title: HEK293T, smallRNA, ASmut3 transfected, rep1

description:
Library name: smallRNA_ASmut3_Rep1
ASmut3_1

value: ASmut3 transfection


title: WT 9.5hr sporulation media rep2

status: Public on Aug 14 2026

type: SRA

city: Atherton

first: Constantine

last: Bartolutti

state: California

address: 69 Santiago Avenue

country: USA

institute: Stanford University

description:
Library name: Sample16
WT_9_5hr_2

library_source: transcriptomic

data_processing:
Used Star align on untrimmed reads to SK1 reference genome - outputs bam files and optionally outputs unique alignment reads
Used samtools index to index the bam files outputted from star align
feature counts command used to assemble raw counts numbers for all files
Assembly: GCA_000766265.2
Supplementary files format and content: .csv files contain RPKM values

molecule: total RNA

organism: Saccharomyces cerevisiae SK1

growth_protocol: Vegetative: Strains were grown with YPD at 30 degrees with shaking. Meiotic: Strains were grown in YPD at 30 degrees until saturation before back dilution and growth in BYTA. Strains were grown at 30 degrees in BYTA until saturation before washing with water and resuspention in sporulation media. Premeiotic starvation: Strains were grown with YPD at 30 degees with shaking until saturation. Strains were back diluted in BYTA media.

extract_protocol:
Cells were harvested via pelleting liquid culture at 6000 RCF then aspirating media before snap freezing in liquid nitrogen. Cells were thawed on ice and resuspended in 625ul TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). An equal volume of citrate-buffered acid phenol (pH 4.3, P4682, Sigma-Aldrich) was added to cells, and they were incubated at 65C for 1 hour in a Thermomixer C (Eppendorf) shaking at 1400 RPM. After microcentrifugation (20,000 g for 10 min) the aqueous phase was transferred to a second tube with 600ul acid phenol. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and transferred to a third tube with 600ul chloroform. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and RNA was precipitated in 100% isopropanol with 350 mM sodium acetate (pH 5.2) overnight at –20C. Pellets were washed with 80% ethanol and resuspended in DEPC water
RNA-seq libraries for three biological replicates were generated with the NEXTflex Rapid Directional mRNA-Seq Bundle with poly(A) beads (NOVA-5138, Bioo Scientific) according to manufacturer’s instructions. 10 mg of total RNA was used as input for all libraries. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp. Libraries were quantified using the Agilent 4200 TapeStation (Agilent Technologies, Inc). Samples were submitted for 100 bp single-end sequencing by the Vincent J. Coates Genomics Sequencing Laboratory with a NovaSeq X.

treatment_protocol: Vegetative cells were harvested in exponential growth phase (OD600=0.6). Premeiotic cells were harvested at times indicated, with 0hr being the time that the cells were transfered from YPD to BYTA media. Meiotic cells were harvested at times indicated, with 0 hr being the time that the cells were transferred into sporulation media.

tag: strain

tag: genotype

value: WT

tag: treatment

value: meiotic


title: Case_56, Chondrosarcoma

type: genomic

city: Bern

first: Jon

last: Brugger

address: Private Address

country: Switzerland

institute: Private

description: Sample ID: 207130360153_R01C01

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using mepylome version 0.10.0 and python 3.13
[processed value definition]  Beta values, calculated with mepylome using the Illumina method

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: KRYO

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

value: Chondrosarcoma

tag: subdiagnosis

value: Metastasis

tag: grade

value: high-grade

tag: origin

value: NL

value: MUT

value: Lung

tag: gender

value: female

tag: status

value: alive

tag: tissue

value: KRYO


title: hac1 5.5hr sporulation media rep1

description:
Library name: Sample17
hac1_5_5hr

value: hac1 delete


title: Case_54, Chondrosarcoma

description: Sample ID: 207130360090_R05C01

value: Femur

tag: age


title: Case_92, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170090_R01C01

source_name: FFPE

value: Dedifferentiated chondrosarcoma

value: SWE

value: male

value: FFPE


title: vegetative + DTT WT exponential rep1

description:
Library name: Sample5
WT_dtt1

value: WT

value: vegetative + DTT


title: HEK293T, smallRNA, ASmut2 transfected, rep1

city: Zurich

first: Jonathan

last: Hall

address: Vladimir-Prelog-Weg 1-5/10

institute: ETH Zurich

description:
Library name: smallRNA_ASmut2_Rep1
ASmut2_1

data_processing:
For RNA-Seq: RNA-Seq reads were aligned to the GRCh38 genome including transcript annotations with STAR v2.7.10b. RNA-Seq reads were counted per gene using HTSeq 2.0.9. with intersection-strict mode and ignoring non-unique alignments.
For smallRNA-Seq: Only unique reads which contained the 3' adapter sequence (AACTGTAGGCACCATCAA) were considered. The 3' adapter sequence and all nucleotides downstream of this sequence were removed from the reads, and only reads >= 15 nucleotides were retained. The occurences of reads were counted for all 48 samples.
Assembly: hg38/GRCh38
Supplementary files format and content: Table with gene read counts for all 48 RNA-Seq samples: All_geneCounts_mRNASeq_samples.out.gz
Supplementary files format and content: Table with processed smallRNA-Seq read counts for all 48 samples: AllReads15nt_smallRNASeq_samples.tab.gz

growth_protocol: HEK293T cells were seeded 6–8 h prior to transfection in 12-well plates (150,000 cells/well).

