title: Vehicle_rep4

data_processing:
Nextpresso pipeline was used to carry out the analysis:
Alignment performed using Bowtie and TopHat aligners
Counts were generated using htseqcount
Normalization and differential expression analysis performed with DEseq2
Genome_build: hg19 and mm10

extract_protocol:
Total RNA was isolated from frozen tissues and cultured cells using ReliaPrep RNA Miniprep Systems (Promega, Z6012). Reverse transcription was performed using TaqMan Reverse Transcription Reagents (ThermoFisher Scientific, N8080234).
Libraries for whole-transcriptome sequencing were constructed using the TruSeq RNA Sample Preparation Kit v2 and sequenced using the 75-bp paired-end protocol on a NextSeq500 (Illumina, San Diego, CA, USA).

tag: mouse strain

value: 7 days vehicle (0.5% methylcellulose, 0.1% Tween80)


title: GFP-CD11b+ cells, rep5

status: Public on Apr 13 2023

type: SRA

city: Guangzhou

first: Suqi

last: Deng

state: Guangdong

address: Huangpu Avenue, Tianhe District, Guangzhou, China

country: China

institute: Jinan University

library_source: transcriptomic

data_processing:
HISAT2 v 2.0.4
Sequenced reads were mapped to the the reference genome using HISAT2 v 2.2.1.
Quantification of gene expression levels were vst-normalized count data processed by DESeq2.
Assembly: m39
Supplementary files format and content: tab-delimited text files include vst normalized count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: MLL-AF9/GFP cells were thawed in PBS and tail-vein injected in CD45.1 recipient mice.

extract_protocol:
RNA was harvested using TRIzol reagent (Life Technologies, Carlsbad, USA). 0.6-3.37 ug of total RNA was used for the construction of sequencing libraries. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations

treatment_protocol: Mice developing AML (GFP% reached 2% in perpipheral blood by flow cytometry) were sacrificed to collect bone marrow cells. Leukaemia cells (GFP+) and bone marrow micro-environment myeloid cells (GFP-CD11b+) were sorted by flow cytometry(BD FACSArial III).

tag: tissue

value: bone marrow

tag: cell type

value: acute myeloid leukemia cells

tag: genotype


title: 10A_M_1323

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: Sex

value: male

tag: strain


title: Vehicle_rep3

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: PDX

tag: xenotransplanted cells

tag: cell line origin

value: human bladder cancer

value: Hsd:Athymic Nude-Foxn1nu

tag: treatment


title: 10A_M_1335


title: 10A_M_1321


title: GFP-CD11b+ cells, rep4


title: 10A_M_1320


title: GFP-CD11b+ cells, rep3


title: GFP+ cells, rep3


title: 10A_M_1319


title: 10A_M_132


title: Vehicle_rep2


title: 10A_M_1318


title: GFP-CD11b+ cells, rep2


title: 10A_M_1316


title: BOTH_r2

data_processing:
Poli A and adapters sequences were cleaned using bbduk software
Nextpresso pipeline was used to carry out the analysis
Alignment performed using TopHat aligner
Gene count matrices were produced using htseqcount
Assembly: mm10 and hg19

extract_protocol:
Total RNA was isolated from frozen tissues and cultured cells using TRItidyG (A4051 PanReac AppliChem) . Reverse transcription was performed using TaqMan Reverse Transcription Reagents (ThermoFisher Scientific, N8080234).
Libraries for sequencing were constructed using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina protocol | Lexogen  and sequenced using the 75-bp  protocol on a NextSeq500 (Illumina, San Diego, CA, USA).

value: ScaBER

value: 14 days [Alpelisib (25mg/kg); Nintedanib (40mg/kg)] combination


title: Vehicle_rep1


title: GFP+ cells, rep1


title: 10A_M_1324


title: GFP-CD11b+ cells, rep1


title: EC_T10_TgW_5

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

country: Belgium

institute: VIB-KU Leuven Center for Brain and Disease Research

data_processing:
Raw FASTQ files were mapped using STAR v2.7.1a
Gene counts were created with RSEM v1.2.28
Assembly: Mus musculus genome (GRCm38), version M24 (Ensembl 99)
Supplementary files format and content: Collated count matrix derived from raw data files

source_name: lung endothelial cells

extract_protocol:
RNA was isolated using TRIzol (Life Technologies). Starting from total RNA, poly-adenylated fragments were isolated, reverse transcribed and converted into indexed sequencing libraries using the KAPA stranded mRNA-seq kit (Sopachem, Eke, Belgium)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All mice used were between 8 and 14 weeks old. Deletion of TRAIL was induced by intraperitoneal injections of tamoxifen (1mg/mouse/day) for 5 or 10 days, respectively, prior to the experiment.

value: lung endothelial cells

value: Tnfsf10 L/L, Cdh5.Cre Tg/W

tag: trail status

value: EC-TRAIL KO


title: 10A_M_1310


title: 10A_M_1312


title: 10A_M_1311


title: 10A_M_131


title: 10A_M_1309


title: Nintedanib_resp_rep2

value: 7 days Nintedanib (40mg/kg)


title: EC_T10_TgW_4


title: 10A_M_1308


title: Nintedanib_resp_rep1


title: 10A_M_1387


title: EC_T10_TgW_3


title: Nintedanib_non_resp_rep2


title: 10A_M_1307


title: 10A_M_1305


title: EC_T10_TgW_1


title: 10A_M_1301


title: Nintedanib_non_resp_rep1


title: 10A_M_1304


title: Nintedanib_resp_rep3


title: BYL_rep3

value: 7 days Alpelisib (25mg/kg)


title: EC_T10_WW_5

value: Tnfsf10 L/L, Cdh5.Cre W/W

value: Control


title: 10A_M_130


title: 10A_M_13


title: BYL_rep4


title: EC_T10_WW_4


title: 10A_M_1299


title: BYL_rep1


title: EC_T10_WW_3


title: 10A_M_1306


title: EC_T10_WW_2


title: BYL_rep2


title: EC_T10_TgW_2


title: 10A_M_1298


title: 10A_M_1294


title: 10A_M_129


title: BOTH_rep4

value: 7 days [Alpelisib (25mg/kg); Nintedanib (40mg/kg)] combination


title: 10A_M_1286


title: BOTH_rep3


title: EC_T10_WW_1


title: 10A_M_1292


title: 10A_M_1303


title: BOTH_rep2


title: BOTH_rep1


title: 10A_M_1293


title: 10A_M_1289


title: 10A_M_1282


title: 10A_M_1284


title: 10A_M_1280


title: 10A_M_1285


title: 10A_M_1279


title: 10A_M_1283


title: DDX42-dTAG cells treated with 1h 500nM dTAGv-1, 8h 5uM WX-02-23

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

data_processing:
For quantification of alternative RNA splicing, fastq files are adapter-trimmed by cutadapt 3.4 and aligned to GRCh38 by STAR 2.7 .6 and analyzed using rMATS (v4.1.1) (Shen et al., 2014) using the GENCODE (v35) GTF annotation for GRCh38 and the following parameters: -t paired --libType fr-unstranded –readLength 150 --novelSS
Supplementary files format and content: hg38
Supplementary files format and content: tsv file represents rMATs output files . For column definitions, see https://github.com/Xinglab/rmats-turbo
Supplementary files format and content: file naming is SAMPLE1_SAMPLE2_EVENTTYPE.MATS.JC.txt

organism: Homo sapiens

growth_protocol: 1.6×10^6 HCT-116 DDX42-dTAG endogenous knock-in cells per sample were seeded into a 6 cm plate and grown for 24h in DMEM with Glutamax and 10% fetal bovine serum (Life Technologies).

extract_protocol: Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer's instructions.

treatment_protocol: Cells were treated for 1h with either DMSO or 500nM dTAGv-1 in 3mL of medium, after which DMSO, 5 µM WX-02-23, 5 µM WX-02-43, or 10 nM pladienolide B were added from 1000x DMSO stocks directly to the supernatant for another 8h.

value: HCT116 DDX42-dTAG


title: DDX42-dTAG cells treated with 1h 500nM dTAGv-1, 8h 10nM PladB

value: Pladienolide B


title: DDX42-dTAG cells treated with 1h 500nM dTAGv-1, 8h DMSO

value: DMSO


title: 10A_M_128


title: 10A_M_1276


title: 10A_M_1275


title: 10A_M_1278


title: KOd_3D_C

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
Sample 20
counts.txt

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version hg38, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in September 2017) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: hg38
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

growth_protocol: 2D cells were grown in Ham's F12 with 5% fetal calf serum (Gibco, Invitrogen), 5 μg/ml bovine insulin (Sigma), 1 μg/ml hydrocortisone (Sigma), 1× penicillin/streptomycin (Gibco, Invitrogen). 3D samples were cultured in DMEM;F12, supplemented with 1× B27 (Gibco, Invitrogen), 20 ng/mL human EGF (PeproTech), 20 ng/mL basic FGF (PeproTech) and 1× penicillin/streptomycin (Gibco, Invitrogen). "wtRosen" samples were cultured in adherent conditions with standard medium until they reached 50% confluency. At that point, the medium was enchanged to 3D medium until cells reached 80% confluency.

extract_protocol:
RNeasy Plus Mini Kit or Micro Kit (Qiagen)
mRNA-sequencing stranded libraries were generated using the TruSeq Illumina kit according to the manufacturer’s instructions.

tag: cell line

value: Breast cancer cell line

value: KOd

tag: growth condition

tag: replicate


title: DDX42-dTAG cells treated with 1h DMSO, 8h 10nM PladB


title: DDX42-dTAG cells treated with 1h DMSO, 8h 5uM WX-02-43


title: KOd_3D_B

description:
Sample 19
counts.txt


title: DDX42-dTAG cells treated with 1h 500nM dTAGv-1, 8h 5uM WX-02-43


title: KOd_3D_A

description:
Sample 18
counts.txt


title: wt_3D_C

description:
Sample 17
counts.txt

value: wt


title: wt_3D_B

description:
Sample 16
counts.txt


title: 10A_M_1274

value: male


title: 10A_M_1272


title: DDX42-dTAG cells treated with 1h DMSO, 8h DMSO


title: 10A_M_1281


title: 10A_M_1271


title: 10A_M_1270


title: 10A_M_127


title: 10A_M_1273


title: wt_3D_A

description:
Sample 15
counts.txt


title: DDX42-dTAG cells treated with 1h DMSO, 8h 5uM WX-02-23


title: JKT-33_DHF

city: Clayton

first: Stephanie

middle: Irene

last: Studniberg

state: VIC

address: 19 Innovation Walk

department: Microbiology

country: Australia

institute: Infection Discovery Program, Monash Biomedicine Discovery Institute

data_processing:
Raw sequence reads in FASTQ file format were aligned to the human reference genome GRCh38/hg38 using the align() function in Bioconductor package Rsubread (v 2.10.5) with default parameters.
Fragments of aligned sequences overlapping Gencode human genes (GRCh38.p13) were quantified with featureCounts, with Gencode v38 primary assembly annotation used in the quantification.
Genes with no symbols, sex-linked genes, immunoglobulin genes, and non-protein-coding genes were filtered out from the analysis. Haemoglobin genes were found to be highly variable and were also filtered from the analysis. Genes with low counts in fewer than 5 samples were determined as unexpressed and filtered out using the filterByExpr function in edgeR.
Filtered counts were normalised using the trimmed mean of M-values method in edgeR (v 3.38.4)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files were written from the R prompt: columns represent gene symbols, total gene length (total base count of all exons) and the number of fragments mapping to the gene.

source_name: PBMCs

extract_protocol:
Total RNA was isolated from 2x10^5 PBMCs using the RNeasy Plus Mini Kit (QIAGEN) following manufacturers' instructions.
Libraries were prepared with either 25ng or 50ng total RNA using Illumina TruSeq RNA Library Prep Kit (<100ng) following manufacturers' instructions.

treatment_protocol: PBMCs were frozen at collection.

