title: WT Sperm WGA DNA (SMRT seq)

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

description: SMRT-seq

data_processing:
Subreads were mapped to the Marchantia (v5.1) genome using pbmm2 (v1.1.0). Base modifications were detected using ipdSummary (v2.0) with the following flags set (--identify 4mC --methylFraction). For 5mCG analysis, circular consensus reads were generated with ccs (v6.4) using the “—hifi-kinetics” option to generate consensus kinetics tags, and primrose (v1.3) was used to predict 5mC modification of each CG motif and generate base modification (“MM”) and base modification probability (“ML”) BAM tags. Pileup-based consensus methylation sites and probabilities were generated by the script “aligned_bam_to_cpg_scores.py” from pb-CpG-tools (v1.1.0) with the “-q 1 -m reference -p model -c 10” options.
Assembly: MpTak1v5.1
Supplementary files format and content: gff files
Library strategy: SMRT-seq

organism: Marchantia polymorpha subsp. ruderalis

source_name: Sperm

growth_protocol: Plants were grown on plates containing 1/2× Gamborg’s B5 medium with 1% agar (Sigma) under constant light at 21 °C. Plants were transferred to jiffy pellets after 2 weeks on plates and placed in a growth chamber at 21 °C with 70% humidity under constant light with far-red irradiation for induction of sexual reproduction, as described previously (Chiyoda et al., 2008).

extract_protocol:
Sperm were isolated as described previously (Schmid et al., 2018; Higo et al., 2016). Sperm DNA was extracted as described (Healey et al., 2014).
Native WT and Mpdn4mt1-1 mutant sperm libraries for SMRT-seq were prepared using the SMRTbell Express Prep kit (v2.0; Pacific Biosciences, Menlo Park, CA, USA) following the low DNA input workflow as described (Kingan et al., 2019). Whole genome amplified libraries were also constructed, utilizing the SMRTbell gDNA Sample Amplification Kit (Pacific Biosciences, Menlo Park, CA, USA). Libraries were sequenced under CCS running mode (one Sequel II SMRT Cell for each native library and one Sequel II SMRT Cell for the amplified libraries) via DNA Link (Seoul, Korea).

treatment_protocol: No special treatment was given.

tag: 4mc/5mc spike_added

value: No

value: Sperm

value: WT

value: Whole Genome Amplified


title: Elp1_MUT_Ptch1_tumor_S1

status: Public on Apr 09 2025

type: SRA

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: 3181756_Patch_ELP1_mut_1

library_source: transcriptomic single cell

data_processing:
barcoded processing, gene counting and aggregation were made using the STARsolo (v2.7.3a)
Assembly: mm10
Supplementary files format and content: Tab-separated files

molecule: nuclear RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
Single cells from developing mouse cerebellar tissue were processed using the microfluidics-based 10x Chromium protocol, according to manufacturer instructions
mouse cerebellar tissue  were isolated and processed using the 10x Chromium technology

tag: tissue

value: tumor

tag: genotype


title: Fsk-oeGFP

type: RNA

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

country: Japan

institute: Doshisha University

description: Gene expression data from B16F10 cells transfected with GFP expression plasmid and treated with forskolin

hyb_protocol: Following fragmentation, 2 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000-7G.

data_processing: The data were analyzed with Expression console  (Build 1.4.1.46) using Affymetrix default analysis settings and RMA scaling as normalization method.

label: biotin

molecule: total RNA

label_protocol: Biotinated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Ambion WT expression kit and Gene Chip WT Terminal Labeling and Hybridization Kit Manual, Affymetrix).

growth_protocol: B16F10 cells were cultured in DMEM supplemented with 10% FBS, 40 μg/ml streptomycin, and 40 units/ml penicillin.

extract_protocol: ISOGEN II extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: B16F10 cells were co-transfected with plasmid DNA and  puromycin resistant vector, and then selected with puromycin. Each stable cells were treated with forskolin for 5 days, and then total RNA were extracted.

value: GFP expression

tag: cell type

value: Mouse cell line derived from melanoma

tag: cell line


title: al7m_H3_ChIP_rep2

city: Cambridge

last: Harris

address: Downing Street

department: Department of Plant Sciences

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
The reads were aligned to the TAIR10 reference genome using Bowtie2 (version 2.5.3), the duplicated reads were removed by Samtools (version 1.19.2). Deeptools (version 3.5.5) was used to generate the tracks using RPGC for normalization. As there were few differences between the biological replicates in all ChIPs, we merged the biological replicates for downstream analysis. The IGV genome browser was used to visualize the data. MACS2 (version 2.2.9.1) was used for peak calling and differential peaks were identified by DiffBind in R. Peaks were annotated by ChIPseeker in R. Deeptools was used to generate the metaplots and heatmaps.
Assembly: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: The arabidopsis seeds were either grew on 1/2 MS plates for 15 days or directly on soil under LD conditions (16 h light and 8 h dark at 22 °C)

extract_protocol:
ChIPs were performed as previously described(Harris et al., 2024) https://doi.org/10.7554/eLife.89353.2. Cells were fixed in vitro with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin wea sonicated by a Diagenode Bioruptor Plus Sonicator.
Libraries were generated with NuGen Ovation Ultra Low System V2 kits following the manufacturer’s instructions.

value: seedling

tag: chip antibody

value: anti-H3 (ab1791, Abcam)


title: Eosinophils, D02_NT_008

city: San Diego

first: Gregory

last: Seumois

state: CA

address: 9420 Athena Cir, La Jolla

institute: La Jolla Institute for immunology

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ-lite v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5)  and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: count matrix with rows as genes and columns as samples

organism: Homo sapiens

source_name: Eosinophils, No Treatment (NT)

growth_protocol: We used primary cell eosinophils isolated directly from blood - No growth procedure was applied

extract_protocol:
At the end of incubation, cells were washed once with 10 ml of PBS (Phosphate Buffer Saline (pH 7.4) and centrifuged at 400 x g for 5 minutes at 4 ˚C. Supernatant was discarded and cell pellet immediately resuspended in 1 ml of Quiazol cell lysis solution (Quiagen). Cell were lysed following the steps described in Rosales et al ,2018 and stroed at - 80 ˚ C till completion of the study and sample collection. RNA extraction was performed unsing miRNAeasy Kit as recommended by manufacterer including DNAse I treatment. Quality of RNA was assess by capillary electrophoresis (Fragment Analyzer), and quantified by qPCR for B2M gene, a stable house keeping gene (Rosales et al. 2018). Tot RNA was stored in -80 ˚C.
Roughly 10 nanograms of purified RNA was amplified according to the Smart-seq2 protocol (Picelli et al. 2023, Rosales et al. 2018). Using poly-dT oligos, mRNA was captured and reverse transcribed into full-length cDNA. The cDNA was then amplified by PCR for 13 cycles. It was then purified using AMPure XP magnetic beads with a 0.8:1 ratio (Beckman Coulter) by an automated platform (Epimotion5075, Eppendorf). Next, 500 picograms of cDNA was used to prepare NextEra XT sequencing libraries with dual indexing(NextEra XT DNA Library Prep Kit # FC-131-1096 and IDT 8bp UDI Index Kits for illumina ).  Whole-transcriptome and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine cDNA quality and quantity as well as to optimize the number of PCR cycles needed, and fragment size. The libraries which passed quality control were pooled and sequenced on the Illumina Sequencing Novaseq6000 platform. Libraries were sequenced to a depth of roughly > 8 million 100 x 100 bp Pair-ended reads per sample (Novaseq XP 4-lane kit v1.5; Illumina).
RNA-seq 100 x 100 Paired-end sequencing reads

treatment_protocol: Eosinophils were isolated from blood using magnetic negative selection following the protocol outlined in Akuthota et al. (2012) and cultured at a concentration of 1 million cells/ml in conditioned culture medium for 48 hours at 37°C with 5% CO2.  Four different conditioned culture media were employed, including a negative control (NT) composed of RPMI1640 supplemented with 10% fetal bovine serum, human recombinant Interleukin-5 (IL-5) at 1 ng/ml, penicillin (500 ng/ml), and streptomycin (500 ng/ml). The remaining three conditioned culture media were "vaped" according to the procedure by Corriden et al. (2020) and supplemented with 10% fetal bovine serum, human recombinant Interleukin-5 (IL-5) at 1 ng/ml, penicillin (500 ng/ml), and streptomycin (500 ng/ml) right before to use. Three E-cigarette vapor extract conditioned media were prepared: EB medium composed solely of RPMI 1640, EVE+ containing "vaped" propylene glycol (PEG) and glycerin (Gly) in a 70:30 vol:vol ratio with nicotine at 59 mg/ml, and EVE– lacking nicotine. Preparation involved the vaping of e-Cigarette loading liquid containing PEG/Gly with or without nicotine, collecting the vapor into RPMI 1640 culture medium, and filtering the conditioned media for sterility using a 0.22 µm Millex-MP disposable polyethersulfone syringe filter (Millipore) before storage at -80°C.

value: Blood

value: primary cell

value: Eosinophil

tag: donor

tag: Sex

value: Male

tag: treatment

value: NoTreatment


title: Fsk-oeNrf3

description: Gene expression data from B16F10 cells transfected with NRF3 expression plasmid and treated with forskolin

value: Nrf3 expression


title: CAR-IL-15 iNK, rep 3

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

description: Library name: CARIL15iNK3

data_processing:
Reads of the samples were trimmed for adapters quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR. The average mapping rate of all samples was 95%. Unique alignment was above 90%. There were 3.33 to 4.82% unmapped reads. The mapping statistics were calculated using Picard software. The samples had 0.47% ribosomal bases. Percent coding bases were between 42-51%. Percent UTR bases were 31-33%, and mRNA bases were between 74-83% for all the samples. Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples had 70-75% non-duplicate reads. The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: iPSC-NK

extract_protocol:
Total RNA was isolated from NK cells using TRIzol reagent according manufacturer’s guide (Invitrogen).
Ligation-based library preparation was performed using Illumina stranded mRNA ligation kit according manufacturer’s guide.

value: iPSC-NK

tag: condition

value: freshly differentiated

value: CAR-IL15 transfected


title: CARJ-Ramos, scRNA-seq

city: Hangzhou

first: Juan

last: Wei

state: Zhejiang

address: 150 Dongfang Rd

country: China

institute: Hangzhou Institute of Medicine, CAS

description: 10x Genomics

data_processing:
scRNA data was processed using standard Cellranger workflow with hg38 reference, tag sequences were manually aligned and counted from fastq data with allowed variation of at most 3 bases
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RMPK for each sample

molecule: polyA RNA

source_name: Ramos and CD19 CAR-Jurkat

growth_protocol: Ramos and CD19 CAR-Jurkat cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum and antibiotics at 37 ℃ under 5% CO2

extract_protocol:
Single-cell suspensions were loaded to 10x Chromium to capture 9000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3) .
cDNA was amplified by PCR for 13 cycles and then subjected to size separation by 8% PAGE electrophoresis into >600 nt fragments containing cDNAs reversely transcripted from cellular mRNAs and <300 nt fragments containing barcoded ssDNA labels. The two cDNA fragments were separately converted into sequencing libraries and merged at a desired ratio (50% for ssDNA labels and 50% for cellular cDNA library).

