title: Y-Ctrl, Brain, Spatial transcriptomics

first: Kai

last: Zhang

address: No. 600 Yishan Road

institute: Shanghai Jiao Tong University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x genome to gene expression count using Space Ranger pipeline to generae FASTQ files.
Sequences were aligned to mm10 gemome to gene expression count using Space Ranger's default setting.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.matx.zg: gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Fresh frozen brain tissues were sectioned into 10-μm thickness by using a Leica CM3050s, and mounted onto the GEX arrays. Sections were placed on Thermocycler Adaptor with the active surface facing up, incubated for 1 min at 37°C, and fixed for 30 min with methyl alcohol at -20°C, followed by staining with H&E. The images were taken by using Leica Aperio Versa 8 at 20× resolution.
Spatial transcriptome sequencing libaries were prepared  with 10x Genomics Visum Sptial Gene Expression & Regeat kit according to the manufacturer's construction.

value: Brain

value: Control


title: O-Ctrl, Brain, Spatial transcriptomics

status: Public on May 03 2025

type: SRA

city: Shanghai

country: China

library_source: transcriptomic

molecule: nuclear RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: O-Ex, Brain, Spatial transcriptomics

value: Exercise


title: Sample_8_dKO_LK_2x

city: Frederick

first: Shweta

last: Singh

state: Maryland

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

country: USA

institute: National Cancer Institute

data_processing:
Trimming for adapters and lowquality bases using Cutadap
Alignment using STAR
Quantification using RSEM
Assembly: mm10
Supplementary files format and content: .txt table with RSEM genes counts

molecule: total RNA

source_name: Donor Lin- ckit+ from bone marrow

growth_protocol: Donor Lin- ckit+ cells were sort purified from the bone marrow cells of competitive bone marrow transplantation recipient mice.

extract_protocol:
RNA was purified using the RNeasy Micro Kit (Qiagen)
Illumina® Stranded Total RNA Prep and Ligation with Ribo-Zero Plus ( kits

tag: cell type

value: Donor Lin- ckit+ from bone marrow

value: Tet2 KO + Id1KO


title: Sample_8_dKO_LK


title: Sample_7_Id1KO_LK_3x

value: Id1 KO


title: Sample_7_Id1KO_LK


title: Sample_6_Tet2KO_LK_3x

value: Tet2 KO


title: Sample_5_WT_LK_3x

value: WT


title: Sample_6_Tet2KO_LK


title: Sample_5_WT_LK


title: KK-Ay mouse with ligature for 3 weeks 3 [KL3]

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

country: Japan

institute: Kyushu University

data_processing:
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
Raw counts for each gene were estimated in each sample usingFeatureCount . Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm38
Supplementary files format and content: excel file includes normalized counts for each Sample with annotation.

source_name: glomeruli

growth_protocol: C57BL/6 and KK-Ay mice were housed under normal diet and ad libitum water.

extract_protocol:
Mouse glomeruli were isolated from the kidneys of perfused mice with Dynabeads M-450 Tosylactivated in PBS. Briefly, the dissected kidneys (1 and 1/2 kidneys) from each mouse were minced and digested in 1 mg/ml of collagenase A (10103578001; Sigma-Aldrich, St-Louis, MO, USA) and 100 U/ml DNase Ⅰ in Hank's Balanced Sult Solution (14175095; Thermo Fisher Scientific, Waltham, MA, USA) at 37℃ for 30 minutes. Then, the digested mixture was passed through a 100 µm cell strainer (542000; Greiner, Kremsmünster, Australia) and placed on a magnet for purification. After washing with PBS twice, glomeruli were collected. The purity of glomeruli was confirmed more than 95% by microscopy.
Glomerular RNA was isolated using PureLink RNA Mini Kit (12183018A; Invitrogen) according to the manufacturer's guidance.
A total amount of 1 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.

treatment_protocol: C57BL/6 and KK-Ay mice at 13 week old were injected with anesthetics containing 4 mg/kg midazolam (LF6476; SANDOZ, Tokyo, Japan), 0.3 mg/kg Dorbene® (9021; Kyoritsu Pharmaceutical, Tokyo, Japan), and 5 mg/kg Vetorphale® (3270952; Meiji Seika Pharma, Tokyo, Japan) at the induction of ligation or euthanasia. Mice were checked for ligatures every week.

value: glomeruli

tag: strain background

value: glomerular cells

value: KK-Ay


title: KK-Ay mouse without ligature 2 [K2]

value: no


title: KK-Ay mouse without ligature 1 [K1]


title: Sample_8_dKO_LK_3x


title: Kidney, Dmrt2 KO, rep1

city: Los Angeles

first: Riana

middle: K

last: Parvez

state: CA

address: 1425 San Pablo St.

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description:
150bp reads
dmrt2_106

data_processing:
Sequence reads were filtered using fastp (0.20.1) (average quality > 20, length > 20)
Filtered reads were aligned using STAR (2.7.0e)
Read count extraction was performed using featureCount (2.0.1)
Assembly: mm39
Supplementary files format and content: txt files contain read counts for all samples and genes

source_name: embryonic kidney

extract_protocol:
Samples were preserved in RNAlater, incubated overnight at 4°C and stored at -80°C until extraction
Whole embryonic kidney RNA was extracted using Qiagen RNeasy Mini Kit according to manufacturer's protocols. RNA was eluted in 30uL nuclease free water.
Samples were shipped to the Genome Technology Access Center at McDonnell Genomic Institute at Washington University in St. Louis for sequencing. Up to 5ug of RNA were used for library prepration; library preparation was performed using the manufacturer's protocol for polyA selection.

value: embryonic kidney

tag: developmental stage

tag: strain

value: Dmrt2 KO


title: KK-Ay mouse with ligature for 3 weeks 1 [KL1]


title: C57BL/6 mouse with ligature for 3 weeks 2 [CL2]


title: Kidney, Dmrt2 KO, rep3

description:
150bp reads
dmrt2_114


title: Sample_7_Id1KO_LK_2x


title: C57BL/6 mouse without ligature 3 [C3]


title: C57BL/6 mouse without ligature 2 [C2]


title: C57BL/6 mouse without ligature 1 [C1]


title: semimembranosus PSE rep2

city: urumqi

first: Zequan

last: Xu

address: Line 311, Nongda East Road

institute: Xinjiang agriculture university

data_processing:
SOAPnuke (v1.5.2) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.Bowtie2 (v2.2.5) was then employed to align the clean reads to the reference coding gene set
Gene expression was normalised by fragments per kilobase of transcript per million fragments (FPKM), based on the length and read count mapped to each gene
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Sus scrofa

source_name: semimembranosus

extract_protocol:
Muscle tissue was ground in liquid nitrogen, and total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany). We extracted total RNA from the muscle tissues after using DNase I treatment (RNase-Free DNase Set, Qiagen, Germany) to remove contaminating DNA.
RNA libraries were prepared for sequencing using BGIseq500 platform

value: semimembranosus

value: normal RYR1 type

value: normal quality from PSE carcasses

tag: age

value: postmortem 20 minutes


title: C57BL/6 mouse with ligature for 3 weeks 3 [CL3]


title: semimembranosus PSE rep3


title: semimembranosus PSE rep1


title: semimembranosus NO rep3

value: normal quality from NO carcasses


title: semimembranosus NO rep2


title: longissimus lumborum PSE rep2

source_name: longissimus lumborum

value: longissimus lumborum

value: PSE quality from PSE carcasses


title: longissimus lumborum NO rep3


title: longissimus lumborum PSE rep3


title: C57BL/6 mouse with ligature for 3 weeks 1 [CL1]


title: semimembranosus NO rep1


title: longissimus lumborum NO rep2


title: longissimus lumborum NO rep1


title: Pwp1_siRNA_rep1

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

institute: Kyoto University

data_processing:
The sequencing reads were mapped to the mouse genome (mm10) using STAR aligner software (v2.7.10.a). The mapped reads were fed to RSEM (v1.3.3) to calculate the expression levels.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by RSEM (v1.3.3).

molecule: polyA RNA

source_name: Embryo

growth_protocol: Mouse morula stage embryos were in vitro produced by in vitro fertilization (IVF) and further cultured in KSOM up to 72 hpi.

extract_protocol:
RNA-seq library was generated from ten morula stage embryos (siControl and siPwp1 groups), by using SMART-Seq v4 PLUS Kit (Takara Bio USA) according to the manufacturer’s manual.
SMART-Seq v4 PLUS Kit (Takara Bio USA) was used according to the manufacturer’s manual.

treatment_protocol: The culture was chemically semi-defined (bovine serum albumin was added). The one-cell stage embryos at 3 hpi were electropolated with siControl or siPwp1 and further cultured up to morula stage (72 hpi).

value: Embryo

value: ICR

value: morula stage embryo

value: in vitro produced, siPwp1 treated from the one-cell stage


title: Pwp1_siRNA_rep2


title: siRNA_Control_rep1

value: in vitro produced, siControl treated from the one-cell stage


title: longissimus lumborum PSE rep1


title: S10DE23

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped onto the R64.1.1 assembly of Saccharomyces cerevisiae genome using STAR version 2.5.3a. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 104 and “union” mode.
Assembly: sacCer3
Supplementary files format and content: Tab-separated text file with raw read counts per Ensembl Gene.

