title: C2007

description: Single nucleotide polymorphism array

value: 10 Trisomy


title: 12J_M_294

status: Public on May 21 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

tag: age

tag: strain


title: C2023

type: genomic

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

country: China

institute: Fujian Maternity and Child Health Hospital

description: Single nucleotide polymorphism array

hyb_protocol: DNA was digested, amplified, purified, fragmented, labeled and hybridized according to the standard Affymetrix protocol.

scan_protocol: SNP arrays were scanned with GeneChip Scanner 3000 7G System.

data_processing: Raw CEL data was annotated using GRCh37 (hg19) genome version and was converted into CYCHP form through the ChAS. SNP array was further analyzed using ChAS.

label: biotin

organism: Homo sapiens

source_name: Chorionic villus

extract_protocol: Fetal DNA samples were extracted from chorionic villi, amniotic fluid or skin tissues using the QIAGEN DNA Mini Kit (Qiagen, Valencia, CA, USA).

tag: maternal age

tag: pregnant outcome

value: Early embryo growth arrest

tag: prenatal diagnosis

value: No clinical Variations

tag: chromosomal abnormality


title: 12J_M_295


title: C2002

description: Single nucleotide polymorphism array

label_protocol: DNA was digested, amplified, purified, fragmented, labeled and hybridized according to the standard Affymetrix protocol.

value: Pathogenic CNVs

value: 17 Trisomy


title: C2004

description: Single nucleotide polymorphism array


title: C2003

description: Single nucleotide polymorphism array


title: 12J_M_292


title: 12J_M_291


title: C2026

description: Single nucleotide polymorphism array


title: 12J_M_293


title: C2001

description: Single nucleotide polymorphism array

value: 16 Trisomy


title: C2000

description: Single nucleotide polymorphism array

value: 21 Trisomy


title: C1999-A

description: Single nucleotide polymorphism array


title: 12J_M_290


title: C1994

description: Single nucleotide polymorphism array

value: 22 Trisomy


title: C1998

description: Single nucleotide polymorphism array

value: 13 Trisomy


title: 12J_M_289


title: 12J_M_288


title: C1995

description: Single nucleotide polymorphism array


title: 12J_M_287


title: 12J_M_285


title: 12J_M_286


title: C1993

description: Single nucleotide polymorphism array


title: 12J_M_284


title: C1990

description: Single nucleotide polymorphism array


title: C1987

description: Single nucleotide polymorphism array

value: 5,7 Trisomy


title: 12J_M_282


title: C1988

description: Single nucleotide polymorphism array


title: C1984

description: Single nucleotide polymorphism array


title: C1983

description: Single nucleotide polymorphism array


title: 12J_M_280


title: C1980

description: Single nucleotide polymorphism array

source_name: Skin tissues


title: 12J_M_279


title: 12J_M_277


title: C1973

description: Single nucleotide polymorphism array


title: C1971

description: Single nucleotide polymorphism array

value: 9 Trisomy


title: 12J_M_281


title: C1974

description: Single nucleotide polymorphism array


title: 12J_M_276


title: C1982

description: Single nucleotide polymorphism array


title: C1970

description: Single nucleotide polymorphism array


title: 12J_M_283


title: 12J_M_274


title: 12J_M_275


title: C1967

description: Single nucleotide polymorphism array


title: C1969

description: Single nucleotide polymorphism array


title: C1966

description: Single nucleotide polymorphism array

value: 8 Trisomy


title: 12J_M_271


title: C1964

description: Single nucleotide polymorphism array


title: 12J_M_272


title: C1963

description: Single nucleotide polymorphism array


title: 12J_M_270


title: C1960

description: Single nucleotide polymorphism array


title: 12J_M_278


title: 12J_M_269


title: 12J_M_268


title: C1958

description: Single nucleotide polymorphism array


title: 12J_M_267


title: C1956

description: Single nucleotide polymorphism array


title: C1953

description: Single nucleotide polymorphism array


title: 12J_M_265


title: 12J_M_264


title: C1952

description: Single nucleotide polymorphism array


title: C1951

description: Single nucleotide polymorphism array


title: C1949-A

description: Single nucleotide polymorphism array

value: 3 Trisomy


title: C1950

description: Single nucleotide polymorphism array


title: 12J_M_273


title: C1948

description: Single nucleotide polymorphism array


title: C1944

description: Single nucleotide polymorphism array

value: Chromosomal deletions/duplications


title: C1943

description: Single nucleotide polymorphism array


title: C1948-A

description: Single nucleotide polymorphism array


title: 12J_M_266


title: C1941

description: Single nucleotide polymorphism array

value: Triploidy


title: 12J_M_262


title: 12J_M_259


title: C1945

description: Single nucleotide polymorphism array


title: 12J_M_258


title: 12J_M_191


title: 12J_M_260


title: 12J_M_256


title: 12J_M_257


title: C1955

description: Single nucleotide polymorphism array


title: 12J_M_190


title: 12J_M_188


title: 12J_M_263


title: C1931

description: Single nucleotide polymorphism array


title: C1935

description: Single nucleotide polymorphism array

value: 14 Trisomy


title: 12J_M_187


title: 12J_M_189


title: C1929

description: Single nucleotide polymorphism array


title: C1925

description: Single nucleotide polymorphism array

value: 7 Trisomy


title: 12J_M_261


title: 12J_M_186


title: C1924

description: Single nucleotide polymorphism array


title: 12J_M_184


title: 12J_M_185


title: C1940

description: Single nucleotide polymorphism array

value: 15 Trisomy


title: 12J_M_183


title: 12J_M_182


title: 12J_M_181


title: 12J_M_175


title: 12J_M_178


title: C1912

description: Single nucleotide polymorphism array

value: Early embryo growth arrest


title: C1917

description: Single nucleotide polymorphism array


title: 12J_M_176


title: C1911

description: Single nucleotide polymorphism array

value: No clinical Variations


title: 12J_M_177


title: 12J_M_174


title: C1919

description: Single nucleotide polymorphism array

value: Pathogenic CNVs


title: 12J_M_173


title: C1898

description: Single nucleotide polymorphism array


title: C1895

description: Single nucleotide polymorphism array


title: C1894

description: Single nucleotide polymorphism array

value: Variants of unknown significance (VOUS)


