: Raw counts for RNAseq
Supplementary files format and content: Peaks for RIPseq

source_name: bone marrow-derived macrophages

extract_protocol:
RNA extraction and sequencing: Total RNA was extracted from the isolated BMDMs using TRIzol. After rRNA depletion, the remaining RNA was prepared for library preparation following Illumina's instructions. The resulting libraries were sequenced using Illumina Sequencing Technology. RIP-seq for IFIH1-bound RNA complexes: RNA extracts from the isolated BMDMs were subjected to RNA-binding protein immunoprecipitation (RIP) using the Magna RIPTM kit. The IFIH1-bound RNA complexes were enriched by incubating the RNA extracts with IFIH1 antibody-bound beads and RIP immunoprecipitation buffer. The purified RNAs from the IFIH1-bound complexes were then sequenced using Illumina Sequencing Technology, with 5% input RNA as a negative control to reduce noise.
Provide at least 1 ug (2-5 ug preferred) of total RNA at a concentration of at least 50 ng/ul (1 ug for Poly-A enrichment; 2 ug for ribo-depletion libraries; using less starting material is possible, but we can't guarantee results). Please make sure that your RNA isolation protocol employs a DNAse digestion step or other means to remove DNA from the sample. On an agarose gel, DNA contamination will be visible as a smear of band of fragments considerably larger than the RNA (>10 kb).  To verify the purity of the RNA samples the 260/280 ratio should be between 1.8 and 2.1 and 260/230 ratio should be higher than 1.5.  Poly-A enrichment, ribo-depletion and strand specific library prep are among the commonly requested types of service (more technical details on this appear below). Libraries for slightly degraded RNA samples should be prepared using ribo-depletion protocols. If possible please avoid RNA extraction protocols involving Trizol or related phenol containing reagents (silica column based kits are less likely to retain contaminants). If using Trizol, protocols that contain a column based cleanup (e.g. Direct-zol, TRIzolPlus) have to be used.  Please note that an additional column cleanup is mandatory for RNA samples isolated from PAXgene tubes or with PAXgene kits. RNA samples should be eluted in molecular biology grade water, always stored in a -80 degree freezer and shipped on dry ice.  All RNA samples require a Bioanalyzer sample QC (or equivalent).  Such QC traces can be submitted by the customers or we can run the QC  for a fee instead.

value: bone marrow-derived macrophages


title: Tumor_HET_b


title: AL155_4

value: dendritic cell


title: Tumor_HET_a


title: Tumor_WT_c


title: AL118_4


title: Input


title: IFIH1-RIP2

value: IFIH1 antibody


title: DRG10_GW21_S1_L001_R1_001


title: DRG9_GW17_S1_L001_R1_004


title: Tumor_WT_b


title: DRG9_GW17_S1_L001_R1_003


title: IFIH1-RIP


title: A156_1

value: MDDCs cultured with control jurkat cells


title: mmu-M1C

description: RNAseq-mus.txt


title: DRG9_GW17_S1_L001_R1_001


title: A118_1


title: PHD2-KO

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

description: 10x Genomics

data_processing:
Cell Ranger
Seurat
Monocle3
Assembly: mm10
Supplementary files format and content: gz compressed tab-separated values files and matrix files

source_name: mESC

extract_protocol:
Cells were trypsinized into single cells and subjected to a standard procedure for sample preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: DRG9_GW17_S1_L001_R1_002


title: A155_1


title: Tumor_WT_a


title: IgAV_4_TCR

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

data_processing:
Raw sequencing data was processed using the 10x CellRanger pipeline, cellranger count to and cellranger vdj generate a UMI count matrix
Assembly: GRCh38
Supplementary files format and content: the UMI count matrixes which were generated by cellranger count and cellranger vdj are provided

source_name: PBMC

extract_protocol: Ficoll centrifugation to isolate PBMC. RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

tag: diagnosis

value: IgA vasculitis (IgAV)

tag: subject status

value: IgAVN


title: mmu-M1B

description: RNAseq-mus.txt

tag: treatment


title: DRG10_GW21_S1_L001_R1_002


title: mmu-M1A

description: RNAseq-mus.txt


title: WT

description: 10x Genomics

value: WT


title: DRG8_GW14_S1_L001_R1_004


title: IgAV_4_BCR


title: DRG8_GW14_S1_L001_R1_003


title: mmu-M0C

description: RNAseq-mus.txt

value: PBS


title: NTOC lobes day 3 treated with TL1A + IL-18, RNA

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

institute: Ghent University

data_processing:
CITE-Seq samples:The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression and cell surface protein libraries.
scRNA-Seq samples:The Cell Ranger pipeline (10x Genomics, version 6.0.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1 and read 2 for the gene expression libraries.
Read 2 of the gene expression libraries was mapped to the mouse reference genome.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting were performed using the Cell Ranger suite.
CITE-seq reads were quantified using the feature-barcoding functionality.
Assembly: Sample dependent, see above
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format files as produced by the Cellranger pipeline of 10X Genomics

source_name: Neonatal Thymus Organ Culture

growth_protocol: All mice used in this study were C57BL/6N wild-type. Time-mate pregnant females and adult C57BL/6N were purchased by Janvier. All mouse experiments were conducted according to institutional, national, and European animal regulations. Ghent University’s Ethics Committee approved all experimental animal procedures (EC2020-010, EC2022-110 ). Experiments were conducted in agreement with the European Parliament’s Directive 2010/63/EU and the 22-09-2010 Council on the protection of animals used for scientific purposes.

