title: DNAm peripheral blood sample_291


title: DNAm peripheral blood sample_288

status: Public on Jan 14 2023

type: genomic

city: Munich

first: Natan

last: Yusupov

address: Kraepelinstr. 2-10

department: Dept. Genes and Environment

country: Germany

institute: Max Planck Institute of Psychiatry

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi pipline with stratified quantile normalization and subsequently beta-mixture quantile normalization. Batch effects corrected with ComBat

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral whole blood samples according to standard procedures

tag: Sex

value: Female

tag: age

tag: study

value: Former Smoker

tag: bmi

value: Non-Exposed


title: DNAm peripheral blood sample_286

value: Male

value: Never Smoker


title: DNAm peripheral blood sample_285

value: Exposed


title: DNAm peripheral blood sample_296


title: DNAm peripheral blood sample_280


title: DNAm peripheral blood sample_281


title: DNAm peripheral blood sample_279


title: DNAm peripheral blood sample_277


title: DNAm peripheral blood sample_278


title: DNAm peripheral blood sample_276


title: DNAm peripheral blood sample_275


title: DNAm peripheral blood sample_274


title: DNAm peripheral blood sample_272


title: DNAm peripheral blood sample_273


title: DNAm peripheral blood sample_266


title: DNAm peripheral blood sample_271


title: DNAm peripheral blood sample_269


title: DNAm peripheral blood sample_257


title: DNAm peripheral blood sample_261


title: DNAm peripheral blood sample_263


title: DNAm peripheral blood sample_267


title: DNAm peripheral blood sample_264


title: DNAm peripheral blood sample_260


title: DNAm peripheral blood sample_259


title: DNAm peripheral blood sample_258


title: DNAm peripheral blood sample_262


title: DNAm peripheral blood sample_254


title: DNAm peripheral blood sample_255


title: DNAm peripheral blood sample_270


title: DNAm peripheral blood sample_253


title: DNAm peripheral blood sample_252


title: DNAm peripheral blood sample_265


title: DNAm peripheral blood sample_268


title: DNAm peripheral blood sample_250


title: DNAm peripheral blood sample_251


title: DNAm peripheral blood sample_373


title: DNAm peripheral blood sample_248


title: DNAm peripheral blood sample_256


title: DNAm peripheral blood sample_249


title: DNAm peripheral blood sample_246


title: DNAm peripheral blood sample_245


title: DNAm peripheral blood sample_247


title: DNAm peripheral blood sample_242


title: DNAm peripheral blood sample_241


title: DNAm peripheral blood sample_243


title: DNAm peripheral blood sample_233


title: DNAm peripheral blood sample_234


title: DNAm peripheral blood sample_232


title: DNAm peripheral blood sample_235


title: DNAm peripheral blood sample_231


title: DNAm peripheral blood sample_236


title: DNAm peripheral blood sample_240


title: DNAm peripheral blood sample_239


title: DNAm peripheral blood sample_237


title: DNAm peripheral blood sample_238


title: DNAm peripheral blood sample_229


title: DNAm peripheral blood sample_228


title: DNAm peripheral blood sample_226


title: DNAm peripheral blood sample_230


title: DNAm peripheral blood sample_224


title: DNAm peripheral blood sample_244


title: DNAm peripheral blood sample_223


title: DNAm peripheral blood sample_227


title: DNAm peripheral blood sample_225


title: DNAm peripheral blood sample_222


title: DNAm peripheral blood sample_219


title: DNAm peripheral blood sample_218


title: DNAm peripheral blood sample_220


title: DNAm peripheral blood sample_216


title: DNAm peripheral blood sample_217


title: DNAm peripheral blood sample_215


title: DNAm peripheral blood sample_214


title: DNAm peripheral blood sample_213


title: DNAm peripheral blood sample_208


title: DNAm peripheral blood sample_211


title: DNAm peripheral blood sample_221


title: DNAm peripheral blood sample_209


title: DNAm peripheral blood sample_210


title: DNAm peripheral blood sample_212


title: DNAm peripheral blood sample_202


title: DNAm peripheral blood sample_205


title: DNAm peripheral blood sample_204


title: DNAm peripheral blood sample_203


title: DNAm peripheral blood sample_206


title: DNAm peripheral blood sample_200


title: DNAm peripheral blood sample_207


title: DNAm peripheral blood sample_201


title: DNAm peripheral blood sample_196


title: DNAm peripheral blood sample_197


title: DNAm peripheral blood sample_190


title: DNAm peripheral blood sample_199


title: DNAm peripheral blood sample_198


title: DNAm peripheral blood sample_193


title: DNAm peripheral blood sample_195


title: DNAm peripheral blood sample_189


title: DNAm peripheral blood sample_192


title: DNAm peripheral blood sample_194


title: DNAm peripheral blood sample_187


title: DNAm peripheral blood sample_191


title: DNAm peripheral blood sample_182


title: DNAm peripheral blood sample_181


title: DNAm peripheral blood sample_179


title: DNAm peripheral blood sample_186


title: DNAm peripheral blood sample_185


title: DNAm peripheral blood sample_188


title: DNAm peripheral blood sample_177


title: DNAm peripheral blood sample_175


title: DNAm peripheral blood sample_183


title: DNAm peripheral blood sample_178


title: DNAm peripheral blood sample_176


title: DNAm peripheral blood sample_174


title: DNAm peripheral blood sample_172


title: DNAm peripheral blood sample_173


title: DNAm peripheral blood sample_170


title: DNAm peripheral blood sample_171


title: DNAm peripheral blood sample_168


title: DNAm peripheral blood sample_167


title: DNAm peripheral blood sample_169

value: Current Smoker


title: DNAm peripheral blood sample_184


title: DNAm peripheral blood sample_180


title: DNAm peripheral blood sample_162


title: DNAm peripheral blood sample_163


title: DNAm peripheral blood sample_160


title: DNAm peripheral blood sample_161


title: DNAm peripheral blood sample_159


title: DNAm peripheral blood sample_157


title: DNAm peripheral blood sample_158


title: DNAm peripheral blood sample_156


title: DNAm peripheral blood sample_154


title: DNAm peripheral blood sample_164


title: DNAm peripheral blood sample_166


title: DNAm peripheral blood sample_150


title: DNAm peripheral blood sample_153


title: DNAm peripheral blood sample_152


title: DNAm peripheral blood sample_151


title: DNAm peripheral blood sample_165


title: DNAm peripheral blood sample_149


title: DNAm peripheral blood sample_147


title: DNAm peripheral blood sample_148


title: DNAm peripheral blood sample_142


title: DNAm peripheral blood sample_146


title: DNAm peripheral blood sample_145


title: DNAm peripheral blood sample_140


title: DNAm peripheral blood sample_134


title: DNAm peripheral blood sample_138


title: DNAm peripheral blood sample_155


title: DNAm peripheral blood sample_139


title: DNAm peripheral blood sample_132


title: DNAm peripheral blood sample_144


title: DNAm peripheral blood sample_143


title: DNAm peripheral blood sample_133


title: DNAm peripheral blood sample_131


title: DNAm peripheral blood sample_130


title: DNAm peripheral blood sample_141


title: DNAm peripheral blood sample_129


title: DNAm peripheral blood sample_128


title: DNAm peripheral blood sample_125


title: DNAm peripheral blood sample_135


title: DNAm peripheral blood sample_123


title: DNAm peripheral blood sample_121


title: DNAm peripheral blood sample_124


title: DNAm peripheral blood sample_137


title: DNAm peripheral blood sample_122


title: DNAm peripheral blood sample_118


title: DNAm peripheral blood sample_119


title: DNAm peripheral blood sample_120


title: DNAm peripheral blood sample_127


title: DNAm peripheral blood sample_126


title: DNAm peripheral blood sample_136


title: DNAm peripheral blood sample_116


title: DNAm peripheral blood sample_112


title: DNAm peripheral blood sample_111


title: DNAm peripheral blood sample_115


title: DNAm peripheral blood sample_114


title: DNAm peripheral blood sample_108


title: DNAm peripheral blood sample_110


title: DNAm peripheral blood sample_109


title: DNAm peripheral blood sample_113


title: DNAm peripheral blood sample_106


title: DNAm peripheral blood sample_105


title: DNAm peripheral blood sample_107


title: DNAm peripheral blood sample_117


title: DNAm peripheral blood sample_104


title: DNAm peripheral blood sample_98


title: DNAm peripheral blood sample_102


title: DNAm peripheral blood sample_99


title: DNAm peripheral blood sample_100


title: DNAm peripheral blood sample_101


title: DNAm peripheral blood sample_94


title: DNAm peripheral blood sample_103


title: DNAm peripheral blood sample_97


title: DNAm peripheral blood sample_96


title: DNAm peripheral blood sample_95


title: DNAm peripheral blood sample_92


title: DNAm peripheral blood sample_90


title: DNAm peripheral blood sample_91


title: DNAm peripheral blood sample_89


title: DNAm peripheral blood sample_88


title: DNAm peripheral blood sample_85


title: DNAm peripheral blood sample_82


title: DNAm peripheral blood sample_87


title: DNAm peripheral blood sample_86


title: DNAm peripheral blood sample_84


title: DNAm peripheral blood sample_83


title: DNAm peripheral blood sample_93


title: DNAm peripheral blood sample_81


title: DNAm peripheral blood sample_80


title: DNAm peripheral blood sample_79


title: DNAm peripheral blood sample_77


title: DNAm peripheral blood sample_78


title: DNAm peripheral blood sample_76


title: DNAm peripheral blood sample_73


title: DNAm peripheral blood sample_74


title: DNAm peripheral blood sample_75


title: DNAm peripheral blood sample_70


title: DNAm peripheral blood sample_62


title: DNAm peripheral blood sample_63


title: DNAm peripheral blood sample_61


title: DNAm peripheral blood sample_69


title: DNAm peripheral blood sample_71


title: DNAm peripheral blood sample_67


title: DNAm peripheral blood sample_64


title: DNAm peripheral blood sample_65


title: DNAm peripheral blood sample_66


title: DNAm peripheral blood sample_60


title: DNAm peripheral blood sample_59


title: DNAm peripheral blood sample_68


title: DNAm peripheral blood sample_72


title: DNAm peripheral blood sample_54


title: DNAm peripheral blood sample_56


title: DNAm peripheral blood sample_57


title: DNAm peripheral blood sample_55


title: DNAm peripheral blood sample_51


title: DNAm peripheral blood sample_52


title: DNAm peripheral blood sample_53


title: C5

type: RNA

city: Shenzhen

first: Fei

last: Shi

address: Dongbeimen street,Shenzhen, Guangdong, China

country: China

institute: Shenzhen People’s Hospital

hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

data_processing: The gene expression profile data were extracted using Agilent Feature Extraction Software(11.0.1.1),and analyzed using Agilent GeneSpring GX 12.1.