title: C1906

description: Single nucleotide polymorphism array


title: C1903

description: Single nucleotide polymorphism array


title: C1897

description: Single nucleotide polymorphism array


title: C1902

description: Single nucleotide polymorphism array


title: C1893

description: Single nucleotide polymorphism array


title: 12J_M_171


title: C1887

description: Single nucleotide polymorphism array


title: C1888

description: Single nucleotide polymorphism array


title: C1922

description: Single nucleotide polymorphism array


title: 12J_M_172


title: 12J_M_170


title: 12J_M_180


title: 12J_M_179


title: 12J_M_169


title: C1882

description: Single nucleotide polymorphism array


title: C1886

description: Single nucleotide polymorphism array

value: 12 Trisomy


title: C1884

description: Single nucleotide polymorphism array


title: 12J_M_165


title: C1883

description: Single nucleotide polymorphism array


title: 12J_M_168


title: 12J_M_166


title: 12J_M_160


title: 12J_M_161


title: 12J_M_163


title: 12J_M_167


title: C1879

description: Single nucleotide polymorphism array


title: 12J_M_162


title: 12J_M_164


title: C1878

description: Single nucleotide polymorphism array


title: C1874

description: Single nucleotide polymorphism array


title: C1877

description: Single nucleotide polymorphism array


title: C1872

description: Single nucleotide polymorphism array


title: C1880

description: Single nucleotide polymorphism array


title: C1878-A

description: Single nucleotide polymorphism array


title: C1871

description: Single nucleotide polymorphism array


title: 12J_M_157


title: 12J_M_158


title: C1869

description: Single nucleotide polymorphism array


title: C1875

description: Single nucleotide polymorphism array


title: 12J_M_156


title: 12J_M_159


title: 12J_M_155


title: C1866

description: Single nucleotide polymorphism array


title: 12J_M_154


title: C1863

description: Single nucleotide polymorphism array


title: C1864

description: Single nucleotide polymorphism array


title: C1860

description: Single nucleotide polymorphism array

value: 16 Trisomy


title: 12J_M_152


title: C1861

description: Single nucleotide polymorphism array


title: C1859

description: Single nucleotide polymorphism array


title: 12J_M_151


title: 12J_M_153


title: 12J_M_149


title: C1850

description: Single nucleotide polymorphism array


title: 12J_M_148


title: 12J_M_147


title: 12J_M_146


title: C1853

description: Single nucleotide polymorphism array


title: 12J_M_143


title: C1857

description: Single nucleotide polymorphism array


title: 12J_M_142


title: 12J_M_145


title: C1856

description: Single nucleotide polymorphism array


title: C1855

description: Single nucleotide polymorphism array


title: C1835

description: Single nucleotide polymorphism array


title: 12J_M_150


title: C1845

description: Single nucleotide polymorphism array


title: C1858

description: Single nucleotide polymorphism array

value: 18 Trisomy


title: 12J_M_144


title: 12J_M_140


title: 12J_M_141


title: C1854

description: Single nucleotide polymorphism array


title: 12J_M_139


title: C1830

description: Single nucleotide polymorphism array


title: C1849

description: Single nucleotide polymorphism array

value: 13 Trisomy


title: C1827

description: Single nucleotide polymorphism array

value: 22 Trisomy


title: 12J_M_137


title: C1817-A

description: Single nucleotide polymorphism array


title: C1819

description: Single nucleotide polymorphism array


title: C1820

description: Single nucleotide polymorphism array


title: 12J_M_136


title: 12J_M_135


title: C1807

description: Single nucleotide polymorphism array

value: 21 Trisomy


title: C1815

description: Single nucleotide polymorphism array


title: C1803

description: Single nucleotide polymorphism array


title: 12J_M_132


title: C1806

description: Single nucleotide polymorphism array


title: 12J_M_133


title: C1812

description: Single nucleotide polymorphism array


title: 12J_M_130


title: C1808

description: Single nucleotide polymorphism array


title: 12J_M_134


title: 12J_M_129


title: 12J_M_128


title: C1801

description: Single nucleotide polymorphism array


title: C1797

description: Single nucleotide polymorphism array


title: C1796

description: Single nucleotide polymorphism array


title: 12J_M_138


title: 12J_M_125


title: 12J_M_126


title: C1793

description: Single nucleotide polymorphism array


title: 12J_M_124


title: 12J_M_123


title: C1792

description: Single nucleotide polymorphism array

value: 15, 22 Trisomy


title: C1805

description: Single nucleotide polymorphism array


title: 12J_M_122


title: 12J_M_121


title: C1791

description: Single nucleotide polymorphism array


title: C1798

description: Single nucleotide polymorphism array


title: C1790

description: Single nucleotide polymorphism array


title: C1784

description: Single nucleotide polymorphism array


title: C1786

description: Single nucleotide polymorphism array


title: 12J_M_117


title: 12J_M_119


title: 12J_M_118


title: C1785

description: Single nucleotide polymorphism array


title: C1781

description: Single nucleotide polymorphism array


title: 12J_M_116


title: 12J_M_131


title: C1777

description: Single nucleotide polymorphism array


title: C1783

description: Single nucleotide polymorphism array


title: C1778

description: Single nucleotide polymorphism array


title: 12J_M_115


title: C1775

description: Single nucleotide polymorphism array


title: 12J_M_111


title: 12J_M_110


title: 12J_M_112


title: C1774

description: Single nucleotide polymorphism array


title: 12J_M_109


title: C1770

description: Single nucleotide polymorphism array


title: C1767

description: Single nucleotide polymorphism array


title: 12J_M_108


title: 12J_M_127


title: 12J_M_120


title: C1764

description: Single nucleotide polymorphism array

value: 8 Trisomy


title: C1763

description: Single nucleotide polymorphism array

value: 14,21 Trisomy


title: C1760

description: Single nucleotide polymorphism array

value: 15 Trisomy,45,X


title: C1766

description: Single nucleotide polymorphism array


title: 12J_M_105


title: 12J_M_113


title: 12J_M_103


title: C1754

description: Single nucleotide polymorphism array


title: 12J_M_104


title: 12J_M_106


title: 12J_M_114


title: 12J_M_101


title: 12J_M_100


title: C1771

description: Single nucleotide polymorphism array


title: C1742

description: Single nucleotide polymorphism array


title: 12J_M_102


title: 12J_M_99


title: 12J_M_98


title: C1741

description: Single nucleotide polymorphism array


title: 12J_M_97


title: 12J_M_107


title: C1735

description: Single nucleotide polymorphism array


title: 12J_M_95


title: C1725

description: Single nucleotide polymorphism array

source_name: Amniotic fluid


title: C1724

description: Single nucleotide polymorphism array


title: C1759

description: Single nucleotide polymorphism array


title: 12J_M_94


title: C1752

description: Single nucleotide polymorphism array


title: C1722

description: Single nucleotide polymorphism array


title: C1721

description: Single nucleotide polymorphism array


title: C1718

description: Single nucleotide polymorphism array

value: 20 Trisomy


title: C1716

description: Single nucleotide polymorphism array


title: C1746

description: Single nucleotide polymorphism array


title: C1714

description: Single nucleotide polymorphism array


title: C1710

description: Single nucleotide polymorphism array

value: Chromosomal deletions/duplications


title: 12J_M_89


title: 12J_M_87


title: 12J_M_92


title: 12J_M_86


title: C1712

description: Single nucleotide polymorphism array


title: 12J_M_91


title: C1731

description: Single nucleotide polymorphism array


title: 12J_M_88


title: C1708

description: Single nucleotide polymorphism array


title: 12J_M_84


title: 12J_M_85


title: 12J_M_96


title: C1709

description: Single nucleotide polymorphism array


title: 12J_M_82


title: 12J_M_93


title: C1706

description: Single nucleotide polymorphism array

value: Triploidy


title: 12J_M_81


title: C1704

description: Single nucleotide polymorphism array

value: Early embryo growth arrest


title: C1717

description: Single nucleotide polymorphism array

value: 14 Trisomy


title: 12J_M_90


title: 12J_M_80


title: C1703

description: Single nucleotide polymorphism array

value: Pathogenic CNVs


title: 12J_M_79


title: C1702

description: Single nucleotide polymorphism array


title: C1701

description: Single nucleotide polymorphism array

value: No clinical Variations


title: 12J_M_77


title: 12J_M_78


title: C1698

description: Single nucleotide polymorphism array


title: C1697

description: Single nucleotide polymorphism array


title: C1692

description: Single nucleotide polymorphism array


title: C1689

description: Single nucleotide polymorphism array


title: C1693

description: Single nucleotide polymorphism array

value: 10 Trisomy


title: 12J_M_83


title: C1690

description: Single nucleotide polymorphism array


title: C1707

description: Single nucleotide polymorphism array


title: 12J_M_76


title: 12J_M_72


title: 12J_M_75


title: 12J_M_74


title: 12J_M_73


title: 12J_M_71


title: C1685

description: Single nucleotide polymorphism array


title: 12J_M_70


title: 12J_M_69


title: C1683

description: Single nucleotide polymorphism array


title: C1680

description: Single nucleotide polymorphism array


title: 12J_M_68


title: C1679

description: Single nucleotide polymorphism array


title: 12J_M_66


title: 12J_M_67


title: C1678

description: Single nucleotide polymorphism array


title: C1696

description: Single nucleotide polymorphism array


title: 12J_M_65


title: C1699

description: Single nucleotide polymorphism array


title: C1674

description: Single nucleotide polymorphism array


title: C1659

description: Single nucleotide polymorphism array

value: 7,21 Trisomy


title: 12J_M_63


title: C1658

description: Single nucleotide polymorphism array


title: 12J_M_64


title: C1655

description: Single nucleotide polymorphism array


title: C1642

description: Single nucleotide polymorphism array


title: C1632

description: Single nucleotide polymorphism array


title: 12J_M_60


title: 12J_M_59


title: 12J_M_61


title: 12J_M_58


title: C1637

description: Single nucleotide polymorphism array

value: 18 Trisomy


title: 12J_M_55


title: 12J_M_57


title: C1598

description: Single nucleotide polymorphism array


title: 12J_M_53


title: 12J_M_54


title: C1499

description: Single nucleotide polymorphism array


title: C1497

description: Single nucleotide polymorphism array


title: 12J_M_52


title: C1461

description: Single nucleotide polymorphism array


title: C1494

description: Single nucleotide polymorphism array

value: 16 Trisomy


title: C1460

description: Single nucleotide polymorphism array


title: 12J_M_51


title: 12J_M_50


title: 12J_M_62


title: C1454

description: Single nucleotide polymorphism array


title: 12J_M_49


title: C1430

description: Single nucleotide polymorphism array

value: 12, 15 Trisomy


title: C1500

description: Single nucleotide polymorphism array


title: 12J_M_56


title: C1429

description: Single nucleotide polymorphism array

value: 22 Trisomy


title: 12J_M_47


title: C1433

description: Single nucleotide polymorphism array


title: C1420

description: Single nucleotide polymorphism array


title: 12J_M_45


title: 12J_M_46


title: C1418

description: Single nucleotide polymorphism array


title: BM Lane 2

city: Stanford

first: Juliana

last: Idoyaga

address: 299 Campus Drive

institute: Stanford University

library_source: transcriptomic

data_processing:
Processed using 10x CellRanger pipeline version 3.1.0 in the Stanford Functional Genomics Facility. Reads were aligned using the mm10 genome.
Downstream analysis was performed using Seurat V3. Cells were selected for number of genes over 300, number of total counts less than 50000, and % of mitochondrial genes less than 20%. Data was normalized using the “LogNormalize” method (scale factor 10000) of Seurat’s NormalizeData function.
Assembly: mm10
Supplementary files format and content: Counts matrix post quality control
Supplementary files format and content: demultiplexed count-unnormalized

molecule: total RNA

source_name: Bone Marrow

extract_protocol:
Cells were CD135 enriched and sorted for live
Constructed by Stanford Functional Genomics Facility using Single Cell 3' V3 kit from 10x Genomics per manufacturer's protocols.

tag: tissue

value: Bone Marrow

tag: genotype

value: WT


title: LM2-4175_KLF4 over-expression replication 2

type: RNA

description: Gene expression data from KLF4 over-expressed LM2-4175 cells

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to affymetrix human U133 plus 2.0 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000

data_processing: Raw data were normalized by RMA algorithm

source_name: LM2-4175_KLF4 over-expression

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: Breast cancer cells LM2-4175 were cultured on plates in 10% FBS.

extract_protocol: Cellular RNA was isolated by Tri-Reagent using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: The stable KLF4 over-expressed LM2-4175 cell lines were generated by transduction a lentiviral-mediated expression plasmid.

tag: cell line

tag: cell type

value: breast cancer cell line

tag: genotype/variation

value: KLF4 overexpression


title: LM2-4175_KLF4 over-expression replication 1


title: GC_B_Cell_KO2

city: New York

first: Ryan

last: Smolkin

state: NY

address: 408 E 69th St

institute: MSKCC

data_processing:
Reads were combined into single Fastq files for each sample for those samples (2 and 6) that were sequenced separately
Files were converted to Sam Format and Illumina adapters were marked (GATK v4.1.9.0)
Low quality reads were trimmed (GATK v4.1.9.0 -QT10)
Reads were aligned (STAR v2.7.7a with standard options) to mm10
Duplicate reads were removed (GATK v 4.1.9.0)
Combined reads were counted against gencode.vM25 using featureCounts (-t exon -g gene_id)
FeatureCounts output was further processed to generate a TPM matrix in R
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: GC B Cell

extract_protocol:
Total RNA was extracted from LDHA-sufficient and -deficient cells by standard Trizol purification
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: GC B Cell


title: GC_B_Cell_KO3


title: LM2-4175_control replication 3

description: Gene expression data from LM2-4175 cells

value: control


title: GC_B_Cell_WT3


title: GC_B_Cell_WT1


title: Spleen Lane 2

source_name: Spleen

value: Spleen


title: GC_B_Cell_WT2


title: GC_B_Cell_KO1


title: LM2-4175_control replication 2


title: C1411

description: Single nucleotide polymorphism array

value: Early embryo growth arrest


title: 12J_M_43


title: 12J_M_48


title: LM2-4175_control replication 1

description: Gene expression data fromLM2-4175 cells


title: C1356

description: Single nucleotide polymorphism array


title: LM2-4175_KLF4 over-expression replication 3


title: C1393

description: Single nucleotide polymorphism array


title: 12J_M_40


title: 12J_M_42


title: C1359

description: Single nucleotide polymorphism array


title: 12J_M_44


title: MIA334A25 Haematopoietic Stem and Progenitor Cells

city: London

first: Dominique

last: Bonnet

state: London

address: 1 Midland Rd

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Adaptor removal and quality trimming done with Trimmomatic v 0.36
Read alingment and gene counts was performed with RSEM v 1.2.31 and STAR v 2.5.2a
Differential expression analysis was carried out with DESeq2 package ( version 1.18.1 )
Genome_build: Ensembl GRCh89 release 89
Supplementary_files_format_and_content: Tab-delimited text include raw counts per gene and per sample (generated by DESeq2).

source_name: Human Bone Marrow

growth_protocol: Bone marrow CD34+ haematopoietic cell were co-cultured with bone marrow Mesenchymal Stromal Cells for 5 days.