extract_protocol:
Samples were split up in 3 groups: (1) non-preprocessed samples, (2) T cell-depleted samples and (3) Thymus epithelial cells (TECs)-enriched sample. We isolated 20 neonatal thymuses per condition were pooled together per condition/treatment: [1] (P0.5), [2] NTOC lobes day 1.5 and [3] NTOC lobes day 3 treated with either vehicleor TL1A+IL-18. For the non-processed sample, single-cell suspensions were obtained as described previously. T cell-depleted sample was obtained  by negative beads enrichment using biotinylated antibodies as follows: (1) Biotin-anti-CD4 [1:100], (2) Biotin-anti-CD8α [1:100], (3) Biotin-anti-CD19 [1:200] and (4) Biotin-anti-Ter-119 [1:200]. Samples were incubated for 15 min at RT. After 15 min incubation, the cells were centrifuged at 400g, 4ºC for 5 min to remove the excess of non-bound antibodies. 150µL of MagniSort™ Streptavidin Negative Selection Beads (eBioscience, #MSNB-6002) were added  per sample and incubated for 10 min at RT. The samples were placed in a MagniSort™ Magnet (eBioscience, #MAG-4902-10) for 5 min at RT and purified-enriched cells were recovered in clean round bottom polystyrene tubes ready for sorting. Thymus epithelial cells (TECs)-enriched samples were obtained by enzymatic digestion with the following digestion mix:  RPMI, 2%FCS, 2mM EDTA (Invitrogen, #15575020), 0.125 mg/mL Liberase™TM (Roche, #5401119001), 1mg/mlDispase II (Roche, #04942078001) and 10ng/mlDNase I (Roche, #10104159001). Thymic lobes were incubated for 30–40min in a 37 °C water bath in the enzymatic solution. After digestion, the remaining pieces were filtered through a 70-μm mesh filter and washed with 5–10ml MACS buffer (1× PBS with 5mM EDTA and 2% FCS). Cells were centrifuged at 400g, 4ºC for 5 min. Lastly, cells were subjected to negative bead enrichment with the following biotinylated antibodies: (1) Biotin-anti-CD4 [1:100], (2) Biotin-anti-CD8β [1:100], (3) Biotin-anti-CD19 [1:200], (4) Biotin-anti-CD11b [1:300], and (4) Biotin-anti-Ter-119 [1:200] and FACS sorted based on CD45- EpCAM+. Sorted cells were finally poled in a (1)20:(2)60:(3)20 ratio. Sequencing was done using the following parameters: Novaseq6000 flowcell 100 cycles kit v1.5 paired reads (28-8-0-91), 100 pM + 1 % PhiX.
Thymic NTOC lobes were processed to single-cell suspension by pressing the organ through a 70 μm cell strainer. NTOC supernatant cells were harvested by repeated pipetting of the NTOC well and filter after the lobes were removed from the well. Samples were spun down at 400g, 4ºC for 7 min. Subsequently, samples were washed once more with 12.5 mL of cold PBS and spin down again at 400g, 4ºC for 7 min. Finally, we added 2mL of ACK lysis buffer (Westburg b.v., #10-548E) to each sample for 2 min at RT. Once incubated, we added 10mL of cold PBS to stop the lysis reaction and samples were centrifuged at 400g, 4ºC during 7 min. If needed, lysis step can be repeated again for better removal of red blood cells. Samples were incubated at 37ºC water bath for 45 min and resuspended with a glass pipette each 15 min. Once incubated, we added 5mL of FACS-EDTA buffer and the cells were transferred to a new 15mL falcon tube through a 70µm cell strainer. Subsequent flow cytometry or FACS preparation of all samples was performed on ice. Antibody staining was performed 30min in the dark. For intracellular staining of transcription factors cells were fixed after extracellular staining using eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set (ThermoFisher, #00-5523-00). For intracellular cytokine measurements, cells were first extracted from each tissue as mentioned above, and incubated with Brefeldin A (Enzo Life Sciences, #BML-G405-0025) and Monensin (Biolegend, #420701) for 4 hours, following extracellular staining and fixation and permeabilisation using BD Cytofix/Cytoperm™ (BD Biosciences, #554714). Fixable Viability Dye eFluor™ 780 (ThermoFisher, #65- 0865-14) was used to exclude dead cells in all flow cytometry and FACS experiments. For counting purposes, we added 10 µL/sample of e123count eBeads (ThermoFisher, #01-1234-42) or samples were counted in a  BD FACSVerse™ Cell Analyzer. Cell suspensions were analyzed with a BD FACSymphony™ A5, BD FACSymphony™ A3 or BD LSRFortessa™ or purified using a BD Symphony S6, BD FACSAria II or III.

