title: AGGREGATE_27


title: T2DM, ScRNA_seq

status: Public on Aug 27 2024

type: SRA

city: Jinan

first: Zhenyu

last: Tian

state: Shandong

address: No. 107, Wenhua west road

country: China

institute: Qilu Hospital of Shandong University

description: 10x Genomics

library_source: transcriptomic

data_processing:
Single-cell mRNA expression data were analyzed using the Cell Ranger Single Cell Software Suite (v2.2.0) to perform quality control, sample demultiplexing, barcode processing, and single-cell 3’ gene counting. Sequencing reads were aligned to the Rattus norvegicus transcriptome
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for rach gene and each cell

molecule: total RNA

organism: Rattus norvegicus

source_name: perivascular adipose tissue

extract_protocol:
We isolated the thoracic aorta and its perivascular adipose tissue (PVAT) from rats for single-cell RNA sequencing (scRNA-seq) and molecular biology experiments. Specifically, rats were anesthetized with an intraperitoneal injection of sodium pentobarbital (60 mg/kg) and perfused transcardially with saline to remove blood. The thoracic cavity was exposed via a midline sternotomy. Carefully, the lungs, liver, kidneys, and spleen were removed to fully expose the heart and aorta. The heart and thoracic aorta were excised and placed in ice-cold PBS. Under the microscope, the heart was removed, and the thoracic aorta along with its surrounding PVAT were carefully separated.
The scRNA-seq libraries were constructed using a Chromium Single Cell 3’ Reagent Kit v2 (10× Genomics) according to the manufacturer’s protocol. Library quantification and quality were assessed by a Qubit fluorometer (Invitrogen)

tag: tissue

value: perivascular adipose tissue

tag: cell line

value: stromal vascular fraction

tag: cell type


title: NC, ScRNA_seq

description: 10x Genomics


title: MIXED1_44

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

data_processing:
Raw data were normalized using Quartile 3 count (Q3) normalization in R as per NanoString's recommendations (code: https://bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html)
Batch correction was performed using Combat-seq
Spatial Deconvolution was performed in the GeoMx DSP Analysis suite using scRNAseq reference datasets (see methods in the preprint for references)
Assembly: Human
Supplementary files format and content: There is one spreadsheet (excel) that contains all the Q3-normalized gene expression data for all 143 sequenced regions.
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: AML bone marrow

extract_protocol:
5 micrometer tissue slices of FFPE bone marrow biopsies (AML or non-leukemic) were cut.
Spatial transcriptomics sequencing libraries were prepared with NanoSTring GeoMx Digital Spatial Profiling slides & reagent kit according to manufacturer's instructions

treatment_protocol: Not applicable (treatment-naïve samples)

value: AML bone marrow

tag: disease state

value: treatment-naïve


title: MIXED2_25


title: CONTROL_1

source_name: Non-leukemic bone marrow

value: Non-leukemic bone marrow


title: AGGREGATE_29


title: normal tissue [CIM072N]

type: genomic

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

hyb_protocol: Bisulfite converted DNA was hybridised to Infinium Human Methylation EPIC BeadChip according to the manufacturer’s recommendations.

scan_protocol: The Illumina HiScan system was used to scan the beadchip platform.

data_processing: Data processing was performed with R software. Briefly, probes with low quality (detection p-value > 0.05), mapped in X/Y chromosomes or to SNPs, and cross-reactive were filtered out using the minfi package. Differences in Type-I and Type-II probes and normalization of the β values were adjusted using the Beta MIxture Quantile dilation (BMIQ) method. Batch effect was corrected with ComBat function from sva package (v.3.44.0).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: normal adjacent breast tissue

label_protocol: Cy5 and Cy3

extract_protocol: Genomic DNA was isolated from 24 fresh frozen macrodissected IBC tissue biopsies and six surrounding normal breast frozen tissues using the QIAsymphony kit (Qiagen, Valencia, CA, USA).

tag: donor id

value: normal adjacent breast tissue


title: 36_LXR-bKO_GW_(LXRa), BMDM cells

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

library_source: genomic

data_processing:
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Assembly: mm10
Supplementary files format and content: Peaks files

organism: Mus musculus

source_name: Bone marrow

growth_protocol: For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRβ-/- mice were isolated and cultured for 7 days in RPMI supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin). To analyze LXRα-dependent response, cells were cultured in RPMI supplemented with 10% FBS, 1% antibiotics (penicillin and streptomycin) and 100 nM of Lipopolysachaaride (LPS) during 3 or 24 hours. Genome-wide locations of LXRα, p65 and H3K27ac acetylation mark were analized in response to treatment with LPS.

extract_protocol:
Cells were fixed with DSG (2 mM) for 30 minutes and 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorruptor plus (Diagenode) and LXR-DNA, p65-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
to create the sequencing library, DNA was end-repaired and ligated to stem-loop adaptors (DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions). Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

value: Bone marrow

value: bone marrow-derived macrophage

tag: genotype

value: LXR-bKO

tag: treatment

value: GW3965 1 µM 24 hours

tag: chip antibody

value: LXRa


title: 37_LXR-bKO_GW+LPS_(LXRa), BMDM cells

value: GW3965 1 µM + Lipopolysaccharide 100 nM 24 hours


title: MIXED1_42


title: MIXED1_43


title: HT29 cells, shControl 4

city: Changsha, Hunan, China

first: Xi

last: Li

address: No.87 Xiangya Road

institute: Xiangya Hospital, Central South University

data_processing:
1) Remove reads with adaptors;
2) Remove reads in which unknown bases are more than 10%;
3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include TPM and read count values for each Sample

extract_protocol:
Total RNA was extracted from each sample using  Trizol the method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human colon cancer cells

value: WT

value: 10% FBS


title: normal tissue [CIM070N]


title: HT29 cells, shControl 3


title: HT29 cells, shControl 2


title: MIXED1_41


title: MIXED2_33


title: tumor tissue [CIM006]

source_name: inflammatory breast cancer tissue

value: inflammatory breast cancer tissue


title: HT29 cells, shControl 1


title: MIXED1_39


title: normal tissue [CIM068N]


title: MIXED1_40


title: MIXED1_38


title: HT29 cells, shALDH1A1, 3

value: ALDH1A1 knockdown


title: HT29 cells, shALDH1A1, 2


title: MIXED2_27


title: HT29 cells, shALDH1A1, 1


title: MIXED1_35


title: MIXED1_37


title: MIXED1_34


title: BarBQ pastrami production chain, mixture, all bacteria, rep 2

city: Haifa

first: May

last: Cohen Hakmon

address: Shikago

country: Israel

institute: Technion

description:
table_supplamentary.qzv
taxa-bar-plots_supplamentary.qzv
supplamentary_quantified_microorganisms.csv

data_processing:
we used Qiime2 to analyze data
Assembly: 16s
Supplementary files format and content: table.qzv
Supplementary files format and content: taxa-bar-plots.qzv
Library strategy: 16S DNA metagenome

organism: food metagenome

source_name: pastami

growth_protocol: from pastrami plant

extract_protocol:
MagMAXTMCORENucleic Acid Purification Kit
The 16S libraries were constructed simultaneously according to Illumina 16S Metagenomic Sequencing Library Preparation using primers amplifying the 16S V3 and V4 region located at positions 341 bp and 805 bp

treatment_protocol: rinsing in ringer solution and then extraction

value: pastami

tag: group

value: mixture


title: MIXED1_33

value: AML bone marrow


title: HT29 cells, shALDH1A1, 4


title: MIXED1_36

value: treatment-naïve


title: normal tissue [CIM011N]


title: BarBQ pastrami production chain, mixture, all bacteria, rep 1


title: BarBQ pastrami production chain, mixture, all bacteria, rep 4


title: MIXED1_31


title: BarBQ pastrami production chain, mixture, live bacteria, rep 3


title: normal tissue [CIM015N]


title: MIXED1_30


title: normal tissue [CIM069N]


title: BarBQ pastrami production chain, mixture, live bacteria, rep 2


title: BarBQ pastrami production chain, mixture, all bacteria, rep 3


title: MIXED1_32


title: MIXED1_29


title: MIXED1_28


title: BarBQ pastrami production chain, mixture, live bacteria, rep 1


title: BarBQ pastrami production chain, after three months in storage, without lactate, rep 5

description:
table_figure_3.qzv
taxa-bar-plots_figure_3.qzv
figure_3_quantified_microorganisms.csv

value: final product


title: MIXED1_27


title: MIXED1_26


title: AGGREGATE_26


title: BarBQ pastrami production chain, after three months in storage, without lactate, rep 3


title: BarBQ pastrami production chain, after three months in storage, without lactate, rep 4


title: MIXED1_25


title: BarBQ pastrami production chain, after three months in storage, with lactate, rep 5


title: AGGREGATE_24


title: BarBQ pastrami production chain, after three months in storage, with lactate, rep 4


title: AGGREGATE_25


title: MIXED2_35


title: BarBQ pastrami production chain, after three months in storage, with lactate, rep 2


title: MIXED1_23


title: BarBQ pastrami production chain, after three months in storage, with lactate, rep 1


title: MIXED1_22


title: MIXED1_21


title: MIXED1_20


title: BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 4


title: BarBQ pastrami production chain, after three months in storage, without lactate, rep 2


title: BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 3


title: BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 2


title: MIXED1_19


title: MIXED1_24


title: BarBQ pastrami production chain, after three months in storage, without lactate, rep 1


title: MIXED1_17


title: BarBQ pastrami production chain, after three months in storage, with lactate, rep 3


title: MIXED1_16


title: BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 4


title: MIXED1_15


title: AGGREGATE_33


title: BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 2


title: BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 3


title: MIXED1_12


title: MIXED1_13


title: MIXED1_11


title: BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 1


title: BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 5


title: MIXED1_14


title: MIXED1_18


title: BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 5


title: MIXED1_48


title: BarBQ pastrami production chain, after six weeks in storage, without lactate, rep 1


title: MIXED2_23


title: BarBQ pastrami production chain, after six weeks in storage, with lactate, rep 5


title: BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 3


title: MIXED2_22


title: BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 4


title: MIXED2_21


title: BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 2


title: BarBQ pastrami production chain, after two weeks in storage, without lactate, rep 1


title: BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 4


title: BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 5


title: MIXED2_20


title: BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 3


title: MIXED2_18


title: MIXED2_19


title: MIXED2_16


title: MIXED2_15


title: BarBQ pastrami production chain, after one week in storage, without lactate, rep 4


title: MIXED2_11


title: BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 1


title: MIXED2_17


title: MIXED2_13


title: BarBQ pastrami production chain, after one week in storage, without lactate, rep 3


