title: Control-1

city: LONDON

first: Fauzy

last: Nasher

address: Keppel Street,

institute: London School of Hygiene and Tropical Medicine

data_processing:
The paired-end reads were trimmed and filtered using Sickle v1.200. Bowtie2 was used to map the reads against the reference sequence: C. jejuni strains 11168H assembly GCA_900117385.1. Cufflinks suite was used to convert annotations from GFF to GTF format and Bedtools was used to generate transcript counts per samples. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as meta data associated with the study (multifactorial design). Adjusted p-value significance cut-off of 0.001 and log fold change cut-off of >1.5 was used for multiple comparison.
Assembly: GCF_000009085.1 (ASM908v1)
Supplementary files format and content: *_EDGE.out.rpkm_0.txt: Tab-delimited text files include #reads and RPKM.

organism: Campylobacter jejuni

source_name: Bacteria

extract_protocol: RNA was extracted using Triazole, quality was checked by agarose gel, library was prepared according to Illumina protocol and was sent for sequencing.

value: Bacteria

tag: c.jejuni strain

tag: c.jejuni genotype

value: Control (25C)

tag: time

value: 4 hrs


title: RBG18871_Young_MSC-L_006

status: Public on Nov 02 2022

type: SRA

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Reads were mapped to the Mus musculus genome (EMSEMBL GRCm38.p4 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: endosteum and central marrow

extract_protocol:
Single endosteal and central marrow stromal cells were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, 93443) and 1U of Superase-In RNase Inhibitor (Ambion). Of note, information regarding expression of surface markers was recorded for each cell. Cells were frozen immediately at -80C until further processing. After thawing on ice, 2 µl of annealing mixture (1 µM oligodT –IDT-, 5mM each dNTPs and a dilution 1:6,000,000 of ERCC RNA Spike-In Mix -Invitrogen-) was added followed by incubation at 72C for 3 minutes. Then 5.7 µl of Reverse Transcription mix (3.5 U/µl of Maxima H minus retrotranscriptase –ThermoFisher-, 0.88 U/µl of Superase-In RNase Inhibitor, 1.75X Maxima RT Buffer, 3.5 µM TSO – Qiagen- and 13.15% PEG 8000 –Sigma-Aldrich-) was added and the mixture was incubated at 42 C for 90 min, followed by 70 C for 15 min. cDNA was further amplified by adding 40 µl of PCR mix (0.03 U/µl of Terra PCR direct polymerase –Takara Bio-, 1.25X Terra PCR Direct Buffer, 0.25 µM IS PCR primer –IDT-). PCR was as follows: 3 min at 98 °C for initial denaturation followed by 21 cycles of 15 s at 98 °C, 30 s at 65 °C, 4 min at 68 °C. Final elongation was performed for 10 min at 72 °C.  Sequences of oligodT, TSO and IS PCR primers were as previously described (PMID: 24385147).
Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6 with a final elution in 25 µl of EB Buffer (Qiagen). The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher). Size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer). Samples were used to construct Nextera XT libraries (Illumina) from 100 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems), pooled and sequenced in an Illumina HiSeq 4000 instrument.

tag: cell population

value: mesenchymal and endothelial cells

value: MSC-L

tag: age

value: Young


title: GK1_B

type: genomic

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchips using standard Illumina protocol

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

data_processing: The SeSAME package was used to extract the DNA methylation value of each probe using the openSesame function. Recommended general masking probes were removed according to the annotation file of Infinium DNA methylation arrays. Differentially methylated probes were identified by the limma package (version 3.46.0) with adjusted p-value < 0.05, absolute delta methylation change > 0.2.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: GEJ TP53/CDKN2A KO organoid 1

label_protocol: Standard Illumina Protocol

growth_protocol: Organoid were embeded in Matrigel and maintained in aDME/F12 based organoid condtion medium

extract_protocol: Genomic DNA was extracted from organoids using Qiagen DNeasy Blood & Tissue kits

tag: genotype

value: TP53/CDKN2A KO


title: RBG18869_Young_MSC-L_004


title: 4F2A_N14-2

type: RNA

city: Daejeon

first: Jeongmin

last: Ha

address: 125, Gwahak-ro, Yuseong-gu

department: Stem Cell Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day14

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Mouse Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

source_name: 4F2A MEF_iNSC rep day14, replicate 2

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: 2'MEFs and 4F2A MEFs were cultured in MEF derivation culture medium (MEF medium; Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 2 mM Glutamax, 0.1 mM nonessential amino acids, and 1% Penicillin/Streptomycin)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: For reprogramming, doxycycline induction was continued the designated day.

tag: ^sample

value: 4F2A iNSC D14 #2

tag: cell line

value: 4F2A MEF

tag: treatment

value: iNSC rep.


title: RBG18872_Young_MSC-L_007


title: GK4_C

source_name: GEJ TP53/CDKN2A KO organoid 4


title: Control-3

country: United Kingdom

tag: cell type

value: WT


title: GK3

source_name: GEJ TP53/CDKN2A KO organoid 3


title: ABZM00502: DNMT3A_6.7 [MARS_scRNA]

city: Rehovot

first: Amos

last: Tanay

address: Herzl

country: Israel

institute: Weizmann Institute of Science

data_processing:
Read-1 files were mapped to the mm9 genome assembly using Bowtie2 (default parameters)
Demultiplexing and UMI counting were based on 8bp of UMI and 7bp of cell-barcodes in Read-2, and performed using the pipeline described in Jaitin et al. 2014

source_name: Cell Bank Riken BioResource Research Center)

growth_protocol: Mouse embryonic stem cells (mESCs) were maintained under standard conditions. Cells were fed with fresh medium every day and were split every 2 days.

extract_protocol:
RNA capture for scRNA MARSseq: single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 2nM poly-dT barcodes,  0.1%triton and RNAse inhibitors.
cDNA MARS-seq library preparation: scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014. For bulk MARS-seq, only differences were were using set of 348 barcoded oligos, which allowed to pool the 384 well plate into VBLOCK KIT reservoir by centrifuge, later in the process. The step of klenow heat inactivation was removed. The volumes of the first RT and Exonuclease I reaction mix were scaled down to 1 and 0.5 μl respectively. Each reaction mix was dispensed by MANTISR (FORMULATRIX).

treatment_protocol: For the epigenetic reset, mESC were cultured in Neurobasal and DMEM-F12 (WITHOUT HEPES) medium (1:1), supplemented with N2B27, 20 ng/ml recombinant human LIF and 2i for two to three passages. Embryoid bodies were established in 25 μl hanging drops on a cover of low-adherent bacterial culture dish, allowing 500 cells/drop to aggregate for 48 hours. After two days 48-56 EBs were pooled into 10 cm low adherent bacterial culture dish.

tag: cell line/mouse line

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

tag: batch index

value: TTTC


title: GK4


title: GN2_B

source_name: GEJ organoid 2

value: Control


title: GN3

source_name: GEJ organoid 3


title: C4-2B MDVR cells, PTUPB 20 μM

city: Sacramento

first: Chengfei

last: Liu

state: CA

address: 4645 2nd Ave Research III building, suite2300

country: USA

institute: University of California, Davis

data_processing:
Data analysis was performed using a Top Hat-Cufflinks pipeline and sequence read mapping/alignment using HISAT
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: C4-2B MDVR

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
An mRNA-Seq paired-end library was prepared using Illumina NovaSeq 6000:2 × 150 cycles/bases (150bp, PE).

value: C4-2B MDVR

value: Prostate cancer cell line

value: 2 days

value: PTUPB 20 uM


title: 4F2A_N12-2

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day12

source_name: 4F2A MEF_iNSC rep day12, replicate 2

value: 4F2A iNSC D12 #2


title: ABZM00503: DNMT3A_7.5 [MARS_scRNA]

value: GGTA


title: RBG18870_Young_MSC-L_005

value: mesenchymal and endothelial cells


title: 4F2A_iNSC

description: Gene expression of iNSCs

source_name: 4F2A MEF_iNSC

value: 4F2A iNSC

value: After rep.


title: GN4

source_name: GEJ organoid 4


title: C4-2B MDVR cells, PTUPB 10 μM

value: PTUPB 10 uM


title: RBG18868_Young_MSC-L_003

value: MSC-L

value: Young


title: RBG18845_Old_MSC-S_019

value: MSC-S

value: Old


title: ABZM00501: DNMT3A_5.7 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: GCGC


title: RBG18867_Young_MSC-L_002


title: GK4_B

value: TP53/CDKN2A KO


title: GK1_A


title: ABZM00504: DNMT3A_7.6 [MARS_scRNA]

value: TCCG


title: ABZM00500: DNMT3A_4.10 [MARS_scRNA]

value: AAAC


title: GN4_A

value: Control


title: ABZM00495: DKO_6.8 [MARS_scRNA]

source_name: Dr. Masaki Okano

value: ATCA


title: GN1_A

source_name: GEJ organoid 1


title: C4-2B MDVR cells, PTUPB 10 μM plus enzalutamide

value: C4-2B MDVR

value: Prostate cancer cell line

value: 2 days

value: PTUPB 10 uM plus enzalutamide


title: RBG18844_Old_MSC-S_018

value: mesenchymal and endothelial cells


title: GN2_A


title: C4-2B MDVR cells, enzalutamide 20 μM

value: enzalutamide 20 uM


title: C4-2B MDVR cells, PTUPB 20 μM plus enzalutamide

value: PTUPB 20 uM plus enzalutamide


title: ABZM00493: DKO_2.1 [MARS_scRNA]

value: ACAG


title: 4F2A_N10-1

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day10

source_name: 4F2A MEF_iNSC rep day10, replicate 1

value: 4F2A iNSC D10 #1

value: 4F2A MEF

value: iNSC rep.


title: RBG18843_Old_MSC-S_017

value: MSC-S

value: Old


title: C4-2B MDVR cells, Control

value: DMSO


title: GN3_A


title: 4F2A_N10-2

source_name: 4F2A MEF_iNSC rep day10, replicate 2

value: 4F2A iNSC D10 #2


title: ABZM00492: DKO_1.2 [MARS_scRNA]

value: TTGG


title: RBG18842_Old_MSC-S_016


title: RBG18866_Young_MSC-L_001

value: MSC-L

value: Young


title: Wet AMD Patient 2_SP2

city: Singapore

first: Christine

last: Cheung

address: 59 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was also processed by NovogeneAIT Genomics (Singapore) using CellRanger (10x Genomics) with reads mapped to the human genome assembly (GRCh38).
Assembly: GRCh38
Supplementary files format and content: Filtered feature-barcode matrices containing detected cellular barcodes
Supplementary files format and content: Feature.tsv and barcode.tsv files containing corresponding row and column indices for respenctive data matrix

molecule: polyA RNA

source_name: Blood outgrowth endothelial cells

growth_protocol: BOECs were generated as per described by Ormiston, M. L. et al. (2015) with modifications. 1 volume of peripheral blood samples (5 – 9 mL per participant) was diluted with 1 volume of phosphate-buffered saline (PBS) and the buffy coat layer was separated via density gradient centrifugation with Ficoll® Paque (GE Healthcare). The buffy coat, which was enriched with peripheral blood mononuclear cells (PBMCs), was carefully collected, washed with PBS, resuspended in heparin-free, EGM-2 medium (Lonza) supplemented with 16% defined foetal bovine serum (FBS; Hyclone) and counted. Plasma was also collected and stored at -80°C. Subsequently, the PBMCs were seeded into collagen I-coated well(s) according to a cell density of ≥1.5 × 10 6 cells/cm 2 . Medium was replaced every two to three days. Outgrowth endothelial colonies should emerge visually between seven to 14 days after seeding. The cells were expanded to the third passage before any applications were performed, including phenotyping and functional evaluation, to opt out unwanted leukocytes. After the third passage, BOECs were cultured on collagen-I-coated tissue culture dishes in heparin-free, EGM-2 with 10% heat-inactivated FBS and medium was replaced every two to three days.