treatment_protocol: The following cytokines were used: Recombinant murine IL-12 (Cat# 210-12, Peprotech, Rocky Hill, NJ). Recombinant murine IL-18 (R&D Systems, #P70380). Recombinant murine TL1A (Peprotech, #1896-TL-010). All lyophilized cytokines were reconstituted in PBS with 0.1% BSA before storing at -80˚C. The concentration of BSA in all vehicle control conditions corresponded to the highest concentration within the specific experiment.  Thymuses  from neonates (P0.5) were surgically removed,  trimmed of fat and connective tissues placed in D-MEM media on ice. 2x- 3x Thymuses per well (indicated for each experiment) were set in 12-well plates over isopore Membrane filters, PC, 0.8 µM, 13 mm (Merck Millipore, #ATTP01300,) in complete media: D-MEM (GIBCO, #31330-038) supplemented with 20 % FCS (TICO EUROPE (Greiner), #71133), 20 μM L-glutamine, 50 μM 2-mercapto-ethanol, 0,8 % penicillin-streptomycin (Sigma-Aldrich, # P4333), 0.4 mM Na pyruvate (Sigma-Aldrich, #Cat S-8636), 1x non-essential amino acids (Sigma-Aldrich, #M7145). 12-well plates were incubated at 37ºC, 5% CO2 for up to 6 days. Cytokines were used at the following concentrations: TL1A [100 ng/mL], IL-12 [4 ng/mL] and IL-18 [40 ng/mL].

value: Neonatal Thymus Organ Culture

value: TL1A+Il-18, Day 3


title: NTOC supernatant day 3 treated with IL-12 + IL-18, RNA


title: IgAV_4_rnaseq


title: mmu-M0B

description: RNAseq-mus.txt


title: DRG8_GW14_S1_L001_R1_002

city: Beijing


title: IgAV_3_TCR

value: xiongzihan:IgAV in convalescence phase


title: DRG8_GW14_S1_L001_R1_001

value: dorsal root ganglion


title: mmu-M0A

description: RNAseq-mus.txt


title: NTOC lobes day 3 treated with IL-12 + IL-18, RNA


title: IgAV_3_BCR


title: NTOC lobes day 3 treated with vehicle (-control), RNA

value: Control, Day 3


title: iSPN-mut, BIPKm18_TomNeg., biol rep 6

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

description: RPKM.RData

data_processing:
Demultiplex sequencing data from pooled lanes.
After a default quality-filtering step (using FastQC_v0.10.1), record in fastq files representing raw data.
Align reads using Bowtie against the murine transcriptome (mouse NCBI build37 Refseq transcripts).
Unique reads were counted using featureCounts (v1.4.5-p1), and the UCSC mm10 annotation file
All output files were quality assessed using MultiQC (v0.7). Non-uniquely mapped reads were discarded. Read counts were then imported into R package DESeq2 (v1.14.1) to perform differential gene expression analysis
Assembly: mm10
Supplementary files format and content: Calculate the count number of reads for each transcript and reads per kilobase of a transcript per million mapped reads (RPKMs).
Supplementary files format and content: Collapse overlapping Refseq transcripts to obtain the highest one expression value per gene locus.

source_name: striatal tissue

extract_protocol:
The protocol used was optimized to prepare cDNA from 200-sorted neurons using the SMARTer® Ultra® Low RNA Kit for Illumina® sequencing.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: striatal tissue

value: All other striatal cell types, except iSPN

tag: genotype

value: Mutant

value: 8 months


title: iSPN-mut, BIPKm17_TomNeg., biol rep 5

description: RPKM.RData

tag: time


title: DRG_GW7_sample2_lane3_S1-3


title: NTOC lobes day 1.5 treated with TL1A + IL-18, RNA


title: DRG_GW7_sample2_lane3_S1-2


title: IgAV_2_BCR

value: wangziyi:IgAV in acute phase


title: IgAV_3_rnaseq


title: IgAV_2_TCR


title: iSPN+mut, BIPKm18_TomPos., biol rep 6

description: RPKM.RData

value: Indirect spiny projection neurons (iSPN)


title: iSPN+mut, BIPKm17_TomPos., biol rep 5

description: RPKM.RData


title: DRG_GW7_sample2_lane3_S1-1


title: iSPN-mut, BIPKm16_TomNeg., biol rep 4

description: RPKM.RData


title: Neonatal thymus day P0.5 (reference), RNA

value: Reference


title: M3

city: Dalian

first: Jihong

last: Yao

address: 9 West Section, Lvshun South Road, Lvshunkou District, Dalian 116044, China

institute: Dalian medical university

description: PA+si-NC

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: The csv format file contains the FPKM value of gene in every sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent  according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The high-throughput sequencing and analyses for mRNAs were carried out by Wefind Biotechnology Co., Ltd. (Wuhan, China). After the samples were qualified, the library was constructed according to the Illumina sample preparation process of the RNA-seq protocol. The purified double-stranded cDNA was selected for fragment size using AMPure XP Beads. The DESeq2 software was used to analyze the differential expression between the sample groups.