extract_protocol:
HEK293T cells were washed with ice-cold PBS and lysed in TRIzol reagent (Invitrogen, #15596-018). RNA was extracted per the manufacturer’s protocol.
For RNA-Seq: Libraries were prepared from 200 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, #RS-122-2103). Libraries were pooled to equal molarity and quantified using the QuantiFluor ONE dsDNA System (Promega, #E4871). Final pools were diluted to 1.4 pM and sequenced on a NextSeq 500 (Illumina) using the High Output 75-cycle kit (#FC-4041005) in single-end 76 bp format with dual 8 bp indexes.
For smallRNA-Seq: 200ng total RNA were used to perform Library preparation using the QIAseq miRNA Library Kit (96) (Qiagen, Cat# 331505) and the QIAseq miRNA 48 Index IL, 96 (Qiagen, Cat# 331595). 15 cycles of PCR were performed. Samples were pooled to equal molarity by series of 48. Each pool was quantified by fluorometry (PicoGreen measurement) in order to be adjusted to equal molarity and the pool was quantified and adjusted to 1.4pM for being used for clustering on the NextSeq 500 instrument (Illumina). In order to take advantage of the UMIs sequences (meant at correcting the data for PCR bias), samples were sequenced single-reads 76 bases using the NextSeq 500 High Output Kit 75-cycles (Illumina, Cat# FC-404-1005).

treatment_protocol: Transfections were performed using Lipofectamine 2000 (Invitrogen, #11668027) with final oligonucleotide concentrations up to 50 nM, following the manufacturer’s instructions. Complexes were formed by incubating reagents for ~25 min before adding to cells. Incubation proceeded for up to 48 h.

tag: cell line

value: ASmut2 transfection


title: HEK293T, smallRNA, miR106a transfected, rep1

description:
Library name: smallRNA_miR106a_Rep1
106a_1

value: miR106a transfection


title: HEK293T, smallRNA, miR106b transfected, rep1

description:
Library name: smallRNA_miR106b_Rep1
106b_1

value: miR106b transfection


title: Case_52, Chondrosarcoma

description: Sample ID: 206644420120_R01C01

value: Chondrosarcoma

value: high-grade

value: NL

tag: follow-up


title: Case_72, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170090_R07C01

value: MUT

value: Pelvis

value: female


title: WT 6hr 45 minute sporulation media rep1

description:
Library name: Sample10
WT_6hr_45min_1

value: meiotic


title: Case_50, Chondrosarcoma

description: Sample ID: 206644420023_R08C01

value: Thorax

value: alive

value: KRYO


title: Case_66, Chondrosarcoma

description: Sample ID: 208404170109_R01C01

value: GX

value: SWE

value: Sternum


title: WT 5.5hr sporulation media rep1

description:
Library name: Sample9
WT_5_5hr_1

value: WT


title: HEK293T, smallRNA, miR106b+let7a transfected, rep3

description:
Library name: smallRNA_miR106b+let7a_Rep3
106b_let7_3

value: miR106b+let7a co-transfected


title: HEK293T, smallRNA, miR106a+let7a transfected, rep3

description:
Library name: smallRNA_miR106a+let7a_Rep3
106a_let7_3

value: miR106a+let7a co-transfection


title: Case_43, Chondrosarcoma

description: Sample ID: 206644420100_R08C01

value: Scapula


title: Case_65, Chondrosarcoma

description: Sample ID: 208404170089_R02C01

value: Chondrosarcoma

value: Femur

value: FFPE


title: vegetative + DTT WTdel exponential rep2

description:
Library name: Sample8
hac1_dtt2

value: hac1 delete

value: vegetative + DTT


title: Case_42, Chondrosarcoma

description: Sample ID: 206644420100_R03C01

value: high-grade

value: NL

value: MUT

value: male


title: Case_90, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170087_R02C01