title: MIXED2_10


title: MIXED2_9


title: MIXED2_12


title: MIXED2_14


title: BarBQ pastrami production chain, after one week in storage, without lactate, rep 1


title: BarBQ pastrami production chain, after one week in storage, with lactate, rep 5


title: BarBQ pastrami production chain, after one week in storage, with lactate, rep 4


title: BarBQ pastrami production chain, after one week in storage, without lactate, rep 2


title: MIXED2_8


title: MIXED2_7


title: BarBQ pastrami production chain, after one week in storage, with lactate, rep 2


title: MIXED2_6


title: BarBQ pastrami production chain, after one week in storage, with lactate, rep 1


title: MIXED2_5


title: BarBQ pastrami production chain, after two weeks in storage, with lactate, rep 2


title: BarBQ pastrami production chain, after slicing, without lactate, rep 5


title: MIXED2_3


title: MIXED2_4


title: BarBQ pastrami production chain, after slicing, without lactate, rep 4


title: MIXED2_1


title: BarBQ pastrami production chain, after slicing, without lactate, rep 2


title: BarBQ pastrami production chain, after one week in storage, with lactate, rep 3


title: MIXED2_2


title: BarBQ pastrami production chain, after slicing, without lactate, rep 1


title: AGGREGATE_21


title: AGGREGATE_23


title: AGGREGATE_19


title: AGGREGATE_20


title: BarBQ pastrami production chain, after cooking, without lactate, rep 2

value: after cooking


title: AGGREGATE_22


title: BarBQ pastrami production chain, after cooking, without lactate, rep 5


title: BarBQ pastrami production chain, after slicing, without lactate, rep 3


title: AGGREGATE_18


title: BarBQ pastrami production chain, after cooking, without lactate, rep 3


title: BarBQ pastrami production chain, after cooking, without lactate, rep 1


title: AGGREGATE_16


title: BarBQ pastrami production chain, mixture, without lactate, rep 5


title: AGGREGATE_17


title: AGGREGATE_15


title: BarBQ pastrami production chain, mixture, without lactate, rep 3


title: BarBQ pastrami production chain, mixture, without lactate, rep 4


title: BarBQ pastrami production chain, mixture, without lactate, rep 2


title: BarBQ pastrami production chain, mixture, without lactate, rep 1


title: BarBQ pastrami production chain, brine, without lactate, rep 5

value: brine


title: BarBQ pastrami production chain, after cooking, without lactate, rep 4


title: AGGREGATE_13


title: MIXED1_45


title: AGGREGATE_12


title: AGGREGATE_10


title: AGGREGATE_9


title: AGGREGATE_11


title: BarBQ pastrami production chain, brine, without lactate, rep 2


title: AGGREGATE_7


title: AGGREGATE_8


title: AGGREGATE_5


title: AGGREGATE_6


title: BarBQ pastrami production chain, after slicing, with lactate, rep 5

description:
table_figure_2.qzv
taxa-bar-plots_figure_2.qzv
figure_2_quantified_microorganisms.csv


title: BarBQ pastrami production chain, after slicing, with lactate, rep 4


title: BarBQ pastrami production chain, after slicing, with lactate, rep 3


title: AGGREGATE_14


title: BarBQ pastrami production chain, after cooking, with lactate, rep 5


title: AGGREGATE_2


title: AGGREGATE_1


title: BarBQ pastrami production chain, after cooking, with lactate, rep 4


title: BarBQ pastrami production chain, after slicing, with lactate, rep 2


title: MIXED1_9


title: MIXED1_10


title: BarBQ pastrami production chain, brine, without lactate, rep 4


title: BarBQ pastrami production chain, after cooking, with lactate, rep 3


title: BarBQ pastrami production chain, after cooking, with lactate, rep 2


title: BarBQ pastrami production chain, brine, without lactate, rep 3


title: MIXED1_7


title: BarBQ pastrami production chain, brine, without lactate, rep 1


title: BarBQ pastrami production chain, after cooking, with lactate, rep 1


title: MIXED1_6


title: BarBQ pastrami production chain, mixture, with lactate, rep 5


title: MIXED1_5


title: AGGREGATE_4


title: BarBQ pastrami production chain, after slicing, with lactate, rep 1


title: AGGREGATE_3


title: BarBQ pastrami production chain, mixture, with lactate, rep 3


title: BarBQ pastrami production chain, mixture, with lactate, rep 2


title: BarBQ pastrami production chain, mixture, with lactate, rep 4


title: BarBQ pastrami production chain, brine, with lactate, rep 5


title: MIXED1_3


title: MIXED1_4


title: MIXED1_2


title: MIXED1_1


title: BarBQ pastrami production chain, brine, with lactate, rep 4


title: TTL-KO-AE 3

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

country: Germany

institute: University of Münster

data_processing:
The sequencing data was automatically demultiplexed using the Illumina BCL Convert Software v3.8.2.
FastQ files underwent pre-trimming and post-alignment quality control rounds using FastQC v0.11.7.#_ENREF_25" \t "Andrews, 2010 #11320 Removal of Illumina adapters and low-quality sequences was performed with Trimmomatic v0.38.#_ENREF_26" \t "Bolger, 2014 #11306 Reads of length <15 bases, as well as leading and/or trailing bases with quality <3 or no base call, and bases with average quality <15 in a 4-base sliding window were removed
Alignment was performed with HISAT2 v2.1
Mapped reads (primary alignments) were sorted by read name using SAMtools v1.8
Read counts were calculated with HTSeq v0.11.2
Assembly: hg38
Supplementary files format and content: Raw read counts

source_name: hiPSC-cardiomyoctes

extract_protocol:
Total RNA isolation
Enrichment of mRNAs with the NEBNext Poly(A) mRNA Magnetic Isolation Module was followed by library preparation using the NEBNext Ultra II RNA Directional Library Prep Kit for Illumina (New England BioLabs).
Single read sequencing took place on a NextSeq 2000 System (Illumina), using the corresponding NextSeq 2000 P3 Reagents (50 cycles), with a read length of 72 base pairs.

value: hiPSC-cardiomyoctes

value: TTL-KO

value: Afterload enhancement

tag: time


title: BarBQ pastrami production chain, brine, with lactate, rep 2


title: MIXED1_8


title: BarBQ pastrami production chain, brine, with lactate, rep 1


title: TTL-KO-AE 2


title: TTL-KO-AE 1


title: BarBQ pastrami production chain, raw material, with lactate, rep 5

value: raw material


title: SVBP-KO-AE 2

value: SVBP-KO


title: SVBP-KO-AE 1


title: BarBQ pastrami production chain, raw material, with lactate, rep 4


title: BarBQ pastrami production chain, raw material, with lactate, rep 3


title: WT-AE 3


title: BarBQ pastrami production chain, mixture, with lactate, rep 1


title: WT-AE 2


title: BarBQ pastrami production chain, raw material, with lactate, rep 2


title: BarBQ pastrami, former batch, rep 5

description:
table_figure_1.qzv
taxa-bar-plots_figure_1.qzv
figure_1_quantified_microorganisms.csv


title: WT-AE 1


title: WT-ID 2

value: Control


title: BarBQ pastrami, former batch, rep 4


title: WT-ID 3

value: WT


title: BarBQ pastrami, former batch, rep 2


title: BarBQ pastrami, former batch, rep 3


title: BarBQ pastrami, former batch, rep 1


title: smoked pastrami, rep 5


title: IRI, Knockout 2, ScRNASeq

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

country: USA

institute: University of Virginia

description:
IRIKO2
10x Genomics

library_source: transcriptomic single cell

data_processing:
FastQ files were generated using Illumina’s BCLConvert.
The FastQ results from Illumina were processed using the 10x Genomics CellRanger tool (v8.0) for sequence alignment with the mm10 reference genome. Seurat (v5.1.0) was utilized for quality control filtering, clustering, and downstream gene expression analysis in R.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Kidney

extract_protocol:
Kidneys were digested with collagenase type1(4mg/ml, Sigma-Aldrich) using VIA Extractor tissue disaggregator (Cytiva LifeSciences) for 7 minutes at 37ºC. The digested tissues were passed through a 70µm cell strainer (BD Bioscience) to obtain a single-cell suspension. The cells were further subjected to Debris Removal Solution (Miltenyi Biotec) and MojoSort Dead Cell Removal (BioLegend) as per the manufacturer’s instructions. The CD4+ T cells were sorted by Influx Cell Sorter (BD Biosciences) using CD45-Percp/Cy5.5, CD25-APC/Cy7, TCRβ-A647, CD4-BV650, CD127-PE and DAPI (live/dead) flow panel.
The generation of single-cell indexed libraries was performed by the University of Virginia, School of Medicine Genome Analysis and Technology Core (GATC), RRID: SCR_018883, using the 10X Genomics Chromium X platform and the Chromium GEM-X Single Cell 3' Chip Kit (P/N 1000690, 1000691, 1000215).  Between 7,000 and 17,000 cells were targeted per sample with cell viabilities ranging between 80 and 95%.  Amplified cDNA was generated following the manufacturer’s protocols for the single cell GEM-X kit (10X Genomics) and QC’d using an Agilent 4200 TapeStation Instrument and the Agilent D5000 HS kit.  Single-cell libraries were prepared from the cDNA following the manufacturer’s protocols.  Individual libraries were QC’d using the Agilent 4200 TapeStation Instrument and the Agilent D5000 HS kit and ThermoFisher’s Qubit 3 using the DNA HS kit.   Libraries were pooled for a QC run on Illumina’s Miseq sequencer running the MiSeq Reagent Nano Kit v2 (300 cycles) (1.4 Million reads/run).  Data from this run was analyzed using 10x Genomic’s Cellranger 8.0.0, and the cell counts generated were used to rebalance the pool for sequencing on Illumina’s NextSeq 2000, using P3-100 cycle kits.

value: Kidney

value: CD4 T Cells

value: Il1rl1fl/fl Foxp3YFP-Cre

tag: age

value: 10 Weeks Old

value: Ischemia-reperfusion Injury


title: BarBQ pastrami production chain, raw material, with lactate, rep 1

value: pastami


title: smoked pastrami, rep 3


title: IRI, Wild Type1, ScRNASeq

description:
IRIWT1
10x Genomics


title: BarBQ pastrami production chain, brine, with lactate, rep 3


title: IRI, Wild Type2, ScRNASeq

description:
IRIWT2
10x Genomics


title: smoked pastrami, rep 2


title: KI-TTL 3

data_processing:
The sequencing data was automatically demultiplexed using the Illumina BCL Convert Software v3.8.2.
FastQ files underwent pre-trimming and post-alignment quality control rounds using FastQC v0.11.7.#_ENREF_25" \t "Andrews, 2010 #11320 Removal of Illumina adapters and low-quality sequences was performed with Trimmomatic v0.38.#_ENREF_26" \t "Bolger, 2014 #11306 Reads of length <15 bases, as well as leading and/or trailing bases with quality <3 or no base call, and bases with average quality <15 in a 4-base sliding window were removed
Alignment was performed with HISAT2 v2.1
Mapped reads (primary alignments) were sorted by read name using SAMtools v1.8
Read counts were calculated with HTSeq v0.11.2
Assembly: mm10
Supplementary files format and content: Raw read counts

source_name: Black Swiss

extract_protocol:
Total RNA isolation from left ventricle tissue
Enrichment of mRNAs with the NEBNext Poly(A) mRNA Magnetic Isolation Module was followed by library preparation using the NEBNext Ultra II RNA Directional Library Prep Kit for Illumina (New England BioLabs).
Single read sequencing took place on a NextSeq 2000 System (Illumina), using the corresponding NextSeq 2000 P3 Reagents (50 cycles), with a read length of 72 base pairs.