value: PBMCs

tag: diagnosis

value: dengue hemorrhagic fever (DHF)


title: JKT-32_DHF


title: 10A_M_1269


title: wt_2D_Rosens_B

description:
Sample 14
counts.txt


title: 10A_M_1266


title: JKT-31_DHF


title: 10A_M_1264


title: JKT-22_DHF


title: 10A_M_1262


title: 10A_M_1263


title: KOd_2D_B

description:
Sample 12
counts.txt


title: 10A_M_1260


title: 10A_M_1261


title: 10A_M_1265


title: KOd_2D_A

description:
Sample 11
counts.txt


title: JKT-30_DHF


title: 10A_M_126


title: wt_2D_Rosens_A

description:
Sample 10
counts.txt


title: JKT-20_DHF


title: 10A_M_1259


title: 10A_M_1258


title: wt_2D_C

description:
Sample 9
counts.txt


title: JKT-27_DF

value: dengue fever (DF)


title: 10A_M_1257


title: 10A_M_1256


title: wt_2D_B

description:
Sample 8
counts.txt


title: JKT-26_DF


title: KOd_2D_C

description:
Sample 13
counts.txt


title: JKT-21_DF


title: 10A_M_1255


title: 10A_M_1252


title: 10A_M_125


title: KOs_3D_B

description:
Sample 5
counts.txt

value: KOs


title: 10A_M_1254


title: wt_2D_A

description:
Sample 7
counts.txt


title: JKT-12_DF


title: JKT-13_DF


title: 10A_M_1251


title: KOs_3D_C

description:
Sample 6
counts.txt


title: Pearson-ErythroidCultureMix-Day12-scATAC-c1

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Pearson-ErythroidCultureMix-Day12-c1_S1_L001

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
Genome_build: hg19
Supplementary_files_format_and_content: Accessible chromatin fragments per ATAC library (tsv) as well as metadata per cell (meta.tsv)

source_name: Differentiated BMMNC

growth_protocol: Primary hematopoietic cells were differentiated in erythroid media containing EPO, SCF, IL-3 and harvested for single cell genomics processing at day 6 and 12 of culture.

extract_protocol:
NP40 lysis, see method sections for full details
10x Genomics scATAC-seq
Customized scATAC-seq (mtscATAC-seq) workflow as described in https://www.nature.com/articles/s41587-020-0645-6

tag: subject status

value: patient with Pearson Syndrome

value: Differentiated BMMNC

tag: time point


title: KOs_3D_A

description:
Sample 4
counts.txt


title: 10A_M_1243


title: 10A_M_1244


title: 10A_M_1240


title: KOs_2D_C

description:
Sample 3
counts.txt


title: 10A_M_1247


title: KOs_2D_A

description:
Sample 1
counts.txt


title: 10A_M_1245


title: 10A_M_1249


title: Pearson-ErythroidCultureMix-Day06-scATAC-c1

description: Pearson-ErythroidCultureMix-Day06-c1_S1_L001


title: 10A_M_1242


title: 10A_M_1237


title: 10A_M_124


title: 10A_M_1241


title: KOs_2D_B

description:
Sample 2
counts.txt


title: 10A_M_1238


title: 10A_M_1235


title: Pearson-CD34-PT3-scATAC

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
Protein abundance tag libraries were computed using kallisto | bustools v0.44
Genome_build: hg19
Supplementary_files_format_and_content: Accessible chromatin fragments per ATAC library (tsv) and protein abundances per ASAP tag (csv)

source_name: Bone marrow mononuclear cells

growth_protocol: Cryopreserved cells were thawed in RPMI with 10% FBS and washed in media prior to live cell sorting +/- CD34 enrichment as indicated before single cell genomics processing.

extract_protocol:
NP40 lysis, see method sections for full details
10x Genomics scATAC-seq
Customized scATAC-seq (mtscATAC-seq & ASAP) workflow as described in https://www.nature.com/articles/s41587-020-0645-6 and https://www.biorxiv.org/content/10.1101/2020.09.08.286914v1

value: Bone marrow mononuclear cells

tag: cd34 enrichment

value: complete


title: Pearson-ErythroidCultureMix-Day12-scATAC-c2

description: Pearson-ErythroidCultureMix-Day12-c2_S2_L001

tag: cell type


title: 10A_M_1234


title: Pearson-ErythroidCultureMix-Day06-scATAC-c2

description: Pearson-ErythroidCultureMix-Day06-c2_S2_L001


title: 10A_M_1233


title: FAC-cyXENs, replicate 1, RNAseq

city: Kunming

first: Mq

last: Peng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

description: Bulk

data_processing:
All reads were mapped to the mouse (GRCm38/mm10), human (GRCh38/hg38), and rhesus macaque genome (Mmul_10/rheMac10) using hisat2 (version 2.2.1) with default settings.
FeatureCoumt (version 2.0.1) was used to estimate read counts.
Stringtie (version 2.1.4) was used to estimate fragments per kilobase of exon per million fragments mapped (FPKM) and transcripts per kilobase of exon model per million mapped reads (TPM) values according to a previous report49, genes with an FPKM value ≥3 were considered as expressed.
genome_build: Mmul_10/rheMac10

organism: Macaca fascicularis

source_name: blastocyst

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
RNA extraction was performed using a RNeasy Mini Kit (QIAGEN) using DNase treatment (QIAGEN). RNA was analyzed using a 2100 Bioanalyzer (Aglient Technologies). (Transcripts per Kilobase Million). For monkey cells, RNA was extracted with Trizol Reagent (15596026, Invitrogen). The RNA (~50ng) reverse transcription reaction and amplification were performed using SuperScript II (18064-071, Invitrogen), and KAPA HiFi HotStart Ready Mix (KK2602, KAPA). The cDNA was analyzed using a 2100 Bioanalyzer (Aglient Technologies). The RNA Library was generated using TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme), then the library was adapted for sequencing on an Illmina NovaSeq 6000 platform (sequenced by Annoroad).

value: Separately cultured cells

tag: tissue type

value: Embryo

value: FTW-cyXENs(FTW-cynomolgus monkey embryonic stem cells)


title: 10A_M_1231

tag: brain region


title: FAC-cyESCs, replicate 3, RNAseq

description: Bulk

value: FTW-cyESCs(FTW-cynomolgus monkey embryonic stem cells)


title: 10A_M_1230

tag: age


title: FAC-cyESCs, replicate 2, RNAseq

description: Bulk


title: FAC-cyXENs, replicate 2, RNAseq

description: Bulk


title: 10A_M_1228

tag: Sex


title: 10A_M_1229

tag: strain


title: Pearson-ASAP-TAG-BMMNC-c4

value: partial


title: 10A_M_1227


title: Pearson-ASAP-TAG-BMMNC-c3


title: 10A_M_1226


title: FAC-cyTSCs, replicate 2, RNAseq

description: Bulk

value: FTW-cyTSCs(FTW-cynomolgus monkey trophoblast stem cells)


title: FAC-cyTSCs, replicate 1, RNAseq

description: Bulk


title: 10A_M_1223


title: 10A_M_1224


title: 10A_M_1222


title: Pearson-ASAP-BMMNC-c5


title: FTW_cy3line, replicate 2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Subsequently, unique molecular identifiers (UMI) matrices from each sample were merged in R and imported to Seurat(v4.1.1).
hisat2 compiler was run on raw fastq files. FeatureCounts was run on the aligned fastqs. Stringtie was run on the aligned fastqs. Concatenated file was processed in Deseq2 (including normalization, estimation of dispersion effects, and differential gene expression).
genome_build: Mmul_10/rheMac10

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (Chromium Single Cell 3’ Reagent Kit v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip G to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. On average, approximately 13,200 single cells were loaded on each channel and approximately 8,000 cells were recovered. Libraries were sequenced on the Illumina NovaSeq 6000 platform

value: Co-cultured cells

value: FTW-cynomolgus monkey embryonic stem cells + FTW-cynomolgus monkey extraembryonic endoderm stem cells + FTW-cynomolgus monkey trophoblast stem cells


title: 10A_M_1219

value: male


title: 10A_M_1232


title: Pearson-ASAP-TAG-BMMNC-c1


title: 10A_M_122


title: Pearson-BMMNC-PT3-scATAC


title: 10A_M_1218


title: Pearson-ASAP-TAG-BMMNC-c5


title: FTW_cy3line, replicate 1, scRNAseq

description: 10x Genomics


title: 10A_M_1221


title: Pearson-ASAP-BMMNC-c4


title: 10A_M_1217


title: FTW_cy2line, replicate 2, scRNAseq

description: 10x Genomics

value: FTW-cynomolgus monkey embryonic stem cells + FTW-cynomolgus monkey extraembryonic endoderm stem cells


title: 10A_M_1214


title: Pearson-ASAP-TAG-BMMNC-c2


title: Pearson-ASAP-BMMNC-c3


title: 10A_M_1216


title: FTW_cy2line, replicate 1, scRNAseq

description: 10x Genomics


title: 10A_M_1213


title: Pearson-ASAP-BMMNC-c2


title: FTW_cyXENs, replicate 2, scRNAseq

description: 10x Genomics

value: FTW-cynomolgus monkey extraembryonic endoderm stem cells


title: 10A_M_1212


title: Pearson-ASAP-BMMNC-c1


title: 10A_M_1211


title: 10A_M_1209


title: FTW_cyXENs, replicate 1, scRNAseq

description: 10x Genomics


title: FTW_cyESCs, replicate 1, scRNAseq

description: 10x Genomics

value: FTW-cynomolgus monkey embryonic stem cells


title: 10A_M_1206


title: Pearson_PBMC_PT2_scRNA

data_processing:
Fastqs were generated using CellRanger mkfastq v3.0
Sequencing reads were aligned using CellRanger count to the hg38 reference genome and transcriptome
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression counts (.mtx) with annotated columns (barcodes) and rows (genes) in additional files

growth_protocol: Cryopreserved cells were thawed in RPMI with 10% FBS and washed in media prior to single cell genomics processing.

extract_protocol:
Standard protocol
10x Genomics 3' scRNA-seq

value: peripheral blood mononuclear cells


title: 10A_M_1207


title: FTW_cyTSCs, replicate 2, scRNAseq

description: 10x Genomics

value: FTW-cynomolgus monkey trophoblast stem cells


title: 10A_M_1208


title: 10A_M_1205


title: Pearson_PBMC_PT3_scRNA

value: patient with Pearson Syndrome


title: 10A_M_1201


title: 10A_M_120


title: FTW_cyTSCs, replicate 1, scRNAseq

description: 10x Genomics


title: Pearson_PBMC_PT1_scRNA


title: 10A_M_1197


title: 10A_M_12


title: Pearson_PBMC_PT2_scATAC

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
Genome_build: hg19
Supplementary_files_format_and_content: Accessible chromatin fragments per ATAC library

source_name: peripheral blood mononuclear cells


title: 10A_M_1196


title: 10A_M_1195


title: Pearson-mix-3 [Celline_scATAC]

source_name: Fibroblast cell line

growth_protocol: All fibroblasts were grown in DMEM containing 15% FBS, L-glutamine, non-essential amino acid and penicillin/streptomycin. Cells were incubated at 37°C with 5% CO2.

tag: donors mixed

value: D1, D2, and D4; D1,D2 = Pearson

value: Fibroblast cell line


title: xh_220707_22-24h_mix

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
For metagenomics annotation, kaiju (Menzel et al., 2016) was used.
The xHYB data was quantified by aligning raw fastq reads to the reference sequences on which the xHYB panel was built.
Trinity (Haas et al., 2013) and SPAdes (Prjibelski et al., 2020) were used for transcript assembly. Transcript assemblies were then used for detection of novel virus contigs.
Supplementary files format and content: tab-separated values
Supplementary files format and content: fasta files

organism: wastewater metagenome

source_name: wastewater

extract_protocol:
Raw influx was filtered by 2 µm and 0.2 µm. Filtrate was either concentrated using Centricon units (60 ml), or used for Ceres nanotrap based extraction according to the manufacturer's protocol (10 ml) with addition of the ER2 reagent.
RNA was extracted using Trizol/Trizol LS (Thermo Fisher) and the Zymo DirectZol kit (cat# R2050), or with the Zymo Biomics RNA Magbead kit (cat# R2137) using either the RNA isolation protocol from this kit's manual or the RNA/DNA combination isolation protocol from the manual of the Zymo Biomics MagBead DNA/RNA kit (cat# R2135).
DNA was extracted using the Zymo RNA Magbead kit (cat# R2137) with the RNA/DNA combination protocol from the manual of the MagBead DNA/RNA kit (cat# R2135), or with the Zymo Biomics DNA Miniprep Kit (cat# D4300)
RNA sequencing libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara). DNA sequencing libraries were prepared by first applying the ResolveDNA Whole Genome Amplification kit (BioSkryb) and subsequently the Nextera XT DNA Library Preparation Kit (Illumina).
A subset of RNA sequencing libraries was subjected to enrichment using the xHYB adventitious agent panel (Qiagen) where indicated in the sample description.