value: Dedifferentiated chondrosarcoma


title: vegetative hac1del exponential rep2

description:
Library name: Sample4
hac1_veg2

value: vegetative


title: vegetative WT exponential rep2

description:
Library name: Sample2
WT_veg2


title: Case_48, Chondrosarcoma

description: Sample ID: 206639830042_R05C01

value: Pelvis

value: alive

value: KRYO


title: vegetative + DTT hac1del exponential rep1

description:
Library name: Sample7
hac1_dtt1


title: Case_64, Chondrosarcoma

description: Sample ID: 208404170105_R04C01

value: SWE

value: Sternum


title: HEK293T, smallRNA, neg control transfected, rep3

description:
Library name: smallRNA_neg_Rep3
neg_3

value: neg control transfection


title: HEK293T, smallRNA, let7a transfected, 50nM, rep1

description:
Library name: smallRNA_let7a_50_Rep1
let7_4

value: let7a 50nM transfection


title: Case_89, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170087_R01C01

value: Humerus

value: female


title: vegetative WT exponential rep1

description:
Library name: Sample1
WT_veg1

value: WT


title: Case_63, Chondrosarcoma

description: Sample ID: 208404170105_R02C01

value: Chondrosarcoma

value: FFPE


title: Day 28 Anchored Middle Region, replicate 3

city: Boulder

first: Jason

last: Burdick

state: Colorado

address: 3415 Colorado Avenue

department: BioFrontiers Institute

institute: University of Colorado, Boulder

description:
Library name: Sample 15
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_25

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Alignment to the appropriate reference genome using STAR aligner v2.7.* with non-canonical splice junction removal and output of unmapped reads. Coordinate sorting of BAM files using samtools v1.21. UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0. Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RustQC v0.2.1. Generation of comprehensive QC report using MultiQC v1.33. Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Differential expression using edgePython v0.2.5. Data processing pipeline from https://plasmidsaurus.com/technical-documentation/rna.
Assembly: ASM4765221v1
Supplementary files format and content: .tsv file with read counts and counts per million for each sample

organism: Bos taurus

source_name: Meniscal fibrochondrocytes

growth_protocol: 3 days in growth media (DMEM + glutaMAX, 10% FBS, 1% pen-strep), followed by 25 days in chondrogenic media (1% P/S, 1% ITS-X, and 1% NEAA by volume, 50 µg ml−1 ascorbic acid, 1×10−7 M dexamethasone, and 10 ng ml−1 transforming growth factor-β3 (TGF-β3) in DMEM + GlutaMAX).

extract_protocol:
Tissues were cut into specified regions, and each region was further dissected into approximate quarters. Bulk RNA was extracted from pieces using a Direct-zol RNA Miniprep Plus Kit (Zymo Research, USA) according to the manufacturer’s instructions. Total RNA concentration was quantified using a spectrophotometer (Nano-drop Technologies, USA).
Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences. Library construction description from https://plasmidsaurus.com/rna#rna-library-prep.

tag: cell type

value: Meniscal fibrochondrocytes

value: Anchored mold, middle region


title: Case_44, Chondrosarcoma

description: Sample ID: 206897320048_R08C01

value: high-grade

value: BSL

value: MUT

value: Femur


title: Case_61, Chondrosarcoma

description: Sample ID: 208404170090_R06C01

value: male


title: Case_49, Chondrosarcoma

description: Sample ID: 206644410004_R08C01

value: NL

value: alive

value: KRYO


title: HEK293T, smallRNA, let7a transfected, 10nM, rep3

description:
Library name: smallRNA_let7a_Rep3
let7_3

value: let7a 10nM transfection


title: Case_38, Chondrosarcoma

description: Sample ID: 206639830002_R03C01

value: Rib


title: vegetative + DTT WT exponential rep2

description:
Library name: Sample6
WT_dtt2

value: vegetative + DTT


title: Case_60, Chondrosarcoma

description: Sample ID: 208404170090_R04C01

value: SWE

value: female


title: Case_37, Enchondroma

description: Sample ID: 207130380071_R07C01

value: Enchondroma

value: low-grade

value: Finger


title: HEK293T, smallRNA, ASmut1+let7a transfected, rep2

description:
Library name: smallRNA_ASmut1+let7a_Rep2
ASmut1_let7_2

value: ASmut1+let7a co-transfection


title: Day 28 Anchored Post Region, replicate 3

description:
Library name: Sample 12
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_19

value: Meniscal fibrochondrocytes

value: Anchored mold, post region


title: Case_45, Chondrosarcoma

description: Sample ID: 207130360143_R08C01

value: Chondrosarcoma

value: high-grade

value: MUT

value: Pelvis


title: Case_73, Chondrosarcoma

description: Sample ID: 208404170090_R02C01

value: GX

value: Humerus

value: male

value: FFPE


title: Case_59, Chondrosarcoma

description: Sample ID: 208404170090_R03C01

value: FAILED

value: Femur


title: Day 28 Anchored Middle Region, replicate 2

description:
Library name: Sample 14
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_24