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
RNeasy kit
RNA-Seq libraries were generated according to manufacturer's instructions from 400 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

value: yeast

value: MATa trp1::TetO:TRP1 lys4::LacO:hphNT1 his3::LacR-GFP:HIS3 TetR-mRFP loxCEN4lox:KanMX GDP-creEDB78:LEU2 hht2-hhf2::[HHT-S10D-HHFS]-URA3 bar1-delta- Ade1; leu2-x

tag: condition

value: Estradiol 3 hours


title: S10DE22


title: S10DE21


title: 8E23

value: MATa lox-CEN4-lox:KanMX GDP-creEBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0


title: 8EtOH3

value: EtOH 3 hours


title: S10DEtOH1


title: 8E21


title: 8EtOH2


title: 8EtOH1


title: OEJMJ4_Input ChIP rep1

city: Hangzhou

first: Chenxu

last: Liu

state: Zhejiang

address: Xihu District, No.866 Yuhangtang Road

department: Horticulture

institute: Zhejiang university

description: Library name: OEJMJ4_Input_rep1

library_source: genomic

data_processing:
For data analysis, Trimmomatic software were used to remove adapter and low quality reads. The clean reads were then aligned to reference genome sequences (ITAG4.0) using the bwa program. The bam file generated by the unique mapped reads as an input file, using MACS2 software for callpeak with cutoff q-value < 0.05. For motif analysis, DNA sequence is compared with the Motif database to obtain the Motif. Peaks were annotated by the bedtools.
Assembly: the reference genome sequences (ITAG4.0) from Sol Genomics Network was used through bwa program
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: leaves

extract_protocol:
2g fresh tomato leaves were collected and fixed with 1% formaldehyde. After plant nucleus chromatin isolated, the DNA was sonicated to 100-400bp. 5% DNA was took as input, and the remaining DNA collected for immunoprecipitation. The primary antibody (Abcam, ab9110, Cambridge, UK) was incubated with fragmented chromatin at 4℃ for 6 hours. The antibody magnetic bead protein DNA complex is washed sequentially with high salt and low salt buffer solutions, and then the IP product is eluted. The IP product and input were cross-linked using RNase A (NEB, T3018L, Ipswich MA, USA) and Proteinase K (NEB, P8107S, Ipswich MA, USA).
The cross-linked input DNA and IP DNA were purified using a QIAquick PCR Purification Kit (QIAGEN, 28106, Hilden, Germany) and DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). The DNA libraries were sequenced on Novaseq PE150 sequencing platform by Romics Biotech (Romics, Shanghai, China).

value: leaves

value: OE-JMJ4 line

value: Cold (4℃)


title: OEJMJ4_HA ChIP rep3

description: Library name: OEJMJ4_HA_rep3


title: OEJMJ4_HA ChIP rep2

description: Library name: OEJMJ4_HA_rep2


title: OEJMJ4_HA ChIP rep1

description: Library name: OEJMJ4_HA_rep1


title: S10DEtOH3


title: OEJMJ4_Input ChIP rep2

description: Library name: OEJMJ4_Input_rep2


title: OEJMJ4_Input ChIP rep3

description: Library name: OEJMJ4_Input_rep3


title: mCh-_3

source_name: Population whole-cell extraction

growth_protocol: Cells were grown at 30°C in YPD medium

extract_protocol:
Cells were collected from three independent experiments, snap frozen and stored at -80°C. Total RNA purification and genomic DNA removal were performed using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, QIAGEN), respectively, following manufacturer’s instructions. Total RNA quantification and quality control were performed using Tape Station 4150 (Agilent).
RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter (IDT for Illumina TruSeq UD Indexes) on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Cells collected at time 0 and time 180 minutes after addition of 1 μM beta-estradiol (E8875, Sigma)

value: Population whole-cell extraction

tag: cell line

value: S288c background

value: Haploid MATa

value: MATa trp1::TetO:TRP1 lys4::LacO:hphNT1 his3::LacR-GFP:HIS3 TetR-mCherry leu2::Cre-EBD78:LEU2 Shs1-loxPmCherry:Cln2(3'UTR)-NatNT2-loxP-GFP ade2

value: mCh- t180


title: mCh-_1


title: mCh*_2

value: mCh* t0


title: mCh*_3


title: mCh-_2


title: cen4-_15

data_processing:
RNAseq reads were aligned to the reference genome Ensembl Saccharomyces cerevisiae release R64-1-1 using STAR aligner version 2.6.1 (3). Gene-level read counts were obtained simultaneously with the alignment process using the corresponding Saccharomyces cerevisiae gtf annotation file from Ensembl.
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files include normalized values (DESeq2) for each Sample.

extract_protocol:
Cells were collected from three independent experiments, snap frozen and stored at -80°C. Total RNA purification and genomic DNA removal were performed using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, QIAGEN), respectively, following manufacturer’s instructions. Total RNA quantification and quality control were performed using Tape Station 4150 (Agilent).
Libraries prepared at Novogene

treatment_protocol: Cells collected at different time points after addition of 1 μM beta-estradiol (E8875, Sigma)


title: mCh*_1


title: siRNA_Control_rep2

value: Embryo

value: ICR

value: morula stage embryo


title: 8E22

value: yeast


title: cen4-_13


title: cen4-_12


title: cen4-_11


title: cen4-_6

value: cen4- t30


title: CEN4_15

value: MATa ura3::GDP-cre EBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0

value: CEN4 t180


title: cen4-_7

value: MATa lox-CEN4-lox:KanMX GDP-creEBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0

value: cen4- t60


title: cen4-_10


title: S10DEtOH2

value: MATa trp1::TetO:TRP1 lys4::LacO:hphNT1 his3::LacR-GFP:HIS3 TetR-mRFP loxCEN4lox:KanMX GDP-creEDB78:LEU2 hht2-hhf2::[HHT-S10D-HHFS]-URA3 bar1-delta- Ade1; leu2-x

value: EtOH 3 hours


title: cen4-_9

value: Population whole-cell extraction


title: cen4-_2

value: S288c background

value: CEN4* t0


title: wk18_male_IC

description: Library name: wk18M_IC

library_source: transcriptomic single cell

data_processing:
Fastq was demultiplexed and aligned by cellranger with the flag set as “ARC-v1”
Cell-gene count matrices were processed using Seurat v4 as described in text
Barcodes of interest were subset
fastq files were generated from bam files for barcodes of interest
Assembly: Homo sapiens, hg38, 10X refdata-gex-GRCh38-2020-A
Supplementary files format and content: raw cell ranger outputs for each sample (barcodes.tsv, features.tsv, and matrix.mtx)

organism: Homo sapiens

source_name: Human kidney

extract_protocol:
Tissue was thawed on ice, and nuclei were isolated. See detailed steps in methods and Kim et al., 2024 Dev Cell.
Chromium Next Gem Single Cell Multiome (Cat No. PN-1000283)

treatment_protocol: Tissue was placed in a cryovial, snap frozen with liquid nitrogen, and stored at -80 celsius until library construction.

value: Human kidney

tag: Sex

value: male

value: Wild type


title: cen4-_4

value: Haploid MATa


title: Donor8_AIM-

city: Augusta

first: Klaus

last: Ley

state: Georgia

address: 1410 Laney Walker Blvd

department: Immunology Center of Georgia

institute: Augusta University

data_processing:
Illumina DRAGEN to convert BCL to fastq files and trime for adapters
Read count extraction and normalization were performed using STAR v.2.7.1 and DESeq2 v1.34
Assembly: GENCODE GRCh38.p13 and GENCODE GRCm39 respectively
Supplementary files format and content: Tab-delimited text files include count values and decoder information for each sample.

source_name: Sorted AIM-_CD4+T cells

extract_protocol:
No RNA extraction. Cells directly sorted into low-input lysis buffer (LI-LB) containing 0.1% Triton X-100 (vol/vol), 1U/µl RNase inhibitor (Takara), 2.5mM dNTPs (Thermo Fisher Scientific).
Double-stranded (ds)-cDNA synthesis and amplification using the Smart-seq2 protocol. Briefly, poly-dT and template-switch oligos were used for mRNA capture and generation of full-length double-stranded cDNA using SuperScript II reverse transcriptase kit (Thermo Fisher). The cDNA was amplified using KAPA HiFi HotStart ReadyMix buffer and purified with AMPure XP magnetic bead (Beckman Coulter). Quality and quantity of cDNA were assessed with Tapestation (Agilent) and Qubit (Invitrogen). For each sample, 1 ng cDNA was used to prepare dual-index barcoded libraries using Nextera XT DNA library prep kit and index kits (Illumina). Libraries were purified with AMPure XP magnetic bead. Good quality libraries, as examined with Tapestation and Qubit, were retained for sequencing. Samples from low, mid and high range Gensini scores (severity of coronary artery disease) were processed together to minimize batch effects. Equimolar concentrations of uniquely indexed libraries were pooled and sequenced using an S4 flow cell on a NovaSeq 6000 (Illumina) to obtain 70 million 100-bp paired-end reads per cluster.

tag: tissue type

value: Blood CD4+T cells

value: Sorted AIM-_CD4+T cells

value: APOB PEPTIDE STIMULATED

tag: time

value: 24 HOURS


title: Donor9_AIM-


title: Donor9_AIM2

source_name: Sorted AIM2_CD4+T cells

value: Sorted AIM2_CD4+T cells


title: CEN4_14

value: MATa ura3::GDP-cre EBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0

value: CEN4 t180


title: wk18_female_IC

description: Library name: wk18F_IC

value: female


title: Donor8_AIM2


title: Donor9_AIM1

source_name: Sorted AIM1_CD4+T cells

value: Sorted AIM1_CD4+T cells


title: CEN4_11

value: CEN4 t120


title: cen4-_1

value: Population whole-cell extraction

value: MATa lox-CEN4-lox:KanMX GDP-creEBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0


title: Donor9_AIM3

source_name: Sorted AIM3_CD4+T cells

value: Sorted AIM3_CD4+T cells


title: cen4-_5

value: S288c background

value: cen4- t30


title: CEN4_12


title: cen4-_8

value: cen4- t60


title: cen4-_14

value: Haploid MATa


title: Donor8_AIM1

value: Blood CD4+T cells


title: cen4-_3

value: CEN4* t0


title: CEN4_10


title: Donor7_AIM-

value: Sorted AIM-_CD4+T cells

value: APOB PEPTIDE STIMULATED


title: CEN4_13


title: Donor7_AIM3

value: 24 HOURS


title: CEN4_8

value: MATa ura3::GDP-cre EBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0

value: CEN4 t60


title: CEN4_7


title: Donor7_AIM2

value: Sorted AIM2_CD4+T cells


title: CEN4_6

value: CEN4 t30


title: Donor7_AIM1

value: Sorted AIM1_CD4+T cells


title: Donor6_AIM3


title: CEN4_4

value: Population whole-cell extraction


title: CEN4_3

value: CEN4 t0


title: CEN4_2


title: Donor6_AIM-


title: Donor6_AIM2


title: 130_CTD-S5p_cen4-_180_2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome sacCer3 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
BigWig files were generated using Homer (Heinz et al. 2010) makeUCSCfile v4.11.0 with default parameters except for “-fragLength 200” and "-norm 5e6" (H4K16ac and H4K12ac) or "-norm 1e6" (all other datasets).
Peaks were called using MACS2 v2.1.1.20160309 on the pool of replicates versus their corresponding input. MACS2 was run with default parameters except for: ’-g 12000000 –nomodel –extsize 200’. For conditions H3K4me3_wt_60 and H3K4me3_mut_180, the additional parameters “–to-large” was added to correct for the high number of reads in the IPs compared to the input.
Assembly: sacCer3
Supplementary files format and content: bigWig, narrowPeak (except for Input and RNAPII samples)