value: Alpha Mouse Liver 12

value: PA+si-NC


title: SOD1-A4V TIC DIFF3

description: ElementBio AVITI

data_processing:
Sequence reads were trimmed using FastX 0.0.14
Trimmed sequence reads were mapped to reference genome Homo_sapiens.Ensembl.GRCh38.88 using STAR 2.5.2b (parameters: --outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate)
Reads in the alignments that overlap with gene features were counted using featureCounts 1.5.3 (parameters: -Q 0 -s 2 -t exon -g gene id)
Normalization of counts for each sample was performed using EDASeq.
Assembly: Homo_sapiens.Ensembl.GRCh38.88
Supplementary files format and content: tab-delimited .txt file containing raw counts for each sample
Supplementary files format and content: tab-delimited .txt file containing FPKM values for each sample

extract_protocol:
RNA was harvested using RNAeasy mini kit (Qiagen). 1.6ug of total RNA for each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library prep kit using manufacturer's instructions.

value: iPSC-derived Astrocytes

value: ALS

value: TIC


title: iSPN+mut, BIPKm16_TomPos., biol rep 4

description: RPKM.RData


title: DRG_GW7_sample2_lane2_S1-4


title: DRG_GW7_sample2_lane3_S1-4


title: DRG_GW7_sample2_lane2_S1-3


title: M2

description: PA+si-NC

value: WT


title: IgAV_1_TCR

value: PBMC

value: IgA vasculitis (IgAV)

value: chengyuxin:IgAV in acute phase with Mycoplasma pneumoniae infection


title: NTOC lobes day 1.5 treated with IL-12 + IL-18, RNA

value: Neonatal Thymus Organ Culture


title: IgAV_1_BCR


title: IgAV_1_rnaseq


title: M1

description: PA+si-NC


title: DRG_GW7_sample2_lane2_S1-2

value: dorsal root ganglion


title: NTOC lobes day 1.5 treated with vehicle (-control), RNA

value: Control, Day 1.5


title: control_3_TCR

value: healthy control


title: DRG_GW7_sample2_lane2_S1-1


title: iSPN+mut, BIPKm2_TomPos., biol rep 3

description: RPKM.RData

value: striatal tissue

value: Mutant

value: 8 months


title: DRG_GW7_sample2_lane1_S1-4


title: iSPN+mut, BIPKm3_TomPos., biol rep 2

description: RPKM.RData

value: Indirect spiny projection neurons (iSPN)


title: IgAV_2_rnaseq

value: wangziyi:IgAV in acute phase


title: control_3_BCR


title: MS3

value: Alpha Mouse Liver 12


title: DRG_GW7_sample2_lane1_S1-3


title: MS1


title: iSPN-mut, BIPKm1_TomNeg., biol rep 1

description: RPKM.RData

value: All other striatal cell types, except iSPN


title: MS2


title: control_3_rnaseq


title: DRG_GW7_sample2_lane1_S1-2


title: control_1_BCR


title: DRG_GW7_sample2_lane1_S1-1


title: control_1_TCR


title: SRSF2_KO

city: Shanghai

first: Zhen

middle: zhen

last: Wang

address: 320 Yueyang Road

institute: Shanghai Insititute of Nutrition and Health, University of Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The Cell Ranger software suite (version 5.0.0) of 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome, down-sample reads as required to generate normalized aggregate data across samples, then a matrix of gene counts versus cells was generated. The unique molecular identifier (UMI) count matrix was analyzed by using the R package Seurat[1] (version 3.1.1).
To get rid of  low-quality cells or likely multiplet captures, a set of criteria were conducted: Cells were removed if the UMI/gene counts out of the limit of mean value +/- 2 fold of standard deviations, assuming that each cell's UMI/gene counts have a Gaussian distribution. Cells were futured removed if > 10% of gene counts belonged to mitochondrialgenes.
The DoubletFinder package[2] (version 2.0.2) was uesd to identify potential doublet.
NormalizeData function in Seurat was used to process library size normalization, then the normalized counts were obtained.
The gene expression measurements for each cell by the total expression were normalized by “LogNormalize”, the global-scaling normalization method, then multiplied by a default scaling factor (10,000), and log-transformed the results.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Supplementary files format and content: rds files include the cell metadata.

source_name: one day old; gene knock out

extract_protocol:
The diaphragms were isolated from one day old WT, SRSF1 KO and SRSF2 KO mice immediately following euthanasia. To obtain single cells, the samples were minced and placed in enzymatic buffer containing dispase II and collagenase XI at 37 ℃ for 30 min. After termination of digestion, the samples were filtered through 40um cell strainers, centrifuged and resuspendend in 20% FBS/F-10 solution. Then the single cells were used for single-cell sequencing.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: diaphragm

value: mixed cell types


title: iSPN-mut, BIPKm66_TomNeg., biol rep 5

description: RPKM.RData

value: 3 months


title: DRG4_GW7_sample1_S1


title: WT

description: 10x Genomics

source_name: one day old

value: wild type


title: IM-DSF

city: Guangzhou

first: Xiangbo

last: Zeng

address: Jinan University

institute: JNU

data_processing:
Hisat2 (version:2.0.4) was used for the alignment of high-quality reads and mapping to the human reference genome (GRCh38). the expression value of each gene was calculated in terms of fragments per kilobase of exon model per million mapped reads (FPKM). the gene expression level in KBM5 cells treated with DMSO,0.25μM DSF, in the absence or presence of TKIs.
Assembly: GRCh38.p14

source_name: blood

extract_protocol: total RNA was extracted and examined for RIN number to inspect the RNA integrity. cDNA library construction and sequencing were performed by Shanghai Biotechnology Corporation with VAHtS Stranded mRNA-seq Library Prep Kit for Illumina®.