treatment_protocol: CAR-J cells and Ramos cells were separately modified with tyrosinase and phenol groups to serve as bait and prey cells. Then, the two cells were mixed at 1:1 and cocultured with amine-ssDNA barcodes at 37 °C for 30 min. After stringent PBS washing, the cells with barcoded DNA tagging were profiled by scRNA-seq.

value: Ramos and CD19 CAR-Jurkat

value: Lymphocyte

value: Ramos (WT) and Jurkat (CD19 CAR-transduced)


title: WT Sperm (SMRT seq)

description: SMRT-seq

data_processing:
Library strategy: SMRT-seq
For BS-seq, low-quality reads and potential adaptor sequence were first trimmed using TrimGalore version 0.4.2 with default parameters. DNA methylation analysis was performed by using miniature-sniffle-mapper (https://github.com/martinjvickers/miniaturesniffle-mapper), which is based on Bismark (Krueger and Andrews, 2011), but with the additional ability to map ambiguous reads.  Methylation data was mapped to the Marchantia chromosome assembly v5.1 (Montgomery et al., 2020) as well as to the pUC19 vector sequence and lambda cl857 genome where appropriate.
For RNA-seq, low-quality reads and potential adaptor sequence were first trimmed using  TrimGalore version 0.4.2 with default parameters. RNA-seq reads were processed into kallisto version 0.43.0 and sleuth package version 0.30.0.
For SMRT seq, subreads were mapped using pbmm2 (v1.1.0) and base modifications were detected using ipdSummary (v2.0)
Genome_build: MpTak1v5.1
Supplementary_files_format_and_content: gff files (BS-seq and SMRT seq). HDF5 binary file, plaintext files, json files (RNA-seq)

source_name: WT Sperm

extract_protocol: WT and dn4mt mutant sperm libraries for SMRT sequencing were prepared using the SMRTbell Express Prep kit v2.0 (Pacific Biosciences, Menlo Park, CA, USA) following the low DNA input workflow as described (Kingan et al., 2019). Libraries were sequenced under CCS running mode with one Sequel II SMRT Cell for each library via DNA Link (Seoul, Korea).

tag: 4mc/5mc spike added

value: No

value: Sperm

value: WT


title: al7m_H3K4me3_ChIP_rep2

value: seedling

value: anti-H3K4me3 (ab8580, Abcam)


title: Ramos, siTNFRSF17, rep3

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website. Then, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM for each sample

source_name: Ramos

growth_protocol: Ramos cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum and antibiotics at 37 ℃ under 5% CO2

extract_protocol:
RNA was extracted using a FastPure cell/tissue total RNA isolation kit (Vazyme). 1 μg total RNA was used for library preparation
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: Ramos cells were harvested and seeded in 6-well plates and kept culturing for 24 h. Next, the cell culture media were replaced with FBS-supplemented RPMI 1640 media without penicillin and streptomycin, and each well was added with transfection reagent (Lipofectamine™ 3000) and mock/TNFRSF17 siRNA solution (diluted by Opti-MEM, final concentration: 30 nM). After incubation at 37 °C for 6 h, the cell supernatants were discarded and replaced with fresh complete cell culture media.

value: Ramos

value: B lymphocyte

value: TNFRSF17 knockdown

value: TNFRSF17 siRNA


title: al7m_H3K4me3_ChIP_rep1


title: CAR-IL-15 iNK, rep 1

description: Library name: CARIL15iNK1


title: Mpdn4mt1-1 knockout Sperm WGA DNA (SMRT seq)

description: SMRT-seq

value: Mpdn4mt1-1 double knockout

value: Whole Genome Amplified


title: CAR-IL-15 iNK, rep 2

description: Library name: CARIL15iNK2

value: iPSC-NK


title: Ramos, siTNFRSF17, rep1


title: Ramos, siTNFRSF17, rep2


title: Mock iNK, rep 3

description: Library name: MockiNK3

value: freshly differentiated


title: al7m_H2AZ_ChIP_rep2

value: anti-H2A.Z (AS10718, Agrisera)


title: al7m_H2AZ_ChIP_rep1


title: Mock iNK, rep 2

description: Library name: MockiNK2


title: Eosinophils, D03_EVEN_029

source_name: Eosinophils, E-cig vapor extract with PEG and Glycerin, no nicotine (EVEneg)

value: Blood

value: primary cell

value: Eosinophil

value: Female

value: EVEneg


title: Ramos, siControl, rep2

value: WT

value: mock siRNA


title: Mock iNK, rep 1

description: Library name: MockiNK1


title: dn4mt knockout Sperm (SMRT seq)

description: SMRT-seq

source_name: dn4mt knockout Sperm

value: No

value: Sperm

value: dn4mt double knockout


title: VC1mM_6

city: Kizugawa

first: Akari

last: Kuwano

state: Kyoto

address: 6-5-4 Kunimidai

institute: Rohto Pharmaceutical Co., Ltd.

description: Gene expression data of human keratinocyte 3D cultured skin with VC addition

hyb_protocol: Labelled cDNA samples were prepared from total RNA using a GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.) according to the manufacturer’s instructions and then hybridized to human Clariom D arrays and human microarrays (Thermo Fisher Scientific, Inc.)

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000 7G instrument (Thermo Fisher Scientific, Inc.), and the data were obtained using GeneChip Command Console software (AGCC, version 4.0).

data_processing:
Raw data were normalized by signal space transformation robust multi-chip analysis (SST-RMA) algorithm ormalization and quality checks such as labelling and hybridization were performed using Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific, Inc.). In addition, PCA, HCA, and the generation of scatter plots and volcano plots were carried out using TAC 4.0 software. GSEA was performed using GSEA software version 4.1.062
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_D_Human
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

source_name: cultured human epidermal equivalent

growth_protocol: Normal human epidermal keratinocytes (#420811D) were purchased from Japan Tissue Engineering Co., Ltd. (Aichi, Japan). Cryopreserved keratinocytes were thawed and suspended in cAssayulture  mMedium containing fetal bovine serum (#402250, Japan Tissue Engineering Co., Ltd.). Cell aliquots were seeded into 24-well culture inserts (Corning Co., Ltd., NY, USA) placed in multiwell culture plates in which each well had been filled with 1.5 mL of culture medium and incubated in a humidified atmosphere of 5% CO2 at 37°C. Keratinocytes seeded in the culture inserts were submerged when the medium was present in the inserts. After 24 h of incubation, the keratinocytes were exposed to the air‒liquid interface to construct an epidermal equivalent by removing the both medium in the 24-well culture inserts and multiwell culture plates

extract_protocol: Total RNA was extracted from a half portion of human epidermal equivalents treated with or without 1.0 mM VC for 14 days using an miRNeasy Mini Kit (Qiagen, Inc.) according to the manufacturer’s instructions.

treatment_protocol: Human epidermal equivalents treated with or without 1.0 mM VC for 14 days

value: human epidermal keratinocyte

value: with VC addition


title: VC1mM_5

label_protocol: Labelled cDNA samples were prepared from total RNA using a GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.) according to the manufacturer’s instructions and then hybridized to human Clariom D arrays and human microarrays (Thermo Fisher Scientific, Inc.)


title: Ramos, siControl, rep3

value: Ramos

value: B lymphocyte


title: Col_FLAG_ChIP_rep2

source_name: whole plant

value: whole plant

value: anti-FLAG M2 (F1804, Sigma-Aldrich)


title: Ramos, siControl, rep1


title: PBNK, donor 3

description: Library name: PBNK3

source_name: peripheral blood NK cell

value: peripheral blood NK cell

value: freshly isolated from healthy donor


title: Col_FLAG_ChIP_rep1


title: AL5_FLAG_ChIP_rep2


title: al7m_H3_ChIP_rep1

value: seedling

value: anti-H3 (ab1791, Abcam)


title: VC1mM_2


title: PBNK, donor 2

description: Library name: PBNK2


title: VC1mM_3


title: old_10

city: Panania

first: Benjamin

middle: John

last: Hunter

state: NSW

address: 118 Horsley Rd

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

description: Pre-mortem

data_processing:
The quality of each RNA sequence (reversely stranded) was assessed using ShortRead. The raw sequences were aligned on hg38 genome assembly (UCSC) with Rsubread version 2.2.1. The alignment was performed on pair-end sequences without trimming. Rsubread was also used for generating the gene count matrix. The gene counts were converted in Count Per Million (CPM), log2 transformed, and then normalised using Voom.
Assembly: The raw sequences were aligned on hg38 genome assembly (UCSC) with Rsubread version 2.2.1.
Supplementary files format and content: CSV. Normalised log2 transformed data with associated Entrez IDs and study IDs.

source_name: Left ventricular myocardium

extract_protocol:
Cryopreserved human myocardium was powderised as described in the proteomic MS methods and weighed to approximately 30mg. Powderised myocardium was lysed and homogenised in 500 µL TRIzol (Invitrogen) using steel balls in the TissueLyser LT (Qiagen) and kept on dry ice between cycles (3-5 x 1 minute). 1-bromo-3-chloropopane (50 µL) was added to each sample and left to incubate for 5 minutes at RT, then spun at 14,000 x g at 4°C for 15 minutes to induce phase separation. RNA-containing aqueous phase was transferred to a sterile tube and an equal volume of isopropanol was added, mixed by inverting, and left for 1 hour at RT. RNA was pelleted at 14,000 x g at 18°C for 15 minutes, supernatant discarded. RNA was then washed in 4°C 70% ethanol twice discarding supernatant after spinning at 14,000 x g at 4°C for 10 minutes and left to dry at RT. RNA was DNase treated for 30 minutes at 37°C and washed again. Pelleted RNA was reconstituted in 15 µL 4°C nuclease free diethyl pyrocarbonate (DEPC). Concentration and quality were tested on NanoDrop (Thermo Fisher Scientific) to a standard of 260nm/280nm = 1.8-2.0 and 260nm/230nm 1.7-2.2. RNA integrity was assessed using an RNA Nano Chip on an Bioanalyzer (Agilent).
RNA-seq libraries were prepared with Illumina Stranded Total RNA prep Ligation with Ribo Zero Plus (100ng input and 11 PCR cycles) according to manufacturer’s instructions. Quality checks were performed using the Qubit dsDNA High Sensitivity Assay Kit and the Revvity LabChip GX Touch. The final sequencing pool was quantified using the Qubit dsDNA High Sensitivity Assay Kit after pooling all libraries equimolar into a single library pool. Sizing was checked using the Agilent High Sensitivity D1000 Tapestation system. The RNA-seq libraries were sequenced using a paired-end 250bp kit on a S4 flow cell of the Illumina NovaSeq 6000 with a final run concentration of 58pM and 1% PhiX.