extract_protocol:
After 24h of sprouting assay, the BOECs embedded in fibrin gels were dissociated, resuspended, counted and resuspended appropriately for loading onto 10X Genomics Chromium Controller chip by facility personnel at Single-cell Omics Centre (SCOC), Genome Institute Singapore (GIS).
Each BOEC cell line was prepared as a separate scRNA-seq library using Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) by SCOC GIS and the final ready-to-sequence libraries were handed over with quantification and quality assessment reports from Bioanalyzer Agilent 2100 using the High Sensitivity DNA chip (Agilent Genomics). Individual libraries were pooled equimolarly and sent for sequencing by NovogeneAIT Genomics (Singapore).

treatment_protocol: To subject BOECs to a sprouting context, a fibrin gel bead sprouting assay was performed as per described (100) with modifications. BOECs were coated onto Cytodex 3 microcarrier beads (Sigma-Aldrich) at 150 cells per bead with agitation for 4 hours and allowed to adhere to the beads overnight. Coated beads were subsequently suspended in  2 mg/ml fibrinogen solution (Sigma-Aldrich) at a concentration of 500 beads/mL and clotted with 0.625 U/ml thrombin (Sigma-Aldrich). Heparin-free EGM-2 with 10% FBS (Gibco) was added to the clotted gels containing the cell-coated beads, and cells were incubated overnight at 37°C and 5% CO 2 for 24h to allow sprout formation.

value: Blood outgrowth endothelial cells

tag: disease

value: Wet AMD

value: Fibrin gel sprouting assay 24h


title: ABZM00494: DKO_2.2 [MARS_scRNA]

value: CTAC


title: Wet AMD Patient 2_SP1


title: Wet AMD Patient 1_SP2


title: RBG18841_Old_MSC-S_015

source_name: endosteum and central marrow

value: mesenchymal and endothelial cells


title: GN1_B

value: Control


title: ABZM00490: DKO_0.3 [MARS_scRNA]

value: AGTC


title: RBG18840_Old_MSC-S_014


title: Wet AMD Patient 1_SP1


title: 4F2A_N8-1

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day8

source_name: 4F2A MEF_iNSC rep day8, replicate 1

value: 4F2A iNSC D8 #1


title: 4F2A_N14-1

source_name: 4F2A MEF_iNSC rep day14, replicate 1

value: 4F2A iNSC D14 #1

value: 4F2A MEF


title: ABZM00489: DNMT3A_7_g.3 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: ATGC


title: Healthy Donor 1_SP2

value: Healthy


title: RBG18839_Old_MSC-S_013

value: MSC-S

value: Old


title: ABZM00491: DKO_1.1 [MARS_scRNA]

value: CATG


title: 4F2A_N6-2

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day6

source_name: 4F2A MEF_iNSC rep day6, replicate 2

value: 4F2A iNSC D6 #2

value: iNSC rep.


title: ABZM00488: DNMT3A_7_g.2 [MARS_scRNA]

value: CTCG


title: Healthy Donor 1_SP1

value: Blood outgrowth endothelial cells

value: Fibrin gel sprouting assay 24h


title: RBG18838_Old_MSC-S_012

value: mesenchymal and endothelial cells


title: PR_RUX_PTX_2

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Briefly, fastq files were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out. The gene-level counts from all studies were then normalized using TMM with edgeR  (Robinson et al., 2010). Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)] were used for analysis.
Assembly: hg19
Supplementary files format and content: csv file of log2(CPM+1) table

growth_protocol: For RNA-seq, cells were seeded in 6 wells at 3x10^4 cells/well for SUM190 and treatments added after 24hrs

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit
RNA-seq libraries were prepared using Roche Kapa mRNA hyper preperation kit

treatment_protocol: Treatments were added after 24hrs and incubated for 72hrs

value: 15nM Ruxolitinib 6.5nM Paclitaxel


title: 4F2A_N6-1

source_name: 4F2A MEF_iNSC rep day6, replicate 1

value: 4F2A iNSC D6 #1


title: 4F2A_N8-2

source_name: 4F2A MEF_iNSC rep day8, replicate 2

value: 4F2A iNSC D8 #2


title: ABZM00487: DNMT3A_7_g.1 [MARS_scRNA]

source_name: Cell Bank Riken BioResource Research Center)

value: GGAC


title: RBG18837_Old_MSC-S_011


title: RBG18836_Old_MSC-S_010


title: ABZM00486: DNMT3A_6.6 [MARS_scRNA]

value: GTCC


title: PR_RUX_PTX_1


title: ABZM00485: DNMT3A_6.5 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: GATC


title: PR_RUX_2

value: 15uM Ruxolitinib


title: ABZM00484: DNMT3A_6.4 [MARS_scRNA]

value: GCAT


title: PR_RUX_1


title: RBG18834_Old_MSC-S_008

value: MSC-S

value: Old


title: ABZM00483: DNMT3A_5.6 [MARS_scRNA]

value: CGGT


title: PR_PTX_High_2

value: 10nM Paclitaxel


title: 4F2A_N2-2

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day2

source_name: 4F2A MEF_iNSC rep day2, replicate 2

value: 4F2A iNSC D2 #2

value: 4F2A MEF

value: iNSC rep.


title: RBG18833_Old_MSC-S_007

value: mesenchymal and endothelial cells


title: 4F2A_N2-1

source_name: 4F2A MEF_iNSC rep day2, replicate 1

value: 4F2A iNSC D2 #1


title: Control-2

source_name: Bacteria

value: Bacteria

value: WT

value: Control (25C)

value: 4 hrs


title: 4F2A_iPSC-1

description: Gene expression of iPSCs

source_name: 4F2A MEF_iPSC, replicate 1

value: 4F2A iPSC-1

value: After rep.


title: 4F2A_iPSC-2

description: Gene expression of iPSCs

source_name: 4F2A MEF_iPSC, replicate 2

value: 4F2A iPSC-2


title: 4F2A_N4-1

description: Gene expression of 4F2A MEFs after reprogramming to iNSCs, day4

source_name: 4F2A MEF_iNSC rep day4, replicate 1

value: 4F2A iNSC D4 #1


title: RBG18832_Old_MSC-S_006

value: MSC-S


title: PR_PTX_High_1


title: ABZM00481: DNMT3A_5.4 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: AAGT


title: RBG18831_Old_MSC-S_005

value: Old


title: ABZM00482: DNMT3A_5.5 [MARS_scRNA]

value: TAGA


title: 4F2A_P16-2

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day16

source_name: 4F2A MEF_iPSC rep day16, replicate 2

value: 4F2A MEF

value: iPSC rep.


title: PR_PTX_Low_1

value: 6.5nM Paclitaxel


title: 4F2A_N4-2

source_name: 4F2A MEF_iNSC rep day4, replicate 2

value: 4F2A iNSC D4 #2

value: iNSC rep.


title: PR_PTX_Low_2


title: RBG18830_Old_MSC-S_004

value: mesenchymal and endothelial cells


title: ABZM00480: DNMT3A_4.9 [MARS_scRNA]

value: GCTG


title: RBG18829_Old_MSC-S_003


title: ABZM00479: DNMT3A_4.8 [MARS_scRNA]

value: AGCT


title: PR_DMSO_2

value: DMSO


title: RBG18828_Old_MSC-S_002


title: ABZM00478: DNMT3A_4.7 [MARS_scRNA]

value: GCCA


title: RBG18827_Old_MSC-S_001


title: PR_DMSO_1


title: 4F2A_N12-1

source_name: 4F2A MEF_iNSC rep day12, replicate 1

value: 4F2A iNSC D12 #1


title: 4F2A_P16-1

source_name: 4F2A MEF_iPSC rep day16, replicate 1


title: ABZM00475: DKO_7_g.3 [MARS_scRNA]

source_name: Dr. Masaki Okano

value: CGAG


title: DR_Dox_High_2

value: 1uM Doxorubicin


title: 4F2A_P14-1

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day14

source_name: 4F2A MEF_iPSC rep day14, replicate 1


title: 4F2A_P12-2

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day12

source_name: 4F2A MEF_iPSC rep day12, replicate 2


title: 4F2A_P14-2

source_name: 4F2A MEF_iPSC rep day14, replicate 2


title: ABZM00474: DKO_7_g.2 [MARS_scRNA]

value: CTGA


title: ABZM00473: DKO_7_g.1 [MARS_scRNA]

value: AGGG


title: RBG18824_Old_AEC_019

source_name: endosteum and central marrow

value: AEC

value: Old


title: RBG18823_Old_AEC_018


title: ABZM00472: DKO_6.7 [MARS_scRNA]

value: TCCG


title: DR_Dox_Low_1

value: 350nM Doxorubicin


title: DR_Dox_Low_2


title: RBG18822_Old_AEC_017


title: ABZM00471: DKO_6.6 [MARS_scRNA]

value: GGTA


title: RBG18825_Old_AEC_020


title: DR_DMSO_2


title: ABZM00470: DKO_6.5 [MARS_scRNA]

value: TTTC


title: DR_DMSO_1


title: RBG18821_Old_AEC_016


title: DR_Dox_High_1


title: RBG18820_Old_AEC_015


title: RBG18819_Old_AEC_014


title: Par_RUX_PTX_2

value: 15nM Ruxolitinib 2.5nM Paclitaxel


title: ABZM00469: DKO_6.4 [MARS_scRNA]

value: GCGC


title: ABZM00468: DKO_5.7 [MARS_scRNA]

value: AAAC


title: ABZM00467: DKO_5.6 [MARS_scRNA]

value: CGCC


title: Par_RUX_2

value: 15uM Ruxolitinib


title: RBG18818_Old_AEC_013

value: mesenchymal and endothelial cells


title: Par_RUX_PTX_1


title: RBG18816_Old_AEC_011


title: Par_Dox_High_2


title: ABZM00466: DKO_5.5 [MARS_scRNA]

value: ACTT


title: RBG18815_Old_AEC_010


title: 4F2A_P6-1

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day6

source_name: 4F2A MEF_iPSC rep day6, replicate 1

value: 4F2A MEF

value: iPSC rep.


title: 4F2A_P10-1

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day10

source_name: 4F2A MEF_iPSC rep day10, replicate 1


title: Par_RUX_1


title: 4F2A_P10-2

source_name: 4F2A MEF_iPSC rep day10, replicate 2


title: 4F2A_P6-2

source_name: 4F2A MEF_iPSC rep day6, replicate 2


title: ABZM00465: DKO_5.4 [MARS_scRNA]

value: TCTA


title: 4F2A_P12-1

source_name: 4F2A MEF_iPSC rep day12, replicate 1


title: 4F2A_P8-1

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day8

source_name: 4F2A MEF_iPSC rep day8, replicate 1


title: 4F2A_P2-1

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day2

source_name: 4F2A MEF_iPSC rep day2, replicate 1


title: 4F2A_P8-2

source_name: 4F2A MEF_iPSC rep day8, replicate 2


title: ABZM00463: DKO_4.6 [MARS_scRNA]

value: ATCA


title: 4F2A_P4-2

description: Gene expression of 4F2A MEFs after reprogramming to iPSCs, day4

source_name: 4F2A MEF_iPSC rep day4, replicate 2


title: 4F2A_P4-1

source_name: 4F2A MEF_iPSC rep day4, replicate 1


title: RBG18814_Old_AEC_009

value: AEC


title: Par_Dox_Low_2

value: 65nM Doxorubicin


title: RBG18817_Old_AEC_012

value: Old


title: ABZM00464: DKO_4.7 [MARS_scRNA]

value: TGAT


title: Par_Dox_High_1

value: 1uM Doxorubicin


title: 4F2A MEF-2

description: Gene expression of 4F2A MEFs before reprogramming

source_name: 4F2A MEF, replicate 2

value: Before rep.