extract_protocol: RNA was extracted using Zymo Direct-zol RNA Kit

tag: stroma layer

value: MSC-MDS

tag: hspcs


title: MIA334A4 Haematopoietic Stem and Progenitor Cells


title: MIA334A26 Haematopoietic Stem and Progenitor Cells


title: MIA334A5 Haematopoietic Stem and Progenitor Cells


title: MIA334A24 Haematopoietic Stem and Progenitor Cells


title: BM Lane 1


title: Spleen Lane 1


title: C1339

description: Single nucleotide polymorphism array

value: Pathogenic CNVs


title: MIA334A43 Haematopoietic Stem and Progenitor Cells

value: MSC-HD


title: MIA334A50 Haematopoietic Stem and Progenitor Cells


title: 12J_M_38


title: C1333

description: Single nucleotide polymorphism array

value: No clinical Variations


title: MIA334A35 Haematopoietic Stem and Progenitor Cells


title: 12J_M_41


title: MIA334A48 Haematopoietic Stem and Progenitor Cells


title: 12J_M_36


title: 12J_M_35


title: 12J_M_39


title: 12J_M_34


title: C1336

description: Single nucleotide polymorphism array

value: Triploidy


title: MIA334A13 Haematopoietic Stem and Progenitor Cells


title: C1250

description: Single nucleotide polymorphism array


title: 12J_M_33


title: MIA334A22 Mesenchymal Stromal Cells

value: Mesenchymal Stromal Cells


title: MIA334A41 Haematopoietic Stem and Progenitor Cells


title: MIA334A40 Haematopoietic Stem and Progenitor Cells


title: 12J_M_37


title: C1263

description: Single nucleotide polymorphism array


title: MIA334A12 Haematopoietic Stem and Progenitor Cells


title: C1262

description: Single nucleotide polymorphism array


title: MIA334A47 Haematopoietic Stem and Progenitor Cells


title: MIA334A46 Haematopoietic Stem and Progenitor Cells


title: MIA334A23 Haematopoietic Stem and Progenitor Cells


title: C1259

description: Single nucleotide polymorphism array


title: MIA334A45 Haematopoietic Stem and Progenitor Cells


title: MIA334A44 Haematopoietic Stem and Progenitor Cells


title: C1245

description: Single nucleotide polymorphism array

value: 16 Trisomy


title: MIA334A3 Mesenchymal Stromal Cells


title: MIA334A21 Mesenchymal Stromal Cells


title: MIA334A20 Mesenchymal Stromal Cells


title: 12J_M_32


title: 12J_M_31


title: MIA334A18 Mesenchymal Stromal Cells


title: C1234

description: Single nucleotide polymorphism array


title: Fantasy love leaves, 25℃, control, biol rep3

city: Ji'nan

first: Chunxia

last: Wu

state: Shandong

address: No.1,University Road,Science Park,Changqing District

department: Life Sciences

institute: Shandong Provincial Key Laboratory of Plant Stress

data_processing:
llumina Novaseq™ 6000 (LC Sceiences,USA) following the vendor’s recommended protocol
Cutadapt (cutadapt-1.9) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
De novo assembly of the transcriptome was performed with Trinity 2.4.0.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG(http://eggnogdb.embl.de/) databases using DIAMOND (2.0.15) with a threshold of Evalue<0.00001.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Anthurium andraeanum

source_name: leaves

growth_protocol: The full-flowering plants were grown in the growth chambers for three days with a 12/12 h day/night cycle at 25℃ (control) and treatment temperatures.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cold treatments, the plants were grown at 15℃ for three days, then the temperature was decreased to 6℃ for three days and then 4℃ for three days. The control plants were grown at 25℃ throughout the experiment.

value: leaves

tag: cultivar

value: Fantasy love

tag: treatment

tag: time


title: C1239

description: Single nucleotide polymorphism array


title: 12J_M_30

tag: brain region


title: C1253

description: Single nucleotide polymorphism array


title: Fantasy love leaves, 25℃, control, biol rep2


title: MIA334A19 Mesenchymal Stromal Cells


title: MIA334A32 Mesenchymal Stromal Cells


title: MIA334A33 Mesenchymal Stromal Cells


title: 12J_M_29

tag: age


title: C1235

description: Single nucleotide polymorphism array


title: C1202

description: Single nucleotide polymorphism array

value: 22 Trisomy


title: 12J_M_27

tag: strain


title: C1227

description: Single nucleotide polymorphism array


title: Fantasy love leaves, 25℃, control, biol rep1


title: Fantasy love leaves, 6℃, 3days, biol rep2


title: 12J_M_26


title: C1219

description: Single nucleotide polymorphism array


title: 12J_M_28


title: 12J_M_25


title: Fantasy love leaves, 6℃, 3days, biol rep1


title: C1231

description: Single nucleotide polymorphism array

tag: maternal age


title: MIA334A31 Mesenchymal Stromal Cells


title: Fantasy love leaves, 4℃, 3days, biol rep3


title: Fantasy love leaves, 6℃, 3days, biol rep3


title: MIA334A29 Mesenchymal Stromal Cells


title: MIA334A10 Mesenchymal Stromal Cells


title: MIA334A30 Mesenchymal Stromal Cells


title: MIA334A2 Mesenchymal Stromal Cells


title: 12J_M_24


title: Fantasy love leaves, 4℃, 3days, biol rep2


title: C1229

description: Single nucleotide polymorphism array

tag: pregnant outcome

value: Chromosomal deletions/duplications


title: 12J_M_23


title: MIA334A1 Mesenchymal Stromal Cells


title: C1228

description: Single nucleotide polymorphism array

tag: prenatal diagnosis


title: Fantasy love leaves, 4℃, 3days, biol rep1


title: 12J_M_22


title: MIA334A17 Mesenchymal Stromal Cells


title: C1223

description: Single nucleotide polymorphism array

tag: chromosomal abnormality

value: 15 Trisomy


title: Oregon leaves, 25℃, 3days, biol rep3

tag: tissue

value: Oregon


title: C1220

description: Single nucleotide polymorphism array


title: 12J_M_21


title: MIA334A16 Mesenchymal Stromal Cells


title: Oregon leaves, 25℃, 3days, biol rep1


title: 12J_M_19


title: Oregon leaves, 25℃, 3days, biol rep2


title: C1205

description: Single nucleotide polymorphism array


title: 12J_M_20


title: C1214

description: Single nucleotide polymorphism array


title: MIA334A15 Mesenchymal Stromal Cells


title: C1204

description: Single nucleotide polymorphism array


title: MIA334A14 Mesenchymal Stromal Cells


title: Oregon leaves, 6℃, 3days, biol rep3


title: 12J_M_18


title: MIA334A8 Mesenchymal Stromal Cells


title: Oregon leaves, 6℃, 3days, biol rep2


title: MIA334A28 Mesenchymal Stromal Cells


title: Oregon leaves, 6℃, 3days, biol rep1


title: 12J_M_17


title: 12J_M_16


title: C1213

description: Single nucleotide polymorphism array


title: MIA334A27 Mesenchymal Stromal Cells


title: MIA334A42 Mesenchymal Stromal Cells

value: +CD34-Healthy (HD3)


title: C1211

description: Single nucleotide polymorphism array


title: Oregon leaves, 4℃, 3days, biol rep2


title: 12J_M_15


title: C1210

description: Single nucleotide polymorphism array


title: 12J_M_14


title: Oregon leaves, 4℃, 3days, biol rep1


title: MIA334A38 Mesenchymal Stromal Cells


title: MIA334A37 Mesenchymal Stromal Cells

value: +CD34-Healthy (HD1)


title: MIA334A36 Mesenchymal Stromal Cells

value: +CD34-Healthy (HD2)


title: C1208

description: Single nucleotide polymorphism array

value: Early embryo growth arrest


title: Oregon leaves, 4℃, 3days, biol rep3


title: C1207

description: Single nucleotide polymorphism array


title: 12J_M_13


title: mouse brain, Striatum, 6-OHDA, mouse3, Visium (V11T17-101_B1)

city: Solna

first: Marco

last: Vicari

address: Tomtebodavägen 23

department: Gene Technology

country: Sweden

institute: KTH, SciLifeLab

data_processing:
A pre-built reference (refdata-gex-mm10-2020-A for the mouse samples and refdata-gex-GRCh38-2020-A for the human samples) was downloaded from 10x Genomics website and used as a reference for data processing with Space Ranger v1.3.1 (SMA_RRST samples) or Space Ranger v1.2.1 (rest of the samples)
Raw fastq files and H&E images were processed with the Space Ranger v1.3.1 or Space Ranger v1.2.1 command line tool to produce the following processed data files: expression matrices (h5 files), scaled H&E images (png files), spot coordinate tables (csv files) and scale factors (json files). Loupe Browser 6 (10x Genomics) was used to manually annotate the tissue sections and produced the following processed data files: csv tables ending with _RegionLoupe.csv, _filter.csv,  _dopamine.csv, _lesion.csv, _region.csv
Assembly: mm10, GRCh38
Supplementary files format and content: Space Ranger processed data files: expression matrices (h5 files), scaled H&E images (png files), spot coordinate tables (csv files) and scale factors (json files). Loupe Browser 6 processed data files: csv tables ending with _RegionLoupe.csv, _filter.csv,  _dopamine.csv, _lesion.csv, _region.csv
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
snap-frozen un-embedded tissue specimens were cryo-sectioned at 10-12um thickeness, placed onto Visium gene expression array, imaged with MALDI-MSI and then processed with the Visium protocol (10x Genomics) or RRST protocol (https://doi.org/10.1038/s41467-023-36071-5)
spatial gene expression libraries were generated following 10X Genomic Visium Spatial Gene Expression protocol (User Guide, CG000239 Rev F) for the standard Visium, iCTRL, iCTRL_FMP-10 and SMA_Visium samples (ref. protocol column above) or The Visium Spatial Gene Expression for FFPE reagent kit (10x Genomics, User Guide CG000407 Rev C, mouse transcriptome, human transcriptome) for the SMA_RRST samples
Visium spatial gene expression (RNA)

value: brain

value: 8 weeks

tag: array id

tag: protocol

value: standard Visium

tag: section

value: coronal section at the Striatum level


title: mouse brain, Substantia Nigra, 6-OHDA, mouse1, Visium (V11T17-101_A1)

value: coronal section at the Substantia Nigra level


title: C1201

description: Single nucleotide polymorphism array

value: Pathogenic CNVs


title: MIA334A34 Mesenchymal Stromal Cells

value: MSC-HD

tag: cell type

value: Mesenchymal Stromal Cells


title: 12J_M_12


title: MIA334A11 Mesenchymal Stromal Cells

tag: stroma layer


title: C1206

description: Single nucleotide polymorphism array

value: 16 Trisomy


title: mouse brain, Substantia Nigra, 6-OHDA, mouse4, FMP-10_iCTRL (V11T16-085_D1)


title: 12J_M_11


title: mouse brain, Substantia Nigra, 6-OHDA, mouse3, FMP-10 (V11T16-085_B1)


title: C1200

description: Single nucleotide polymorphism array

value: No clinical Variations


title: mouse brain, Substantia Nigra, 6-OHDA, mouse4, FMP-10 (V11T16-085_C1)


title: C1182

description: Single nucleotide polymorphism array

value: 14 Trisomy


title: MON468A42 Mesenchymal Stromal Cells

tag: hspcs


title: 12J_M_10


title: 12J_M_9


title: 12J_M_7


title: 12J_M_8


title: MON468A35 Mesenchymal Stromal Cells


title: MON468A41 Mesenchymal Stromal Cells


title: C1195

description: Single nucleotide polymorphism array


title: C1185

description: Single nucleotide polymorphism array


title: MON468A34 Mesenchymal Stromal Cells


title: mouse brain, Substantia Nigra, 6-OHDA, mouse1, FMP-10 (V11T16-085_A1)