molecule: total RNA

source_name: moderate to severe asthmatic subject

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

extract_protocol: Total RNA from each serum sample was isolated with the TRIzol Reagent (Invitrogen life technologies). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: colltecting serum from healthy control and asthmatic patient after informed consent

tag: tissue

value: Serum

tag: disease state

value: moderate to severe asthmatic subject


title: MDA-MB-231, control, rep2

status: Public on Jan 15 2023

type: SRA

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

library_source: transcriptomic

data_processing:
Processing raw data for both format conversion and de-multiplexing were performed by Bcl2Fastq version 2.20 of the Illumina pipeline.
Sequence reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool then adapter sequences were masked with Cutadapt version 1.11 from raw fastq data using the following parameters: --anywhere --overlap 5 --times 2 --minimum-length 35 --mask-adapter.
Then reads were mapped to the mouse Ensembl GRCh38 build reference genome using HISAT2 version 2.2.0 using Gene annotations according to the Ensembl database. Gene-level quantification was performed using salmon version 1.8.0 (12).
To identify differentially expressed genes (DEGs) data was filtered to remove from the analysis the genes having < 10 counts per million across all replicates for each comparison.
The data normalization and differential analysis for gene expression were performed using Bioconductor R package DESeq2 version 1.34 accounting for the presence of batch effects.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: breast

extract_protocol:
Total RNA was extracted from purified from cell pellets of control and KDM5B-NTT-overexpressing cultures using Qiagen RNeasy kits
RNA-Seq libraries from total RNA (1 g) from each sample were prepared using the Illumina TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) according to manufacturer’s instructions.

value: breast

tag: cell line


title: DNAm peripheral blood sample_50


title: DNAm peripheral blood sample_58


title: DNAm peripheral blood sample_48


title: C3


title: DNAm peripheral blood sample_47


title: DNAm peripheral blood sample_45


title: DNAm peripheral blood sample_49


title: C1


title: B2

source_name: Mild asthmatic patient

value: mild asthmatic patient


title: B4


title: B1


title: DNAm peripheral blood sample_42


title: C2


title: C4


title: B5


title: DNAm peripheral blood sample_43


title: DNAm peripheral blood sample_37


title: DNAm peripheral blood sample_38


title: DNAm peripheral blood sample_40


title: DNAm peripheral blood sample_46


title: A3

source_name: healthy control

value: healthy control


title: A5


title: B3


title: DNAm peripheral blood sample_39


title: A4


title: A2


title: A1


title: DNAm peripheral blood sample_36


title: DNAm peripheral blood sample_41


title: DNAm peripheral blood sample_34


title: DNAm peripheral blood sample_35


title: DNAm peripheral blood sample_33


title: DNAm peripheral blood sample_44


title: NeuN_Rbfox3 crRNA 5, 1

city: Beijing

first: Yunfei

last: Li

state: China

address: 38 Xueyuan Road, Haidian District, Beijing

department: Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China

institute: Peking University

description: Transfecting the plasmids encoding RfxCas13d, NeuN and Rbfox3 crRNA 5 into HEK293T cells. Cells were collected for total RNA extraction 24 hour after transfection.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The DESeq2 software was used to identify the differantially expressed genes.
Assembly: human genome version hg38 was used as reference genome.
Supplementary files format and content: Excel spreadsheet includes the FPKM value for each sample.

source_name: HEK293T cells

growth_protocol: HEK293T Cells were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Total RNA was extracted using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: Harvest cells using Trizol reagent 24 hours after transfection with indicated plasmids.

value: HEK293T cells

tag: transfection

value: NeuN_Rbfox3 crRNA 5


title: NeuN_Rbfox3 crRNA 3, 3

description: Transfecting the plasmids encoding RfxCas13d, NeuN and Rbfox3 crRNA 3 into HEK293T cells. Cells were collected for total RNA extraction 24 hour after transfection.

value: NeuN_Rbfox3 crRNA 3


title: NeuN_Rbfox3 crRNA 5, 3


title: NeuN_Rbfox3 crRNA 3, 2


title: DNAm peripheral blood sample_32


title: NeuN_Rbfox3 crRNA 5, 2


title: NeuN_NT crRNA, 3

description: Transfecting the plasmids encoding RfxCas13d, NeuN and NT crRNA into HEK293T cells. Cells were collected for total RNA extraction 24 hour after transfection.

value: NeuN_NT crRNA


title: DNAm peripheral blood sample_31


title: DNAm peripheral blood sample_30


title: DNAm peripheral blood sample_29


title: NeuN_NT crRNA, 1


title: NeuN_Rbfox3 crRNA 3, 1


title: NeuN_NT crRNA, 2


title: EVT_D8_rep2

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to hg39 genome using Hisat2.
FeatureCounts was used to quanlify gene expression
Assembly: hg38
Supplementary files format and content: comma-delimited count values for each Sample.

source_name: trophoblasts

growth_protocol: Trophoblast stem cells (hTSCs) were cultured in hTSC media: DMEM/F12 (Gibco. Cat. 21331-020) supplemented with 50.0uM β-mercaptoethanol (Thermo. Cat. 31350010), 0.2% FBS (Gibco. Cat. 10270), 0.5% Penicillin-Streptomycin-Glutamine (Thermo, Cat.10378016), 0.3% BSA (Gibco. Cat. 15260037),1.0% ITS-X supplement (Gibco. Cat. 51500056), 50.0 µg/mL Vc (Sigma. Cat. 49752-100G), 50.0 ng/mL EGF (R&D, Cat. 236-EG-200), 2.0 µM CHIR99021 (GSK3i. Tocris. Cat. 4423), 0.5 µM A83-01 (Tocris. Cat. 2939), 1.0 µM SB431542 (Tocris. Cat. 1614), 10.0 µM VPA (Stemcell. Cat. 72292) and 5.0 µM Y27632 (Tocris. Cat. 1254).

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher) and was subjected to extract with Direct-zol RNA Microprep kit (Zymo research)
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix 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 AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Indicated trophoblasts were seeded one day before infection and other types of differentiated cells at the suitable time point. On the day of infection, cells were washed with PBS and infected at the indicated multiplicity of infection (MOI) by diluting viruses in basal medium. Cells were incubated at 37°C for 2 hrs. Subsequently, the inoculum was removed, replaced with complete culture medium, and further incubated until harvest. Trophoblasts were submitted for SARS-CoV-2 or MERS-CoV infection at 0.1 MOI for one hour followed by incubation with or without remdesivir and GC376.  Cells were collected at 48hpi for analysis.

tag: strain

tag: genotype

value: wild type

tag: cell type

value: Trophoblast stem cells (hTSCs)

tag: treatment

value: EVT


title: DNAm peripheral blood sample_27

value: Female

value: Former Smoker

value: Non-Exposed


title: EVT_D6_rep1


title: EVT_D8_rep1


title: DNAm peripheral blood sample_25


title: DNAm peripheral blood sample_28

value: Never Smoker


title: DNAm peripheral blood sample_26

value: Male


title: EVT_D4_rep1


title: DNAm peripheral blood sample_23


title: EVT_D2_rep2


title: DNAm peripheral blood sample_22


title: EVT_D2_rep1


title: STB_D6_rep2

value: STB


title: DNAm peripheral blood sample_21


title: DNAm peripheral blood sample_24


title: DNAm peripheral blood sample_19


title: STB_D6_rep1


title: STB_D4_rep2


title: STB_D4_rep1


title: DNAm peripheral blood sample_20


title: DNAm peripheral blood sample_17


title: DNAm peripheral blood sample_18

value: Exposed


title: DNAm peripheral blood sample_16


title: STB_D2_rep1


title: STB_D2_rep2


title: DNAm peripheral blood sample_15


title: DNAm peripheral blood sample_14

value: Current Smoker


title: DNAm peripheral blood sample_13


title: Trophoblast organoids of Day 14 rep2

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to hg39 genome using Hisat2.
FeatureCounts was used to quanlify gene expression
Assembly: hg38
Supplementary files format and content: tab-delimited count values for each Sample.

source_name: trophoblast organoids


title: TSC_C5_GATA2 rep1

source_name: trophoblast stem cells

value: mcherry knock in GATA2 locus


title: Trophoblast organoids of Day 18


title: Trophoblast organoids of Day 20


title: DNAm peripheral blood sample_8


title: DNAm peripheral blood sample_7


title: Trophoblast organoids of Day 14 rep1


title: STB Day4 infection rep3

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to hg39 genome using Hisat2.
FeatureCounts was used to quanlify gene expression
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited count values for each Sample.

tag: infected

value: yes


title: TSC_C5_GATA2 rep2


title: DNAm peripheral blood sample_12


title: DNAm peripheral blood sample_11


title: TSC rep2

source_name: trophoblast stem cells(hTSCs)


title: DNAm peripheral blood sample_10


title: DNAm peripheral blood sample_9


title: TSC rep1


title: STB Day4 Mock rep2

value: no

value: mock


title: STB Day4 Mock rep3


title: STB Day4 infection rep2


title: STB Day4 infection rep1


title: STB Day4 Mock rep1


title: DNAm peripheral blood sample_6


title: DNAm peripheral blood sample_1


title: DNAm peripheral blood sample_2


title: DNAm peripheral blood sample_5


title: STB Day3 infection rep1


title: STB Day3 infection rep2


title: DNAm peripheral blood sample_4


title: BLOOD_Sample2, replicate1, scRNAseq

city: Houston

first: Linghua

last: Wang

address: 1881 East Road,

country: USA

institute: MD Anderson Cancer Center

description:
10x Genomics
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
metadata.tsv.gz

library_source: transcriptomic single cell

data_processing: Sequence data was then put through the 10X genomic cell ranger 3.0 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.

source_name: Blood

extract_protocol: scRNA-seq was performed using 10x Genomics Chromium Single Cell Controller. Sorted cells were washed with 1X PBS and suspended in PBS/0.04% BSA. Cells were double-checked for viability and cell number by using the countess II FL and microscope. All cells were diluted to a concentration of 500-1000 cells/μl in PBS/0.04% BSA before being used for single cell 10X 3’v3. Single cells were captured using the 10X genomic controller according to the bead types and chip used for the experiments. The 10X genomic Chromium Single cell 3’ GEM, library and Gel bead Kit ’v3 (Catalogue #1000075) and chromium chip B single cell kit (Part# 1000073) were used to capture cells on the controller; cell recovery targeted was in a range of 5000 - 10000 cells. Captured cells then undergo a GEM-RT, cDNA amplification, and all purification in accordance to the 10X protocol. Cleanup cDNA was checked via a tape station (Agilent 42000) HSD5000 (Catalogue# Part# 5067-5593) for cDNA traces. 25% of the cDNA was used to generate the library, and the Chromium i7 multiplex kit (Part# 120262) was used to identify each sample. Library cleanup was performed using AMPure beads and QC was done again with tape station D1000 tapes (Part # 5067-5583). Ten libraries of equal amount were pooled to give a final concentration of 10nM and submitted for sequencing with the NovaSeq6000 S2 sequencer, 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC core at MD Anderson.

