title: CEMBA3C_MacaqueM1_R1_P2-1-J11-M13


title: MOLM13-TP53+/+ resting replicate 3

status: Public on Oct 31 2023

type: SRA

city: Zurich

first: Roman

middle: Raffael

last: Schimmer

state: Zurich

address: Raemistrasse 100

department: Department of Medical Oncology and Hematology

country: Switzerland

institute: University Hospital Zurich and University of Zurich

library_source: transcriptomic

data_processing:
Quality control, mapping and differential gene expression analysis was performed using the SUSHI bioinformatics pipeline
Gene set enrichment analysis (GSEA) was performed using the GSEA software jointly developed by UC San Diego and the Broad Institute
Assembly: hg18
Supplementary files format and content: excel file including all genes analysed (gene name, transcript ID, etc) and normalized counts for each above listed sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Isogenic MOLM13 cells harboring wildtype TP53 (MOLM13-TP53+/+) or knockout TP53 (MOLM13-TP53-/-) were cultured in RPMI medium supplemented with GlutaMAX™ (Gibco™, #61870010), 100 U ml-1 of penicillin and 100 mg ml-1 of streptomycin (Penicillin-Streptomycin 5’000 U/mL, Cat. No. 15070063), and 10% FCS (Gibco™, #16000044))

extract_protocol:
RNA was harvested with PicoPure™ RNA isolation kit (Thermo Fisher, #KIT0204) according to the manufacturer's instructions.
RNA libraries were constructed using the Illumina Truseq RNA Library Prep Kit V2

treatment_protocol: MOLM13-TP53 cells were incubated with anti-CD33 CAR T-cells for 6 days at an effector-to-target ratio resulting in incomplete target killing

tag: tissue

tag: cell line

tag: cell type

value: human AML cell line

tag: genotype

value: TP53 WT

tag: treatment


title: MOLM13-TP53+/+ resting replicate 2


title: MOLM13-TP53-/- resting replicate 1

value: TP53 KO


title: MOLM13-TP53-/- co-incubated with anti-CD33 CAR T-cell, replicate 3

value: CAR T-cell therapy


title: MOLM13-TP53+/+ co-incubated with anti-CD33 CAR T-cell, replicate 3


title: MOLM13-TP53-/- resting replicate 2


title: MOLM13-TP53+/+ co-incubated with anti-CD33 CAR T-cell, replicate 1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-J2

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 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: Mmul_10 (rheMac10), annotation: Ensembl release 104
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-seq3

molecule: genomic DNA

organism: Macaca mulatta

extract_protocol:
Motor cortex of brains were dissected.
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.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously22. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

tag: brain region

value: Motor cortex

tag: gender

value: M


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-J14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-I2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-K2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-L13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-M1


title: MOLM13-TP53-/- co-incubated with anti-CD33 CAR T-cell, replicate 2


title: MOLM13-TP53-/- resting replicate 3


title: MOLM13-TP53+/+ co-incubated with anti-CD33 CAR T-cell, replicate 2


title: MOLM13-TP53+/+ resting replicate 1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-L2


title: MOLM13-TP53-/- co-incubated with anti-CD33 CAR T-cell, replicate 1


title: anti-CD33 CAR T-cell, resting, replicate 2

source_name: Blood

value: Blood

value: T-cell


title: anti-CD33 CAR T-cell, resting, replicate 1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-J13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-K1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-K13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-J1


title: Blood, control, VS93

city: Paris

first: Camille

last: Verebi

address: 102 rue de la Santé

country: France

institute: IPNP Inserm U1266

data_processing:
For mRNA sequencing, fastq files were then aligned using the STAR algorithm (version 2.7.6a), against the Ensembl Human genome reference. Reads were then counted using RSEM (v1.3.1), and statistical analyses of read counts were performed using R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0) to determine the proportion of differentially expressed genes between two conditions. We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function), with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustment, and genes with at least 10 reads in at least 3 different samples). Following the package recommendations, we used the Wald test with the contrast function and the Benjamini and Hochberg FDR control procedure to identify the differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: tab delimited text files include FPKM values for each sample
Supplementary files format and content: tab delimited text file includes DESeq normalized abundance measurements for each sample

source_name: Whole Blood

extract_protocol:
Peripheral blood samples were collected from patients in PaxGene tubes after a 12-hour overnight fast. RNA was extracted from blood samples following manufacturer’s procedure using the Paxgene blood miRNA kit (PreAnalytix GmbH, Hombrechtikon, Swtizerland).
Briefly, after globin mRNA depletion libraries were prepared from 3 μg RNA.

value: Whole Blood

tag: condition

value: control


title: Blood, control, VS76


title: Blood, control, VS85


title: Blood, control, VS75


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-I14


title: Blood, control, VS65


title: Blood, control, VS60


title: Blood, control, VS92


title: Blood, control, VS72


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-G2


title: Blood, control, VS69


title: Blood, control, VS54


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-I1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-H2


title: Blood, control, VS78


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-G14


title: Blood, control, VS52


title: Blood, control, VS62


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-I13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-H14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-G13


title: Blood, control, VS67


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-H13


title: Blood, control, VS56


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-H1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-G1


title: Blood, AN77

value: AN


title: Blood, AN46


title: Blood, AN43


title: Blood, AN36


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-E2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-F1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-F13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-F2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-F14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-E14


title: Blood, AN23


title: Blood, AN12


title: Blood, AN16


title: Blood, AN21


title: Blood, AN31


title: Blood, AN02


title: Blood, AN25


title: Blood, AN28


title: Blood, AN09


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-D14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-D2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-C2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-E1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-C1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-C14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-B1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-D1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-A14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-D13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-A2


title: Blood, AN27


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-E13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-B13


title: Blood, AN07


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-C13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-B2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-B14


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-O23


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-A13


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-P11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-P12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-N23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-N24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-O12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-P23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-P24


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-A1


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-O24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-N12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-O11


title: PBS.1

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
All reads were independently aligned with STAR_2.4.0f1 (Dobin et al, 2013) for sequence alignment against the human genome sequence build hg19, downloaded via the UCSC genome browser and SAMTOOLS v0.1.19 (Li et al, 2009) for sorting and indexing reads
Cufflinks (2.0.2) (Trapnell et al, 2012) was used to estimate the expression values (FPKMS), and GENCODE v19 (Derrien et al, 2012) GTF file for annotation.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

molecule: polyA RNA

source_name: breast cancer

extract_protocol:
total RNA was extracted from samples by Trizol lysis and RNeasy Mini Kit (Qiagen, #74106) following the manufacturer’s protocols
cDNA libraries were generated using NEB Ultra II Directional RNA Library Prep (plus Poly A isolation module) kit

value: breast cancer

value: PBS


title: PBS.2


title: PBS.3


title: 124.3

value: O-EV


title: 124.1


title: 124.2


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-M24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-N11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-L24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-M23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-M11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-L11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-L12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-L23


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_312]

city: Bethesda

first: Avindra

last: Nath

state: Maryland

address: 10 Center Drive

institute: NIH/NINDS

data_processing:
Illuminasoftware bcl2fastq v.2.17
RNA sequences were subjected to quality control  through FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Adapters were removed using Trimmomatic: https://github.com/timflutre/trimmomatic
Alignment to the human genome (GRCh38) using STAR
Gene expression levels were quantified using FeaturesCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene expression levels for each sample

extract_protocol:
RNA was extracted from muscle samples using the TRIzol protocol
Five hundred nanograms of RNA were used to prepare the RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep Kit

value: Muscle

tag: Sex

value: Female

tag: subject status

value: post-infectious Myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) volunteer


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_124]

source_name: Vastus Lateralis Muscle, HV, Baseline

value: Male

value: healthy volunteer (HV)


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_313]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_311]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_323]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_305]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_324]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_319]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_322]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_320]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_325]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_316]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_123]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_121]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_122]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_302]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_120]


title: Vastus Lateralis Muscle, PI-ME/CFS, Baseline [MECFS_310]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_117]


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-M12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-K23


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_115]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_119]


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-K24


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_113]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_112]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_101]


title: Vastus Lateralis Muscle, HV, Baseline [MECFS_110]


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-I23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-J24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-J23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-J12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-J11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-I24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-K11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-K12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-H12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-H23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-I12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-H11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-G24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-I11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-H24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-G23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-G12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-F12


title: HBRT-1025:A-A07:TNBC_test_high_AR_low

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
FASTQ files were then processed by the NanoString DND pipeline to generate count data for each target probe in every Amplified Oligonucleotide Item (AOI). First, each AOI was QC checked to ensure contamination was avoided during PCR and library preparation and that sequencing was sufficient. No AOIs were eliminated during QC. Next, we checked for global outliers in the target list. No outliers were identified. In total, none of the 24 AOIs nor any of the 18,676 gene-associated probes were removed during QC. Finally, the dataset was normalized using third quantile (Q3) normalization.
Assembly: hg38
Supplementary files format and content: Raw Counts

source_name: breast

extract_protocol: RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.