title: 12J_M_4


title: C1186

description: Single nucleotide polymorphism array


title: MON468A33 Mesenchymal Stromal Cells


title: 12J_M_3


title: mouse brain, Striatum, 6-OHDA, mouse3, FMP-10_iCTRL (V11L12-109_D1)

value: iCTRL


title: mouse brain, Striatum, 6-OHDA, mouse4, FMP-10 (V11L12-109_C1)


title: C1183

description: Single nucleotide polymorphism array


title: MON468A32 Mesenchymal Stromal Cells


title: C1175

description: Single nucleotide polymorphism array


title: MON468A27 Mesenchymal Stromal Cells


title: mouse brain, Striatum, 6-OHDA, mouse3, FMP-10 (V11L12-109_B1)


title: mouse brain, Striatum, 6-OHDA, mouse3, iCTRL (V11L12-038_C1)


title: MON468A30 Mesenchymal Stromal Cells


title: 12J_M_2


title: mouse brain, Striatum, 6-OHDA, mouse1, FMP-10 (V11L12-109_A1)


title: 12J_M_5


title: C1174

description: Single nucleotide polymorphism array


title: C1176

description: Single nucleotide polymorphism array

value: 9 Trisomy


title: C1173

description: Single nucleotide polymorphism array


title: 12J_M_1


title: mouse brain, Striatum, 6-OHDA, mouse3, DHB (V11L12-038_B1)


title: MON468A29 Mesenchymal Stromal Cells


title: mouse brain, Striatum, 6-OHDA, mouse3, 9-AA (V11L12-038_D1)


title: C1178

description: Single nucleotide polymorphism array


title: mouse brain, Striatum, 6-OHDA, mouse3, DHB (V11L12-038_A1)


title: MON468A26 Mesenchymal Stromal Cells


title: BCR sequencing of pre-GC and GC B cells

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
BCR mRNA

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
BCR analysis was done via a cellranger v6.0.0 and then analyzed further processed via Immcantation (changeo) to detect clonal lineage and mutations (generating the filtered_contig_heavy_clone-pass.tsv table)
Further processing was done with Seurat v4.2.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz,
Supplementary files format and content: 10x Genomics output files for hashtags: umi_barcodes.tsv.gz, umi_features.tsv.gz, umi_matrix.mtx.gz,
Supplementary files format and content: filtered_contig_heavy_clone-pass.tsv for heavy chain alignment and mutation analysis

extract_protocol:
Spleens from three LDHA-sufficient mice and three LDHA-deficient mice were isolated into single cell suspensions. Cells were then stained with standard flow cytometry antibodies, as well as hashtag B2m and CD45 antibodies to barcode each mouse with a unique Oligonucleotide Hash Tag. Cells were sorted for viability and B cell-positivity, as well as based on GL7 expression (see S5c). Purified Hash-tagged cells were counted and resuspended at a concentration of 1000 cells/ul. Cells suspension was  verified to have viability of >80% using a Countess II.
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Approximately 30,000 cells were targeted, where several samples were multiplexed together on one lane of 10X Chromium, following cell hashing protocol. Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics).
The scRNA-seq and scBCR-seq libraries were prepared using the 10x Single Cell Immune Profiling Solution Kit, according to the manufacturer’s instructions. Briefly, amplified cDNA was used for both 5′ gene expression library construction and TCR enrichment. For gene expression library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected with SPRIselect beads, PCR-amplified with sample indexing primers (98 °C for 45 s; 14–16 cycles of 98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s; 72 °C for 1 min), and double-sided size-selected with SPRIselect beads. For BCR library construction, BCR transcripts were enriched from 2 μl of amplified cDNA by PCR (primer sets 1 and 2: 98 °C for 45 s; 10 cycles of 98 °C for 20 s, 67 °C for 30 s, 72 °C for 1 min; 72 °C for 1 min).
Following BCR enrichment, enriched PCR product was fragmented and end-repaired, size-selected with SPRIselect beads, PCR-amplified with sample-indexing primers (98 °C for 45 s; 9 cycles of 98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s; 72 °C for 1 min), and size-selected with SPRIselect beads. Final libraries (GEX, TCR and HTO) were sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 10 cycles, i5 – 10 cycles, R2 – 90 cycles).

value: Spleen

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: library type

value: mRNA

tag: antibodies/tags


title: C1172

description: Single nucleotide polymorphism array

value: Early embryo growth arrest


title: Combined scRNAseq of 3 LDHA-sufficient and 3 LDHA-deficient pre-GC and GC B cells

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

molecule: polyA RNA

value: pre-GC and GC B cells


title: human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_C1)

value: brain

value: 94 years

value: section of human post-mortem caudate nucleus


title: 12J_M_0


title: MON468A22 Mesenchymal Stromal Cells


title: C1166

description: Single nucleotide polymorphism array


title: JH_AIDKO_3

data_processing:
Paired-end fastq files were demultiplexed and recombined into discrete samples.
FastqToSam (GATK v4.1.9.0) converted each sample to SAM format  remove adapters and low-quality bases (MarkIlluminaAdapters with standard options), 2) bbmap v38.93 to clump duplicate reads into clusters (6 passes, 0 substitutions allowed), 3) grep to include only clusters with at least 100 reads (utilizing the VDJ recombination as a cellular barcode), 4) bbmap v38.93 to align to a custom JH4 reference genome (see below), 5) GATK v4.1.9.0 to convert back to fastq format, 6) realignment with bbmap v38.93, 7) GATK v4.1.9.0 to remove read groups allowing for pileup into a unique text file.Pileup output was processed in R v4.2.1.
MarkIlluminaAdapters (GATK v4.1.9.0) with standard options called Illumina adapters
Low-quality bases and reads were removed with ClipReads (GATK v4.1.9.0) with QT cutoff of 10
Reads were converted back to Fastq with SamToFastq (Clipping_Attribute XT, Clipping_Action 2, Non_Pf True)
Clumpify in bbtools v38.93 was used for deduplication (dedupe, addcount=t, passes=6, subs=0)
Grep to extract paired reads with >10 copies
bbmap (bbtools v38.93) to map (minid=0.25) to custom reference genome (V1-64:D3-1:J4:J4_intron)
Reads were converted back to Fastq with SamToFastq (Clipping_Attribute XT, Clipping_Action 2, Non_Pf True)
bbmap (bbtools v38.93) to map a second time (minid=0.25) to custom reference genome (V1-64:D3-1:J4:J4_intron)
AddOrReplaceReadGroups (GATK v4.1.9.0) to add read groups (to allow PileupSpark to work properly) and to sort by coordinate
PileupSpark (GATK v4.1.9.0) to generate pileups
Custom R Code to generate mutation rates for each sample at each position (1100-1139, excluding 1108 to remove consistent prior observation of high background mutation rate at that position) in the JH4 intron
Assembly: Custom JH4 intron is available at github/ryashka/LDHA
Supplementary files format and content: Pileup for each sample, Combined mutation rate matrix
Library strategy: JH4-Seq

source_name: Splenic GC B cells

extract_protocol:
Germinal center B cells were sorted from the spleen of NP-CGG-immunized mice at day 14. Genomic DNA was harvested using DNeasy Blood & Tissue Kit (QIAGEN) according to the manufacturer’s protocol, except for the elution step in which the DNA on the spin column was eluted in 50mL of elution buffer.
The reverse complement primer probes (RC-probes) targeting the JH4 intron (Fwd: 5’-CATAACAAAGGTTAAAAATAAAGAC-3’ and Rev: 5’-GCCTGACATCTGAGGACTC-3’) were synthesized by NimaGen and used for the generation of indexed amplicons by reverse complementary PCR (RC-PCR). The addition of Illumina universal indexes and sequence adapters to the JH4-specfic RC-probes and the amplification of the intronic sequence with these RC-generated region-specific indexing primers were performed in a probe-polymerase mix. The mix was composed of 1) RC-PCR HiFi Master Mix, 2) RC-probe mix, 3) RC-PCR probe dilution buffer (all from NimaGen), and 4) 80 to 100 ng of genomic DNA. The following thermocycling program was used: 1) 98°C for 2 minutes, 2) 98°C for 10 seconds, 58°C for 10 minutes at a ramp rate of 0.1°C/second, and 72°C for 1 minute, 3) 98°C for 10 seconds, 80°C for 1 second, 58°C for 1 hour and 30 minutes at a ramp rate of 0.1°C/second, and 72°C, 4) go to step 3 once, 5) 98°C for 10 seconds, 80°C for 1 second, 58°C for 2 minutes at a ramp rate of 0.5°C/second, and 72°C for 1 minutes, 6) go to step 5 33 times, 6) 4°C hold. PCR amplicons were purified using Agencourt AMPure XP beads (Beckman Coulter) and resuspended in 50mL of low EDTA Tris-EDTA buffer. Indexed amplicons were sequenced on a NovaSeq platform, and an average of 10 to 20 million 150 bp paired-end reads were generated for each sample (Memorial Sloan Kettering Cancer Center Integrated Genomics Operations, New York, USA).

value: Splenic GC B cells

tag: genotype

value: AID(Cre/Cre)


title: Hashtag sequencing for scRNAseq of pre-GC and GC B cells

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

value: HTO

value: Anti CD45 + Anti MHC classI :WT--/TotalSeq-C0305 ; WT--/TotalSeq-C0306 ; WT--/TotalSeq-C0307 ; KO--/TotalSeq-C0308 ; KO--/TotalSeq-C0309 ; KO--/TotalSeq-C0310


title: MON468A25 Mesenchymal Stromal Cells

value: Mesenchymal Stromal Cells


title: MON468A24 Mesenchymal Stromal Cells


title: MON468A20 Mesenchymal Stromal Cells


title: C1171

description: Single nucleotide polymorphism array

value: Pathogenic CNVs

value: 16 Trisomy


title: JH_AIDKO_4


title: human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_B1)


title: human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_A1)


title: MON468A21 Mesenchymal Stromal Cells


title: CCD18co treated with OSM

city: San Diego

last: Maruggi

address: 10777 Science Center Dr

institute: Pfizer

description:
CH7
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg39
Supplementary files format and content: Tab-separated values files, matrix files, and 10X Loupe files

source_name: CCD18co cells

extract_protocol:
CCD18co cells were dissociated from in-vitro culture by Trypsinization, counted, and processed as illustrated in the 10X Genomics 3' RNA sequencing pipeline
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell line

value: CCD18co cells

tag: treatment

value: OSM


title: JH4_KO6


title: CCD18co treated with TL1a

description:
CH6
10x Genomics

value: Recombinant TL1a


title: MON468A19 Mesenchymal Stromal Cells


title: human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_D1)

tag: age


title: 2.5M_cold shock_24h

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

country: Japan

institute: Meijo University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with Bowtie. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: Halothece sp. PCC7418 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000317635.1/)
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample

organism: Halothece sp. PCC 7418

source_name: Halothece

growth_protocol: Halothece cells were photoautotrophically cultured at 30ºC in blue-green 11 (BG11) media plus Turk Island salt solution (TISS) containing 0.5 or 2.5 M NaCl under continuous cool white fluorescent light intensity of 70 µE m-2 s-1.