tag: strain

value: Black Swiss

tag: Sex

value: female


title: WT-ID 1


title: KI-TTL 1


title: kabanos, batch C, rep 4

source_name: kabanos

value: kabanos

value: final product


title: smoked pastrami, rep 1


title: kabanos, batch C, rep 3


title: KI-Empty 2


title: KI-Empty 3


title: KI-Empty 1


title: kabanos, batch C, rep 2


title: kabanos, batch C, rep 1


title: kabanos, batch B, rep 5


title: IRI, Knockout 1, ScRNASeq

description:
IRIKO1
10x Genomics


title: IRI, Knockout 3, ScRNASeq

description:
IRIKO3
10x Genomics


title: kabanos, batch B, rep 3


title: kabanos, batch B, rep 4


title: smoked pastrami, rep 4


title: WT-Empty 1


title: WT-Empty 2


title: Sog1R4_1.5

city: Riverside

first: Shiyang

last: He

state: CA

address: 3401 Watkins Drive, Boyce Hall

department: Biochemistry

institute: UCR

data_processing:
The quality of RNA-seq data was examined by FastQC v0.11.7.
The samples that have significantly more than 20M reads are downsampled to ~20M reads with seqtk 1.3-r106.
The raw sequencing data were mapped to the Arabidopsis thaliana genome version TAIR10 using the alignment algorithm STAR 2.7.3a.
PCR duplications were removed with bamUtil 1.0.14.
Reads count for each sample was calculated with featureCounts v2.0.0.
FPKM values were calculated with cufflinks v2.2.1.
The differentially expressed genes were identified with the DESeq2_1.36.0 package.
The volcano plots were drawn using the ggplot2_3.4.0package.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include  Feature Counts for each Sample.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown in a Percival 136LLVL growth chamber set at 20oC with a 24 hr light cycle.

extract_protocol:
Following 84h after sowing, seedlings were collected and flash frozen in liquid nitrogen after which total RNA was isolated using the RNAeasy kit per manufacturer’s instructions (Qiagen).
mRNA was isolated from approximately 10μg of total RNA using magnetic poly(A) capture beads following manufacturer’s instructions (PerkinElmer). The resulting mRNA was used for cDNA synthesis by the Rapid Directional RNA-Seq Library Prep Kit (PerkinElmer) and AMPure XP beads (Beckman Coulter Life Sciences) following manufacturer’s instructions.

treatment_protocol: Seedlings of Col-0 wt, als3-1 and sog1-7 were sterilized and cold treated after which they were planted on soaked gel medium with either 0 or 1.50mM AlCl3 (pH 4.2).

value: seedlings

tag: ecotype


title: KI-TTL 2


title: BarBQ pastrami production chain, after one week in storage, without lactate, rep 5


title: WT-Empty 3


title: kabanos, batch B, rep 1


title: kabanos, batch A, rep 5


title: kabanos, batch B, rep 2


title: kabanos, batch A, rep 2


title: kabanos, batch A, rep 4


title: kabanos, batch A, rep 3


title: sausage, batch C, rep 5

source_name: sausage

value: sausage


title: ColR4_1.5

value: wt


title: Sog1R3_0.0

value: 0 mM AlCl3 (pH 4.2)


title: Sog1R4_0.0


title: sausage, batch C, rep 4


title: ColR4_0.0


title: Sog1R2_0.0


title: kabanos, batch A, rep 1


title: Sog1R3_1.5


title: Sog1R2_1.5


title: ColR3_0.0


title: sausage, batch C, rep 3


title: ColR3_1.5


title: sausage, batch C, rep 2


title: sausage, batch C, rep 1


title: ColR2_1.5


title: ColR2_0.0


title: Als3R4_1.5


title: sausage, batch B, rep 5


title: sausage, batch B, rep 3


title: Als3R3_1.5


title: sausage, batch B, rep 4


title: sausage, batch B, rep 2


title: Als3R3_0.0


title: sausage, batch B, rep 1


title: sausage, batch A, rep 5


title: Als3R2_0.0


title: Als3R2_1.5


title: sausage, batch A, rep 3


title: sausage, batch A, rep 4


title: sausage, batch A, rep 2


title: sausage, batch A, rep 1


title: BarBQ pastrami, batch C, rep 4


title: 4644OAGFPNEG

city: San Francisco

first: Tien

last: Peng

state: California

address: 513 Parnassus Avenue

department: medicine

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: 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: Lung

extract_protocol:
Dissected mouse lung was 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) after perfusion with PBS and removed from the chest. The lung was incubated in digestion cocktail for 45 mins at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM). The mixture was passed through a 70 μm cell strainer and resuspended in red blood cell (RBC) lysis buffer, then passed through a 40 μm cell strainer. Cell suspensions were incubated with the appropriate conjugated antibodies in sorting buffer for 30 min at 4C and washed with FACS buffer. Doublets and dead cells were excluded based on forward and side scatter and SYTOX Blue (Invitrogen, S34857), respectively.  The following antibodies were used for staining: CD45-BV421 (BD, 563890), CD31-BV421 (Invitrogen, 48-0311-82), EpCAM-BV421 (BD, 563214). Immune (CD45-biotin, Biolgened, Cat#103104), epithelial (CD326-biotin, Biolegend, Cat#118204) and endothelial (CD31-Biotin, Biolegend, Cat#102404) cells are removed with EasySep mouse streptavidin RapidShperes (StemCell, 19860A). FACS was performed on a BD FACS Aria using FACSDiva Software. CD45- CD31- EpCAM- cells were sorted for mesenchymal cells, the GFP+ fibroblasts were further separated and were sorted into FACS buffer.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.
droplet-based single cell RNA-Seq

value: Lung

value: fibroblasts and tumor cells


title: 2470GFPNEG

description: 10x Genomics


title: BarBQ pastrami, batch C, rep 3


title: 2470GFPPOS

description: 10x Genomics


title: BarBQ pastrami, batch C, rep 2


title: GATA6+/+ Day 2 IgG biol rep 1

city: New York

first: Joseph

middle: A.

last: Bisson

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
SEACR-based analysis: The libraries were clustered on a pair end flow cell and sequenced for 50 cycles on an Illumina NextSeq500 Sequencing System. FASTQ files were aligned to the GENCODE GRCh38 build of the human genome using bowtie2 with the –-dovetail parameter. The resulting BAM files were sorted and indexed using samtools and then converted to bedgraph format using bedtools. Peaks were subsequently called using SEACR to identify enrichment in target data by selecting the top 1% of regions by AUC (stringent threshold). The DiffBind R Bioconductor package was used to interrogate differential binding for GATA6 vs IgG controls.
MACS2/HOMER (BasePair.com software): Transcription factor motif enrichment analysis and peak calling was performed using Basepair software with a CUT&RUN Peaks, Motif (MACS2, HOMER) pipeline (basepairtech.com).
Assembly: GRCh38
Supplementary files format and content: Annotated peaks from SEACR-based and MACS2-based analysis (.xlx files)
Library strategy: CUT&RUN

extract_protocol:
500,000 H1-GATA6+/+ cells were harvested approximately 52 hrs after starting the cardiac differentiation protocol and CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher 14-1048) according to the manufacturer’s protocol.  Anti-GATA6 (n=3 independent biological replicates) (Cell Signaling Technology 5851) and Rabbit Anti-IgG (n=2 independent biological replicates) negative control (Epicypher 13-0042) antibodies were used at a 1:50 dilution (~0.5g).
The DNA libraries were prepared with approximately 5 ng of CUT&RUN enriched DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs E7645) and NEBNextMultiplex Oligos for Illumina(96 Unique Dual Index Primer Pairs) (New England Biolabs E6440); 14 PCR cycles were used to amplify the adaptor ligated target DNA

value: hESC

value: WT

value: In vitro cardiac-directed differentiation (day 2)


title: GATA6+/+ Day 2 G6 biol rep 2


title: GATA6+/+ Day 2 G6 biol rep 1


title: Als3R4_0.0


title: BarBQ pastrami, batch C, rep 1


title: GATA6+/+ Day 2 G6 biol rep 3


title: BarBQ pastrami, batch B, rep 3


title: BarBQ pastrami, batch B, rep 4


title: BarBQ pastrami, batch B, rep 1


title: CSMN_P525L_03-07-2019

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

data_processing:
bcl2fastq2 2.19.1
Fragments were aligned to thehuman reference genome hg38with support of theEnsembl 92splice sites using the alignergsnap (v2018-07-04)
Counts per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation usingfeatureCounts (v1.6.3)
Assembly: hg38
Supplementary files format and content: Tab separated file with the output of featureCounts. Each columns is either describing characteristics of a gene (gene name, ensembl_id, strand, position, chromosom) or a sample. Each row list genes with the details of the gene and the counts per gene per sample.