extract_protocol:
Cells were fixed with 1% (vol/vol) formaldehyde for 30 min. Formaldehyde was quenched for 5 min by adding glycine to a final concentration of 125 mM. Cells were washed with cold Tris-buffered saline, resuspended in lysis buffer [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1% (vol/vol) Triton X-100, 0.1% (vol/vol) Na-deoxycholate, and protease inhibitor cocktail] and were sonicated twice for 15 min by performing alternating cycles of 30 s pulses followed by a 30 s cool-down period using a Diagenode Bioruptor Pico. After centrifugation, supernatants were immunoprecipitated at 4C using anti-H4K12ac, H4K16ac, H3K4me3, Pol II, Pol II CTD-S2p and Pol II CTD-S5p (table S3) and protein A and G Dynabeads (10001D and 10003D, Thermo Fisher Scientific). Beads were first washed with lysis buffer, followed by washing with lysis buffer containing 500 mM NaCl, then with wash buffer [10 mM Tris (pH 8.0), 250 mM LiCl, 0.5% (vol/vol) Nonidet P-40, 0.5% (wt/vol) Na-deoxycholate and 1 mM EDTA], and finally with TE buffer [10 mM Tris (pH 8.0) and 1 mM EDTA]. Elution was performed in 50 mM Tris (pH 8.0), 10 mM EDTA, 1% (wt/vol) SDS at 65C, and the cross-link was reversed 5 hours at 65C. After RNase DNase free (04716728001, Merck) and proteinase K treatment (03115828001, Merk), DNA fragments were purified using QIAquick PCR purification kit (28104, Qiagen). DNA fragments were used for ChIPseq experiments
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 2,5 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: chip antibody

value: RNA Pol II CTD-S5p

value: 180 min


title: CEN4_5

value: S288c background


title: CEN4_1


title: Donor5_AIM1


title: Donor6_AIM1


title: Donor4_AIM-


title: Donor5_AIM3

value: Sorted AIM3_CD4+T cells


title: 128_CTD-S5p_cen4-_60_2

value: Haploid MATa

value: 60 min


title: Donor5_AIM-

value: Blood CD4+T cells


title: 127_CTD-S5p_cen4-_30_2

value: 30 min


title: Donor4_AIM1

value: APOB PEPTIDE STIMULATED


title: 129_CTD-S5p_cen4-_120_2

value: 120 min


title: Donor40_AIM-

value: Sorted AIM-_CD4+T cells

value: 24 HOURS


title: 126_CTD-S5p_cen4-_0_2

value: 0 min


title: 125_CTD-S5p_cen4-_180_1


title: CEN4_9

value: MATa ura3::GDP-cre EBD78:LEU2 his3-delta-1 leu2-delta-0 ura3-delta-0 met15-delta-0