value: Anchored mold, middle region


title: Case_39, Chondrosarcoma

description: Sample ID: 206639830042_R08C01

value: NL

value: alive

value: KRYO


title: Case_41, Chondrosarcoma

description: Sample ID: 206644420023_R02C01

value: female


title: vegetative hac1del exponential rep1

description:
Library name: Sample3
hac1_veg1

value: hac1 delete

value: vegetative


title: Case_40, Chondrosarcoma

description: Sample ID: 206644410047_R01C01

value: Chondrosarcoma


title: HEK293T, smallRNA, ASmut1+let7a transfected, rep3

description:
Library name: smallRNA_ASmut1+let7a_Rep3
ASmut1_let7_3

value: ASmut1+let7a co-transfection


title: Day 28 Anchored Post Region, replicate 2

description:
Library name: Sample 11
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_18

value: Meniscal fibrochondrocytes

value: Anchored mold, post region


title: HEK293T, smallRNA, mock transfected, rep3

description:
Library name: smallRNA_mock_Rep3
mock_3

value: mock transfection


title: HEK293T, smallRNA, Smut+let7a transfected, rep3

description:
Library name: smallRNA_Smut+let7a_Rep3
Smut_let7_3

value: Smut+let7a co-transfection


title: HEK293T, smallRNA, ASmut3+let7a transfected, rep2

description:
Library name: smallRNA_ASmut3+let7a_Rep2
ASmut3_let7_2

value: ASmut3+let7a co-transfection


title: Case_88, Dedifferentiated chondrosarcoma

description: Sample ID: 208404170072_R06C01

value: Dedifferentiated chondrosarcoma

value: high-grade

value: SWE

value: MUT

value: Pelvis

value: male

value: FFPE


title: Case_35, Enchondroma

description: Sample ID: 207130370087_R05C01

value: Enchondroma

value: Cellular

value: low-grade

value: NL

value: WT

value: Femur

value: alive

value: KRYO


title: Case_58, Chondrosarcoma

description: Sample ID: 208404170089_R08C01

value: Chondrosarcoma

value: Tibia


title: Case_36, Enchondroma

description: Sample ID: 207130380071_R06C01

value: BSL

value: Finger


title: HEK293T, smallRNA, Smut+let7a transfected, rep2

description:
Library name: smallRNA_Smut+let7a_Rep2
Smut_let7_2

value: Smut+let7a co-transfection


title: Case_62, Chondrosarcoma

description: Sample ID: 208404170090_R08C01

value: high-grade

value: SWE

value: MUT

value: female


title: Case_57, Chondrosarcoma

description: Sample ID: 207953370145_R05C01

value: Pelvis

value: male


title: HEK293T, smallRNA, miR106b+let7a transfected, rep2

description:
Library name: smallRNA_miR106b+let7a_Rep2
106b_let7_2

value: miR106b+let7a co-transfected


title: HEK293T, smallRNA, miR106a+let7a transfected, rep2

description:
Library name: smallRNA_miR106a+let7a_Rep2
106a_let7_2

value: miR106a+let7a co-transfection


title: Case_34, Enchondroma

description: Sample ID: 207130370087_R04C01

value: Enchondroma

value: Cellular

value: low-grade

value: NL

value: Humerus


title: Day 28 Anchored Middle Region, replicate 1

description:
Library name: Sample 13
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_23

value: Meniscal fibrochondrocytes

value: Anchored mold, middle region


title: Case_33, Enchondroma

description: Sample ID: 207130360115_R07C01

value: BSL

value: Finger

value: FFPE


title: Day 28 Unanchored Middle Region, replicate 3

description:
Library name: Sample 9
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_16

value: Unanchored mold, middle region


title: HEK293T, smallRNA, ASmut2+let7a transfected, rep2

description:
Library name: smallRNA_ASmut2+let7a_Rep2
ASmut2_let7_2

value: ASmut2+let7a co-transfection


title: HEK293T, smallRNA, neg control transfected, rep2

description:
Library name: smallRNA_neg_Rep2
neg_2

value: neg control transfection


title: Case_32, Enchondroma

description: Sample ID: 207130360115_R05C01

value: MUT

value: alive


title: Day 28 Unanchored Middle Region, replicate 1

description:
Library name: Sample 7
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_14


title: Case_4, Clear cell chondrosarcoma

description: Sample ID: 208524740120_R05C01

value: CC

value: Clear cell chondrosarcoma

value: GX

value: SWE

value: Spine

value: male


title: Day 28 Unanchored Middle Region, replicate 2

description:
Library name: Sample 8
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_15


title: Case_31, Enchondroma

description: Sample ID: 207130360064_R06C01

value: Enchondroma

value: Ollier's disease

value: low-grade

value: NL

value: Foot

value: KRYO


title: Day 28 Anchored Post Region, replicate 1

description:
Library name: Sample 10
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_17