source_name: Skin

growth_protocol: Differentiation of hiPSC into spinal motor neurons (MNs) was carried out based on the protocol from Reinhardt et al. 2013. Briefly, spinal motor neurons were cultured in N2B27 medium with 2 ng/ml BDNF (Promega), 2 ng/ml GDNF (Sigma-aldrich), 1 ng/ml TGFβ-3 (Promega), 100 µM dbcAMP (Sigma-aldrich) and 200 µM ascorbic acid and were matured for 21 DIV. Differentiation of hiPSC into cortical neurons (CN) was based on the protocol published by Burkhardt et al. (Burkhardt, Martinez et al. 2013, Japtok, Lojewski et al. 2015). Briefly, hiPSC were detached and replated at high density on a Matrigel®-coated dish in mTeSR1 medium with 10 µM Y-27632 inhibitor. Next day, Y-27632 was withdrawn and the cells were cultivated in mTeSR1 for the next 3-5 days to reach confluent cell layer. After that, neuronal differentiation was induced by applying neuronal differentiation medium (NDM: DMEM-F12/Neurobasal medium at 50:50 ratio, 1% penicillin/streptomycin/glutamine, 1% MEM Non-Essential Amino Acid Solution (ThermoFischer Scientific), 0.5% B27 supplement without vitamin A, 0.5% N2 supplement, 100 µM β-Mercaptoethanol (ThermoFischer Scientific), 5 µg/ml insulin (ThermoFischer Scientific) supplemented with 1.5 µM Dorsomorphin and 10 µM SB-431542. The cells were cultivated for 10 days and on day 11 Dorsomorphin and SB-431542 were withdrawn. The cells were kept in NDM without supplements until day 15 and then 0.05 µM retinoic acid was added. Cells were cultivated like this until day 20. After that, the cells were detached using accutase for 10 minutes at 37°C and replated on the poly-L-ornithine and laminin-coated dish at the density of 192,000 cells/cm2 in NDM supplemented with 0.05 retinoic acid, 2 ng/ml BDNF and 2 ng/ml GDNF. Additionally, only on the day of splitting, 10 µM Y-27632 inhibitor was added. The cells were maintained in these conditions until day 45 and then they were split as previously and replated onto a fresh poly-L-ornithine and laminin-coated dish at a density of 200,000 cells/cm2 in NDM supplemented with 0.05 retinoic acid, 2 ng/ml BDNF and 2 ng/ml GDNF. Additionally, only on the day of splitting, 10 µM Y-27632 inhibitor was added. The cells were maintained in these conditions until day 45 and then they were finally split for their respective assay and replated onto a fresh poly-L-ornithine and laminin-coated dish in the same medium.

extract_protocol:
mRNA was isolated from 30 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions.
mRNA was isolated from 30 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation NEB Next Adapter for Illumina of the NEB Next Multiplex Oligos for Illumina Kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. During the following 15 cycles PCR enrichment, unique dual index primer (Truseq design) were incorporated. After two XP bead purifications (with a ratio of 0.9:1 to the sample volume), libraries were quantified using the Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina Nextseq 550 system in 75 bp single-end mode to an average depth of 30 million fragments per library.

treatment_protocol: not applicable

value: Skin

tag: cell line_(ipsc_source)

value: Fibroblast

value: iPSC-derived spinal motor neurons

value: FUS-P525L eGFPhet (mutant)

value: Not applicable


title: CSMN_P525L_20-02-2019


title: BarBQ pastrami, batch B, rep 5

value: pastami


title: CSMN_WT_20-02-2019

value: FUS-WT eGFPhet (isogenic control)


title: BarBQ pastrami, batch A, rep 5

value: final product


title: 4644OAGFPPOS

description: 10x Genomics


title: CSMN_P525L_08-05-2019


title: BarBQ pastrami, batch A, rep 4


title: MN_P525L_04-07-2019


title: GATA6+/+ Day 2 IgG biol rep 2

description: JB_6765_WT_w4_NEGATIVE_CTRL_Rb_IgG_11_2_21


title: BarBQ pastrami, batch A, rep 3


title: CSMN_WT_08-05-2019


title: MN_WT_04-07-2019


title: BarBQ pastrami, batch A, rep 1


title: MN_P525L_21-03-2019


title: GATA6-/- Day 3 biol rep 2

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing. Day 2 and Day 5 RNA-seq alignment (GRChg19) and differential gene expression analysis were performed as described (Ref: 73, Anelli et al. 2017). Day 3 RNA-seq reads were aligned and mapped to the GRCh38 human reference genome by STAR (Version 2.5.2) and transcriptome resconstruction was performed by Cufflinks (Version 2.1.1) after trimming adaptors with cutadapt (Version 1.18). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM). Raw read counts per gene were extracted using HTSeq-count v0.11.277. Gene expression profiles were constructed for differential expression, cluster, and principle component analyses with the DESeq2 package. For differential expression analysis, pairwise comparisons between two or more groups using parametric tests where read-counts follow a negative binomial distribution with a gene-specific dispersion parameter were performed. Corrected p-values were calculated based on the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Day 2 and Day 5 data was aligned to hg19. Day 3 data was aligned to hg38
Supplementary files format and content: CSV files contains ENSID, gene symbol, and normalized counts for each sample for Day 2 and Day 3 RNA-seq
Supplementary files format and content: CSV file contains ENSID, gene symbol, and raw counts for each sample for Day 5 RNA-seq

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (QIAGEN)
Day 2 and Day 5 sample libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina), Day 3 sample libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's protocols.

value: Homozygous KO

value: In vitro cardiac-directed differentiation (day 3)


title: BarBQ pastrami, batch A, rep 2


title: MN_WT_21-03-2019


title: GATA6+/- Day 3 biol rep 1

value: Heterozygous KO


title: MN_WT_27-03-2019


title: GATA6-/- Day 3 biol rep 1


title: BarBQ pastrami, batch B, rep 2


title: GATA6+/- Day 3 biol rep 2


title: RSAD2-2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: hg19)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes
Assembly: Hg19
Supplementary files format and content: RSEM Count file is in Text

source_name: Macrophages (MDMs)

growth_protocol: Monocytes were cultured in IMDM+10% human serum and allowed to differentiate into MDMs for 6 days.

extract_protocol:
RNA was extracted using Rneasy plus mini kit (Qiagen)
Done by Genomics core

treatment_protocol: MDMs were infected with HIV-1 followed by two rounds of siRNA treatment to knockdown RSAD2 and then harvested for analysis

value: Macrophages (MDMs)

value: HIV infected MDM treated with siRSAD2 donor 2


title: RSAD2-3

value: HIV infected MDM treated with siRSAD2 donor 3


title: RSAD2-1

value: HIV infected MDM treated with siRSAD2 donor 1


title: NC-3

value: HIV infected MDM treated with siControl donor 3


title: NC-2

value: HIV infected MDM treated with siControl donor 2


title: CSMN_WT_03-07-2019

value: Skin


title: GATA6+/+ Day 3 biol rep 2

value: hESC

value: WT


title: SCZ5_ALN

city: Reutlingen

first: Hansjuergen

last: Volkmer

address: Markwiesenstr 55

institute: NMI at the University of Tuebingen

data_processing:
Illumina bcl2fastq (version 2.20) was used to demultiplex sequenced reads.
Sequence reads were trimmed for adaptor sequence using Skewer (version 0.2.2).
Trimmed sequence raw reads were mapped to the reference genome hg19.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw reads per gene
Supplementary files format and content: tab-delimited text files include DESeq2 normalized reads

growth_protocol: iPSC were differentiated into dopaminergic neurons via lentiviral overexpression of lineage-specific transcription factors (ASCL1, LMX1B, NURR1).

extract_protocol:
Dopaminergic neurons were harvested using Accutase and pelleted. RNA was extracted using RNeasy Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMART-Seq stranded total RNA Kit (Takara) following manufacturer's protocols.

treatment_protocol: Homogenous dopaminergic neuron populations were obtained by incorporation of a pyromycin resistance gene at the 3' end of NURR1 and separated by a 2A peptide sequence.

value: differentiated dopaminergic neurons from induced pluripotent stem cells

value: female

value: untreated dopaminergic neurons

value: Day 21


title: SCZ4_ALN

value: male


title: NC-1

value: HIV infected MDM treated with siControl donor 1


title: GATA6+/+ Day 3 biol rep 1

value: In vitro cardiac-directed differentiation (day 3)


title: SCZ2_ALN


title: U3

value: Uninfected MDM donor 3


title: U1

value: Macrophages (MDMs)

value: Uninfected MDM donor 1


title: MN_P525L_27-03-2019

value: Fibroblast

value: iPSC-derived spinal motor neurons

value: FUS-P525L eGFPhet (mutant)

value: Not applicable


title: 36 weeks , Overweight, Rep 9

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Raw FASTQ files were trimmed of auto-detected adapter sequences and filtered for read quality using TrimGalore (0.6.5) in paired-end mode.
Reads were aligned against the GRCh38 reference genome using STAR (2.7.9a) in paired-end mode. Resultant BAM files were sorted by coordinate and gzip-compressed.
Aligned reads were counted using the FeatureCounts utlility from subread (2.0.1) in unstranded mode (s=0), using the same annotation GTF used to construct the STAR reference.
Assembly: GRCh38
Supplementary files format and content: EukmRNAseq_counts.csv: Comma-seperated Values (CSV) table, count matrix used for input into DESeq2. Genes are listed as rows, and columns represent unique samples. The last 5 columns are gene annotations extracted from the reference GTF using the ENSEMBL ids found in the row names.

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

extract_protocol:
RNA was extracted using Trizol/BCP and Rneasy mini kit (QIAgen) and quantified using Qubit Flurometer
messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand of cDNA synthesis. This was followed by end repair, A-tailing, adapter ligation, size selection, amplification and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Blood samples from the pregnant women who were either normal weight or overweight at prepregnancy were collected at 12, 24, and 36 weeks of gestation for peripheral blood mononuclear cells isolation. PBMCs were isolated using FICO/Lite-LyphoH density gradient method.

tag: visit time

value: 36 weeks

tag: subject category

value: Overweight


title: CTR3_ALN

tag: tissue


title: Cardiac_Organoid_COVID

city: Palo Alto

first: Nazish

last: Sayed

address: 240 Pasteur Dr

institute: Stanford University

library_source: other

data_processing:
FASTQ format files were processed using default parameters with 10x Genomics Cell Ranger Arc (2.0.0) count function
ArchR a R package is used to process the single cell multiome ddata
First created a  ArchR project using the fragment files of two samples and imported scRNA using import10xFeaatureMatrix function
Dimensional reduction is performed, and resoultion 0.2 is used to cluster cells.
Supplementary files format and content: fragement file and feature matrix in tsv, h5 format
Library strategy: Single Cell Multiome ATAC + Gene Expression

molecule: other

source_name: cardiac organoid

growth_protocol: COs were fabricated with iPSC-CM and iPSC-ECs. To generate COs, the cells were dispensed at a final cell density of 1 × 106 cells/ml into an agarose mold replica (Microtissues® Inc) featuring a 9 x 9 microwell array. Cell sedimentation into the microwells and self-assembly of the COs occurred over 48 hours. After 48 hours, spontaneously beating COs were then maintained in RPMI-B27 with insulin at 37°C and 5% CO2 until further experiments with SARS-CoV2.