title: 4F2A_P2-2

source_name: 4F2A MEF_iPSC rep day2, replicate 2


title: ABZM00462: DKO_4.5 [MARS_scRNA]

source_name: Dr. Masaki Okano

value: CTAC


title: RBG18813_Old_AEC_008


title: 4F2A MEF-3

source_name: 4F2A MEF, replicate 3


title: Par_Dox_Low_1


title: ABZM00461: DKO_4.4 [MARS_scRNA]

value: ACAG


title: RBG18812_Old_AEC_007


title: 4F2A MEF-1

source_name: 4F2A MEF, replicate 1


title: ABZM00460: DKO_3.3 [MARS_scRNA]

value: TTGG


title: RBG18811_Old_AEC_006


title: 2'MEF_P'12

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day12 (LIF D5-12)

source_name: 2'MEF_iPSC rep. (LIF D5-12) day12


title: Par_PTX_High_2

value: 10nM Paclitaxel


title: ABZM00459: DKO_3.2 [MARS_scRNA]

value: CATG


title: Par_PTX_High_1


title: Par_PTX_Low_2

value: 2.5nM Paclitaxel


title: ABZM00458: DKO_3.1 [MARS_scRNA]

value: AGTC


title: Par_PTX_Low_1


title: RBG18809_Old_AEC_004

source_name: endosteum and central marrow

value: mesenchymal and endothelial cells


title: RBG18810_Old_AEC_005


title: RBG18808_Old_AEC_003


title: ABZM00457: DKO_0.2 [MARS_scRNA]

value: TAAG


title: Par_DMSO_2

value: DMSO


title: RBG18807_Old_AEC_002


title: ABZM00456: DKO_0.1 [MARS_scRNA]

value: GTAG


title: Par_DMSO_1


title: 2'MEF_P12

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day12 (LIF D0-12)

source_name: 2'MEF_iPSC rep. (LIF D0-12) day12

value: iPSC rep.


title: Primary TNBC, patient 24, section 2

city: Los Angeles

first: John

last: Carpten

address: 1450 Biggy St

institute: University of Southern California

description: 10x Genomics spatial transcriptomics data

data_processing:
Raw sequencing data was processed through the spaceranger mkfastq pipeline, version 1.1.0 (10x Genomics), to create FASTQ files.
FASTQ files were processed through the spaceranger count pipeline, version 1.1.0 (10x Genomics), for demultiplexing, genome alignment, UMI counting, and spatial alignment.
Assembly: GRCh38
Supplementary files format and content: .h5 file contains matrix of raw expresssion data (UMI counts) per tissue-associated barcode for use in R or Python analysis
Supplementary files format and content: .json file contains scale factors relating pixels in tissue_hires_image.png to original full resolution tissue image
Supplementary files format and content: .png file contains downsampled tissue image
Supplementary files format and content: .csv file contains spatial cordinates for tissue barcodes
Supplementary files format and content: .cloupe file provides a user friendly interface for data exploration when opened with Loupe Browser (10x Genomics)
Library strategy: spatial transcriptomics (10x Genomics)

source_name: TNBC tumor tissue

extract_protocol:
Fresh tissue was snap frozen in liquid nitrogen, then embedded in O.C.T. compound for cryosectioning. Two sections were obtained per patient sample and were mounted on 10x Genomics Visium Gene Expression slides.
Libraries were constructed according to the 10x Genomics Spatial Gene Expression protocol. Briefly, tissues on slides were permeabilized to allow RNA to bind to oligonucleotides on the slide surface via polyA capture. cDNA was synthesized on-slide from immobilized RNA, then collected and used to generate sequencing libraries containing unique sample indices, as well as P5 and P7 primers for Illumina-compatible sequencing

tag: tissue

value: TNBC tumor tissue


title: RBG18806_Old_AEC_001

value: AEC

value: Old


title: 2'MEF_N12

description: Gene expression of 2'MEFs after reprogramming to iNSCs, day12

source_name: 2'MEF_iNSC rep. day12

value: iNSC rep.


title: 2'MEF_D12

description: Gene expression of 2'MEFs after reprogramming to iDPs, day12

source_name: 2'MEF_iDP rep. day12

value: iDP rep.


title: 2'MEF_P'10

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day10 (LIF D5-12)

source_name: 2'MEF_iPSC rep. (LIF D5-12) day10


title: Primary TNBC, patient 24, section 1


title: RBG18805_Young_MSC-S_020

value: MSC-S

value: Young


title: RBG18804_Young_MSC-S_019


title: Primary TNBC, patient 23, section 2


title: ABZM00453: DKO_6.1 [MARS_scRNA]

value: AGGG


title: RBG18803_Young_MSC-S_018


title: 2'MEF_P10

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day10 (LIF D0-12)

source_name: 2'MEF_iPSC rep. (LIF D0-12) day10


title: ABZM00451: DKO_5.2 [MARS_scRNA]

value: GGTA


title: ABZM00452: DKO_5.3 [MARS_scRNA]

value: TCCG


title: Primary TNBC, patient 23, section 1


title: RBG18835_Old_MSC-S_009


title: ABZM00455: DKO_6.3 [MARS_scRNA]

value: CGAG


title: Primary TNBC, patient 22, section 2


title: Primary TNBC, patient 22, section 1


title: RBG18802_Young_MSC-S_017


title: 2'MEF_P'8

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day8 (LIF D5-12)

source_name: 2'MEF_iPSC rep. (LIF D5-12) day8


title: RBG18800_Young_MSC-S_015


title: ABZM00450: DKO_5.1 [MARS_scRNA]

value: TTTC


title: 2'MEF_N10

description: Gene expression of 2'MEFs after reprogramming to iNSCs, day10

source_name: 2'MEF_iNSC rep. day10


title: 2'MEF_D10

description: Gene expression of 2'MEFs after reprogramming to iDPs, day10

source_name: 2'MEF_iDP rep. day10


title: Primary TNBC, patient 21, section 2


title: 2'MEF_N8

description: Gene expression of 2'MEFs after reprogramming to iNSCs, day8

source_name: 2'MEF_iNSC rep. day8


title: 2'MEF_D8

description: Gene expression of 2'MEFs after reprogramming to iDPs, day8

source_name: 2'MEF_iDP rep. day8


title: ABZM00448: DKO_4.2 [MARS_scRNA]

value: AAAC


title: RBG18799_Young_MSC-S_014

value: mesenchymal and endothelial cells


title: ABZM00447: DKO_4.1 [MARS_scRNA]

value: CGCC


title: 2'MEF_P8

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day8 (LIF D0-12)

source_name: 2'MEF_iPSC rep. (LIF D0-12) day8


title: Primary TNBC, patient 20, section 2


title: RBG18801_Young_MSC-S_016


title: ABZM00446: DNMT3A_6.3 [MARS_scRNA]

source_name: Cell Bank Riken BioResource Research Center)

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: ACTT


title: Primary TNBC, patient 20, section 1

value: TNBC tumor tissue


title: 2'MEF_P'6

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day6 (LIF D5-12)

source_name: 2'MEF_iPSC rep. (LIF D5-12) day6

value: iPSC rep.


title: RBG18797_Young_MSC-S_012


title: ABZM00445: DNMT3A_6.2 [MARS_scRNA]

value: TCTA


title: ABZM00449: DKO_4.3 [MARS_scRNA]

source_name: Dr. Masaki Okano

value: GCGC


title: RBG18796_Young_MSC-S_011


title: 2'MEF_N6

description: Gene expression of 2'MEFs after reprogramming to iNSCs, day6

source_name: 2'MEF_iNSC rep. day6

value: iNSC rep.


title: RBG18795_Young_MSC-S_010

source_name: endosteum and central marrow

value: MSC-S


title: ABZM00444: DNMT3A_6.1 [MARS_scRNA]

value: TGAT


title: 2'MEF_P4

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day4

source_name: 2'MEF_iPSC rep. day4


title: ABZM00443: DNMT3A_5.3 [MARS_scRNA]

value: ATCA


title: 2'MEF_D6

description: Gene expression of 2'MEFs after reprogramming to iDPs, day6

source_name: 2'MEF_iDP rep. day6

value: iDP rep.


title: 2'MEF_P6

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day6 (LIF D0-12)

source_name: 2'MEF_iPSC rep. (LIF D0-12) day6


title: Primary TNBC, patient 21, section 1

source_name: TNBC tumor tissue


title: RBG18798_Young_MSC-S_013

value: Young


title: Primary TNBC, patient 18, section 2


title: 2'MEF_C4

description: Gene expression of 2'MEFs after dox induction without LIF, day4

source_name: 2'MEF_Common re. day4

value: PDR


title: RBG18794_Young_MSC-S_009


title: Primary TNBC, patient 18, section 1

description: 10x Genomics spatial transcriptomics data


title: ABZM00442: DNMT3A_5.2 [MARS_scRNA]

value: CTAC


title: RBG18793_Young_MSC-S_008


title: RBG18792_Young_MSC-S_007


title: ABZM00441: DNMT3A_5.1 [MARS_scRNA]

value: ACAG


title: 2'MEF_C2

description: Gene expression of 2'MEFs after dox induction without LIF, day2

source_name: 2'MEF_Common rep. day2


title: RBG18791_Young_MSC-S_006

value: mesenchymal and endothelial cells


title: Primary TNBC, patient 17, section 1


title: Primary TNBC, patient 19, section 1


title: ABZM00440: DNMT3A_4.6 [MARS_scRNA]

value: TTGG


title: Primary TNBC, patient 8, section 2


title: 2'MEF_P2

description: Gene expression of 2'MEFs after reprogramming to iPSCs, day2

source_name: 2'MEF_iPSC rep. day2


title: whole_blood_TTM050_CPC5

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

data_processing:
After trimming the adapters, quality control of the RNA-seq data was performed using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the human reference genome (GRCh38) using STAR with default set-up
We used DCC with default set-up for circRNA identification.
We used featureCounts function from Rsubread package to obtain the counts of linear RNAs from GENCODE and LNCipedia database
We DESeq2 to identify differentially expressed linear RNAs and circRNAs
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files include raw counts of each linear RNA and circRNA

source_name: whole blood

extract_protocol:
RNA extraction and library preparation were performed from PAXgeneTM Blood RNA tubes
A strand-specific RNA-Seq library was prepared using the Ovation Human Blood RNA-Seq Library Systems (NuGEN Technologies, San Carlos, USA) from the human whole blood samples

tag: outcome

tag: subject status

value: cardiac arrest patient

value: whole blood


title: whole_blood_TTM049_CPC5


title: NG1 iPSC

description: Gene expression of NGFP1 iPSCs

source_name: 2'MEF_NGFP1 iPSCs

value: After rep.


title: RBG18790_Young_MSC-S_005


title: ABZM00439: DNMT3A_4.5 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: CATG


title: Primary TNBC, patient 8, section 1

value: TNBC tumor tissue


title: whole_blood_TTM048_CPC5


title: RBG18789_Young_MSC-S_004


title: Primary TNBC, patient 7, section 2


title: RBG18788_Young_MSC-S_003


title: whole_blood_TTM047_CPC5


title: ABZM00438: DNMT3A_4.4 [MARS_scRNA]

value: AGTC


title: Primary TNBC, patient 7, section 1


title: Primary TNBC, patient 17, section 2


title: ABZM00425: TKO_7.6 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: GCGC


title: ABZM00424: TKO_7.5 [MARS_scRNA]

value: AAAC


title: 2'MEF

description: Gene expression of 2'MEFs before reprogramming

value: Before rep.