value: breast

tag: tissue type

value: Triple Negative Breast Cancer Subtype

value: stained high for AR


title: HBRT-1186:A-B11:TNBC_test_high_AR_high


title: CHTN-018:A-B05:TNBC_test_low_AR_low

value: stained low for AR


title: HBRT-1025:A-A06:TNBC_test_high_AR_high


title: CHTN-018:A-B04:TNBC_test_low_AR_high


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-G11

value: Motor cortex

value: M


title: HBRT-1186:A-B10:TNBC_test_high_AR_low


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-F23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-F11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-E23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-E24


title: Human whole white blood cells, Untreated rep1

city: Khantharawichai

first: Nuchsupha

last: Sunthamala

state: Mahasarakham

address: Department of Biology, Faculty of Science, Mahasarakham University

department: Biology

country: Thailand

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimited text file includes raw count for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM value for each sample

source_name: Whole white blood cells

growth_protocol: White blood cells (WBCs) were separated from the blood samples using red blood cell (RBC) lysis buffer and centrifugation. The isolated WBCs were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco, Thermo Fisher, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Thermo Fisher, USA) and antibiotic-antimycotic (Gibco, Thermo Fisher, USA). The WBCs were incubated at 37°C with 5% CO2.

extract_protocol:
The cells were then collected for total RNA extraction by using Rneasy mini plus (QIAGEN) and RNA quality was checked by gel electrophoresis.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Whole WBCs were cultured in serum-free RPMI-1640 medium and treated with Dapphitkhai and Chanthaleela at concentration of 500 µg/mL. A negative control group consisted of unstimulated WBCs. The WBCs were incubated at 37°C with 5% CO2 for 24 h.

value: Whole white blood cells

value: Human white blood cells

value: Wild type

value: Untreated


title: Human whole white blood cells, Chanthaleela treated rep1

institute: Faculty of Science, Mahasarakham University

value: Chanthaleela treated for 24 hr


title: Human whole white blood cells, Dapphitkhai treated rep2

value: Dapphitkhai treated for 24 hr


title: Human whole white blood cells, Chanthaleela treated rep3


title: Human whole white blood cells, Dapphitkhai treated rep3


title: Human whole white blood cells, Dapphitkhai treated rep1


title: Human whole white blood cells, Untreated rep3


title: Human whole white blood cells, Untreated rep2


title: Human whole white blood cells, Chanthaleela treated rep2


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-F24


title: K562:Kasumi-1 100:1

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Demultiplexing of raw reads using cellranger mkfastq
Alignment against GRCh38 and generation of count matrices using cellranger count
Assembly: GRCh38
Supplementary files format and content: count matrix, barcode list and feature list in csv file format

source_name: cell line

extract_protocol:
Ficoll-based extraction of bone marrow mononuclear cells and cryopreservation in FCS with 10% DMSO until analysis. Thawing in PBS supplemented with 10% FCS and 10% bovine DNase I, grade II. Bead-based dead cell removal with negative-selection strategy (Miltenyi). Resuspension in PBS with 0.04% ultra-pure BSA.
Standard 5' 10x Genomics single cell RNA sequencing protocol according to manufacturer's instructions.

value: cell line

tag: status

value: cell line mix


title: AML1022.1 GoT

source_name: bone marrow

value: bone marrow

value: AML relapse post-HSCT


title: AML1022.1 nanoranger


title: K562:Kasumi-1 1:1.5


title: de-novo AML2

value: initial diagnosis


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-E12


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-D11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-E11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-C24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-D12


title: de-novo AML1


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-C23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-B24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-C11


title: K562:Kasumi-1 1:100


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-B23


title: K562:Kasumi-1 1:15


title: Ctrl.IP

city: jinan

first: qingxia

last: hu

address: qingdao street 6699

country: China

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
Illumina NovaSeq6000 software used for basecalling.
Cutadapt software (v1.9.3) removes adapter sequences from high-throughput sequencing reads
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Hisat2 software（v2.0.4）
MACS 3 software was used to analyze m6A sites
diffReps software was used to analyze differentially-methylated-sites
Assembly: Homo-sapies-HG19
Supplementary files format and content: tab-delimited text file includes raw counts for each samle
Supplementary files format and content: tab-delimited text files include RPKM values for each samle

source_name: prostate

extract_protocol:
The MeRIP assay was performed according to the protocol of RNA Immunoprecipitation Kit (GS-ET-006, Cloudseq, Shanghai, China). Cells cultured in 15cm dishes were collected with PBS, then scraped with RIP lysis buffer which containing protease inhibitor and RNase inhibitors
Both the input without immunoprecipitation and the IP samples were used for MeRIP-seq library generation using NEBNext® Ultra II Directional RNA Library Prep kit (New England Biolabs)

value: prostate


title: sh.IP


title: sh.Input


title: Ctrl.Input


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-C12


title: 4C_LNPK_WT_sample2_rep2

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
library strategy: QHR4C-seq
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample

source_name: cultured cell

extract_protocol:
1 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: cultured cell

value: HEK 293T cell line

value: human embryonic kidney 328T cell

value: wildtype


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-D24

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-D23


title: ALL2


title: ALL4

value: dasatinib 140 mg daily; ABL001 40 mg daily; and prednisone 120 mg daily


title: de-novo AML3


title: ALL3

value: dasatinib 140 mg daily and prednisone 120 mg daily


title: ALL1


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-A24


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-B11


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-A23


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-B12


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-P21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-O9


title: 4C_LNPK_WT_sample1_rep2

value: human embryonic kidney 326T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-P22


title: 4C_LNPK_single_CBS3_KO_sample2_rep1

value: human embryonic kidney 319T cell

value: CBS3 del -/-


title: 4C_LNPK_single_CBS3_KO_sample1_rep2

value: human embryonic kidney 318T cell


title: 4C_LNPK_single_CBS5_KO_sample1_rep2

value: human embryonic kidney 322T cell

value: CBS5 del -/-


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-O22


title: 4C_LNPK_single_CBS5_KO_sample2_rep2

value: human embryonic kidney 324T cell


title: 4C_LNPK_WT_sample1_rep1

value: human embryonic kidney 325T cell


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-A12


title: 4C_LNPK_double_CBS3_and_5_KO_sample3_rep2

value: human embryonic kidney 316T cell

value: CBS3 and 5 del -/-


title: 4C_LNPK_single_CBS3_KO_sample1_rep1

value: cultured cell

value: HEK 293T cell line

value: human embryonic kidney 317T cell


title: 4C_LNPK_single_CBS3_KO_sample2_rep2

value: human embryonic kidney 320T cell


title: 4C_LNPK_single_CBS5_KO_sample1_rep1

value: human embryonic kidney 321T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-O21

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-6-B11-A11


title: 4C_LNPK_WT_sample2_rep1

value: human embryonic kidney 327T cell

value: wildtype


title: 4C_LNPK_single_CBS5_KO_sample2_rep1

value: human embryonic kidney 323T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-P9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-P10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-M9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-N10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-N9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-O10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-N21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-M22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-N22


title: 4C_LNPK_double_CBS3_and_5_KO_sample2_rep1

value: human embryonic kidney 313T cell


title: 4C_LNPK_double_CBS3_and_5_KO_sample3_rep1

value: human embryonic kidney 315T cell


title: 4C_GT2_single_CBS3_KO_sample1_rep2

value: human embryonic kidney 300T cell

value: CBS3 del -/-


title: 4C_GT2_single_CBS3_KO_sample1_rep1

value: human embryonic kidney 299T cell


title: 4C_GT2_double_CBS3_and_5_KO_sample3_rep1

value: human embryonic kidney 297T cell


title: 4C_GT2_single_CBS3_KO_sample2_rep1

value: human embryonic kidney 301T cell


title: 4C_GT2_double_CBS3_and_5_KO_sample2_rep2

value: cultured cell

value: human embryonic kidney 296T cell

value: CBS3 and 5 del -/-


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-M10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-K21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-L10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-K22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-K10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-K9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-J9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-L9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-L22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-J22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-L21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-M21


title: 4C_LNPK_double_CBS3_and_5_KO_sample2_rep2

value: HEK 293T cell line

value: human embryonic kidney 314T cell


title: 4C_GT2_single_CBS5_KO_sample2_rep2

value: human embryonic kidney 306T cell

value: CBS5 del -/-


title: 4C_LNPK_double_CBS3_and_5_KO_sample1_rep1

value: human embryonic kidney 311T cell


title: 4C_GT2_WT_sample2_rep1

value: human embryonic kidney 309T cell

value: wildtype


title: 4C_GT2_WT_sample1_rep2

value: human embryonic kidney 308T cell


title: 4C_GT2_single_CBS5_KO_sample1_rep1

value: human embryonic kidney 303T cell


title: 4C_GT2_WT_sample1_rep1

value: human embryonic kidney 307T cell


title: 4C_GT2_WT_sample2_rep2

value: human embryonic kidney 310T cell


title: 4C_GT2_single_CBS5_KO_sample1_rep2

value: human embryonic kidney 304T cell


title: 4C_LNPK_double_CBS3_and_5_KO_sample1_rep2

value: human embryonic kidney 312T cell


title: 4C_GT2_single_CBS3_KO_sample2_rep2

value: human embryonic kidney 302T cell

value: CBS3 del -/-


title: 4C_GT2_single_CBS5_KO_sample2_rep1

value: cultured cell

value: human embryonic kidney 305T cell


title: 4C_GT2_double_CBS3_and_5_KO_sample3_rep2

value: HEK 293T cell line

value: human embryonic kidney 298T cell

value: CBS3 and 5 del -/-


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-J21

value: Motor cortex

value: M


title: 4C_GT2_double_CBS3_and_5_KO_sample2_rep1

value: human embryonic kidney 295T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-J10


title: 4C_GT2_double_CBS3_and_5_KO_sample1_rep2

value: human embryonic kidney 294T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-I9


title: 4C_CBS4_WT_for_single_KO_rep2

data_processing:
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample
Library strategy: QHR4C-seq