value: Meniscal fibrochondrocytes

value: Anchored mold, post region


title: Case_23, Chondrosarcoma

description: Sample ID: 208404170105_R03C01

value: Chondrosarcoma

value: high-grade

value: Tibia

value: female

value: FFPE


title: HEK293T, smallRNA, mock transfected, rep2

description:
Library name: smallRNA_mock_Rep2
mock_2

value: mock transfection


title: Day 28 Unanchored Post Region, replicate 3

description:
Library name: Sample 6
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_10

value: Unanchored mold, post region


title: HEK293T, smallRNA, ASmut3+let7a transfected, rep1

description:
Library name: smallRNA_ASmut3+let7a_Rep1
ASmut3_let7_1

value: ASmut3+let7a co-transfection


title: Case_2, Clear cell chondrosarcoma

description: Sample ID: 208416810014_R06C01

value: CC

value: Clear cell chondrosarcoma

value: GX

value: SWE


title: Case_46, Chondrosarcoma

description: Sample ID: 208404170109_R02C01

value: FAILED

value: Pelvis

value: male


title: Case_30, Enchondroma

description: Sample ID: 207130360064_R05C01

value: Enchondroma

value: Cellular

value: low-grade

value: NL

value: Hand

value: alive

value: KRYO


title: HEK293T, smallRNA, ASmut1+let7a transfected, rep1

description:
Library name: smallRNA_ASmut1+let7a_Rep1
ASmut1_let7_1

value: ASmut1+let7a co-transfection


title: Case_28, Enchondroma

description: Sample ID: 207130360064_R02C01

value: Ollier's disease

value: MUT

value: Femur


title: Case_3, Clear cell chondrosarcoma

description: Sample ID: 208416810030_R01C01

value: CC

value: Clear cell chondrosarcoma


title: Case_29, Enchondroma

description: Sample ID: 207130360064_R03C01

value: Tibia


title: Day 28 Unanchored Post Region, replicate 1

description:
Library name: Sample 4
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_8

value: Meniscal fibrochondrocytes

value: Unanchored mold, post region


title: Day28 Blob, replicate 3

description:
Library name: Sample 3
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_7

value: No mold


title: HEK293T, smallRNA, Smut+let7a transfected, rep1

description:
Library name: smallRNA_Smut+let7a_Rep1
Smut_let7_1

value: Smut+let7a co-transfection


title: Thal_CON_F_30

city: Zürich

first: Juliet

last: Richetto

address: Winterthurerstrasse 260

institute: University of Zürich

description: Library name: 745_T

data_processing:
Reads were quality-checked using FastQC. Low-quality ends were clipped (5’: 4 bases; 3’: 4 bases) and sequencing adaptors removed using Fastp. Trimmed reads were mapped to the mouse genome (GRCm39 release M31-2023-01-30) and gene-level quantifications were calculated with Kallisto using the SUSHI data analysis framework
Assembly: GRCm39 release M31-2023-01-30
Supplementary files format and content: ene-level quantifications calculated with Kallisto

molecule: polyA RNA

organism: Mus musculus

source_name: Brain - Thalamus

extract_protocol:
RNA was extracted with the Qiagen AllPrep DNA/RNA mini kit
RNA libraries for RNA-seq were prepared using thew Illumina Stranded mRNA Prep, Ligation following the manufacturers instructions.

value: Brain - Thalamus

value: Maternal housing control

tag: Sex

value: Female


title: Thal_CON_F_29

description: Library name: 744_T


title: HEK293T, smallRNA, miR106b+let7a transfected, rep1

description:
Library name: smallRNA_miR106b+let7a_Rep1
106b_let7_1

value: miR106b+let7a co-transfected


title: Day28 Blob, replicate 1

description:
Library name: Sample 1
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_5


title: HEK293T, smallRNA, let7a transfected, 10nM, rep2

description:
Library name: smallRNA_let7a_Rep2
let7_2

value: let7a 10nM transfection


title: Thal_CON_M_28

description: Library name: 739_T

value: Male


title: HEK293T, smallRNA, miR106a+let7a transfected, rep1

description:
Library name: smallRNA_miR106a+let7a_Rep1
106a_let7_1

value: miR106a+let7a co-transfection


title: 149128_Esophagus_Tumor

city: Boston

first: Liyang

last: Diao

state: MA

address: 201 Brookline Ave. Suite 1001

institute: Rome Therapeutics

description: Library name: ILS52171FT1

data_processing:
RNA-seq reads were aligned to the human reference genome using STAR aligner (Dobin et al., 2013) with default parameters.
Locus-specific LINE-1 expression was quantified using L1EM (McKerrow & Fenyö, 2020) restricted to intact LINE-1 loci from L1Base2.
Expression was normalized to transcripts per million (TPM) and summed across intact loci.
For comparative analyses, repeat-naïve quantifications were also generated by counting reads mapping to L1Hs loci without ORF filtering.
Expression values were merged with protein expression and immunopeptidomics results for downstream correlation analyses.
Assembly: Human genome reference GRCh38 (GENCODE/Ensembl annotation; L1Base2 intact LINE-1 loci set).
Supplementary files format and content: L1EM locus-level output files in comma-delimited format with normalized TPM values.