value: blood


title: SRSF1_KO

description: 10x Genomics


title: DRG5_GW10_sample1_S1

data_processing:
Barcode filtering and sequence alignment were performed with software Cell Ranger (http://10xgenomics.com). Reads were aligned to the human reference genome (hg19)
raw counts extraction, normalization, dimensional reduction analysis and further downstream analysis were mainly performed with the R package Seurat
Assembly: hg19
Supplementary files format and content: a gzip tab-delimited txt file include raw gene expression counts for each sample

extract_protocol:
Human fetal DRG samples across GW7-21 were collected in ice-cold oxygenated artificial cerebrospinal fluid at PH 7.4. DRG samples were transferred into 2 ml ice-cold EZ PREP and were homogenized by grinding with a glass Dounce tissue grinder . Transfer the tissue homogenate into a 15 ml tube, add 2 ml of EZ PREP, incubate on ice for 5 minutes and centrifuge at 500 g at 4℃ for 5 minutes. The supernatant was removed and the nuclei were resuspended in 4 ml ice-cold EZ PREP, and the incubation and centrifugation were repeated once. Then, the nuclei were washed in Nuclei Suspension Buffer and centrifuge at 500 g at 4℃ for 5 minutes. Nuclei were resuspended and filtered through a 70 μm cell strainer, and the nuclei concentration was adjusted to 1,000 nuclei/μl.
The libraries were generated by using the Chromium Next GEM Single Cell 3' Kit v3 according to the 10x GENOMICS official instructions, and processed on the Illumina platform for sequencing with 150 bp paired-end reads


title: iSPN+mut, BIPKm66_TomPos., biol rep 5

description: RPKM.RData


title: iSPN+mut, BIPKm65_TomPos., biol rep 4

description: RPKM.RData


title: DRG_GW8_sample1_lane3-S2-4


title: control_2_TCR

data_processing:
Raw sequencing data was processed using the 10x CellRanger pipeline, cellranger count to and cellranger vdj generate a UMI count matrix
Assembly: GRCh38
Supplementary files format and content: the UMI count matrixes which were generated by cellranger count and cellranger vdj are provided
Library strategy: scTCR-seq

value: PBMC


title: IM


title: Bd21, root, ammonium, rep3

value: Whole root

value: ammonium nutrition


title: iSPN-mut, BIPKm65_TomNeg., biol rep 4

description: RPKM.RData


title: DSF


title: iSPN-mut, BIPKm63_TomNeg., biol rep 3

description: RPKM.RData


title: iSPN+mut, BIPKm1_TomPos., biol rep 1

description: RPKM.RData


title: DRG3_GW10_sample2_S1

value: dorsal root ganglion


title: control_1_rnaseq

value: healthy control


title: control_2_rnaseq


title: NTOC supernatant day 6 treated with TL1A, ADT

data_processing:
CITE-Seq samples:The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression and cell surface protein libraries.
scRNA-Seq samples:The Cell Ranger pipeline (10x Genomics, version 6.0.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1 and read 2 for the gene expression libraries.
Read 2 of the gene expression libraries was mapped to the mouse reference genome.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting were performed using the Cell Ranger suite.
CITE-seq reads were quantified using the feature-barcoding functionality.
Assembly: Sample dependent, see above
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format files as produced by the Cellranger pipeline of 10X Genomics
Library strategy: CITE-Seq

extract_protocol:
All viable cells (DAPI-) from Day 6 NTOC supernatant treated with: TL1A and TL1A+IL-18 were FACS-purified (Aria III, BD Biosciences) and pelleted by centrifugation at 400g for 5 mins. Cells were incubated with CD16/CD32 mAb (BD Bioscience, #553142) for 20mins at 4°C to avoid non-specific Fc receptor binding of CITE-seq antibodies, prior CITE-seq performance. Cells were washed twice with  PBS with 2% FCS used directly in downstream CITE-seq analysis. We FACS-purified 15.000 cells per sample (treatment) were loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to create single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library kit, version 3 (NTOC supernatant) and version NextGEM 3.1 (Thymus lobes & NTOC lobes) (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos.
Thymic NTOC lobes were processed to single-cell suspension by pressing the organ through a 70 μm cell strainer. NTOC supernatant cells were harvested by repeated pipetting of the NTOC well and filter after the lobes were removed from the well. Samples were spun down at 400g, 4ºC for 7 min. Subsequently, samples were washed once more with 12.5 mL of cold PBS and spin down again at 400g, 4ºC for 7 min. Finally, we added 2mL of ACK lysis buffer (Westburg b.v., #10-548E) to each sample for 2 min at RT. Once incubated, we added 10mL of cold PBS to stop the lysis reaction and samples were centrifuged at 400g, 4ºC during 7 min. If needed, lysis step can be repeated again for better removal of red blood cells. Samples were incubated at 37ºC water bath for 45 min and resuspended with a glass pipette each 15 min. Once incubated, we added 5mL of FACS-EDTA buffer and the cells were transferred to a new 15mL falcon tube through a 70µm cell strainer. Subsequent flow cytometry or FACS preparation of all samples was performed on ice. Antibody staining was performed 30min in the dark. For intracellular staining of transcription factors cells were fixed after extracellular staining using eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set (ThermoFisher, #00-5523-00). For intracellular cytokine measurements, cells were first extracted from each tissue as mentioned above, and incubated with Brefeldin A (Enzo Life Sciences, #BML-G405-0025) and Monensin (Biolegend, #420701) for 4 hours, following extracellular staining and fixation and permeabilisation using BD Cytofix/Cytoperm™ (BD Biosciences, #554714). Fixable Viability Dye eFluor™ 780 (ThermoFisher, #65- 0865-14) was used to exclude dead cells in all flow cytometry and FACS experiments. For counting purposes, we added 10 µL/sample of e123count eBeads (ThermoFisher, #01-1234-42) or samples were counted in a  BD FACSVerse™ Cell Analyzer. Cell suspensions were analyzed with a BD FACSymphony™ A5, BD FACSymphony™ A3 or BD LSRFortessa™ or purified using a BD Symphony S6, BD FACSAria II or III.