value: CEN4 t60


title: Donor40_AIM3


title: Donor40_AIM2

value: Sorted AIM2_CD4+T cells


title: 122_CTD-S5p_cen4-_30_1

value: Population whole-cell extraction


title: Donor3_AIM1

value: Sorted AIM1_CD4+T cells


title: 121_CTD-S5p_cen4-_0_1

value: RNA Pol II CTD-S5p


title: Donor38_AIM-


title: 124_CTD-S5p_cen4-_120_1

value: S288c background


title: Donor40_AIM1


title: Donor38_AIM3

value: Sorted AIM3_CD4+T cells


title: Donor3_AIM-


title: 120_CTD-S5p_CEN4_180_2

value: Haploid MATa

value: 180 min


title: 118_CTD-S5p_CEN4_60_2

value: 60 min


title: Donor37_AIM3

value: Blood CD4+T cells


title: 123_CTD-S5p_cen4-_60_1


title: 116_CTD-S5p_CEN4_0_2


title: Donor37_AIM1

value: APOB PEPTIDE STIMULATED


title: 112_CTD-S5p_CEN4_30_1

value: 30 min


title: 115_CTD-S5p_CEN4_180_1


title: Donor37_AIM-

value: Sorted AIM-_CD4+T cells


title: Donor38_AIM2

value: 24 HOURS


title: Donor36_AIM3


title: 119_CTD-S5p_CEN4_120_2

value: 120 min


title: Donor37_AIM2


title: Donor36_AIM-


title: Donor38_AIM1


title: Donor36_AIM2


title: 110_CTD-S2p_cen4-_180_2

value: RNA Pol II CTD-S2p


title: 113_CTD-S5p_CEN4_60_1


title: 114_CTD-S5p_CEN4_120_1


title: 117_CTD-S5p_CEN4_30_2


title: Donor36_AIM1


title: Donor35_AIM-


title: 109_CTD-S2p_cen4-_120_2


title: 107_CTD-S2p_cen4-_30_2


title: Donor34_AIM-


title: Donor35_AIM2


title: 105_CTD-S2p_cen4-_180_1


title: 106_CTD-S2p_cen4-_0_2

value: 0 min


title: Donor33_AIM-


title: 111_CTD-S5p_CEN4_0_1


title: 100_CTD-S2p_CEN4_180_2


title: 102_CTD-S2p_cen4-_30_1


title: 101_CTD-S2p_cen4-_0_1


title: 99_CTD-S2p_CEN4_120_2


title: 103_CTD-S2p_cen4-_60_1


title: Donor33_AIM2

value: Sorted AIM2_CD4+T cells


title: Donor33_AIM3


title: Donor32_AIM-


title: Donor32_AIM3


title: 98_CTD-S2p_CEN4_60_2

value: Population whole-cell extraction


title: Donor32_AIM2


title: 97_CTD-S2p_CEN4_30_2


title: 108_CTD-S2p_cen4-_60_2


title: Donor35_AIM3


title: Donor32_AIM1

value: Sorted AIM1_CD4+T cells


title: Donor31_AIM-


title: 95_CTD-S2p_CEN4_180_1


title: Donor34_AIM3


title: Donor31_AIM3


title: Donor34_AIM2


title: 104_CTD-S2p_cen4-_120_1


title: Donor33_AIM1


title: 93_CTD-S2p_CEN4_60_1


title: Donor31_AIM2


title: Donor30_AIM-


title: Donor30_AIM3


title: 91_CTD-S2p_CEN4_0_1


title: 94_CTD-S2p_CEN4_120_1


title: 89_H4K16ac_cen4-_120_2


title: Donor30_AIM2


title: Donor30_AIM1


title: 90_H4K16ac_cen4-_180_2


title: 88_H4K16ac_cen4-_60_2


title: 86_H4K16ac_cen4-_0_2


title: 96_CTD-S2p_CEN4_0_2


title: 85_H4K16ac_cen4-_180_1


title: Donor29_AIM-


title: 84_H4K16ac_cen4-_120_1


title: Donor29_AIM3


title: Donor29_AIM2


title: 83_H4K16ac_cen4-_60_1


title: 81_H4K16ac_cen4-_0_1


title: Donor31_AIM1


title: Donor29_AIM1


title: 80_H4K16ac_CEN4_180_2


title: Donor28_AIM-


title: 92_CTD-S2p_CEN4_30_1


title: Donor28_AIM3


title: 87_H4K16ac_cen4-_30_2


title: 82_H4K16ac_cen4-_30_1


title: Donor2_AIM-


title: Donor28_AIM2


title: 78_H4K16ac_CEN4_60_2


title: 79_H4K16ac_CEN4_120_2


title: 77_H4K16ac_CEN4_30_2


title: Donor27_AIM-


title: Donor28_AIM1


title: 76_H4K16ac_CEN4_0_2


title: 75_H4K16ac_CEN4_180_1


title: Donor2_AIM1


title: 74_H4K16ac_CEN4_120_1


title: Donor27_AIM2


title: Donor27_AIM1


title: Donor26_AIM-


title: 73_H4K16ac_CEN4_60_1


title: Donor26_AIM3


title: 72_H4K16ac_CEN4_30_1


title: 71_H4K16ac_CEN4_0_1


title: Donor26_AIM2


title: 70_RNAPolII_cen4-_180_2

value: RNA Pol II


title: 68_RNAPolII_cen4-_60_2

value: S288c background


title: 67_RNAPolII_cen4-_30_2


title: Donor26_AIM1


title: Donor27_AIM3

value: Sorted AIM3_CD4+T cells


title: Donor25_AIM-


title: Donor25_AIM2


title: Donor25_AIM3


title: 66_RNAPolII_cen4-_0_2

value: Haploid MATa


title: 65_RNAPolII_cen4-_180_1

value: 180 min


title: Donor25_AIM1


title: Donor24_AIM-


title: Donor24_AIM3


title: 64_RNAPolII_cen4-_120_1


title: 63_RNAPolII_cen4-_60_1

value: 60 min


title: Donor24_AIM2

value: Blood CD4+T cells


title: 62_RNAPolII_cen4-_30_1


title: 60_RNAPolII_CEN4_180_2


title: Donor23_AIM-

value: APOB PEPTIDE STIMULATED


title: 59_RNAPolII_CEN4_120_2


title: 61_RNAPolII_cen4-_0_1


title: Donor23_AIM2


title: Donor22_AIM-


title: Donor23_AIM1


title: Donor22_AIM2


title: Donor23_AIM3


title: 57_RNAPolII_CEN4_30_2

value: 30 min


title: 58_RNAPolII_CEN4_60_2


title: 52_RNAPolII_CEN4_30_1


title: Donor22_AIM3


title: 55_RNAPolII_CEN4_180_1


title: Donor24_AIM1


title: Donor22_AIM1


title: 54_RNAPolII_CEN4_120_1


title: 50_H4K12ac_cen4-_180_2


title: 51_RNAPolII_CEN4_0_1


title: Donor21_AIM3


title: Donor21_AIM-

value: Sorted AIM-_CD4+T cells


title: Donor21_AIM1

value: 24 HOURS


title: 48_H4K12ac_cen4-_60_2


title: Donor21_AIM2


title: 56_RNAPolII_CEN4_0_2


title: Donor20_AIM-


title: 49_H4K12ac_cen4-_120_2

value: 120 min


title: 47_H4K12ac_cen4-_30_2


title: 53_RNAPolII_CEN4_60_1


title: 46_H4K12ac_cen4-_0_2


title: Donor20_AIM3


title: 45_H4K12ac_cen4-_180_1


title: Donor20_AIM1


title: 44_H4K12ac_cen4-_120_1


title: Donor1_AIM2


title: Donor1_AIM1


title: 43_H4K12ac_cen4-_60_1


title: Donor19_AIM3


title: 41_H4K12ac_cen4-_0_1


title: Donor20_AIM2


title: 42_H4K12ac_cen4-_30_1


title: 40_H4K12ac_CEN4_180_2


title: 39_H4K12ac_CEN4_120_2


title: Donor19_AIM1


title: 38_H4K12ac_CEN4_60_2


title: 37_H4K12ac_CEN4_30_2


title: Donor18_AIM-


title: Donor19_AIM-


title: Donor18_AIM2


title: Donor18_AIM1


title: 36_H4K12ac_CEN4_0_2


title: 35_H4K12ac_CEN4_180_1


title: Donor18_AIM3


title: 34_H4K12ac_CEN4_120_1


title: Donor17_AIM3


title: 32_H4K12ac_CEN4_30_1


title: Donor17_AIM-


title: Donor17_AIM2


title: 30_H3K4me3_cen4-_180_2


title: 31_H4K12ac_CEN4_0_1


title: Donor17_AIM1


title: 29_H3K4me3_cen4-_120_2


title: Donor16_AIM-


title: Donor19_AIM2


title: Donor16_AIM3


title: Donor16_AIM2


title: 28_H3K4me3_cen4-_60_2


title: 27_H3K4me3_cen4-_30_2


title: Donor15_AIM-


title: 26_H3K4me3_cen4-_0_2


title: Donor15_AIM3


title: 25_H3K4me3_cen4-_180_1


title: Donor16_AIM1


title: 24_H3K4me3_cen4-_120_1


title: Donor15_AIM2


title: Donor15_AIM1


title: 23_H3K4me3_cen4-_60_1


title: 33_H4K12ac_CEN4_60_1


title: Donor14_AIM3


title: Donor14_AIM-


title: 21_H3K4me3_cen4-_0_1


title: 20_H3K4me3_CEN4_180_2


title: 19_H3K4me3_CEN4_120_2


title: 18_H3K4me3_CEN4_60_2


title: Donor13_AIM3


title: Donor14_AIM1


title: 17_H3K4me3_CEN4_30_2


title: Donor13_AIM2


title: Donor13_AIM1


title: 14_H3K4me3_CEN4_120_1


title: Donor12_AIM-


title: 13_H3K4me3_CEN4_60_1


title: 12_H3K4me3_CEN4_30_1


title: 11_H3K4me3_CEN4_0_1


title: 22_H3K4me3_cen4-_30_1


title: 10_input_cen4-_180_1


title: Donor12_AIM2


title: Donor12_AIM1


title: Donor11_AIM-


title: Donor14_AIM2


title: 9_input_cen4-_120_1


title: Donor12_AIM3


title: Donor11_AIM3


title: Donor11_AIM1


title: Donor13_AIM-


title: 6_input_cen4-_0_1


title: 7_input_cen4-_30_1


title: Donor10_AIM3


title: 5_input_CEN4_180_1


title: 16_H3K4me3_CEN4_0_2


title: Donor10_AIM-


title: 15_H3K4me3_CEN4_180_1


title: Donor11_AIM2


title: 8_input_cen4-_60_1


title: Donor10_AIM2


title: 3_input_CEN4_60_1


title: Donor10_AIM1


title: il4M2-3

city: Chengdu

first: Jing

last: Li

state: Sichuan

address: huimin road 211

institute: Sichuan Agricultural University

data_processing:
Kallistov0.44.0
Use from the ensemble Sus_scrofa. Sscrofa11.1.104. GTF and Sus_scrofa Sscrofa11.1. Cdna. All. The fa. Gz file as reference genome, using R for downstream analysis.
Assembly: Ss11.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Macrophage

growth_protocol: BMDMs were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Life Technologies, China,15596026). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit ( NEB, USA, 7530) following manufacturer's protocols.

treatment_protocol:
After 4h purification, M1 macrophages were induced with 100ng/ml IFN-γ (Proteintech, USA, HZ-1301) and 20ng/ml LPS (sigma, USA, L4516).
After 4h purification, M1 macrophages were induced with 20ng/ml GM-CSF (absin, China, abs04132).
After 4h purification,M2 macrophages were induced with 10ng/ml IL-10(Proteintech, USA, HZ-1145), and 10ng/ml IL-4 (Proteintech, USA, HZ-1004).
After 4h purification,M2 macrophages were induced with 20ng/ml M-CSF (absin, China, abs00846).

value: Macrophage

value: Macrophage induced differentiation

tag: agent

value: 10ng/ml IL-10and 10ng/ml IL-4


title: il4M2-2


title: 2_input_CEN4_30_1

value: Population whole-cell extraction


title: Ccrl2-/CM

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data of cardiac macrophages in the hearts of mice with heart failure

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Affymetrix Clariom_S_Mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: Co-culture cardiomyocytes with CCRL2-Mφ secretome for 48 h.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Ccrl2+ and Ccrl2- macrophages were sorted from the six mixed hearts of WT mice at 1 week after TAC using Cell Sorter

extract_protocol: After co-culture, CFs and CMs were prepared for microarray analysis.

treatment_protocol: Ccrl2+ and Ccrl2- macrophages were sorted from the heart tissue and then co-cultured with cardiac fibroblasts (CFs) or cardiomyocytes (CMs)

value: heart

value: 15-16 weeks old


title: 1_input_CEN4_0_1

value: S288c background

value: 0 min


title: il4M2-1


title: Sham/CM

source_name: Co-culture cardiomyocytes with PBS for 48 h.


title: ATAC_seq_GSC23_shLBR.568

city: Pittsburgh

first: Tingting

last: Duan

state: PA

address: 5117 Centre Avenue

institute: University of Pittsburgh

data_processing:
Raw FASTQ files were trimmed using Trim Galore and aligned to the hg38 human genome using Bowtie2 with default parameters. Samtools was used to sort and index the BAM files. For subsequent visualization, bigwig files were generated using the Deeptools “bamCoverage” script using default settings.
Assembly: hg38
Supplementary files format and content: Bigwig generaged by Deeptools

source_name: Glioblastoma

extract_protocol:
100,000 cells/sample were collected and  treated with Dnase. Cell pallets were washed and Cryopreserved before library construction.
Nuclei were extracted and QC was performed. After the QC, the nuclei pellets were resuspended in the Tn5 transposase reaction mix consisting of transposase and equimolar adapter1 and adapter 2. The mix of transposition reaction was incubated at 37°C for 30 min. PCR wass then performed to enrich the library. The final libraries were purified with the AMPure beads and library quality was assessed.

value: Glioblastoma

value: GSC

value: shRNA


title: Ccrl2-/CF

source_name: Co-culture cardiac fibroblasts with CCRL2-Mφ secretome for 48 h.


title: ATAC_seq_GSC23_shLBR.2173


title: CEN4t180_2

data_processing:
Reads were mapped to Saccharomyces cerevisiae genome (assembly sacCer3) using the ENCODE ATAC pipeline v2.0.2 that uses bowtie2 (Langmead and Salzberg 2012) v2.3.4.3 to align reads. Parameters used for the different tools are available here. Briefly, Bowtie2 is used to map reads to the reference genome with default parameters except for “-X2000.” Then samtools view v1.9 (Li et al. 2009) is used to remove reads (unmapped, mate unmapped, not primary alignment reads, reads failing platform, low quality reads (MAQ <30)) with the following parameters “samtools view -F 1804 -q 30.” Then, duplicated reads are marked with Picard MarkDuplicates v2.20.7 (“Picard Tools - By Broad Institute” n.d.) and removed with samtools with the following parameter “-F 1804.”
Normalized BigWig files were generated using Homer (Heinz et al. 2010) makeUCSCfile v4.11.1 with the following parameter ’-norm 1e7 -style dnase’.
Peak calling was done using the Encode ATAC pipeline v2.0.2. macs2 v2.2.4 with the following parameters “–shift 75 –extsize 150 –nomodel -B –SPMR –keep-dup all –call-summits” was used to call the peaks.The pipeline was run for all condition separately. Peak set retained for further analyses is the overlap / optimal one.
Assembly: sacCer3
Supplementary files format and content: Visualisation tracks are in bigwig.
Supplementary files format and content: Narrowpeak files: the peak calling result file is a BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue.

extract_protocol:
ATAC-seq experiments were performed in duplicates as previously described (Hendrickson et al. 2018). Briefly, 1–5 million yeast cells were collected and washed with spheroplasting buffer (SB) [40 mM HEPES pH 7.5, 10 mM MgCl2, 1 M sorbitol]. Then, cells were resuspended with 190 μL SB and 10 μL of 10 mg/mL zymolyase in SB. After 30 minutes incubation at 30°C, spheroplasted cells were washed twice with 200 μL of SB. Then, the pellet was resuspended in 50 μL transposition mix (25 μLTagment DNA Buffer, 22.5 μL nuclease-free water, 2.5 μL Nextera Tagment DNA Enzyme 1) using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina 20034197). The solution was incubated at 37°C during 30 minutes and purified using the DNA Clean & Concentrator™-5 Kit (Zymo Research) and eluting in 11 μL of nuclease-free water.
For the library amplification, each PCR reaction had 25 μL NEBNext Hi-Fidelity 2× PCR Master Mix (New England Biolabs M0541S), 7.5 μL of nuclease-free water, 6.25 μL Universal Primer Ad1 (10 μM), 6.25 μL barcoded reverse primer (Ad2.[1–16]) (10 μM) (table S2 and (13) for ATAC-seq primer sequences) and 5 μL purified transposed DNA. The PCR amplification was: 1 cycle: 72°C for 5 min; 1 cycle: 98°C for 30 s; 10 cycles [98°C for 10 s, 63°C for 30 s, 72°C for 1 min]; hold at 4°C. PCR products were purified and size-selected using SPRIselect beads (Beckman-Coulter, Villepinte, France) to remove free primers and other reagents. This step was repeated twice using a ratio (volume of beads/volume of PCR) equal to 1.4/1. ATAC-seq libraries were sequenced on an Illumina HiSeq 4000 sequencer as paired-end 100 base reads. Image analysis and base calling were performed using RTA version 2.7.7 and bcl2fastq version 2.20.0.422.

value: Haploid MATa

value: CEN4 t180

value: 180 min

value: 1 μM beta-estradiol


title: mcsfM2-2

value: 20ng/ml M-CSF


title: mcsfM2-3


title: CEN4t0_2

value: CEN4 t0


title: Ccrl2+/CF

source_name: Co-culture cardiac fibroblasts with CCRL2+Mφ secretome for 48 h.