title: Primary TNBC, patient 6, section 2


title: whole_blood_TTM045_CPC5


title: Primary TNBC, patient 6, section 1


title: ABZM00422: DNMT3B_7.5 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: ACTT


title: whole_blood_TTM043_CPC5


title: ABZM00423: DNMT3B_7.6 [MARS_scRNA]

value: CGCC


title: ABZM00421: DNMT3A_7.4 [MARS_scRNA]

value: TCTA


title: whole_blood_TTM042_CPC5


title: RBG18786_Young_MSC-S_001

value: mesenchymal and endothelial cells

value: MSC-S

value: Young


title: Primary TNBC, patient 5, section 2


title: RBG18785_Young_AEC_020

value: AEC


title: ABZM00420: DNMT3A_7.3 [MARS_scRNA]

value: TGAT


title: whole_blood_TTM040_CPC5

value: cardiac arrest patient

value: whole blood


title: Primary TNBC, patient 4, section 2

value: TNBC tumor tissue


title: ABZM00419: DNMT3A_7.2 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: ATCA


title: whole_blood_TTM039_CPC5


title: RBG18782_Young_AEC_017


title: Primary TNBC, patient 4, section 1


title: RBG18783_Young_AEC_018


title: whole_blood_TTM038_CPC5


title: RBG18787_Young_MSC-S_002


title: RBG18781_Young_AEC_016


title: Primary TNBC, patient 3, section 2


title: ABZM00415: J1_WT_7.2 [MARS_scRNA]

source_name: J1 (SCRC1010, ATCC)

value: J1 (SCRC1010, ATCC)

value: CATG


title: ABZM00418: DNMT3A_7.1 [MARS_scRNA]

value: CTAC


title: whole_blood_TTM044_CPC5


title: whole_blood_TTM037_CPC5


title: RBG18784_Young_AEC_019


title: ABZM00414: J1_WT_7.1 [MARS_scRNA]

value: AGTC


title: RBG18780_Young_AEC_015


title: RBG18779_Young_AEC_014


title: whole_blood_TTM036_CPC5


title: Primary TNBC, patient 2, section 1


title: Primary TNBC, patient 2, section 2


title: whole_blood_TTM035_CPC5


title: Primary TNBC, patient 5, section 1


title: ABZM00413: TKO_4.3 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: ATGC


title: whole_blood_TTM033_CPC5


title: RBG18776_Young_AEC_011


title: RBG18778_Young_AEC_013


title: Primary TNBC, patient 3, section 1


title: RBG18777_Young_AEC_012


title: RBG18775_Young_AEC_010


title: Primary TNBC, patient 15, section 1


title: ABZM00411: TKO_4.1 [MARS_scRNA]

value: GGAC


title: Primary TNBC, patient 1, section 2


title: Primary TNBC, patient 15, section 2


title: Primary TNBC, patient 1, section 1


title: whole_blood_TTM031_CPC5


title: ABZM00409: DNMT3B_4.2 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: GATC


title: ABZM00408: DNMT3B_4.1 [MARS_scRNA]

value: GCAT


title: whole_blood_TTM034_CPC5


title: RBG18774_Young_AEC_009

value: mesenchymal and endothelial cells

value: AEC

value: Young


title: whole_blood_TTM030_CPC5

value: cardiac arrest patient

value: whole blood


title: ABZM00407: DNMT3A_4.3 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: CGGT


title: ABZM00412: TKO_4.2 [MARS_scRNA]

value: CTCG


title: Primary TNBC, patient 14, section 2

value: TNBC tumor tissue


title: whole_blood_TTM028_CPC5


title: RBG18773_Young_AEC_008


title: Primary TNBC, patient 14, section 1


title: whole_blood_TTM032_CPC5


title: ABZM00406: DNMT3A_4.2 [MARS_scRNA]

value: TAGA


title: whole_blood_TTM029_CPC5


title: RBG18772_Young_AEC_007


title: RBG18771_Young_AEC_006


title: ABZM00410: DNMT3B_4.3 [MARS_scRNA]

value: GTCC


title: Primary TNBC, patient 13, section 2


title: Primary TNBC, patient 13, section 1


title: whole_blood_TTM027_CPC5


title: whole_blood_TTM026_CPC5


title: Primary TNBC, patient 12, section 2


title: ABZM00404: DNMT3A_0.2 [MARS_scRNA]

value: GCTG


title: RBG18769_Young_AEC_004


title: ABZM00403: DNMT3A_0.1 [MARS_scRNA]

value: AGCT


title: whole_blood_TTM025_CPC1


title: RBG18770_Young_AEC_005


title: whole_blood_TTM024_CPC1


title: RBG18768_Young_AEC_003


title: ABZM00454: DKO_6.2 [MARS_scRNA]

value: CTGA


title: ABZM00402: TKO_3.6 [MARS_scRNA]

value: GCCA


title: Primary TNBC, patient 11, section 2


title: whole_blood_TTM023_CPC1


title: ABZM00401: TKO_3.5 [MARS_scRNA]

value: TAAG


title: Primary TNBC, patient 12, section 1


title: RBG18767_Young_AEC_002


title: Primary TNBC, patient 11, section 1


title: RBG18765_Old_mOPr_013

value: mOPr

value: Old


title: ABZM00405: DNMT3A_4.1 [MARS_scRNA]

value: AAGT


title: Primary TNBC, patient 9, section 2


title: whole_blood_TTM021_CPC1


title: ABZM00399: DNMT3B_3.7 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: CGAG


title: RBG18764_Old_mOPr_012

value: mesenchymal and endothelial cells


title: whole_blood_TTM022_CPC1

value: cardiac arrest patient

value: whole blood


title: ABZM00400: TKO_3.4 [MARS_scRNA]

value: GTAG


title: Primary TNBC, patient 9, section 1

value: TNBC tumor tissue


title: RBG18763_Old_mOPr_011


title: whole_blood_TTM020_CPC1


title: ABZM00397: DNMT3B_3.5 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: AGGG


title: whole_blood_TTM019_CPC1


title: whole_blood_TTM018_CPC1


title: RBG18762_Old_mOPr_010


title: RBG18766_Young_AEC_001

value: AEC

value: Young


title: RBG18761_Old_mOPr_009


title: 21478

city: Christchurch

first: Anna

last: Pilbrow

address: 2 Riccarton Avenue

country: New Zealand

institute: University of Otago, Christchurch

data_processing:
The bioinformatics pipeline was designed to detect mRNAs, lncRNAs and circRNAs and generate data on putative novel lncRNA and circRNA transcripts. The pipeline is freely available to download at https://github.com/zoeward-nz/PhD.
Libraries were de-multiplexed, adapter- and quality-trimmed using Trimmomatic (Bolger et. al. Bioinformatics 2014, 30:2114-2120) and quality assessed using Fastqc tools (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Resulting reads were aligned to the human reference genome (build GRCh38) using STAR2 (Dobin et. al. Bioinformatics 2013, 29:15-21), assembled into transcripts in StringTie (Pertea et. al. Nat Biotechnol 2015, 33:290-295), quantified using Salmon software (Patro et. al. Nat Methods 2017, 14:417-419) and aggregated to the gene or transcript level using the GENCODE.v33 annotation (Soneson et. al. F1000Res 2015,4:1521).
Gene/transcript expression was compared between groups using negative binomial generalised linear models with DESeq2 (Love et. al. Genome Biol 2014, 15:550) (false discovery rate α<0.01) as previously described (Rademaker et. al. J Am Heart Assoc 2021, 10:e021312). For gene level analyses (annotated mRNA and lncRNA transcripts), only transcripts expressed at greater or equal to 1 transcript per million (TPM) in at least 90% of samples were considered to be robustly expressed and included in the analysis.
CircExplorer2 (Zhang et. al. Genome Res 2016, 26:1277-1287) was used for circRNA detection and the same detection threshold was applied to minimise detection of false-positive circRNAs (greater or equal to1 TPM in at least 90% of samples).
To detect putative novel lncRNAs, filtering was relaxed to include low abundance transcripts with a read count of greater or equal to 1 in at least 50% of samples. To minimise detection of false-positive novel lncRNAs, only multi-exonic transcripts aligning to the main chromosomes (not scaffold chromosomes) were included in the analysis.
Assembly: human reference, build GRCh38
Supplementary files format and content: Data for annotated genes (mRNAs, lncRNAs) are provided as raw TPM (not normalised for library size).

source_name: plasma

extract_protocol:
RNA extraction and clean-up from plasma was performed with Norgen Plasma/Serum RNA Purification kits (Norgen Biotek Corporation, Thorold, Canada) according to manufacturer’s instructions. This kit purifies RNA from up to 5 mL of fresh or frozen serum/plasma and concentrates high purity, cell-free circulating and exosomal RNA using a two-column method. RNA was quantified using the QubitTM adapted protocol (Li et. al. BMC Mol Biol 2015, 16:9) and stored at -80°C prior to sequencing.
RNA libraries were prepared using 8μl input total RNA and the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio, USA). All libraries were normalised, and equimolarly pooled before being paired-end sequenced on an Illumina NovaSeq 6000 S1 flowcell using v1.5 chemistry, generating ~100 million reads per sample at 2×100 bp read length. Library preparation was performed by the Otago Genomics Facility (Dunedin, New Zealand) and sequencing was performed by the Ramaciotti Centre for Genomics, Sydney, Australia.

treatment_protocol: Pateint samples were selected from the Coronary Disease Cohort Study (Prickett et. al. Clin Chem 2017, 63:316-324) and control samples were selected from the Canterbury Healthy Volunteers Study (Ellis et. al. Circ Cardiovasc Genet 2011, 4:636-646).  Plasma collected from 61 patients ~4 months after admission to hospital with an acute coronary syndrome (i.e. once the patients were stable and early left ventricular remodelling was underway), were selected for RNA-Seq analysis, along with plasma from 31 heart-healthy controls. The patient group included all patients from the Coronary Disease Cohort Study who developed de novo heart failure within 3 years of their index hosptial admission and had at least 5 mL plasma available (n=30, HF+) and a matched group of patients who remained free of HF over a median 5.0 years follow-up (n=31, HF-). HF- patients and controls (n=31) were matched to the HF+ group based nearest matching for age, sex, ethnicity, body mass index, smoking status and activity. In addition HF- patients were matched to the HF+ group based on nearest matching for heart rate, left ventricular ejection fraction, E/e’, creatinine, previous medical history (hypertension, diabetes, myocardial infarction, valve disease, peripheral vascular disease, cerebrovascular accident, pulmonary disorder, coronary artery bypass grafting, percutaneous coronary intervention), severity of disease (plasma NT-proBNP, plasma high‐Sensitivity Troponin I) and medications (beta blockers, angiotensin converting enzyme inhibitors, angiotensin-receptor blockers, statins and diuretics). Matching was performed with the MatchIt package (https://github.com/kosukeimai/MatchIt) in R.