value: Left ventricular myocardium


title: old_7

description: Pre-mortem


title: VC0mM_6

description: Gene expression data of human keratinocyte 3D cultured skin without VC addition

value: without VC addition


title: VC1mM_1


title: VC1mM_4


title: old_9

description: Pre-mortem


title: 19_ABD_RNA_seq

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 19

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous adipose tissues

extract_protocol:
RNA was extracted with Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen #74804)
Library prepration and sequencing was performed by GENEWIZ

value: subcutaneous adipose tissues

value: male

tag: bmi

tag: whr

tag: race

value: African American

tag: age


title: ChiPSC12, ETV6::RUNX1, clone 1,scRNA-seq

city: Düsseldorf

first: Vera

middle: Helena

last: Jepsen

address: Moorenstraße 5

country: Germany

institute: University Hospital Düsseldorf

description:
518-12
10x Genomics, 5 sequencing runs per sample

data_processing:
Raw sequencing data was processed using the 10X Genomics CellRanger software (v6.0.2). Raw BCL-files were demultiplexed and processed to Fastq-files using the CellRanger mkfastq pipeline. Alignment of reads and UMI counting was performed via the CellRanger count pipeline to generate a gene-barcode matrix (genome version: GRCh38, Ensemble release 98). The CellRanger aggr pipeline was used for aggregation and sequencing depth normalization.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files (H5 archives)

source_name: Cellartis Human iPS Cell Line 12 (ChiPSC12, Takara, #Y00280)

growth_protocol: Feeder-free differentiation of hiPSCs was performed using the STEMdiff Hematopoietic kit (Stemcell Technologies) according to the manufacturer’s instructions. On day 12, suspension cells were harvested and used for downstream analyses.

extract_protocol:
Following in vitro differentiation of hiPSCs, hematopoietic progenitor cells of 5 wells were pooled, filtered and resuspended in PBS with 0.04% BSA (Biowest). Cell viability was determined to be >70% using the BD Rhapsody Single-Cell Analysis system (BD Biosciences).
Single-cell suspensions were used for single-cell droplet library generation on the 10X Chromium Controller system using the Chromium Single Cell 3’ NextGEM Reagent kit v3.1 (10X Genomics) according to the manufacturer’s instructions.

value: hematopoietic progenitor cells (HPCs)


title: old_8

description: Pre-mortem


title: 18_ABD_RNA_seq

description: Library name: 18

value: Caucasian


title: ChiPSC12, WT, scRNA-seq

description:
518-11
10x Genomics, 5 sequencing runs per sample

value: Cellartis Human iPS Cell Line 12 (ChiPSC12, Takara, #Y00280)


title: 17_ABD_RNA_seq

description: Library name: 17

value: Hispanic


title: AL5_FLAG_ChIP_rep1


title: old_4

description: Pre-mortem


title: PBNK, donor 1

description: Library name: PBNK1

value: WT


title: 16_ABD_RNA_seq

description: Library name: 16

value: Black


title: OB hypothalamic cells, GEX

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

data_processing:
Sequenced reads were mapped to mm10 genome assembly using cellranger version 6.0.0 (Chow, DIO) or 7.0.1 (OB)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-Seq

source_name: Hypothalamus, brain

extract_protocol:
single cell extraction protocol
10X Genomics 3' v3 kit

tag: group

value: OB

value: Hypothalamus, brain

value: Rapamycin or Vehicle


title: HW8, WT, scRNA-seq

description:
518-9
10x Genomics, 5 sequencing runs per sample

source_name: HW8 (National Cancer Institute, NIH)

value: HW8 (National Cancer Institute, NIH)


title: old_6

description: Pre-mortem


title: 15_ABD_RNA_seq

description: Library name: 15

value: Latino


title: hfd (DIO) hypothalamic cells, HTO

library_source: other

molecule: protein

value: hfd (DIO)


title: HW8, ETV6::RUNX1, clone 1, scRNA-seq

description:
518-10
10x Genomics, 5 sequencing runs per sample


title: old_11

description: Pre-mortem

value: Left ventricular myocardium


title: old_13

description: Pre-mortem


title: S84_Leaf_rep4

city: Auckland

first: Yongyan

last: Peng

state: Auckland

address: 120 Mt Albert Road

department: Kiwifruit New Cultivars

country: New Zealand

institute: Plant and Food Research

data_processing:
The FASTQ file read quality was evaluated, and Fastp (v0.21) was used for trimming (Chen et al., 2018). Reads with a quality below a PHRED score of 20 were trimmed from the 3’end, and reads < 36 bp in length were excluded. The remaining reads were mapped against the Mt4.0v2 transcriptome (Young et al., 2011; Tang et al., 2014) using Salmon (v0.8.2). DESeq2 (v1.24.0) (Love et al., 2014) was used for normalization and differential expression analyses. Differentially expressed transcripts were filtered using a cut-off adjusted p-value ≤ 0.05 and log2 fold-change ≥ 1 or ≤ −1.
Assembly: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary files format and content: Excel file including raw counts for each sample
Supplementary files format and content: excel file including normalised TPM counts for each sample

organism: Medicago truncatula

source_name: leaf

growth_protocol: All Medicago plants used for this research were grown under vernalized long-days (VLD) which is a floral-inductive condition. To sow plants, seeds were scarified using sandpaper (p600 grit), sterilised in a chlorine solution (Millipore, USA) for 10 minutes and germinated overnight shaking in water at 15°C. Seedlings were vernalized for 3 weeks at 4°C on moist filter paper in a petri dish. The seedlings were planted directly into seed-raising mix (Daltons, NZ) in small 6-cell punnets placed on rockwool mats. The plants were sub irrigated with hydroponics (Gibeaut et al., 1997) (without Na2O3Si) and grown in a controlled greenhouse under white fluorescent light in long-days (16/8 hours light/dark) at an intensity of ~160-200 μmol m−2s−1 at 22°C.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany) according to the user manual. RNA quantity and quality were checked by a NanoPhotometer® N60 (Implen, Germany) and a Bioanalyzer 2100 (Agilent Technologies, USA).
Directional strand specific mRNA libraries (polyA enrichment)

treatment_protocol: Harvested tissue was snap-frozen in liquid nitrogen and homogenised by metal beads in a Geno/Grinder® 2010 (New Jersey, USA).

value: leaf

tag: genetic modification

value: Mting1-7/Mting2-2 double mutant

tag: developmental stage

value: 21 days old

value: vernalised long day


title: S84_Leaf_rep3

tag: tissue


title: VC0mM_3

value: human epidermal keratinocyte

value: without VC addition


title: hfd (DIO) hypothalamic cells, GEX


title: VC0mM_5


title: OB hypothalamic cells, HTO


title: 13_ABD_RNA_seq

description: Library name: 13

value: subcutaneous adipose tissues

value: male

value: Caucasian


title: S84_Leaf_rep2

tag: genotype


title: VC0mM_2

tag: cell type


title: chow hypothalamic cells, HTO

value: chow


title: 11_ABD_RNA_seq

description: Library name: 11

value: female

value: African American


title: chow hypothalamic cells, GEX

value: Hypothalamus, brain

value: Rapamycin or Vehicle


title: young_5

description: Pre-mortem


title: young_8

description: Pre-mortem


title: S84_Apex_rep3

source_name: apex

value: apex


title: VC0mM_1


title: S84_Apex_rep2


title: 12_ABD_RNA_seq

description: Library name: 12

value: South Asian


title: young_11

description: Pre-mortem

value: Left ventricular myocardium


title: 14_ABD_RNA_seq

description: Library name: 14


title: 9_ABD_RNA_seq

description: Library name: 9


title: young_3

description: Pre-mortem


title: S84_Apex_rep1


title: sciatic nerve, replicate 5, scRNAseq

first: Xiaolong

last: Xin

address: Research Building 866 Yu Hang Tang Road, Zhejiang University Zijingang Campus

department: School of Basic Medical Sciences

institute: Zhejiang University

description:
Library name: P60
10x Genomics

data_processing:
Cell, the official analysis software of 10x Genomics, was used Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) to the original data to identify the data filtering, alignment, quantitative, recycling cells, Finally, the gene expression matrix of each cell was obtained.
Follow-up the Seurat (https://satijalab.org/seurat/) for further cell filtration, standardization, the classification of the cells, each subgroup analysis and Marker gene screening differentially expressed genes.
The single-cell subpopulation classification analysis process includes the following steps:  (1) After removing low-quality cells, the LogNormalize method of "Normalization" function of Seurat software was used to homogenize the expression amount.  (2) Dimensionality was reduced by Principal component analysis (PCA), and the variables were reduced and then the homogenized expression values were used for PCA (Principal component analysis) analysis. The first 10 principal components were selected from the results of PCA analysis for subsequent clustering and grouping analyses.  (3) Clustering and grouping analysis: Seurat software used a clustering algorithm based on graph theory to cluster and group cells. It mainly includes the following steps:  a) Construct the clustering relationship between cells: construct the KNN clustering relationship graph based on Euclidean distance by using significant principal components;  b) Optimizing the weight value of clustering relationship distance between cells: using Jaccard similarity to optimize the weight value of intercellular distance;  c) Clustering and clustering: cell clusters were identified by clustering algorithm based on shared nearest neighbor (SNN) module optimization, that is, the k-nearest neighbors were first calculated and the SNN graph was constructed, and then the modularity function was optimized to determine the clusters.
Seurat was used to analyze differentially expressed genes in different cell populations by bimod likelihood ratio statistical test to screen genes that were up-regulated in different cell populations.  The screening conditions for up-regulated genes were as follows:  1. The gene is expressed in more than 10% of the cells in the target or control subsets;  (2) P value ≤0.01;  3. Gene expression fold logFC≥0.26, that is, gene up-regulation fold ≥2^0.26;
Gene Ontology(GO) is an international standardized classification system of gene functions. It provides a set of dynamically updated controlled vocabulary to comprehensively describe the properties of genes and gene products in organisms. There are three GO ontologies, which describe the molecular function, cellular component and biological process of a gene. The basic unit of GO is a term(entry, node), and each term corresponds to an attribute. GO functional significant enrichment analysis was performed by mapping all significantly differentially expressed genes to each term in the Gene Ontology database, calculating the number of genes in each term, and then applying hypergeometric test to find out the GO entries that were significantly enriched in significantly differentially expressed genes compared with the whole genome background.
Assembly: mm9
Supplementary files format and content: .rds, P7~P60 single-cell data from mice
Supplementary files format and content: .rds, Single cell data for P14 DRG from mice