treatment_protocol: Raw influx from Berlin wastewater treatment plants was provided by municipial water authorities (BWB). Samples were mostly taken as 2 hours composite samples (see time point in sample name), stored at four degrees, and processed within 12 hours.

tag: geographic location

tag: tissue

value: wastewater

tag: processing

value: Concentration

tag: nucleic acid_extraction

value: Trizol/Zymo DirectZol

tag: enrichment

value: xHYB adv. agents


title: xh_220707_22-24h_mix_CeresBiomCombiRNA

value: Ceres nanotrap

value: Zymo Biomics magbead (DNA/RNA combi protocol)


title: 10A_M_1193


title: xh_220707_20-22h_mix_CeresBiomCombiRNA


title: xh_220707_20-22h_mix


title: 10A_M_1194


title: Pearson-mix-5 [Celline_scATAC]

value: D1-D5; D1-D3 = Pearson


title: 10A_M_119


title: 10A_M_1188


title: Pearson_PBMC_PT3_scATAC


title: 10A_M_1192


title: xh_220629_22-24h_mix


title: 10A_M_1189


title: INPUT_WT3

data_processing:
Reads were aligned with bowtie2 (version Bowtie2/2.3.2) to the human genome (UCSC version hg38AnalysisSet). The output was sorted and indexed with samtools (version SAMtools/1.7). Duplicated reads were marked with picard (version picard/2.9.2).
For each sample, peaks where called with macs2 (version MACS2/2.1.1.20160309) using the options '-q 0.01 --nomodel --shift -75 --extsize 150 -g 2700000000 --keep-dup all'.
Called peaks were merged across biological replicates. The maximal peak distance for merging was set to the average fragment size (150). The log fold-change over input was calculated for this merged peak set (based on the total library size in each sample) and filtered for a log2[fold-change]>1.
The resulting merged and filtered peaks were converted to bigBed format using the UCSC command line tool bedToBigBed.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig file, Coverage tracks per sample were generated by tiling the genome in 20bp windows, counting overlapping reads per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.

growth_protocol: Cells were cultured in Ham's F12 with 5% fetal calf serum (Gibco, Invitrogen), 5 μg/ml bovine insulin (Sigma), 1 μg/ml hydrocortisone (Sigma), 1× penicillin/streptomycin (Gibco, Invitrogen) in monolayer, until they reached 80% confluency,

extract_protocol:
After cross-linking (1% formaldehyde) and nuclei isolation, nuclei were lysed and sonicated in 50mM Hepes/KOH pH7.5, 500mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% DOC, 0.1%SDS and protease inhibitors, followed by overnight incubation with the respective antibodies and antibody/protein/chromattin conjugate pulldown using magnetic beads. The samples were then reverse cross-linked and DNA was purified using a phenol/chloroform extraction method.
10 ng of DNA were used for the library preparation using the KAPA Hyper Prep Kit (Roche), according to the manufacturer's instructions. QC of libraries was done with Fragment Analyzer using the High Sensitivity NGS Fragment ANalysis Kit (both from AATI).

tag: cell line

value: Breast cancer cell line

tag: genotype

value: WT

tag: replicate

tag: chip antibody

value: none (input)


title: INPUT_WT2


title: 10A_M_1187

value: male


title: 10A_M_1202


title: 10A_M_1190


title: xh_220629_22-24h_mix_CeresBiomCombiRNA


title: INPUT_WT1


title: xh_220629_20-22h_mix_CeresBiomCombiRNA


title: 10A_M_1186


title: INPUT_KOS3

value: KOS


title: 10A_M_1183


title: 10A_M_1181


title: 10A_M_1182


title: INPUT_KOS2


title: Pearson_PBMC_PT1_scATAC

tag: subject status

value: peripheral blood mononuclear cells


title: 10A_M_1180


title: xh_220623_24h_mix_1


title: 10A_M_1179


title: 10A_M_118


title: INPUT_KOS1

tag: cell type


title: xh_220629_20-22h_mix


title: INPUT_KOD3

value: KOD


title: 10A_M_1178


title: 10A_M_1177


title: xh_220616_22-24h_mix


title: 10A_M_1172


title: 10A_M_1171


title: xh_220616_20-22h_mix


title: 10A_M_1184


title: xh_220607_22-24h_mix


title: 10A_M_1199


title: INPUT_KOD2


title: xh_220607_22-24h_mix_CeresBiomCombiRNA


title: 10A_M_1170


title: INPUT_KOD1


title: FAC-cyESCs, replicate 1, RNAseq

description: Bulk

tag: treatment

value: Separately cultured cells

tag: tissue type

value: Embryo

value: FTW-cyESCs(FTW-cynomolgus monkey embryonic stem cells)


title: 10A_M_1174

tag: brain region

tag: age


title: 10A_M_117

tag: Sex

tag: strain


title: xh_220623_24h_mix_2

tag: geographic location

value: wastewater


title: H3K9ME3_WT3

value: anti-H3K9me3 (39161, ActiveMotif)


title: 10A_M_1169


title: 10A_M_1168


title: H3K9ME3_WT2


title: xh_220607_20-22h_mix_CeresBiomCombiRNA

tag: tissue


title: H3K9ME3_WT1


title: 10A_M_1167


title: 10A_M_1165


title: 10A_M_1166


title: 10A_M_1164


title: H3K9ME3_KOS3


title: xh_220602_22-24h_mix

tag: processing

value: Concentration

value: Trizol/Zymo DirectZol


title: H3K9ME3_KOS2


title: xh_220602_22-24h_mix_CeresBiomCombiRNA

value: Ceres nanotrap

tag: nucleic acid_extraction

value: xHYB adv. agents


title: 10A_M_1161


title: 10A_M_116


title: 10A_M_1160


title: xh_220602_22-24h_mix_CeresBiomRNA

value: Zymo Biomics magbead

tag: enrichment


title: 10A_M_1163


title: H3K9ME3_KOS1

tag: cell line

value: Breast cancer cell line


title: xh_220602_20-22h_mix


title: 10A_M_1156


title: 10A_M_1157


title: xh_220602_20-22h_mix_concBiomCombiRNA

value: Zymo Biomics magbead (DNA/RNA combi protocol)


title: H3K9ME3_KOD2

tag: genotype


title: 10A_M_1155


title: xh_220607_20-22h_mix


title: 10A_M_1159


title: xh_220602_20-22h_mix_CeresBiomRNA


title: H3K9ME3_KOD1

tag: replicate


title: 10A_M_1153


title: 10A_M_1151


title: xh_220602_20-22h_mix_CeresBiomCombiRNA


title: xh_220527_22-24h_mix


title: H3K4ME3_WT3

value: WT

tag: chip antibody

value: anti-H3K4me3 (ab8580, Abcam)


title: 10A_M_115

value: male


title: 10A_M_1148


title: 10A_M_1149


title: H3K4ME3_WT2


title: 10A_M_1150


title: H3K4ME3_WT1


title: 10A_M_1147


title: 10A_M_1146


title: 10A_M_1145


title: 10A_M_1144


title: H3K9ME3_KOD3


title: H3K4ME3_KOS3

value: KOS


title: H3K4ME3_KOS2


title: xh_220527_22-24h_mix_CeresTrizolElu_PCRinhibRemov

value: Trizol from Ceres beads, then Trizol/Zymo DirectZol

tag: additional processing

value: PCR inhibitor removal column


title: 10A_M_1152


title: H3K4ME3_KOS1

tag: cell type


title: xh_220527_22-24h_mix_CeresTrizolElu


title: 10A_M_1140


title: 10A_M_114


title: 10A_M_1142


title: xh_220527_20-22h_mix


title: 10A_M_1138


title: xh_220527_22-24h_mix_PCRinhibRemov


title: xh_220527_22-24h_mix_concBiomCombiRNA


title: xh_220527_20-22h_mix_PCRinhibRemov


title: H3K4ME3_KOD3

value: KOD


title: 10A_M_1137


title: 10A_M_1136


title: xh_220527_20-22h_mix_concBiomCombiRNA


title: H3K4ME3_KOD2


title: H3K4ME3_KOD1


title: 10A_M_1134


title: 10A_M_1141


title: 10A_M_1143


title: H3K27ME3_WT3

value: anti-H3K27me3 (ab6002, Abcam)


title: xh_220527_20-22h_mix_CeresTrizolElu

value: wastewater


title: 10A_M_1133


title: 10A_M_1132


title: 10A_M_1131


title: xh_220527_20-22h_mix_CeresTrizolElu_PCRinhibRemov


title: H3K27ME3_WT1


title: H3K27ME3_WT2


title: xh_220511_22-24h_mix


title: sgLXRB-1 CAR-T Cell 3 [sgLXRB-1-3]

city: Shanghai

first: Haochen

last: Yang

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
We used Cutadapt (v1.15) software to filter the sequencing data to get high quality Clean Data for further analysis.
Reads were aligned to an assembly of Homo Sapiens (GRCh38) using STAR software (V2.7.10b) (https://github.com/alexdobin/STAR).
We used HTSeq (V0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene.
Assembly: hg38
Supplementary files format and content: Comma-separated values files include RAW count mapped to gene for each sample

source_name: T Cell

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
The sequencing libraries were generated and sequenced on NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.

value: T Cell

tag: treatment


title: 10A_M_1130


title: 10A_M_1135


title: 10A_M_113


title: xh_220511_22-24h_mix_PCRinhibRemov

value: Concentration


title: 10A_M_1129


title: 10A_M_1128


title: H3K27ME3_KOS2


title: xh_220511_20-22h_mix

value: Trizol/Zymo DirectZol


title: sgLXRB-1 CAR-T Cell 1 [sgLXRB-1-1]


title: xh_220511_20-22h_mix_PCRinhibRemov


title: xh_220511_20-22h_mix_CeresBiomRNA

value: Ceres nanotrap


title: sgNTC CAR-T Cell 2 [sgNTC-2]

value: sgNTC


title: xh_220427_22-24h_mix

value: xHYB adv. agents


title: H3K27ME3_KOD3

value: Breast cancer cell line


title: 10A_M_1125


title: sgNTC CAR-T Cell 3 [sgNTC-3]


title: 10A_M_1124


title: H3K27ME3_KOD1


title: 10A_M_1126


title: H3K27ME3_KOS3


title: 27HC Treat CAR-T Cell 3 [27HC-3]

value: 27-HC Treatment


title: 27HC Treat CAR-T Cell 2 [27HC-2]

value: WT


title: xh_220427_20-22h_mix


title: H3K27AC_WT3

value: anti-H3K27ac (ab4729, Abcam)


title: H3K27AC_WT2


title: 10A_M_1122

value: male


title: xh_220511_22-24h_mix_CeresBiomRNA

value: Zymo Biomics magbead


title: H3K27ME3_KOS1

value: KOS


title: xh_220421_22-24h_mix_mix_CeresTrizolElu


title: 10A_M_1127


title: 10A_M_1121


title: xh_220421_22-24h_mix


title: sgLXRB-1 CAR-T Cell 2 [sgLXRB-1-2]


title: 10A_M_1123


title: H3K27AC_WT1


title: H3K27ME3_KOD2


title: sgNTC CAR-T Cell 1 [sgNTC-1]