value: plasma

value: HVOL


title: AK0294

value: HF-


title: RBG18760_Old_mOPr_008

value: mOPr


title: ABZM00395: DNMT3A_3.1 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: TTTC


title: ABZM00396: DNMT3A_3.2 [MARS_scRNA]

value: TCCG


title: whole_blood_TTM017_CPC1


title: ABZM00394: TKO_2.2 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: GCGC


title: whole_blood_TTM016_CPC1

value: cardiac arrest patient


title: 35801


title: 21445


title: 7772


title: ABZM00393: TKO_2.1 [MARS_scRNA]

value: AAAC


title: whole_blood_TTM015_CPC1

value: whole blood


title: RBG18759_Old_mOPr_007

value: mesenchymal and endothelial cells

value: Old


title: RBG18758_Old_mOPr_006


title: ABZM00398: DNMT3B_3.6 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: CTGA


title: ABZM00392: DNMT3B_2.2 [MARS_scRNA]

value: CGCC


title: whole_blood_TTM014_CPC1


title: RBG18757_Old_mOPr_005


title: 17485

value: plasma


title: 46897

value: HVOL


title: RBG18756_Old_mOPr_004


title: ABZM00391: DNMT3B_2.1 [MARS_scRNA]

value: ACTT


title: whole_blood_TTM013_CPC1


title: ABZM00390: DNMT3A_2.2 [MARS_scRNA]

value: TCTA


title: 4343


title: RBG18754_Old_mOPr_003

value: mOPr


title: whole_blood_TTM012_CPC1


title: whole_blood_TTM011_CPC1


title: ABZM00389: DNMT3A_2.1 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: TGAT


title: 42893


title: whole_blood_TTM010_CPC1


title: ABZM00388: TKO_1.2 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: ATCA


title: ABZM00387: TKO_1.1 [MARS_scRNA]

value: CTAC


title: RBG18753_Old_mOPr_002


title: 27273


title: whole_blood_TTM008_CPC1

value: cardiac arrest patient


title: 19260


title: ABZM00386: DNMT3B_1.2 [MARS_scRNA]

value: ACAG


title: whole_blood_TTM007_CPC1

value: whole blood


title: RBG18745_Old_OPr_009

value: mesenchymal and endothelial cells

value: OPr

value: Old


title: 23186


title: whole_blood_TTM009_CPC1


title: RBG18744_Old_OPr_008


title: ABZM00384: DNMT3A_1.2 [MARS_scRNA]

value: CATG


title: ABZM00385: DNMT3B_1.1 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TTGG


title: RBG18743_Old_OPr_007


title: whole_blood_TTM005_CPC1


title: 20186

value: plasma

value: HVOL


title: RBG18752_Old_mOPr_001

value: mOPr


title: 19977


title: RBG18742_Old_OPr_006


title: 29256


title: ABZM00383: DNMT3A_1.1 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: AGTC


title: ABZM00365: J1_WT_6.3 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTCG


title: whole_blood_TTM003_CPC1


title: ABZM00364: J1_WT_6.2 [MARS_scRNA]

value: GGAC


title: whole_blood_TTM004_CPC1

value: cardiac arrest patient


title: 20908


title: RBG18747_Old_OPr_010


title: 29478


title: 31108


title: RBG18738_Old_OPr_005


title: UNΔ Normal EC gRNA 4&5 H4_5Q_3

state: Singapore

address: Experimental Medicine Building 59 Nanyang Drive, Level 3

description:
UNΔ Normal EC gRNA 4&5
Subjected to CRISPR-Cas9 nucleofection but no deletion at rs6903956

data_processing:
Reads were aligned using STAR aligner v2.4.1a to human genome (hg38) with default parameters.
Raw read counts were converted to log2-counts-per-million (logCPM) and the mean-variance relationship modelled with precision weights approach with voom transformation.
For differential expression analysis, raw counts were normalized using edgeR R package v3.34.0 (Robinson et al., 2010) using a trimmed mean of M values (TMM) and differentially expressed genes were identified using limma R package v3.46.0 (Ritchie et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized (TMM) gene counts for every technical replicate.
Supplementary_files_format_and_content: Differential expressed table with various comparisons. Benjamini and Hochberg (1995) P-value adjustment method was used,

source_name: Endothelial Cells

growth_protocol: Endothelial Cells were differentiated from patient derived induced pluripotent stem cells and maintained in EGM-2 + 10% FBS

extract_protocol:
Total RNA was isolated from the iPSC-derived endothelial cells as per manufacturer’s instructions (RNeasy Micro Kit, Qiagen).
PolyA library preparation and 150 base-pair paired end sequencing was performed by Novogene sequencing facility (Singapore) using an Illumina HiSeq sequencer. The average sequencing depth was 60 million reads.

value: induced pluripotent stem cell differentiated endothelial cell


title: RBG18735_Old_OPr_003


title: whole_blood_TTM006_CPC1

value: whole blood


title: UNΔ Normal EC gRNA 4&5 H4_5Q_2


title: RBG18736_Old_OPr_004

value: mesenchymal and endothelial cells


title: 23368


title: ABZM00363: J1_WT_6.1 [MARS_scRNA]

value: GTCC


title: ABZM00343: J1_WT_4.3 [MARS_scRNA]


title: UNΔ Normal EC gRNA 4&5 H4_5Q_1


title: ABZM00342: J1_WT_4.2 [MARS_scRNA]


title: RBG18734_Old_OPr_002

value: OPr

value: Old


title: 29451


title: Δ Normal EC gRNA 4&5 H4_5F_3

description:
Δ Normal EC gRNA 4&5
Subjected to CRISPR-Cas9 nucleofection with a 63-89bp deletion at rs6903956


title: RBG18733_Old_OPr_001


title: 41593


title: ABZM00341: J1_WT_4.1 [MARS_scRNA]


title: Δ Normal EC gRNA 4&5 H4_5F_2


title: RBG18731_Young_mOPr_015

value: Young


title: ABZM00330: TKO_7.4 [MARS_scRNA]

source_name: Cell Bank Riken BioResource Research Center)

value: TKO_Cell Bank Riken BioResource Research Center

value: TGAT


title: Δ Normal EC gRNA 4&5 H4_5F_1


title: RBG18729_Young_mOPr_013


title: 20973

value: plasma

value: HVOL


title: UNΔ Normal EC gRNA 4&1 H4_1F_3

description:
UNΔ Normal EC gRNA 4&1
Subjected to CRISPR-Cas9 nucleofection but no deletion at rs6903956


title: 9049


title: RBG18730_Young_mOPr_014

value: mOPr


title: RBG18728_Young_mOPr_012


title: ABZM00329: TKO_7.3 [MARS_scRNA]

value: ATCA


title: 43956


title: ABZM00328: TKO_7.2 [MARS_scRNA]

value: CTAC


title: 34781


title: ABZM00326: TKO_5.4 [MARS_scRNA]

value: TTGG


title: UNΔ Normal EC gRNA 4&1 H4_1F_1


title: ABZM00327: TKO_7.1 [MARS_scRNA]

value: ACAG


title: RBG18727_Young_mOPr_011


title: Δ Normal EC gRNA 4&1 H4_1D_3

description:
Δ Normal EC gRNA 4&1
Subjected to CRISPR-Cas9 nucleofection with a 63-89bp deletion at rs6903956


title: 23948


title: 39901


title: ABZM00325: TKO_5.3 [MARS_scRNA]

value: CATG


title: RBG18726_Young_mOPr_010


title: RBG18725_Young_mOPr_009


title: ABZM00324: TKO_5.2 [MARS_scRNA]

value: AGTC


title: Δ Normal EC gRNA 4&1 H4_1D_2

value: induced pluripotent stem cell differentiated endothelial cell


title: 28247


title: Δ Normal EC gRNA 4&1 H4_1D_1


title: ABZM00323: TKO_5.1 [MARS_scRNA]

value: ATGC


title: RBG18724_Young_mOPr_008

value: mesenchymal and endothelial cells


title: 26770


title: RBG18723_Young_mOPr_007


title: UNΔ Normal EC gRNA 4&1 H4_1F_2


title: ABZM00322: TKO_3.3 [MARS_scRNA]

value: CTCG


title: WT Normal EC H_3

description:
WT Normal EC
No CRISPR-Cas9 nucleofection


title: ABZM00321: TKO_3.2 [MARS_scRNA]

value: GGAC


title: WT Normal EC H_2


title: RBG18722_Young_mOPr_006

value: Young


title: RBG18721_Young_mOPr_005


title: 17241


title: 20217


title: CH0289

value: HF+


title: ABZM00320: TKO_3.1 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: GTCC


title: RBG18720_Young_mOPr_004


title: WT Normal EC H_1


title: 22214

value: plasma

value: HVOL


title: ABZM00319: TKO_0.2 [MARS_scRNA]

value: GATC


title: RBG18719_Young_mOPr_003

value: mOPr


title: RBG18718_Young_mOPr_002


title: Δ CAD EC gRNA 4&5 H07_4_5F_2

description:
Δ CAD EC gRNA 4&5
Subjected to CRISPR-Cas9 nucleofection with a 63-89bp deletion at rs6903956


title: AK0383


title: Δ CAD EC gRNA 4&5 H07_4_5F_3


title: CH0311


title: ABZM00318: TKO_0.1 [MARS_scRNA]

value: GCAT


title: Δ CAD EC gRNA 4&5 H07_4_5F_1


title: RBG18717_Young_mOPr_001


title: AK0538


title: ABZM00317: TKO_0_serum.2 [MARS_scRNA]

value: CGGT


title: UNΔ CAD EC gRNA 4&2 H07_4_2BP_3

description:
UNΔ CAD EC gRNA 4&2
Subjected to CRISPR-Cas9 nucleofection but no deletion at rs6903956


title: ABZM00316: TKO_0_serum.1 [MARS_scRNA]

value: TAGA


title: RBG18714_Young_OPr_013

value: OPr


title: UNΔ CAD EC gRNA 4&2 H07_4_2BP_2

value: induced pluripotent stem cell differentiated endothelial cell


title: AK0216


title: UNΔ CAD EC gRNA 4&2 H07_4_2BP_1


title: RBG18712_Young_OPr_011


title: ABZM00300: DNMT3B_7_g.1 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: CTGA


title: ABZM00301: DNMT3B_7_g.2 [MARS_scRNA]

value: CGAG


title: AK0469


title: Δ CAD EC gRNA 4&2 H07_4_2BM_3

description:
Δ CAD EC gRNA 4&2
Subjected to CRISPR-Cas9 nucleofection with a 63-89bp deletion at rs6903956


title: ABZM00299: DNMT3B_7.4 [MARS_scRNA]

value: AGGG


title: RBG18711_Young_OPr_010

value: mesenchymal and endothelial cells

value: Young


title: ABZM00298: DNMT3B_7.3 [MARS_scRNA]

value: TCCG


title: CH0009

value: HF+


title: Δ CAD EC gRNA 4&2 H07_4_2BM_2


title: RBG18710_Young_OPr_009


title: ABZM00297: DNMT3B_7.2 [MARS_scRNA]

value: GGTA


title: Δ CAD EC gRNA 4&2 H07_4_2BM_1


title: WT CAD EC H07_3

description:
WT CAD EC
No CRISPR-Cas9 nucleofection


title: CH0418

value: plasma


title: RBG18705_Young_OPr_006


title: ABZM00295: DNMT3B_5.4 [MARS_scRNA]

value: GCGC


title: WT CAD EC H07_2

description:
WT CAD EC
No CRISPR-Cas9 nucleofection


title: AK0399


title: RBG18709_Young_OPr_008


title: RBG18713_Young_OPr_012


title: WT CAD EC H07_1

description:
WT CAD EC
No CRISPR-Cas9 nucleofection


title: ABZM00294: DNMT3B_5.3 [MARS_scRNA]

value: AAAC


title: AK0274


title: CH0138


title: ABZM00293: DNMT3B_5.2 [MARS_scRNA]