source_name: Esophagus

extract_protocol:
Frozen esophageal tumor, tumor-adjacent normal, and healthy control tissues were pulverized using a Covaris cryoPREP instrument. Total RNA was extracted using standard column-based RNA purification according to the manufacturer’s instructions. RNA integrity was assessed by Bioanalyzer prior to library preparation.
RNA-seq libraries were prepared from high-quality total RNA using a poly(A)-enrichment method followed by stranded mRNA library construction (Illumina TruSeq stranded mRNA kit or equivalent). Indexed libraries were quantified by qPCR and pooled for sequencing.

value: Esophagus

tag: disease state

value: Tumor


title: Thal_CON_F_31

description: Library name: 746_T


title: Thal_CON_M_27

description: Library name: 738_T


title: Case_24, Chondrosarcoma

description: Sample ID: 206644420109_R04C01

value: Chondrosarcoma

value: high-grade

value: NL

value: MUT

value: Femur

value: female

value: alive

value: KRYO


title: Day28 Blob, replicate 2

description:
Library name: Sample 2
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_6

value: Meniscal fibrochondrocytes

value: No mold


title: HEK293T, smallRNA, let7a transfected, 10nM, rep1

description:
Library name: smallRNA_let7a_Rep1
let7_1


title: 149128_Esophagus_NADJ

description: Library name: ILS52171FA1

value: NADJ


title: Day 28 Unanchored Post Region, replicate 2

description:
Library name: Sample 5
Columns in 7F4W83-expression-matrix.tsv:  7F4W83_9

value: Unanchored mold, post region


title: Case_26, Enchondroma

description: Sample ID: 206897320048_R01C01

value: Enchondroma

value: low-grade

value: BSL

value: Toe

value: male

value: FFPE


title: 3074262_Esophagus_Tumor

description: Library name: ILS51764FT1

value: Esophagus

value: Tumor


title: Thal_CON_M_25

description: Library name: 622_T

value: Brain - Thalamus

value: Maternal housing control

value: Male


title: Thal_CON_F_26

description: Library name: 628_T

value: Female


title: HEK293T, smallRNA, mock transfected, rep1

description:
Library name: smallRNA_mock_Rep1
mock_1

value: mock transfection


title: 3074262_Esophagus_NADJ

description: Library name: ILS51764FA1


title: Case_21, Chondrosarcoma

description: Sample ID: 206644420023_R07C01

value: Chondrosarcoma

value: high-grade

value: NL

value: MUT

value: Scapula

value: alive

value: KRYO


title: HEK293T, smallRNA, neg control transfected, rep1

description:
Library name: smallRNA_neg_Rep1
neg_1

value: neg control transfection


title: Case_22, Chondrosarcoma

description: Sample ID: 206644420100_R04C01

value: Femur

value: male


title: CPI-637_rep2

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

description: Library name: CPI-637_rep2

data_processing:
Reads were quality trimmed and adapters were removed using Trim Galore (v0.6.6).
The processed reads were pseudo‑aligned to the GRCh38 human transcriptome (Ensembl v107) using Salmon (v1.9.0), and transcript‑level abundances were quantified as transcripts per million (TPM).
Transcript‑level abundance estimates were summarized into gene‑level counts using the tximport package (v1.32.0).
Downstream gene-level analyses were performed with the EdgeR package (v4.10.0).
All statistical calculations were performed in the R programming language (v4.6.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes TMM normalised counts for each sample (log2-transformed with an offset value of 1.0)
Supplementary files format and content: Tab-delimited text file includes FPKM calculated counts for each sample

source_name: placenta

growth_protocol: TSCs were seeded either in TSC medium or in EVT‑A medium, with or without 1 µM A‑485 or 3 µM CPI. On day 3, TSCs were collected for RNA isolation, while EVTs were refreshed with EVT‑B medium, again with or without 1 µM A‑485 or 3 µM CPI. EVTs were harvested for RNA isolation on day 5. A detailed culture protocol is provided in van Voorden et al., 2023 (DOI: 10.1073/pnas.2217405120).

extract_protocol:
Cells were washed in PBS and lysed directly in the culture plate using RLT Plus Buffer (RNeasy Plus Mini Kit, QIAGEN, 74136) supplemented with 1% 2‑mercaptoethanol. Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, 74136) according to the manufacturer’s protocol.
Total RNA libraries were prepared using the KAPA mRNA Capture HyperPrep Kit (Roche, 0000162206), followed by 150 bp paired‑end sequencing on an Illumina NovaSeq X Plus system.