value: Neonatal Thymus Organ Culture


title: CTR


title: iSPN+mut, BIPKm63_TomPos., biol rep 3

description: RPKM.RData

value: striatal tissue

value: Mutant


title: control_2_BCR

data_processing:
Raw sequencing data was processed using the 10x CellRanger pipeline, cellranger count to and cellranger vdj generate a UMI count matrix
Assembly: GRCh38
Supplementary files format and content: the UMI count matrixes which were generated by cellranger count and cellranger vdj are provided
Library strategy: scBCR-seq


title: HFSD2 (high-fat and sucrose diet)

city: Chengdu

first: Danian

last: Chen

address: 37 Guoxue Xiang Street

institute: West China Hospital, Sichuan University

data_processing:
the sequencing quality was first assessed using FastQC, and poor-quality 5′ end reads were trimmed using a Perl script and then mapped onto the rat genome using TopHat2, allowing for up to 2 mismatches as default settings.
Reads mapped onto multiple genomic locations were discarded, and a custom R script was used to calculate the fragments per kilobase million (FPKM) of each gene and obtain the expression profile of each sample
Assembly: orycun2

organism: Oryctolagus cuniculus

source_name: Retina

growth_protocol: Male Chinchilla rabbits at the age 12-16 weeks old (3.5±0.5kg) (Dongfang Breeding Co., Pizhou, China) were housed in individual cages and a room with controlled humidity (45±5%) and temperature (22±6 C) under 12/12-h light-dark cycle

extract_protocol:
Total RNAs were extracted from dissected rabbit retinas using TRIzol (Thermo Fisher) and treated with RNAse-free DNAse I (New England Biolabs) to remove genomic DNA. The yield of total RNA was assessed using NanoDrop Microvolume Spectrophotometers (NanoDrop Technologies).
The cDNA libraries were prepared using an Illumina TruSeq RNA sample preparation kit, and the quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Male adult Chinchilla rabbits fed with a regular control diet (ND, standard rabbit chow), HFD (adding 10% lard and 0.5% cholesterol in the standard chow), HSD (adding 40% sucrose in the standard chow), and HFSD (adding 10% lard, 0.5% cholesterol, and 35% sucrose in the standard chow) for six months

value: Retina

value: WT

value: High-fat and sucrose diet for six months


title: iSPN-mut, BIPKm62_TomNeg., biol rep 2

description: RPKM.RData

value: All other striatal cell types, except iSPN


title: DRG_GW8_sample1_lane3-S2-1


title: NTOC supernatant day 6 treated with TL1A + IL-18, RNA

value: TL1A + IL-18


title: HSD2 (high-sucrose diet)

value: High-sucrose diet for six months


title: HSD1 (high-sucrose diet)


title: iSPN+mut, BIPKm62_TomPos., biol rep 2

description: RPKM.RData

value: Indirect spiny projection neurons (iSPN)

value: 3 months


title: iSPN+mut, BIPKm61_TomPos., biol rep 1

description: RPKM.RData


title: DRG_GW8_sample1_lane2_S2_4


title: iSPN-wt, IPNKm72_TomNeg., biol rep 4

description: RPKM.RData

value: 8 months


title: NTOC supernatant day 6 treated with TL1A, RNA


title: HFSD1 (high-fat and sucrose diet)


title: DRG_GW8_sample1_lane2_S2_3


title: iSPN-mut, BIPKm61_TomNeg., biol rep 1

description: RPKM.RData


title: DRG_GW8_sample1_lane3-S2-3


title: Bladder urothelial carcinoma paired normal tissue, CR-hPB137

city: Nanjing

first: Weipu

last: Mao

state: Jiangsu

address: No 87, Dingjiaqiao District

department: Urology

institute: southeast university zhongda hospital

data_processing:
Sequencing data were aligned to the human reference genome (GRCh38) and processed using CellRanger 2.1.1 (10x Genomics)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include UMI counts for each cell