tag: cancer type

value: Not Applicable

value: Lymphocytes

value: Blood

tag: tissue type

value: Healthy normal tissue

value: Not applicable


title: STB Day3 infection rep3

value: wild type


title: rat spleen 6mA MeDIP-seq

first: Shunmin

last: He

address: 1 Beichen West Road,  Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: genomic

data_processing:
MeDIP-seq reads were aligned to the dm6 genome assembly using bowtie2 with with parameters “--no-mixed --no-discordant --non-deterministic --very-sensitive-local”
MACS2 callpeak was used to identify enrichment peaks with parameters “-f BAMPE –B” and a default q-value (FDR) cutoff of 0.05, and used IgG as a control
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result

organism: Rattus norvegicus

source_name: rat spleen 6mA

extract_protocol:
Genomic DNA was extracted from Drosophila and other animal tissues using the Wizard genomic DNA purification Kit (Promega) following the manufacturer’s instructions. 5 µg of fragmented genomic DNA was immunoprecipitated with 5 µg of rabbit 6mA antibody (Abcam) or rabbit IgG overnight at 4°C in a final volume of 500 µl immunoprecipitation buffer. Then the mixture was incubated with 50 µl protein A/G agarose beads for 2 h at 4°C and then washed three times with 1 ml of immunoprecipitation buffer. The beads were then treated with proteinase K and the methylated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation for library construction.
End repair, 3′-adenylation, adaptor ligation, and PCR amplification were performed according to Illumina TruSeq DNA sample preparation procedures. Libraries were sequenced using the Illumina Hiseq2500 V4 platform.

value: SD Rat

value: spleen

value: 2 months


title: BLOOD_Sample1, replicate1, scRNAseq


title: rat hippocampus 6mA MeDIP-seq

source_name: rat hippocampus 6mA

value: hippocampus


title: STAD_Sample9, replicate1, scRNAseq

source_name: Peritoneal cavity

value: STAD

value: Peritoneal cavity

value: Metastatic tumor tissue

value: Naïve


title: STB Day3 Mock rep2


title: STAD_Sample8, replicate1, scRNAseq

source_name: Stomach

value: Stomach

value: Primary tumor tissue


title: STAD_Sample7, replicate1, scRNAseq


title: STB infection drug GC376 48hpi  rep2

value: yes


title: EVT_D4_rep2

value: Trophoblast stem cells (hTSCs)

value: EVT


title: DNAm peripheral blood sample_3

value: Female

value: Never Smoker

value: Non-Exposed


title: STB Day3 Mock rep3

value: wild type

value: no

value: mock


title: STAD_Sample6, replicate1, scRNAseq

value: Lymphocytes

value: Not Applicable


title: rat Input

source_name: rat Input

value: SD Rat

value: testis

value: 2 months


title: STB infection drug GC376 48hpi  rep1


title: STB infection drug Remd 48hpi  rep2

value: remdesivir


title: STAD_Sample4, replicate1, scRNAseq

value: STAD

value: Peritoneal cavity

value: Metastatic tumor tissue

value: Naïve


title: STAD_Sample5, replicate1, scRNAseq

value: Blood

value: Uninvolved normal tissue


title: STAD_Sample3, replicate1, scRNAseq

value: Stomach

value: Primary tumor tissue


title: STB infection drug Remd  48hpi rep1

value: wild type

value: yes


title: STB infection drug infection 48hpi rep1


title: STAD_Sample1, replicate1, scRNAseq


title: STB infection drug infection 48hpi  rep2


title: OV_Sample2, replicate1, scRNAseq

value: OV

value: Not applicable


title: OV_Sample1, replicate1, scRNAseq

value: Lymphocytes

value: Not Applicable


title: STB Day3 Mock rep1

value: no

value: mock


title: LN_2_Sample13, replicate1, scRNAseq

source_name: Lymph node

value: DLBCL

value: Lymph node


title: STB infection drug mock  48h rep2


title: LN_2_Sample12, replicate1, scRNAseq


title: STB infection drug mock 48h rep1


title: LN_2_Sample11, replicate1, scRNAseq


title: LN_2_Sample9, replicate1, scRNAseq


title: LN_2_Sample10, replicate1, scRNAseq


title: YY3L: young isochronic parabiont 3 left

city: Cambridge

first: Lee

middle: L

last: Rubin

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: 10X Genomics

data_processing:
Cell Ranger (version 2.0) (10X Genomics) was used to perform sample de-multiplexing, barcode processing and single cell gene unique molecular identifier (UMI) counting, while a digital expression matrix was obtained for each experiment with default parameters, mapped to the 10x reference for mm10, version 1.2.0.
After the initial sequencing, the samples in each pool were re-pooled based on the actual number of cells detected by Cell Ranger, aiming to sequence each sample to a similar depth (number of reads/cell) (median: 40,007). Multiple NextSeq runs were conducted to achieve over 70% sequencing saturation as determined again by Cell Ranger (median: 75%).
Basic processing and visualization of the scRNA-seq data were performed using the Seurat package (version 3.2.1.9002) in R (version 3.6.1)
Meta data with cell types and subpopulations after filtering, with nCount_RNA, nFeature_RNA, percent mito, percent ribo, are in the additional meta data file within the processed data section.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Raw tab-separated values files and matrix for filtered barcodes
Supplementary files format and content: Processed tab-separated values files and matrix for filtered barcodes
Supplementary files format and content: Metadata cell types and subpopulation for filtered barcodes

organism: Mus musculus

source_name: brain

extract_protocol:
Brain cells were processed through all steps to generate stable cDNA libraries. Briefly, after dissociation, cells were diluted in ice-cold PBS containing 0.4% BSA at a density of 1,000 cells/ul.
For every sample, 17,400 cells were loaded into a Chromium Single Cell™ Chip (10x Genomics) and processed following the manufacturer™s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3™ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics). Libraries were pooled based on their molar concentrations. Pooled libraries were then loaded at 2.07 pM and sequenced on a NextSeq 500 instrument (Illumina) with 26 bases for read1, 57 bases for read2 and 8 bases for Index1.

value: brain

value: male

value: 3-4 months old

value: isochronic parabiosis


title: YY4L: young isochronic parabiont 4 left

description: 10X Genomics


title: YY4R: young isochronic parabiont 4 right

description: 10X Genomics


title: YY2R: young isocrhonic parabiont 2 right

description: 10X Genomics


title: YY3R: young isochronic parabiont 3 right

description: 10X Genomics


title: YY2L: young isochronic parabiont 2 left

description: 10X Genomics


title: YY1R: young isochronic parabiont 1 right

description: 10X Genomics


title: LN_2_Sample8, replicate1, scRNAseq


title: LN_2_Sample7, replicate1, scRNAseq


title: LN_2_Sample6, replicate1, scRNAseq


title: LN_2_Sample5, replicate1, scRNAseq


title: YX8L: young animal 8

description: 10X Genomics

value: 2-3 months old

value: unpaired


title: YY1L: young isochronic parabiont 1 left

description: 10X Genomics


title: STAD_Sample2, replicate1, scRNAseq

value: STAD

value: Stomach

value: Uninvolved normal tissue

value: Naïve


title: LN_2_Sample4, replicate1, scRNAseq

value: Primary tumor tissue

value: Not applicable


title: LN_2_Sample3, replicate1, scRNAseq

value: Lymphocytes

value: Not Applicable


title: YX7R: young animal 7

description: 10X Genomics


title: RfxCas13d_N5 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Rbfox3 crRNA 6 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The DESeq2 software was used to identify the differantially expressed genes.
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: Excel spreadsheet includes the FPKM value for each sample.

source_name: N2A cells

growth_protocol: N2A Cells were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

treatment_protocol: Harvest cells using Trizol reagent 48 hours after transfection with indicated plasmids.

value: N2A cells


title: YX5R: young animal 5

description: 10X Genomics


title: YX6L: young animal 6

description: 10X Genomics


title: YX4R: young animal 4

description: 10X Genomics


title: LN_2_Sample1, replicate1, scRNAseq

value: DLBCL


title: RfxCas13d_T6 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Mapt crRNA 6 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: YX2L: young animal 2

description: 10X Genomics


title: YX3R: young animal 3

description: 10X Genomics


title: YX1L: young animal 1

description: 10X Genomics


title: LC_5_Sample23, replicate1, scRNAseq

source_name: Lung

value: NSCLC

value: Lung


title: LC_5_Sample24, replicate1, scRNAseq

value: EGFR TKIs


title: YO8X: young heterochronic parabiont 8

description: 10X Genomics

value: brain

value: male

value: 3-4 months old

value: heterochronic parabiosis


title: RfxCas13d_T4 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Mapt crRNA 4 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: YO7X: young heterochronic parabiont 7

description: 10X Genomics


title: YO9X: young heterochronic parabiont 9

description: 10X Genomics


title: RfxCas13d_M3 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Map2 crRNA 3 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: YO6X: young heterochronic parabiont 6

description: 10X Genomics


title: LC_5_Sample22, replicate1, scRNAseq


title: YO5X: young heterochronic parabiont 5

description: 10X Genomics


title: RfxCas13d_M1 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Map2 crRNA 1 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: RfxCas13d_K8 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Sik3-S crRNA 8 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: YO4X: young heterochronic parabiont 4

description: 10X Genomics


title: RfxCas13d_K1 crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and Sik3-S crRNA 1 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: LC_5_Sample21, replicate1, scRNAseq


title: YO3X: young heterochronic parabiont 3

description: 10X Genomics


title: LC_5_Sample20, replicate1, scRNAseq


title: YO2X: young heterochronic parabiont 2

description: 10X Genomics


title: RfxCas13d_NT crRNA, rep 2

description: Transfecting the plasmids encoding RfxCas13d and NT crRNA into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: LC_5_Sample19, replicate1, scRNAseq


title: RfxCas13d, rep 2

description: Transfecting the plasmid encoding RfxCas13d into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: OY9X: old heterochronic parabiont 9

description: 10X Genomics

value: 20-22 months old


title: LC_5_Sample18, replicate1, scRNAseq


title: OY8X: old heterochronic parabiont 8

description: 10X Genomics


title: LC_5_Sample17, replicate1, scRNAseq


title: OY7X: old heterochronic parabiont 7

description: 10X Genomics


title: dRfxCas13d_N5 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Rbfox3 crRNA 6 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: dRfxCas13d_T6 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Mapt crRNA 6 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: OY4X: old heterochronic parabiont 4

description: 10X Genomics


title: OY3X: old heterochronic parabiont 3

description: 10X Genomics


title: EVT_D6_rep2

value: wild type

value: Trophoblast stem cells (hTSCs)