title: ATAC_seq_GSC23_shCONT


title: CEN4t0_1


title: CEN4t180_1


title: lpsM1-4

value: Macrophage

value: 100ng/ml IFN-gamma and 20 ng/ml LPS


title: 4_input_CEN4_120_1

value: 120 min


title: lpsM1-3

value: Macrophage induced differentiation


title: cen4-t180_2

value: Population whole-cell extraction


title: ATAC_seq_T387_shLBR.2173


title: Trem2 Mac

source_name: Trem2⁺ macrophage from mouse hearts at 8 wks post-TAC

growth_protocol: Lyve1+, CD74+, Ccrl2+, and Trem2+ macrophages were sorted from the six mixed hearts of WT mice at 1 week after TAC using Cell Sorter (FACSAria III; BD Bioscience, New Jersey, USA)

extract_protocol: Briefly, total RNA was reverse transcribed, amplified with Whole Transcript Pico Reagent Kit (Affymetrix, Thermo Fisher Scientific, California, USA), labeled, and hybridized with Affymetrix Clariom S Array (mouse) according to manufacturer instructions. Hybridized GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip Scanner 3000 7G. Robust Multichip Average (RMA) algorithms were employed for background correction, normalization, and summary of the AffyBatch probe-level data to obtain gene expression data. Microarray data sets were analyzed using the Agilent Genespring GS 11 software.

treatment_protocol: The microarray assay was performed as described previously.Total cell RNA was extracted with TRIzol.

value: heart

value: 15-16 weeks old


title: ATAC_seq_T387_shLBR.568


title: GSC23_shLBR-2 replicate2

data_processing:
For RNA-seq, raw FASTQ reads were trimmed using Trim Galore, followed by transcript mapping with Hisat2 to human reference genome (hg38). Samtools was used for sorting, indexing and format conversion from SAM files. Quantification and differential analysis were performed using FeatureCounts and DESeq2 with paired sample analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include mRNA raw counts for each sample

extract_protocol:
Cellular total RNA was isolated using TRIzol (cat: 15596018; Life Technologies) followed by Direct-zol RNA Miniprep kit (cat: R2052; Zymo Research).The procedure of ChIP assays was according to the ChIP kit (cat: 17-10085, Millipore) instruction manual provided by the manufacturer.
Total RNA was extracted and used for library construction using the Illumina TruSeq Stranded Total RNA Library Prep Kit, which was performed by Novogene.

treatment_protocol: GSCs are transduced with either control shRNA or shLBR. KD of LBR is verified before extracting RNA for sequencing.

value: LBR KD


title: CD163 Mac

source_name: CD163⁺ macrophage from mouse hearts at 8 wks post-TAC


title: cen4-t180_1

value: S288c background


title: Ccrl2+/CM

source_name: Co-culture cardiomyocytes with CCRL2+Mφ secretome for 48 h.


title: Sham/CF

source_name: Co-culture cardiac fibroblasts with PBS for 48 h.


title: mcsfM2-1


title: ATAC_seq_T387_shCONT

value: Glioblastoma

value: GSC


title: Ccrl2 Mac

source_name: Ccrl2⁺ macrophage from mouse hearts at 8 wks post-TAC


title: GSC23_shLBR-2 replicate1


title: cen4-t0_2

source_name: Population whole-cell extraction

value: Haploid MATa

value: CEN4* t0

value: 0 min


title: lpsM1-1


title: R_DSS_d10_Rep3

city: Wien

first: Cornelia

last: Vesely

state: Österreich

address: Schwarzspanierstr 17

department: Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description: Library name: R_DSS_d10_Rep3

data_processing:
Convert BAM to FASTQ with SamToFastq --ClIPPING_ACTION X --CLIPPING_ATTRIBUTE XT
Quality control with fastp -q 25 -u 10 -l 50 -y -x
STAR read mapping per sample with GRCm38 M25 reference --outFIlterType BySJout
Read count using R featureCounts genocode vM25 gtf and strandSpecific 2
Assembly: GRCm38 GENCODE M25
Supplementary files format and content: bulkRNAseq_cnt.csv raw counts
Supplementary files format and content: bulkRNAseq_cpm.csv counts per million

source_name: distal colon

growth_protocol: Mice were maintained according to national laws in individually ventilated cages.

extract_protocol:
At the endpoint, colons were isolated, measured and distal colon was homogenized for RNA isolation by Trizol.
Total RNA was subjected to poly-A RNA enrichment (NEBNext® Poly(A) mRNA Isolation Module, NEB,) followed by stranded library preparation (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina, NEB), multiplexed and sequenced on a NextSeq Illumina platform to a minimum of 30 Mio reads per sample.

treatment_protocol: DSS-colitis was induced in 8-10-week-old male mice by adding 2-2.5% DSS in the drinking water for seven days, followed by three days with regular drinking water. Body weight and health status of the animals were monitored throughout the experiment. Mice were euthanized on day ten.

value: distal colon


title: CD74 Mac

source_name: CD9⁺ macrophage from mouse hearts at 8 wks post-TAC


title: GSC23_shLBR-1 replicate2


title: gmM1-4

value: 20ng/ml GM-CSF


title: GSC23_shLBR-1 replicate1


title: R_DSS_d10_Rep2

description: Library name: R_DSS_d10_Rep2


title: cen4-t0_1


title: N2 + dietary restriction 0 (DR0), rep 3

city: Lausanne

first: Terytty Yang

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

description: Library name: RC3

data_processing:
After sequencing on the Illumina NovaSeq 6000 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa --sjdbGTFfile Caenorhabditis_elegans.WBcel235.89.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
genome build: ce11
Supplementary files format and content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

organism: Caenorhabditis elegans

growth_protocol: Synchronized worm eggs obtained by bleaching were fed with HT115 control bacteria until Adult Day 1 stage. Worms were then transferred onto NGM plates containing 10 μg/mL kanamycin (to prevent bacteria from further growing) and fed with undiluted (AL, ad libitum control), diluted (DR1, dietary restriction 1) HT115 bacteria food, or no bacteria (DR0, dietary restriction 0) for 24 h.

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard Illumina NovaSeq 6000 protocols with polyA enrichment

treatment_protocol: Dietary restriction treatment was started from Adult Day1 stage and worms were harvested 24 h after treatment.

value: WT

tag: dietary restrition

value: dietary restriction 1 (DR0), no food


title: R_DSS_d10_Rep1

description: Library name: R_DSS_d10_Rep1


title: lpsM1-2

value: Macrophage

value: 100ng/ml IFN-gamma and 20 ng/ml LPS


title: GSC23_shCONT-replicate2

value: control shRNA


title: GSC23_shCONT-replicate1


title: N2 + dietary restriction 0 (DR0), rep 1

description: Library name: RC1


title: R_DSS_d10_Rep4

description: Library name: R_DSS_d10_Rep4


title: Q_DSS_d10_Rep3

description: Library name: Q_DSS_d10_Rep3


title: N2 + dietary restriction 0 (DR0), rep 2

description: Library name: RC2


title: gmM1-2

value: Macrophage induced differentiation


title: Q_DSS_d10_Rep2

description: Library name: Q_DSS_d10_Rep2


title: gmM1-1


title: T387_shLBR-2 replicate2


title: R_DSS_d5_Intestine

description: Library name: R_DSS_d5_Intestine

library_source: other

data_processing:
CellRanger multi v 7.1.0
Per sample BAM files were converted to fastq.gz for submission with CellRanger bamtofastq
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: CellRanger filtered count matrix in H5 format

molecule: other

source_name: large intestine

extract_protocol:
For flow cytometry, cells were resuspended in antibody mixtures  and stained for 30min in the dark and viable CD45+ and CD45- cells were sorted using a FACS ARIA into 1xPBS/0.2% BSA. Sorted cells were then pooled, counted and fixed for 18hrs at 4°C in 1mL of freshly prepared fixation buffer (Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling).
On the next day, cells were pelleted, resuspended in freezing solution and stored at -80°C until processing for fixed single cell sequencing. Library preparation was performed using the Chromium mouse transcriptome probe set v1.0.1 protocol. Libraries were sequenced on an Illumina HiSeq 4000.

treatment_protocol: DSS-colitis was induced in 8-10-week-old male mice by adding 2-2.5% DSS in the drinking water for five days. Body weight and health status of the animals were monitored throughout the experiment. Mice were euthanized on day five.

value: large intestine


title: Q_DSS_d10_Rep1

description: Library name: Q_DSS_d10_Rep1


title: T387_shLBR-2 replicate1


title: R_Baseline_d5_Intestine

description: Library name: R_Baseline_d5_Intestine


title: N2 + dietary restriction 1 (DR1), rep 2

description: Library name: RB2

value: dietary restriction 1 (DR1), diluted food


title: N2 + dietary restriction 1 (DR1), rep 3

description: Library name: RB3


title: T387_shLBR-1 replicate2

value: LBR KD


title: R_Ctr_d10_Rep2

description: Library name: R_Ctr_d10_Rep2


title: Q_DSS_d5_Intestine

description: Library name: Q_DSS_d5_Intestine


title: R_Ctr_d10_Rep1

description: Library name: R_Ctr_d10_Rep1


title: gmM1-3


title: N2 + dietary restriction 1 (DR1), rep 1

description: Library name: RB1


title: N2 + ad libitum (AL), rep 3

description: Library name: RA3

value: ad libitum (AL) control


title: Q_Ctr_d10_Rep2

description: Library name: Q_Ctr_d10_Rep2


title: WT_DSS_d5_Intestine

description: Library name: WT_DSS_d5_Intestine


title: Q_Baseline_d5_Intestine

description: Library name: Q_Baseline_d5_Intestine


title: T387_shCONT-replicate2

value: Glioblastoma


title: N2 + ad libitum (AL), rep 2

description: Library name: RA2


title: Q_Ctr_d10_Rep1

description: Library name: Q_Ctr_d10_Rep1


title: T387_shCONT-replicate1

value: GSC


title: CPT2 single KO bio rep 3

status: Public on May 02 2025

city: Columbus

first: Gang

last: Xin

state: OH

address: 460 W 12th Ave

department: MI&I

institute: The Ohio State University

data_processing:
bcl2fastq
HISAT2
DESeq2 v1.42.0
Assembly: mm10
Supplementary files format and content: csv file includes raw counts of each sample

source_name: heart

extract_protocol:
RNA was isolated with the PureLink RNA Mini Kit (Thermo Fisher). Genomic DNA was removed from RNA preparations by DNAse digestion using RNase-Free DNase Set (QIAGEN) according to the manufacturer's instructions.
Sequencing libraries were constructed using the Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer's instructions.