extract_protocol:
Total RNA was extracted utilizing TRIzol LS Reagent (Thermo Fisher Scientific), according to the manufacturer’s protocol.
RNA samples were utilized to construct the libraries, which were sequenced at Macrogen (Japan).

treatment_protocol: For heat shock stress treatment, the cells were cultured to the exponential growth phase (OD730 = 0.6-0.8) at 30ºC for at least eight days, then, the temperature was increased to 37ºC.The cells were cultured for 24 h before harvesting. For cold shock stress treatment, the cells were cultured to the exponential growth phase (OD730 = 0.6-0.8) at 30ºC for at least eight days, then, the temperature was decreased to 23ºC.The cells were cultured for 24 h before harvesting.

value: Halothece

value: WT

value: cold shock under 2.5 M NaCl

tag: time


title: MON468A17 Mesenchymal Stromal Cells

value: MSC-HD


title: C1170

description: Single nucleotide polymorphism array

tag: pregnant outcome

value: Early embryo growth arrest

value: 13 Trisomy


title: 2.5M_heat shock_24h

value: heat shock under 2.5 M NaCl


title: MON468A16 Mesenchymal Stromal Cells


title: JH4_WT6

value: Splenic GC B cells

value: Ldha(fl/fl)Aicda(Cre/+)


title: JH4_WT7


title: 2.5M_ctr

description:
Halothece_2.5M_heatshock.xlsx
Halothece_2.5M_coldshock.xlsx

value: control for heat or cold shock treatment under 2.5 M NaCl

value: 0 h


title: JH4_KO7


title: human post-mortem brain, Striatum, PD, Visium (V11T17-101_D1)

value: brain

value: 94 years

value: standard Visium

value: section of human post-mortem caudate nucleus


title: CCD18co treated with TGFb

description:
CH5
10x Genomics

value: CCD18co cells

value: Recombinant TGFb


title: 0.5M_heat shock_24h

value: Halothece

value: heat shock under 0.5 M NaCl


title: 0.5M_ctr

description:
Halothece_0.5M_heatshock.xlsx
Halothece_0.5M_coldshock.xlsx

value: WT

value: control for heat or cold shock treatment under 0.5 M NaCl


title: MON468A10 Mesenchymal Stromal Cells

value: MSC-HD

value: Mesenchymal Stromal Cells


title: CCD18co treated with IL1b

description:
CH4
10x Genomics

value: Recombinant IL1b


title: JH_AIDKO_2

value: Splenic GC B cells

value: AID(Cre/Cre)


title: CCD18co treated with TNFa

description:
CH3
10x Genomics

value: Recombinant TNFa


title: 0.5M_cold shock_24h

value: cold shock under 0.5 M NaCl


title: JH4_KO4

value: Ldha(fl/fl)Aicda(Cre/+)


title: JH_AIDKO_1


title: 0.5M_acclimated

treatment_protocol: To acclimate to low or high salinity, the cells were cultured to the exponential growth phase (OD730 = 0.6-0.8) at 30ºC under 0.5 or 2.5 M NaCl conditions, respectively, for at least eight days.

value: the cells were acclimated to 0.5 M NaCl condition

value: 0 h


title: MON468A9 Mesenchymal Stromal Cells


title: CCD18co treated with IL36

description:
CH2
10x Genomics

value: Recombinant IL36


title: CLS1, 0H

city: Taipei

first: Wan-Yi

last: Shie

address: No.1, Changde St., Jhongjheng District, Taipei City 100, Taiwan R.O.C.

country: Taiwan

institute: National Taiwan University

data_processing:
RNA sequencing was performed on Illumina NovaSeq 6000 at a depth of ~40 million reads per sample and 150bp paired-end reads. Bases with low quality and sequences from adapters in raw data were removed using program FASTQ (version 0.20.0).
The filtered reads were mapped with Bowties2 and aligned to the human reference genome hg19. The software FeatureCounts (v2.0.1) in Subread package was applied for the quantification of the gene abundance.
Differentially expressed genes (DEGs) were identified by DESeq2 (version 1.28.0) or EdgeR (version 3.36.0), depends on whether having biological replicates or not.
Assembly: human reference genome hg19
Supplementary files format and content: Tab-delimited text files include read count for each Sample

source_name: lung

growth_protocol: Human CLS1 was isolated from a lung adenocarcinoma patient as described in, and cultured in RPMI1640 medium supplemented with 10% fetal bovine serum and 1 mM sodium pyruvate at 37 0C in a humidified incubator.

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Thermo Fisher) and RNeasy Mini Kit (QIAGEN), only samples with an integrity number >9.0 underwent cDNA library construction.
Purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 μg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan.

treatment_protocol: Long-term acidosis treatment, pH of the culture media was titrated by the addition of 1N HCl to pH7.4 or pH6.6, mother cells were stocked from the population that has undergone 44 passages (about 2 months). In experiments where short-term acid stimulation was assessed, cells were maintained in the pH media for 24 hours.

value: lung

value: CLS1 cells

value: lung adenocarcinoma

value: no acidosis

value: 0 hour


title: CLS1, pH6.6, 24H

value: WT

value: pH 6.6 culture medium

value: 24 hours


title: CLS1, pH7.4, rep 2, exp 2

value: pH 7.4 culture medium

value: 2 months


title: JH4_WT5

value: Splenic GC B cells


title: MON468A13 Mesenchymal Stromal Cells

value: MSC-HD

value: Mesenchymal Stromal Cells


title: MCF7-P EtOH input

city: Houston

first: Xiaoyong

last: Fu

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw fastq reads were aligned separately to the reference genomes of human (hg19) and Drosophila melanogaster (dm3) using Bowtie 2 v2.3.4.1. Uniquely mapped reads with up to 2 mismatches were used for subsequent peak calling.
We used HOMER v4.9.1 to call peaks for ER (FDR < 0.05, DESeq FDR < 0.1 for duplicates), using the input DNA as background control. Differential peaks were analyzed using merged peaks with the cutoff P-value < 0.01 and fold-change > 2.
ER ChIP-Seq BAM files were downsampled for spike-in normalization using Picard v2.17.8 (Broad Institute). Scaling factors were calculated based on the spiked-in chromatin reads aligned to the reference genome of Drosophila melanogaster (dm3).
Genome_build: hg19
Genome_build: dm3
Supplementary_files_format_and_content: We used HOMER v4.9.1 makeUCSCfile command to create bedGraph files, and used ENCODE bedGraphToBigWig tool to covert bedGraph to bigwig files.

source_name: breast cancer MCF7 cells

growth_protocol: MCF7-P cells were maintained in RPMI/1640 medium, supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG). The isogenic MCF7-P line with doxycycline (Dox)-inducible FOXA1 overexpression was maintained in the presence of 200 μg/ml Geneticin (Invitrogen).

extract_protocol:
Breast cancer cells were grown to 85% confluence in 15-cm plates and cross-linked with 1% formaldehyde (10 min) followed by quenching (125 mM glycine). Cells were washed in cold PBS and harvested by cell scraper in cold PBS with protease inhibitors (Roche). Cells were centrifuged at 3,220g for 5 min, snap-frozen, and stored at -80°C at 1×10^7 cells per pellet. Pellets were resuspended in cytosolic and then nuclear lysis buffer, and chromatin was sheared at 4°C using a water-bath sonicator (Bioruptor, Diagenode) for 20 min at high output (30 s on, 30 s off). Sonicated lysates were cleared by centrifuging at 20,000g for 10 min and diluted 4 times before pre-incubation with protein-A/G beads (Santa Cruz) for 30 min at 4°C. ChIP was performed by overnight incubation at 4°C with antibodies against human ER (Santa Cruz Biotechnology, sc-543X) and Drosophila melanogaster histone variant H2Av (Active Motif, # 61752) to pull down spiked-in chromatin for normalization control, followed by an additional 1 h incubation with protein-A/G beads. Beads were washed consecutively with low and high salt wash buffer, once with LiCl wash buffer, and once with TE buffer. DNA was eluted in elution buffer (50 mM NaHCO3 and 1% SDS) and then supplemented with 300 mM NaCl. Cross-links were reversed overnight at 67°C. RNA was digested at 37°C with 0.1 mg/ml RNase A for 30 min. DNA was purified with a PCR purification kit (Qiagen).
Indexed libraries were prepared from ChIP DNA using the KAPA Hyper Library Preparation Kit (Kapa Biosystems). Libraries were amplified by 12 cycles of PCR, and then assessed for size distribution using the 4200 TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher). The indexed libraries were multiplexed, 10 libraries per pool. The pool was quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) and then sequenced on the Illumina HiSeq 2000.

treatment_protocol: MCF7-P cells constructed with Dox-inducible FOXA1 overexpression were incubated with 1 μg/ml Dox for 5 days before fixation for chromatin extraction. MCF7-P cells were pre-starved in phenol red-free RPMI medium supplemented with 10% charcoal-stripped fetal bovine serum for 48 h, then treated with 0.1% ethanol (as control) or 100 nM 17β-estradiol for 1 h.

tag: sample type

value: Parental

tag: chip antibody


title: JH4_KO5


title: MON468A12 Mesenchymal Stromal Cells


title: MON468A8 Mesenchymal Stromal Cells


title: CCD18co control cells

description:
CH1
10x Genomics

value: CCD18co cells

value: DMSO


title: CLS1, pH7.4, rep 1, exp 2

tag: tissue


title: MON468A4 Mesenchymal Stromal Cells


title: MCF7-P E2 ER rep2

value: ER (Santa Cruz Biotechnology, sc-543X)


title: JH4_KO3

value: Ldha(fl/fl)Aicda(Cre/+)


title: 2.5M_acclimated

value: Halothece

value: the cells were acclimated to 2.5 M NaCl condition


title: MON468A14 Mesenchymal Stromal Cells


title: JH4_KO1


title: MON468A3 Mesenchymal Stromal Cells


title: JH4_WT4

value: Ldha(+/+)Aicda(Cre/+)


title: CLS1, pH6.6, rep 2, exp 2

value: lung

value: CLS1 cells

value: lung adenocarcinoma


title: CLS1, pH6.6, rep 1, exp 2

value: WT

value: pH 6.6 culture medium


title: JH4_KO2


title: JH4_WT3


title: MON468A2 Mesenchymal Stromal Cells


title: MCF7-P EtOH ER


title: MCF7-P E2 ER rep1


title: FOXA1+Dox input


title: CLS1, pH7.4, rep 1, exp 1

value: pH 7.4 culture medium

value: 2 months


title: FOXA1-Dox input


title: MON468A5 Mesenchymal Stromal Cells

value: MSC-HD


title: UL38_3

city: Rochester

first: Joshua

last: Munger

state: New York

address: 601 Elmwood Ave, Room 3-7544, Box 712

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
Raw read counts were obtained using featurecounts from the subread1.5.0p3 package and gencode 25 human gene annotations using only uniquely aligned reads (default) and including multi-mapping reads (-M)
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36
Each sample was mapped individually to the human reference genome (GRCh38.p7, primary assembly + gencode 25 annotation) with STAR2.5.2b
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with a false-discovery rate adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: GRCh38.p7, primary assembly + gencode 25 annotation
Supplementary files format and content: gene names, abundance values, log2 fold changes, and significance scores (p-values).