value: EVT


title: dRfxCas13d_T4 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Mapt crRNA 4 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: OY2X: old heterochronic parabiont 2

description: 10X Genomics


title: YO1X: young heterochronic parabiont 1

description: 10X Genomics


title: OY1X: old heterochronic parabiont 1

description: 10X Genomics


title: dRfxCas13d_M3 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Map2 crRNA 3 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: OY11X: old heterochronic parabiont 11

description: 10X Genomics


title: OY10X: old heterochronic parabiont 10

description: 10X Genomics


title: LN_2_Sample2, replicate1, scRNAseq

value: Lymph node

value: Primary tumor tissue


title: dRfxCas13d_M1 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Map2 crRNA 1 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: LC_5_Sample15, replicate1, scRNAseq

value: Lymphocytes

value: Uninvolved normal tissue


title: LC_5_Sample14, replicate1, scRNAseq

value: Not Applicable


title: LC_5_Sample16, replicate1, scRNAseq


title: OX6X: old animal 6

description: 10X Genomics

value: 21-22months old

value: unpaired


title: OX7X: old animal 7

description: 10X Genomics


title: LC_5_Sample12, replicate1, scRNAseq

value: NSCLC

value: Metastatic tumor tissue

value: Pozio


title: E28 DZ, scATACseq

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw sequencing data aligned to the pig genome ATAC reference Sscrofa11 (10× reference database was prepared with gene annotation gff3 data v11.1.98 and genomic fasta data v11.1.98 downloaded from the Ensemble).
The digital peaks matrix was quantified using the Cell Ranger ATAC (10× Genomics, v1.2.0) analysis pipeline. The following analysis was performed with the Seurat R package (v3.1.1) and Signac R package (v0.2.2). We kept only those valid barcodes that passed the following thresholds: (1) number of fragments ranging from 2000 to 30,000, (2) mitochondria ratio less than 2%, (3) transcription start site (TSS) enrichment score (by TSSEnrichment function) between 2 and 40, (4) strength of the nucleosome signal per cell (by NucleosomeSignal function) less than 5 and (5) fraction of reads overlapping peaks per cell greater than 50%. After this stringent quality control, we obtained 48,514 single cells.
Normalization and latent semantic indexing (LSI) dimensionality reduction were performed for each sample independently with the RunTFIDF and RunSVD functions. Batch correction by samples was applied by Signac on the first 50 LSI components. We applied the UMAP and TSNE algorithms to the first 50 LSI components corrected by Signac. We identified 15 distinct clusters using the Seurat function FindClusters (resolution equal to 0.3)
Supplementary files format and content: Sscrofa11
Supplementary files format and content: barcodes.tsv, peaks.bed, matrix.mtx

organism: Sus scrofa

source_name: myotome

extract_protocol:
Somite tissues of ZZ and DZ at  E18, E21, and myotome tissues at E28 were isolated and transferred to RPMI1640 medium (GIBCO, 11875093) containing 10% Fetal Bovine Serum (HyClone, SH30070.03) on ice. Then, the tissues were washed with PBS three times and transferred to pre-warmed digestion medium containing 100 μg/mL DNase Ⅰ (Sigma-Aldrich, DN25) and 0.1 g/mL Collagenase I (Sigma, C2674) in RPMI1640. Tissues were shaken vigorously for 30 s and further incubated at 37°C for 30 to 40 minutes in an incubator with general shaking every 6 minutes to release cells. Released cells passed through a 70 μm cell strainer (BD, 352350) and were collected in 15 mL tubes. Sample viability was assessed via Trypan Blue (ThermoFisher) and an automatic cell counter (Countstar). Cells derived from different embryo ages and pigs were sorted and processed independently in all experiments. Thus, each cell can be traced back to the embryos and tissues it came from.
scATAC-seq was performed using the 10× Chromium platform. All protocols to generate scATAC-seq data, including sample preparation, library preparation, and instrument and sequencing settings, are described below and are available at https://support.10xgenomics.com/single-cell-atac.

value: myotome

tag: developmental stage

value: embryonic day (E) 28

tag: breed

value: DurocxTibetan pigs (DZ)


title: OX4X: old animal 4

description: 10X Genomics

value: brain

tag: Sex

value: male


title: dRfxCas13d_K1 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Sik3-S crRNA 1 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

value: N2A cells


title: dRfxCas13d_K8 crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and Sik3-S crRNA 8 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: OY5X: old heterochronic parabiont 5

description: 10X Genomics

tag: age

value: 20-22 months old

value: heterochronic parabiosis


title: OY6X: old heterochronic parabiont 6

description: 10X Genomics


title: dRfxCas13d_NT crRNA, rep 2

description: Transfecting the plasmids encoding dRfxCas13d and NT crRNA into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: LC_5_Sample10, replicate1, scRNAseq

description:
10x Genomics
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
metadata.tsv.gz

value: Lung

value: Primary tumor tissue

value: Naïve


title: E21 DZ, scATACseq

description: 10x Genomics

source_name: Somite

value: Somite

value: embryonic day (E) 21


title: OX8X: old animal 8

description: 10X Genomics

value: 21-22months old

value: unpaired


title: dRfxCas13d, rep 2

description: Transfecting the plasmid encoding dRfxCas13d into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: E21 ZZ, scATACseq

description: 10x Genomics

value: Tibetan pigs (ZZ)


title: LC_5_Sample9, replicate1, scRNAseq

value: NSCLC

value: Lymphocytes

value: Not Applicable

value: Uninvolved normal tissue


title: RfxCas13d_N5 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Rbfox3 crRNA 6 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: OX2X: old animal 2

description: 10X Genomics

value: brain


title: OX5X: old animal 5

description: 10X Genomics

value: male


title: E18 DZ, scATACseq

description: 10x Genomics

value: embryonic day (E) 18

value: DurocxTibetan pigs (DZ)


title: LC_5_Sample13, replicate1, scRNAseq

value: EGFR TKIs


title: OO6R: old isochronic parabiont 6 right

description: 10X Genomics

value: 20-22 months old

value: isochronic parabiosis


title: RfxCas13d_T6 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Mapt crRNA 6 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

value: N2A cells


title: LC_5_Sample7, replicate1, scRNAseq

value: Lung

value: Primary tumor tissue

value: Not available


title: LC_5_Sample8, replicate1, scRNAseq

source_name: Liver

value: Liver

value: Metastatic tumor tissue


title: OO6L: old isochconic parabiont 6 left

description: 10X Genomics


title: E28 ZZ, scATACseq

description: 10x Genomics

value: myotome

value: embryonic day (E) 28

value: Tibetan pigs (ZZ)


title: LC_5_Sample11, replicate1, scRNAseq

source_name: Kidney

value: NSCLC

value: Lymphocytes

value: Not Applicable

value: Kidney

value: Pozio


title: LC_5_Sample6, replicate1, scRNAseq

value: Uninvolved normal tissue


title: OO5R: old isocrhonic parabiont 5 right

description: 10X Genomics

value: brain

value: male

value: 20-22 months old


title: LC_5_Sample5, replicate1, scRNAseq

value: Lung


title: RfxCas13d_M3 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Map2 crRNA 3 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

value: N2A cells


title: OX3X: old animal 3

description: 10X Genomics

value: 21-22months old

value: unpaired


title: E28 ZZ, scRNAseq

description: 10x Genomics

data_processing:
Raw sequencing data were aligned to the pig gene expression reference Sscrofa11 (the 10× reference database was prepared with the gene annotation gff3 dataset v11.1.98 and genomic fasta dataset v11.1.98, which were downloaded from Ensemble).
The CellRanger (10× Genomics) analysis pipeline was used to generate a digital gene expression matrix from these data. The raw digital gene expression matrix (UMI counts per gene per cell) was filtered, normalized, and clustered using R [v3.5.2, https://www.R-project.org/].
Cell and gene filtering was performed as follows: cells with fewer than 200 genes detected, or more than 30,000 UMIs and cells containing greater than 10% of reads from mitochondrial genes were removed.
Assembly: Sscrofa11
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Somite tissues of ZZ and DZ at  E18, E21, and myotome tissues at E28 were isolated and transferred to RPMI1640 medium (GIBCO, 11875093) containing 10% Fetal Bovine Serum (HyClone, SH30070.03) on ice. Then, the tissues were washed with PBS three times and transferred to pre-warmed digestion medium containing 100 μg/mL DNase Ⅰ (Sigma-Aldrich, DN25) and 0.1 g/mL Collagenase I (Sigma, C2674) in RPMI1640. Tissues were shaken vigorously for 30 s and further incubated at 37°C for 30 to 40 minutes in an incubator with general shaking every 6 minutes to release cells. Released cells passed through a 70 μm cell strainer (BD, 352350) and were collected in 15 mL tubes. Sample viability was assessed via Trypan Blue (ThermoFisher) and an automatic cell counter (Countstar). Cells derived from different embryo ages and pigs were sorted and processed independently in all experiments. Thus, each cell can be traced back to the embryos and tissues it came from.
Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics, PN120263) following the manufacturer’s instruction. After droplet generation, samples were transferred onto a pre-chilled 8-well tube (Eppendorf), and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x Genomics, followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted at a ratio of 1:4  and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).


title: OO5L: old isochronic parabiont 5 left

description: 10X Genomics

value: isochronic parabiosis


title: E21 DZ, scRNAseq

description: 10x Genomics

value: Somite

value: embryonic day (E) 21

value: DurocxTibetan pigs (DZ)


title: LC_5_Sample4, replicate1, scRNAseq

value: NSCLC

value: Primary tumor tissue

value: EGFR TKIs


title: OX1X: old animal 1

description: 10X Genomics


title: E21 ZZ, scRNAseq

description: 10x Genomics

value: Tibetan pigs (ZZ)


title: RfxCas13d_K8 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Sik3-S crRNA 8 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: LC_5_Sample2, replicate1, scRNAseq

value: Lymphocytes

value: Not Applicable


title: E18 ZZ, scATACseq

description: 10x Genomics

value: embryonic day (E) 18


title: OO4R: old isochronic parabiont 4 right

description: 10X Genomics

value: brain

value: male


title: LC_5_Sample3, replicate1, scRNAseq

value: Lung


title: E18 DZ, scRNAseq

description: 10x Genomics


title: LC_5_Sample1, replicate1, scRNAseq

value: Uninvolved normal tissue


title: OO4L: old isochronic parabiont 4 left

description: 10X Genomics

value: 20-22 months old


title: OO3R: old isochronic parabiont 3 right

description: 10X Genomics


title: E28 DZ, scRNAseq

description: 10x Genomics

value: myotome

value: embryonic day (E) 28


title: RfxCas13d_K1 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Sik3-S crRNA 1 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

value: N2A cells


title: E18 ZZ, scRNAseq

description: 10x Genomics

value: Somite


title: BRCA_2_Sample1, replicate1, scRNAseq

source_name: Breast

value: Breast

value: Not applicable


title: RfxCas13d_T4 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Mapt crRNA 4 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: E16 ZZ, scRNAseq

description: 10x Genomics

value: embryonic day (E) 16


title: OO2R: old isochronic parabiont 2 right

description: 10X Genomics

value: isochronic parabiosis


title: E16 DZ, scRNAseq

description: 10x Genomics

value: DurocxTibetan pigs (DZ)


title: dRfxCas13d_N5 crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and Rbfox3 crRNA 6


title: RfxCas13d, rep 1

description: Transfecting the plasmid encoding RfxCas13d into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.