title: xh_220421_20-22h_mix


title: H3K27AC_KOS3


title: 27HC Treatment Control CAR-T Cell 2 [27HC-CTRL2]

value: 27-HC Treat Control


title: 10A_M_1120


title: xh_220421_20-22h_mix_CeresTrizolElu


title: 27HC Treatment Control CAR-T Cell 1 [27HC-CTRL1]


title: 10A_M_112


title: xh_220413_22-24h_mix


title: 27HC Treat CAR-T Cell 1 [27HC-1]


title: 27HC Treatment Control CAR-T Cell 3 [27HC-CTRL3]


title: 10A_M_1119


title: Treatment Control CAR-T Cell 3 [CTRL3]

value: Treat Negative Control


title: 10A_M_1116


title: H3K27AC_KOS1


title: Treatment Control CAR-T Cell 1 [CTRL1]


title: 10A_M_1118


title: xh_220404_20-22h_mix


title: 10A_M_1117


title: RO 48-8071 treat CAR-T Cell 2 [RO2]


title: RO 48-8071 treat CAR-T Cell 3 [RO3]


title: 10A_M_1115


title: H3K27AC_KOD1

value: KOD


title: Treatment Control CAR-T Cell 2 [CTRL2]


title: xh_220404_22-24h_mix

value: wastewater


title: Pearson_invitro_culture_Day12_c7_scRNA

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
Soupercell was run with default parameters on the CellRanger bam file and processed to annotate healthy/Pearson cells
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression abundances (hdf5) and donor demultiplexing (tsv) per library

tag: subject status

value: patient with Pearson Syndrome

value: Differentiated BMMNC

tag: day collected


title: xh_220413_20-22h_mix

value: Concentration

value: Trizol/Zymo DirectZol


title: 10A_M_1114

tag: brain region

tag: age


title: xh_220404_20-22h_mix_CaptuElu

value: captuvir eluate


title: xh_220404_20-22h_mix_beforeCaptu

value: before captuvir

value: xHYB adv. agents


title: Pearson_invitro_culture_Day12_c8_scRNA


title: RO 48-8071 treat CAR-T Cell 1 [RO1]

value: T Cell


title: H3K27AC_KOS2

value: Breast cancer cell line


title: Pearson_invitro_culture_Day12_c6_scRNA


title: H3K27AC_KOD2

value: anti-H3K27ac (ab4729, Abcam)


title: H3K27AC_KOD3


title: xh_220404_20-22h_mix_CaptuEluConc

value: captuvir concentrated eluate


title: RGX-104 treat CAR-T Cell 3 [RGX3]

value: WT


title: 10A_M_1113

tag: Sex

value: male

tag: strain


title: xh_220404_20-22h_mix_CaptuFT

tag: geographic location

tag: tissue

value: captuvir flowthrough


title: RGX-104 treat CAR-T Cell 2 [RGX2]


title: 10A_M_111


title: xh_220204_22-24h_mix

tag: processing

tag: nucleic acid_extraction


title: RGX-104 treat CAR-T Cell 1 [RGX1]


title: GW3965 treat CAR-T Cell 2 [GW2]


title: Pearson_invitro_culture_Day6_c2_scRNA


title: xh_220119_22-24h_mix

tag: enrichment


title: xh_220204_20-22h_mix


title: 10A_M_1106


title: xh_220119_20-22h_mix


title: Pearson_invitro_culture_Day6_c1_scRNA


title: 10A_M_1107


title: Pearson_invitro_culture_Day6_c4_scRNA


title: Pearson_invitro_culture_Day6_c3_scRNA


title: 10A_M_1108


title: 10A_M_1105


title: GW3965 treat CAR-T Cell 1 [GW1]

tag: genotype


title: xh_220113_22-24h_mix


title: GW3965 treat CAR-T Cell 3 [GW3]


title: xh_220113_20-22h_mix


title: In vitro CAR-T Cell 3 [Vitro3]

value: In Vitro


title: 10A_M_1109


title: Adult, replicate 1-2, scRNAseq

city: Birmingham

first: Aaron

last: Silva Sanchez

state: AL

address: 1825 University Boulevard

department: Medicine

institute: The University of Alabama at Birmingham

description: 10x Genomics

data_processing:
An aggregate count matrix was generated using Cell Ranger (version 6.1.2, 10x Genomics). Briefly, cell barcodes were demultiplexed, and reads were aligned to the mm10 genome using the cellranger multi pipeline. The cell ranger aggr was then used to normalize counts across samples.
We next processed the aggregated matrix using the R package Seurat (version 4.2.0). Cells with a total number of genes (nFeature_RNA) between 200 and 3500 and a gene count (nCount_RNA) lower than 15,000 were kept. We further excluded cells whose mitochondrial gene counts accounted for more than 10% of total counts.
Using the expression of lineage genes (Ms4a1, Cd19, Ighd, Igha, Sdc1, Mzb1, Cd3e, Cd3g, Lck, Cd8a, Cd8b1, Cd4, Tcrg-C1, Trdc, Klrb1b, Klrb1c, Klrc1, Klrd1, Klrg1, Klra7, Nkg7, Lyz2, Cd68, Fcgr1, Ccr2, Ly6g, Zbtb46, Il12b, Siglech, Siglecf), we excluded non-DC contaminants from downstream analyses. The Seurat file was saved in the rds format.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files and rds file

source_name: Lung

extract_protocol:
Lungs from neonatal and adult Zbtb46-YFP mice were processed. Two replicates in the same group (NEO or AD) were stained with TotalSeq-B anti-mouse Hashtag1 and Hashtag2 (BioLegend), respectively. Cells were then stained with LIVE/DEAD AQUA, CD45.2, and DCs were purified by FACS sorting of live CD45.2 YFP+ cells.
Single cell libraries were prepared according to the protocol for Chromium Single Cell 3' Reagent Kit v2 (10X Genomics). Briefly, sorted DCs from the same group of mice were combined. DCs, barcoded single cell 3ʹ gel beads and partitioning oil were then loaded onto a Single Cell A Chip, and single cell Gel Bead-In-EMulsions (GEMs) were generated by Chromium controller. Barcoded cDNA was then produced by the incubation of GEMs and amplified by PCR after the GEMs were broken to generate sufficient mass. Sequencing libraries were finally constructed with the P5 primer, sample index and P7 primer added.

value: Dendritic cells

value: Lung

value: 8 weeks


title: Neonatal, replicate 1-2, scRNAseq

description: 10x Genomics

value: 7 days


title: Liver_RNA Mouse, C70

city: Bethesda

first: Alexander

middle: V

last: Sorokin

state: MD

address: 10 Center Drive, Bldg 10, Magnuson CC, Room 5D-03

institute: NIH, NHLBI

data_processing:
[mapping and quantification of gene expression]  The “Demultiplex QIAseq UPX 3' reads” tool of the CLC Genomics Workbench 20.0.3 was used to demultiplex the raw sequencing reads according to the sample indices. The “Quantify QIAseq UPX 3' workflow” was used to process the demultiplexed sequencing reads with default settings. In short, the reads are trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality and ambiguous nucleotides. They are then deduplicated using unique molecular identifier (UMIs). Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups, if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing a SNP (the biggest group is chosen). The reads were then mapped to the mouse genome GRCm38 and annotated using the NCBI RefSeq GRCm38.p6 annotation.
[differential gene expression]  The 'Empirical analysis of DGE' algorithm of the CLC Genomics Workbench 20.0.3 (https://digitalinsights.qiagen.com) was used for differential expression analysis with default settings. It is an implementation of the 'Exact Test' for two-group comparisons developed by Robinson and Smyth (30) and incorporated in the EdgeR Bioconductor package (31). Genes with log-adjusted p value less than 0.05 were considered significantly deregulated. Falls discovery rate (FDR)-adjusted p value less than 0.05 was only applicable in aorta samples analyses, thus for consistency of gene changes representation across the groups, we applied only log-adjusted p value in final report.
[heatmaps, hierarchical clustering and computational analyses]  'log CPM' (Counts per Million) values were calculated for each gene. The CPM calculation uses the effective library sizes as calculated by the TMM normalization. After this, a Z-score normalization was performed across samples for each gene: the counts for each gene are mean centered and scaled to unit variance. Rows and columns were clustered using Euclidean distance as distance measure and average linkage as clustering method. The Heatmap was plotted using the R package pheatmap (https://CRAN.R-project.org/package=pheatmap). Pathway analysis was performed with significantly changed genes through the use of Ingenuity Pathway Analysis (IPA, QIAGEN) (32). The principal component analysis (PCA) figure was generated using the CLC Genomics Workbench 20.0.3. 'log CPM' (Counts per Million) values were calculated for each gene. The CPM calculation uses the effective library sizes as calculated by the TMM normalization. After this, a Z-score normalization was performed across samples for each gene: the counts for each gene were mean centered and scaled to unit variance. Genes or transcripts with zero expression across all samples or invalid values (NaN or +/- Infinity) were removed.
Supplementary_files_format_and_content: Cumulative comparative results per each gene, Excel file

source_name: Liver_RNA Mouse

extract_protocol:
After euthanasia, mouse ear and other tissues have been preserved in the TRIzol (Invitrogen) until further RNA isolation (n=4-5 per each experimental group). Arterial system and liver have been flushed with 1x cold PBS. Aorta has been isolated from the heart origin up to iliac bifurcation with perivascular fat removed along the whole distance.
The RNA isolation was performed using the QIAGEN RNeasy kit according to manufacturer's protocol. The Starting volume was approx. 30mg and elution was 30ul. The library preparation was done using the QIAseq UPX 3’ Transcriptome Kit (QIAGEN). A total of 10ng purified RNA was converted into cDNA NGS libraries. During reverse transcription, each cell is tagged with a unique ID and each RNA molecule is tagged with a unique molecular index (UMI). Then RNA was converted to cDNA. The cDNA was amplified, during the PCR indices were added and the libraries were purified. Library preparation QC was performed using Agilent Bioanalyzer. Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using qPCR. The library pool was then sequenced on a NextSeq500 sequencing instrument according to the manufacturer instructions with 100bp read length for read 1 and 27bp for read2. Raw data was de-multiplexed and FASTQ files for each pool was generated using the bcl2fastq software (Illumina inc.).

treatment_protocol: After 2 weeks on an Omega-3 FA Deficient (OD) diet, 14 weeks old mice were randomly assigned to one of 3 experimental diets (n=5): 1) OD diet, 2) EPA Rich (EPA) diet (3.0 g EPA/kg • diet per day), or 3) DHA Rich (DHA) diet (3.0 g EPA/kg • diet per day) for another 12-week feeding period. Supplementation with either EPA or DHA was calculated according to a metabolic body weight formula (27) to produce a human (70 kg) equivalent dose of 4 g/day of EPA or DHA. All feeds were stored in vacuum at 4°C and were changed twice a week. All procedures were approved by the Animal Care and Use Committee of the NHLBI (#H-0275R1).