value: CGCC


title: RBG18702_Young_OPr_004


title: AK0549


title: U87 cells, shY1_rep1

first: Wei

middle: Kang

state: Shanghai

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences

institute: Chinese Academy of Sciences

description:
shY1_rep1
RNA-seq

data_processing:
We used trimmomatic(v0.39) to remove Illumina adapter and low quality sequence(setting: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Trimmed reads were mapped to hg38 genome using hisat2( v2.2.1) with default papameter.
Reads were counted for each gene by htseq-count, and differential expression was performed with the R package edgeR (v3.28.1).
Genes with low counts were filtered by keeping only genes with rowSums(cpm(y) > 1) > = (number of samples per group), and the logCPM from edgeR was converted to RPKM using the formula RPKM = 2^(logCPM-log2(gene length in kb).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

growth_protocol: U87 cells were maintained in Dulbecco’s Modified Eagle’s medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNAs were isolated using TRIzol (Invitrogen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: human Glioblastoma cell line

value: YB-1 KD


title: AK0589


title: RBG18707_Young_OPr_007

value: OPr


title: ABZM00296: DNMT3B_7.1 [MARS_scRNA]

value: TTTC


title: CH0089


title: RBG18700_Young_OPr_003


title: U87 cells, shLuc_rep2

description:
shLuc_rep2
RNA-seq

value: control KD


title: U87 cells, shLuc_rep1

description:
shLuc_rep1
RNA-seq


title: RBG18698_Young_OPr_002


title: ABZM00291: DNMT3B_3.4 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TCTA


title: AK0599


title: AK0095


title: AK0223


title: MTA1

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

library_source: genomic

data_processing:
Base-Calling was performed by CASAVA version 1.4
The high quality reads were mapped to the Human genome 19 of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed.
The expression peaks were detected by MACS (Model-based Analysis for ChIP-Seq) using the parameter
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bed files were generated using MACS2.

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS). Cells were maintained in a humidified incubator equilibrated without CO2 at 37 ℃.

extract_protocol:
10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer‘s instructions.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For a ChIP assay, approximately 1 x 10^6 cells were used.The chromatin DNA precipitated by antibodies against RUNX2 and MTA1. The DNA was obtained using Cleavage Under Targets and Tagmentation (CUT&Tag) kit.

tag: chip antibody

value: MTA1 (Cell Signaling Technology)


title: RBG18697_Young_OPr_001

value: mesenchymal and endothelial cells


title: U87 cells, shY1_rep2

description:
shY1_rep2
RNA-seq


title: RUNX2

value: RUNX2 (Cell Signaling Technology)


title: RBG18703_Young_OPr_005

value: Young


title: EV004: Old_Endosteum

city: New York

first: Emmanuelle

last: Passegue

state: NY

department: Columbia Stem Cell Initiative

institute: Columbia University Irving Medical Center

data_processing:
Raw fastq files were aligned and processed to count matrices using CellRanger v2.1.1
Top 2,300 barcodes were selected for samples EV001, EV002, EV003 and top 2,858 were selected for EV004 using the "cellranger count" function with "force-cells=2300" for EV001, EV002 and EV003, or "force-cells=null" for EV004.
Genome_build: mm10
Supplementary_files_format_and_content: h5 files contain a matrix of selected cellular barcodes, Ensembl IDs, official gene symbols and read counts.

source_name: Endosteal stroma

growth_protocol: Mice were maintained in CUIMC animal facilities under SPF conditions.

extract_protocol:
Bone chips (endosteum) were harvested by crushing bones and washing away marrow with ice-cold HBSS. Marrow plugs (central marrow) were harvested by flushing intact plugs with ice-cold HBSS. All samples were subjected to collagenase digestion as indicated in the manuscript to liberate stromal cells, filtered through 100 micron mesh, and stained for surface protein expression. Live Ter119-/CD45- cells from each compartment were directly sorted into filter-sterilized alphaMEM supplemented with 10% FBS and purity was confirmed to be >95% by running freshly sorted cells on the same sorter.
Libraries were constructed following manufacturer's instructions for Chromium Single Cell 3' Library & Bead Kit v2 (10X Genomics). 5,000 cells were loaded for each sample and samples were sequenced in a HiSeq4000 sequencer (Illumina) to obtain an average of ~286 million reads per sample

value: Endosteal stroma

value: Bone marrow stromal cells

value: 24 months


title: CH0452

value: plasma

value: HF+


title: CH0076


title: EV003: Young_Endosteum

value: 10 weeks


title: ABZM00288: DNMT3B_3.1 [MARS_scRNA]

value: CTAC


title: ABZM00292: DNMT3B_5.1 [MARS_scRNA]

value: ACTT


title: ABZM00287: DNMT3B_0.4 [MARS_scRNA]

value: ACAG


title: EV002: Old_CentralMarrow

source_name: Central marrow stroma

value: Central marrow stroma


title: Hyperoxia_3

city: ChengDu

first: Yanrong

last: Long

address: No. 17, Section 3, Renmin South Road, Wuhou District

department: State Key Laboratory of Biotherapy

institute: Sichuan University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: mm10

source_name: lung

growth_protocol: mice reared in normoxia or hyperoxia

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: mice were either maintained in room air (21% O2) or in hyperoxia (80% O2) from P0 to P14.

value: lung

value: edothelial cells

value: WT

value: Hyperoxia

value: Day 14


title: AK0218


title: Hyperoxia_2


title: AK0072


title: ABZM00290: DNMT3B_3.3 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TGAT


title: ABZM00286: DNMT3B_0.3 [MARS_scRNA]

value: TTGG


title: EV001: Young_CentralMarrow

value: Bone marrow stromal cells


title: Hyperoxia_1


title: ABZM00285: DNMT3B_0.2 [MARS_scRNA]

value: CATG


title: BMP-D7-3

city: Hefei

first: Chen

last: Kan

address: Meishan Road 81

institute: Anhui Medical University

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.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0). Pvalue <0.05 and |FoldChange|≥1.5 were set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

source_name: tibial muscle

growth_protocol: After CTX injury in tibial muscle at different time point, mice were sacrificed and target muscle were collected.

extract_protocol:
RNA was harvested using Trizol reagent according to the manufacturer’s instructions.
Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: WT and mutant mice were treated by cardiotoxin.

tag: genotype/variation

tag: strain


title: ABZM00284: DNMT3B_0.1 [MARS_scRNA]

value: AGTC


title: CH0326

value: plasma

value: HF+


title: AK0239


title: Air_4

value: Normoxia

tag: time


title: ABZM00259: J1_WT_3.2 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CGGT


title: AK0319


title: BMP-D7-2


title: Air_3


title: BMP-D7-1


title: BMP-D3-3


title: ABZM00258: J1_WT_3.1 [MARS_scRNA]

value: TAGA


title: Hyperoxia_4

value: lung


title: BMP-D3-2


title: Air_2

value: edothelial cells


title: AK0531


title: CH0250


title: ABZM00243: J1_WT_2.4 [MARS_scRNA]

value: CGCC


title: Air_1

value: WT


title: CH0121


title: BMP-D3-1


title: WT-D3-3


title: WT-D3-2


title: ABZM00240: J1_WT_1.1 [MARS_scRNA]


title: ABZM00241: J1_WT_1.2 [MARS_scRNA]

value: TCTA


title: AK0056


title: Female Hypo Control BiologicalReplicate1

city: New Delhi

first: Arpita

last: Konar

address: Mathura Road

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
sequenced reads were trimmed for adapter sequences and repeat sequences using Trimmomatic
FPKM values were calculated using the Tuxedo pipeline
Assembly: mm9
Supplementary files format and content: csv files include FPKM values for each Sample.  txt file includes normalized abundance values (FPKM values of all transcripts).

source_name: Hypo

extract_protocol:
RNA was isolated from hypothalamus and PFC of male and female mice using Trizol reagent. Approximately, 1µg of RNA was taken per sample and RNA sequencing libraries were made using TruSeq v2 Library Prep Kit as per manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both male and female mice were exposed to fear inducing stressors at their peripuberty (P28-P42) and checked for aggressive behaviour at their adulthood (P90) by resident intruder paradigm.

value: Balb/c

tag: Sex

value: female

value: Adult (post natal day 90)

tag: sample group

value: Female Control

value: Hypo


title: AK0488


title: WT-D3-1

tag: age


title: Female Hypo Experimental BiologicalReplicate3

value: Female peripubertal stress induced non-aggressive (SNagg)


title: Female Hypo Control BiologicalReplicate2


title: BMP-D1-3


title: CH0251

value: plasma


title: ABZM00213: J1_WT_2.2 [MARS_scRNA]


title: ABZM00212: J1_WT_2.1 [MARS_scRNA]


title: BMP-D1-2


title: AK0570

value: HF-


title: ABZM00242: J1_WT_2.3 [MARS_scRNA]

value: ACTT


title: ABZM00187: J1_WT_7_g.3 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CTGA


title: Female Hypo Control BiologicalReplicate3


title: Female Hypo Experimental BiologicalReplicate2


title: AK0499


title: Female PFC Control BiologicalReplicate2

source_name: PFC

value: PFC


title: Female PFC Control BiologicalReplicate3


title: BMP-D1-1


title: ABZM00186: J1_WT_7_g.2 [MARS_scRNA]

value: AGGG


title: AK0300


title: WT-D1-3


title: CH0242


title: AK0362


title: CH0203


title: ABZM00289: DNMT3B_3.2 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: ATCA


title: Female PFC Experimental BiologicalReplicate1


title: AK0470


title: WT-D1-2

value: WT


title: ABZM00185: J1_WT_7_g.1 [MARS_scRNA]

value: TCCG


title: AK0286


title: Female PFC Control BiologicalReplicate1

value: Balb/c


title: ABZM00188: J1_WT_7_g.4 [MARS_scRNA]

value: CGAG


title: ABZM00180: J1_WT_5.4 [MARS_scRNA]

value: CGCC


title: ABZM00179: J1_WT_5.3 [MARS_scRNA]


title: BMP-D0-3


title: WT-D1-1


title: AK0477


title: Female PFC Experimental BiologicalReplicate2

value: female

value: Adult (post natal day 90)


title: Female Hypo Experimental BiologicalReplicate1

value: Female peripubertal stress induced non-aggressive (SNagg)

value: Hypo


title: BMP-D0-1


title: BMP-D0-2


title: WT-D0-3


title: ABZM00178: J1_WT_5.2 [MARS_scRNA]

value: TCTA


title: ABZM00172: J1_WT_0.2 [MARS_scRNA]

value: CATG


title: Male Hypo Control BiologicalReplicate3

value: male

value: Male Control


title: ABZM00171: J1_WT_0.1 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AGTC


title: ABZM00173: J1_WT_0.3 [MARS_scRNA]

value: TTGG


title: Male Hypo Control BiologicalReplicate2


title: Female PFC Experimental BiologicalReplicate3

value: PFC


title: AK0593

value: plasma

value: HF-


title: CH0125


title: Male Hypo Experimental BiologicalReplicate3

value: Balb/c

value: Male peripubertal stress induced escalated aggressive (SEagg)


title: WT-D0-2

value: WT


title: ABZM00177: J1_WT_5.1 [MARS_scRNA]

value: TGAT


title: CH0212


title: CH0295


title: scrCCB077_mm10

city: Leuven

first: Gabriele

last: Bergers

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven-VIB CCB

description: Cell Ranger version 3.1.0

data_processing:
Sequenced data were mapped to the mouse genome (build mm10) using Cell Ranger software (10x Genomics, version 3).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar: Tar archives include filtered_feature_bc_matrix files (barcodes.tsv,  features.tsv, matrix.mtx), by CellRanger.