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: wildtype


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-I22


title: 4C_GT2_double_CBS3_and_5_KO_sample1_rep1

value: human embryonic kidney 293T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-I21


title: 4C_CBS4_single_CBS5_KO_sample2_rep2

value: CBS5 del -/-


title: 4C_CBS4_WT_for_single_KO_rep1

value: human embryonic kidney 303T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-I10


title: 4C_CBS4_single_CBS5_KO_sample1_rep2

value: human embryonic kidney 300T cell


title: 4C_CBS4_single_CBS5_KO_sample1_rep1

value: human embryonic kidney 299T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-H9


title: 4C_CBS4_single_CBS5_KO_sample2_rep1

value: human embryonic kidney 301T cell


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-H10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-G9


title: 4C_CBS2_WT_for_single_KO_rep2


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-G22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-H22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-H21


title: 4C_CBS2_WT_for_single_KO_rep1

value: human embryonic kidney 297T cell


title: 4C_CBS2_single_CBS3_KO_sample2_rep2

value: cultured cell

value: human embryonic kidney 296T cell

value: CBS3 del -/-


title: 4C_CBS2_single_CBS3_KO_sample1_rep2

value: HEK 293T cell line


title: 4C_CBS2_single_CBS3_KO_sample2_rep1


title: 4C_CBS2_single_CBS3_KO_sample1_rep1


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-P8


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-A9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-E9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-A10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-F10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-B21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-C10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-C22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-B22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-F9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-D22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-E10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-G21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-F22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-D9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-G10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-B10


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-A21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-E22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-A22


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-C9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-B9


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-F21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-E21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-D21


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-C21


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-P7


title: CEMBA3C_MacaqueM1_R1_P1-5-B11-D10


title: RNA_CBS5_KO_sample2_rep1

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.

value: Human embryonic kidney 293T


title: RNA_CBS5_KO_sample2_rep2


title: RNA_CBS5_KO_sample1_rep2


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-P20

value: Motor cortex


title: RNA_CBS3_KO_sample1_rep2


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-O7

value: M


title: RNA_293T_WT_for_CBS3del_rep1


title: RNA_293T_WT_for_CBS5del_rep1


title: RNA_CBS3_KO_sample2_rep2


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-P19


title: RNA_CBS3_KO_sample1_rep1


title: RNA_CBS5_KO_sample1_rep1


title: RNA_wt_for_g_del_rep2

source_name: cortex

value: cortex

value: cortex-neuron

value: neuron


title: RNA_293T_WT_for_CBS3del_rep2

value: human embryonic kidney 293T cell

value: wildtype


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-O8


title: RNA_CBS3_KO_sample2_rep1


title: RNA_293T_WT_for_CBS5del_rep2


title: tumoroïd patient 414

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

institute: Transgene SA

data_processing:
The 3 first bases from read 2 were trimmed using Trimmomatic (3 extra G added by the library preparation protocol)
PCR duplicates were removed using Unique molecular identifiers (UMIs) using the program dedup from the package UMI-tools
Reads were aligned using STAR to an artificial genome containing the whole mouse genome (GRCm38) and mBT-001 viral genome.
Readcount for each murin and viral gene was quantified using HTSeq-count
Assembly: GRCh38

source_name: tumoroïd

growth_protocol: NSCLC biopsies were dissociated (with intermittent agitation and enzymatic media) to generate a heterogeneous suspension of tumor cells. Then, heterologous microvessels (a vascular unit derived from the adipose tissue) were added to this suspension of tumor cells to generate our scaffold-free tumoroid model (at a ratio of 1:1). The formation of tumoroids is done in ultra-low-attachment plates and within 7 days.

extract_protocol:
Total RNA was extracted from whole tumours using the kit Qiagen kitRNeasy Plus Mini.
Strand specific 3' mRNA sequencing libraries were prepared by Integragen, SA.

value: tumoroïd

tag: patient id


title: heathy tissue biopsy patient 414 rep1

description: HlePatHea

source_name: heathy tissue biopsy

value: heathy tissue biopsy


title: organoïd patient 414

source_name: organoid

value: organoid


title: heathy tissue biopsy patient 414 rep2


title: tumor biopsy patient 414 rep2

source_name: tumor biopsy

value: tumor biopsy


title: tumor biopsy patient 414 rep1

description: HlePatTum


title: tumor biopsy patient 554


title: organoïd patient 554


title: heathy tissue biopsy patient 554


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-O20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-N19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-N20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-N8


title: tumoroïd patient 554


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-O19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-N7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-M8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-L20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-M7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-K8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-M19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-K20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-K7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-L7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-L8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-M20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-K19


title: heathy tissue biopsy patient 469


title: tumor biopsy patient 469


title: organoïd patient 469


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-L19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-J20


title: tumoroïd patient 469


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-J8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-J19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-I8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-J7


title: MOLM13dBRD9_3

city: Kobe

first: Weijia

last: Zang

address: Hyogo, Kobe, Chuo Ward, Minatojima Minamimachi, 6 Chome−３−7

department: Department of Hematology-Oncology

country: Japan

institute: Foundation for Biomedical Research and Innovation at Kobe

data_processing:
RNA-seq rawdata was cleaned by FastP(PE mode) and aligned to mm10 by Hisat2(2.2.1)
Alignment results were filtered by Samtools and converted to BAM files
Read counted by FeatureCount from Subreads Packages(R)
Assembly: mm10
Supplementary files format and content: raw data, gene count

source_name: MOLM13 parental cells

growth_protocol: The MOLM13 cell lines were cultured in RPMI with 10% FCS and 1% P/S

extract_protocol:
RNA was extracted using RNeasy columns (Qiagen) per manufacturer’s instructions.
RNA was poly(A)-selected, and unstranded Illumina libraries were prepared with the standard TruSeq protocol

treatment_protocol: MOLM13 parental cells received DMSO and 100nM dBRD9 treatment  for 4 days.

value: hematopoietic cells (MOLM13 cells)

value: MOLM13 parental cells

value: 50nM dBRD9


title: MOLM13dBRD9_1


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-I7


title: MOLM13dBRD9_2


title: Input_K562dBRD9

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

description: genomic DNA immunoprecipitated without antibody

data_processing:
The adapter sequences were removed from the FASTQs using Trimmomatic (0.39).
The cleaned FASTQs were aligned using Bowtie2 (2.4.4) to the human reference genome GRCh38.
The duplicated reads were removed using picard (2.26.2) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: hematopoietic cells (K562 cells)

growth_protocol: The K562 cell lines were cultured in RPMI with 10% FCS and 1% P/S

extract_protocol:
Cells were fixed with 2mM DSG (Thermo Fisher Scientific, 20593) for 30 min at room temperature and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1 mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 10 min at 37°C.Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4°C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated.Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 ml of 10% Triton X-100 and 30 ml of 5M NaCl were added. The sample was then incubated with 20 ml of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4°C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4°C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4°C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65°C. RNA and protein were digested with 0.2 mg/ml RNase A for 30 min at 37C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: K562 parental cells received DMSO and 100nM dBRD9 treatment  for 4 days.