value: DHA-suppl

value: liver


title: 10A_M_1104

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2


title: Pearson_invitro_culture_Day12_c5_scRNA

value: patient with Pearson Syndrome

value: Differentiated BMMNC


title: In vitro CAR-T Cell 1 [Vitro1]


title: 10A_M_1103


title: xh_220105_22-24h_mix

value: wastewater

value: Concentration

value: Trizol/Zymo DirectZol

value: xHYB adv. agents


title: 10A_M_1101


title: xh_220105_20-22h_mix


title: 10A_M_1100


title: Intratumoral CAR-T Cell 2 [TIL2]

value: T Cell

value: In Vivo(Intratumoral)


title: Intratumoral CAR-T Cell 3 [TIL3]

value: WT


title: xh_211223_22-24h_mix


title: Liver_RNA Mouse, C58

value: EPA-suppl


title: 10A_M_110

value: male


title: Intratumoral CAR-T Cell 1 [TIL1]


title: In vitro CAR-T Cell 2 [Vitro2]

value: In Vitro


title: xh_211208_22-24h_mix


title: Liver_RNA Mouse, C22


title: Liver_RNA Mouse, C46

value: Omega-3 Deficient


title: 10A_M_11


title: xh_211208_20-22h_mix


title: Liver_RNA Mouse, C34


title: 10A_M_1099


title: Liver_RNA Mouse, C10


title: xh_211124_22-24h_mix


title: 10A_M_1098


title: Liver_RNA Mouse, C93


title: xh_211124_20-22h_mix


title: 10A_M_1097


title: xh_211223_20-22h_mix


title: xh_211117_22-24h_mix


title: 10A_M_1096


title: ACC-422, radiation treatment, bio rep 3

first: Corey

middle: W

last: Speers

address: 1700 6th Ave S

department: Radiation Oncology

institute: University of Alabama Birmingham

data_processing:
Raw sequencing reads aligned using HISAT2
Aligned reads mapped to genes using htseq-count
Differential gene expression analysis with DeSeq2
Assembly: hg38
Supplementary files format and content: tab-delimited tsv files include raw read counts for each sample

source_name: Breast

growth_protocol: Cells were grown in an incubator at 37°C with 5% CO2. MDA-MB-453 cells were grown in DMEM media containing 1% penicillin/streptomycin and 10% fetal bovine serum (FBS). ACC-422 cells were grown in MEM media containing  1X Insulin-Transferrin-Selenium-Ethanolamine, 1% penicillin/streptomycin and 15% fetal bovine serum (FBS).

extract_protocol:
For each sample, RNA was collected using TRIzol and isolated using the miRNeasy mini kit (Qiagen 217004).
Poly(A) mRNA library preparation  was performed by the Advanced Genomics Core at the University of Michigan using NEB PolyA enrichment and NEB Ultra 2 stranded kits.

treatment_protocol: MDA-MB-453 and ACC-422 cells were plated in media containing FBS and left to adhere overnight. The following day, cells were pretreated in media without phenol red containing CSS instead of FBS for 48 hours. After this pretreatment, cells were stimulated with 1 nM R1881, 2 mM enzalutamide, or 4 Gy RT for 24 hours. Cells treated with a combination of R1881 with RT or enzalutamide with RT first received a 24-hour pretreatment with R1881, following by 4 Gy RT, and RNA was collected 24 hours post-RT.

value: Breast

tag: cell line

value: Breast cancer cells

value: radiation treatment


title: ACC-422, radiation treatment and R1881, bio rep 1

value: radiation treatment +R1881


title: ACC-422, radiation treatment and R1881, bio rep 3


title: ACC-422, radiation treatment and R1881, bio rep 2


title: Liver_RNA Mouse, C81

value: liver


title: ACC-422, radiation treatment, bio rep 2


title: 10A_M_1092

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: Liver_RNA Mouse, C69

value: DHA-suppl


title: Liver_RNA Mouse, C57


title: ACC-422, radiation treatment, bio rep 1


title: xh_211028_22-24h_mix

value: wastewater


title: 10A_M_1090


title: xh_211028_20-22h_mix

value: Concentration


title: 10A_M_109


title: xh_211013_20-22h_mix

value: Trizol/Zymo DirectZol


title: Liver_RNA Mouse, C45


title: Liver_RNA Mouse, C33


title: Liver_RNA Mouse, C21


title: ACC-422, R1881, bio rep 3


title: ACC-422, R1881, bio rep 2


title: 10A_M_1088


title: xh_210929_22-24h_mix

value: xHYB adv. agents


title: Liver_RNA Mouse, C9


title: xh_210929_20-22h_mix


title: SKIN_EAR, C92

value: skin


title: xh_211117_20-22h_mix


title: 10A_M_1085


title: ACC-422, no treatment, bio rep 3

value: no treatment


title: ACC-422, R1881, bio rep 1


title: xh_210916_22-24h_mix


title: ACC-422, no treatment, bio rep 2


title: SKIN_EAR, C80


title: ACC-422, no treatment, bio rep 1


title: 10A_M_1083


title: xh_210722_20-22h


title: SKIN_EAR, C68


title: SKIN_EAR, C56


title: 10A_M_1084


title: xh_210916_20-22h_mix


title: MDA-MB-453, radiation treatment and R1881, bio rep 2


title: xh_210622_22-24h


title: 10A_M_1082


title: 10A_M_1086


title: MDA-MB-453, radiation treatment and R1881, bio rep 1


title: SKIN_EAR, C44


title: xh_210622_20-22h


title: 10A_M_1080


title: SKIN_EAR, C32


title: 10A_M_1081


title: MDA-MB-453, radiation treatment, bio rep 3


title: 10A_M_1079


title: xh_210610_22-24h


title: SKIN_EAR, C20


title: MDA-MB-453, radiation treatment and R1881, bio rep 3


title: xh_210610_20-22h


title: MDA-MB-453, radiation treatment, bio rep 2


title: xh_210604_22-24h


title: MDA-MB-453, radiation treatment, bio rep 1


title: 10A_M_1076


title: xh_210604_20-22h


title: SKIN_EAR, C8


title: SKIN_EAR, C91


title: xh_210527_22-24h


title: 10A_M_1074


title: MDA-MB-453, R1881, bio rep 3


title: MDA-MB-453, R1881, bio rep 2


title: SKIN_EAR, C79


title: MDA-MB-453, R1881, bio rep 1


title: MDA-MB-453, no treatment, bio rep 3


title: SKIN_EAR, C55


title: SKIN_EAR, C67


title: SKIN_EAR, C43


title: MDA-MB-453, no treatment, bio rep 2


title: 10A_M_1072


title: 10A_M_1073


title: xh_210519_20-22h


title: 10A_M_1077


title: 10A_M_1071


title: SKIN_EAR, C31


title: MDA-MB-453, no treatment, bio rep 1


title: xh_210527_20-22h


title: xh_210422_22-24h


title: 10A_M_1070


title: xh_210422_20-22h


title: 10A_M_1075


title: 10A_M_107


title: DDX42 SMInput treated with PladB (rep2)

description: DDX42_PladB.reproducible_enriched_windows.tsv

data_processing:
Processed using Skipper https://github.com/YeoLab/skipper
Skipper trims the read, extract UMI, align to the genome and deduplicate
To find enriched windows, it models the CLIP libraries crosslinking-induced truncation(CITs)  with beta-binomial model with GC-bias of each window as a varaible
overdispersion parameters are estimated from two input replicates
Assembly: hg38
Supplementary files format and content: wig files represent crosslinking-induced truncation(CITs) for plus and minus strands
Supplementary files format and content: tsv file represents reproducible genomic enriched window

source_name: HCT116 colon cancer cell line

growth_protocol: 5×10^6 HCT-116 DDX42-dTAG endogenous knock-in cells per sample were seeded into a 10 cm plate and grown for 24h in DMEM with Glutamax and 10% fetal bovine serum (Life Technologies).

extract_protocol:
HCT116 replicates were treated with 400 mJ of UV using the CL-1000 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with HA antibody-bound Dynabeads (antibody: CST 3724S). Subsequent protocol was followed as detailed in Van Nostrand et al, Methods Mol Biol 2017. Sequencing was performed on Illumina Novaseq 6000 single-end reads and data processed through Dr. Yeo's seCLIP pipeline.
Libraries were constructed as per the (s)eCLIP protocol using Illumina 50x forward and 70x reverse primers.

treatment_protocol: Cells were treated with 5 µM WX-02-23, 5 µM WX-02-43, 100 nM pladienolide B, or vehicle control from 1000x DMSO stocks in 7mL medium for 3h

value: HCT116, DDX42 HA-tagged

value: Pladienolide B

tag: clip antibody

value: none (input)


title: DDX42 CLIP treated with PladB (rep2)


title: Aorta_RNA Mouse, C19

source_name: Aorta_RNA Mouse

value: aorta


title: xh_210415_22-24h


title: Aorta_RNA Mouse, C7

value: EPA-suppl


title: xh_210415_20-22h


title: xh_210519_22-24h


title: DDX42 CLIP treated with PladB (rep1)


title: 10A_M_1068

value: male


title: Aorta_RNA Mouse, C78


title: DDX42 SMInput treated with PladB (rep1)


title: Aorta_RNA Mouse, C66


title: 10A_M_1067


title: xh_210408_22-24h


title: xh_210408_20-22h


title: 10A_M_1066


title: xh_210325_KW2_morning


title: Aorta_RNA Mouse, C54


title: 10A_M_1065


title: Aorta_RNA Mouse, C42


title: DDX42 SMInput treated with WX-02-43 (rep2)

description: DDX42_WX-2-43.reproducible_enriched_windows.tsv


title: DDX42 CLIP treated with WX-02-43 (rep1)


title: 10A_M_1064


title: Aorta_RNA Mouse, C30

value: Omega-3 Deficient


title: Aorta_RNA Mouse, C90


title: xh_210304_KW6


title: DDX42 SMInput treated with WX-02-43 (rep1)


title: xh_210325_KW2_22-24


title: Aorta_RNA Mouse, C18


title: 10A_M_1069


title: DDX42 CLIP treated with WX-02-23 (rep2)

description: DDX42_WX-2-23.reproducible_enriched_windows.tsv


title: 10A_M_1063


title: xh_210304_KW3


title: DDX42 CLIP treated with WX-02-43 (rep2)


title: DDX42 SMInput treated with WX-02-23 (rep2)


title: 10A_M_1061


title: 10A_M_1060


title: xh_210304_KW1


title: DDX42 CLIP treated with WX-02-23 (rep1)


title: 10A_M_106


title: DDX42 SMInput treated with WX-02-23 (rep1)


title: Aorta_RNA Mouse, C6


title: Aorta_RNA Mouse, C77


title: Aorta_RNA Mouse, C89


title: 10A_M_1058


title: DNA_220719_22-24hmix_cer_BIOMcombi

data_processing:
For metagenomics annotation, kaiju (Menzel et al., 2016) was used.
The xHYB data was quantified by aligning raw fastq reads to the reference sequences on which the xHYB panel was built.
Trinity (Haas et al., 2013) and SPAdes (Prjibelski et al., 2020) were used for transcript assembly. Transcript assemblies were then used for detection of novel virus contigs.
Supplementary files format and content: tab-separated values
Supplementary files format and content: fasta files
Library strategy: DNA-seq

value: Ceres nanotrap

value: Zymo Biomics magbead (DNA/RNA combi protocol)


title: Aorta_RNA Mouse, C65


title: DNA_220719_20-22mix_cer_BIOMcombi


title: Aorta_RNA Mouse, C53


title: 10A_M_1056


title: DDX42 CLIP treated with DMSO (rep2)

description: DDX42_DMSO.reproducible_enriched_windows.tsv

value: DMSO


title: DNA_220707_22-24hmix_cer_BIOMminiprep

value: Zymo Biomics DNA miniprep


title: DNA_220707_22-24hmix_cer_BIOMcombi

value: wastewater


title: 10A_M_1054


title: xh_210304_KW2

value: Concentration


title: 10A_M_1055


title: DNA_220707_20-22mix_cer_BIOMcombi


title: DDX42 SMInput treated with DMSO (rep2)


title: DDX42 CLIP treated with DMSO (rep1)


title: 10A_M_1052


title: 10A_M_1053


title: Lev-diazirine-comp-2

city: Stanford

first: Linglan

last: Fang

state: California

address: 369 N-S AXIS STAUFFER I, RM-107-CHEMISTRY-KOOL LAB

institute: Stanford University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
Trimmed sequence reads were mapped to GRCh38 using bowtie2 (parameters: non-deterministic)
Read count extraction were performed using icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
RBRP scores were calculated using RBRP scripts (https://github.com/linglanfang/RBRP)
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly
Supplementary files format and content: bigWig files include RBRP scores and log-transformed p-value
Supplementary files format and content: tab- and comma-delimited text files include RPKM values for each sample

source_name: embryonic kidney

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
To isolate total cellular RNA, cells were lysed with 6 mL of Trizol LS reagent according to the Supplementary Information. RNAs were then purified with a Zymo Quick-RNA Midiprep kit according to the manufacturer’s protocol. To enrich poly(A)+ transcripts, a 250-µg aliquot of total cellular RNA was diluted to 600 µg/mL with RNA storage buffer and then purified with Poly(A)Purist MAG kit according to the manufacturer’s protocol. The captured RNAs were further purified with RNeasy Mini columns according to the manufacturer’s protocol, and stored as 500-ng aliquots at -80 ˚C.
RNA libraries for RNA-seq were prepared using a customized protocol developed in our lab (bioRxiv 2022.07.18.500496; doi: https://doi.org/10.1101/2022.07.18.500496)