growth_protocol: MRC5 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Cell cycles were synchronized via serum free media for 24 hours

value: Fibroblasts

value: transduced to express HCMV UL38 gene


title: JH4_WT1

value: Splenic GC B cells


title: UL38_2


title: FOXA1+Dox ER ChIPSeq rep2

value: Parental


title: CLS1, pH6.6, rep 2, exp 1


title: UL38_1


title: CLS1, pH6.6, rep 1, exp 1


title: EV_3

value: transduced to express an empty vector (control)


title: FOXA1-Dox ER ChIPSeq rep1

value: ER (Santa Cruz Biotechnology, sc-543X)


title: FOXA1+Dox ER ChIPSeq rep1


title: CLS1, pH7.4, rep 2, exp 1


title: EV_2


title: ZR75-1-P_FOXA1_plus.Dox rep2

data_processing:
Raw reads were mapped to the human genome (hg19) using STAR v2.5.1.
Relative transcript abundance was calculated by Fragments Per Kilobase of transcript per Million mapped reads (FPKMs) using Cufflinks v2.2.1. RNA-seq quality control was done using RseQC v2.6.2.
Differential gene expression was calculated using Cuffdiff program of Cufflinks v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited csv files include FPKM values for 600MPE parental and endocrine-resistant models, and cuffdiff outputs of comparison of ER+ breast cancer cells (T47D and ZR75-1) with ectopic FOXA1 overexpression (+Dox) vs. non-overexpression (-Dox).

source_name: breast cancer ZR75-1 cells

growth_protocol: 600MPE parental cells were kept in DMEM medium with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG). Estrogen deprivation-resistant (EDR) cells were kept in phenol-red free (PRF) DMEM medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS and 1% PSG. Tamoxifen-resistant (TamR) cells were kept in PRF DMEM medium supplemented with 10% heat-inactivated CS-FBS and 1% PSG, with the addition of 100 nM 4-OH-tamoxifen (H7904, Sigma). Cells (T47D and ZR75-1) with inducible FOXA1 overexpression were kept in RPMI medium supplemented with 10% FBS and 1% PSG. All cells have been authenticated by short tandem repeats DNA profiling and are routinely tested for mycoplasma negative using the MycoAlert Mycoplasma Detection Kit (Lonza).

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Cells were maintained in their original media and harvested for RNA extraction. Cells with inducible FOXA1 overexpression were treated with -/+Dox (1 μg/ml) for 48 h before RNA extraction.

value: endocrine-sensitive parental


title: Sut5-DDR2-plus

city: NEW YORK

first: Lingling

last: Hu

address: 1300 York Avenue LC-902

institute: Weill Cornell Medicine

data_processing:
A counts matrix was obtained. DESeqDataSet was generated using this unnormalized counts matrix. Differential expression analysis was performed using the ‘DESeq’ function and results tables were generated using the ‘results’ function to compare the DDR2+ vs. CTSK+ groups50. Log fold change shrinkage was performed using the ‘lfcShrink’ function with the ‘apeglm’ method51 for visualization and ranking of genes. Results were exported as .csv files (one with all the genes, and one with the subset of genes with adjusted P value < 0.05). 2-D PCA plots of the samples were generated by the first two principal components using the ‘plotPCA’ function.
Assembly: mm10
Supplementary files format and content: Normalized read counts for each sample

source_name: Calvarial suture

extract_protocol:
Total mRNA was freshly extracted from FACS-isolated CSC populations from P7 Ctsk-Cre mice (n=5) using RNeasy Plus Micro Kit (Qiagen, cat. 74034). Total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies).
cDNA synthesis and amplification were performed by SMART-Seq v4 ultra-low input RNA kit (Takara Bio, USA) starting with 1 ng of total RNA from each sample. 150 pg of qualified full-length double-strand cDNA was used and processed for Illumina library construction with the Nextera XT DNA Library Preparation Kits (Illumina). Then the normalized cDNA libraries were pooled and sequenced on an Illumina NovaSeq6000 sequencer with pair-end 50 cycles.

value: Calvarial suture

value: FACS-isolated calvarial stem cells


title: ZR75-1-P_FOXA1_plus.Dox rep1


title: Sut5-PSC


title: Sut4-PSC


title: ZR75-1-P_FOXA1_minus.Dox rep2


title: JH4_WT2

value: Ldha(+/+)Aicda(Cre/+)


title: FOXA1-Dox ER ChIPSeq rep2


title: 600MPE-TamR rep2

source_name: breast cancer 600MPE cells

value: tamoxifen-resistant derivative


title: ZR75-1-P_FOXA1_minus.Dox rep1


title: HUVEC_I130-3

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
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 GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38

source_name: HUVEC

extract_protocol: Trizol (Invitrogen) was used for RNA isolation from white adipose tissue.

treatment_protocol: we performed intramuscular deliver of negativ control mimic or mir-130b mimic into the ischemic gastrocnemius following femoral artery ligation in db/db mice (4 injections in total). Two weeks post injury, gastrocnemius muscle was harvested and EC fraction was isolated by using CD31 antibody-bound magnetic beads. RNA-Seq analysis was performed using Illumina HiSeq2500 V4 2x150 bp  (Genewiz, South Plainfield, NJ).

value: HUVEC

value: Transfected with miR-130 mimic


title: 600MPE-TamR rep1


title: Sut3-DDR2-plus

value: WT


title: HUVEC_I130-2


title: T47D-P_FOXA1_plus.Dox rep2

source_name: breast cancer T47D cells


title: Sut2-PSC


title: HUVEC_I130-1


title: 600MPE-EDR rep2


title: Sut4-DDR2-plus


title: T47D-P_FOXA1_plus.Dox rep1


title: Sut2-DDR2-plus


title: HUVEC_INS-3

value: Transfected with non-specific mimic


title: EV_1


title: T47D-P_FOXA1_minus.Dox rep2


title: Sut1-PSC


title: 600MPE-EDR rep1


title: Sut3-PSC


title: T47D-P_FOXA1_minus.Dox rep1


title: Sut1-DDR2-plus


title: Tet2 KO_3

status: Public on May 20 2023

first: Yue

last: Wei

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
Basecalling was done by HiSeq Control Software (HD 3.4.0.38).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the cpm (count per million mapped fragments) value for each gene was calculated by R/Bioconductor package edgeR (version 3.8.6).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are cpm values (estimated by edgeR) for all the samples.

source_name: bone marrow LSK cells

extract_protocol:
bone marrow LSK cells were isolated by FACS and frozen in Picopure RNA extraction buffer in -80C. RNA was harvested using Picopure RNA extraction kit. 10-20 ng Total RNA for the construction of sequencing libraries.
RClontech SMARTer v4 + Nextera kit was to prepare the libraries

tag: strain

value: untreated

value: Vav Cre/ Tet2 flox/flox

value: bone marrow LSK cells


title: 600MPE-P rep2


title: Tet2 KO_1


title: 600MPE-P rep1


title: HUVEC_INS-2


title: KDM6B OE_3

value: Vav human KDM6B


title: KDM6B OE_2


title: KDM6B OE_1


title: Tet2 KO_2


title: double lesion_3

value: Vav human KDM6B/ Vav Cre/ Tet2 flox/flox


title: double lesion_1


title: double lesion_2


title: Vav Cre_3

value: Vav Cre


title: Vav Cre_1


title: MIP56_Podo_4

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
FASTQ files were quality trimmed with Trimmomatic
Reads were mapped to mm10 using RNA STAR
Count matrix was calculated using Htseq tools
EdgeR was used for all comparisons
Genome_build: GRCm38/mm10

source_name: Enzyme-dissociated cells

extract_protocol:
RNA was isolated with trizol according to manufacturer’s instructions with glycogen included as a carrier. Each sample was treated with DNase I (Roche) for 10 minutes and then RNA was further column purified with MinElute RNeasy kit (#28004, Qiagen).
RNA quality was ascertained by RNA-Pico on Agilent Bioanalyzer. RNA-seq libraries were constructed using Ovation RNA-Seq System V2 followed by Ovation Ultralow System V2 using Nugen protocols M01114 v5 and M01379v3.1. Libraries were quantitated by Qubit and size profile determined using Bioanalyzer. All libraries had a mean size of ~300 bp and were similar concentrations (~10 ng/ul) Libraries were finally quantitated by qPCR and 2 pools prepared in equimolar ratios for sequencing. 200 pM of each pool based upon qPCR was used for clustering. Libraries were sequenced at 80 bp single base pair reads using Illumina HiSeq 3000.

treatment_protocol:
For adult male surgeries, the animals were housed under standard conditions with 12h light/dark cycles and ad libitum access to food and water. At 8 weeks of age, male CD1 mice were anesthetized with 4% isoflurane (Bayer) and maintained with 2% isoflurane and 0.25 l/min oxygen during surgery. The animals were intubated and ventilated (Minivent, Harvard Apparatus) with a tidal volume of 250 µl and a respiration rate of 133 strokes/min. A thoracotomy at the 3rd and 4th intercostal space was performed and the pericardial sac removed. The left descending coronary artery was permanently ligated with 7-0 prolene suture (Ethicon). Following ligation, blanching of the myocardium was observed to determine if adequate ischaemia was achieved. The chest wall was then sutured closed, the mouse removed from anesthesia, supplied with s.c. injection of buprenorphine (0.05mg/kg) as required and allowed to recover from the surgery. Sham mice had the same procedure except MI was not performed.
Adult CD-1 (ICR) mice were anaesthetized with an i.p injection of ketamine (100 mg/kg) and Xylazil (12.5 mg/kg) 3 days post-surgery. Hearts were quickly dissected and washed in perfusion buffer (120.4 mmol/l NaCl, 14.7 mmol/l KCl, 0.6 mmol/l KH2PO4, 0.6 mmol/l Na2HPO4, 1.2 mmol/l MgSO4•7H2O, 4.6 mmol/l NaHCO3, 10 mmol/l Na-HEPES, 30 mmol/l taurine, 5.5 mmol/l glucose and 10 mM 2,3-Butanedione 2-monoxime). The aorta was then cannulated with a 21-gauge cannula, secured with 3-0 silk suture and perfused with 37◦C, oxygenated perfusion buffer using a Langendorff apparatus (4ml/min). Once all blood was washed from the heart, digestion buffer (200 µg/ml Liberase DH (Roche) in perfusion buffer) was passed through the heart for ~8 minutes (until the hearts appeared waxy in color and flaccid to the touch). During perfusion, atria and excess tissue was removed. After enzymatic digestion, hearts were minced with fine scissors into small pieces and triturated to release cells. Cell isolates were passed through a 100 µm cell strainer and centrifuged at 30xg for 3 minutes at room temperature. Supernatant (containing the non-myocyte cells) was collected and the myocyte pellet was washed with perfusion buffer and re-centrifuged. The supernatant was again collected and the purified myocyte pellet was lysed with 1 ml of Trizol (ThermoFisher). The non-myocyte supernatant was centrifuged at 500xg for 5 minutes and FACS was performed.
Following cell extraction, the non-myocyte fraction was resuspended in 100ul 5 mg/ml bovine serum albumin in PBS solution. Cell isolates were then incubated at 4°C for 20 minutes with 3 ug of CD90-APC (A14727, ThermoFisher), CD45-FITC (130-102-778, Miltenyi Biotec), CD31-BV421 (102423, BioLegend) and Podoplanin-PE/Cy7 (127411, BioLegned). The stained cells were washed in PBS/BSA solution and sorted using a BD FACS ARIA cell sorter. Each purified cell population was centrifuged at 1000xg for 5 minutes, cell media was aspirated and 1 ml Trizol was added to isolate RNA.