value: hematopoietic, parental cells

value: 100nM dBRD9

tag: chip antibody


title: CTCF_K562dBRD92

description: genomic DNA immunoprecipitated with previous antibody

value: anti-CTCF (Millipore, 07-729)


title: MOLM13DMSO_2

value: DMSO


title: MOLM13DMSO_3


title: MOLM13DMSO_1


title: hPSC-derived Monocyte/Macrophages, Day 14, scRNA-seq

city: Cincinnati

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Standard 10x Genomics Cell Ranger (v3.0.2) pipeline to generate FASTQ and generate filtered matrices.
Assembly: hg19 for Day 28 and Day 37 HCO as well as HCO TXP
Assembly: hg38 for Day 22 HCO and Day 14 Monocyte/Macrophage
Supplementary files format and content: tab seperated value files and matrix files

source_name: hPSC-derived monocyte/macrophages

extract_protocol:
For Day 22 and Day 37 HCOs and Day 14 Macrophages: Organoid were washed with cold Cell Recovery solution and minced in HBSS with Mg2+ and Ca2+ 1% BSA. Original supernatants collected and spun down and readded into the sample. HCOs were mechanically and enzymatically digested enzymes from Neural Tissue Dissociation Kit as recommended by Manufacturer's instructions for 45-60 minutes at 37C. Samples were shaken and fluxed through a P1000 then P200 tip every 10 mins. Dissociated cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in 2% FBS in HBSS with y-27632 and 1% BSA. Day 14 Macrophages were subjected to the same mechanical and enzymatic manipulations as the dissociated HCOs.
For Day 28 HCOs Hematopoietic Floaters: Supernatants of Day 28 HCOs was collected, spun down, and resuspended in HBSS with BSA and did not undergo enzymatic digestion.
For HCO TXP: Organoid was removed from mouse kidney capsule after 15 weeks in vivo growth. The organoid was separated from surrounding kidney capsule and outer most muscle layer, opened, and flushed the lumen of mucus. HCOs were shaken in 5mL TryPLe + 5uL y-27632 for 60 minutes at 4C. Cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in 2% FBS in PBS without Mg++ or Ca++ with y-27632. Cells were stained with Sytox Blue viability dye and sorted on a FACS Aria cell sorter and 100,000 live cells were collected in 5mL PBS with 5% FBS, 0.5% BSA, 5uL y-27632.
Library was performed according to the manufacter’s instructions (single cell Chromium 3’ v3 GEM protocol, 10x Genomics) loading 12,800 cell for approximately 8,000 captured cells. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip 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. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hPSC-derived monocyte/macrophages

value: WA01 hESC

value: hematopoietic

tag: age

value: 14 days post-hPSC


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-H20

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-H19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-I19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-I20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-H7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-G7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-G8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-H8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-E8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-F20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-F8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-F19


title: hPSC-derived HCO, Day 22, biol rep 1, scRNA-seq

description: 10x Genomics

source_name: hPSC-derived colonic organoids

value: hPSC-derived colonic organoids

value: hiPSC 115.3

value: epithelial, mesenchymal, hematopoietic

value: 22 days post-hPSC


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-G19


title: hPSC-derived HCO, Day 22, biol rep 2, scRNA-seq

description: 10x Genomics


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-G20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-E7


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-E20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-E19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-F7


title: dBRD9_3 [human_Brd9_bulkRNA-seq]

data_processing:
Raw FASTQs were processed using nf-core/rnaseq (3.10.1).
Assembly: GRCh38
Supplementary files format and content: txt


title: CTL_1 [human_Brd9_bulkRNA-seq]


title: CTL_3 [human_Brd9_bulkRNA-seq]


title: CTCF_K562DMSO2


title: dBRD9_2 [human_Brd9_ATAC-seq]

extract_protocol: Cells harvest was followed by a transposition reaction and purification followed the manual of ATAC-seq kit from Active motif (#13150)


title: CTL_2 [human_Brd9_bulkRNA-seq]


title: dBRD9_2 [human_Brd9_bulkRNA-seq]


title: Input_K562DMSO


title: dBRD9_3 [human_Brd9_ATAC-seq]


title: dBRD9_1 [human_Brd9_bulkRNA-seq]


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-D8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-D19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-D20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-D7


title: CTL_2 [human_Brd9_ATAC-seq]


title: CTL_3 [human_Brd9_ATAC-seq]


title: CTL_1 [human_Brd9_ATAC-seq]


title: LNCaP_25HD

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

description: condensation disruption control sample

data_processing:
Basecalls performed using Illuminal CASAVA software.
GRO-seq reads were aligned to human genome (hg19) using bowtie with “--best --strata –m 1 –v 2” parameters. Duplicated reads were eliminated for subsequent analysis.
To balance the clonal amplification bias and total useful reads, only at most three reads was allowed for each unique genomic position.
edgeR 3.16.5 was used to call the differential eRNAs.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: prostate cancer cells

growth_protocol: LNCaP obtained from ATCC were cultured in RPMI1640 media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Cells were subjected to nuclear run-on for 5 minutes at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE I, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: To test the role of AR condensation on enhancer assembly and gene expression, we used 1,6 hexanediol (1,6 HD) to chemically disrupt phase separation in cells (2,5HD was used as control for 1,6HD). Before experiment, the LNCaP cells were hormone-stripped in phenol red-free RPMI1640 medium plus 5% charcoal-treated FBS for 3 days, followed by four different treatments for 2 hours: 1. ethanol as vehicle control; 2. 100 nM DHT as hormone stimulation sample; 3. 100 nM DHT plus 2.5% 1,6 HD as condensation disruption condition; 4. 100 nM DHT plus 2.5% 2,5 HD as condensation disruption control condition.

value: LNCaP

value: DHT+2,5HD:stripping 3 days, DHT 100nM + 2.5% 2,5 HD  2hr

tag: fraction

value: Nascent RNA


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-C8

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 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: Mmul_10 (rheMac10), annotation: Ensembl release 104
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-seq3

extract_protocol:
Motor cortex of brains were dissected.
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: CEMBA3C_MacaqueM1_R1_P1-4-B11-C19


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-C20


title: TAF15IDR_shCtrl_noDOX_DHT

data_processing:
Basecalls performed using Illuminal CASAVA software.
The adaptor was removed by using cutadapt v1.11 with parameters "-m 20 -e 0.1". The clean reads were aligned to the hg19 genome assembly using bowtie2 v2.2.9 with parameters "-mm --very-sensitive --no-discordant -X 2000", and only primary alignments were retained. The alignments were shifted with +4 for plus strand and -5 for minus strand.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Assembly: hg19
Supplementary files format and content: bigWig file

growth_protocol: LNCaP obtained from ATCC were cultured in RPMI1640 media supplemented with 10% FBS. The established doxycycline-inducible stable cell lines with pInducer20 vectors that contain different AR cDNAs were maintained at RPMI1640 medium with G418 (600 μg/ml) for stable selection. All cell lines were cultured in a 5% CO2 humidified incubator at 37°C.

extract_protocol: 50,000 cells were harvested for each condition. After purification of nuclei, transposition was performed with Tn5 transposase from Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030). ATAC-seq library prep was performed as in Buenrostro et al, 2015. Libraries were sequenced with Illumina NovaSeq6000.

treatment_protocol: To test the role of AR condensation on enhancer accessibility, we used 1,6 hexanediol (1,6 HD) to chemically disrupt phase separation in cells (2,5HD was used as control for 1,6HD). Before experiment, the LNCaP cells were hormone-stripped in phenol red-free RPMI1640 medium plus 5% charcoal-treated FBS for 3 days, followed by four different treatments for 2 hours: 1. ethanol as vehicle control; 2. 100 nM DHT as hormone stimulation sample; 3. 100 nM DHT plus 2.5% 1,6 HD as condensation disruption condition; 4. 100 nM DHT plus 2.5% 2,5 HD as control condition. To test the enhancer regulation function of different AR cDNAs (WT vs mutants), we have set up the doxycycline-inducible stable cell lines with pInducer20 vectors that contain different AR cDNAs. For the rescue experiments, doxycycline-inducible AR-overexpressing LNCaP cell lines were infected by either control or AR shRNA lentivirus and selected with 1 μg/ml puromycin and collected for experiments within 5 days (first two days in regular medium and last three days in stripping media before hormone treatment). 20 ng/ml doxycycline was added to the overexpressing samples for 2 days before the 2 hours of vehicle or DHT treatment and collection for ATAC-seq experiments.

tag: transfection

value: LNCap stable line with pInducer20-TAF15IDR-ARdIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-TAF15IDR-ARdIDR:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: TAF15IDR_shCtrl_DOX_Veh

value: pInd-TAF15IDR-ARdIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: TAF15IDR_shCtrl_DOX_DHT

value: pInd-TAF15IDR-ARdIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-B8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-B7


title: TAF15IDR_shAR_noDOX_Veh

value: pInd-TAF15IDR-ARdIDR:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: TAF15IDR_shAR_noDOX_DHT

value: pInd-TAF15IDR-ARdIDR:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: TAF15IDR_shAR_DOX_Veh

value: pInd-TAF15IDR-ARdIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: dBRD9_1 [human_Brd9_ATAC-seq]

value: hematopoietic, parental cells

value: 100nM dBRD9


title: input

city: Zhoushan

first: Longmei

last: Qiu

state: Zhejiang Province

address: 1 Haida South Road, Dinghai District, Zhoushan City, Zhejiang Province

institute: Zhejiang Ocean University

data_processing:
Raw fastq sequences were treated with Trimmomatic tools (v 0.36) using the following options: TRAIL- ING: 20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Genomic alignment (version from UCSC genome browser) was using bowtie2 (version: 2.5.1) to get uniquely mapping reads.
MACS3 (version 3.0.0a7) was employed to perform peak calling with the corresponding input sample serv- ing as control. Then using Hommer(version:4.11.1) to annotate the Peaks. The nucleotides in Peaks region were used for detection of the consensus m6A motif by DREME (version: 5.5.1) and MEME (version: 5.5.1). Motif central enrichment was performed by CentriMo (version: 5.5.1).
Assembly: "Our research team conducted whole-genome sequencing of Mytilus coruscus, but it has not been made public yet."