value: heart


title: N2 + ad libitum (AL), rep 1

description: Library name: RA1


title: WT_Baseline_d5_Intestine

description: Library name: WT_Baseline_d5_Intestine


title: CPT2/USP30 double KO bio rep2


title: CPT2/USP30 double KO bio rep1


title: CPT2H-KO bio rep 5


title: CPT2H-KO bio rep 3


title: CPT2H-KO bio rep 2


title: CPT2 single KO bio rep 1


title: CPT2/USP30 double KO bio rep3


title: CPT2H-KO bio rep 4


title: CPT2 single KO bio rep 2


title: CPT2H-KO bio rep 1


title: wild type bio rep 5


title: T387_shLBR-1 replicate1


title: wild type bio rep 3


title: Lymp_G4.Lymp.YY.2.2

city: Asahikawa

first: Hiraku

last: Yanada

institute: Asahikawa Medical University

description: Library name: Sample5

data_processing:
Raw reads were trimmed and quality-filtered using Trim Galore! (v0.6.7), Trimmomatic (v0.39), and Cutadapt (v3.7). Trimmed reads were aligned to the GRCh38 human genome using STAR (v2.7.10a). Gene-level counts were generated using featureCounts (v2.0.1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes transcript-level FPKM values for each sample. Tab-delimited text file includes raw gene counts generated by featureCounts.

source_name: Lymph

extract_protocol:
Deparaffinization: Perform 2 rounds of xylene treatment to remove paraffin, followed by washes in 100% ethanol.  Drying & Proteinase K digestion: Dry the pellet, then incubate with digestion buffer containing Proteinase K at 37–56°C for 15 min to 3 h.  RNA isolation: Use a Qiagen RNeasy FFPE Kit to purify RNA.  DNase treatment was performed to remove residual genomic DNA.  Quantification and QC: RNA concentration was measured using NanoDrop, and RNA integrity was assessed using a Bioanalyzer.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit (Clontech, 634442), MGIEasy Universal Library Conversion Kit (App-A) following manufacturer's protocols.

value: Lymph

value: 1st line CBDCA+PEM, 2nd line Sotorasib


title: Lymp_G4.Lymp.YY.2

description: Library name: Sample4


title: wild type bio rep 2


title: wild type bio rep 4


title: Lymp_G4.Lymp.YY.1

description: Library name: Sample3


title: Lung_G3.Lung.YY.2

description: Library name: Sample2

source_name: Lung

value: Lung


title: PBMC, NR, WGS, KAS25

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description: Library name: KAS25_NR_WGS

data_processing:
The sequenced reads were aligned using bwa to cellranger reference GRCh38 (GRCh38-2020-A).
The aligned reads were then processed by freebayes to find variants (-iXu -C 2 -n 3 -E 1 --min-coverage 5 --pooled-continuous).
Assembly: hg38
Supplementary files format and content: vcf files
Library strategy: WGS

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral venous blood via standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation.
The library was constructed using MGIEasy Universal DNA Library Prep Kit v1.0. The experimental process was conducted according to manufacturer's instruction without modification. The final libraries were sequenced on DNBSEQ-G400.

value: PBMC

tag: responsiveness

value: Non responder


title: PBMC, NR, WGS, KAS24

description: Library name: KAS24_NR_WGS

tag: tissue


title: PBMC, NR, WGS, KAS23

description: Library name: KAS23_NR_WGS


title: PBMC, NR, WGS, KAS22

description: Library name: KAS22_NR_WGS


title: PBMC, NR, WGS, KAS21

description: Library name: KAS21_NR_WGS


title: PBMC, NR, WGS, KAS20

description: Library name: KAS20_NR_WGS


title: Lung_G3.Lung.YY.1

description: Library name: Sample1


title: PBMC, NR, WGS, KAS18

description: Library name: KAS18_NR_WGS


title: PBMC, NR, WGS, KAS16

description: Library name: KAS16_NR_WGS


title: Thalamus_sound-exposed mouse

city: Noda

first: Satoka

last: Kasai

state: Chiba

address: 2641, Yamazaki

institute: Tokyo University of Science

hyb_protocol: Hybridization of labelled cRNA was performed on SurePrint G3 Mouse 8x60K ver. 2.0 (Design ID: 074809) using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2600D scanner.

data_processing: Agilent Feature Extraction Software (v 12.0.3.1) was used for background subtraction and LOWESS normalization.

source_name: mouse thalamus, exposed to pain-stimulated sound stress, 4h

label_protocol: Labelled cRNA was synthesised from total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Adult C57BL/6N mice (males, 7 weeks) were obtained from Japan SLC (Shizuoka, Japan), and used for all behavioral and biochemical studies. Mice were housed at the Institute for Experimental Animals, Tokyo University of Science, under standard conditions (23°C ± 1°C; 12-h light/dark cycle, lights on at 8:00 a.m.) in standard mouse cages with sawdust bedding and food and water ad libitum.

extract_protocol: Total RNA was isolated from the thalamus using the RNeasy Lipid Tissue Mini Kit (Qiagen, Netherlands), according to the manufacturer’s recommendations.

treatment_protocol: The thalamus region of the brain was fractionated from mice after 1 day of sound stress exposure for 4h.

tag: gender

value: male

value: thalamus

value: 7-weeks old

source_name: mouse thalamus, control


title: PBMC, R, WGS, KAS14

description: Library name: KAS14_R_WGS

value: Responder


title: PBMC, R, WGS, KAS12

description: Library name: KAS12_R_WGS


title: PBMC, R, TNFi, Post, scRNA, KAS07_KAS08

data_processing:
The sequenced reads were aligned using cellranger count (v7.1.0) to cellranger reference GRCh38 (GRCh38-2020-A).
Aligned files were aggregated with cellranger aggr (v7.1.0; --nosecondary)
Mulitplexed samples were seperated based on individual variants using souporcell, and annotate sample with
Assembly: hg38
Supplementary files format and content: Gene expression matrix

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral venous blood via standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation.
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.1. The experimental process was conducted according to manufacturer's instruction without modification. The final libraries were sequenced on DNBSEQ-G400.

tag: treatment

value: TNFi


title: PBMC, R, TNFi, Post, scRNA, KAS03


title: PBMC, NR, WGS, KAS15

description: Library name: KAS15_NR_WGS


title: wild type bio rep 1

tag: genotype

value: WT


title: PBMC, R, TNFi, Pre, scRNA, KAS06_KAS08


title: PBMC, R, TNFi, Pre, scRNA, KAS02


title: PBMC, R, TNFi, Pre, scRNA, KAS03


title: PBMC, NR, TNFi, Pre, scRNA, KAS24_KAS25


title: PBMC, NR, TNFi, Post, scRNA, KAS24_KAS25


title: PBMC, NR, IL17i, Pre, scRNA, KAS15_KAS16_KAS17


title: PBMC, NR, IL17i, Post, scRNA, KAS15_KAS16_KAS17


title: PBMC, R, TNFi, Pre, scRNA, KAS12_KAS13_KAS14


title: PBMC, R, TNFi, Post, scRNA, KAS12_KAS13_KAS14


title: PBMC, NR, WGS, KAS19

description: Library name: KAS19_NR_WGS


title: PBMC, NR, WGS, KAS17

description: Library name: KAS17_NR_WGS


title: PBMC, R, TNFi, Pre, scRNA, KAS09_KAS10_KAS11


title: PBMC, NR, IL17i, Post, scRNA, KAS04


title: PBMC, NR, TNFi, Post, scRNA, KAS04


title: PBMC, NR, TNFi, Pre, scRNA, KAS04


title: PBMC, NR, IL17i, Post, scRNA, KAS18_KAS19_KAS20


title: PBMC, NR, IL17i, Pre, scRNA, KAS18_KAS19_KAS20


title: PBMC, NR, IL17i, Post, scRNA, KAS21_KAS22_KAS23


title: PBMC, R, WGS, KAS13

description: Library name: KAS13_R_WGS


title: PBMC, NR, IL17i, Pre, scRNA, KAS05


title: PBMC, NR, IL17i, Pre, scRNA, KAS21_KAS22_KAS23


title: PBMC, R, TNFi, Post, scRNA, KAS01


title: PBMC, R, TNFi, Pre/Post, scRNA, KAS06_KAS07

value: TNFi or TNFi_base


title: PBMC, R, TNFi, Pre, scRNA, KAS01


title: PBMC, NR, TNFi, Post, scRNA, KAS05


title: PRV+DEX 1 (mRNA-seq)

city: Chongqing

first: Zhang

last: Chen

address: No. 160 Xueyuan Road, Changyuan Street

institute: Southwest University

data_processing:
HiSeqTM2500/4000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
In order to make samples with different gene lengths, different experiments and different sequencing data volumes comparable, people introduced the concept of FPKM. FPKM (Fragments per kilobase of Exon Model per million mapped reads) is the number of Fragments per thousand base length from a gene in each million reads. FPKM takes into account the effects of sequencing depth and gene length on Reads count, and is the most commonly used method to measure gene expression level at present.HTSeq software was used to analyze the gene expression level of each sample, and the model was UNION. The number of genes and the expression level of individual genes at different expression levels were counted in the results file. In general, the FPKM value of 0.1 or 1 is used as the threshold of gene expression.
There was first normalization of the original Read count, which mainly corrected the sequencing depth. Then, the hypothesis testing probability (P-value) is calculated by statistical model. Finally, multiple hypothesis testing correction (BH) was performed to obtain the FDR value (error detection rate, PADJ is the common form, padJ is used to represent FDR below).
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include FPKM values for each sample .Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

growth_protocol: PC-12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with Nase-free DNase I (Takara, Kusatsu, Japan). Sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® and 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dexamethasone treatment after pseudorabies virus infection


title: PBMC, R, TNFi, Post, CITE, KAS02


title: PRV 2 (mRNA-seq)

value: pseudorabies virus treatment


title: PBMC, NR, TNFi, Pre, scRNA, KAS05


title: PRV+DEX 3 (mRNA-seq)


title: PRV+DEX 2 (mRNA-seq)


title: PBMC, NR, IL17i, Pre, scRNA, KAS04


title: sorted B-cells, scATAC-seq from individual patient WM54

city: New York

first: Gareth

last: Morgan

address: 550 1st Avenue

institute: NYU Langone Health

description:
Library name: WM54-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence

library_source: genomic single cell

data_processing:
ATAC-seq objects were generated from fragment files using ArchR, includng QC, data normalization, batch correction, and identification of single-cell transcription factor motif deviations via chromVAR
Gene expression count matrices were generated using cellranger v5 and processed in R using Seurat v4, including QC, library integration, data normalization, and clustering. Gene expression objects were subsequently integrated into ArchR-derived ATAC-seq objects.
Assembly: Human hg38
Supplementary files format and content: filtered cellrnager outputs (barcodes, features, matrix)
Supplementary files format and content: ATAC-seq fragment files

source_name: bone marrow

extract_protocol:
B-cells were flow sorted from bone marrow by first sorting live cells using Dapi-, and then selecting for B-cells which were CD14-/CD3-/CD19+.
Libraries were pooled as per 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (CG000365 - Rev C).