title: dRfxCas13d_T6 crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and Mapt crRNA 6


title: OO2L: old isochronic parabiont 2 left

description: 10X Genomics


title: OO1R: old isochronic parabiont 1 right

description: 10X Genomics


title: dRfxCas13d_T4 crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and Mapt crRNA 4


title: monkey Input

organism: Macaca mulatta

source_name: monkey Input

value: rhesus monkey

value: heart

value: 3 years


title: OO3L: old isochronic parabiont 3 left

description: 10X Genomics

value: brain

value: male


title: TIL, patient P4, pre, GEX

city: Boston

first: Stephanie

last: Dougan

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description:
mRNA
10X Genomics

data_processing:
CellRanger 5 was used for alignment of FASTQs against the GRCh38 transcriptome and subsequent feature counting.
CITE-seq-Count 1.4.4 was used to count hashtag oligos in HTO libraries.
Assembly: GRCh38
Supplementary files format and content: For GEX libraries: CellRanger counts output in HDF5 format. For TCR libraries: productive TCR contigs in comma-separated format. For HTO libraries: oligo UMI counts in sparse matrix format (gzipped).

source_name: Tumor

extract_protocol:
PBMCs were isolated from whole blood by Ficoll centrifugation. Tumor biopsies were mechanically and enzymatically digested. CD45+ CD3+ T cells were sorted from all samples by flow cytometry then washed with 0.05% BSA in PBS for sequencing.
Libraries were constructed according to the standard protocol provided by 10X Genomics for 5' v2 immunoprofiling with feature barcoding.

value: Tumor

value: Tumor-infiltrating lymphocyte

value: Ribociclib and anti-PD1


title: RfxCas13d_NT crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and NT crRNA into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

value: N2A cells


title: dRfxCas13d_M3 crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and Map2 crRNA 3


title: PBMC, hashed patients P4 and P6, pre and post, TCR

description:
TCR-amplified mRNA
10X Genomics

source_name: Blood

value: Blood

value: Peripheral blood T cell


title: PBMC, hashed patients P4 and P6, pre and post, HTO

description:
HTO RNA
10X Genomics

tag: antibodies/tags

value: BioLegend TotalSeq-C0251:P4 pre; TotalSeq-C0252:P4 post; TotalSeq-C0253:P6 pre;  TotalSeq-C0254:P6 post


title: OO1L: old isochronic parabiont 1 left

description: 10X Genomics

value: 20-22 months old

value: isochronic parabiosis


title: dRfxCas13d_M1 crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and Map2 crRNA 1


title: PBMC, hashed patients P4 and P6, pre and post, GEX

description:
mRNA
10X Genomics


title: dRfxCas13d_K8 crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and Sik3-S crRNA 8


title: Gp130 ecKO 3

city: Sagamihara

first: Junya

last: Ito

state: Kanagawa

address: 1-17-71 Fuchinobe, Chuo-ku

department: School of Veterinary Medicine

country: Japan

institute: Azabu University

data_processing:
The FASTQ files were processed for removal of adaptor sequences, trimmed and quality-based filtered using fastp v0.23.2
The trimmed reads were removed ribosomal RNA using SortMeRNA v4.3.6
The removed reads were mapped onto the reference genome of Mus musculus (GRCm39) using STAR v2.7.10a
Mapped reads were counted using RSEM v1.3.3.
Differential expression analysis was performed in R v4.2.1 using the EdgeR v 3.38.4 package.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: uterus

extract_protocol:
RNA was isolated using RNeasy plus mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using SureSelect Strand-Specific RNA Library Prep kit following manufacturer's protocols.

value: uterus

tag: background strain

value: Gp130 conditional knockout

tag: time

value: day 4 (1600h) of pregnancy


title: Gp130 ecKO 2

tag: tissue


title: PBMC, hashed patients P3 and P5, pre and post, HTO

description:
HTO RNA
10X Genomics

value: BioLegend TotalSeq-C0251:P3 pre; TotalSeq-C0252:P3 post; TotalSeq-C0253:P5 pre;  TotalSeq-C0254:P5 post


title: Gp130 ecKO 1


title: TIL, patient P4, pre, TCR

description:
TCR-amplified mRNA
10X Genomics


title: monkey brain 6mA MeDIP-seq

source_name: monkey brain 6mA

value: rhesus monkey

value: brain

value: 3 years


title: DMAD_KD_SMRT-seq

data_processing:
The raw data in hax.h5 format was aligned to dm6 genome using RS_Modification_and_Motif_Analysis.1 protocol with the default parameters and only the alignment results were used in the subsequent analysis.
The polymerase kinetics information was further loaded to alignment results by loadChemistry.py and loadPulses scripts.
All the datasets from the same sample were merged and sorted by using cmph5tools.
6mA site was identified using ipdSummary.py script
Genome_build: dm6

organism: Drosophila melanogaster

source_name: w1118 SMRT seq

extract_protocol:
Genomic DNA was extracted from DMAD KD fly head  using the Wizard genomic DNA purification Kit (Promega)
Genomic DNA was converted to SMRTbell templates using SMRTbell Template Prep Kit 1.0. DNA polymerase was bound to the prepared DNA template libraries using the DNA/Polymerase Binding Kit P6 v2.

tag: strain background

tag: genotype/variation

value: DMAD knock down

value: head


title: PBMC, hashed patients P3 and P5, pre and post, TCR

description:
TCR-amplified mRNA
10X Genomics

value: Ribociclib and anti-PD1


title: monkey spleen 6mA MeDIP-seq

source_name: monkey spleen 6mA

tag: strain

value: spleen


title: RfxCas13d_M1 crRNA, rep 1

description: Transfecting the plasmids encoding RfxCas13d and Map2 crRNA 1 into N2a cells. GFP-positive cells were collected for total RNA extraction 48 hour after transfection.

tag: cell line

value: N2A cells

tag: transfection


title: Control 1

tag: genotype

value: WT


title: 6h embryo dsRNA(Jumu) (replicate 1)

data_processing:
FastQC was used to make sure that the sequencing data were high quality
Reads were aligned to the dm6 genome assembly using Tophat2
Differential expression analysis was carried out by cuffdiff
Genome_build: dm6
Supplementary_files_format_and_content: fpmk

molecule: polyA RNA

source_name: w1118  6h dsRNA(Jumu) rep 1

extract_protocol:
Total RNAs were isolated from embryos at indicated stages using TRIzol reagent (Invitrogen) and mRNAs were then purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module according to the user manual.
Illumina sequencing libraries were constructed according to the manufacturer’s instructions. The libraries were then sequenced using the Illumina Hiseq2500 V4 platform

value: embryo


title: TIL, patient P5, pre, TCR

description:
TCR-amplified mRNA
10X Genomics

value: Tumor

tag: cell type

value: Tumor-infiltrating lymphocyte

tag: treatment


title: TIL, patient P6, pre, TCR

description:
TCR-amplified mRNA
10X Genomics


title: dRfxCas13d, rep 1

value: Transfecting the plasmid encoding dRfxCas13d


title: 6h embryo dsRNA(GFP) (replicate 1)

description: processed data file: dsRNA_GFP_FPKM.txt

data_processing:
FastQC was used to make sure that the sequencing data were high quality
Reads were aligned to the dm6 genome assembly using STAR or Tophat2
Differential expression analysis was carried out by cuffdiff
Genome_build: dm6

source_name: w1118  6h dsRNA(GFP)

extract_protocol:
Total RNAs were isolated from embryos at indicated stages using TRIzol reagent (Invitrogen) and mRNAs were then purified using a Dynabeads mRNA DIRECT Kit (Invitrogen) according to the user manual.
Illumina sequencing libraries were constructed according to the manufacturer’s instructions. The libraries were then sequenced using the Illumina Hiseq2500 V4 platform

value: control


title: 6h embryo dsRNA(DMAD) (replicate 2)

description: processed data file: dsRNA_DMAD_FPKM.txt

source_name: w1118  6h dsRNA(DMAD)

value: DMAD knockdown


title: 6h embryo dsRNA(DMAD) (replicate 1)


title: dRfxCas13d_K1 crRNA, rep 1

source_name: N2A cells

value: Transfecting the plasmids encoding dRfxCas13d and Sik3-S crRNA 1


title: 6h embryo dsRNA(Jumu) (replicate 2

source_name: w1118  6h dsRNA(Jumu) rep 2


title: Drug_aCTLA4, scTCR-seq

city: Seoul

first: AREUM

last: JO

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of KOREA

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were performed using the Cell Ranger software v5.0.0 multi pipeline with mm10-2020-A and vdj-GRCm38-alts-ensembl-5.0.0 reference genomes.
Assembly: mm10
Supplementary files format and content: Output files of 10x Cell Ranger software: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

source_name: tissue

extract_protocol:
Single cell suspension was generated from the tissue following the manufacturer's recommentations (Tumor Dissociation Kit, mouse, Miltenyi). Total RNA capture and cDNA amplification were performed according to the manufacter’s protocol (Single Cell 5' Immune Profiling v1.1 protocol, 10x Genomics). Briefly, Single-cell suspensions were loaded onto the 10x Chromium system targeting 5,000 cells. For each single cell, total RNA from the cell lysate contained in gel bead-in-emulsion (GEM) was captured with UMI and 10x barcoded gel bead and then reverse transcribed to cDNA. The barcoded cDNAs were pooled and amplified.
Library was constructed according to the manufacter’s instructions (Single Cell 5' Immune Profiling v1.1 protocol, 10x Genomics).

treatment_protocol: For the anti-CTLA-4 treatment group, 100 μg of anti-CTLA-4(9H10) was intraperitoneally injected on days 5, 8, and 11 after tumor inoculation.

value: 100ug anti-CTLA-4(9H10)

value: tissue

value: balb/c

value: 6 weeks old


title: dRfxCas13d_NT crRNA, rep 1

value: Transfecting the plasmids encoding dRfxCas13d and NT crRNA


title: Drug_aCTLA4, scBCR-seq

description: 10x Genomics


title: TIL, patient P6, pre, GEX

description:
mRNA
10X Genomics


title: Drug_Control, scTCR-seq

description: 10x Genomics

value: phosphate-buffered solution (PBS) on days 5, 8, and 11 after tumor inoculation. Mice were sacrificed 13 days after tumor inoculation. Tissue specimens were analyzed by immunofluorescence tissue staining, scRNAseq(10x genemics).