source_name: Mus musculus

extract_protocol:
12 males and 10 females for P0, 10 males and 11 females for P7, 10 males and 8 females for P14, 9 males and 6 females for P28, and 5 males and 8 females for P60, to facilitate scRNA-seq library preparation. DRGs at the lumbar level of P14 mice were meticulously dissected from 4 males and 4 females to facilitate snRNA-seq library preparation. The harvested neural tissues were placed in a culture dish containing an appropriate volume of calcium-free and magnesium-free PBS on ice, sectioned into 0.5 mm² pieces, and subsequently dissociated into single cells using a dissociation medium containing 0.35% collagenase IV, 2 mg/ml papain, and 120 Units/ml DNase I, maintained in a 37°C water bath. The enzymatic digestion was terminated using 1×PBS with 10% fetal bovine serum. The resulting cell suspension was passed through a 70-30 μm cell strainer and centrifuged at 300 g for 5 minutes at 4°C. The cell pellet was then resuspended in 100 μl of 1× PBS (0.04% BSA) and supplemented with 1 ml of 10× red blood cell lysis buffer, allowing it to incubate at RT for 2-10 minutes. Subsequent centrifugation at 300 g for 5 minutes at room temperature was performed. The cells were resuspended in 100 μl of a Dead Cell Removal MicroBeads solution, and non-viable cells were eliminated using the Miltenyi® Dead Cell Removal Kit. The final cell suspension was prepared in 50 μl of 1× PBS (0.04% BSA). Overall cell viability was verified via trypan blue exclusion, yielding a viability rate exceeding 85%. Single-cell suspensions were quantified using a hemocytometer or a Countess II Automated Cell Counter, with the cell concentration adjusted to 700-1200 cells/μl.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Mus musculus

tag: cell line

value: Schwann cell

value: glia

tag: batch

value: scan data


title: young_7

description: Pre-mortem


title: 10_ABD_RNA_seq

description: Library name: 10

value: Hispanic


title: S82_Leaf_rep3

value: leaf

value: Mting2-2 mutant

value: 15 days old

value: vernalised long day


title: 8_ABD_RNA_seq

description: Library name: 8

value: subcutaneous adipose tissues


title: S82_Leaf_rep2


title: sciatic nerve, replicate 4, scRNAseq

description:
Library name: P28
10x Genomics


title: young_9

description: Pre-mortem


title: 7_ABD_RNA_seq

description: Library name: 7

value: female

value: Black


title: young_10

description: Pre-mortem


title: sciatic nerve, replicate 3, scRNAseq

description:
Library name: P14
10x Genomics


title: Dorsal root ganglion, replicate 1, scRNAseq

description:
Library name: DRGP14
10x Genomics

value: Neuron

value: neuron


title: S82_Leaf_rep1


title: sciatic nerve, replicate 2, scRNAseq

description:
Library name: P7
10x Genomics


title: 6_ABD_RNA_seq

description: Library name: 6

value: Caucasian


title: VC0mM_4

value: human epidermal keratinocyte

value: without VC addition


title: S82_Apex_rep4

value: apex


title: sciatic nerve, replicate 1, scRNAseq

description:
Library name: P0
10x Genomics

value: Mus musculus

value: Schwann cell


title: 5_ABD_RNA_seq

description: Library name: 5

value: Mixed


title: Normal 1 TCR

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

institute: Wuhan University

data_processing:
cellranger (v3.1.0) is used to map reads to reference genome (GRCh38.p12) and generate gene expression matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count

source_name: Bone marrow

extract_protocol:
BM mononuclear cells (BMMCs) were isolated by Centrifugation (300g for 5 min at 4 °C) after mixing 3 volume red blood cell lysis buffer (Solarbio life science R1010) and samples containing 1 volume IMDM medium (Gibco, 12440053) on ice 10 min. Cells were stained in FACS sorting buffer containing DPBS (Solarbio life science, D1040) with 2% FBS, 1% penicillin–streptomycin (Gibco, 15140122) and 1 mmol I−1 EDTA (Beyotime Biotechnology, C0196) with FITC anti-human CD3 (clone HIT3a; BioLegend, 300306) for 30 min at 4 °C. After staining, cells were washed once and resuspended in FACS sorting buffer and sorted on BD FACS Aria II.
Total BM mononuclear cells (viability was between 85%-95%) from healthy donor or CML patients were loaded onto the 10x Genomics chromium single-cell platform and libraries were constructed using a Chromium single cell 3′ library kit V3 (10x Genomics, 1000075). Libraries of CD3+ cells from healthy donors or patients with CML were constructed using the Chromium single cell 5′ library (10x Genomics, 1000165) and V(D)J enrichment (10× Genomics, 1000005) kits.

value: Bone marrow

value: T cell


title: 4_ABD_RNA_seq

description: Library name: 4


title: S82_Apex_rep3

value: Mting2-2 mutant


title: S82_Apex_rep2

value: 15 days old


title: ZB5_3

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

description:
Library name: Sample 10
conditional KO animal 5

data_processing:
trimming with Cutadapt
mappping with RNA star
read counts measured with featureCounts
Differential gene expression analysis with DESeq2
Assembly: mm10
Supplementary files format and content: Excel file containing the results of the DEG_seq analysis

source_name: E12 Embryonic Cortex

extract_protocol:
RNeasy kit (Qiagen)
PolyA enrichment

value: E12 Embryonic Cortex

value: Emx1 Cre/+; Zbtb7a fl/fl (cKO)

value: litter 5


title: 3_ABD_RNA_seq

description: Library name: 3

value: subcutaneous adipose tissues

value: female


title: 2_ABD_RNA_seq

description: Library name: 2


title: Normal 2 TCR


title: young_4

description: Pre-mortem

value: Left ventricular myocardium


title: ZB3_4

description:
Library name: Sample 8
conditional KO animal 4

value: litter 3


title: Normal 3 TCR


title: ZB3_2

description:
Library name: Sample 7
Wildtype animal 4

value: Emx1 Cre/ +; Zbtb7a +/+ (WT)


title: ZB5_2

description:
Library name: Sample 9
Wildtype animal 5


title: Normal 1 CD3


title: CML patient 6 TCR


title: 1_ABD_RNA_seq

description: Library name: 1

value: African American


title: ZB3_1

description:
Library name: Sample 6
Wildtype animal 3


title: HepG2_shHELLS

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

data_processing:
Low quality and/or adapter-contaminated portions of sequenced reads were trimmed using Trim Galore (version 0.6.6) with Cutadapt (version 3.4).
Trimmed reads were then aligned to the reference human genome (GRCh37) using Bowtie2 (version 2.4.5; the following parameters were used: " --local --vary-sensitive-local --no-mixed --no-discordant") with gene annotation information (GENCODE release 19).
Aligned reads showing low quality (mapping quality less than 10) were further removed using Samtools (version 1.10)
Initial peaks were identified using MACS3 (version 3.0.0a7) with the following parameters: "-B -g hs --broad".
Reliable peaks were identified by analyzing the bdgcmp output with the bdgbroadcall function of MACS3
Assembly: bigwig files were generated using the bedGraphToBigWig tool with the mapped read files
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

source_name: Liver

growth_protocol: All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The construction of library was performed using NEBNext Ultra DNA Library Prep Kit.

treatment_protocol: shRNA were selected in the presence of 1.25 μg/mL puromycin.

value: Liver

value: Cell line

tag: antibody

tag: transfection

value: shHELLS


title: S81_Leaf_rep2

value: leaf

value: Mting1-7 mutant

value: 14 days old

tag: treatment

value: vernalised long day


title: S81_Leaf_rep1


title: S81_Leaf_rep3


title: S81_Apex_rep4

value: apex


title: ZB1_8

description:
Library name: Sample 5
Wildtype animal 2

value: E12 Embryonic Cortex

value: litter 1


title: CML patient 5 TCR

value: Bone marrow

value: T cell


title: CML patient 3 TCR


title: CML patient 2 TCR


title: ZB1_7

description:
Library name: Sample 4
conditional KO animal 3

value: Emx1 Cre/+; Zbtb7a fl/fl (cKO)


title: S81_Apex_rep3


title: S81_Apex_rep2


title: WM793_R3

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Adaptors and poly-A trimmed using cutadapt
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC
Counts per gene from STAR were used as input to generate normalized gene expression matrix using EdgeR {Robinson, 2010 }.
Genome_build: hg38
Supplementary_files_format_and_content: edgeR normalized gene expression as logCPM

growth_protocol: Cell lines were grown at 37°C with 10% CO2 in media recommended in CCLE or ATTC (RPMI-1640 or DMEM, Gibco BRL, Invitrogen) supplemented with 100U/ml penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Libraries were prepared using recommended Illumina protocols
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

tag: disease state

value: melanoma


title: S11_Leaf_rep3

value: Mting1-1/Mting2-11 double mutant


title: ZB1_6

description:
Library name: Sample 3
conditional KO animal 2


title: WM793_R2


title: WM793_R1


title: Normal 3 CD3


title: Normal 2 CD3


title: ZB1_3

description:
Library name: Sample 2
conditional KO animal 1


title: HepG2_shCont

value: shControl


title: S11_Leaf_rep1


title: WM266.4_R1


title: S11_Leaf_rep2


title: ZB1_2

description:
Library name: Sample 1
Wildtype animal 1

value: Emx1 Cre/ +; Zbtb7a +/+ (WT)


title: WM266.4_R2


title: S11_Apex_rep3


title: CML patient 6 CD3


title: WM115_R3


title: WM115_R2


title: CML patient 1 TCR


title: S11_Apex_rep2


title: CML patient 3 CD3


title: S11_Apex_rep1


title: WM266.4_R3


title: corpus callosum, 0.2% cuprizone chow, rep 1

city: Notre Dame

first: Katrina

middle: L

last: Adams

state: Indiana

address: 100 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

description:
Library name: cc1
10X 3p v3.1

data_processing:
The BCL files were demultiplexed to fastq files, adapter trimming was performed and samples were aligned to mm10 using Cell Ranger (v6.0.1).
Assembly: Mus musculus, mm10
Supplementary files format and content: gzipped fastq files, paired end with read , read 2, index 1 and index 2. Each sample was run on two lanes, which are uploaded separately.
Supplementary files format and content: Filtered feature barcode matrices are included (the barcodes, features and matrix files).

source_name: corpus callosum

extract_protocol:
Pooled tissue was transferred to chilled glass dounce with 1mL of lysis buffer + 1% TritonX100 + 1 μM DTT (Sigma Nuclei Pure Prep Kit, Cat #NUC-201). Samples were dounced on ice 10 times with pestle A, then 10 times with pestle B. The suspension was passed through a 40μM FlowMi cell strainer. Dounces were rinsed with 1mL of low sucrose buffer and passed through the cell strainer as well. Samples were centrifuged at 300 rcf, at 4°C, for 5 mins in a fixed-angle centrifuge. Supernatant was carefully decanted, and the pelleted nuclei were washed with 1.5mL of low sucrose buffer, and centrifuged again at 300 rcf, at 4°C, for 5 mins. Pelleted nuclei were then resuspended in 500μL Nuclei wash buffer (PBS + 1% UltraPure BSA + 0.2U/μL Protector RNase inhibitors) + 900μL of 1.8M sucrose cushion buffer, then carefully layered on top of 500μL 1.8M sucrose cushion buffer in a 2mL low-bind tube. Samples were centrifuged at 13,000 rcf, at 4°C, for 45 mins. Supernatant was removed, and nuclei were resuspended in 1mL of Nuclei wash buffer, passed through a 40μM FlowMi cell strainer and counted using a Cell Countess II. Approximately 6,000 nuclei were loaded per sample onto the 10X chromium controller per manufacturer's instructions.
Single nuclei libraries were generated using the 10X single cell 3’ reagents and protocol (v3.1). Libraries were sequenced on an Illumina Novaseq6000, with an average number of 80,000 reads per cell for each sample.