value: Lymphatic endothelial cell (CD45-/CD31+/Podoplanin+)

value: Myocardial infarction


title: MIP56_Podo_3


title: HUVEC_INS-1


title: MIP1_Podo_4

treatment_protocol:
For neonatal surgeries, timed pregnant CD1 female mice were housed under standard conditions with 12h light/dark cycles and ad libitum access to food and water. At postnatal day 1 mice (P1), neonatal MI surgeries were performed as previously described (Mahmoud, A.I., et al. (2014) Nat. Protocols 9, 305-311). Sham mice had the same procedure except MI was not performed.
Neonatal CD-1 (ICR) mice were decapitated 3 days after surgery and cardiac ventricles were dissected and washed in ADS buffer (116.3 mmol/l NaCl, 20mmol/l HEPES, 1mmol/l NaH2PO4, 5.5mmol/l glucose, 5.36 mmol/l KCl, 0.83 mmol/l MgSO4,) and then cut into small pieces and pooled into groups of 6 ventricles per cell stirrer. Hearts were then digested at 37◦C under constant agitation for 30-40 minutes (or until tissue was fully homogenized). The digestion buffer was made with 200 µg/ml Liberase DH (Roche) in ADS buffer. Myocytes and non-myocytes were then separated by percoll® as described above. Cell isolates were then layered on percoll gradients and centrifuged at 2100xg for 30 minutes. The bottom layer (containing myocytes) and the top layer (containing enriched non-myocytes) were then collected separately and washed twice in ADS. The myocyte fraction was then lysed in Trizol. FACS was then performed on the non-myocyte fraction.
Following cell extraction, the non-myocyte fraction was resuspended in 100ul 5 mg/ml bovine serum albumin in PBS solution. Cell isolates were then incubated at 4°C for 20 minutes with 3 ug of CD90-APC (A14727, ThermoFisher), CD45-FITC (130-102-778, Miltenyi Biotec), CD31-BV421 (102423, BioLegend) and Podoplanin-PE/Cy7 (127411, BioLegned). The stained cells were washed in PBS/BSA solution and sorted using a BD FACS ARIA cell sorter. Each purified cell population was centrifuged at 1000xg for 5 minutes, cell media was aspirated and 1 ml Trizol was added to isolate RNA.


title: MIP56_Podo_1


title: MIP1_Podo_3


title: MIP1_Podo_2


title: ShamP56_Podo_4

value: Sham-operation


title: MIP1_Podo_1


title: ShamP56_Podo_3


title: ShamP56_Podo_2


title: ShamP56_Podo_1


title: Vav Cre_2


title: ShamP1_Podo_2


title: ShamP1_Podo_3


title: MIP56_Podo_2


title: B12

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

description:
Panc1
abundance.kallisto_B12

data_processing:
Raw sequencing data was mapped to a human transcriptome library (GRCh38) using kallisto (v0.46.1) with 30 bootstrap intervals.
Data was imported into R and length scaled TPM values were calculated using functions tximport and summarizeToGene (library tximport)
Assembly: GRCh38.103
Supplementary files format and content: Length scaled TPM values sumamrised on gene level (tab separated file)

growth_protocol: The PDAC-derived cell line BxPC3 (classical-like subtype) and Panc-1 (basal-like subtype) were cultured in DMEM high glucose with 10% fetal bovine serum and 1% Penicillin-Streptomycin-Glutamine (Sigma-Aldrich, St. Louis, USA) at 37°C, 5% CO2 in a humidified atmosphere.

extract_protocol:
RNA was extracted from each SCDCL using the AllPrep RNeasy Mini Kit (Qiagen N.V., Venlo, Niederlande) as indicated by the manufacturer in the instruction manual. RNA samples were sequenced at Novogene Europe, Cambridge, United Kingdom.
Poly-A enrichment and strand-specific library preparation were used.

treatment_protocol: To measure the sensitivity to gemcitabine (Sigma-Aldrich, St. Louis, USA), cells of the respective parental cell population growing in log phase (2,000 cells of BxPC3 and 1,500 cells of Panc-1 per well) were seeded in 96-well plates. After a period of 24 hours, the cells were treated with gemcitabine concentrations ranging from 2.5 to 320 nmol/L for 72 hours. After this time, the survival fraction of the cells was determined. For this purpose, cell metabolism was used as a surrogate parameter for viability by using the CellTiter-Blue assay (Promega, Madison, USA).

value: single cell-derived cell line

value: gemcitabine


title: B7

description:
Panc1
abundance.kallisto_B7


title: B4

description:
Panc1
abundance.kallisto_B4


title: B10

description:
Panc1
abundance.kallisto_B10


title: B8

description:
Panc1
abundance.kallisto_B8


title: B9

description:
Panc1
abundance.kallisto_B9


title: B11

description:
Panc1
abundance.kallisto_B11


title: B14

description:
Panc1
abundance.kallisto_B14


title: B3

description:
Panc1
abundance.kallisto_B3


title: B13

description:
Panc1
abundance.kallisto_B13


title: B6

description:
Panc1
abundance.kallisto_B6


title: B2

description:
Panc1
abundance.kallisto_B2


title: B23

description:
BxPC3
abundance.kallisto_B23


title: ShamP1_Podo_4


title: B1

description:
Panc1
abundance.kallisto_B1


title: ShamP1_Podo_1


title: B26

description:
BxPC3
abundance.kallisto_B26


title: B22

description:
BxPC3
abundance.kallisto_B22


title: B25

description:
BxPC3
abundance.kallisto_B25


title: B16

description:
BxPC3
abundance.kallisto_B16


title: B20

description:
BxPC3
abundance.kallisto_B20


title: B21

description:
BxPC3
abundance.kallisto_B21


title: B18

description:
BxPC3
abundance.kallisto_B18


title: B24

description:
BxPC3
abundance.kallisto_B24


title: B5

description:
Panc1
abundance.kallisto_B5


title: B19

description:
BxPC3
abundance.kallisto_B19


title: B17

description:
BxPC3
abundance.kallisto_B17


title: B15

description:
BxPC3
abundance.kallisto_B15


title: NC, IL-6, biol rep5

city: Nantes

first: Anais

last: Defois

address: 1 place Alexis Ricordeau

country: France

institute: Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR 1229

description:
A679_HVC_5_IL6
ExpressionMatrix_NTS-258-1(1).csv

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Chondrocytes

growth_protocol: Primary human chondrocytes were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNAs were extracted using the RNA XS kit according to the manufacturer instruction (Macherey-Nagel, NucleoSpin RNA XS, 740902)
the libraries was prepared from 10 ng of total RNA. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach, which enriches for 3’ends of cDNA. 38.5 nM of full-length cDNAs was used as input to the Nextera DNA Flex library prep kit (ref 20018704, Illumina), which enriches for 3′ends of cDNA. Size library is controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350-800bp (major pic at 484 pb) was run on an Illumina NovaSeq 6000 using a NovaSeq 6000 SP Reagent Kit 100 cycles according to manufacturer’s protocol (NovaSeq 6000 Sequencing System Guide Document #1000000019358v11, Illumina).
3’seq-RNA

treatment_protocol: Pro-inflammatory treatments (IL-1b at 1ng/mL OR TNF-a at 25ng/mL OR IL-6/IL6Rs at 50 ng/mL) were applied during 24h

tag: disease

value: non-OA

value: Chondrocytes


title: NC, IL-6, biol rep4

description:
A673_HVC_5_TNF
ExpressionMatrix_NTS-258-1(1).csv


title: NC, IL-6, biol rep1

description:
A649_HVC_4_IL6
ExpressionMatrix_NTS-258-1(2).csv


title: NC, IL-6, biol rep2

description:
A667_HVC_5_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: NC, IL-6, biol rep3

description:
A670_HVC_5_IL1b
ExpressionMatrix_NTS-258-1(2).csv


title: NC, TNF, biol rep4

description:
A643_HVC_4_IL1b
ExpressionMatrix_NTS-258-1(2).csv

value: TNF


title: NC, TNF, biol rep5

description:
A646_HVC_4_TNF
ExpressionMatrix_NTS-258-1(2).csv


title: NC, TNF, biol rep3

description:
A640_HVC_4_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: NC, TNF, biol rep1

description:
A499_HVC_3_TNF
ExpressionMatrix_NTS-258-1(1).csv


title: NC, IL-1b, biol rep4

description:
A493_HVC_3_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: NC, IL-1b, biol rep3

description:
A476_HVC_2_IL6
ExpressionMatrix_NTS-258-1(2).csv


title: NC, IL-1b, biol rep5

description:
A496_HVC_3_IL1b
ExpressionMatrix_NTS-258-1(2).csv


title: Smartseq2, MI, MAD2L1BP (R285*), rep2

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
The raw data were qualitatively controlled using Fast QC (version 0.11.9), followed by fastp (version 0.23.2) to remove the linker and low-quality reads
Clean reads were mapped to the human reference genome (hg38) using STAR (version 2.7.6a).
The mapping files containing the reads matching the human genome were used RSEM to calculate gene and transcript expression values, and raw read counts.
Using the DESeq2 R package to analyze the differential expression between the control group and the experimental group, fold change>=2 and qvalue<=0.05.
Assembly: hg38
Supplementary files format and content: Genome sequencing depth file and expression count file

source_name: ovary

extract_protocol:
MI oocytes were washed at least five times in 1XPBS, and directly lysed in Lysis Buffer MasterMix (0.3% TritonX-100, 40U/µL RNase inhibitor, 2.5µM oligodT30VN, and 2.5µM dNTP mix)
Library was performed according to the Smart-seq2 method (Simone Picelli, et al. Nature Protocols, 2014).
Smart-seq2

value: ovary

value: MI oocyte


title: Smartseq2, MI, Control, rep2

value: WT


title: Smartseq2, MI, Control, rep1


title: Smartseq2, MI, MAD2L1BP (R285*), rep1


title: NC, IL-1b, biol rep1

description:
A470_HVC_2_IL1b
ExpressionMatrix_NTS-258-1(1).csv


title: NC, No treatment, biol rep3

description:
A389_HVC_1_TNF
ExpressionMatrix_NTS-258-1(1).csv

value: No treatment


title: OAC, IL-6, biol rep5

description:
A623_HAC_5_IL6
ExpressionMatrix_NTS-258-1(1).csv

value: OA


title: OAC, IL-6, biol rep4

description:
A620_HAC_5_TNF
ExpressionMatrix_NTS-258-1(2).csv


title: NC, No treatment, biol rep2

description:
A386_HVC_1_IL1b
ExpressionMatrix_NTS-258-1(1).csv


title: NC, No treatment, biol rep1

description:
A383_HVC_1_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: NC, TNF, biol rep2