extract_protocol:
Human iPSC-derived COs were digested with freshly prepared Liberase solution (R&D) for 10 mins. Digestion was halted by resuspending in RPMI-B27 with insulin and EGM2 medium. After passing through a 70 μm strainer, viability of the cells was checked and then prepped for nuclei isolation. Cells were washed with ice-cold Wash buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 0.1% Tween-20, and 1 U/μl RNase inhibitor), spun down and resuspended in 100 μl chilled Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 0.1% Tween-20, 0.01% Digitonin, 0.1% Nonidet P40 Substitute and 1 U/μl RNase inhibitor). Cells were lysed for 5 mins on ice followed by resuspension in 1 ml chilled wash buffer. After spinning for 5 mins at 500 rcf, nuclei pellet was resuspended in 50 μl Nuclei buffer (10x Genomics) and 1 U/μl RNase inhibitor.
Briefly, an estimated 10,000 nuclei per sample were captured as per instructions from the10X chromium Single Cell Multiome ATAC and Gene Expression Reagent Kits V1 User Guide. Joint scRNA- and scATAC-seq libraries were prepared using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions

treatment_protocol: SARS-CoV-2 pseudovirus was obtained commercially (Montana Molecular). COs were infected with SARS-CoV-2 pseudovirus at the titer of 2x1010 VG/ml in RPMI-B27 + EGM2 (for COs) for respective time periods.

value: exposedd to SARS-CoV-2 pseudovirus


title: Cardiac_Organoid_No COVID


title: SCZ1_ALN

tag: cell line

value: differentiated dopaminergic neurons from induced pluripotent stem cells


title: U2

tag: cell type

value: Uninfected MDM donor 2


title: CTR2_ALN

value: female

value: untreated dopaminergic neurons


title: GATA6+/+ Day 3 biol rep 3

value: hESC

value: WT


title: 24 weeks, Overweight, Rep 10

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: 24 weeks


title: CTR1_ALN

value: Day 21


title: SH1245_TR_GU02DN

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: counts.csv is a comma-separated-values file with rows corresponding to a gene, columns corresponding to a sample, and values giving the number of reads aligned to the gene.

source_name: CTC

extract_protocol:
Single cells were picked or sorted into lysate buffer and RNA was released.
single cell cDNA was amplified using SMART-seq2 protocol

value: CTC

tag: donor

value: EpCAM- and PSMA-


title: SH1404_TR_GU02DN


title: SH1328_TR_GU02DN


title: SH1233_TR_GU02DN


title: 36 weeks , Overweight, Rep 8


title: SH1402_TR_GU02DN


title: 24 weeks, Overweight, Rep 9


title: SH1150_TR_GU02DN


title: SH1151_TR_GU02DN


title: 12 weeks, Overweight, Rep 10

value: 12 weeks


title: KPC-3403 anti-PD-1 + TGFB-TRAP

city: Baltimore

first: Heng Chung

last: Kung

state: Maryland

address: 1650 Orleans Street

department: Department of Oncology

institute: Johns Hopkins University School of Medicine

data_processing:
The demultiplexing, barcode processing, gene counting were conducted using CellRanger v6.1.2 (10X Genomics)
Assembly: mm10
Supplementary files format and content: Tab separated values and matrix files

molecule: nuclear RNA

source_name: KPC PDAC Orthotopic Tumor

extract_protocol:
Briefly, fresh sucrose density buffer containing sucrose (0.344 g/mL, Sigma-Aldrich), 10 mM HEPES (Gibco), 5 mM CaCl2 (Sigma-Aldrich), 3 mM magnesium acetate tetrahydrate (Sigma-Aldrich), 1 mM DTT (Sigma-Aldrich), and 0.2 U/mL NxGen RNase inhibitor (Lucigen) was prepared. Frozen mouse orthotopic KPC PDAC tumors were mechanically homogenized into powder form using mortar and pestle in liquid nitrogen. Lysis buffer containing 0.1% Triton-X (Sigma-Aldrich), 0.2 U/mL NxGen RNase inhibitor (Lucigen), and sucrose density buffer was added to the homogenized tissue and let sit for 3 min on ice. Following lysis, the crude homogenate was pipetted over a 100 mm cell strainer, washed with sucrose density buffer, and centrifuged at 400 rcf for 5 min at 4°C on low brake setting. The supernatant was aspirated, and the pellet was resuspended in resuspension buffer containing PBS + 1% BSA (Sigma-Aldrich) and 0.2 U/mL RNase inhibitor (Lucigen) over a 35 mm filter flow tube. Amplified cDNA was generated from RNA from each single nuclei using the Chromium Next GEM Single Cell V(D)J Reagent Kits v.1.1, per the manufacturer’s instructions.
Amplified cDNA was generated from RNA from each single nuclei using the Chromium Next GEM Single Cell V(D)J Reagent Kits v.1.1, per the manufacturer’s instructions.

value: KPC PDAC Orthotopic Tumor

value: anti-PD-1, TGFB-TRAP


title: SH1142_TR_GU02DN


title: KPC-3403 anti-PD-1 + anti-IL-1B

value: anti-PD-1, anti-IL-1B


title: KPC-3403 anti-IL-1B

value: anti-PD-1 isotype, anti-IL-1B


title: KPC-3403 anti-PD-1

value: anti-PD-1, TGFB-TRAP isotype


title: SH1141_TR_GU02DN


title: KPC-3403 TGFB-TRAP

value: anti-PD-1 isotype, TGFB-TRAP


title: 36 weeks , Normal Weight, Rep 10

value: 36 weeks

value: Normal Weight


title: SH1135_TR_GU02DN


title: SH895_TR_GU02CTC

value: EpCAM+ and/or PSMA+


title: 36 weeks , Overweight, Rep 7

value: Overweight


title: SH890_TR_GU02CTC


title: SH893_TR_GU02CTC


title: KPC-3403 Control

value: anti-PD-1 isotype, TGFB-TRAP isotype


title: 12 weeks, Overweight, Rep 9

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: KPC-4545 anti-PD-1 + TGFB-TRAP


title: 24 weeks, Overweight, Rep 8

value: 24 weeks


title: SH889_TR_GU02CTC


title: KPC-4545 anti-PD-1


title: SH887_TR_GU02CTC


title: SH886_TR_GU02CTC


title: SH1139_TR_GU02DN


title: KPC-4545 anti-IL-1B


title: 24 weeks, Normal Weight, Rep 7


title: GATA6-/- Day 5 biol rep 2

value: hESC

value: Homozygous KO

value: In vitro cardiac-directed differentiation (day 5)


title: SH885_TR_GU02CTC

value: CTC


title: SH879_TR_GU02CTC


title: SH882_TR_GU02CTC


title: SH829_TR_GU02CTC


title: KPC-4545 Control

value: KPC PDAC Orthotopic Tumor


title: KPC-4545 TGFB-TRAP


title: SH897_TR_GU02CTC


title: SH828_TR_GU02CTC


title: 36 weeks , Overweight, Rep 6


title: GATA6-/- Day 5 biol rep 1


title: 36 weeks , Normal Weight, Rep 9


title: 24 weeks , Normal Weight, Rep 4


title: KPC-4545 anti-PD-1 + anti-IL-1B


title: SH827_TR_GU02CTC


title: GATA6+/- Day 5 biol rep 2

value: Heterozygous KO


title: 12 weeks, Normal Weight, Rep 10

value: 12 weeks


title: MMPhigh_1

city: Bengaluru

first: Maneesha

middle: S

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur

department: MBGU

country: India

institute: JNCASR

data_processing:
The cell ranger 2.1.1 pipeline (10X genomics) was used to align reads to the mm10 reference genome, and barcode matrices were generated using the default parameters.
Assembly: UCSC mm10
Supplementary files format and content: Barcodes, features and matrix files

source_name: mouse embryonic AGM cells

extract_protocol:
Freshly sorted CD31+ AGM cells based on TMRM intensity- MMPlow and MMPhigh were resuspended in 1X PBS with 2% FBS. Cell suspension was loaded into the Single Cell B Chip (10X Genomics) and processed in the Chromium single cell controller (10X Genomics), targeting a maximum of 10000 cells per lane.
The single cell mRNA library was prepared using the Chromium Single Cell 3’ Reagent kit v3 instructions (10x Genomics) according to manufacturer’s instructions.

value: mouse embryonic AGM cells


title: SH823_TR_GU02CTC


title: MMPhigh_2

growth_protocol: Freshly sorted CD31+ AGM cells based on TMRM intensity- MMPlow and MMPhigh were resuspended in 1X PBS with 2% FBS.


title: GATA6+/- Day 5 biol rep 1


title: 24 weeks , Normal Weight, Rep 3


title: MMPlow_2


title: MMPlow_1


title: SH888_TR_GU02CTC


title: 24 weeks, Normal Weight, Rep 6


title: GATA6+/+ Day 5 biol rep 2

value: WT


title: SH822_TR_GU02CTC


title: SH820_TR_GU02CTC


title: 36 weeks , Normal Weight, Rep 8


title: CCCP_rep2

data_processing:
Quality check of the sequenced FASTQ files was done using FastQC tool, followed by trimming, which involves removal of adaptor sequences and low-quality bases (Q<20) from the ends of the reads using Fastp.
UCSC mm10 was used as the reference genome, and indexed using Hisat2. Trimmed reads were aligned to the indexed genome using Hisat2.
The resulting sequence Alignment/Map (SAM) files were sorted by coordinates and converted to Binary Alignment/Map (BAM) files using Samtools.
Gene expression values were calculates using the Feature counts package of the Subread R package, and summarised counts for each gene was obtained.
Assembly: UCSC mm10
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: AGM

growth_protocol: AGM tissue from E10.5 and E11.5 embryos was dissected and cultured on a 0.65μm membrane filter at the gas-liquid interface for 48 hours 1.5mL MyeloCult media, supplemented with 10-6M hydrocortisone.

extract_protocol:
RNA from control and CCCP treated AGM explants was isolated through TRIzol method, and quantified using Qubit high-sensitivity assay kit on Qubit 4 fluorimeter.
mRNA isolation was done using NEBNext Poly(A) mRNA Magnetic Isolation Module. cDNA stranded library construction was performed using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads.

treatment_protocol: 5μM CCCP was used to treat the explants for 48 hours

value: AGM

value: Embryonic HSCs

value: CCCP treated


title: GATA6+/+ Day 5 biol rep 1


title: SH819_TR_GU02CTC

value: EpCAM+ and/or PSMA+


title: 24 weeks, Normal Weight, Rep 5

value: Normal Weight


title: CCCP_rep1


title: UN_rep2

value: Untreated


title: 12 weeks, Overweight, Rep 8

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: Overweight


title: SH817_TR_GU02CTC


title: GATA6-/- Day 2 biol rep 3

value: hESC

value: In vitro cardiac-directed differentiation (day 2)


title: GATA6-/- Day 2 biol rep 2

value: Homozygous KO


title: 12 weeks, Normal Weight, Rep 9


title: SH816_TR_GU02CTC

value: CTC


title: GATA6-/- Day 2 biol rep 1


title: UN_rep1


title: 12 weeks, Normal Weight, Rep 8


title: GATA6+/- Day 2 biol rep 3


title: WT_MEF_clone5_immortalized

city: St. John's

first: Michael

last: Leitges

state: NL

address: 300 Prince Philip Drive

department: Division of BioMedical Sciences, Faculty of Medicine

country: Canada

institute: Memorial University of Newfoundland

data_processing:
The quality of the FASTQ files were analyzed using FASTQC (version 0.12.0)
Pair-end reads obtained from RNA-seq data were mapped to the mouse reference genome (mm10) using STAR (version 2.7.10a) software with default parameters
Samtools (version 1.18) as used to convert the sequence alignment map (SAM) files were subsequently into the Binary Alignment Map (BAM) format.
Gene counts were assigned based on reads uniquely mapped to annotated genes in the Ensembl Mus_musculus.GRCm38.102.gtf using featureCounts function of Subread (version 2.0.6)
Assembly: mm10/GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: MEFs were cultured in DMEM – high glucose (Sigma-Aldrich) supplemented with 10% FCS, 1X non-essential amino acids (Cytiva), 1% Pen Strep (Gibco) and β-mercaptoethanol (Gibco).