title: 6h embryo dsRNA(Jumu)

source_name: w1118  6h dsRNA(Jumu)

value: Jumu knockdown


title: fat body 6mA MeDIP-seq

source_name: larva fat body 6mA

value: fat body

value: larva


title: fat body IgG MeDIP-seq

source_name: larva fat body IgG


title: TIL, patient P3, post, TCR

description:
TCR-amplified mRNA
10X Genomics

value: Ribociclib and anti-PD1


title: TIL, patient P3, post, GEX

description:
mRNA
10X Genomics


title: NAcMed(biol rep 3)

first: Jincan

last: Ke

state: Guangdong

address: 190 KaiYuan Road, Huangpu District

department: Center for Cell Lineage and Development

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Adapters and low-quality reads were removed by fastp (v0.20.0)
Then raw reads were mapped to the GRCm38 mouse genome by HISAT2 (v2.1.0)
All mapped reads were processed by StringTie (v1.3.4) and FeatureCounts (v1.6.3) to quantify gene-expression levels, measured by transcripts per million (TPM) and gene counts using default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Medial shell of the NAc

extract_protocol:
cDNA was harvested using Geo-seq
cDNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumima

value: Medial shell of the NAc

value: Mouse neural cell

value: WT


title: NAcMed(biol rep 5)


title: NAcMed(biol rep 2)


title: NAcMed(biol rep 1)


title: NAcMed(biol rep 4)


title: mouse spleen 6mA MeDIP-seq

source_name: mouse spleen 6mA

value: spleen

value: 3 months


title: TIL, patient P5, pre, GEX

description:
mRNA
10X Genomics

source_name: Tumor

value: Tumor

value: Tumor-infiltrating lymphocyte


title: Control 3

value: uterus

value: day 4 (1600h) of pregnancy


title: NAcLat(biol rep 5)

source_name: Lateral shell of the NAc

value: Lateral shell of the NAc


title: NAcLat(biol rep 4)


title: head 6mA MeDIP-seq

source_name: WT head 6mA

value: head


title: TIL, patient P2, pre, GEX

description:
mRNA
10X Genomics


title: 6h embryo dsRNA(GFP) (replicate 2)

description: processed data file: dsRNA_GFP_FPKM.txt

value: control

value: embryo


title: NAcLat(biol rep 3)


title: head IgG MeDIP-seq

source_name: WT head IgG


title: mouse hippocampus 6mA MeDIP-seq

source_name: mouse hippocampus 6mA

value: hippocampus


title: 0.75h embryo DNA and DMAD-CD pull down seq

source_name: w1118 embryo DMAD-CD pull down


title: TIL, patient P2, pre, TCR

description:
TCR-amplified mRNA
10X Genomics


title: NAcLat(biol rep 2)


title: TIL, patient P1, post, GEX

description:
mRNA
10X Genomics


title: VPA, iPSC-derived neurons, biol rep 3

city: Providence

first: Calvin

middle: S

last: Leung

state: RI

address: 70 Ship Street

department: MCB

institute: Brown University

data_processing:
Read quality was accessed using FastQC (version 0.11.9)
Raw reads were mapped to the Ensembl reference genome 104 (GRCh38) using Salmon (version 1.5.2).
Differentially expressed genes were detected using the DESeq2 R package (version 1.32.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample.

source_name: iPSC line I-93-7

extract_protocol:
Total RNA was extracted using the mirVANA RNA isolation kit (ThermoFisher).
Libaries were generated using the Illumina Tru-Seq kit following manufactuer's protocols.

treatment_protocol: iPSC-derived neurons were treated with 200µg/ml VPA or DMSO at day 64 of neuronal induction and were harvested after 24 hours for RNA extraction.

value: iPSC line I-93-7

value: iPSC-derived neurons

value: VPA


title: NAcLat(biol rep 1)


title: TIL, patient P1, pre, TCR

description:
TCR-amplified mRNA
10X Genomics

value: Ribociclib and anti-PD1


title: TIL, patient P1, pre, GEX

description:
mRNA
10X Genomics


title: Drug_Control, scRNA-seq

description: 10x Genomics

value: phosphate-buffered solution (PBS) on days 5, 8, and 11 after tumor inoculation. Mice were sacrificed 13 days after tumor inoculation. Tissue specimens were analyzed by immunofluorescence tissue staining, scRNAseq(10x genemics).

value: tissue

value: balb/c

value: 6 weeks old


title: VPA, iPSC-derived neurons, biol rep 2


title: PBMC, hashed patients P1 and P2, pre and post, HTO

description:
HTO RNA
10X Genomics

source_name: Blood

value: Blood

value: Peripheral blood T cell

value: BioLegend TotalSeq-C0251:P1 pre; TotalSeq-C0252:P1 post; TotalSeq-C0253:P2 pre;  TotalSeq-C0254:P2 post


title: ULC

city: Shanghai

first: Pengjun

address: 600 Yishan Rd

institute: Sixth People's Hospital affiliated to Shanghai Jiaotong University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  * MT% < 20%;   * Cell Gene Number < 5000;  * Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Barcode information in CLS.png
Genome_build: mm10
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: contralateral medial vestibular nuclei

extract_protocol:
brains were dissected and made to slices. MVN tissue were dissociated to single cell.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols
scRNA-seq

treatment_protocol: unilateral labrythectomy

value: medial vestibular nucleus


title: vehicle, iPSC-derived neurons, biol rep 3

value: Vehicle


title: VPA, iPSC-derived neurons, biol rep 1


title: ULI

source_name: ipsilateral medial vestibular nuclei


title: B_cell_Aff3het_rep2

city: Tokushima

first: Koji

last: Yasutomo

address: 3-18-15 Kuramoto-cho

department: Graduate school of Biomedical Sciences

institute: Tokushima University

description: Gene expression after 3 days culture with LPS/IL4 of Aff3+/- mouse B cells

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel was set to Green and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Aff3+/- Spleen B cell, LPS/IL4_3d, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using RNeasy plus Mini kit (Qiagen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: CD43-negative B cells were purified from Aff3+/- or Aff3-/- mouse spleen, and cultured in the presence of 10 ug/mL LPS and 10 ng/mL IL-4 for 3 days, and total RNA was extracted from these cells and used for the analysis.


title: PBMC, hashed patients P1 and P2, pre and post, TCR

description:
TCR-amplified mRNA
10X Genomics


title: VN

source_name: control medial vestibular nuclei


title: vehicle, iPSC-derived neurons, biol rep 1


title: B_cell_Aff3ko_rep1

description: Gene expression after 3 days culture with LPS/IL4 of Aff3-/- mouse B cells

source_name: Aff3-/- Spleen B cell, LPS/IL4_3d, replicate 1


title: TIL, patient P1, post, TCR

description:
TCR-amplified mRNA
10X Genomics

value: Tumor

value: Tumor-infiltrating lymphocyte


title: vehicle, iPSC-derived neurons, biol rep 2


title: Control 2h 6 RNA

status: Public on Jan 13 2023

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center

data_processing:
Reads were trimmed applying the tool TrimGalore version 0.4.4_dev. The adaptor sequence “AGATCGGAAGAGC” (Illumina TruSeq, Sanger iPCR; auto-detected) as well as 3 bp from the 5’ end and 15 bp from the 3’ end were removed. In addition, sequences that became shorter than 18 bp (after quality trimming) were removed using TrimGalore’s default settings.
Reads were mapped to the mm10 transcriptome build GRC38.93 from ENSEMBL using boWTie version 0.12.7 with its standard options.
Reads falling into genes were counted from BAM files applying a suited R/Bioconductor workflow (function SummarizeOverlaps with mode ‘Union’). Duplicated reads were removed. For ribosomal footprinting samples, reads in the coding part of genes (CDS) were counted, for total RNA samples reads in the whole gene body were counted.
Genome_build: mm10, GRCm38.93
Supplementary_files_format_and_content: Counts of deduplicated reads overlapping CDS for ribosome-protected libraries or gene bodies for total RNA in each sample

source_name: Brain

extract_protocol:
Cells were collected, washed and lysed in Polysome lysis buffer (20 mM Tris-HCl, pH 7.4, 120 mM KCl, 5 mM MgCl2, 14 mM β-mercaptoethanol, 1% NP-40, 100 µg/ml CHX, 1x complete protease inhibitor cocktail (Roche), 100 u/ml RNase Inhibitor (Thermo Fisher)). Lysates containing 40 μg of total RNA were treated with 100 U of RNaseI (Ambion) for 45 min and stopped by addition of 50 U of SUPERaseIn (Ambion). Samples were centrifuged through 25% sucrose cushion at 100,000 rpm for 1 h and the pelleted RNA was extracted with the Direct-Zol RNA Miniprep kit (Zimo). Ribosomal RNA was depleted with the Gold Ribo-Zero kit (Illumina). Resulted RNA samples were resolved by electrophoresis in a 15% NOVEX TBE-Urea gel (Thermo Fisher). Gel slices including ribosome footprints corresponding to a fuzzy band of the 26-34 nt size range were cut out from the gel, crushed by centrifugation in 0.5 ml gel-breaker tubes (Segmatic) and extracted in 0.5 ml 10 mM Tris-HCl pH 7.0 by incubation for 15 min at 70°C. RNA was recovered by precipitation with isopropanol in presence of 0.3 M sodium acetate pH 5.5 and 20 μg Glycoblue (Thermo Scientific). For the parallel total mRNA sequencing, we used the same NSC lysates prepared as described above at the amount of 20 μg of total RNA. RNA was extracted with phenol/chloroform as described (Faye et al. 2014). RNA samples were treated with 3 U of TURBO DNase (Ambion) for 15 min at 37°C. RNA was again extracted with phenol/chloroform and recovered with ethanol precipitation in the presence of 0.3 m sodium acetate pH 5.2. Ribosomal RNA was depleted with the Gold Ribo-Zero kit (Illumina). After depletion 80 ng of each RNA sample was used to synthesized cDNA and make a library using the NEBNext Ultra Directional RNA library kit for Illumina (NEB).
Recovered RNA was dephosphorylated with T4 PNK (NEB) in the absence of ATP. Indexed libraries were generated using the SMARTer smRNA-Seq kit for Illumina (Takara).

treatment_protocol: Cells were treated with vehicle or IFN-β 48 hours after seeding and incubated at 37°C 25% CO2 for the corresponding incubation time. Then, NSCs were incubated for 5 min with 0.1 mg/ml CHX at 37°C 25% CO2.