source_name: E0771 TU EC - DPAg

extract_protocol:
For the isolation of immune cells, tumors were excised, mechanically minced and incubated with serum-free RPMI containing 3 U/ml Collagenase I (Worthington Biochemical), 133 U/ml Collagenase IV (Worthington Biochemical) and 10 U/ml DNase I (Worthington Biochemical) and rotated at 37°C for 30 min. Enzymatic digestion was blocked by adding RPMI-1640 containing 2mM EDTA and 2% FBS. The remaining tumor aggregates were dissociated mechanically. The single cell suspension was then passed thought a 70µm strainer and red blood cells were lysed by incubation with 3 ml of ACK Lysis Buffer (15 mM NH4Cl, 10 mM KHCO3, 0.1 mM Na2EDTA) for 3 minutes at RT. Tumor-infiltrating lymphocytes were further enriched using Lymphoprep (Stemcell technologies) and density gradient centrifugation (800 x g for 30 min, without break or acceleration, RT). The interphase cells were collected and washed with PBS before flow cytometry staining. For the isolation of ECs, tumors were minced and incubated with enzymes A, D and R (Tumor Dissociation Kit, Miltenyi) in combination with mechanical dissociation by gentleMACS™ Dissociator (Miltenyi). Tumor endothelial cells were enriched by removing immune cells and tumor cells using the positive selection anti-mouse CD45 (TIL) MicroBeads (Miltenyi) and the positive selection anti-mouse CD326 (EpCAM) MicroBeads (Miltenyi). The negative fraction that contained the remaining endothelial cells was collected and washed with PBS before flow cytometry staining. CD45-CD31+ ECs were sorted with a BD FACSAria III (BD Biosciences).
The single cell suspensions were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), aiming for 6,000 cells per library. Samples were processed using kits pertaining to V2 barcoding chemistry of 10x Genomics. Single samples were always processed in a single well of a PCR plate, allowing all cells from a sample to be treated with the same master mix and in the same reaction vessel. For each experiment, all samples were processed in parallel in the same thermal cycler. Libraries were sequenced on an Illumina NovaSeq 6000.

tag: tumor model

value: DPAg

value: Tumor endothelial cells


title: scrCCB094_mm10

description: Cell Ranger version 3.1.0

source_name: PyMT TU EC - DPAg + anti-IFNg

value: FvBN

value: PyMT

value: DPAg + anti-IFNg


title: CH0033


title: CH0155


title: Male Hypo Experimental BiologicalReplicate2

value: male

value: Adult (post natal day 90)

value: Hypo


title: delta-cyaA with 4.0mM cAMP rep2

city: Bangalore

first: Shweta

last: Chakraborty

state: Karnataka

address: Rajiv Gandhi Nagar, Kodigehalli

institute: National Centre for Biological Sciences

description: log phase bacteria grown in LB at 37 degree Celsius at 180rpm

data_processing:
Illumina HiSeq-2500 for sequencing
BWA was used for indexing the reference genome and aligning the reads(q>20)
SAMtools(v1.2) and BEDtools(v2.25.0) were used to filter reads and determine the read counts per gene.
Normalisation and differential gene expression calling was done using EdgeR(3.28.1) and custom R scripts.
Assembly: Escherichia coli K12 MG1655 , Ref Seq: NC_000913.2
Supplementary files format and content: Tab-delimited text files containing read counts per gene(cyaA_readcounts.table).
Supplementary files format and content: Tab-delimited text files containing EdgeR(v3.28.1) normalised counts per million per sample(cyaA_logCPM_values.table).

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Cells were grown in LB, with or without cAMP, at 37 degrees Celsius at 180rpm.

extract_protocol:
Total RNA was extracted using the TRIzol-chloroform extraction methods, followed by removal of genomic DNA contamination. To enrich for mRNA 16S and 23S rRNA were depleted using Ambion Microbe Express Riboclean-up kits(AM1905).
Libraries for each sample were prepared using the NEB NextUltra directional RNA library prep kit followed by single end sequencing using Illumina HiSeq 2500 platform.

treatment_protocol:
Delta-cyaA E.coli cells were treated with 10 different concentrations of extracellular cAMP ranging from 0mM to 4mM. Cells were harvested when the population reached its maximum growth rate followed by mRNA isolation and sequencing.
Extracellular cAMP concentrations used: 0mM, 0.01mM,  0.05mM,  0.1mM,  0.3mM,  0.6mM, 0.8mM, 1.0mM, 2.0mM, 4.0mM

tag: genotype

value: delta-cyaA

tag: growth phase

value: log phase

value: 4.0mM cAMP


title: delta-cyaA with 4.0mM cAMP rep1

tag: treatment


title: delta-cyaA with 2.0mM cAMP rep2

value: 2.0mM cAMP


title: scrCCB076_mm10

description: Cell Ranger version 3.1.0

source_name: E0771 TU EC - UT

value: Untreated

tag: cell type


title: AK0542

value: plasma

value: HF-


title: Male PFC Control BiologicalReplicate3

value: Balb/c

value: Male Control

value: PFC


title: Male PFC Control BiologicalReplicate2


title: delta-cyaA with 1.0mM cAMP rep2

value: 1.0mM cAMP


title: delta-cyaA with 2.0mM cAMP rep1


title: scrCCB073_mm10

description: Cell Ranger version 3.1.0

source_name: E0771 TU IC - DPAg

value: DPAg

value: Tumor immune cells


title: Male Hypo Control BiologicalReplicate1


title: Male PFC Experimental BiologicalReplicate3

value: Male peripubertal stress induced escalated aggressive (SEagg)


title: Male Hypo Experimental BiologicalReplicate1

value: male


title: AK0055


title: WT-D0-1

value: WT


title: scrCCB074_mm10

description: Cell Ranger version 3.1.0

source_name: PyMT TU EC - UT

value: FvBN

value: PyMT

value: Tumor endothelial cells


title: scrCCB075_mm10

description: Cell Ranger version 3.1.0

source_name: PyMT TU EC - DPAg


title: delta-cyaA with 1.0mM cAMP rep1

value: delta-cyaA

value: log phase


title: AK0058


title: scrCCB054_mm10

description: Cell Ranger version 3.0.2

source_name: PyMT TU IC - DPAg


title: Male PFC Control BiologicalReplicate1

value: Adult (post natal day 90)


title: AK0623

value: plasma


title: scrCCB072_mm10

description: Cell Ranger version 3.1.0

source_name: E0771 TU IC - UT

value: Untreated


title: scrCCB053_mm10

description: Cell Ranger version 3.0.2

source_name: PyMT TU IC - UT


title: delta-cyaA with 0.6mM cAMP rep2

value: 0.6mM cAMP


title: PP_STm_aCCR2

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

data_processing:
FASTQ files were aligned to the mouse mm10 reference genome using 10x Genomics Cell Ranger software v5.0.1
The UMI count matrix was converted to Seurat objects using R package Seurat
SCTransform function was used to normalize each dataset
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Peyer's patch

growth_protocol: sorted live cells from Peyer's patches 3 days after STm infection with daily aCCR2 antibody treatment

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

value: Peyer's patch

tag: mouse strain

value: wild type

value: STm infected, aCCR2 antibody treatment


title: delta-cyaA with 0.6mM cAMP rep1


title: Male PFC Experimental BiologicalReplicate2

value: Balb/c

value: PFC


title: CH0078

source_name: plasma

value: HF-


title: Young_GFP-pos_p16INK4a+ cells

city: San Francisco

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description: single cell RNA sequencing of adult young murine lung p16INK4a+ stromal cells

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v1.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: adult murine lung p16INK4a+ cells

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 °C and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 °C and washed with FACS buffer. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence and GFP+ cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.

treatment_protocol: Animals were injured with naphthalene by administering naphthalene dissolved in corn oil IP at 150 mg/kg one time. Lung tissue was collected at 14 days post injury. Old and young animals were collected at the same time and mesenchyme was harvested.

value: lung

tag: developmental stage

value: adult


title: PP_STm_C

value: STm infected


title: Young_GFP-neg_p16INK4a- cells

description: single cell RNA sequencing of adult young murine lung p16INK4a- stromal cells

tag: tissue


title: delta-cyaA with 0.8mM cAMP rep2

value: 0.8mM cAMP


title: Male PFC Experimental BiologicalReplicate1

value: male

value: Male peripubertal stress induced escalated aggressive (SEagg)


title: CH0261


title: delta-cyaA with 0.8mM cAMP rep1

value: delta-cyaA

value: log phase


title: PP_control

growth_protocol: Column seperated live Peyer's patch cells

value: untreated


title: AK0524

value: plasma


title: Old_GFP-pos_p16INK4a+ cells

description: single cell RNA sequencing of adult old murine lung p16INK4a+ stromal cells

value: old murine lung p16INK4a+ stromal cells


title: delta-cyaA with 0.3mM cAMP rep2

value: 0.3mM cAMP


title: AK0556


title: AK0618


title: delta-cyaA with 0.3mM cAMP rep1


title: CH0222


title: CH0152


title: delta-cyaA with 0.05mM cAMP rep2

value: 0.05mM cAMP


title: Yap_CUT&RUN

city: Houston

first: Jun

last: Wang

state: TX

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

data_processing:
Library strategy: CUT&RUN
Following sequencing of CUT&RUN libraries, the raw fastq files were mapped using Bowtie2 (version v2.2.5) with the following options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
For mapping Yeast spike-in fragments, we used the following options in addition to those stated directly above: --no-overlap --no-dovetail.
Peaks were called from aligned BAM files using MACS2 callpeaks with the narrowPeak option and a P-value cutoff of 1e-5.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were converted to bigWig format for visualization.

source_name: O9-1 neural crest cells

growth_protocol: Neural crest cells (O9-1 cells) were routinely cultured (typically  × 10e6 cells into a 10 cm plate) on matrigel coated plastic plate in basal medium (15% FBS, 0.1 mM minimum essential media (MEM) nonessential amino acids, 1 mM sodium pyruvate, 55 μM beta-mercaptoethanol, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine in DMEM) supplemented with 103 units/mL leukemia inhibitory factor, and 25 ng/mL fibroblast growth factor-basic

extract_protocol:
DNA were isolated with Yap, IgG and H3K27me3 antibodies, respectively, and were extracted following the guidelines of Peter J Skene and Steven Henikoff’s protocol. Briefly, collected cells were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories, BP531), permeabilized with digitonin and incubated with Yap1 (Novus, NB110-58358, 1:50), Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology, 9733, 1:50) and anti-rabbit IgG (Millipore Sigma, 12370, 1:50) antibodies separately overnight at 4oC. Protein A/G–Micrococcal Nuclease (pA/G-MNase) fusion protein was added into each sample to a final concentration of 700 ng/mL for 10 min at room temperature after washing away unbound antibodies. Next, the samples were washed with digitonin buffer and added 150 µL digitonin buffer, pre-chilled on ice, and added CaCl2 to a final concentration of 2 mM to activate the pAG-MNase enzyme for DNA digesting. After 2 h digestion at 4oC, the reactions were terminated by 100 uL STOP buffer, and the protein-DNA complexes were released by incubating the tubes at 37˚C for 10 min on a ThermoMixer at 500 rpm. Finally, DNA fragments were extracted by phenol-chloroform and ethanol and quantified by Qubit analysis following the manufacturer’s instructions (ThermoFisher Scientific, Q32851). pA/G-MNase was a generous gift from Dr. Steven Henikoff.
CUT&RUN libraries were prepared using the SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio Inc, R400674) following the manufacturer’s instructions and sequenced with paired-end 50 bp reads on an Illumina NovaSeq 6000 instrument.