treatment_protocol: Saline/LPC: injection of 1uL of 1% LPC into the corpus callosum on one side, and saline on the contralteral side. Cuprizone (0.2%) treatment administered in food for 5 weeks.

value: corpus callosum

value: cuprizone chow


title: corpus callosum, normal chow, rep 1

description:
Library name: cn1
10X 3p v3.1

value: normal chow


title: corpus callosum, normal chow, rep 2

description:
Library name: cn2
10X 3p v3.1


title: corpus callosum, LPC, rep 2

description:
Library name: cl2
10X 3p v3.1

value: LPC injection


title: WM115_R1


title: CML patient 1 CD3


title: corpus callosum, 0.2% cuprizone chow, rep 2

description:
Library name: cc2
10X 3p v3.1


title: S10_Leaf_rep3

value: leaf

value: Mting2-11 mutant


title: corpus callosum, LPC, rep 1

description:
Library name: cl1
10X 3p v3.1


title: CML patient 5 CD3


title: S10_Leaf_rep1

value: 14 days old

value: vernalised long day


title: S10_Apex_rep3

value: apex


title: WM9_R2


title: corpus callosum, saline control, rep 2

description:
Library name: cs2
10X 3p v3.1

value: saline injection


title: corpus callosum, saline control, rep 1

description:
Library name: cs1
10X 3p v3.1


title: Normal 2 BM

value: Bone marrow


title: Normal 3 BM


title: WM9_R3


title: CML patient 6 BM


title: S10_Apex_rep2


title: CML patient 2 CD3

value: T cell


title: S10_Apex_rep1


title: IGR39_R3


title: S10_Leaf_rep2


title: CML patient 5 BM


title: S9_Leaf_rep4

value: Mting1-1 mutant


title: CML patient 3 BM


title: IGR39_R1

value: melanoma


title: CML patient 2 BM


title: E18p5_sample_1

city: Los Angeles

first: Jifan

last: Feng

address: 2250 Alcarza Street CSA 103

institute: University of Southern California

description: Library name: E18p5_scRNAseq_mouse_palate_1

data_processing:
Sequencing was performed using a NovaSeq 6000 (Illumina) or NovaSeq XPlus (Illumina), and the quality control, sequence alignment, and read counts were processed and quantified using Cell Ranger (v9.0.0) through the 10x Genomics Cloud Analysis platform (10x Genomics).
Assembly: Mouse GRCm39 (GENCODE vM33/Ensembl110 annotations)
Supplementary files format and content: Matrix table with raw gene counts for every gene
Supplementary files format and content: H5 files from 10X Cell Ranger pipeline containing matrix, features, and barcodes information.

source_name: Embryonic Palate

extract_protocol:
Maxillary tissues of the palatal region from E12.5, E13.5, E14.5, E15.5, and E18.5 embryos (3 biological replicates per stage) were dissected and dissociated using Multi Tissue Dissociation Kit 3 (130-110-204, Miltenyi Biotec) at 37°C and 600 rpm for 15-30 minutes in a thermomixer (Thermo Fisher Scientific, 2231000269).
The single-cell suspension was filtered using MACS® SmartStrainers (30 µm) (130-098-458 Miltenyi Biotec) and processed into a single-cell library using 10x Genomics Chromium single-cell 3’ v3 reagent kits (10x Genomics, PN-1000269) according to the manufacturer’s protocol.

value: Embryonic Palate


title: WM9_R1


title: S9_Leaf_rep3


title: IGR37_R3


title: E13p5_sample_1

description: Library name: E13p5_scRNAseq_mouse_palate_1


title: S9_Leaf_rep2


title: CML patient 1 BM


title: E12p5_sample_3

description: Library name: E12p5_scRNAseq_mouse_palate_3


title: IGR37_R2


title: Healthy_control_H22 (mRNA)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on MGISeq-2000 or NovaSeq 6000 platform in a 100+100-base paired-end mode.
On NovaSeq 6000 platform, Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Mapped read counts for each gene-sample combination were quantified with featureCounts ( -M -O --fraction option) of subread-2.0.0 package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: blood

extract_protocol:
Toal RNA was harvested using PAXgene Blood RNA System (BD Biosciences, San Jose, CA).
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

value: blood

value: Healthy


title: S9_Apex_rep3


title: S9_Apex_rep2


title: E12p5_sample_1

description: Library name: E12p5_scRNAseq_mouse_palate_1


title: IGR37_R1


title: IGR39_R2


title: SkMel30_R3


title: E15p5_sample_1

description: Library name: E15p5_scRNAseq_mouse_palate_1


title: SkMel30_R2


title: Healthy_control_H20 (mRNA)


title: MCPIP3(EKO) mouse 3;  skin.

city: Krakow

first: Agata

last: Lichawska-Cieslar

address: Gronostajowa 7

department: Faculty of Biochemistry, Biophysics and Biotechnology

country: Poland

institute: Jagiellonian University

description: Library name: tg 3 skin

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2)
Raw reads were aligned to mm10 using STAR (version 2.7.3)
Assembly: mm10
Supplementary files format and content: raw counts

source_name: skin

extract_protocol:
Collected tissue samples were snap-frozen in liquid nitrogen and stored at -80°C  prior to analysis. For RNA isolation, the samples were homogenized in Fenozol (A&A Biotechnology, Gdansk, Polska) using a tissue homogenizer (OMNI International, Kennesaw, GA, USA). RNA samples were subjected to DNase I treatment and concentration using RNA Clean and Concentrator-5 (Zymo Research, Irvine, CA, USA).
100 ng of total RNA was used for library preparation using TruSeq Stranded mRNA (Illumina).

value: skin


title: S9_Apex_rep1


title: Healthy_control_H16 (miRNA)

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 101-base single-end mode.
Before analysis of the small RNA-Seq data, reads were trimmed the 3' adapter sequence (AGATCGGAAGAGCACACGTCT).
Trimmed reads were mapped on miRBase human miRNA dataset and FANTOM5 dataset using miRDeep2 software.
Quantification was also performed with miRDeep2 software.
Assembly: miRBase human miRNA dataset and FANTOM5 dataset (Nature Biotechnology volume 35, pages872–878 (2017))
Supplementary files format and content: tab-delimited text files include count data for each sample

extract_protocol:
Toal RNA was harvested using PAXgene Blood RNA System (BD Biosciences, San Jose, CA).
Each library was prepared using NEBNext Multiplex Small RNA Library Prep Set for illumina (New England Biolabs).


title: E14p5_sample_1

description: Library name: E14p5_scRNAseq_mouse_palate_1


title: SkMel30_R1


title: MCPIP3(EKO) mouse 2;  skin.

description: Library name: tg 2 skin


title: Healthy_control_H25 (miRNA)


title: S8_Leaf_rep3

value: Wild type R108


title: MCPIP3(EKO) mouse 1;  skin.

description: Library name: tg 1 skin


title: Control mouse 4; skin

description: Library name: WT 4 skin


title: SkMel28_R3


title: Healthy_control_H22 (miRNA)


title: Healthy_control_H24 (miRNA)


title: S8_Leaf_rep1


title: S8_Apex_rep3


title: SkMel28_R2


title: MCPIP3(EKO) mouse 4;  skin.

description: Library name: tg 4 skin


title: Healthy_control_H21 (miRNA)


title: Healthy_control_H20 (miRNA)


title: Control mouse 2; skin

description: Library name: WT 2 skin


title: A375M_R3


title: Healthy_control_H19 (miRNA)


title: S8_Apex_rep1


title: SkMel28_R1


title: Control mouse 1; skin

description: Library name: WT 1 skin


title: A375M_R2


title: TLDR-Seq_HeLa_libamp_R10_bc3

city: Copengagen

first: Albin

last: Sandelin

address: Ole Maaløes Vej 5

department: Department of Biology, Section for Computational and RNA Biology

country: Denmark

institute: University of Copenhagen

description: Library name: TLDR-Seq_HeLa_libamp_bc3

data_processing:
Reads were basecalled with a modified version of dorado 0.7.4  using the parameter --no-trim  --estimate-poly-a
Reads  that passed the basecalling default threshold  were demultiplexed with cutadapt v6.3.7
mESC  and HeLa-S3 demultiplexed reads were respectively mapped with minimap2 (2.24-r1122) to the Gencode v35 mouse transcriptome or to the Gencode v39 human transcriptome
Transcript quantification was then performed with bambu 3.5.1
Assembly: hg38 (HeLa-S3) and mm39 (mESC)
Supplementary files format and content: Processed data file are tab separated files containing 3 fields: transcript_name, counts, cpm

extract_protocol:
RNA was harvested using the TRIzol Plus RNA purification kit and Phasemaker tubes Complete system, DNaseI treated and purified using the Purelink RNA Mini kit. RNA quality is assessed on the RNA Bioanalyzer. 8ug of RNA was used as an input per sample for the TLDR-sequencing library prep
TLDR-seq library prep was carried out as as follows; Input RNA was dephosphorylated then quantified on the nanodrop. 5 ug of dephosphorylated RNA was used for 3'-end A1 adapter ligation with T4 RNA ligase 2 truncated KQ. Unligated A1 adapters were deadenylated and degraded. cDNA was synthesised using Induro reverse transcriptase, with partially reverse transcribed RNAs digested with RNaseONE. Samples are enriched for m7G capped RNA by cap trapping technology. The cDNA strand of the enriched capped RNA were ligated with barcoded 5'-linkers (A2_bc). The second strand cDNA was generated using LongAmp HotStart Taq 2x Master mix. For amplified samples, PCR amplification was carried out using LongAmp HotStart Taq 2x Master mix. Endprep/dA-tailing and nanopore adapter ligation was carried out using the SQK-LSK114 kit and sequenced on MinIOn flow cells (FLO-MIN114 - R10.4.1)


title: A375M_R1


title: Healthy_control_H15 (miRNA)


title: Healthy_control_H14 (miRNA)


title: PMN-MDSCs_DMSO_H3K27ac_CUT&Tag Rep2

city: Tianjin

first: Lin

last: Zhu

address: Qixiangtai Road

institute: Tianjin Medical University

description: Library name: PMN-MDSCs_DMSO_H3K27ac_CUT_Tag Rep2

data_processing:
FastQC software was used for quality control. Then we mapped reads to mm10 mouse genome assembly with bowtie2 . SAMtools was used for quality filtering. After file format conversion, peak calling was performed by Macs2  with macs2 callpeak.
Assembly: mm10
Supplementary files format and content: Bigwig file
Library strategy: CUT&Tag

source_name: Spleen

extract_protocol:
A total of 1 × 10^5 PMN-MDSCs were collected after in vitro treatment with GC7 or DMSO for 16 hours. Two replicates per group underwent CUT&Tag analysis utilizing an antibody against H3K27ac.
CUT&Tag libraries were prepared using hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following manufacturer's protocols.