value: bone marrow

tag: cell type

value: B-cell

value: MYD88 mutated

tag: disease state

value: Waldenstrom macroglobulinemia

tag: subtype

value: PC-like

tag: batch

tag: sampleID


title: sorted B-cells, scATAC-seq from individual patient WM47

description:
Library name: WM47-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence

value: MBC-like


title: sorted B-cells, scATAC-seq from individual patient WM65

description:
Library name: WM65-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: Control 3 (mRNA-seq)

tag: cell line


title: sorted B-cells, scATAC-seq from individual patient WM46

description:
Library name: WM46-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: PRV 3 (mRNA-seq)


title: PRV 1 (mRNA-seq)


title: Control 2 (mRNA-seq)


title: PBMC, R, TNFi, Post, scRNA, KAS09_KAS10_KAS11

value: PBMC


title: sorted B-cells, scRNA-seq from individual patient WM43

description:
Library name: WM43-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scRNA-seq from individual patient WM65

description:
Library name: WM65-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scRNA-seq from individual patient WM54

description:
Library name: WM54-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: Control 1 (mRNA-seq)


title: sorted B-cells, scRNA-seq from individual patient WM25

description:
Library name: WM25-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scATAC-seq from individual patient WM25

description:
Library name: WM25-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scATAC-seq from individual patient 04-006

description:
Library name: 04-006-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scRNA-seq from individual patient WM46

description:
Library name: WM46-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scRNA-seq from individual patient 04-006

description:
Library name: 04-006-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scATAC-seq from individual patient 04-003

description:
Library name: 04-003-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scATAC-seq from individual patient WM43

description:
Library name: WM43-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scRNA-seq from individual patient 01-190

description:
Library name: 01-190-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scATAC-seq from individual patient 01-190

description:
Library name: 01-190-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scRNA-seq from individual patient 01-163

description:
Library name: 01-163-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scATAC-seq from individual patient 01-163

description:
Library name: 01-163-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scRNA-seq from individual patient 01-131

description:
Library name: 01-131-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: sorted B-cells, scATAC-seq from individual patient 01-076

description:
Library name: 01-076-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scATAC-seq from individual patient 01-115

description:
Library name: 01-115-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: sorted B-cells, scRNA-seq from individiual patient 01-076

description:
Library name: 01-076-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: SNCAdupl_rep1

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

description: Library name: SNCAdupl_rep1

data_processing:
ATAC-seq FASTQ files were trimmed to 30 bp prior to mapping to hg38 genome with Bowtie2 with default parameters.
HOMER was used to convert aligned reads into ‘‘tag directories’’ for further analysis.
To call peaks, we used HOMER’s findPeaks with “-style factor -size 200 -minDist 200 – L 0 – C 0 -fdr 0.9”. Next, we ran IDR pairwise on ATAC-seq for each condition. We applied Irreproducibility Discovery Rate (IDR) analysis for replicates.
We used DESeq2 using HOMER’s getDIffExpression to identify differential chromatin accessibility with fold change >2 and p-adj <0.05.
Assembly: hg38
Supplementary files format and content: raw counts
Supplementary files format and content: peak file

source_name: fibroblast

extract_protocol:
Approximately 1 × 1,000,000 iPSC-derived neurons were resuspended in 47.5 µl lysis buffer (10mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPA, CA-630 in water) at RT.
After the addition of 2.5 µl DNA enzyme I (Illumina), cells were incubated at 37°C for 30 min. DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research), eluted with 11 µl of elution buffer, and amplified using NEBNext High-fidelity 2× PCR MasterMix (New England BioLabs) with the Nextera primer Ad1 (1.25µM) and a unique Ad2.n barcoding primer (1.25µM) for 8-10 cycles. The resulting libraries were size selected by gel excision to 165-250 bp, purified, and single end sequenced using a NovaSeq 6000 (Illumina) sequencer for 51 cycles according to the manufacturer’s instructions.

value: fibroblast

value: IPSC

value: iPSC-derived dopaminergic neurons

value: SNCA isogenic


title: SNCAiso_rep3

description: Library name: SNCAiso_rep3

value: SNCA duplication


title: SNCAiso_rep4

description: Library name: SNCAiso_4

data_processing:
FASTQ files from RNA-seq experiments were mapped to hg38 using STAR with default parameters. Differentially expressed genes were assessed with DESeq2 (81) at p-adj (adjusted p value) < 0.05 and FC (fold change) > 2 where indicated.
After mapping, tag directories were created using the HOMER command makeTagDirectory.
The gene expression raw counts were quantified by HOMER’s analyzeRepeats command with the option “-condenseGenes -count exons -noadj”.
Differential gene expression was calculated using the HOMER command “getDiffExpression.pl”. TPM (transcript per kilobase million) were quantified for all genes matching accession number to raw counts.
Assembly: hg38
Supplementary files format and content: raw
Supplementary files format and content: TPM

extract_protocol:
Approximately ~200,000 iPSC-derived neurons were stored in TRIzol. Total RNA was extracted from homogenates and cells using the Direct-zol RNA MicroPrep Kit.
Total RNA was extracted from homogenates and cells using the Direct-zol RNA MicroPrep Kit (Zymo Research R2052) and stored at -80°C until RNA-seq library preparation. mRNAs were enriched by incubation with Oligo d(T) Magnetic beads (NEB, S1419S) in 2× DTBB buffer (20 mM Tris-HCl pH 7.5, 1 M LiCl, 2mM EDTA, 1% lithium dodecyl sulfate, 0.1% Triton X-100) at 65°C for 2 minutes and were incubated at room temperature while rotating for 15 minutes. Beads were washed 1× with RNA Wash Buffer 1 (10mM TrisHCl pH 7.5, 0.15M LiCl, 1mM EDTA, 0,1% lithium dodecyl sulfate 0.1% Triton X-100) and 1× with RNA Wash Buffer 3 (10mM Tris-HCl pH 7.5, 0.15 M NaCl, 1mM EDTA) before elution in RNA Elution Buffer (10mM Tris-HCl pH 7.5, 1mM EDTA) at 80°C for 2 minutes. PolyA selection was performed a second time, and samples were washed 1× with Wash Buffer 1, 1× with Wash Buffer 3, and 1× with 1× SuperScript III first-strand buffer. Beads were resuspended in 10 µL 2× SuperScript III buffer plus 10 mM DTT, and RNA was fragmented at 94°C for 9 minutes and immediately chilled on ice before the next step. For first-strand synthesis, 10 µL of fragmented mRNA, 0.5 µL Random primers (50 µM) (Thermo Fisher), 0.5 µL SUPERase-In (Ambion), 1µL dNTPs (10mM), and 1µL of DTT (10mM) were heated for 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100mM), 0.1 µL Actinomycin D (2µg/uL), 0.2uL of 1% Tween-20 (Sigma) and 0.5µL of SuperScript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 1 minute, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to the manufacturer’s instruction and eluted with 10 µL nuclease-free wate. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL RNase H (5U/uL), 1.05 µL of water, 1µL of DNA Polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C overnight. The following day, the dUTP marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to a final concentration of 13% PEG, eluted with 40 µL elution buffer (DNA elution buffer from Zymo ChIP Clean and Concentrator Kit). The purified dsDNA underwent end repair by blunting, A-tailing, and adaptor ligation as previously described (79) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR amplified for 16 cycles, size for 200-500bp size range, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a NovaSeq 6000 for 51 cycles according to the manufacturer’s instructions.


title: SNCAiso_rep2

description: Library name: SNCAiso_rep2


title: sorted B-cells, scRNA-seq from individual patient 01-115

description:
Library name: 01-115-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: SNCAdupl_rep4

description: Library name: SNCAdupl_rep4


title: SNCAdupl_rep3

description: Library name: SNCAdupl_rep3


title: SNCAiso_rep1

description: Library name: SNCAiso_rep1


title: SNCAiso_rep1

description: Library name: SNCAiso_1


title: SNCAiso_rep2

description: Library name: SNCAiso_2


title: SNCAdupl_rep3

description: Library name: SNCAdupl_3


title: SNCAdupl_rep4

description: Library name: SNCAdupl_4


title: SNCAiso_rep3

description: Library name: SNCAiso_3


title: sorted B-cells, scRNA-seq from individual patient 04-003

description:
Library name: 04-003-RNA
3' mRNA; read 1 contains cell barcode and UMI and read 2 contains transcript sequence


title: SNCAdupl_rep2

description: Library name: SNCAdupl_2


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 8

city: Guangzhou

first: Shangxin

state: Guangdong

address: No. 651 Dongfeng East Road, Yuexiu District, Guangzhou Province, China

institute: Sun Yat-Sen University Cancer Center

description:
Library name: TLS-9 | 023 | Geometric Segment
FFPE spatial transcriptome sequencing

data_processing:
Raw fastq files were run through the GeoMx NGS pipeline 2.0.0 or 2.2.0.2 to produce DCC files which were uploaded to the DSP instrument. The DCC files produce a raw count matrix that was downloaded from the DSP.
Assembly: GRCh38.p13
Supplementary files format and content: GeoMx_ROI_metadata.xlsx: ROI information
Supplementary files format and content: GeoMx_Hs_CTA_v1.0.pkc: probe metadata

source_name: nasopharyngeal carcinoma tissue

extract_protocol:
On average, 4 μm-thick FFPE sections were cut and placed on a silde as tissue microarray.
TMA sections are deparaffinized, then heated in ER2 solution (provided by Leica) at 100°C for 20 minutes. Subsequently, they are treated with 1 µg/ml of proteinase K (from Ambion) at 37°C for 15 minutes using a BOND RXm autostainer (Leica). Following this, an overnight in situ hybridization is conducted as described, utilizing a final probe concentration of 4 nM per probe. After preparation, the slides are stained with immunofluorescent antibodies to aid in identifying tissue morphology. Specifically, pan-cytokeratin is used to label epithelial cells, CD45 for immune cells, CD20 for B cells, and SYTO13 for DNA staining. These stained slides are then loaded onto a GeoMx instrument for scanning. For each tissue core, a circular region of interest (ROI) measuring 500 μm in diameter is selected. Post-selection, a pathologist (M.R.) annotates each ROI to estimate the content of tumor cells, T cells, and B cells (%). Libraries were constructed with Nanostring DSP reagents and in accordance with the Illumina GeoMx library preparation protocol.

value: nasopharyngeal carcinoma tissue


title: SNCAdupl_rep1

description: Library name: SNCAdupl_1


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 7

description:
Library name: TLS-9 | 021 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 6

description:
Library name: TLS-9 | 020 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: TLS-9 | 019 | Geometric Segment
FFPE spatial transcriptome sequencing


title: sorted B-cells, scATAC-seq from individual patient 01-131

description:
Library name: 01-131-ATAC
ATAC; read 1 contains cell barcode and UMI and read 2 contains ATAC sequence