tag: cell line

value: O9-1 neural crest cells


title: delta-cyaA with 0.1mM cAMP rep2

value: 0.1mM cAMP


title: Old_GFP-neg_p16INK4a- cells

description: single cell RNA sequencing of adult old murine lung p16INK4a- stromal cells

value: old murine lung p16INK4a- stromal cells


title: AK0293

value: HF-


title: AK0365


title: Cre-_mice4

city: Novato

first: Lisa

last: Ellerby

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
Sequenced reads were trimmed for adaptor sequence and bases with quality score lower than 20 using Trim Galore! 0.6.4 with parameters trim_galore --fastqc --length 25 --cores 4 --paired --retain_unpaired
The external and internal rRNA contamination were filtered through SortMeRNA 2.1b with parameters sortmerna --ref $sortmernaREF --reads $merge --aligned $aligned --other $filtered -m 5120 --fastx --paired_out --log -a 30 -v
The filtered raw reads were mapped to the Genome Reference Consortium Mouse Build 38 striosome release 6(GRCm38.p6) assembly by GENCODE using STAR 2.7.2b with parameters STAR --runThreadN 15 --genomeDir Mus_musculus.GRCh38.p6.genome/ --sjdbGTFfile gencode.vM22.annotation.gtf --readFilesIn $read1 $read2 --outSAMtype BAM SortedByCoordinate
The raw counts of reads mapped to known genes were summarized by featureCounts, using GENECODE release M22 annotation with parameters featureCounts -a gencode.vM22.annotation.gtf -o final_counts.txt -g 'gene_name' -T 4 $dirlist
Then R Bioconductor package DESeq2 were used to normalize raw read counts logarithmically and perform differential expression analysis.
Genome_build: mm10(GRCm38.p6)
Supplementary_files_format_and_content: Microsoft excel table files include raw counts and log transformed values for each sample.

source_name: Striatum

extract_protocol:
Dissected striatum at 4 months of age was analyzed The collected cells were subject to  RNA extraction.
TruSeq RNA Sample Prep Kit v2 protocol  (Illumina, San Diego, CA, USA). Briefly, ribosomal RNA was removed using the Ribo-Zero rRNA  Removal Kit (Human/Mouse/Rat) (Illumina), the remaining RNA fragmented and cDNA  synthesized with random hexamers, end-repaired and ligated with appropriate adaptors for  sequencing. After size selection and purification using AMPure XP beads (Beckman Coulter,  CA, USA), 6 bp barcode bases were introduced at one end of the adaptors. The size and  concentration of the RNA-Seq libraries was measured by Bioanalyzer and Qubit fluorometry  (Life Technologies, Grand Island, NY, USA), and the rRNA-depleted libraries sequenced on the  Illumina HiSeq 2500 System with 100 nucleotide paired-end reads.

value: Striatum

value: 4 month

tag: gender

value: Female

tag: cre status

value: Negative


title: IgG_CUT&RUN

tag: chip antibody

value: anti-rabbit IgG (Millipore Sigma, 12370)


title: H3K27me3_CUT&RUN

value: Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology, 9733)


title: delta-cyaA with 0.05mM cAMP rep1

tag: strain

value: delta-cyaA


title: CH0167


title: D9_Cre_Bcl11b_tm1.1_Lead_mice3

value: Positive


title: AK0147


title: delta-cyaA with 0.01mM cAMP rep1

value: log phase

value: 0.01mM cAMP


title: Cre-_mice2


title: delta-cyaA with 0.1mM cAMP rep1


title: PP_STm

city: Rehovot

institute: Weizmann Institute of Science

value: Peyer's patch

value: wild type

value: STm infected


title: delta-cyaA with 0.01mM cAMP rep2


title: D9_Cre_Bcl11b_tm1.1_Lead_mice2


title: D9_Cre_Bcl11b_tm1.1_Lead_mice4


title: wild-type E.coli rep2

value: wild-type

value: no treatment


title: delta-cyaA E.coli mutant (0mM cAMP) rep2


title: Liver patient 30

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned with STAR (v.2.7.8a) to the human genome assembly (GRCh38, Ensembl release 101)
FeatureCounts (v.2.0) was employed for exon read counting
Quality of raw sequencing was assessed using FastQC (v.0.11.9) and MultiQC (v. v1.10.1)
Genetic variants were removed from raw sequencing reads using BAMboozle (v.0.5.0)
Assembly: GRCh38, Ensembl release 101
Supplementary files format and content: txt files with gene-level counts

source_name: Liver biopsy

extract_protocol:
Needle biopsies of liver tissue were homogenized using FastPrep-24™ and RNA purified using TRIzol-RNA lysis reagent according to the manufacturer’s instructions. Purified RNA was quantified using Qubit 3.0 Fluorometer and RNA quality was assessed using Fragment Analyzer 5200
NEBNext Ultra RNA Library Prep Kit for Illumina were used for construction of libraries according to the manufacture's protocol. RNA was paired-end sequenced using the NovaSeqTM 6000 platform

value: Liver biopsy

tag: tissue preservation

value: snap frozen

tag: steatosis, activity,_and_fibrosis_score

value: NAFL

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Liver patient 29

tag: Sex


title: Cre-_mice1

value: Striatum

tag: age

value: 4 month


title: wild-type E.coli rep1

tag: genotype

tag: growth phase


title: delta-cyaA E.coli mutant (0mM cAMP) rep1

tag: treatment


title: Liver patient 28

value: Male

value: NASH


title: D14_5997_p16INK4a+GFP+ cells

source_name: adult murine lung p16INK4a+ cells 14 dpi (naphthalene)

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 °C and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 °C and washed with FACS buffer. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence and GFP+ cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.
droplet-based single cell RNA-Seq

treatment_protocol: Animals were injured with naphthalene by administering naphthalene dissolved in corn oil IP at 150 mg/kg one time. Lung tissue was collected at 14 days post injury.

value: adult

value: 14 days post Naphthalene injury

value: lung

tag: cell type

value: p16INK4a+ stromal cells


title: Liver patient 25


title: hpm_F_WAA5(ex vivo): WT GBS infected

first: Itai

last: Yanai

address: 435 East. 30th St.

institute: NYU Langone Health

description: ex vivo

data_processing:
Basecalls was done using cellranger mkfastq V3.0.0
alignment, filtering, counting and umi counting was doe using cellranger count V3.0.0
Assembly: human GRCh38
Supplementary files format and content: expression matrix of umi ocunts

source_name: human placental macrophages

growth_protocol: human placental cells were dissociated into suspension, macrophages were selected by CD14 expression and cultured overnight

extract_protocol:
human placental macrophages were isolated by selection of CD14+ expression by magnetic beads from single cell suspension
10x single cell RAN seq V3

treatment_protocol: macrophages were infected with GBS or PBS control. After 1 hour excess GBS was washed away and cells were incubated for an additional 3 hours.

value: placental

value: macrophage

value: WT GBS infected


title: D9_Cre_Bcl11b_tm1.1_Lead_mice1

value: Female

value: Positive


title: hpm_F_KBA4(ex vivo): BH/c KO GBS infected

description: ex vivo

value: BH/c KO GBS infected


title: Liver patient 27

value: Liver biopsy


title: hpm_F_WBA6(ex vivo): WT GBS infected

description: ex vivo


title: Liver patient 23

value: RNAlater


title: ALF042A

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

country: Australia

institute: CSL Limited

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using star (v2.6.1)13 with default parameters except for the --quantMode TranscriptomeSAM setting.
Reads were summarized at the gene level using featureCounts tool from the Subread package (v1.6.4)14, in a strand-specific manner.

source_name: Lung,ILD.Apex,Whole lung

extract_protocol:
RNA was extracted from whole lung tissue according to manufacturer’s protocol (Fibrous Tissue Mini kit, Qiagen #74704). RNA quality was verified with the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Samples with RNA integrity numbers (RIN) over 6 were used for RNA sequencing.
cDNA libraries were prepared for sequencing using standard strand specific TrueSeq kits with ribosomal RNA and Globin mRNA depletion. At least 20 million 100 bp single-end reads were generated per sample using Illumina HiSeq 3000 (Illumina, California, USA) using standard protocols at the Australian Genome Research Facility (AGRF, Melbourne, Australia).

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

value: Disease

tag: diseasegroup

value: ILD

value: F

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: IPF

tag: smokingstatus

value: Never

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: hpm_F_CBA2(ex vivo): control

description: ex vivo

tag: tissue

value: placental

tag: cell type

value: macrophage

tag: treatment

value: control


title: METTL3-m6A-MeRIP-seq-Input1

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

data_processing:
QC check
Read mapping (hisat2)
Peakcalling (exome peak)
RNA methylaytion diffenetial analysis
Assembly: hg38
Supplementary files format and content: bigWig

source_name: METTL3 overexpressing THP-1 cells, input

extract_protocol:
For m6A-seq, total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2 and incubated with anti-m6A polyclonal antibody (Sigma Aldrich) for 3 h at 4℃. Then mix the products above with protein A/G magnetic beads (Thermo Fisher) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The beads were then separated and washed with IP buffer three times. A NEBNext Ultra RNA library prep kit (NEB) was used to establish the library for the purified mRNA fragments. Each group was sequenced with an Illumina NovaSeq 6000 sequencer, and the single-end sequencing length was 150 bp. Reads were compared with human genome version GRCH38 through TopHat. If a gene had more than one subtype, the longest subtype was retained. ExomePeak (P < 0.01) was used to identify differential m6A-modified peaks between IP and input samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
m6A-Seq

treatment_protocol: THP-1 cells were transfected with METTL3 and its negative control lentivirus.The positively infected cells were selected with 1 μg/mL puromycin.

tag: cell line

value: AML

tag: genotype

value: METTL3 overexpression

tag: rip antibody


title: METTL3-m6A-MeRIP-seq-Input3


title: METTL3-m6A-MeRIP-seq-IP3

source_name: METTL3 overexpressing THP-1 cells, IP

value: anti-m6A polyclonal antibody


title: Liver patient 26

value: Liver biopsy

tag: Sex

value: Male

tag: tissue preservation

value: snap frozen

tag: steatosis, activity,_and_fibrosis_score

value: NAFL

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: Liver patient 22

value: Female

value: RNAlater

value: No-NAFLD


title: ALF032C

source_name: Lung,IPF.Apex,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker


title: METTL3-m6A-MeRIP-seq-IP1

tag: cell line

tag: cell type

value: AML

tag: genotype

tag: rip antibody


title: Liver patient 24

tag: tissue

tag: Sex

tag: tissue preservation

tag: steatosis, activity,_and_fibrosis_score

tag: kleiner fibrosis_grade

tag: nafld activity_score


title: ALF012B

source_name: Lung,NDC.Base,Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

tag: diseasenormal

value: Normal

tag: diseasegroup

value: NDC

tag: gender

value: F

tag: diagnosis

tag: age

tag: lungweight mg

value: Current

tag: severity

value: Unknown

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: hpm_F_KAA3(ex vivo): BH/c KO GBS infected

description: ex vivo

tag: tissue

value: placental

tag: cell type

value: macrophage

tag: treatment

value: BH/c KO GBS infected


title: NC-m6A-MeRIP-seq-Input3

source_name: THP-2-NC, input

tag: cell line

tag: genotype

value: control

tag: rip antibody


title: ALF025C

source_name: Lung,NDC.Apex,Whole lung

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus


title: METTL3-m6A-MeRIP-seq-IP2

value: METTL3 overexpression

value: anti-m6A polyclonal antibody


title: hpm_F_CAA1(ex vivo): control

description: ex vivo

tag: tissue


title: METTL3-m6A-MeRIP-seq-Input2

tag: cell type

value: AML