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, ID:  80204)
Poly A-enriched RNA library preparation and sequencing was outsourced to Centre d’expertise et de services Génome Québec (Montreal, Canada)

treatment_protocol: Modified NIH 3T3 spontaneous immortalization protocol. Primary MEFs were passaged serially until they reached senescence. Once MEFs became senescent, culture media was shifted to MEF culture medium with 20% FCS. Prolonged cell culture gave rise to spontaneously immortalized cells (colonies), which then established immortalized MEF cell lines

tag: clone

value: Mouse Embryonic Fibroblast

value: immortalized Mouse Embryonic Fibroblast

value: immortalized


title: 12 weeks, Normal Weight, Rep 7

value: 12 weeks


title: SH811_TR_GU02CTC


title: SH810_TR_GU02CTC


title: WT_MEF_clone4_immortalized

tag: genotype

value: WT


title: GATA6+/- Day 2 biol rep 2

value: Heterozygous KO

tag: treatment


title: 24 weeks, Normal Weight, Rep 4

value: 24 weeks


title: SH809_TR_GU02CTC


title: GATA6+/- Day 2 biol rep 1


title: WT_MEF_clone3_immortalized


title: SH808_TR_GU02CTC


title: 12 weeks, Normal Weight, Rep 6


title: WT_MEF_clone5_primary

value: primary Mouse Embryonic Fibroblast

value: primary


title: GATA6+/+ Day 2 biol rep 3


title: WT_MEF_clone4_primary


title: SH807_TR_GU02CTC

value: EpCAM+ and/or PSMA+


title: 24 weeks, Overweight, Rep 6


title: GATA6+/+ Day 2 biol rep 2


title: GATA6+/+ Day 2 biol rep 1


title: 12 weeks, Overweight, Rep 7


title: 36 weeks , Overweight, Rep 5

value: 36 weeks


title: SH804_TR_GU02CTC


title: ARtfm Th17 IgG

city: Nashville

first: Dawn

middle: C

last: Newcomb

state: TN

address: 1161 21st Ave South, T-1218 MCN

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
fragments were trimmed using Trimmomatic (v0.39) and mapped onto mouse genome GRCm38.p6 using bowtie2 (v2.3.5.1).
Alignment SAM files were transformed into BAM and bigwig files using samtools (v.9) and deeptolls (v3.3.1).
MACS2 (v2.2.7.1) was used for calling peaks and DiffBind compared differential peaks between groups to make the MA plots.
GREAT (v4.0.4) was used to determine significantly different gene ontology (GO) pathways and genomic regions based on region-based binomial q-value FDR<0.05.
Assembly: mm10
Supplementary files format and content: bigWig narrow peak
Library strategy: CUT&RUN

source_name: spleen

extract_protocol:
CUT&RUN was performed using CUT&RUN kit with magnetic bead-based method per manufacturer instructions (Cell Signaling Technology).
Using the KAPA HyperPrep Kit, DNA was extracted and constructed into sequencing libraries.

value: spleen

value: male

value: ArTfm

tag: chip antibody

value: IgG


title: SH800_TR_GU02CTC


title: Male Th17 IgG

value: Male


title: Female Th17 IgG

value: female


title: SH801_TR_GU02CTC

value: CTC


title: P7_P56_MO-VIS-SSs

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Fastq files were multiplexed with custom pipeline using the indexes in the tsv files
Assembly: mm10
Supplementary files format and content: RDS file containing a barcodes counts

source_name: cortical neurons anterogradely labeled

extract_protocol:
Tissue was put in Trizol for total RNA extraction.
1st strand cDNA synthesis was performed with Superscript III reverse transcriptase and barcoded RT primer (sample identifier) Samples were then pooled, cleaned and concentrated via Ampure XP magnetic beads 2nd strand cDNA synthesis. Clean up of cDNA was done using Qiagen MinElute PCR clean up kit. The sample were then treated with exonucleases followed by nested PCRs to amplify target transcripts and adding Illumina sequencing sequences Gel purification was then done using Qiagen MinElute gel extraction kit and libraries were cleaned with Ampure XP magnetic beads
Custom to barcodes

value: cortical neurons anterogradely labeled


title: P0-P3-P56_MO-SSp


title: 12 weeks, Overweight, Rep 6

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: Overweight


title: SH799_TR_GU02CTC


title: P3-P56_MO-SSp


title: 24 weeks, Overweight, Rep 7


title: 36 weeks , Overweight, Rep 4


title: P7-P10-P21-P56_MO-SSp-SSs-2


title: SH797_TR_GU02CTC


title: ARtfm 3 Th17 H3K27Me3


title: SH805_TR_GU02CTC


title: SH796_TR_GU02CTC


title: 12 weeks, Overweight, Rep 5

value: 12 weeks


title: ARtfm 2 Th17 H3K27Me3


title: 24 weeks, Normal Weight, Rep 3

value: Normal Weight


title: P7-P10-P21-P56_MO-SSp-SSs-1


title: ARtfm 1 Th17 H3K27Me3


title: WT_MEF_clone3_primary

value: Mouse Embryonic Fibroblast

value: WT


title: 24 weeks, Overweight, Rep 5

value: 24 weeks


title: 36 weeks , Normal Weight, Rep 7


title: SH793_TR_GU02CTC

value: EpCAM+ and/or PSMA+


title: Female 2 Th17 H3K27Me3


title: Female 3 Th17 H3K27Me3


title: SH792_TR_GU02CTC


title: P7-P56_MO-VIS


title: 24 weeks , Normal Weight, Rep 2


title: Male 3 Th17 H3K27Me3


title: subcortically projecting cortical neurons, S2_P7_1

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex at P7 sample 1
PTsubset_wholeCell_2452PT_P7vsP21.rds

data_processing:
Fastq were processed with cellranger (v6.1.1)
Assembly: mm10
Supplementary files format and content: RDS file containing a Seurat object with count matrix, normalized counts, UMAP, and cell annotations
Supplementary files format and content: RDS file containing a Seurat Object with count matrix, normalized counts, UMAP, and age annotations

extract_protocol:
Chromium Single Cell 3' GEM (V3.1)
Chromium Single Cell 3' library (V3.1)
snRNA-seq


title: 12 weeks, Overweight, Rep 4


title: 36 weeks , Overweight, Rep 3

value: 36 weeks


title: SH790_TR_GU02CTC


title: subcortically projecting cortical neurons, S2_P7_2

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex at P7 sample 2
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: SH789_TR_GU02CTC


title: Male 1 Th17 H3K27Me3

value: spleen


title: subcortically projecting cortical neurons, MO_P7_1

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex at P7 sample 1
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: P7-P28-P56_MO-VIS


title: subcortically projecting cortical neurons, MO_P7_2

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex at P7 sample 2
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: SH794_TR_GU02CTC


title: Granulosa cells-PMSG_48h_HCG_6h_rep3

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: Granulosa cells

extract_protocol:
Granulosa cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected at 0h, 1h and 6h after 5IU PMSG(48h) and 5IU HCG induction

value: Kunming

value: ovary

value: Granulosa cells

value: post natal day 21

value: 48h after PMSG injection and 6h after HCG injection


title: subcortically projecting cortical neurons, S1_P7_2

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex at P7 sample 2
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: 36 weeks , Overweight, Rep 2


title: SH788_TR_GU02CTC

value: CTC


title: 24 weeks, Overweight, Rep 4


title: SH787_TR_GU02CTC


title: Female 1 Th17 H3K27Me3

value: female


title: subcortically projecting cortical neurons, S1_P7_1

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex at P7 sample 1
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: Granulosa cells-PMSG_48h_HCG_6h_rep2


title: P7-28-56_MO-VIS

value: cortical neurons anterogradely labeled


title: 12 weeks, Normal Weight, Rep 5

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: SH791_TR_GU02CTC


title: SH785_TR_GU02CTC


title: 12 weeks, Overweight, Rep 3

value: 12 weeks

value: Overweight


title: subcortically projecting cortical neurons, S2_P21_2

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex at P21 sample 2
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: Granulosa cells-PMSG_48h_HCG_6h_rep1


title: SH734_TR_GU02CTC


title: Male 2 Th17 H3K27Me3

value: male


title: subcortically projecting cortical neurons, S2_P21_1

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex at P21 sample 1
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: Granulosa cells-PMSG_48h_HCG_1h_rep3

value: 48h after PMSG injection and 1h after HCG injection


title: 12 weeks, Normal Weight, Rep 4

value: Normal Weight


title: 36 weeks , Normal Weight, Rep 5


title: SH730_TR_GU02CTC

value: EpCAM+ and/or PSMA+


title: Granulosa cells-PMSG_48h_HCG_1h_rep1


title: SH733_TR_GU02CTC


title: 12 weeks, Normal Weight, Rep 3


title: Granulosa cells-PMSG_48h_HCG_0h_rep3

value: 48h after PMSG injection


title: subcortically projecting cortical neurons, MO_P21_2

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex at P21 sample 2
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: SH727_TR_GU02CTC


title: 36 weeks , Normal Weight, Rep 4

value: 36 weeks


title: SH728_TR_GU02CTC


title: 36 weeks , Normal Weight, Rep 6


title: subcortically projecting cortical neurons, S1_P21_1

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex at P21 sample 1
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: SH726_TR_GU02CTC


title: Granulosa cells-PMSG_48h_HCG_0h_rep1

value: Kunming


title: SH725_TR_GU02CTC


title: 36 weeks , Normal Weight, Rep 3


title: Granulosa cells-PMSG_48h_HCG_0h_rep2

value: ovary


title: 24 weeks, Normal Weight, Rep 2

value: 24 weeks


title: subcortically projecting cortical neurons, MO_P21_1

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex at P21 sample 1
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: SH724_TR_GU02CTC


title: 36 weeks , Overweight, Rep 1


title: Granulosa cells-PMSG_48h_HCG_1h_rep2

value: Granulosa cells

value: post natal day 21


title: subcortically projecting cortical neurons, S1_P21_3

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex at P21 sample 3
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: subcortically projecting cortical neurons, S2_P8_P21