extract_protocol: Single cells from the tissues were obtained by using the standard protocols of cell dissociation using a Human Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer's instructions. Barcoded sequencing libraries were generated using Chromium Single Cell 3' v2 Reagent Kits and sequenced using the HiSeq 4000 platform (Illumina)


title: NTOC supernatant day 6 treated with TL1A + IL-18, ADT


title: DRG_GW8_sample1_lane1_S2-4


title: iSPN+wt, IPNKm72_TomPos., biol rep 4

description: RPKM.RData


title: DRG_GW8_sample1_lane2_S2_2


title: HFD2  (High-fat diet)

value: High-fat diet for six months


title: Bladder Ewing sarcoma paired normal tissue, CR-hPB121


title: DRG_GW8_sample1_lane2_S2_1


title: ND2 (normal diet)

value: Regular diet for six months


title: DRG_GW8_sample1_lane3-S2-2


title: ND1 (normal diet)


title: HFD1 (High-fat diet)


title: Primary bladder urothelial carcinoma, CR-hPB136

value: Primary bladder urothelial carcinoma


title: iSPN+wt, IPNKm67_TomPos., biol rep 3

description: RPKM.RData


title: iSPN-mut, BIPKm2_TomNeg., biol rep 3

description: RPKM.RData


title: DRG_GW8_sample1_lane1_S2-3

value: dorsal root ganglion


title: MB2

city: changchun

first: Yongji

last: Wu

address: academic article

institute: Jllin hospital of chinese medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two groups was performed using the DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: knee articular cartilage

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index

value: knee articular cartilage

value: Excessive mechanical load


title: iSPN-wt, IPNKm67_TomNeg., biol rep 3

description: RPKM.RData

value: striatal tissue


title: MB3


title: iSPN-wt, IPNKm66_TomNeg., biol rep 2

description: RPKM.RData


title: Aged_HET_d

city: Boston

first: Joan

last: Brugge

address: 240 Longwood Avenue

institute: Harvard Medical School

data_processing:
Paired-end reads were processed and mapped to the mm10 mouse genome using Cell Ranger v6.
Filtering eliminated genes detected in < 20 cells, and discard cells with (1) UMI counts < 1,000 or > 100,000, (2) gene counts < 500 or > 8,000, and (3) mitochondrial gene ratio > 10%.
Assembly: mm10
Supplementary files format and content: Li_Brugge_10XscRNAseq_GeneCellMatrix_RNAcounts.csv: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample
Supplementary files format and content: Li_Brugge_10XscRNAseq_Metadata_GEO.csv: Metadata table containing meta data information for each cell, including sample of origin and designated cell type

source_name: Mammary gland (#4, abdominal glands)

value: Mammary gland (#4, abdominal glands)


title: Aged_HET_c


title: DRG_GW8_sample1_lane1_S2-1


title: iSPN+wt, IPNKm66_TomPos., biol rep 2

description: RPKM.RData


title: iSPN-mut, BIPKm3_TomNeg., biol rep 2

description: RPKM.RData

value: Mutant


title: Aged_HET_b


title: iSPN-wt, IPNKm64_TomNeg., biol rep 1

description: RPKM.RData

value: WT


title: KB2


title: DRG1_GW8_sample2


title: Aged_HET_a


title: KB3


title: KB1


title: Primary bladder Ewing sarcoma, CR-hPB120

value: Primary bladder Ewing sarcoma


title: UNC2400,Day6,Rep2

data_processing:
RNAseq reads were trimmed using trim_galore program and aligned to the hg38 genome using STAR tools.  Duplicate reads were removed using picard.   Reads were counted or genes using featureCounts. Differential analysis for genes was performed using edgeR package.   Genome track bigwig files were calculated using bamCoverage tool form deepTools package.
Reads were also counted or repeat elements using featureCounts,  and differential analysis for repeats was performed using edgeR package.
Assembly: hg38

extract_protocol:
BT16 samples treated with UNC1999 or UNC2400 at 5 μM were harvested at day 4 and day 6. Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, catalog No. 74104).
For RNA-seq samples, libraries were prepared using TruSeq Stranded Total RNA kit (Illumina).

value: ATRT


title: Aged_WT_d


title: iSPN-wt, IPNKm59_TomNeg., biol rep 5

description: RPKM.RData

value: All other striatal cell types, except iSPN


title: UNC2400,Day6,Rep3


title: iSPN+wt, IPNKm64_TomPos., biol rep 1

description: RPKM.RData


title: DRG_GW8_sample1_lane1_S2-2


title: UNC2400,Day6,Rep1


title: iSPN+wt, IPNKm59_TomPos., biol rep 5

description: RPKM.RData


title: Aged_WT_c


title: Aged_WT_b


title: MB1


title: UNC2400,Day4,Rep3


title: UNC2400,Day4,Rep2


title: single cell ATAC seq library of cynomolgus samples (day0 to 10)