organism: Mytilus coruscus

source_name: Digestive gland

extract_protocol:
The digestive gland cells of mussels were extracted and 20 mL formaldehyde fixative was added to make the final concentration 1%. After incubation at room temperature on a 100 × g for 10 minutes, the cells were added 10 mL of glycine termination solution with a 5 minutes centrifugation at 300 × g, 4°C. The cells were then washed twice with phosphate buffer containing 1 mM PMSF to remove any remaining formaldehyde. After washing, 1 mL of lysis buffer was added, lysed on ice for 30 minutes, followed by a cells collection by centrifugation at 5000 × g, 4°C for 10 minutes. Next, 350 μL of pre-warmed digestion buffer was added, and the mixture was incubated at 37°C for 5 minutes. The cut chromatin was separated, and 10 μL of input DNA was labeled and kept as a control for ChIP samples. The ChIP reaction system was prepared and then incubated overnight at 4°C on a rotating shaker. Subsequently, the magnetic beads were washed, and the chromatin was eluted. Uncross linking and proteinase K treatment were performed afterward. Finally, the resulting DNA was purified, and the detailed steps were described in the Magnetic Chromatin Immunoprecipitation Kit (Active Motif, CA, USA).
The CHIP DNA was assessed by Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit(ThermoFisher Scientifc,USA) .The ChIP-Seq libraries were constructed following the Illumina ChIP-Seq library gener- ation protocol. Briefly, chip DNA was fragmented to approximately 200bp , Subsequently, the fragments were repaired end and added A-tailing following by adaptor ligation. The adaptor-ligated DNA was enrichment with a low-cycle according to instructions of NEBNext® UltraTMDNA Library Prep Kit for Illumina (NEB, USA). The DNA library products were assessed using the Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit (Thermo Fisher Scientific, USA), the libraries were then sequenced with pair-end 150 bp by Illumina platform (Illumina,USA)at Ribobio Co. Ltd (Ribobio, China).

tag: tissue

value: Digestive gland

value: M. coruscus digests glandular cells


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-A7

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-B20


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-A8


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-B19


title: FUSIDR_shCtrl_noDOX_Veh

tag: cell line

value: LNCap stable line with pInducer20-FUSIDR-ARdIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-FUSIDR-ARdIDR:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: ChIP-DNA

tag: cell type

tag: antibody

value: INFO REQUESTED


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-A20


title: TAF15IDR_shCtrl_noDOX_Veh

value: LNCaP

tag: treatment

value: pInd-TAF15IDR-ARdIDR:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-A19

tag: brain region


title: CEMBA3C_MacaqueM1_R1_P1-4-B11-C7

tag: gender


title: FUSIDR_shCtrl_DOX_Veh

value: pInd-FUSIDR-ARdIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: UT105.3

data_processing:
Data was aligned using hg38 and STAR 2.0
Counts were normalized using TMM
Assembly: hg38

source_name: breast

value: breast

value: breast cancer


title: UT105.1


title: R1881.3


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-P6


title: R1881.2


title: FUSIDR_shCtrl_DOX_DHT

value: pInd-FUSIDR-ARdIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-P5


title: R1881.1


title: FUSIDR_shAR_noDOX_Veh

value: pInd-FUSIDR-ARdIDR:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: TAF15IDR_shAR_DOX_DHT

value: LNCap stable line with pInducer20-TAF15IDR-ARdIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-TAF15IDR-ARdIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: Donor_93_VDJ

city: Cambridge

first: Jonathan

last: Hsu

address: 840 Memorial Dr 4th Floor

institute: Marengo Therapeutics

description:
10x Genomics
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
93_vloupe.vloupe

data_processing:
Cell Ranger v6.0.1 was used to demultiplex FASTQ reads. Data quality was checked using FastQC and MultiQC v1.9.
The output from Cell Ranger was imported in R using Seurat. Empty droplets (nFeatures < 300), duplicates (nFeatures > 4000) and dead cells (percentage mitochondrial genes > 5) were removed. Data were then processed and log normalized with Seurat's standard processing steps for downstream analyses.
Protein abundance data (Antibody Derived Tag, ADT) were normalized using a centered log-ratio (CLR) approach prior scaling.
Information about TRBV usage were extracted from VDJ data, so that cells using TRBV6-1, TRBV6-5, TRBV6-2 and TRBV10-3 were used to group cells targeted by α-TRBV6-5AM.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: vloupe

source_name: PBMC isolated from blood

growth_protocol: Antibody-stimulated Cells were grown in X-VIVO 15 supplemented with 5% human AB serum, IL-2 (100 U/ml), IL-15 (10 ng/ml), and penicillin/streptomycin; unstimulated cells were rested overnight in the same media without cytokines

extract_protocol:
Cells were harvested and resuspended in ice-cold PBS supplemented with 1% BSA, 2mM EDTA (staining buffer); processed using a dead cell removal kit according to the manufacturer’s instructions (Miltenyi). Flow-through was supplemented with Fc block (Biolegend, 1:10 dilution), then cells from each condition were pooled and labelled with a cocktail of barcoded antibodies against various markers and for cell hashing for 30 mins at 4˚C; washed 3 times with staining buffer; and resuspended in 50 µl of ice-cold PBS supplemented with 0.04% BSA at ≤106 cells per ml for loading.
Cells from different conditions were labeled with DNA-barcoded antibodies (TotalSeq-C0251, hashtag 1; TotalSeq-C0253, hashtag 3, TotalSeq-C0254, hashtag 4; Biolegend), then pooled. Libraries were generated using the Chromium Single-Cell 5’ Reagent Kits v2 (10X Genomics), following the manufacturer's instructions.

treatment_protocol: Cells were left unstimulated or stimulated for 7 days with plate-bound antibodies.

value: PBMC isolated from blood

value: T cells


title: FUSIDR_shCtrl_noDOX_DHT

value: pInd-FUSIDR-ARdIDR:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: Donor_64_VDJ

description:
10x Genomics
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
64_vloupe.vloupe


title: Donor_9_VDJ

description:
10x Genomics
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
9_vloupe.vloupe


title: UT105.2

extract_protocol: RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.


title: Donor_5_VDJ

description:
10x Genomics
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
5_vloupe.vloupe


title: Donor_4_VDJ

description:
10x Genomics
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
4_vloupe.vloupe


title: Donor_93_CSP


title: Donor_64_CSP


title: Donor_9_CSP


title: Donor_5_CSP


title: Donor_4_CSP


title: FUSIDR_shAR_DOX_Veh

value: pInd-FUSIDR-ARdIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: Donor_89_VDJ

description:
10x Genomics
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
89_vloupe.vloupe


title: FUSIDR_shAR_DOX_DHT

value: pInd-FUSIDR-ARdIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: FUSIDR_shAR_noDOX_DHT

value: LNCap stable line with pInducer20-FUSIDR-ARdIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-FUSIDR-ARdIDR:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: Donor_89_GEX


title: Donor_64_GEX


title: Donor_89_CSP


title: Donor_9_GEX


title: Donor_5_GEX


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-N6

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-P17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-O5


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-N5


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-P18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-O6


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-O17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-O18


title: Donor_4_GEX


title: Donor_93_GEX


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-N18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-N17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-M6