value: Spleen

value: primary cell

value: PMN-MDSCs

value: WT

value: DMSO


title: S8_Leaf_rep2

value: leaf

value: 14 days old

value: vernalised long day


title: PMN-MDSCs_DMSO_H3K27ac_CUT&Tag Rep1

description: Library name: PMN-MDSCs_DMSO_H3K27ac_CUT_Tag Rep1


title: TLDR-Seq_HeLa_libamp_R10_bc2

description: Library name: TLDR-Seq_HeLa_libamp_bc2


title: 501mel_R3


title: Healthy_control_H11 (miRNA)


title: TLDR-Seq_HeLa_libamp_R10_bc1

description: Library name: TLDR-Seq_HeLa_libamp_bc1


title: PMN-MDSCs_GC7_H3K27ac_CUT&Tag Rep2

description: Library name: PMN-MDSCs_GC7_H3K27ac_CUT_Tag Rep2


title: Healthy_control_H9 (miRNA)


title: Control mouse 3; skin

description: Library name: WT 3 skin


title: TLDR-Seq_HeLa_libNoamp_bc9

data_processing:
Reads were basecalled with Guppy 6.4.2 using the parameter 'trim_strategy none'.
Reads  that passed the basecalling mean_qscore_template > 9 threshold  were demultiplexed with cutadapt v6.3.7
mESC  and HeLa-S3 demultiplexed reads were respectively mapped with minimap2 (2.24-r1122) to the Gencode v35 mouse transcriptome or to the Gencode v39 human transcriptome
Transcript quantification was then performed with Nanocount (v1.0.0)
Assembly: hg38 (HeLa-S3) and mm39 (mESC)
Supplementary files format and content: Processed data file are tab separated files containing 5 fields: transcript_name, raw, est_count, tpm, transcript_length

extract_protocol:
RNA was harvested using the TRIzol Plus RNA purification kit and Phasemaker tubes Complete system, DNaseI treated and purified using the Purelink RNA Mini kit. RNA quality is assessed on the RNA Bioanalyzer. 8ug of RNA was used as an input per sample for the TLDR-sequencing library prep
TLDR-seq library prep was carried out as as follows; Input RNA was dephosphorylated then quantified on the nanodrop. 5 ug of dephosphorylated RNA was used for 3'-end A1 adapter ligation with T4 RNA ligase 2 truncated KQ. Unligated A1 adapters were deadenylated and degraded. cDNA was synthesised using Induro reverse transcriptase, with partially reverse transcribed RNAs digested with RNaseONE. Samples are enriched for m7G capped RNA by cap trapping technology. The cDNA strand of the enriched capped RNA were ligated with barcoded 5'-linkers (A2_bc). The second strand cDNA was generated using LongAmp HotStart Taq 2x Master mix. For amplified samples, PCR amplification was carried out using LongAmp HotStart Taq 2x Master mix. Endprep/dA-tailing and nanopore adapter ligation was carried out using the SQK-LSK110 kit and sequenced on MinIOn flow cells (FLO-MIN106 - R9.4.1)


title: PMN-MDSCs_GC7_H3K27ac_CUT&Tag Rep1

description: Library name: PMN-MDSCs_GC7_H3K27ac_CUT_Tag Rep1


title: 501mel_R1


title: 501mel_R2


title: S8_Apex_rep2

value: apex


title: CHL1_R3


title: Healthy_control_H8 (miRNA)


title: TLDR-Seq_HeLa_libNoamp_bc8


title: Healthy_control_H7 (miRNA)


title: TLDR-Seq_HeLa_libNoamp_bc7


title: PMN-MDSCs_flox Rep 1

description: Library name: PMN-MDSCs_flox Rep 1

data_processing:
Raw reads were filtered to get high-quality clean reads by using Cutadapt. Subsequently, reads were aligned to the mouse reference genome utilizing the HISAT2 package. StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
A total of 3×10^5 PMN-MDSCs were isolated from neonatal spleen (PND7) and total RNA was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dhps flox


title: CHL1_R1


title: Healthy_control_H1 (miRNA)


title: PMN-MDSCs_cko Rep 1

description: Library name: PMN-MDSCs_cko Rep 1

value: Dhps cko


title: TLDR-Seq_HeLa_libNoamp_bc5


title: PMN-MDSCs_cko Rep 2

description: Library name: PMN-MDSCs_cko Rep 2


title: SEPSIS_patient_P28 (miRNA)


title: HBL_R2

source_name: HBL

value: HBL

value: melanoma


title: CD45+CD11b- cells isolated from CT26 tumor tissue, treated with aPD-1/aLAG-3, responding, ADT

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

description: Library name: R_adt

data_processing:
CITE-seq data was demultiplexed using illumina bcl2fastq2.20
Demultiplexed data was processed using cellranger count workflow
Assembly: mm10
Supplementary files format and content: Cellranger output files : barcodes.tsv.gz, features.tsv.gz. matrix.mtx.gz
Library strategy: CITE-seq

source_name: Tumor

extract_protocol: 10x Genomics Chromium Single Cell 3′ Library & Gel Bead Kit v.3.1

value: Tumor


title: TLDR-Seq_HeLa_libNoamp_bc4


title: SEPSIS_patient_P24 (miRNA)

value: blood


title: TLDR-Seq_HeLa_libNoamp_bc3


title: HBL_R1


title: TLDR-Seq_HeLa_libNoamp_bc2


title: SEPSIS_patient_P17 (miRNA)


title: CD45+CD11b- cells isolated from CT26 tumor tissue, treated with aPD-1/aLAG-3, non-responding,  ADT

description: Library name: NR_adt


title: Mettl14LKO-3-input

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

institute: Nanjing agricultural university

description:
Library name: sample12
input

data_processing:
Reads were quality controlled using FastQC (v0.11.5) and TrimGalore (v0.6.0).
rRNA sequence were removed by using bowtie2(v2.3.4.1) with --ungz or --un-conc-gz parameter.
The retained reads were aligned to GRCm38/mm10 by HISAT2 (v2.2.1) with default parameters.
Bigwig files were obtained by using bamCoverage function in deepTools (v3.5.1) and visualized in IGV (v11.0.19).
Read counts were quantified by using featureCounts (v1.6.0).
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA quality and integrity were assessed by NanoDrop ND 1000 spectrophotometry and agarose gel electrophoresis. Dynabeads Oligo (dT)25 was employed to isolate the mRNA containing PolyA in total RNA pool. The isolated mRNA was then sonicated into fragments of 150-200 bp through 30 cycle of ultrasound, with each cycle comprising 30 s on and 30 s off.  A total of 50 ng of fragmented mRNA was used as input. In the immunoprecipitation (IP) process, 25 μL of protein G beads (NEB, Cat. S1430) were pre-incubated with 1 μL of anti-m6Aantibody (NEB, Cat. E1610S) in reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) at 4°C for 30 min. Following this, a 250 μL mixture containing 950 ng of mRNA, 50 μL IP buffer (750 mM NaCl, 50 mM Tris-HCl, 0.5% NP-40), and 5 μL RNA inhibitor was added to antibody and incubated for 1 h at 4℃. Subsequently, beads were washed sequentially in the following solutions: twice in reaction buffer, twice in low salt buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), and twice in high salt buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). RNA was then eluted from beads with 100 μL of buffer RLT (QIAGEN, Cat. 1015762) by incubation for 1 min and then purified using a clean and concentrate RNA kit according to the manufacturer’s protocol. (Zymo research, Cat. R1017).
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara), according to the manufacturer’s protocol.

value: liver


title: CD45+CD11b- cells isolated from CT26 tumor tissue, treated with aPD-1/aLAG-3, responding, GEX

description: Library name: R_mRNA


title: SEPSIS_patient_P16 (miRNA)


title: PMN-MDSCs_flox Rep 2

description: Library name: PMN-MDSCs_flox Rep 2


title: Healthy_control_H2 (miRNA)

value: Healthy


title: SEPSIS_patient_P15 (miRNA)


title: Mettl14LKO-2-input

description:
Library name: sample11
input


title: TLDR-Seq_HeLa_libNoamp_bc12


title: TLDR-Seq_HeLa_libNoamp_bc1


title: CHL1_R2


title: CD45+CD11b- cells isolated from CT26 tumor tissue, treated with aPD-1/aLAG-3, non-responding, GEX

description: Library name: NR_mRNA


title: TLDR-Seq_HeLa_libNoamp_bc6


title: H3K4me1 replicate 2

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute for Biological Intelligence

description: Library name: Sample 40

data_processing:
Raw sequencing reads were mapped to the Mus musculus reference genome (mm10) using Bowtie2
Signal tracks were then generated in bigWig format for visualization in genome browsers.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: ganglionic eminence

extract_protocol:
Ganglionic ememenece of mouse e16.5 were dissected and dissoliated into single cell using gentle macs neural dissociation kit.
The EpiCypher Cut&Run protocol was used for sample preparation, and the NEB kit was used for library processing.

value: ganglionic eminence

value: wildtype

tag: chip antibody


title: Mettl14LKO-1-input

description:
Library name: sample10
input


title: SEPSIS_patient_P14 (miRNA)


title: H3K4me1 replicate 1

description: Library name: Sample 39


title: WT2-input

description:
Library name: sample8
input


title: TLDR-Seq_HeLa_libNoamp_bc10


title: WT3-input

description:
Library name: sample9
input


title: SEPSIS_patient_P11 (miRNA)


title: NFIB Cut&Run replicate 1

description: Library name: Sample 37

value: NFIB


title: NFIB Cut&Run replicate 2

description: Library name: Sample 38


title: SEPSIS_patient_P13 (miRNA)


title: SEPSIS_patient_P10 (miRNA)


title: TLDR-Seq_HeLa_libamp_bc3


title: Mettl14LKO-3-IP

description:
Library name: sample6
immunoprecipitation


title: WT1-input

description:
Library name: sample7
input

value: WT


title: TLDR-Seq_HeLa_libamp_bc1


title: TLDR-Seq_HeLa_libamp_bc2


title: SEPSIS_patient_P9 (miRNA)


title: gibbon-iPS-0023F-1

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

description: Library name: iPSC_0023F-1

data_processing:
Trim Galore was used for adapter and quality trimming with the -fastqc option (https://zenodo.org/records/7598955). Sequencing reads from small ape cells were mapped to nomLeu3 using STAR (PMID: 23104886), and uniquely mapped reads were retained for further analyses. BAM files were converted to BED format, and PCR duplicates were removed. The intersectBed tool in Bedtools was used to sum reads of overlapping exons of genes homologous to those of hg38 (PMID: 20110278). Only the first read of paired-end reads was included in the count. Transcripts per kilobase million (TPM) values were calculated for normalization using Pandas.
Assembly: nomLeu3
Supplementary files format and content: txt file including TPM value of gene expressions