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

country: Germany

institute: University Leiden

library_source: genomic single cell

data_processing:
For time course single-cell multiome sequencing experiments, CellRanger ARC (v2.0.0) provided by 10x Genomics was used to demultiplex binary Illumina base call (BCL) files into FASTQ files, align the data against the GRCh38 (human), GRCm39 (mouse), and Macaca_fascicularis_6.0 (cynomolgus) reference, filter reads, as well as count barcodes and scRNA and scATAC molecules to generate feature-barcode matrices.
To mitigate technical cross-species batch effects, we pooled an equal number of cells from the three species for each of the samples.
Assembly: human genome GRCh38 (GENCODE v32/Ensembl98) and mouse genome GRCm39 obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0)
Supplementary files format and content: For every species (containing RNA counts and ATAC counts for all timepoints): matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx; the numbers 1 to 8 in the cell barcodes do correspond to the timepoints 0 to 10 days (0d, 8h, 1d, 2d, 3d, 4d, 7d and 10d).

organism: Macaca fascicularis

source_name: 56A1 cynomolgus induced pluripotent stem cells

growth_protocol: PSCs were singularized using Accutase (Sigma Aldrich) and counted on the Countess II FL Automated Cell Counter (Invitrogen). For human ESCs and cynomolgus iPSCs 1.25 x 105 cells/cm2 were seeded onto Matrigel coated plates in UPPS media supplemented with 10 µM Y-27632 (R&D Systems) and incubated overnight, resulting in confluent cultures the following day for each species. For neural induction, media was exchanged to NPC differentiation and maintenance media consisting of 1:1 DMEM/F12 and Neuropan (PAN Biotech) supplemented with 0.5x N2 and B27 supplements, 1x MEM-NEAA, 1x GlutaMAX, 0.1 mM 2-Mercaptoethanol, 5 µg/mL Insulin, human recombinant (all Thermo Fisher Scientific), 10 µM SB431542 and 100 nM LDN193189 (both Peprotech). Cells were washed with Dulbecco’s phosphate buffered saline (DPBS; Thermo Fisher Scientific) before daily media exchange.

extract_protocol:
Time course scATAC and scRNA libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturer’s protocol. Samples were collected at 0h, 8h, 1d, 2d, 3d, 4d, 7d and 10d post neural induction and cells of all three species were combined in equal amounts prior to the library preparation. The aimed target recovery was 10,000 single nuclei for sequencing.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturers instructions
scRNAseq and scATACseq

treatment_protocol: Neural induction for up to 10 days

value: UPPS (pluripotency, day0) and NPC differentiation and maintenance media

value: scATAC


title: UNC2400,Day4,Rep1

city: Toronto


title: iSPN+wt, IPNKm116_TomPos., biol rep 4

description: RPKM.RData

value: Indirect spiny projection neurons (iSPN)

value: 3 months


title: Young_HET_c

extract_protocol:
Tissues were dissociated into single cells by enzymatic digestion using procedure described previously in Li, et al., Cell Reports. 33, 108566 (2020).
Single cell capturing and cDNA library generation were performed using the 10X Chromium 3’ library construction kit v2 (normal samples) or v3 (tumor samples) following the manufacturer’s instruction.


title: single cell gene expression library of cynomolgus samples (day0 to 10)

value: 56A1 cynomolgus induced pluripotent stem cells

value: mRNA


title: UNC1999,Day6,Rep3


title: Young_HET_b


title: Salp14-C-3

city: New Haven

first: Yingjun

last: Cui

state: CT

address: 300 Cedar St, New Haven, CT, TAC S410/Erol Fikrig

department: Internal Medicine

institute: Yale University

data_processing:
reads were trimmed then  aligned to genome using STAR, reads were normalized and gene expression was quantified with DeSeq2.
Assembly: Genome assemblyCavpor3.0

organism: Cavia porcellus

source_name: skin

extract_protocol:
Total RNAs were extracted from skin sample of guinea pigs using QUICK-RNA MiniPrep kit (Zymo).
200 ng of mRNA was used to contruct cDNA library using TruSeq RNA Library Prep Kit v2

value: skin

value: Salp14-C mRNA


title: iSPN+wt, IPNKm115_TomPos., biol rep 3

description: RPKM.RData


title: UNC1999,Day6,Rep2

first: Sajid

last: Marhon

address: 101 College Street

institute: Princess Margaret Cancer Centre


title: Young_HET_a


title: Salp14-C-2


title: Salp14-C-1


title: iSPN-wt, IPNKm114_TomNeg.,  biol rep 2

description: RPKM.RData


title: UNC1999,Day6,Rep1


title: Young_WT_c


title: iSPN+wt, IPNKm114_TomPos.,  biol rep 2

description: RPKM.RData


title: UNC1999,Day4,Rep3


title: Luc-3

value: Luciferase mRNA


title: iSPN-wt, IPNKm113_TomNeg., biol rep 1

description: RPKM.RData


title: Young_WT_b


title: Young_WT_a


title: Luc-2


title: Aged_WT_a


title: iSPN-wt, IPNKm116_TomNeg., biol rep 4

description: RPKM.RData


title: Luc-1


title: UNC1999,Day4,Rep2


title: iSPN+wt, IPNKm113_TomPos., biol rep 1

description: RPKM.RData