description:
A502_HVC_3_IL6
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, IL-6, biol rep2

description:
A614_HAC_5_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: NC, No treatment, biol rep5

description:
A467_HVC_2_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: NC, IL-1b, biol rep2

description:
A473_HVC_2_TNF
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, TNF, biol rep4

description:
A630_HAC_4_IL1b
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, TNF, biol rep5

description:
A633_HAC_4_TNF
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, IL-1b, biol rep4

description:
A523_HAC_3_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, TNF, biol rep3

description:
A627_HAC_4_CTL
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, IL-6, biol rep3

description:
A617_HAC_5_IL1b
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, TNF, biol rep1

description:
A529_HAC_3_TNF
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, IL-1b, biol rep1

description:
A513_HAC_2_IL1b
ExpressionMatrix_NTS-258-1(2).csv


title: NC, No treatment, biol rep4

description:
A392_HVC_1_IL6
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, IL-1b, biol rep5

description:
A526_HAC_3_IL1b
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, IL-1b, biol rep3

description:
A519_HAC_2_IL6
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, IL-1b, biol rep2

description:
A516_HAC_2_TNF
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, No treatment, biol rep5

description:
A510_HAC_2_CTL
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, No treatment, biol rep3

description:
A399_HAC_1_TNF
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, IL-6, biol rep1

description:
A636_HAC_4_IL6
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, No treatment, biol rep1

description:
A396_HAC_1_CTL
ExpressionMatrix_NTS-258-1(1).csv


title: OAC, No treatment, biol rep4

description:
A405_HAC_1_IL6
ExpressionMatrix_NTS-258-1(2).csv


title: OAC, No treatment, biol rep2

description:
A402_HAC_1_IL1b
ExpressionMatrix_NTS-258-1(2).csv


title: Patient 1104 CPC-EV total RNA

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

data_processing:
Small RNA sequencing files were aligned and hits were determined using the Qiagen GeneGlobe console with QIAseq miRNA Quantification tool. Default parameters were used: 3’ adapters were trimmed using cutadapt, reads with less than 16 base pair insert sequences or less than 10 base pair unique molecular index sequences were removed, reads were aligned with Bowtie aligner, GRCh38 and miRBase v21 references.
Total RNAseq files from Novogene and Emory Yerkes Nonhuman Primate Genomics core were aligned, and gene counts were determined with the STAR aligner in the Illumina BaseSpace app, RNA-Seq Alignment. Reads were aligned with hg19 reference genome.
Assembly: total RNA: hg19,miRNA: GRCh38
Supplementary files format and content: Total RNA: aligned reads in txt file
Supplementary files format and content: small RNA: read numbers from Qiagen quantification tool in xlsx

source_name: cardiac biopsy

growth_protocol: Cells collected from the right atrial appendage of patients with congenital heart disease were separated for c-kit+ progenitor cells using magnetic cell sorting. Cells were cultured in Ham’s F-12 medium (Corning Cellgro®, Corning, NY, USA) with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% L-glutamine and 0.04% human fibroblast growth factor-β. Extracellular vesicles collected from conditioned media of cell culture, isolated via ultracentrifugation.

extract_protocol:
RNA isolated with Qiagen miRNeasy ket, according to manufacturer's procedures. Purified RNA was analyzed (2100 Bioanalyzer and TapeStation Controller, Agilent Genomics) for miRNA and RNA size, quality, and quantity.
For miRNA library preparation, we used the QIAseq miRNA Library Kit from Qiagen. For total RNA library preparation, we used Clontech SmartER Pico + rRNA depletion, and sequencing on the NovaSeq6000 to a depth of 25-30 million reads/sample at 100SR.

value: cardiac biopsy

tag: patient age

value: <1 week

value: extracellular vesicle from c-kit+ progenitor cell

tag: disease state

value: congenital heart disease

value: Hypoplastic left heart sydrome


title: Patient 938 CPC-EV total RNA

value: 5 years

tag: cell type

value: subaortic membrane resection, mitral valve ring


title: Patient 1103 CPC-EV total RNA


title: Patient 1105 CPC-EV total RNA


title: OAC, TNF, biol rep2

description:
A532_HAC_3_IL6
ExpressionMatrix_NTS-258-1(1).csv


title: Patient 1106 CPC-EV total RNA


title: Patient 1107 CPC total RNA

value: c-kit+ progenitor cell


title: Patient 1101 CPC-EV total RNA


title: Patient 1102 CPC-EV total RNA


title: ICC4958 Drought Rep2

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

description: Transcriptome

data_processing:
The FASTQ files obtained were pre-processed using NGS QC Toolkit (v2.3.3) to remove adapters and low-quality reads. Low-quality reads with Phred score >20 were filtered.
Filtered high-quality reads were mapped on the chickpea genome (v1.0) using TopHat2 pipeline (v2.1.1).
A consensus reference-guided assembly of the transcriptome data was generated using Cufflinks (v2.2.1).
Differential expression of genes was determined by Cuffdiff (v2.2.1).
Genome_build: Kabuli chickpea genome (v1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in the drought sensitive and tolerant cultivars under control and drought conditions

organism: Cicer arietinum

source_name: root

growth_protocol: Cicer arietinum ICC4958, ICC1882 seedling were grown in a growth chamber

extract_protocol:
Total RNA was extracted using TRI Reagent. RNA quantification was performed and quality was assessed using Agilent Bioanalyzer. cDNA libraries were prepared and sequencing was performed on Illumina HiSeq platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Drought stress was imposed on 16 day old plants by withholding water for 11 days, control samples were watered on alternate days. The roots were harvested from both stress and control samples from 27 days old seedlings.

tag: condition

value: Drought

tag: phenotype

value: drought-tolerant

value: root

value: 27 days old


title: Patient 1107 CPC-EV total RNA


title: Patient 1106 CPC total RNA


title: Patient 1105 CPC total RNA


title: ICC4958 Drought Rep1

description: Transcriptome


title: Patient 1104 CPC total RNA


title: ICC4958 Control Rep2

description: Transcriptome

value: Control


title: ICC4958 Control Rep1

description: Transcriptome


title: Patient 1102 CPC total RNA


title: ICC1882 Drought Rep1

description: Transcriptome

value: drought-sensitive


title: ICC1882 Drought Rep2

description: Transcriptome


title: Patient 1092 CPC-EV total RNA

value: 4 years

value: Atrial septal defect


title: ICC1882 Control Rep2

description: Transcriptome


title: Patient 1092 CPC-EV miRNA


title: Patient 1101 CPC total RNA


title: Patient 1106 CPC-EV miRNA


title: Patient 938 CPC-EV miRNA


title: ICC1882 Control Rep1

description: Transcriptome


title: Patient 1107 CPC-EV miRNA


title: HCC1187-sh-SOX9-AS1_3

city: Ciudad de México

first: Mireya

last: Cisneros-Villanueva

state: Ciudad de Mexico

address: Periférico Sur No. 4809, Arenal Tepepan, 4809

country: Mexico

institute: Instituto Nacional de Medicina Genómica

data_processing:
The sequencing of RNA-seq libraries was carried out on the NextSeq 500 platform (Illumina, USA) at an average depth of 23 million raw paired reads per sample.
Quality control of raw fastq files was determined using FastQC (v. 0.11.9) and MultiQC (v. 1.11).
Adapter sequences, poor quality reads with Q values ≤22 and reads with fragment sizes ≤70 bp were filtered through Trimmomatic (v. 0.39).
The alignment of raw reads to GRCh38 (Homo sapiens) reference genome and the generation of bam files were carried out with Hisat2 (v. 2.1.0) and samtools, respectively.
Abundance estimation and mapped reads counting was performed with featureCounts (v. 2.0.0). All the analyses were carried out in the Unix-Bash environment of Linux platform
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: cell line

growth_protocol: MDA-MB-468 cells were maintained in DMEM and HCC1187 cells were maintained in RPMI-1640 both were supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen).  1 µg of total RNA was used for the construction of sequencing libraries
Paired-end RNA-seq libraries with fragments of 76 bp were generated from total RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols

treatment_protocol: Cells were transfected during 48 hours

value: cell line

value: basal-like cells

value: SOX9-AS1 knockdown

value: sh-SOX9-AS1 rep3


title: Patient 1104 CPC-EV miRNA

value: cardiac biopsy

value: <1 week

value: extracellular vesicle from c-kit+ progenitor cell

value: congenital heart disease


title: Patient 1103 CPC-EV miRNA

value: Hypoplastic left heart sydrome


title: Patient 1101 CPC-EV miRNA


title: Patient 1102 CPC-EV miRNA


title: Patient 1103 CPC total RNA

value: c-kit+ progenitor cell


title: Patient 1107 CPC miRNA


title: HCC1187-sh-SOX9-AS1_1

value: sh-SOX9-AS1 rep1


title: HCC1187-sh-CONTROL_3

value: shCONTROL

value: sh-LacZ rep3


title: HCC1187-sh-SOX9-AS1_2

value: sh-SOX9-AS1 rep2


title: HCC1187-sh-CONTROL_2

value: sh-LacZ rep2


title: Patient 1105 CPC-EV miRNA


title: MDA-MB-468-sh-SOX9-AS1_2


title: MDA-MB-468-sh-SOX9-AS1_3


title: Patient 1106 CPC miRNA


title: Patient 1105 CPC miRNA


title: MDA-MB-468-sh-CONTROL_3


title: MDA-MB-468-sh-SOX9-AS1_1


title: Patient 1104 CPC miRNA


title: Patient 1103 CPC miRNA


title: MDA-MB-468-sh-CONTROL_1

value: sh-LacZ rep1


title: Patient 1101 CPC miRNA


title: Patient 1102 CPC miRNA


title: Thatcher, Mock, 14 days, (Tc14), rep3

city: Ottawa

first: Michele

last: Loewen

state: Ontario

address: 100 Sussex Drive

country: Canada

institute: National Research Council of Canada (NRC)

data_processing:
Adaptor and quality trimming performed with fastp (Phred Score > 20, min read length > 50).
Quantification with Salmon in mapping-based mode
Differential gene expression analysis with DESeq2.
Assembly: IWGSC_RefSeqv2.1_HC_CDS_assembly
Supplementary files format and content: Transformed (vsd) transcript values from DESeq2 in tab-delimited format

organism: Triticum aestivum

source_name: flag leaf

growth_protocol: Plants were grown in Sunshine Mix #8 with a 16 hour/8 hour 22°C/17°C day/night cycle.

extract_protocol:
Total RNA was extracted using the Zymo Direct-zol RNA Miniprep kit (Infected samples) or the Monarch NEB Total RNA Miniprep kit (Mock samples)
cDNA libraries for infected samples were prepared using the TruSeq Stranded mRNA kit; cDNA libraries for mock samples were preparred using an Illumina Stranded mRNA, Ligation kit.

treatment_protocol: For infection, rust urediniospores were applied at the beginning of anthesis

value: flag leaf

value: Thatcher

value: Mock 14 days


title: Thatcher, Mock, 14 days, (Tc14), rep4