value: placenta

value: Trophoblast

tag: batch

tag: time

value: Day 5


title: Case_20, Chondrosarcoma

description: Sample ID: 206644420023_R04C01

value: WT

value: Radius


title: Case_19, Chondrosarcoma

description: Sample ID: 206644420023_R03C01

value: female


title: Case_18, Chondrosarcoma

description: Sample ID: 206644410047_R06C01


title: Thal_CON_M_23

description: Library name: 608_T

value: Brain - Thalamus

value: Maternal housing control

value: Male


title: 149084_Esophagus_Tumor

description: Library name: 616946FT2

value: Esophagus

value: Tumor


title: 142133_Esophagus_Tumor

description: Library name: ILS36521FT1


title: A485_rep2

description: Library name: A485_rep2

treatment_protocol: TSCs were seeded either in TSC medium or in EVT‑A medium, with or without 1 µM A‑485 or 3 µM CPI. On day 3, TSCs were collected for RNA isolation, while EVTs were refreshed with EVT‑B medium, again with or without 1 µM A‑485 or 3 µM CPI. EVTs were harvested for RNA isolation on day 5. A detailed culture protocol is provided in van Voorden et al., 2023 (DOI: 10.1073/pnas.2217405120).


title: 142133_Esophagus_NADJ

description: Library name: ILS36521FA2

value: NADJ


title: RNA-seq, THP1 Marophages, DMSO, 1 ng/mL IFNa 2hr, 10 uM STM2457 24hr, replicate 2

first: Edward

last: Courvan

address: 3415 Colorado Ave

institute: University of Colorado

description: Library name: RS_IFN_STM_2

data_processing:
Plasmidsaurus: Reads were filtered and trimmed with fastp v0.24.0 with poly-X tail trimming, 3' quality based tail trimming, a Phred 15 quality score filter, and 50 bp minimum length filter.
Plasmidsaurus: Quality filtered reads were aligned with STAR v2.7.11 and sorted with samtools v1.22.1. PCR Duplicates removed using UMIcollapse v1.1.0. Count natrix produced with Feature Counts
Assembly: GRCh38.p14
Supplementary files format and content: csv containing raw counts

source_name: THP1 Macrophage

growth_protocol: THP1 monocytes were grown in RPMI supplemented with 10% fetal bovine serum. THP1 macrophages were differentiated by 48 hr of 50 ng/mL PMA treatment followed by 48 hr rest after removing PMA

extract_protocol:
RNA was harvested using RNeasy mini kit followed by TURBO DNase treatment and RNA Clean XP bead purification.
Library preparation and sequencing was performed by Plasmidsaurus. Library strategy uses a 3' end counting protocol.

treatment_protocol: THP macrophages were treated with either 0.1% DMSO or 10 uM STM2457 in DMSO for 24 hours. Samples receiving IFNa treatment were stimulated four 4 hours and all samples were harvested after 28 hours from initial treatment.

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

tag: treatment -_stm2457

tag: treatment -_ifna

value: 1 ng/mL IFNa, 4 hr


title: CPI-637_rep1

description: Library name: CPI-637_rep1

tag: treatment


title: Thal_CON_M_21

description: Library name: 591_T


title: 149311_Esophagus_NADJ

description: Library name: 616901FA1


title: 149084_Esophagus_NADJ

description: Library name: 616946FA1


title: Case_15, Chondrosarcoma

description: Sample ID: 206639830020_R06C01

value: Chondrosarcoma

value: high-grade

value: NL

value: MUT

value: Spine

value: alive

value: KRYO


title: Case_14, ACT

description: Sample ID: 207130380071_R08C01

value: ACT

value: low-grade

value: BSL

value: Fibula

value: female

value: FFPE


title: Case_13, ACT

description: Sample ID: 206644420109_R08C01

value: Femur

value: male


title: 3069396_Esophagus_Normal

description: Library name: 1248211F

value: Esophagus

value: Normal


title: 94787_Esophagus_Normal

description: Library name: 1236965F


title: Thal_SIR_M_15

description: Library name: 432_T

value: Brain - Thalamus

value: Maternal housing SIR

value: Male


title: RNA-seq, THP1 Marophages, DMSO, 1 ng/mL IFNa 2hr, replicate 3

description: Library name: RS_IFN_3

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

tag: genotype

value: WT

value: DMSO

value: 1 ng/mL IFNa, 4 hr


title: Case_10, ACT

description: Sample ID: 206644420074_R01C01

value: ACT

tag: grade

value: low-grade

value: NL

value: MUT

value: alive

value: KRYO


title: 78987_Esophagus_Normal

description: Library name: 1205934F


title: HEK293T, smallRNA, ASmut2+let7a transfected, rep1

description:
Library name: smallRNA_ASmut2+let7a_Rep1
ASmut2_let7_1

value: ASmut2+let7a co-transfection


title: Case_27, Enchondroma

description: Sample ID: 207130360064_R01C01

value: Enchondroma

tag: subdiagnosis

value: Cellular (Ollier's disease)