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-M5


title: Exp4_Veh

description: Veh

value: LNCaP

value: No transfection, regular LNCaP cells

value: Veh:stripping 3 days, ethanol


title: ERIDR_shAR_noDOX_Veh

value: LNCap stable line with pInducer20-ERIDR-ARdIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-ERIDR-ARdIDR:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: ERIDR_shAR_DOX_DHT

value: pInd-ERIDR-ARdIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: ERIDR_shCtrl_DOX_DHT

value: pInd-ERIDR-ARdIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: ERIDR_shCtrl_DOX_Veh

value: pInd-ERIDR-ARdIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: ERIDR_shCtrl_noDOX_DHT

value: pInd-ERIDR-ARdIDR:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-M18


title: ERIDR_shAR_noDOX_DHT

value: pInd-ERIDR-ARdIDR:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: ERIDR_shAR_DOX_Veh

value: pInd-ERIDR-ARdIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-M17


title: Exp4_DHT

description: DHT treatment

value: DHT:stripping 3 days, DHT 100nM 2hr


title: ERIDR_shCtrl_noDOX_Veh

value: pInd-ERIDR-ARdIDR:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: Exp4_DHT_25HD

description: DHT plus 25HD

value: DHT+2,5HD:stripping 3 days, DHT 100nM + 2.5% 2,5 HD  2hr


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-L6


title: Exp4_DHT_16HD

description: DHT plus 16HD

value: DHT+1,6HD:stripping 3 days, DHT 100nM + 2.5% 1,6 HD  2hr


title: PT, replicate 1, scRNAseq

city: taiyaun

first: ruijing

last: Zhang

address: Wuyi Road, Xinghualing District, Taiyuan City, Shanxi Province

institute: The Second Hospital of Shanxi Medical University

description: 10x Genomics

data_processing:
The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. Overall, all cells passed the quality control threshold : all genes expressed in less than three cells （defaultparameters：1 cell）were removed,number of genes expressed per cell > 500 as low and <5000 as high cut-off,UMI counts less than 500,the percent of mitochondrial-DNA derived gene-expression <25%.  To visualize the data, we further reduced the dimensionality of all cells using Seurat and used t-SNE to project the cells into 2D space. The steps includes:1,Using the LogNormalize method of the "Normalization" function of the Seurat software to calculated the expression value of genes; 2,PCA (Principal component analysis) analysis was performed using the normalized expression value, Within all the PCs, the top 10 PCs were used to do clustering and t-SNE analysis；3,To find clusters, selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method. Marker genes for each cluster were identified with the Wilcoxon rank-sum test （defaultparameters is"bimod" : Likelihood-ratio test）with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which are expressed in more than 10% of the cells in a cluster and average log(Fold Change) of greater than 0.25（defaultparameters：0.26）
cell barcode appendices: PT is represented by '-1' and NC is represented by '-2'
Assembly: human NCBI genome build 36
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: peripheral blood mononuclear cells

extract_protocol:
Place a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers.  Tissue s were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS，V/V）, then pipetting 5-10 times with a Pasteur pipette。The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells  using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: peripheral blood mononuclear cells

tag: diagnosis

value: ESRD

value: PBMC

tag: cell barcode_appendix


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-L5

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: Motor cortex

value: M


title: 11667MAPool01-N__CS13_Aorta

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

data_processing:
Cell Ranger 2.1.0
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: subset_HE.h5ad: Haematopoietic and endothelial single cell analysis AnnData object from CS13 dorsal aorta data integrated with publicly available data from CS13-CS15 dorsal aortae (Zeng, et al. 2019, accession GSE135202 (including samples GSM3993422, GSM3993424, GSM3993425 and GSM3993426)).
Supplementary files format and content: subset_mesenchymal.h5ad: Mesenchymal and epithelial single cell analysis AnnData object from CS13 dorsal aorta data integrated with publicly available data from CS13-CS15 dorsal aortae (Zeng, et al. 2019, accession GSE135202 (including samples GSM3993422, GSM3993424, GSM3993425 and GSM3993426)).

source_name: Carnegie stage 13 dorsal aorta

extract_protocol: The dorsal aorta was dissected from a CS13 human embryo and dissociated into single cells in 1mg/ml Collagenase-Dispase (Roche) and 0.12 mg/ml of DNase I (Roche) for 35 min in a 37°C rotating water bath. 10X libraries were prepared according to manufacturer’s guidelines (Single Cell 3′ Reagent Kit v2, 10x Genomics).

value: Carnegie stage 13 dorsal aorta


title: NC, replicate 1, scRNAseq

description: 10x Genomics

value: healthy


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-L17

first: Joseph


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-L18


title: CS14_Dorsal_Outer_Rep2 (DO_2)

description:
Dorsal more distal mesenchyme up to the notochord
CS14_gene_counts.csv

data_processing:
Adaptor trimming with flexbar/2.5
Alignment with STAR/2.5.1b
Feature counts with BEDTools/2.27.1 multicov function
Assembly: Homo_sapiens.GRCh38.86
Supplementary files format and content: CS13_gene_counts.csv = raw read counts for all CS13 samples
Supplementary files format and content: CS14_gene_counts.csv = raw read counts for all CS14 samples

source_name: CS14 embryo

extract_protocol: The previously published LCM-Seq protocol (Nichterwitz, et al. 2016) was used for RNA-Seq library preparation from LCM material in lysis buffer. LCM caps were vortexed for 15 s and spun in a tabletop centrifuge (8000 g) for 5 min. 5 μL lysate was added to 2 μL 10mM dNTP mix (Thermo Fisher) and 1 μL 10 μM oligodT (5′-AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3′, (IDT)). This was vortexed briefly and spun in a microcentrifuge for 30 s (700 g) then incubated at 72°C for 3 min and immediately snap cooled on ice. To each reaction, 2 μl SSRTIV 5 × buffer, 0.5 μl 100 mM DTT, 0.5 μl 200 U μl−1 SSRTIV (all Thermo Fisher), 2 μl 5 M betaine (Sigma-Aldrich), 0.1 μl 1 M MgCl2 (Sigma-Aldrich), 0.25 μl 40 U μl−1 RNase inhibitor (Takara) and 0.1 μl 100 μM TSO-LNA-oligo 5′- AAGCAGTGGTATCAACGCAGAGTACATrGrG+G −3′, Exiqon) was added. The reverse transcription reaction was performed in a thermal heat cycler with the following conditions; 90min 42°C, 10 cycles of (2 min 50°C, 2 min 42°C) and 15 s 70°C. For the amplification reaction 12.5 μl 2X KAPA HiFI Hotstart Mix (KAPA Biosystems), 0.2 μl 10 μM ISPCR primers (IDT, 5′ - AAG CAG TGG TAT CAA CGC AGA GT – 3′) and 2.3 μl nuclease-free H2O (Invitrogen) was added to each reaction. This was heat cycled as follows: 3 min 98°C, 18 cycles of (20 s 98°C, 15 s 67°C, 6 min 72°C) and 5 min 72°C. After bead purification using AMPure XP beads (Beckman Coulter), the concentration of the cDNA library was measured with an Agilent 2200 TapeStation using the High Sensitvity DNA 5000 kit (Agilent). 1 ng of cDNA from this reaction was amplified and barcoded using the Nextera XT DNA sample preparation kit and Nextera XT index kit (Illumina) following the manufacturer’s protocol. The libraries were purified again using AMPure XP beads, analyzed on the Tapestation 2200 using High Sensitivity DNA 100 Kit and quantified using the Qubit fluorometer and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

tag: tissue region

value: CS14 embryo


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-K6


title: RNA NMPdiff

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: R2 fastq files contain the UMIs of the Ovation SoLo RNA-Seq kit used

data_processing:
Prior to mapping, the first 5 nucleotides of the forward and reverse reads were trimmed using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html) according to manufacturer’s instructions (NuGEN). The resulting reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using TopHat2 (v2.1.1) and bowtie (v1.2.2) and the RefSeq annotation in gtf format (UCSC), providing the options ‘--no-coverage-search --no-mixed --no-discordant -g1 --mate-inner-dist 250 --mate-std-dev 100 --library-type fr-secondstrand’. Read duplications resulting from the PCR amplification of the library were removed using the NuDup deduplication script provided by NuGEN (http://nugentechnologies.github.io/nudup/). Wiggle files were generated with BEDTools version 2.23.0, converted to bigwig format and visualized in the Integrated Genome Browser. FPKM values were calculated using Cufflinks (v2.2.1) with options ‘-u --no-effective-length-correction -b’.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

organism: Mus musculus

source_name: FACS sorted T+/Noto- cells from in vitro differentiated cultures

growth_protocol: To initiate NMP differentiation, ESCs were removed from feeders by dissociation using 0.05% trypsin and then plated onto tissue culture plates for four short successive periods (25’, 20’, 15’, 10’) to remove feeders. To induce differentiation, a protocol slightly modified from Gouti et al. was used. In short, cells were plated on CellBINDSurface dishes precoated with 0.1% gelatin at a density of 1 x 104 cells per cm2 in a medium consisting of ‘N2B27’ medium (Gouti et al., Plos Biol 2014), supplemented with 10 ng/ml bFGF for 3 days (d1-d3). From d2-d3 5 µM CHIR99021 was added to the medium.

extract_protocol:
Total RNA from approximately 200-20000 cells was isolated using the RNeasy Micro kit (Qiagen) and genomic DNA was digested on column with the addition of an extra 1ul of RNase-free DNase I (Roche) to ensure complete digestion.
Sequencing libraries were prepared using the Ovation SoLo RNA-Seq system (NuGen) according to manufacturer’s recommendations, starting at step A.9 with 12 µl purified DNA. After each amplification step, libraries were quantified with the Qubit the High Sensibility DNA assay (Thermo Fisher 12102). Library size was validated using DNA High Sensitivity Bioanalyzer chips (Agilent 5067-4626).