value: 8-12 weeks

value: Neural stem cells

value: Ventricular-subventricular zone


title: B_cell_Aff3het_rep1

source_name: Aff3+/- Spleen B cell, LPS/IL4_3d, replicate 1


title: PBMC, hashed patients P1 and P2, pre and post, GEX

description:
mRNA
10X Genomics


title: B_cell_Aff3ko_rep2

source_name: Aff3-/- Spleen B cell, LPS/IL4_3d, replicate 2


title: IFNb 2h 5 RNA


title: Control 2h 5 RNA


title: Drug_aCTLA4, scRNA-seq

description: 10x Genomics

source_name: tissue

value: 100ug anti-CTLA-4(9H10)


title: IFNb 2h 3 RNA


title: Control 2h 3 RNA


title: IFNb 2h 2 RNA


title: Control 2h 2 RNA


title: Control 2h 6 Footprint

data_processing:
Library strategy: Ribo-seq
Reads were trimmed applying the tool TrimGalore version 0.4.4_dev. The adaptor sequence “AGATCGGAAGAGC” (Illumina TruSeq, Sanger iPCR; auto-detected) as well as 3 bp from the 5’ end and 15 bp from the 3’ end were removed. In addition, sequences that became shorter than 18 bp (after quality trimming) were removed using TrimGalore’s default settings.
Reads were mapped to the mm10 transcriptome build GRC38.93 from ENSEMBL using boWTie version 0.12.7 with its standard options.
Reads falling into genes were counted from BAM files applying a suited R/Bioconductor workflow (function SummarizeOverlaps with mode ‘Union’). Duplicated reads were removed. For ribosomal footprinting samples, reads in the coding part of genes (CDS) were counted, for total RNA samples reads in the whole gene body were counted.
Genome_build: mm10, GRCm38.93
Supplementary_files_format_and_content: Counts of deduplicated reads overlapping CDS for ribosome-protected libraries or gene bodies for total RNA in each sample


title: IFNb 2h 6 Footprint


title: Control 2h 3 Footprint


title: IFNb 2h 3 Footprint


title: IFNb 2h 2 Footprint


title: IFNb 2h 5 Footprint


title: Control 2h 5 Footprint


title: Control 14h 2 RNA

description: totalGenecounts.csv.gz


title: IFNb 14h 1 RNA

description: totalGenecounts.csv.gz


title: Control 2h 2 Footprint


title: IFNb 14h 2 RNA

description: totalGenecounts.csv.gz


title: Control 14h 4 RNA

description: totalGenecounts.csv.gz


title: Control 14h 1 RNA

description: totalGenecounts.csv.gz


title: IFNb 14h 3 RNA

description: totalGenecounts.csv.gz


title: Control 14h 4 Footprint

description: ribobCDScounts.csv.gz


title: Control 14h 3 RNA

description: totalGenecounts.csv.gz


title: Control 14h 3 Footprint

description: ribobCDScounts.csv.gz


title: IFNb 14h 4 RNA

description: totalGenecounts.csv.gz


title: IFNb 14h 2 Footprint

description: ribobCDScounts.csv.gz


title: IFNb 14h 4 Footprint

description: ribobCDScounts.csv.gz


title: Control 14h 2 Footprint

description: ribobCDScounts.csv.gz


title: IFNb 14h 1 Footprint

description: ribobCDScounts.csv.gz


title: Control 14h 1 Footprint

description: ribobCDScounts.csv.gz


title: SynIP_4

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: C57/BL6NTac IP  WT

data_processing:
Aligned to mouse genome (mm10) using STAR spliced read aligner
Count the reads with htseq-count
Normalization (TMM), quantitation and differential expression analysis using Bioconductor packages
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts

extract_protocol:
Brain tissue was lysed with lysis buffer, IP RNA was isolated with anti-HA conjugated magnetic beads, and RNA was extracted with Qiagen RNeasy micro kit. Bulk tissue was lysed and RNA was extracted with the Qiagen RNeasy micro kit.
Libraries prepared using the Illumina TruSeq Stranded RNA (100 ng) + RiboZero Gold Library Prep Kit  and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

treatment_protocol: Groups with IP samples were injected with astrocyte or neuron specific RiboTag (gfaABC1D Rpl22-HA or hSyn1 Rpl22-HA)

tag: animal id

tag: condition

value: IP

tag: group

value: WT


title: SynIP_3

description: C57/BL6NTac IP  WT


title: SynIP_1

description: C57/BL6NTac IP  WT


title: Input_1

description: C57/BL6NTac Input  WT

value: Input


title: PBMC, hashed patients P3 and P5, pre and post, GEX

description:
mRNA
10X Genomics

value: Ribociclib and anti-PD1


title: Input_4

description: C57/BL6NTac Input  WT


title: Input_2

description: C57/BL6NTac Input  WT


title: JS9232_KO

description: C57/BL6NTac Bulk  Sapap3KO

value: Bulk


title: JS9231_KO

description: C57/BL6NTac Bulk  Sapap3KO


title: JS9234_WT

description: C57/BL6NTac Bulk  WT


title: IFNb 14h 3 Footprint

description: ribobCDScounts.csv.gz


title: Input_3

description: C57/BL6NTac Input  WT


title: JS9230_KO

description: C57/BL6NTac Bulk  Sapap3KO


title: JS9235_WT

description: C57/BL6NTac Bulk  WT


title: JS8485_IP_KO

description: C57/BL6J-Dlgap3 KO IP  Sapap3KO

value: C57/BL6J-Dlgap3 KO


title: JS9195_KO

description: C57/BL6NTac Bulk  Sapap3KO


title: JS8719_IP_KO

description: C57/BL6J-Dlgap3 KO IP  Sapap3KO


title: JS9195_WT

description: C57/BL6NTac Bulk  WT


title: JS9233_WT

description: C57/BL6NTac Bulk  WT


title: mouse Input

data_processing:
MeDIP-seq reads were aligned to the dm6 genome assembly using bowtie2 with with parameters “--no-mixed --no-discordant --non-deterministic --very-sensitive-local”
MACS2 callpeak was used to identify enrichment peaks with parameters “-f BAMPE –B” and a default q-value (FDR) cutoff of 0.05, and used IgG as a control
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result

source_name: mouse Input

value: spermatocyte

value: 3 months


title: JS8487.9_IP_WT

description: C57/BL6J IP  WT


title: SynIP_2

description: C57/BL6NTac IP  WT


title: JS8483_IP_KO

description: C57/BL6J-Dlgap3 KO IP  Sapap3KO


title: JS8272_IP_WT

description: C57/BL6J IP  WT


title: JS8715_IP_WT

description: C57/BL6J IP  WT


title: JS8719_In_KO

description: C57/BL6J-Dlgap3 KO Input  Sapap3KO


title: JS8720_In_KO

description: C57/BL6J-Dlgap3 KO Input  Sapap3KO


title: JS8486_IP_WT

description: C57/BL6J IP  WT


title: JS8715_In_WT

description: C57/BL6J Input  WT


title: JS8487.9_In_WT

description: C57/BL6J Input  WT


title: Y357_IP

description: C57/BL6NTac IP  Control

value: Control


title: JS8483_In_KO

description: C57/BL6J-Dlgap3 KO Input  Sapap3KO


title: JS8485_In_KO

description: C57/BL6J-Dlgap3 KO Input  Sapap3KO


title: JS8486_In_WT

description: C57/BL6J Input  WT


title: JS8272_In_WT

description: C57/BL6J Input  WT


title: JS8720_IP_KO

description: C57/BL6J-Dlgap3 KO IP  Sapap3KO


title: Y353_IP

description: C57/BL6NTac IP  Control


title: Y356_IP

description: C57/BL6NTac IP  Control


title: Y357_input

description: C57/BL6NTac input  Control

value: input


title: Y356_input

description: C57/BL6NTac input  Control


title: Y352_IP

description: C57/BL6NTac IP  Control


title: Y353_input

description: C57/BL6NTac input  Control


title: Y352_input

description: C57/BL6NTac input  Control


title: h2a.z_27°C_rep3

first: Fengyue

last: Zhao

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Hisat2 version 2.1.10
Reads per gene were counted by HTseq version 0.11.2
Transcripts per million (TPM) values were generated using R. Differential gene expression analysis was performed using DESeq2 version 1.26.0
Assembly: TAIR10
Supplementary files format and content: *.txt, TPM values for all samples

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings

growth_protocol: 7-day-old seedlings grown at 21°C were shfited to 27°C for 12 hours under short-day conditions

extract_protocol:
Total RNA was extracted with Minibest Plant RNA Extraction Kit (Takara, 9769)
Libraries were prepared with the NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, 7530L) according to the manufacture’s instruction

value: 7-day-old seedlings


title: h2a.z_27°C_rep1


title: h3.3kd;h2a.z_27°C_rep1


title: Col_27°C_rep3

value: Col


title: h3.3kd;h2a.z_27°C_rep2


title: h2a.z_27°C_rep2


title: h3.3kd_27°C_rep1


title: Col_27°C_rep2


title: h3.3kd_27°C_rep3


title: HTR5-GFP;ino80-5_Nucleosome_rep2

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Duplicated reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard)
Broad HTR5-GFP peaks were called using MACS2 version 2.1.2 with default parameters
For data visualization, data from two biological replicates were merged and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp
The HTR5-GFP enrichment was measured by computing the log2 ratios of the scores of HTR5-GFP to mononucleosomal DNA
Assembly: TAIR10
Supplementary files format and content: *.bw: Normalized HTR5-GFP coverage relative to Nucleosome (log2 ratio)

growth_protocol: 7-day-old seedlings grown at 21°C under short-day conditions

extract_protocol:
Materials were fixed with 1% formaldehyde and ground with liquid nitrogen into fine powder. After nuclei extraction, mononucleosomes were generated with micrococcal nuclease (MNase) (NEB, M0247S) digestion. Immunoprecipitation was performed with anti-GFP antibody (Thermo Fisher Scientific, A11122).
Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture’s instruction

tag: chip antibody


title: Col_27°C_rep1


title: h3.3kd_27°C_rep2


title: HTR5-GFP;ino80-5_IP_rep1

value: anti-GFP (Thermo Fisher Scientific, #A11122)


title: h3.3kd;h2a.z_27°C_rep3


title: HTR5-GFP;elf7-3_Nucleosome_rep1


title: HTR5-GFP_Nucleosome_rep2


title: HTR5-GFP;elf7-3_Nucleosome_rep2


title: HTR5-GFP;elf7-3_IP_rep1


title: HTR5-GFP;elf7-3_IP_rep2


title: HTR5-GFP_Nucleosome_rep1


title: HTR5-GFP_IP_rep1


title: h3.3kd;h2a.z_rep3


title: h3.3kd;h2a.z_rep1


title: h3.3kd;h2a.z_rep2


title: h2a.z_rep3


title: h2a.z_rep1


title: h2a.z_rep2


title: h3.3kd_rep3


title: HTR5-GFP;ino80-5_IP_rep2


title: Col_rep3


title: h3.3kd_rep2


title: Col_rep2


title: HTR5-GFP_IP_rep2


title: elf7-3_27°C_rep3

growth_protocol: 7-day-old seedlings grown at 21°C or 27°C under short-day conditions