value: embryonic kidney

value: Human embryonic kidney

value: cells contain Adenovirus 5 DNA (PMID:11967234)

value: Cells were treated with Lev-diazirine for 30 minutes, then washed with PBS and irradiated with UV


title: Linker-1, RBRP

description:
diff_RBRP_Das.sim.bw
diff_RBRP_HCQ.sim.bw
diff_RBRP_Lev.sim.bw

value: Cells were treated with Linker-AI for 30 minutes


title: Lev-diazirine-comp-1


title: PT1_rep2_mtDOGMA_TSA_sup

description: Surface protein in supernatant

data_processing:
Fastqs were generated using CellRanger-Arc mkfastq v1.0
Sequencing reads were aligned using CellRanger-Arc count to the hg38 reference genome and transcriptome
RNA/ATAC data were aggregated using CellRanger-Arc aggr v1.0 between the two replicates
Assembly: hg38
Supplementary files format and content: Aggregated gene expression counts with cells x peaks matrix (h5), ATAC fragments (tsv), and surface proteins (.csv) per cell
Library strategy: multiome

extract_protocol:
10x Genomics multiome protocol
10x Genomics multiome scRNA-seq with adaptations for mtDNA and surface proteins described here: https://www.nature.com/articles/s41587-021-00927-2 (DOGMA-seq)

value: peripheral blood mononuclear cells


title: PT1_rep2_mtDOGMA_TSA_preAMP

description: Surface protein pre amplificaiton


title: DNA_220629_22-24hmix_cer_BIOMminiprep


title: DNA_220629_22-24hmix_cer_BIOMcombi


title: 10A_M_1051

source_name: C57BL/6J Male P56 Mouse Brain


title: 10A_M_1050


title: DNA_220629_20-22hmix_cer_BIOMminiprep


title: 10A_M_105


title: Linker-2, RBRP


title: Lev-diazirine-1


title: Lev-comp-1, RBRP

description:
diff_RBRP_Lev.sim.bw
neglog10P-value_Lev.sim.bw

value: Cells were treated with Levofloxacin for 30 minutes, followed by treatment wit Lev-AI for 30 minutes


title: PT1_rep1_mtDOGMA_TSA_preAMP

description: Surface protein pre amplificaiton


title: DNA_220629_20-22hmix_cer_BIOMcombi


title: DDX42 SMInput treated with DMSO (rep1)

value: HCT116, DDX42 HA-tagged

value: none (input)


title: Lev-comp-2, RBRP


title: Lev-2, RBRP

value: Cells were treated with Lev-AI for 30 minutes


title: DNA_220623_24hmix_cer_BIOMminiprep


title: DNA_220707_20-22hmix_cer_BIOMminiprep


title: Lev-1, RBRP


title: 10A_M_1047

value: male


title: DNA_220623_24hmix_cer_BIOMcombi

value: Ceres nanotrap


title: DNA_220616_20-22hmix_cer_BIOMcombi

value: Zymo Biomics magbead (DNA/RNA combi protocol)


title: DNA_220616_22-24hmix_cer_BIOMcombi


title: HCQ-comp-1, RBRP

description:
diff_RBRP_HCQ.sim.bw
neglog10P-value_HCQ.sim.bw

value: Cells were treated with Hydroxychloroquine for 30 minutes, followed by treatment wit HCQ-AI for 30 minutes


title: tag-PT3-Day14v1

library_source: genomic single cell

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
Protein abundance tag libraries were computed using kallisto | bustools v0.44
Assembly: hg38
Supplementary files format and content: Accessible chromatin fragments per ATAC library (tsv) and protein abundances per ASAP tag (csv)

source_name: Human T cells in culture

treatment_protocol: Thawed cryopreserved PBMCs were resuspended to 1M/ml density in either complete medium supplemented with  complete medium supplemented with IL2 and ImmunoCult Human CD3/CD28 T cell activation then profiled 9 days after the initial culture.

tag: patient id

tag: day in culture


title: tag-PT3-Day14v2


title: DNA_220607_22-24hmix_cer_BIOMcombi


title: 10A_M_1043


title: 10A_M_1048


title: 10A_M_1045


title: PT3-Day21


title: DNA_220607_22-24hmix_centri_BIOMcombi


title: HCQ-2, RBRP

tag: cell type

tag: treatment

value: Cells were treated with HCQ-AI for 30 minutes


title: PT1_rep1_mtDOGMA_TSA_sup

description: Surface protein in supernatant


title: Lev-diazirine-2


title: 10A_M_1044


title: HCQ-comp-2, RBRP


title: HCQ-1, RBRP


title: 10A_M_1042


title: 10A_M_1049


title: PT3-Day14v2


title: 10A_M_1041


title: DNA_220607_20-22hmix_cer_BIOMcombi

value: wastewater


title: Exp-Lev-2, RNA-seq

value: Cells were treated with Levofloxacin for 60 minutes


title: PT3-Day14v1


title: DNA_220607_20-22hmix_centri_BIOMcombi

value: Concentration


title: 10A_M_1040


title: Exp-Lev-1, RNA-seq

value: embryonic kidney

value: Human embryonic kidney


title: PT1-Day14-HCmix-Rep2


title: 10A_M_104


title: DNA_220602_22-24hmix_cer_BIOMcombi


title: PT1-Day14-HCmix-Rep1


title: Exp-HCQ-1, RNA-seq

value: cells contain Adenovirus 5 DNA (PMID:11967234)

value: Cells were treated with Hydroxychloroquine for 60 minutes


title: DNA_220602_22-24hmix_centri_BIOMcombi


title: 10A_M_1038


title: Exp-DMSO-1, RNA-seq

description:
RNA-seq_Das.txt
RNA-seq_HCQ.txt
RNA-seq_Lev.csv

value: Cells were treated with DMSO for 60 minutes


title: Exp-DMSO-2, RNA-seq


title: CPEO1_mtscATAC

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
Assembly: hg38
Supplementary files format and content: Accessible chromatin fragments per ATAC library

value: Peripheral blood mononuclear cell

tag: disease

value: CPEO


title: KSS1_mtscATAC

value: KSS


title: DNA_220525_22-24hmix_centri_BIOMcombi


title: anterior capsule of the lens, HM3

city: Tianjin

first: Jing

last: Sun

state: Tianjin

address: No. 251, Fukang Road, Nankai District, Tianjin, China

institute: Tianjin medical university eye hospital

library_source: other

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.1), the high quality clean reads were aligned to the reference genome (UCSC hg19) with bwa software v(v0.7.12).
Then, circle-map software (v1.1.4) was used to detect eccDNA within all samples, and samtools (v0.2) software was used to get raw soft-clipped read counts of the break point.
Then edgeR (v0.6.9) software was used to perform normalization and differentially expressed eccDNA filter by p-value and fold change. bedtools (v2.27.1) software was used to annotate the eccDNAs.
GO and Pathway enrichment analysis were performed based on the differentially expressed eccDNA-associated genes. IGV (v2.4.10) software was used for eccDNA visualization.
Assembly: UCSC hg19
Supplementary files format and content: eccDNA_Expression_Profiling_1_.xlsx

molecule: other

source_name: anterior capsule of the lens

extract_protocol:
eccDNA enriched from 25 ng of plasma/serum DNA were processed using Nextera XT DNA Library Preparation Kit (Illumina)
DNA libraries were sequenced on Illumina NovaSeq 6000 with 150bp paired end mode according to the manufacturer’s instructions.
Circle-Seq eccDNA

value: anterior capsule of the lens

tag: condition

value: nuclear cataract along with high myopia

value: CCC

tag: molecule type

value: extrachromosomal circular DNA


title: 10A_M_1035

tag: brain region

tag: age

tag: Sex

value: male


title: DNA_220525_20-22hmix_centri_BIOMcombi

tag: geographic location

tag: tissue

value: Zymo Biomics magbead (DNA/RNA combi protocol)


title: Exp-Das-1, RNA-seq

value: Cells were treated with Dasatinib for 60 minutes


title: RNA_WW_220719_22-24hmix_cer_BIOMcombi

value: wastewater

tag: processing

value: Ceres nanotrap

tag: nucleic acid_extraction


title: anterior capsule of the lens, HM1


title: DMSO-2, RBRP

value: embryonic kidney

tag: genotype

value: Cells were treated with DMSO for 30 minutes


title: Exp-HCQ-2, RNA-seq

tag: cell line

value: Human embryonic kidney

value: cells contain Adenovirus 5 DNA (PMID:11967234)


title: 10A_M_1031

tag: strain


title: 10A_M_1030


title: 10A_M_1039


title: DMSO-1, RBRP


title: anterior capsule of the lens, HM2


title: DNA_220602_20-22hmix_cer_BIOMcombi


title: KSS2_mtscATAC


title: 10A_M_103


title: anterior capsule of the lens, C3

value: nuclear cataract


title: DNA_220602_20-22hmix_centri_BIOMcombi

value: Concentration


title: 10A_M_1037


title: Das-comp-2, RBRP

description:
diff_RBRP_Das.sim.bw
neglog10P-value_Das.sim.bw

value: Cells were treated with Dasatinib for 30 minutes, followed by treatment wit Das-AI for 30 minutes


title: Exp-Das-2, RNA-seq


title: RNA_WW_220719_20-22hmix_cer_BIOMcombi


title: RNA_WW_220719_20-22hmix

value: Trizol/Zymo DirectZol


title: anterior capsule of the lens, C2

value: anterior capsule of the lens


title: anterior capsule of the lens, C1


title: 10A_M_1029


title: 10A_M_1034


title: RNA_WW_220707_22-24hmix_cer_BIOMcombi


title: Das-comp-1, RBRP


title: Das-2, RBRP

value: Cells were treated with Das-AI for 30 minutes


title: 10A_M_1028


title: RNA_WW_220707_20-22hmix_cer_BIOMcombi


title: 10A_M_1027


title: iPSC-neurons, PTBP2 eCLIP, rep3

city: Philadelphia

first: Jennine

middle: M

last: Dawicki-McKenna

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

data_processing:
eCLIP libraries were demultiplexed, and inline random 8-mers were removed from the start of read 1 and appended to the read name using a script modified from the Yeo lab’s eclipdemux [https://github.com/YeoLab/eclipdemux]. Inline random 4-mers were removed from the start of read 2 using Trimmomatic v0.32.
Adapter sequences were removed in two rounds with Cutadapt v1.18 using commands recommended by ENCODE’s eCLIP-seq Processing Pipeline.
Paired-end reads were aligned to the human genome (GRCh38.primary_assembly.genome.fa, gencode.v39.primary_assembly.annotation.gtf) with STAR v2.7.1a (--alignEndsProtrude 15 ConcordantPair --outFilterMultimapNmax 100 --outSAMattributes NH HI AS NM MD). Multimappers were further filtered prior to peak calling (see peak calling below).
rRNA and tRNA tracks were downloaded from UCSC Table Browser (RepeatMasker's rmsk track and filtering for rRNA or tRNA), and rRNAs and tRNAs were removed in a two-step process. First, bedtools intersect (v2.15.0, -f 0.90) was used to identify all rRNA/tRNA reads. In the second step, qnames from round 1 were used to mask potentially multi-mapping rRNAs/tRNAs in the alignment file using Picard Tools v1.141 FilterSamReads.
PCR duplicate removal was performed using collapse_duplicates.py from the Xing lab (Zhang and Xing, 2017) with modifications.
Peak calling was performed using CLAM v1.2 (Zhang and Xing, 2017). Briefly, CLAM preprocessor was used to separate multi-mapped and uniquely mapped reads. Multi-mapped reads (--max-multihits of 10) were re-aligned to the genome with a probability. CLAM peakcaller was used in multi-replicate mode with size-matched input as background (n = 3 replicates each for IP and input) using default values for --qval-cutoff (0.05), --fold-change (2-inf), and --binsize (50). Finally, peak annotation was performed with CLAM peak_annotator.
bigWig files were prepared using Yeo lab’s makebigwigfiles [https://github.com/YeoLab/makebigwigfiles].
bigBed files were prepared using ENCODE's bedToBigBed.
Assembly: hg38
Supplementary files format and content: narrow_peak.combined.bb files contain CLAM peak calls in bigBed format
Supplementary files format and content: [BA4|iPSCNs]_[Input|PTBP2]_[rep].tar files contain minus/plus strand signal of unique reads in bigWig format

source_name: Human frontal cortex (Brodmann area 4)

growth_protocol: For generation of mature iPSC-neurons, we used a protocol, modified from a combination of previous studies (Telezhkin et al., 2016; Yan et al., 2013). Experiments were performed when neurons matured to day 40-50 of differentiation.