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: TLS-9 | 017 | Geometric Segment
FFPE spatial transcriptome sequencing


title: SNCAiso_rep4

description: Library name: SNCAiso_rep4


title: NPC-19, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: TLS-9 | 014 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: TLS-9 | 015 | Geometric Segment
FFPE spatial transcriptome sequencing


title: SNCAdupl_rep2

description: Library name: SNCAdupl_rep2


title: NPC-19, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: TLS-9 | 013 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: TLS-9 | 016 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-19, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: TLS-9 | 012 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-19, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: TLS-9 | 011 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN-21, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: TLS-9 | 004 | Geometric Segment
FFPE spatial transcriptome sequencing

source_name: chronic nasopharyngitis tissue

value: chronic nasopharyngitis tissue


title: NPC-14, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: TLS-9 | 006 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-14, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: TLS-9 | 007 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN-21, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: TLS-9 | 003 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN-21, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: TLS-9 | 002 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN-21, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: TLS-9 | 001 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN06, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: MIPCC-DSP-20201224B-02 | 021 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-14, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: TLS-9 | 009 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN06, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: MIPCC-DSP-20201224B-02 | 020 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-14, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: TLS-9 | 005 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-19, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: TLS-9 | 010 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-14, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: TLS-9 | 008 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC02, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: MIPCC-DSP-20201224B-02 | 019 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC04, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 6

description:
Library name: MIPCC-DSP-20201224B-02 | 016 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC08, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201224B-02 | 018 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC03, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: MIPCC-DSP-20201224B-02 | 015 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC02, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: MIPCC-DSP-20201224B-02 | 014 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC08, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201224B-02 | 011 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN06, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: MIPCC-DSP-20201224B-02 | 007 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC-21, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: TLS-9 | 018 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC07, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201224B-02 | 010 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN05, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 6

description:
Library name: MIPCC-DSP-20201224B-02 | 006 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN05, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: MIPCC-DSP-20201224B-02 | 005 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC03, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: MIPCC-DSP-20201224B-02 | 003 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN05, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: MIPCC-DSP-20201224B-02 | 004 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC01, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: MIPCC-DSP-20201019B-04 | 020 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC04, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 5

description:
Library name: MIPCC-DSP-20201224B-02 | 002 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC04, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 4

description:
Library name: MIPCC-DSP-20201224B-02 | 001 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC01, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201019B-04 | 019 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN06, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201019B-04 | 006 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC01, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201019B-04 | 016 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN06, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201019B-04 | 005 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN05, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201019B-01 | 022 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC03, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201019B-01 | 015 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC02, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201019B-01 | 007 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN05, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201019B-04 | 001 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC02, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: MIPCC-DSP-20201019B-01 | 008 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC03, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: MIPCC-DSP-20201019B-01 | 016 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC04, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 2

description:
Library name: MIPCC-DSP-20201019B-01 | 018 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC04, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: MIPCC-DSP-20201019B-01 | 019 | Geometric Segment
FFPE spatial transcriptome sequencing


title: CN05, chronic nasopharyngitis tissue, PanCK-CD45+CD20+ ROI biol rep 3

description:
Library name: MIPCC-DSP-20201019B-04 | 002 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC02, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201019B-01 | 005 | Geometric Segment
FFPE spatial transcriptome sequencing


title: NPC03, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201019B-01 | 013 | Geometric Segment
FFPE spatial transcriptome sequencing


city: Singapore

first: Cheng Gee

last: Koh

state: Singapore

address: 60, Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
Library name: F6_2
MDA-MB-231 cells, Compressed 386.5 Pa biological replicate 6

data_processing:
We carried out low-counts filtering, count normalization using the trimmed mean of M-values (TMM) method and log2-transformed the counts per million (CPM) values in edgeR version 3.40.2 (Robinson et al., 2009). Since UMAP projections of the principal components (PCA-UMAP) indicated mild batch effects, batch correction was performed using removeBatchEffect function in limma version 3.54.2 (Ritchie et al., 2015) on the log-CPM values, where the batch variable was specified as the biological replicate
Differential expression analysis was done using limma with voom transformation (Law et al., 2014) to obtain log2-fold changes (LFCs) for RCU2 versus RCU0, RCU1 versus RCU0 and RCU0.5 versus RCU0.
Over-representation analysis (ORA) was done with pre-defined gene sets in gprofiler2 version 0.2.1 (Kolberg et al., 2020), on a subset of differential genes which fulfilled the criteria of having an absolute LFC higher than or equal to 1.5, and an adjusted p-value of <=0.05.
Gene sets with Benjamini–Hochberg false discovery rate (FDR) below 0.05 were deemed as significantly enriched.
To determine the direction of regulation of these enrichments, LFCs were sorted into ranked gene lists for gene set enrichment analysis (GSEA) implemented in clusterProfiler version 4.6.2 (Wu et al., 2021), using only the significant gene sets. A positive normalized enrichment score (NES) would indicate upregulation of the gene set and vice versa for a negative NES.
Assembly: Genome indexes were generated using STAR version 2.7.9a (Dobin et al., 2013) with the comprehensive Gencode v39 gene annotation. Raw paired-end FASTQ reads were aligned to the human reference genome GRCh38 and then quantified using STAR aligner (Dobin et al., 2013)
Supplementary files format and content: Tab-delimited text files include raw counts per sample.
Supplementary files format and content: Csv file contained combined raw counts of the samples.

growth_protocol: MDA-MB-231 cells were maintained in DMEM high glucose supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Qiagen RNEasy mini kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Triple Negative Breast Cancer Cell Line

value: WT

value: 386.5 Pa compression


description:
Library name: F6_3
MDA-MB-231 cells, Compressed 773 Pa biological replicate 6

value: 773 Pa compression


description:
Library name: F6_1
MDA-MB-231 cells, Uncompressed 0 Pa biological replicate 6

value: Uncompressed


description:
Library name: F6_4
MDA-MB-231 cells, Compressed 1546 Pa biological replicate 6

value: 1546 Pa compression


description:
Library name: F5_4
MDA-MB-231 cells, Compressed 1546 Pa biological replicate 5


description:
Library name: F5_3
MDA-MB-231 cells, Compressed 773 Pa biological replicate 5


description:
Library name: F5_2
MDA-MB-231 cells, Compressed 386.5 Pa biological replicate 5


description:
Library name: F5_1
MDA-MB-231 cells, Uncompressed 0 Pa biological replicate 5


description:
Library name: F4_4
MDA-MB-231 cells, Compressed 1546 Pa biological replicate 4


description:
Library name: F4_3
MDA-MB-231 cells, Compressed 773 Pa biological replicate 4


description:
Library name: F4_1
MDA-MB-231 cells, Uncompressed 0 Pa biological replicate 4


description:
Library name: F3_3
MDA-MB-231 cells, Compressed 773 Pa biological replicate 3


description:
Library name: F3_4
MDA-MB-231 cells, Compressed 1546 Pa biological replicate 3


description:
Library name: F4_2
MDA-MB-231 cells, Compressed 386.5 Pa biological replicate 4


description:
Library name: F3_2
MDA-MB-231 cells, Compressed 386.5 Pa biological replicate 3


description:
Library name: F3_1
MDA-MB-231 cells, Uncompressed 0 Pa biological replicate 3


description:
Library name: F2_2
MDA-MB-231 cells, Compressed 386.5 Pa biological replicate 2


description:
Library name: F2_3
MDA-MB-231 cells, Compressed 773 Pa biological replicate 2


description:
Library name: F1_4
MDA-MB-231 cells, Compressed 1546 Pa biological replicate 1


description:
Library name: F1_3
MDA-MB-231 cells, Compressed 773 Pa biological replicate 1


description:
Library name: F1_1
MDA-MB-231 cells, Uncompressed 0 Pa biological replicate 1


description:
Library name: F1_2
MDA-MB-231 cells, Compressed 386.5 Pa biological replicate 1


title: NPC04, nasopharyngeal carcinoma tissue, PanCK-CD45+CD20+ ROI biol rep 1

description:
Library name: MIPCC-DSP-20201019B-01 | 003 | Geometric Segment
FFPE spatial transcriptome sequencing


title: AML34_NUP98r

city: Vienna

first: Kaan

last: Boztug

state: Vienna

address: Zimmermannplatz 10

institute: St. Anna Children's Cancer Research Institute

description: ATAC-seq

data_processing:
Sequencing adapter trimming and initial filtering with fastp ver 0.20.1
Alignment with bowtie 2 ver 2.4.4 to GRCh38 using the --very-sensitive parameter
PCR duplicate marking with samblaster ver 0.1.24
Sorting and filtering based on ENCODE blacklisted regions (PMID: 31249361) with samtools ver 1.12.
Indexing using samtools ver 1.12.
Peak calling using MACS2 v2.2.7.1 with flags --nomodel --keep-dup auto --extsize 147
workflow can be found at: https://zenodo.org/records/13763301
Assembly: GRCh38
Supplementary files format and content: Peak files in BED format generated with MACS2

source_name: Bone marrow

growth_protocol: Fresh-frozen bone marrow mononuclear cells were rapidly thawed and resuspended in IMDM. Cells were subsequently washed once with PBS. Blasts populations were identified via flow-cytometry using a routine diagnostics panel and subsequently 50.000 blasts were sorted for DNA-isolation and library prepration.

extract_protocol:
We performed DNA-islation and library prepration on 50.000 sorted blasts using the Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina, CA, USA) as described by Shashikant et al. (PMID:  30948010)
Library construction was performed as described in Shashikant et al. (PMID:  30948010)

value: Bone marrow

value: leukemic blast


title: AML55_NUP98r

description: ATAC-seq


title: AML29_NUP98r

description: ATAC-seq


description:
Library name: F2_1
MDA-MB-231 cells, Uncompressed 0 Pa biological replicate 2


title: AML93_ETV6

description: ATAC-seq


title: AML06_NUP98r

description: ATAC-seq


title: AML12_NUP98r

description: ATAC-seq


title: AML17_NUP98r

description: ATAC-seq


title: AML43_NK

description: ATAC-seq

value: normal karyotype


title: AML31_BCRABL1

description: ATAC-seq


title: AML24_UBTF

description: ATAC-seq

value: trisomy 8, UBTF


title: AML65_KMT2Ar

description: ATAC-seq


title: AML23_KMT2Ar

description: ATAC-seq


title: AML81_other

description: ATAC-seq

value: other


title: AML28_NK

description: ATAC-seq


description:
Library name: F2_4
MDA-MB-231 cells, Compressed 1546 Pa biological replicate 2