value: genetically modified F1G4 (C57BL/6N x SV129) mES cells

value: in vitro generated neuromesodermal progenitors

tag: genotype

value: TRE::Foxa2-IRES-EGFP (Rosa26 locus); T::H2B-mCherry-T2A-irTA (BAC); Noto::H2B-mTurquoise (BAC)

value: A single cell suspension of in vitro differentiated cells was filtered through a 35µm mesh before cell sorting on a FACS Aria II (Becton Dickinson), the cell suspension was filtered through a 35µm mesh. Cells were sorted directly into Eppendorf tubes containing 350µl RLT buffer (Qiagen) and 3.5ul b-mercaptoethanol.


title: RNA MPdiff

growth_protocol: To initiate MP differentiation, ESCs were removed from feeders by dissociation using 0.05% trypsin and then plated onto tissue culture plates for four short successive periods (25’, 20’, 15’, 10’) to remove feeders. To induce differentiation, a protocol slightly modified from Gouti et al. was used. In short, cells were plated on CellBINDSurface dishes precoated with 0.1% gelatin at a density of 1 x 104 cells per cm2 in a medium consisting of ‘N2B27’ medium (Gouti et al., Plos Biol 2014), supplemented with 10 ng/ml bFGF for 3 days (d1-d3). From d2-d4 µM CHIR99021 was added to the medium.

value: FACS sorted T+/Noto- cells from in vitro differentiated cultures

value: in vitro generated mesodermal progenitors


title: Trem2+Mac

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from Trem2+Mac sorted fromthe heart tissue of WT mice post-IR

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on Clariom S Array(mouse, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

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

label: biotin

source_name: Trem2+Mac sorted from the heart tissue of WT mice post-IR

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

growth_protocol: 10-week-old C57BL/6 male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: For microarray profiling, the macrophages total RNA was isolated with TRIzol (Invitrogen) from hearts at each time point according to manufacturer's instructions.

treatment_protocol: Heart cells were sorted by gating for CD45+CD11b+ cells via flow cytometry into populations of Trem2+, Lyve1+, MHCII+, and MerTK- macrophages.

tag: strain

value: male

value: heart


title: RNA NotoPdiff

source_name: FACS sorted Noto+/T+ cells from in vitro differentiated cultures

growth_protocol: To initiate NotoP differentiation, ESCs were removed from feeders by dissociation using 0.05% trypsin and then plated onto tissue culture plates for four short successive periods (25’, 20’, 15’, 10’) to remove feeders. To induce differentiation, a protocol slightly modified from Gouti et al. was used. In short, cells were plated on CellBINDSurface dishes precoated with 0.1% gelatin at a density of 1 x 104 cells per cm2 in a medium consisting of ‘N2B27’ medium (Gouti et al., Plos Biol 2014), supplemented with 10 ng/ml bFGF for 3 days (d1-d3). From d2-d4 µM CHIR99021 was added to the medium. For induction of Foxa2 expression, 1ng/ml doxycycline was applied from d2-d4.

value: in vitro generated notochord progenitor-like cells


title: 2 Weeks Infected, mRNA

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description: GEX (3' mRNA) library: read 1 file contains cell barcode and UMI; read 2 file contains transcript

data_processing:
Sequencing data derived from each run underwent processing using distinct software tailored to the library type. mRNA libraries were processed using the CellRanger software (v. 6.0) from 10X Genomics and the mouse mm10 genome (GRCm38). The ADT and HTO libraries were processed using CITE-Seq-Count (v. 1.4.3), available at https://hoohm.github.io/CITE-seq-Count/. This processing yielded raw count matrices for both mRNA and proteins. Downstream data analysis was conducted in Seurat (v. 4.3), following methods outlined by Stuart et al. Cells with less than 200 unique genes or with over 30% of the total reads belonging to mitochondria were filtered out. The HTOs multiplexed samples were then demultiplexed using the MULTIseqDemux() function in Seurat. This step allowed for the removal of doublets and empty droplets and ensured the correct assignment of identities to each sample.
All scRNA-seq datasets from individual timepoints were preprocessed using Seurat's regularized negative binomial regression, where both the number of counts and the percentage of mitochondrial reads were regressed out, as per Hafemeister and Satija. For analysis of the macrophage populations in the uninfected naïve lungs we used the previously generated datasets from Pisu et al. Metadata columns, namely “Timepoint”, “Batch”, “Infection Status”, and “Vaccination Status”, were added to each dataset prior to subsequent steps.
Datasets were combined into a unified Seurat object. The raw counts contained in the RNA slot of the merged object were used as an input for Harmony integration. Raw counts underwent log-normalization, followed by the identification of the top 3,000 variable genes. These genes were scaled and centered. PCA was then performed on these values. Integration in Harmony incorporated “Batch”, “Infection Status”, “Timepoint”, and “Vaccination Status” as covariates.
Using the Harmony-aligned embeddings, graph-based cluster detection was achieved utilizing principal components (PCs) that had been marked statistically significant by the jackstraw method. For community detection, we employed the Louvain algorithm. Cell types for each identified cluster were annotated using both reference-based and canonical marker genes.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CiteSeq-count output files for ADT and HTO: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-Seq

source_name: Lung

extract_protocol:
At 2, 4, and 6 weeks post-infection (w.p.i.), mice were euthanized. Lungs were aseptically removed and immersed in PBS containing 5% FBS and Collagenase IV (250U/mL). To preserve the gene expression profiles of both the host and bacteria, samples were immediately processed using a GentleMACS tissue dissociator (Miltenyi Biotec) and maintained on ice. The dissociated lung material was subsequently strained through a 70-µM mesh, and red blood cells were lysed using ammonium-chloride-potassium (ACK) lysis buffer (Lonza). Cells from infected mice (n = 5/timepoint) were washed in PBS containing 5% FBS, resuspended in sorting buffer (PBS, 1% FBS, 5 mM EDTA, and 25 mM Hepes), filtered through a 40-µM strainer, and sorted. Throughout the sorting, samples were kept at 4°C and directly collected into Cell Staining Buffer (BioLegend). Sorted cells were centrifuged at 500 g for 5 min and then resuspended in 50 µl of cell staining buffer containing 0.25 µg of TruStain FcX PLUS (BioLegend), followed by a 10 min incubation at 4°C. An ADT plus HTO antibody cocktail mix (50 µl) was then added to the samples, and the cells were further incubated for 30 min at 4°C. After two washes in cell staining buffer, differentially tagged samples (e.g., hspx′::GFPhigh/hspx′::GFPlow) were combined and resuspended in 1× Dulbecco’s PBS. The samples were then fixed by slowly adding ice-cold methanol to a final concentration of 90% (vol/vol) and stored at −20°C overnight.
Post-fixation, the samples were brought out of the BSL3 facility, equilibrated on ice for 15 min, and washed twice with rehydration buffer (1× Dulbecco’s PBS with 1.0% BSA [Thermo Fisher Scientific] and 0.5 U/µl RNase Inhibitor [Sigma-Aldrich]). The cell count was determined prior to loading onto the 10× chip. For mRNA library preparation, we adapted the 10× protocol (CG000206 Rev D), making a minor alteration in step 2.2. Specifically, we incorporated 1 μl of ADT and HTO additive primers (0.2 μM stock) following the method described by Stoeckius et al76. HTO and ADT libraries were prepared according to BioLegend's standard protocols.
The mRNA, HTO, and ADT libraries underwent quality control assessment using an Agilent Fragment Analyzer. Their concentrations were determined using the QX200 digital PCR system from Bio-Rad. Libraries were pooled in the same sequencing run at specific ratios: 90% mRNA, 5% ADT, and 5% HTO. Sequencing was performed on the Nextseq 2k (50bp kit) or NextSeq500 (Illumina) using the 75-bp NextSeq kit. The cycle distribution was: read 1 (28 cycles), i7 index (8 cycles), and read 2 (55 cycles for nextseq 500 and 52 cycles for nextseq 2k). Sequencing depth exceeded 50,000 reads/cell.

value: Lung

value: mCherry+

tag: timepoint

value: 2 Weeks

value: Unvaccinated

tag: infection

tag: library type

value: mRNA


title: 6 Weeks Bystander, ADT

description: ADT: Read 1 contains Cell Barcode and UMI, Read 2 contains Antibody barcode.