extract_protocol:
Crosslinked neurons or brain tissues were lysed in eCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40 (Igepal CA630), 0.1% SDS, 0.5% sodium deoxycholate) containing proteinase inhibitor and RNAse inhibitor. Cell or tissue lysis was assisted with sonication by using a Bioruptor on the low setting for 5 min, cycling 30 s on and 30 s off.  For each 1 mL lysate, 5 µL Turbo DNAse I (Thermo Fisher #AM2239) and high dose RNAse I (Thermo Fisher #AM2295; 1:5 diluted in cold DPBS) or low dose RNAse I (1:50 dilution for neurons, and 1:100 dilution for brain) were added. The microspin tubes were placed in a Thermomixer preheated to 37 °C for exactly 5 min, shaken at 1,200 rpm, and then put on ice to terminate the reaction.
Immunoprecipitated-RNA was dephosphorylated with FastAP enzyme (Thermo Scientific #EF0652) and T4 PNK (New England BioLabs #M0201L), and an adapter labeled with an IRDye®800CW fluorochrome (/5Phos/rNrNrNrN rArGrA rUrCrG rGrArA rGrArG rCrArC rArCrG rUrCrU rGrArA rArA/3IR800CWN/) was ligated to the 3′ end. Labeled RBP-RNA complexes were eluted using 1x LDS loading buffer (Thermo Fisher) and resolved on 4-12% Bis-Tris gels, transferred to nitrocellulose membrane, and imaged. RNA-protein complexes were visualized with LI-COR Odyssey imaging system, and a region including ~75 kDa above protein size (by comparing with high RNAse I sample) was cut from the membrane. RNA was isolated from the membrane via protease K/SDS treatment. After reverse transcription with a modified primer (5’-TTC AGA CGT GTG CTC TTC CG-3’), a 5′ adapter containing 8-nt UMI (/5phos/NNNNNNNN AGATCGGAAGAGCGTCGTGTAGGG/3ddC/) was ligated to cDNA. All of the remaining steps were essentially performed according to the eCLIP procedure (van Nostrand et al., 2016).

treatment_protocol: For iPSC-derived neurons, differentiated neurons seeded in 1x 6-well plate (~1x106 cells/well) were irradiated with ultraviolet (UV) light once at 400mJ/cm2 and once at 200 mJ/cm2 on iced water. For postmortem human brain BA4 region, the tissue (Brodmann Area 4) from each of three different donors was first pulverized in liquid nitrogen, and the powder in a chilled 10-cm tissue culture plate on dry ice was UV-crosslinked at 400 mJ/cm2 three times (Spengler et al., 2016).

value: Human frontal cortex (Brodmann area 4)

tag: antibody

value: PTBP2 (EMD Millipore ABE431)


title: RNA_WW_220707_22-24hmix


title: iPSC-neurons, PTBP2 eCLIP, rep2


title: RNA_WW_220719_22-24hmix


title: 10A_M_1025

value: male


title: 10A_M_1024


title: RNA_WW_220707_20-22hmix


title: RNA_WW_220629_22-24hmix_cer_BIOMcombi

value: Zymo Biomics magbead (DNA/RNA combi protocol)


title: iPSC-neurons, PTBP2 eCLIP, rep1


title: 10A_M_1022


title: iPSC-neurons, Size-matched input, rep2


title: iPSC-neurons, Size-matched input, rep3


title: 10A_M_1020


title: ATAC dTAG_3

city: Goettingen

first: Shyam

last: Ramasamy

address: Am Fassberg 11

department: Genome Organization and Regulation

institute: Max Planck Insitute for Multidisciplinary Sciences

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
ATAC-seq data analysis was performed as described in the Methods section of the paper.
Paired-end reads were processed for adapter removal and mapped to the hg38 reference genome using Bowtie2.
Assembly: hg38
Supplementary files format and content: Normalised bigwig files

source_name: Epithelial Tumor Colon

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cell pellets were resuspended in cold lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) and incubated on ice for 3 min.
The tagmentation reactions were performed at 37°C and 1000 rpm for 30 min. The indexed samples were amplified using Nextera indexing primers and NEBNext High-Fidelity PCR Master Mix (NEB, M0541).

treatment_protocol: Cells were treated as described in the Methods section of the paper

value: Epithelial Tumor Colon

value: human colon cancer cells

value: dTAG


title: ATAC dTAG_1


title: ATAC dTAG_2


title: 10A_M_102

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: iPSC-neurons, Size-matched input, rep1


title: ATAC DMSO_3

value: DMSO


title: RNA_WW_220629_22-24hmix

data_processing:
For metagenomics annotation, kaiju (Menzel et al., 2016) was used.
The xHYB data was quantified by aligning raw fastq reads to the reference sequences on which the xHYB panel was built.
Trinity (Haas et al., 2013) and SPAdes (Prjibelski et al., 2020) were used for transcript assembly. Transcript assemblies were then used for detection of novel virus contigs.
Supplementary files format and content: tab-separated values
Supplementary files format and content: fasta files

value: wastewater


title: RNA_WW_220629_20-22hmix


title: RNA_WW_220629_20-22hmix_cer_BIOMcombi

value: Ceres nanotrap


title: Human cortex, PTBP2 eCLIP, rep3


title: Das-1, RBRP

value: embryonic kidney

value: Human embryonic kidney

value: cells contain Adenovirus 5 DNA (PMID:11967234)


title: 10A_M_1019


title: ATAC DMSO_1


title: Human cortex, PTBP2 eCLIP, rep2


title: RNA_WW_220623_24hmix_2

value: Concentration


title: 10A_M_1018


title: 10A_M_1017


title: Human cortex, PTBP2 eCLIP, rep1


title: RNA_WW_220623_24hmix_1

value: Trizol/Zymo DirectZol


title: 10A_M_1016


title: ATAC DMSO_2


title: Human cortex, Size-matched input, rep3


title: RNA_WW_220616_20-22hmix


title: Human cortex, Size-matched input, rep2


title: Human cortex, Size-matched input, rep1


title: 10A_M_1015


title: 10A_M_1013


title: ChIP-seq dTAG_3

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
ChIP-seq data analysis was performed as described in the Methods section of the paper.
Paired-end reads were processed for adapter removal and mapped to the hg38 reference genome using Bowtie2. Spike-ins from Drosophila chromatin were used for normalization.
Assembly: hg38
Supplementary files format and content: Normalised bigwig files

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 minutes.
Antibody incubations, washes, DNA extraction, indexing of libraries were performed as described in the methods section

treatment_protocol:
Cells were treated as described in the Methods section of the paper
The samples were incubated with 1.32  µg of HA-Tag (Cell Signaling Technology, C29F4) and 1 µg of Drosophila spike in (Active Motif, 61686) antibodies.


title: ChIP-seq Input_dTAG_1


title: ChIP-seq Input_dTAG_2


title: ChIP-seq Input_dTAG_3


title: ChIP-seq Input_DMSO_2


title: 10A_M_1014


title: RNA_WW_220607_22-24hmix


title: ChIP-seq Input_DMSO_1


title: ChIP-seq Input_DMSO_3


title: ChIP-seq dTAG_2


title: RNA_WW_220607_22-24hmix_cer_BIOMcombi


title: 10A_M_1011


title: RNA_WW_220607_20-22hmix


title: RNA_WW_220602_20-22hmix_centri_BIOMcombi


title: 10A_M_1010


title: ChIP-seq dTAG_1


title: RNA_WW_220616_22-24hmix


title: RNA_WW_220602_20-22hmix_cer_BIOMcombi


title: 10A_M_101


title: RNA_WW_220607_20-22hmix_cer_BIOMcombi


title: RNA_WW_220602_22-24hmix_cer_BIOMcombi


title: 10A_M_1009


title: 10A_M_1012


title: SH-SY5Y, H3K27ac Rep2

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

data_processing:
150bp paired-end reads for the CUT&Tag-seq were trimmed for adapters using the Trimmomatic tool and aligned to the hg38 genome through local Bowtie2 (version 2.4.5) with these parameters for pair-end mapping: --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. For analyses, multi-mapped reads were filtered out and only uniquely mapped reads were retained with samtools flag of -q 2 -f 0x200. The bam files were sorted and indexed using the samtools (version 1.9) sort and the samtools index. Merging of multiple replicates was performed using samtools merge.
The sorted bam files were used to generate bed, bedgraph and bigwig formats for individual modifications. Sorted bam files were subjected to bigwig generation via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 –normalize Using BPM or CPM --scaleFactor=1.0 --smoothLength 60 --extendReads 150 --centerReads options. The signal was normalized to IgG through bigwigCompare with option –operation first or subtract. For TDF, sequencing runs involving knockout systems, the corresponding bigwig files were normalized by factoring in the reads mapped to E. coli in WT (icas9) and KO (MSL1/3 KO).
Peak-calling and analyses  The reads were extracted from the bam to bed by the bedtools bamtobed option. Further reads were processed as mentioned in the SEACR (version 1.3) manual to get the bedgraph. These bedgraph files were subjected to peak calling through SEACR with a stringent p-value of ≤1e-6 with the norm and relaxed options.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

growth_protocol: H9 hPSC line were grown on geltrex coated plates (ThermoFisher Scientific, A1413302) in mTeSR™ Plus medium (StemCell Technologies, #100-0276) supplemented with 100 U/ml penicillin-streptomycin (Gibco, 15140122) and passaged every 3-4 days with ReLeSR™ (StemCell Technologies, 100-0484) according to manufacturer’s protocols. TDF MSL-LOF and WT lines were grown in MEM (Gibco, 11095080) supplemented with 10% FBS (Sigma, F7524), 1X Glutamax (Gibco, 35050061), 1X non-essential amino acid solution (Sigma, M7145) and 100 U/ml penicillin-streptomycin. HEK293T and HeLa cells were grown in DMEM, high glucose (Lonza, BE12-614Q) supplemented with 10% FBS (Sigma, F7524), 1X Glutamax (Gibco, 35050061) and 100 U/ml penicillin-streptomycin. PC3 and LNCaP cells were grown in RPMI medium (Gibco, 21875034) supplemented with 10% FBS (Sigma, F7524) and 100 U/ml penicillin-streptomycin. RWPE1 cells were grown in keratinocyte serum-free medium (Gibco, 10724011) supplemented with 100 U/ml penicillin-streptomycin. K562 cells were grown in Iscove’s Modified Dulbecco’s Medium (Lonza, BE12-722F) supplemented with 10% FBS (Sigma, F7524) and 100 U/ml penicillin-streptomycin. SH-SY5Y cells were grown in DMEM / F12 (1:1) medium (Gibco, 11320033) supplemented with 10% FBS (Sigma, F7524) and 100 U/ml penicillin-streptomycin. All the cell lines were tested for Mycoplasma contamination using EZ-PCR Kit (Geneflow, K1-0210).