organism: Hylobates lar

source_name: iPSC

growth_protocol: Skin specimens were obtained from two lar gibbons (Hylobates lar) (GAIN-ID: 0023 [Jessica, a 24-year-old female] and GAIN-ID: 0247 [Kyutaro, a 21-year-old male]), one Abbott’s gray gibbon (Hylobates abbotti) (GAIN-ID: 0159 [Anna, an estimated 46-year-old female]), and two siamangs (Symphalangus syndactylus) (GAIN-ID: 0105 [Matsu, a 32-year-old female] and GAIN-ID: 0297 [Peach, an 11-year-old female]). These samples were provided by the Japan Monkey Centre, the Toyohashi Zoo and Botanical Park, and the Great Ape Information Network (GAIN) for primary cultures. Each skin specimen was minced into small pieces and transferred onto tissue culture dishes (353002; Corning, Glendale, AZ, USA) with 15% fetal bovine serum (FBS)/Dulbecco’s modified Eagle’s medium (DMEM) medium, which consists of DMEM with high glucose (044-29765; Wako, Osaka, Japan) supplemented with 15% FBS, 1× non-essential amino acids (139-15651; Wako), 1× GlutaMAX Supplement (35050061; Gibco, Waltham, MA, USA), 1 mM sodium pyruvate (190-14881; Wako), 0.11 mM 2-mercaptoethanol (21985-023; Gibco), and 100 units/ml penicillin and 100 µg/ml streptomycin (168-23191; Wako). Fibroblast outgrowth from the skin pieces was observed after approximately one week of culture. The fibroblasts were subsequently passaged though single-cell dissociation with 0.25% trypsin/ethylenediaminetetraacetic acid (EDTA) and expanded in 15% FBS/DMEM medium on 0.1% gelatin-coated culture dishes at 37°C with 5% CO2. Small ape skin fibroblasts were seeded at 1.0 × 105 cells/well on 0.1% gelatin-coated culture plates. The following day, the cells were transduced with six human reprogramming factors (OCT3/4, KLF4, SOX2, c-MYC, LIN28, and NANOG) using SRV iPSC-3 Vector (S1011626A; Tokiwa Bio, Ibaraki, Japan) at a multiplicity of infection (MOI) of 3 for GAIN-ID: 0247, 0159, 0105, 0297. For GAIN-ID: 0023, transduction was performed with four human reprogramming factors (OCT3/4, KLF4, SOX2, and c-MYC) using the SRV iPSC-1 Vector (S1011624A; Tokiwa Bio) at an MOI of 3. The transduction procedure involved incubating the cells with the respective SRV vectors at room temperature for 2 hours, followed by overnight incubation at 37°C with 5% CO2. 24 hours post-transduction, the cells were dissociated with 0.25% trypsin/EDTA and reseeded onto iMatrix-511-coated 24-well culture plates at 1.0 × 104 cells/well. The medium was changed every other day under two different conditions. For condition A, cells were cultured in 15% FBS/DMEM medium from day 1 to day 7, followed by StemFit AK02N medium (AK02N; Ajinomoto, Tokyo, Japan) without supplements from day 7 to approximately day 21. Thereafter, the cells were maintained in StemFit AK02N medium. For condition B, StemFit AK02N medium without supplements was used from day 1 to day 7 or 14, followed by continued culture in StemFit AK02N medium. Emerging EGFP+ reprogrammed colonies were manually picked and cultured in StemFit AK02N medium on iMatrix-511-coated culture plates.　To remove SRV vectors from expanded EGFP+ reprogrammed cells, small interfering RNA (siRNA) transfection was performed according to the manufacturer’s instructions (S1011626A; Tokiwa Bio). Briefly, EGFP+ reprogrammed cells, after several serial passages, were dissociated with TrypLE Express (12604021; Gibco) and seeded at 0.75 × 104 cells/well in StemFit AK02N medium supplemented with 10 μM Y-27632 (036-24023; Wako) on iMatrix-511-coated 24-well culture plates. On the next day, the medium was replaced with fresh StemFit AK02N medium. The cells were transfected with siRNA (sense: CAAUAGUUCACGCUGAAAGUG; anti-sense: CUUUCAGCGUGAACUAUUGCU) using Lipofectamine RNAiMAX (13778100; Thermo Fisher Scientific, Waltham, MA, USA) on day 1 and 4 after plating. The siRNA-transfected cells were passaged upon reaching sub-confluency and maintained in StemFit AK02N medium on iMatrix-511-coated culture plates. For subcloning SRV-free iPSCs, the siRNA-transfected cells were seeded at 0.5 × 103 cells/cm2, and EGFP- colonies were manually picked up and expanded as iPSCs in StemFit AK02N medium on iMatrix-511-coated culture dishes.

extract_protocol:
Total RNA was extracted using ISOGEN (317-02503; Nippon Gene, Tokyo, Japan) and Direct-Zol RNA Miniprep (R2050; Zymo Research, Irvine, USA).
cDNA library preparation and sequencing were performed by Azenta Japan (Tokyo, Japan). Briefly, cDNA libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs) and sequenced on an Illumina NovaSeq with a 2 x 150 bp paired-end configuration. Each sample yielded approximately 20 million sequencing reads.

value: iPSC


title: HBL_R3


title: gibbon-SRV3-0247M-A4

description: Library name: SRV_0247M-A4

source_name: SRV+ cells

value: SRV+ cells


title: TRAM_Hif1aKO_FG-2

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

department: Medicine

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using kallisto 0.46.1
The Kallisto index was made with default parameters and the GENCODE (Release 39 (GRCh38.p13) and was run in quant mode with default parameters
Assembly: Mus_musculus_GRCm39
Supplementary files format and content: tsv

source_name: TR-AM

growth_protocol: RPMI 1640  supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total
Oligo-dT mRNA directional

treatment_protocol: 1µg/ml 4-Hydroxytamoxifen

value: TR-AM

value: Primary

value: Macrophage


title: SEPSIS_patient_P4 (miRNA)


title: Mettl14LKO-2-IP

description:
Library name: sample5
immunoprecipitation


title: Control, heart

city: Rizhao

first: Wei

last: Qin

state: Shandong

address: 669 Xueyuan Road, Donggang District, Rizhao, Shandong, China

institute: Jining Medical University

description: Library name: Sample 1

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.12.0 (https://github.com/singleron-RD/CeleScope/) with default parameters.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Heart

growth_protocol: Mice were kept in the environment with a 12:12 h light/dark cycle (ambient temperature of 23 °C) and fed a standard laboratory diet.

extract_protocol:
Cardiac tissues were harvested from mice and washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). Nuclei isolation was performed using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China).
The isolated nuclei were resuspended in PBSE. The concentration of single nucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. The single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies), and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). Sequencing was performed on an Illumina novaseq 6000 instrument with 150 bp paired end reads.

treatment_protocol: The mice of PD-1 inhibitor were intraperitoneally injected with InVivoPlus anti-mouse PD-1 antibody (Bioxcell, West Lebanon, USA) at a dose of 5 mg/kg on the 1st and 14th days of a 28-day cycle. The mice of control were intraperitoneally injected with PBS at the same time.

value: Heart

value: PBS


title: SEPSIS_patient_P8 (miRNA)


title: SEPSIS_patient_P2 (miRNA)


title: TRAM_Hif1aKO_FG-3


title: WT2-IP

description:
Library name: sample2
immunoprecipitation


title: Mettl14LKO-1-IP

description:
Library name: sample4
immunoprecipitation


title: Fibroblast-0247M

description: Library name: Fibroblast_0247M

source_name: fibroblasts

value: fibroblasts


title: TLDR-Seq_HeLa_libNoamp_bc11


title: TRAM_Hif1aKO-3


title: SEPSIS_patient_P7 (miRNA)


title: CIH group replicate3

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10x Blocking Agent and 1 μL of 25x Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2x Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-circRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities.

source_name: IP enriched m6A methylated circRNAs

label_protocol: The “IP” RNAs and “Sup” RNAs digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched “IP” RNAs and “Sup” RNAs were then added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific activity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: We placed mice assigned to receive CIH in a specially designed chamber, which contained oxygen sensors for measuring the concentration of O2 in the chamber. Cages were connected to a gas regulator that controls the infusion of sufficient nitrogen to reduce O2 to 6% for 60 seconds, after which the gas control system allows for a rapid replacement of oxygen leading to a quick restoration of O2 to 21% for another 60 seconds. This 2-minutes CIH cycle was repeated 30 times per h, 8 h/day, for a total duration of 8 weeks.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissues from heart tissues and promptly cooled at -80℃ refrigerator.

value: heart

tag: strain

value: BALB/c

source_name: supernatant unmodified circRNAs


title: TRAM_Hif1aKO-2


title: WT3-IP

description:
Library name: sample3
immunoprecipitation


title: CIH group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: TRAM_Hif1aKO_FG-1


title: Sbj1_mAb24

type: protein

city: Siena

first: Viola

last: Viviani

address: Via Fiorentina, 1

country: Italy

institute: GSK

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit). The array was then incubated 1h a room temperature (RT) with mAbs diluted 0,5 ug/ml for anti-human IgG-specific analysis. After two washing with 0.1% Tween in PBS buffer (TPBS), arrays were incubated with an AlexaFluor 647-conjugated IgG anti-human (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before and washed once in PBS, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a InnoScan 710AL (Innopsys) and the 16-bit images were generated with Mapix software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data  was performed using in-house developed R scripts. For each protein the fluorescence intensity data of the replicates was subtracted by local background values surrounding each spot and averaged, hence resulting in a single data point per sample named Mean Fluorescence Intensity (MFI).

label: AlexaFluor 647-conjugated anti-human IgG secondary antibody

source_name: recombinant HumAbs

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol:
Protein extracted from samples.
Briefly: bacterial pellets were either resuspended in equilibration buffer (50?mM NaH2PO4 and 300?mM NaCl, pH 8.0) before mechanical lysis by sonication or resolubilized in B-PER Bacterial Protein Extraction Reagent (B-PER, Thermo Fisher, 1?g/10?ml) or Cell-Lytic Express (Sigma-Aldrich). The unbroken cells and bacterial debris were removed by centrifugation and proteins were purified from the supernatant by IMAC (immobilized metal-ion-affinity chromatography) purification using cobalt-based chelating columns (Hitrap TALON Crude; Merck) according to the manufacturer?s instructions. Columns were washed with equilibration buffer, and proteins bound to the resin were then eluted with imidazole gradient (from 0?mM to 250?mM imidazole) in equilibration buffer. Samples were dialyzed in PBS. The recombinant PorA and PorB proteins were instead purified from inclusion bodies. PorA bacterial pellets were dissolved in Guanidine 6?M, 50?mM Tris-HCl, pH 8.5, whereas PorB bacterial pellets were lysed in 8?M Urea, 50?mM Tris-HCl, pH 8,0. The solubilized inclusion bodies were concentrated in an Amicon concentrator, 10?kDa cutoff (Millipore). Then samples were diluted into a refolding buffer (200?mM CAPS, 400?mM NaCl, 50?mM Tris-HCl, 0.3% Lauryl-N,N-dimethylamine-N-Oxide [LDAO], pH 11). The mixtures were stirred ON at 4?°C and the pH was adjusted to 8.0 with 1?N HCl. The refolded porins were loaded onto an IMAC column (HisTrap HP, GE Healthcare), washed with PBS?+?0,1% LDAO (PBSL) and eluted with PBSL containing 300?mM imidazole. The samples were concentrated with Amicon (10?kDa cutoff) and then loaded onto an S-300 Sephacryl column (GE Healthcare) and the protein was eluted in 0,1% PBSL.