library_source: other

molecule: protein

value: mCherry- CD45+

value: 6 Weeks

value: ADT

tag: adt


title: 2 Weeks Infected, ADT


title: 6 Weeks Bystander, mRNA


title: 4 Weeks Infected, ADT

value: 4 Weeks


title: 6 Weeks Infected, HTO

description: HTO: Read 1 contains Cell Barcode and UMI, Read 2 contains Antibody tag

value: HTO

tag: hto

value: TotalSeq Hashtag 1 murine (cat. # 155801), Hashtag 2 murine (cat. # 155803)


title: 6 Weeks Infected, mRNA

tag: tissue


title: 4 Weeks Bystander, mRNA


title: 2 Weeks Infected, HTO


title: 2 Weeks Bystander, mRNA


title: 4 Weeks Bystander, ADT


title: 2 Weeks Bystander, ADT


title: 4 Weeks Infected, mRNA


title: MerTK-Mac

description: Gene expression data from MerTK-Mac sorted fromthe heart tissue of WT mice post-IR

source_name: MerTK-Mac sorted from the heart tissue of WT mice post-IR

value: MerTK-Mac


title: CS14_Ventral_Outer_Rep2 (VO_2)

description:
Ventral more distal mesenchyme down to the gonadal epithelium
CS14_gene_counts.csv

value: CS14 embryo


title: CS14_Dorsal_Mid_Rep2 (DM_2)

description:
Dorsal sub-aortic mesenchyme
CS14_gene_counts.csv


title: 4 Weeks Infected, HTO


title: 6 Weeks Infected, ADT


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-K5

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-K18


title: CS14_Ventral_Mid_Rep2 (VM_2)

description:
Ventral sub-aortic mesenchyme
CS14_gene_counts.csv


title: G + 4

city: Raleigh

first: Terri

middle: A

last: Long

state: NC

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
sequenced using an Illumina HiSeq 2500 sequencing machine .
125bp single end reads
Adapters and low quality reads were filtered out using fastQC and fastq-mcf.
Assembly: Clean reads were mapped against the TAIR 10 reference genome using the tophat2
Supplementary files format and content: RPKM were acquired using RSubread, followed by edgeR to identify differentially expressed genes (DEGs), using a maximum false discovery rate (FDR) of 0.05 and minimum log fold change threshold of 0.75.

organism: Arabidopsis thaliana

source_name: Protoplast of root epidermal cells (GFP-positive)

growth_protocol: Plants grown vertically on top of mesh placed on MS

extract_protocol:
Roots were roots were harvested from both +Fe and -Fe conditions for protoplast collection, followed by fluorescence-activated cell sorting in triplicates. RNA was extracted from FACS epidermal protoplast using RNAeasy Plant RNA Purification Kit (Qiagen).
RNA libraries were prepared for sequencing by performing cDNA synthesis and amplification using the NEBNext® Poly(A) mRNA Magnetic Isolation Module followed by the NEBNext® Ultra™ II Directional RNA Library Prep and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)

treatment_protocol: Iron-sufficient (+Fe) media is standard Murashige and Skoog media with 0.05% MES, 1% sucrose, 1% agar, and 0.1 mM FeEDTA. Iron deficient (−Fe) media is as mention above minus the 0.1mM FeEDTA, with the addition of 300 μM ferrozine, an iron chelator

value: Root Cells

value: Plus Iron

tag: age

value: 8 day old plus 12 hours

tag: gfp localization

value: Epidermis

tag: condition

value: 36hrs = 8d 12 hrs (7 d +Fe/ 36hrs +Fe)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-K17


title: G - 4

tag: treatment

value: Minus Iron

value: 36hrs = 8d 12 hrs (7 d +Fe/ 36hrs -Fe)


title: G - 2


title: E + 3

value: 8 day old

value: 24hrs = 8d (7d +Fe/ 24hrs +Fe)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-J6

tag: brain region


title: E + 2


title: C - 2

value: 7 day old plus 12 hours

value: 12hrs = 7d +Fe/ 12hrs -Fe


title: C - 3


title: CS14_Ventral_Outer_Rep1 (VO_1)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-J5

tag: gender


title: E - 1

value: 24hrs = 8d (7d +Fe/ 24hrs -Fe)


title: F-2

value: 8 day old plus 6 hours

value: 30hrs = 8d 6hrs (7d +Fe/ 30 hrs -Fe)


title: D + 2

value: 7 day old plus 18 hours

value: 18hrs = 7d +Fe/ 18hrs +Fe


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-J17

value: Motor cortex

value: M


title: D - 2

value: Root Cells

value: 18hrs = 7d +Fe/ 18hrs -Fe


title: CS14_Dorsal_Mid_Rep1 (DM_1)

value: CS14 embryo


title: CS14_Ventral_Inner_Rep2 (VI_2)

description:
Ventral inner layer of the dorsal aorta including endothelium and some adjacent mesenchyme
CS14_gene_counts.csv


title: CS14_Dorsal_Inner_Rep2 (DI_2)

description:
Dorsal inner layer of the dorsal aorta including endothelium and some adjacent mesenchyme
CS14_gene_counts.csv


title: G + 3

value: Plus Iron

value: 8 day old plus 12 hours

value: Epidermis

value: 36hrs = 8d 12 hrs (7 d +Fe/ 36hrs +Fe)


title: CS14_Dorsal_Outer_Rep1 (DI_1)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-I6


title: F-1

value: Minus Iron


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-J18


title: CS14_Ventral_Mid_Rep1 (VM_1)


title: G - 1

value: 36hrs = 8d 12 hrs (7 d +Fe/ 36hrs -Fe)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-I5


title: D + 1


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-I18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-I17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-H6


title: Lyve1+Mac

description: Gene expression data from Lyve1+Mac sorted fromthe heart tissue of WT mice post-IR

source_name: Lyve1+Mac sorted from the heart tissue of WT mice post-IR

value: male

value: heart

tag: cell type


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-H5


title: CS14_Ventral_Inner_Rep1 (VI_1)


title: CS13_Gonadal_Epithelium_Proximal_Rep2 (GEP_2)

description:
Gonadal epithelium most proximal to the dorsal aorta
CS13_gene_counts.csv

source_name: CS13 embryo

value: CS13 embryo


title: CS13_Ventral_Outer_Rep2 (VO_2)

description:
Ventral sub-aortic mesenchyme down to the gonadal epithelium
CS13_gene_counts.csv


title: CS14_Dorsal_Inner_Rep1 (DI_1)


title: MHCII+Mac

description: Gene expression data from MHCII+Mac sorted fromthe heart tissue of WT mice post-IR

source_name: MHCII+Mac sorted from the heart tissue of WT mice post-IR

value: MHCII+Mac


title: CS13_Dorsal_Outer_Rep2 (DO_2)

description:
Dorsal sub-aortic mesenchyme up to notochord
CS13_gene_counts.csv


title: CS13_Dorsal_Inner_Rep2 (DI_2)

description:
Dorsal inner layer of the dorsal aorta including endothelium and some adjacent mesenchyme
CS13_gene_counts.csv


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-H18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-H17


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-G6


title: CS13_Gonadal_Epithelium_Distal_Rep2 (GED_2)

description:
Gonadal epithelium more distal to the dorsal aorta
CS13_gene_counts.csv


title: F + 1

value: 8 day old plus 6 hours

value: 30hrs = 8d 6hrs (7d +Fe/ 30 hrs +Fe)


title: E + 1

value: 8 day old

value: 24hrs = 8d (7d +Fe/ 24hrs +Fe)


title: C + 1

value: Root Cells

value: 7 day old plus 12 hours

value: 12hrs = 7d +Fe/ 12hrs +Fe


title: C + 3

value: Plus Iron


title: F + 3


title: D - 3

value: 7 day old plus 18 hours

value: 18hrs = 7d +Fe/ 18hrs -Fe


title: C + 2

value: Epidermis


title: C - 1

value: Minus Iron

value: 12hrs = 7d +Fe/ 12hrs -Fe


title: D - 1


title: F + 2


title: G + 1

value: 8 day old plus 12 hours

value: 36hrs = 8d 12 hrs (7 d +Fe/ 36hrs +Fe)


title: E - 3

value: 24hrs = 8d (7d +Fe/ 24hrs -Fe)


title: F - 3

value: 30hrs = 8d 6hrs (7d +Fe/ 30 hrs -Fe)


title: E - 2


title: B + 3

value: 7 day old plus 6 hours

value: 6hrs = 7d +Fe/ 6hrs + Fe


title: CS13_Ventral_Inner_Rep2 (VI_2)

description:
Ventral inner layer of the dorsal aorta including endothelium and some adjacent mesenchyme
CS13_gene_counts.csv

value: CS13 embryo


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-G5

value: Motor cortex

value: M


title: D + 3

value: Root Cells

value: 18hrs = 7d +Fe/ 18hrs +Fe


title: CS13_Gonadal_Epithelium_Distal_Rep1 (GED_1)


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-G18


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-G17


title: CS13_Gonadal_Epithelium_Proximal_Rep1 (GEP_1)


title: B + 1

value: Plus Iron


title: CS13_Dorsal_Outer_Rep1 (DO_1)


title: B - 1

value: 6hrs = 7d +Fe/ 6hrs -Fe


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-F6


title: CEMBA3C_MacaqueM1_R1_P1-3-B11-F5


title: A2

value: 7 day old

value: Zero time point


title: B - 3

value: Minus Iron

value: Epidermis


title: CS13_Ventral_Outer_Rep1 (VO_1)