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex. P8 and P21 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: 24 weeks, Overweight, Rep 3


title: Granulosa cells Gm12840-/- rep2

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

treatment_protocol: Samples were collected at 6h after 5IU PMSG(48h) and 5IU HCG induction

value: 48h after PMSG injection and 6h after HCG injection


title: subcortically projecting cortical neurons, S1_P21_2

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex at P21 sample 2
PTsubset_wholeCell_2452PT_P7vsP21.rds


title: SH723_TR_GU02CTC

value: CTC


title: Granulosa cells Gm12840-/- rep1


title: 12 weeks, Overweight, Rep 2


title: SH721_TR_GU02CTC


title: SH720_TR_GU02CTC


title: Granulosa cells WT rep3

value: wild type


title: 24 weeks, Overweight, Rep 2

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: Granulosa cells Gm12840-/- rep3


title: subcortically projecting cortical neurons, S1_P8_P21

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex. P8 and P21 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: subcortically projecting cortical neurons, S1_P4_P12

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: subcortically projecting cortical neurons, S1_P10+56

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from primary somatosensory cortex. P10 and P56 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: Granulosa cells WT rep1


title: 12 weeks, Overweight, Rep 1

value: 12 weeks


title: 12 weeks, Normal Weight, Rep 1


title: subcortically projecting cortical neurons, P_Vis_P8+21

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from primary visual cortex  cortex. P8 and P21 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: SH719_TR_GU02CTC


title: SH714_TR_GU02CTC


title: Retina_18w_F10

city: Leuven

first: Lieve

last: Moons

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

data_processing:
Reads were trimmed using Trim-Galore! (v0.6.7), a wrapper for Cutadapt (v3.4) and FastQC (v0.11.9)
Trimmed reads were mapped to the custom-built transcriptome using STAR (v2.7.0)
Mapped reads were cleaned using Samtools (v1.9.4)
Gene counts were generated by HTseq (v0.11.2) and comparative analysis between individual ages was performed using EdgeR (v3.42.4)
Assembly: PRJEB5837
Supplementary files format and content: Tab-delimited text file including raw counts for each sample

organism: Nothobranchius furzeri

source_name: Neural Retina

growth_protocol: Killifish of the GRZ-AD inbred strain were housed in a standarised system maintaining constant pH (7.0), conducitivty (600µs) and temperature (28,0°C).

extract_protocol:
Fish were euthanized using 0.1% tris buffered tricaine. Retinas were collected after retinal pigment epithelium removal. Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
Libraries were generated using the QuantSeq 3' (Lexogen) mRNA protocol according to the manufacturer's protocol.

value: Neural Retina

value: Wildtype

tag: condition

value: 18 weeks


title: 12 weeks, Normal Weight, Rep 2

value: Normal Weight


title: SH708_TR_GU02CTC

value: EpCAM+ and/or PSMA+


title: subcortically projecting cortical neurons, S2_P4_P12

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: subcortically projecting cortical neurons, P_Vis_P4+12

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from primary visual cortex cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: 36 weeks , Normal Weight, Rep 2


title: Retina_18w_F09


title: subcortically projecting cortical neurons, S2_P10+56

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex. P10 and P56 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: Retina_18w_F08


title: SH705_TR_GU02CTC


title: Granulosa cells WT rep2


title: subcortically projecting cortical neurons, P_S2_P8+21

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex. P8 and P21 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: 24 weeks , Normal Weight, Rep 1


title: Retina_18w_F07


title: subcortically projecting cortical neurons, P_S2_P4+12

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from supplemental somatosensory cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: 36 weeks , Normal Weight, Rep 1


title: SH704_TR_GU02CTC


title: Retina_18w_F06


title: Retina_18w_F05


title: SH703_TR_GU02CTC


title: subcortically projecting cortical neurons, P_S1_P8+21

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from primary somatosensory cortex. P8 and P21 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: subcortically projecting cortical neurons, P_MO_P8+21_2

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from motor cortex. P8 and P21 were pooled in one 10X library. Technical replicate.
L5ET-DEV_Abe_2024.rds


title: Retina_18w_F04


title: HL60-shSDHA-2-R3

city: Hangzhou

first: Meidan

last: Ying

address: No.866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: Zhejiang University

data_processing:
First, the raw image files were obtained, then base calling and error filtering were performed to finally obtain the raw sequencing reads that can be used for analysis. The raw reads obtained from sequencing were filtered to get clean reads for data analysis. Seqtk was used for filtering. Hisat2 (version: 2.0.4) 's spliced mapping algorithm was applied for genome mapping of the preprocessed reads, using default parameters. The mapping generated alignment results in BAM format. Analyze the curve of the number of detected genes increasing with the increase of sequencing amount. We first used Stringtie (version: 1.3.0) to count the number of fragments for each gene after Hisat2 alignment, then performed normalization using the TMM (trimmed mean of M values) method, and finally calculated the FPKM value for each gene using a perl script. Assembly: hg38 Supplementary files format and content: gene_expression.txt include FPKM values and counts of each group.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Haematopoietic and Lymphoid

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US). According to the experimental protocol, purified Total RNA was used for mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, 3' end A addition, adapter ligation, and enrichment to construct the sequencing library.
RNA Libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

value: Haematopoietic and Lymphoid

value: Adult Acute Myeloid Leukemia cell

value: SDHA Knockdown


title: subcortically projecting cortical neurons, P_S1_P4+12

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from primary somatosensory cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: SH702_TR_GU02CTC


title: subcortically projecting cortical neurons, P_MO_P8+21

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from motor cortex. P8 and P21 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: 24 weeks, Overweight, Rep 1

value: Overweight


title: Retina_18w_F03


title: Breast_adjacent_tissue_scRNAseq

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
The barcode processing and gene counting were made using Cell Ranger software v 6.0.1. The feature-barcode matrices are contained intheTSVfiles.
Assembly: GRCh38
Supplementary files format and content: The feature files contain the gene ID, the barcode file contains the identification of the cell, the matrix file containsthecounts.

source_name: Breast cancer adjacent tissue

extract_protocol:
Breast tissue was acquired from three Tru-Cut biopsies. The tissue was sectioned into small fragments and cryopreserved in FBS (Gibco) supplemented with 10% dimethyl sulfoxide (DMSO, Sigma). Upon thawing, the tissue was enzymatically dissociated using Accumax solution (Sigma) and incubated for 30 minutes. The resulting cell suspension was filtered through a 40 µm filter, followed by processing using the Dead Cell Removal Kit (Miltenyi Biotec #130090101) through two rounds to ensure sufficient viability.
The scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3´Reagent Kits v3.1 (Dual Index) following the manufacturer's instructions (10X Genomics). Briefly, the cell suspension was minimally manipulated as described above and loaded onto the Chromium Next GEM Chip G, avoiding bubble formation. Then the chip was inserted into the Chromium Single Cell Controller. Subsequently, the cDNA library was produced, cleaned, and amplified using 11 cycles of the specified PCR program. Libraries were constructed by adding the appropriate adapters and indices (Dual Index TT Set A) provided by the manufacturer. The final amplification was carried out with 12 cycles of the specified PCR program.

value: Breast cancer adjacent tissue

value: Breast tissue


title: HL60-shSDHA-2-R2


title: Retina_18w_F02


title: SH691_TR_GU02CTC


title: HL60-shSDHA-2-R1


title: SH707_TR_GU02CTC


title: SH689_TR_GU02CTC


title: subcortically projecting cortical neurons, MO_P8_P21

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex. P10 and P56 were pooled in one 10X library sample 2
L5ET-DEV_Abe_2024.rds


title: subcortically projecting cortical neurons, P_MO_P4+12

description:
AAV2-retro injection into the basilar pons. Retrogradely labelled nuclei were collected from motor cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: HL60-shSDHA-1-R3


title: WBC6_healthy donor1

source_name: White Blood Cell from a healthy donor

value: White Blood Cell from a healthy donor


title: Retina_12w_F10


title: subcortically projecting cortical neurons, MO_P8

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex at P8
L5ET-DEV_Abe_2024.rds


title: Retina_18w_F01


title: HL60-shSDHA-1-R2


title: WBC4_healthy donor1


title: HL60-shSDHA-1-R1


title: subcortically projecting cortical neurons, MO_P4_P12

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex. P4 and P12 were pooled in one 10X library.
L5ET-DEV_Abe_2024.rds


title: Retina_12w_F08


title: Retina_12w_F09


title: HL60-shCtrl-R3

value: WT

value: shCtrl


title: BRx68_single_cell_3

source_name: Cell from CTC-derived cell line

value: Cell from CTC-derived cell line


title: HL60-shCtrl-R2


title: Liver, LeuD, WT, 15 bio rep2

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley rd

department: Nutritional Sciences

institute: Rutgers University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes.
Assembly: GRCm39
Supplementary files format and content: Processed data contains the Deseq output of comparisons between our experimental groups.

source_name: Liver

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Plus Kit (Zymo Research) following instructions provided by the manufacturer.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’-ends and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated with the TapeStation System (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific). Further validation of the libraries was carried out by quantitative PCR (KAPA Biosystems) of selected genes.

treatment_protocol: WT and GCN2 KO mice were individually housed and given ad libitum access to food and water and placed on their normal 12-h light-dark cycle. Following a 2-day adjustment period to a control diet, the mice either remained on the control diet (Control) or were switched to a leucine-devoid diet (LeuD) at the start of the dark cycle. 24-hours following this switch, the lights were turned off and stayed off for the remaining 8-day period. Following the 8-day darkness period, the mice were killed under red light at either circadian time (CT) 03 or 15, and their livers were collected and immediately snap frozen in liquid nitrogen.