treatment_protocol: Recombinant expressed monoclonal antibodies in mammalian cells

tag: subclass

value: PBMC


title: PD-1 inhibitor, heart

description: Library name: Sample 2

value: PD-1 inhibitor


title: gibbon-SRV1-0023F-1

description: Library name: SRV_0023F-1


title: Control group replicate3

address: 福建省泉州市鲤城区中山北路34号


title: TRAM_Hif1aKO-1


title: Sbj3_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: TRAM_FG-2


title: Colorectal carcinoma cells-RUNX1

first: Li

middle: ming

last: yue

address: 163 Xianlin Dadao

institute: Nanjing university

data_processing:
Sequenced reads were aligned to the human genome, and reads with more than two aligned positions were removed. The remaining tags were further filtered by quality score and redundancy. Only nonredundant reads that passed the quality score were retained for downstream analysis. ChIP-seq tags and whole genome sequencing tags were then analyzed using MACS to identify the peaks based on p < 0.005
The remaining tags were further filtered by quality score and redundancy.
Only nonredundant reads that passed the quality score were retained for downstream analysis.
ChIP-seq tags and whole genome sequencing tags were then analyzed using MACS to identify the peaks based on p < 0.005
Genome_build: mm9
Supplementary_files_format_and_content: wig, peak text files

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed using a ChIP assay kit (Millipore, Temecula, USA) according to the manufacturer’s instructions. Briefly, cells were fixed with formaldehyde and homogenized. Nuclei were pelleted, and DNA was sheared by sonication and immunoprecipitated with anti-RUNX1 antibody or negative control immunoglobulin G using protein A/G beads. DNA was released from immunoprecipitate complexes using proteinase K and purified. Chromatin was sheered by 8 sonication cycles to generate DNA fragments with an average size of 200 bp for ChIP-seq analysis and 4 sonication cycles to generate DNA fragments with an average size of 600 bp for ChIP-qPCR.
For high-throughput sequencing, 10-20 ng DNA was used to make the ChIP-seq library according to the instructions from Illumina’s ChIP-seq Sample Prep kit. The ChIP-seq library was loaded on Illumina’s cluster station and sequenced with Illumina Genome Analyzer IIx.

value: Human colorectal carcinoma cells

value: RUNX1(Santa Cruz Biotechnology, #sc-365644)


title: TRAM_Ctr-3

value: Ctr


title: Control group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: Sbj2_mAb19

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: CT26_TRX_1

city: Amsterdam

first: Judy

last: van Beijnum

state: Noord Holland

address: CCA rm 2.52, De Boelelaan 1118

department: Medical Oncology

country: Netherlands

institute: VUMC

description: Library name: 7797_25_TRX_1

data_processing:
bcl2fastq2 versie v2.15.0.4
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw counts for all samples

source_name: sc. Flank tumor

growth_protocol: B16F10 and CT26 cells were maintained in DMEM supplemented with 10% FCS and 1% Pen/Strep and glutamine supplements. 1e5 tumor cells were injected in the flank of C57BL/6 or Balb/C mice and harvested 3 weeks p.i.

extract_protocol:
RNA was extracted using Trizol according to the manufacturers instructions
TruSeq RNA Library Prep Kit v2 (Illumina Inc., San Diego)

treatment_protocol: Mice were vaccinated with recombinant proteins

value: sc. Flank tumor

value: Mouse colrectal cancer

value: TRX


title: Sbj2_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: CIH group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: TRAM_FG-3

value: WT


title: TRAM_Ctr-2

value: TR-AM


title: WT1-IP

description:
Library name: sample1
immunoprecipitation

value: liver


title: CT26_TRX_3

description: Library name: 7797_27_TRX_4


title: Sbj2_mAb4

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Fibroblast-0023F

description: Library name: Fibroblast_0023F


title: CT26_TRX_2

description: Library name: 7797_26_TRX_2


title: TRAM_FG-1

value: Primary

value: Macrophage


title: Control group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: B16F10_VEA_C1Q_3

description: Library name: 7797_24_C1q_14_3

value: Mouse melanoma


title: IgG CUT&RUN Repeat 2

city: Sioux Falls

first: Louis-Jan

last: Pilaz

address: 2301 E 60th Street North

institute: Sanford Research

description:
Library name: Sample 17
ZBTB7A CUT&RUN

data_processing:
trimming with Trim Galore
mappping with Bowtie2
read counts measured with featureCounts
merging all repeats together
1x normalization with bamCoverage
Assembly: mm10
Supplementary files format and content: Bedgraph files
Library strategy: CUT&Run

source_name: E12 Embryonic Cortex

growth_protocol: Embryonic day 12 mouse cortices (n=3 each group) were dissected, and cells were dissociated with the Accumax (Sigma-Aldrich A7089) following the manufacturer’s instructions. CUT&RUN was performed according to the published protocol (Skene and Henikoff 2017, eLife) (n=3 biological replicates/antibody/genotype). 10,000 cells were used for each experiment, and 3 biological replicates were performed for each antibody and genotype.

extract_protocol:
Skene and Henikoff 2017, eLife
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645, E7103) with index primers (NEB, E7645-S). Pippen size selection was used to remove the primer dimers.

value: E12 Embryonic Cortex

value: CD1 strain


title: HepG2_shCont

type: genomic

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

institute: Konkuk University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

source_name: liver cancer cell line

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted  using genomic DNA extraction Kit according to standard instructions


title: B16F10_VEA_C1Q_2

description: Library name: 7797_23_C1q_13_5


title: BMDM_Hif1aKO_FG-3

source_name: BMDM

value: BMDM


title: Sbj2_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: IgG CUT&RUN Repeat 3

description:
Library name: Sample 18
ZBTB7A CUT&RUN


title: Sbj2_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: B16F10_VEA_C1Q_1

description: Library name: 7797_22_C1q_13_4


title: H3K4Me1 CUT&RUN Repeat 2

description:
Library name: Sample 14
ZBTB7A CUT&RUN


title: BMDM_Hif1aKO_FG-1


title: BMDM_Hif1aKO_FG-2


title: B16F10_VEA_EMI_2

description: Library name: 7797_20_EMI_11_2

value: TRXtr-EMI


title: TRAM_Ctr-1


title: B16F10_VEA_EMI_3

description: Library name: 7797_21_EMI_12_2


title: B16F10_VEA_EMI_1

description: Library name: 7797_19_EMI_12_5


title: Sbj1_mAb20

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: H3K4Me1 CUT&RUN Repeat 1

description:
Library name: Sample 13
ZBTB7A CUT&RUN


title: B16F10_VEA_TRX_3

description: Library name: 7797_18_TRX_1_4


title: GATAD2B CUT&RUN Repeat 3

description:
Library name: Sample 12
ZBTB7A CUT&RUN


title: BMDM_Hif1aKO-3


title: B16F10_VEA_TRX_2

description: Library name: 7797_17_TRX_2_3


title: BMDM_Hif1aKO-1


title: IgG CUT&RUN Repeat 1

description:
Library name: Sample 16
ZBTB7A CUT&RUN


title: BMDM_Hif1aKO-2


title: H3K4Me1 CUT&RUN Repeat 3

description:
Library name: Sample 15
ZBTB7A CUT&RUN


title: GATAD2B CUT&RUN Repeat 2

description:
Library name: Sample 11
ZBTB7A CUT&RUN


title: Sbj1_mAb17

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb3

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb18

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: B16F10_VEA_TRX_1

description: Library name: 7797_16_TRX_2_1


title: Sbj2_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: HepG2_shHELLS


title: GATAD2B CUT&RUN Repeat 1

description:
Library name: Sample 10
ZBTB7A CUT&RUN


title: B16F10_Combi_LOX_3

description: Library name: 7797_15_LOX_12_2

value: TRXtr-LOX


title: H3K27Ac CUT&RUN Repeat 3

description:
Library name: Sample 9
ZBTB7A CUT&RUN


title: delta_bbr_1

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: QELSC083AX_20231031153015__31__A_balh_delta_bbr_37_h_S285

data_processing:
All reads mappings were performed against our own unpublished Amycolatopsis balhimycina genome.
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness).
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.443 based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript)
Assembly: own unpublished Amycolatopsis balhimycina genome
Supplementary files format and content: counts.txt: A tab separated matrix with samples as columns and genes as rows

organism: Amycolatopsis balhimycina

source_name: bacterial cell

growth_protocol: A. balhimycina wildtype, Δtba and Δbbr were cultivated in balhimycin production conditions for 37 h

extract_protocol:
RNA was extracted using the “Zymo Quick RNA Fungal/Bacterial Kit” (Zymo Research, CN#R2014) according to the manufacturer’s instructions. The RNA integrity was checked by agarose gel electrophoresis and residual DNA was removed by DNAseI treatment using the “DNA-free™ DNA Removal Kit” (ThermoFischer, CN#AM1906). Successful digestion was initially checked by PCR. The total RNA was quantified with a “Qubit RNA BR Assay Kit” (Thermo Fisher) and RNA integrity was checked by an Agilent 2100 BioAnalyzer with the “RNA 6000 Pico kit” (Agilent).
Library preparation and ligation were performed using “Illumina Stranded Total RNA Prep” and “Ribo-Zero Plus Microbiome”, respectively, according to the manufacturer’s instructions. In brief, 100 ng of total RNA per sample were subjected to rRNA depletion, followed by cDNA library construction, adapter ligation, and 15 cycles of barcoding PCR. The obtained libraries were quantified with the “Qubit 1x DNA HS Assay Kit” (Thermo Fisher) and the fragment distribution was checked with an Agilent 2100 BioAnalyzer using the “High Sensitivity DNA Kit” (Agilent). Libraries were subsequently pooled and sequenced on an Illumina NovaSeq 6000 device using “NovaSeq 6000 SP Reagent Kit” (v1.5) (100 cycles) with a run mode 75,10,10,0. The average number of reads obtained was 13-21x106. The sequencing was demultiplexed with the latest version of the nextflow pipeline: nf-core/demultiplex. For demultiplexing, “bcl2fastq” was used and the quality was checked with “fastp”.

value: bacterial cell

value: delta bbr

value: genetic modification (knockout)


title: BMDM_FG-1


title: B16F10_Combi_LOX_1

description: Library name: 7797_13_LOX_12_3

value: sc. Flank tumor


title: H3K27Ac CUT&RUN Repeat 2

description:
Library name: Sample 8
ZBTB7A CUT&RUN


title: B16F10_Combi_LOX_2.

description: Library name: 7797_14_LOX_11_2


title: delta_tba_2

description: QELSC082AP_20231031153015__23__A_balh__delta_tba_37_h_S276

value: delta tba


title: H3K27Ac CUT&RUN Repeat 1

description:
Library name: Sample 7
ZBTB7A CUT&RUN

value: WT


title: delta_tba_1

description: QELSC081AH_20231031153015__21__A_balh_delta_tba_37_h_S275


title: BMDM_Ctr-3

value: Ctr


title: BMDM_Ctr-2


title: BMDM_FG-3