extract_protocol:
CUT&Tag was performed according to the protocol of Kaya-Okur et al (1) with modifications to tissue processing as described below. ~100,000 cells were pelleted by centrifugation for 3 min at 600 x g at room temperature and resuspended in 500μl of ice-cold NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, and 20 % glycerol and cOmplete EDTA free protease inhibitor tablet) and was let to sit for 10 min on ice. Nuclei were pelleted by centrifugation for 4 min at 1300 x g at 4°C, resuspended in 500μl of wash buffer and held on ice until beads were ready. Required amount of BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc) were transferred into binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2), washed once in the same buffer, each time placing them on a magnetic rack to allow the beads to separate from the buffer and resuspended in binding buffer. 10 μl of beads was then added to each tube containing cells and rotated on an end-to-end rotator for 10 minutes. After a quick spin to remove liquid from the cap, tubes were placed on a magnet stand to clear, the liquid was withdrawn and 800μl of antibody buffer containing 1μg of primary antibodies: normal rabbit IgG (Santa Cruz Cat no sc-2027), H3K27ac (Abcam, ab4729), H4K16ac (Abcam, ab109463), H3K122ac (Abcam, ab33309), H3K4me1(Abcam, ab8895), H3K36me3 (Abcam, ab9050)) H3K4me3 (Millipore, 07-473),  H3K27me3 (Abcam, ab192985) and H3K9me3 (Abcam, ab176916)) was added and incubated at 4ºC overnight in a nutator. Secondary antibodies (guinea pig α-rabbit antibody, Antibodies online, ABIN101961) were added 1:100 in Dig-wash buffer (5% digitonin in wash buffer) and 100 µL was squirted in per sample while gently vortexing to allow the solution to dislodge the beads from the sides and incubated for 60 min on a nutator. Unbound antibodies were washed in 1 ml of Dig-wash buffer three times. 100 μl of (1:250 diluted) protein-A-Tn5 loaded with adapters in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine with Roche cOmplete EDTA free protease inhibitor) was added to the samples, placed on nutator for 1 hour and washed three times in 1 ml of Dig-300 buffer to remove unbound pA-Tn5. 300 µL Tagmentation buffer (Dig-300 buffer + 5 mM MgCl2) was added while gentle vortexing and samples were incubated at 37ºC for 1 hr on an incubator. Tagmentation was stopped by adding 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. Samples were mixed by full speed vortexing for ~2 seconds and incubated for 1 hr at 55ºC to digest proteins. DNA was purified by phenol: chloroform extraction using phase-lock tubes (Quanta Bio) followed by ethanol precipitation.
Libraries were prepared using NEBNext HiFi 2x PCR Master mix (M0541S) with a 72ºC gap-filling step followed by 13 cycles of PCR with 10-second combined annealing and extension for the enrichment of short DNA fragments. Libraries were sequenced in Novaseq 6000 (Novogene) with 150bp paired-end reads.

treatment_protocol: All KO and WT TDF lines were treated with 1μg/ml doxycycline (Sigma) for 4 to 7 days

value: Neuroblastoma Bone-marrow Epithelial Cells

value: H3K27ac(Abcam, ab4729)


title: ChIP-seq DMSO_3


title: SH-SY5Y, H3K27ac Rep1


title: ChIP-seq DMSO_2


title: RNA_WW_220602_22-24hmix_cer_BIOM

value: Zymo Biomics magbead


title: 10A_M_1008

city: La Jolla


title: Micro-Capture-C Triptolide_18

description:
ANGPT2_Triptolide_HCT-116_merged.wig
DCBLD2_Triptolide_HCT-116_merged.wig
DDIT4_Triptolide_HCT-116_merged.wig
EREG_Triptolide_HCT-116_merged.wig
ERRFI1_Triptolide_HCT-116_merged.wig
HMGA2_Triptolide_HCT-116_merged.wig
HS3ST1_Triptolide_HCT-116_merged.wig
IRS1_Triptolide_HCT-116_merged.wig
ITPRID2_Triptolide_HCT-116_merged.wig
KITLG_Triptolide_HCT-116_merged.wig
KRR1_Triptolide_HCT-116_merged.wig
KRT19_Triptolide_HCT-116_merged.wig
KRT80_Triptolide_HCT-116_merged.wig
MTAP_Triptolide_HCT-116_merged.wig
MYC_Triptolide_HCT-116_merged.wig
PCDH7_Triptolide_HCT-116_merged.wig
PHLDA1_Triptolide_HCT-116_merged.wig
SPRY4_Triptolide_HCT-116_merged.wig
TRIB1_Triptolide_HCT-116_merged.wig
VTI1A_Triptolide_HCT-116_merged.wig

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
Assembly: hg38
Supplementary files format and content: Normalised wiggle files
Library strategy: Micro-Capture-C (MCC)

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 minutes and permeabilised with 0.05% digitonin. Chromatin was digested by MNase and religated. Decrosslinking and DNA extraction was performed. Samples were sonicated using a S220 focused-ultrasonicator (Covaris).
Micro-Capture-C libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were amplified using 6 cycles on the thermocycler. Capture enrichment was done with IDT biotinylated DNA oligonucleotides and washes were performed using Roche KAPA HyperCapture Reagent Kit Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity NGS Analysis Kit.

value: Triptolide


title: SH-SY5Y, H4K16ac Rep2


title: ChIP-seq DMSO_1


title: Micro-Capture-C Triptolide_17


title: SH-SY5Y, H4K16ac Rep1


title: RWPE, H3K27ac Rep1

source_name: RWPE

value: RWPE

value: Prostate Epithelial Cells


title: 10A_M_1006

value: male


title: RWPE, H4K16ac Rep1


title: 10A_M_1007


title: RNA_WW_220602_20-22hmix


title: RNA_WW_220527_22-24hmix_cer_trizol_PCRinh_rem

value: Trizol from Ceres beads, then Trizol/Zymo DirectZol

tag: additional processing

value: PCR inhibitor removal column


title: Micro-Capture-C Triptolide_16

value: Epithelial Tumor Colon

tag: cell type

value: human colon cancer cells


title: 10A_M_1005


title: RNA_WW_220602_22-24hmix

value: wastewater


title: RWPE, IgG Rep1

value: IgG(Santa Cruz Biotechnology, sc-2027)


title: Micro-Capture-C Triptolide_15

tag: treatment


title: RNA_WW_220527_20-22hmix_cer_trizol_PCRinh_rem

value: Ceres nanotrap


title: PC3, H3K27ac Rep2

value: Prostate Mesenchymal Adenocarcinoma


title: 10A_M_1003


title: 10A_M_1004


title: Micro-Capture-C Triptolide_14


title: PC3, H3K27ac Rep1


title: RNA_WW_220527_22-24hmix_PCRinh_rem

value: Concentration


title: Micro-Capture-C Triptolide_13


title: 10A_M_1002


title: PC3, H4K16ac Rep2


title: RNA_WW_220602_20-22hmix_cer_BIOM


title: 10A_M_1001


title: RNA_WW_220527_22-24hmix_cer_trizol

value: Trizol/Zymo DirectZol


title: Micro-Capture-C Triptolide_12


title: Micro-Capture-C Triptolide_11


title: PC3, IgG Rep1


title: 10A_M_1000


title: 10A_M_100


title: 10A_M_1


title: RNA_WW_220527_22-24hmix


title: RNA_WW_220527_20-22hmix


title: LNCaP, H3K27ac Rep1

source_name: LNCaP

value: LNCaP

value: Prostate Epithelial Carcinoma


title: LNCaP, H3K27ac Rep2

value: H3K27ac(Abcam, ab4729)


title: RNA_WW_220527_20-22hmix_cer_trizol


title: Micro-Capture-C Triptolide_10

value: Triptolide


title: Micro-Capture-C Triptolide_8


title: 4T1-HA tumors, Micelle IL-12, anti-PD-1_4

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.7.0f).
Mapped reads were counted by FeatureCounts (version 1.6.4 ).
Genome_build: mm10
Supplementary_files_format_and_content: raw count
Genome_build: mm10
Supplementary_files_format_and_content: csv file including raw counts

source_name: Tumor tissue

extract_protocol:
Total RNA was isolated from tumor tissues using TRIzol (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and RNeasy spin columns (Qiagen, Venlo, The Netherlands) according to the manufacturer's protocols.
Libraries were prepared using Illumina NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer's protocols.

value: BALB/c

value: inoculated with 4T1-HA cells

value: 4T1-HA tumors


title: RNA_WW_220527_20-22hmix_PCRinh_rem

extract_protocol:
Raw influx was filtered by 2 µm and 0.2 µm. Filtrate was either concentrated using Centricon units (60 ml), or used for Ceres nanotrap based extraction according to the manufacturer's protocol (10 ml) with addition of the ER2 reagent.
RNA was extracted using Trizol/Trizol LS (Thermo Fisher) and the Zymo DirectZol kit (cat# R2050), or with the Zymo Biomics RNA Magbead kit (cat# R2137) using either the RNA isolation protocol from this kit's manual or the RNA/DNA combination isolation protocol from the manual of the Zymo Biomics MagBead DNA/RNA kit (cat# R2135).
DNA was extracted using the Zymo RNA Magbead kit (cat# R2137) with the RNA/DNA combination protocol from the manual of the MagBead DNA/RNA kit (cat# R2135), or with the Zymo Biomics DNA Miniprep Kit (cat# D4300)
RNA sequencing libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara). DNA sequencing libraries were prepared by first applying the ResolveDNA Whole Genome Amplification kit (BioSkryb) and subsequently the Nextera XT DNA Library Preparation Kit (Illumina).
A subset of RNA sequencing libraries was subjected to enrichment using the xHYB adventitious agent panel (Qiagen) where indicated in the sample description.


title: RNA_WW_220527_22-24hmix_centri_BIOM

value: Zymo Biomics magbead


title: Micro-Capture-C Triptolide_9


title: LNCaP, H4K16ac Rep1


title: 4T1-HA tumors, Micelle IL-12, anti-PD-1_3


title: Micro-Capture-C Triptolide_7


title: 4T1-HA tumors, Micelle IL-12, anti-PD-1_2


title: RNA_WW_220527_20-22hmix_centri_BIOM


title: 4T1-HA tumors, Micelle IL-12, anti-PD-1_1


title: Micro-Capture-C Triptolide_6


title: K562, H3K27ac Rep2

value: Lymphoblasts


title: PC3, H4K16ac Rep1


title: RNA_WW_220511_22-24hmix_cer_BIOM


title: 4T1-HA tumors, Micelle IL-12_4


title: RNA_WW_220511_20-22hmix_cer_BIOM


title: K562, H3K27ac Rep1


title: K562, H4K16ac Rep2


title: Micro-Capture-C Triptolide_4

value: Epithelial Tumor Colon


title: Micro-Capture-C Triptolide_3

value: human colon cancer cells


title: K562, H4K16ac Rep1


title: RNA_WW_220511_22-24hmix_PCRinh_rem

value: wastewater

value: PCR inhibitor removal column


title: RNA_WW_220511_20-22hmix_PCRinh_rem


title: 4T1-HA tumors, Micelle IL-12_2


title: Micro-Capture-C Triptolide_5


title: Micro-Capture-C Triptolide_2


title: LNCaP, IgG Rep1

value: IgG(Santa Cruz Biotechnology, sc-2027)


title: K562, IgG Rep1


title: Micro-Capture-C Triptolide_1


title: 4T1-HA tumors, Free IL-12, anti-PD-1_4

value: Free IL-12_anti-PD-1


title: Tiled-Micro-Capture-C dTAG_12

description:
dTAG_HMGA2_merged_chimeric.txt
dTAG_ITPRID2_merged_chimeric.txt
dTAG_MTAP_merged_chimeric.txt
dTAG_MYC_merged_chimeric.txt

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
ICE normalization (Imakaev et al. Nature Methods 2012)
Assembly: hg38
Supplementary files format and content: Chimeric junctions files: tab-delimited text files listing the locations of the identified valid junctions
Library strategy: Tiled-Micro-Capture-C

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 minutes and permeabilised with 0.05% digitonin. Chromatin was digested by MNase and religated. Decrosslinking and DNA extraction was performed. Samples were sonicated using a S220 focused-ultrasonicator (Covaris).
Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

value: dTAG


title: HeLa, H3K27ac Rep1

source_name: HeLa

value: HeLa

value: Adenocarcinoma Epithelial cells