value: Liver

tag: time

tag: diet

value: LeuD


title: BRx68_single_cell_2


title: Retina_12w_F06

value: Neural Retina

value: 12 weeks


title: Retina_12w_F07

value: Wildtype


title: Liver, Control, WT, 15 bio rep3

value: Control


title: BRx68_single_cell_1


title: Retina_12w_F05


title: Liver, Control, GCN2 KO, 15 bio rep3

value: GCN2 KO


title: SH636_TR_GU01DN

value: CTC

value: EpCAM- and PSMA-


title: HL60-Suc-24h-R3

value: Haematopoietic and Lymphoid

value: Adult Acute Myeloid Leukemia cell

value: Succinate 24h


title: Liver, Control, WT, 15 bio rep2


title: HL60-Suc-24h-R2


title: HL60-Suc-3h-R3

value: Succinate 3h


title: Liver, Control, GCN2 KO, 15 bio rep2


title: WBC1_healthy donor1

value: White Blood Cell from a healthy donor


title: SH626_TR_GU01DN


title: Retina_12w_F03


title: SH611_TR_GU01DN


title: subcortically projecting cortical neurons, MO_P10+56

description:
AAV2-retro injection into the spinal cord. Retrogradely labelled nuclei were collected from motor cortex. P10 and P56 were pooled in one 10X library sample 1
L5ET-DEV_Abe_2024.rds


title: HL60-Suc-3h-R2

value: WT


title: Retina_12w_F02


title: Liver, LeuD, GCN2 KO, 03 bio rep3


title: SH466_TR_GU01CTC

value: EpCAM+ and/or PSMA+


title: Retina_12w_F01


title: HL60-Suc-0h-R3

value: saline


title: Liver, Control, GCN2 KO, 15 bio rep1

value: Liver


title: Retina_06w_F10

value: 6 weeks


title: SH462_TR_GU01CTC


title: HL60-shCtrl-R1

value: shCtrl


title: SH464_TR_GU01CTC


title: Retina_12w_F04

value: Neural Retina

value: 12 weeks


title: Liver, LeuD, GCN2 KO, 03 bio rep2

value: LeuD


title: Breast_tumor_HiC

data_processing:
FASTQ data was processed using seqtk to eliminate low quality sequences. Hi-C matrix was build using runHiC (version 0.8.7).
FASTQ data was processed using seqtk to eliminate low quality sequences. Valid pairs were obtained using runHiC (version 0.8.7).
Assembly: GRCh38
Supplementary files format and content: .mcool matrix. Containing a Hi-C multi-resolution contact matrix.
Supplementary files format and content: .pairs file containing the filtered interacting pairs from Hi-C experiment.

source_name: Breast cancer primary tumor

extract_protocol:
Breast tissue was acquired from three Tru-Cut biopsies. The tissue was sectioned into small fragments and cryopreserved in FBS (Gibco) supplemented with 10% dimethyl sulfoxide (DMSO, Sigma). Upon thawing, the tissue was enzymatically dissociated using Accumax solution (Sigma) and incubated for 30 minutes. The resulting cell suspension was filtered through a 40 µm filter, followed by processing using the Dead Cell Removal Kit (Miltenyi Biotec #130090101) through two rounds to ensure sufficient viability. Cells were cross-linked with 2% formaldehyde. Then cell nuclei were obtained with a lysis buffer (10 mM Tris-HCl pH 8, 0.2% IGEPAL CA-630, 10 mM NaCl, 1X cOmpleteR protease inhibitors cocktail). For genome digestion, 125 U of DpnII (New England Biolabs) were added. The ligation spet was performed using 50 U Weiss of T4 DNA Ligase enzyme (Thermo Scientific, 5 U Weiss/μl), and the crosslink was reversed. DNA was purified using a Phenol-Chloroform-Isoamyl alcohol mix (25:24:1) and shared with a Covaris Sonicator.
Hi-C libraries were generated using the TruSeq Illumina system.

value: Breast cancer primary tumor

value: Triple negative breast cancer


title: HL60-Suc-0h-R2


title: Liver, LeuD, WT, 15 bio rep3


title: SH457_TR_GU01CTC

value: CTC


title: Breast_tumor_scRNAseq

source_name: Breast cancer tumor

value: Breast cancer tumor


title: Retina_06w_F09

value: Wildtype


title: Liver, LeuD, GCN2 KO, 03 bio rep1

value: GCN2 KO


title: Liver, Control, GCN2 KO, 03 bio rep3

value: Control


title: Retina_06w_F05


title: CCL2KD_CMEC_Pseudo

address: 240 Pasteur Drive, 3500 BMI

data_processing:
RNAseq reads are trimmed using trimmomatic and HISAT2 tool is used for alignment
RPKM values are calculated using excel and read counts using featureCounts
differential analysis is perfomed using deseq2
Assembly: hg38
Supplementary files format and content: raw counts

source_name: iPSC

growth_protocol: SARS-CoV-2 pseudovirus was obtained commercially (Montana Molecular) where these pseudoviruses (as BSL-1 baculoviruses) were pseudotyped with Spike (S) proteins. As per manufacturer’s instructions, these pseudovirus does not replicate inside the cells, but exhibit high affinity for the host receptor ACE2 in ECs. iPSC-ECs or COs were infected with SARS-CoV-2 pseudovirus at the titer of 2x1010 VG/ml in EGM2 media (for iPSC-ECs) or a mixture of RPMI-B27 + EGM2 (for COs) for respective time periods.

extract_protocol:
Total RNA was extracted from COs using RNeasy plus mini-Kit (Qiagen) as per manufacturer’s instructions
Dyna Oligo(dT) beads (Life technologies) were used to purify mRNA and then fragmentated to 200-300 bp fragments to prepare index-tagged paired-end cDNA libraries as previously descibed7. Illumina sequencing adapters were ligated to cDNA fragments through PCR and sequencing was performed on Novaseq 6000. Obtained fastq (paired end) sequencing reads were mapped to human reference genome (hg38) using STAR (2.5.4b), and quantified raw counts and RPKM values were annotated using Homer (analyzeRepeats.pl). Heatmaps were generated through normalized DESEQ2 counts. Gene ontology analysis was conducted using R package.

value: iPSC

value: iPSC-CM, iPSC-EC

value: pseudovirus


title: Retina_06w_F08


title: Retina_06w_F06


title: Liver, LeuD, GCN2 KO, 15 bio rep3


title: CCL2KD_CM_Pseudo

value: iPSC-CM


title: SH454_TR_GU01CTC

value: EpCAM+ and/or PSMA+


title: SH453_TR_GU01CTC


title: Liver, Control, GCN2 KO, 03 bio rep2

value: Liver


title: CCL2KD_CMEC_Pseudo2


title: SH445_TR_GU01CTC


title: SH446_TR_GU01CTC


title: CCL2KD_CM_Pseudo2


title: Liver, Control, WT, 03 bio rep1

value: WT


title: Retina_06w_F04

value: Neural Retina

value: 6 weeks


title: Liver, LeuD, WT, 03 bio rep2

value: LeuD


title: SH461_TR_GU01CTC


title: Retina_06w_F03


title: CCL2KD_CMEC_Mock

value: mock


title: SH440_TR_GU01CTC


title: CCL2KD_CMEC_Mock2


title: Retina_06w_F02


title: Retina_06w_F07


title: Liver, LeuD, WT, 03 bio rep3


title: SH443_TR_GU01CTC


title: Liver, Control, WT, 15 bio rep1


title: Retina_06w_F01


title: SH437_TR_GU01CTC


title: Liver, Control, WT, 03 bio rep3


title: CMEC_Mock

value: control

value: Mock


title: Liver, Control, GCN2 KO, 03 bio rep1


title: SH436_TR_GU01CTC

value: CTC


title: Liver, Control, WT, 03 bio rep2


title: CM_Mock_2


title: SH396_TR_GU01CTC


title: AML42

type: RNA

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

institute: Princess Máxima Center for Pediatric Oncology

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v22

hyb_protocol: As per Nanostring's recommendations

scan_protocol: nCounter MAX/FLEX

data_processing: Normalized using ROSALIND® according to Nanostring's recommendations

source_name: diagnostic bone biopsy (trephine) taken from the crista

extract_protocol: RNeasy FFPE KIT (Qiagen) according to manufacturers recommendations

tag: disease

value: childhood AML

value: bone biopsy

tag: immune infiltration status

value: depleted


title: AML43

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v23


title: CM_Mock

value: iPSC


title: SH394_TR_GU01CTC

data_processing:
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: counts.csv is a comma-separated-values file with rows corresponding to a gene, columns corresponding to a sample, and values giving the number of reads aligned to the gene.

source_name: CTC


title: Liver, LeuD, GCN2 KO, 15 bio rep2

value: GCN2 KO


title: Liver, LeuD, WT, 03 bio rep1


title: AML33

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v20


title: SH391_TR_GU01CTC


title: CMEC_Live_Plus_2

value: iPSC-CM, iPSC-EC

value: Live COVID Virus


title: CMEC_Live_Plus


title: AML30

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v18


title: AML32

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v19


title: Liver, LeuD, WT, 15 bio rep1


title: SH390_TR_GU01CTC

value: EpCAM+ and/or PSMA+


title: CM_Live_Plus_2

value: iPSC-CM


title: CM_Live_Plus


title: Pt7

source_name: artery

value: artery

tag: disease state

value: Long Covid


title: SH389_TR_GU01CTC


title: BCaT_104

city: TLALPAN

first: Cristian

last: Arriaga

state: Federal District

address: AV. SAN FERNANDO, COL. SECCIÓN XVI

institute: Mexican National Cancer Institute

data_processing:
The quality of the sequencing files was determined with the reports generated with the FastQC 0.12.0
Reads were mapped to the human reference with STAR aligner v.2.7.1a
Gene expression quantification was done with featureCounts from the rsubread package on the STAR bam files
Gene expression quantification was also done by aligning to the transcriptome withSalmon v.1.10.3. Data were normalized to TPM and is included as matrix (processed file bcat_counts.csv)
Differential expression analysis was performed with DEseq2 v.1.44.0
Assembly: Reads were mapped to the human reference genome assembly version hg38 (gencode v40)
Supplementary files format and content: Count matrix from Salmon counts is included. Each row correspond to Ensembl gene ID, and each column correspond to the ID of BCaT samples.

source_name: Biopsy from primary mammary adenocarcinoma (thick needle)

extract_protocol:
RNA was isolated using the AllPrep kit (QIAGEN, No. 80204); RNA concentration and quality analysis (RIN value) were performed by Tape Station 2200 bioanalyzer (Agilent Technologies)
1 ug of RNA with RIN associated greater than 8.0 were used to generate sequencing libraries using the TruSeq Stranded mRNA library prep kit from illumina according to the manufacturer’s instruction

value: Breast cancer

tag: molecular subtype

value: Luminal B

tag: group

value: Non-responder (RD)

value: Neoadjuvant Chemotherapy


title: SH393_TR_GU01CTC

extract_protocol:
Single cells were picked or sorted into lysate buffer and RNA was released.
single cell cDNA was amplified using SMART-seq2 protocol


title: AML34

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v21


title: CMEC_Mock_2

value: control

value: Mock


title: SH388_TR_GU01CTC

value: CTC


title: AML29

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v17

value: childhood AML

value: bone biopsy