extract_protocol:
Total RNA was extracted with Minibest Plant RNA Extraction Kit (Takara, 9769)
Libraries were prepared with the NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction


title: HTR5-GFP;ino80-5_Nucleosome_rep1


title: elf7-3_27°C_rep2


title: Col_rep1


title: elf7-3_27°C_rep1


title: elf7-3_21°C_rep3


title: elf7-3_21°C_rep2


title: h3.3kd_27°C_rep2


title: h3.3kd_27°C_rep1


title: Control 2

source_name: uterus

value: uterus

value: day 4 (1600h) of pregnancy


title: h3.3kd_21°C_rep1


title: h3.3kd_21°C_rep2


title: elf7-3_21°C_rep1


title: h3.3kd_27°C_rep3


title: Col_27°C_rep2


title: h3.3kd_21°C_rep3


title: Col_27°C_rep1


title: h3.3kd_rep1


title: Col_21°C_rep2


title: Col_21°C_rep3


title: Col_21°C_rep1


title: HL-60 RPF, pooled

city: Palo Alto

first: Abolfazl

last: Arab

address: 3160 Porter Dr

institute: Arc Institute

description: ribosome-protected mRNA fragments

data_processing:
The adapters in the sequencing reads were removed using cutadapt87 (v3.1) with options ‘— trimmed-only -m 15 -a AGATCGGAAGAGCAC‘. The PCR duplicates in the reads were collapsed using CLIPflexR88 (v0.1.19). The UMIs for each read were extracted using UMI-tools 89 (v1.1.1) with the options ‘extract—bc-pattern=NN‘ for the 5’ end and options ‘extract—3prime—bc-pattern=NNNNN‘ for the 3’ end. Reads corresponding to rRNA and other non-nuclear mRNA were removed by aligning out the reads using Bowtie290 (v2.4.2) on a depletion reference (rRNA, tRNA and mitochondrial RNA sequences). This depletion reference was built from the hg38 noncoding transcriptome (Ensembl91,92 version 96). The reads that did not align to the depletion reference were aligned to the hg38 mRNA transcriptome (Ensembl version 96) using Bowtie2 with options ‘— sensitive—end-to-end—norc‘. The mRNA transcriptome was built using the cDNA longest CDS reads of Homo sapiens downloaded from the Ensembl release version. The resulting reads were converted to BAM files and then sorted using samtools (v1.11). The duplicate reads in the sorted files were removed using UMI-tools (v1.1.1) with options ‘dedup‘.
Ribolog was used to compare translational efficiency across conditions93 (https://github.com/goodarzilab/Ribolog). Briefly, Ribolog applies a logistic regression to model individual Ribo-seq and RNA-seq reads in order to provide estimates of logTER (i.e., logFC in TE) and its associated p-value across the coding transcriptome.
Assembly: hg38
Supplementary files format and content: tab-delimited text file that includes gene level differential translational efficiency.
Library strategy: Ribo-seq

extract_protocol:
At 72 hours, approximately 10x10^6 cells were lysed in ice cold polysome buffer (20 mM Tris pH 7.6, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) supplemented with 1% v/v Triton X-100 and 25 U/mL Turbo DNase (Invitrogen). The lysates were triturated through a 27G needle and cleared for 10 min at 21,000 g at 4°C. The RNA concentrations in the lysates were determined with the Qubit RNA HS kit (Thermo). Lysate corresponding to 15 µg RNA was diluted to 200 µl in polysome buffer and digested with 0.75 µl RNaseI (Epicentre) for 45 min at room temperature. The RNaseI was then quenched by 5 µl SUPERaseIN (Thermo).     Monosomes were isolated using MicroSpin S-400 HR (Cytiva) columns, pre-equilibrated with 3 mL polysome buffer per column. 100 µl digested lysate was loaded per column (two columns were used per 200 µl sample) and centrifuged 2 min at 600 g. The RNA from the flow through was isolated using the RNA Clean and Concentrator-25 kit (Zymo). In parallel, total RNA from undigested lysates were isolated using the same kit.    Ribosome protected footprints (RPFs) were gel-purified from 15% TBE-Urea gels as 17-35 nt fragments. RPFs were then end-repaired using T4 PNK (New England Biosciences) and pre-adenylated barcoded linkers were ligated to the RPFs using T4 Rnl2(tr) K227Q (New England Biosciences). Unligated linkers were removed from the reaction by yeast 5’-deadenylase (New England Biosciences) and RecJ nuclease (New England Biosciences) treatment. RPFs ligated to barcoded linkers were pooled, and rRNA-depletion was performed using riboPOOLs (siTOOLs) per the manufacturer’s recommendations. Linker-ligated RPFs were reverse transcribed with ProtoScript II RT (New England Biosciences) and gel-purified from 15% TBE-Urea gels.
Ribosome protected footprints (RPFs) were gel-purified from 15% TBE-Urea gels as 17-35 nt fragments. RPFs were then end-repaired using T4 PNK (New England Biosciences) and pre-adenylated barcoded linkers were ligated to the RPFs using T4 Rnl2(tr) K227Q (New England Biosciences). Unligated linkers were removed from the reaction by yeast 5’-deadenylase (New England Biosciences) and RecJ nuclease (New England Biosciences) treatment. RPFs ligated to barcoded linkers were pooled, and rRNA-depletion was performed using riboPOOLs (siTOOLs) per the manufacturer’s recommendations. Linker-ligated RPFs were reverse transcribed with ProtoScript II RT (New England Biosciences) and gel-purified from 15% TBE-Urea gels. cDNA was then circularized with CircLigase II (Epicentre) and used for library PCR. First, a small-scale library PCR was run supplemented with 1X SYBR Green and 1X ROX (Thermo) in a qPCR instrument. Then, a larger scale library PCR was run in a conventional PCR instrument, performing a number of cycles that resulted in ½ maximum signal intensity during qPCR. Library PCR was gel-purified from 8% TBE gels and sequenced on a SE50 run on an Illumina HiSeq4000.cDNA was then circularized with CircLigase II (Epicentre) and used for library PCR. First, a small-scale library PCR was run supplemented with 1X SYBR Green and 1X ROX (Thermo) in a qPCR instrument. Then, a larger scale library PCR was run in a conventional PCR instrument, performing a number of cycles that resulted in ½ maximum signal intensity during qPCR. Library PCR was gel-purified from 8% TBE gels and sequenced on a SE50 run on an Illumina HiSeq4000.

treatment_protocol: Cells were seeded into 6-well plates at 100,000 cells/mL in duplicate and were treated with decitabine (100 nM at 0, 24 and 48 hours) or DMSO.

value: cancer cell line

value: 72 hours


title: HL-60 RNA, decitabine, 72 hours, replicate 2

value: decitabine


title: HL-60 m6A, decitabine, 72 hours, replicate 2

data_processing:
MeRIP-seq reads were aligned to the hg38 reference genome using STAR (version 2.7.3a) with reference annotation GENCODE (version 34). RADAR was used to perform peak calling and differential methylation analysis. Both STAR and RADAR were used with default parameters.
Differentially methylated peaks were defined as FDR < 0.1 and logFC > 0.5. Wilcoxon test and t-test functions were used to test for global m6A hypermethylation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file in bed12 format that includes differential methylated m6A peaks

extract_protocol:
At 72 hours, total RNA was extracted as previously described (PMID: 30212448). 2 µg of the fragmented total RNA per sample was used for RNA immunoprecipitation (IP) with 5 µg of the anti-m6A antibody (ABE572, Millipore).
RNA-seq libraries from input and IP samples were prepared using the SMARTer Pico Input Mammalian v2 RNA-seq kit (Takara) and sequenced as SE50 runs on an Illumina HiSeq4000.

value: WT


title: HL-60 m6A, DMSO, 72 hours, replicate 2

value: DMSO


title: HL-60 m6A, DMSO, 72 hours, replicate 1


title: HL-60 m6A, decitabine, 72 hours, replicate 1


title: HL-60 input, DMSO, 72 hours, replicate 1


title: HL-60 input, DMSO, 72 hours, replicate 2


title: Col_27°C_rep3


title: HL-60 RNA, DMSO, 72 hours, replicate 1


title: HL-60 input, decitabine, 72 hours, replicate 2


title: HL-60 RNA, decitabine, 72 hours, replicate 1


title: HL-60, RG3039, 72 hours, replicate 2

description: 3' RNA-seq

data_processing:
The Salmon-tximport-DESeq2 pipeline was used for differential gene expression analysis. Salmon (version 1.2.1) was first used to quantify transcript abundance. A Salmon index was generated using the GENCODE (version 34) genome annotation, and subsequently the `salmon quant` tool was used with the `--validateMappings` option to calculate transcript abundances. Then, the R package tximport was used to import Salmon results into R and perform data preparation. The `summarizeToGene` function was used to collapse transcript abundances to the gene level. From here, the R package DESeq2 was used for differential gene expression analysis. We first extracted normalized counts for each RNA-seq experiment using DESeq2 by running the `estimateSizeFactors` function and then the `counts` function with option `normalized=TRUE`. For each individual experiment, the DESeq2 statistical model was modified based on the experimental design.
The STAR-featureCounts-REMBRANDTS-limma pipeline for differential RNA stability analysis. RNA-seq sequencing reads were first aligned to the hg38 reference genome using STAR5 (version 2.7.3a). Then, featureCounts was used to quantify intron and exon level counts. Finally, REMBRANDTS was used to calculate mRNA stability as previously described (PMID: 29030541; https://github.com/csglab/REMBRANDTS). Briefly, the package estimates a gene-specific bias function that is subtracted from Δexon–Δintron calculations to provide unbiased mRNA stability measurements. To assess differential RNA stability changes, we used limma, which was designed for microarray experiments and serves a similar function to DESeq2, though it supports negative values (relevant for RNA stability analysis). The model designs used here are analogous to the designs for differential expression analysis and based on the experiment design.
iPAGE was used to perform gene ontology analysis (see https://github.com/abearab/pager).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each Sample

extract_protocol:
At 72 hours, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and assessed on a BioAnalyzer 2100 (Agilent) for library quantification and quality control. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 using single-end, 50–base pair sequencing.

treatment_protocol: Cells were seeded into 6-well plates at 100,000 cells/mL in duplicate and were treated with decitabine (100 nM on days 0, 1 and 2), RG3039 (2 uM on day 0), both drugs or DMSO.


title: HL-60, RG3039, 72 hours, replicate 1

description: 3' RNA-seq


title: HL-60 input, decitabine, 72 hours, replicate 1


title: HL-60, decitabine, 72 hours, replicate 1

description: 3' RNA-seq


title: HL-60, DMSO, 72 hours, replicate 1

description: 3' RNA-seq