tag: origin

value: Hand


title: Case_25, Enchondroma

description: Sample ID: 206036380095_R07C01

value: BSL

value: Finger

tag: gender

value: female

value: FFPE


title: Thal_CON_F_24

description: Library name: 610_T

tag: tissue

value: Brain - Thalamus

value: Maternal housing control

value: Female


title: Thal_SIR_F_12

description: Library name: 420_T

value: Maternal housing SIR


title: Case_8, ACT

description: Sample ID: 206644410004_R06C01

value: ACT

value: low-grade

value: Tibia

tag: age

value: male

tag: status


title: Thal_CON_M_22

description: Library name: 598_T

value: Male


title: Case_16, Chondrosarcoma

description: Sample ID: 206639830020_R08C01

value: Chondrosarcoma

value: high-grade

value: NL

value: MUT

value: Scapula

tag: follow-up

value: alive

value: KRYO


title: Thal_CON_F_20

description: Library name: 587_T


title: A485_rep1

description: Library name: A485_rep1

value: placenta

tag: cell line

tag: cell type

value: Trophoblast

value: Day 5


title: RNA-seq, THP1 Marophages, DMSO, 1 ng/mL IFNa 2hr, 10 uM STM2457 24hr, replicate 3

description: Library name: RS_IFN_STM_3

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

value: WT

value: 1 ng/mL IFNa, 4 hr


title: Thal_CON_M_19

description: Library name: 579_T

value: Brain - Thalamus

value: Maternal housing control

tag: Sex


title: Thal_SIR_F_11

description: Library name: 418_T

value: Maternal housing SIR

value: Female


title: GSC4121 shDCPS657_1

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

country: China

institute: Fudan University

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport function to obtain gene expression matrix.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files including RNA count and abundance (Transcripts Per Million, TPM)  values

source_name: patient-derived cells

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Mini Kit (Catalog 74136) according to the manufacturer’s instructions.
Total RNA was used for library construction using Illumina TruSeq Total RNA Library Prep Kit. The library was sequenced as paired-end 150bp read.

value: patient-derived cells

value: glioblastoma stem cells


title: RNA-seq, THP1 Marophages, DMSO, 1 ng/mL IFNa 2hr, 10 uM STM2457 24hr, replicate 1

description: Library name: RS_IFN_STM_1


title: Thal_CON_F_17

description: Library name: 559_T


title: RNA-seq, THP1 Marophages, DMSO, replicate 3

description: Library name: RS_CTL_3

value: DMSO

value: ctl


title: Case_7, ACT

description: Sample ID: 206639830002_R08C01

value: ACT

value: low-grade

value: NL

value: MUT

value: Femur

value: female

value: alive


title: 3056752_Esophagus_Normal

description: Library name: 1359824F

value: Esophagus

tag: disease state

value: Normal


title: GSC4121 shDCPS339_2


title: RNA-seq, THP1 Marophages, 10 uM STM2457 24hr, replicate 3

description: Library name: RS_STM_3

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

value: WT


title: Thal_CON_M_16

description: Library name: 554_T

value: Brain - Thalamus

value: Maternal housing control

value: Male


title: RNA-seq, THP1 Marophages, 10 uM STM2457 24hr, replicate 2

description: Library name: RS_STM_2


title: Thal_SIR_F_10

description: Library name: 410_T

value: Maternal housing SIR

value: Female


title: RNA-seq, THP1 Marophages, 10 uM STM2457 24hr, replicate 1

description: Library name: RS_STM_1

value: ctl


title: RNA-seq, THP1 Marophages, DMSO, replicate 2

description: Library name: RS_CTL_2

value: DMSO


title: RNA-seq, THP1 Marophages, DMSO, replicate 1

description: Library name: RS_CTL_1


title: Case_12, ACT

description: Sample ID: 206644420109_R01C01

value: ACT

value: low-grade

value: NL

value: KRYO


title: Case_6, ACT

description: Sample ID: 206639830002_R07C01

value: MUT

value: Foot

value: male

value: alive


title: Case_11, ACT

description: Sample ID: 206644420100_R01C01

value: Femur

value: female


title: Thal_SIR_F_9

description: Library name: 408_T

value: Brain - Thalamus


title: Case_5, ACT

description: Sample ID: 206639830002_R04C01


title: 3065955_Esophagus_Normal

description: Library name: 1214977F

value: Esophagus

value: Normal


title: GSC4121 shCONT_2

value: patient-derived cells

value: glioblastoma stem cells

value: shCONT


title: Case_1, Clear cell chondrosarcoma

description: Sample ID: 201904410006_R07C01

value: CC

value: Clear cell chondrosarcoma

value: GX

value: SWE

value: FFPE


title: sgMETTL13_Ribo_rep2

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

description: Library name: sgMETTL13_Ribo_rep2

library_source: other

data_processing:
Total RNA samples: Sequencing reads were preprocessed using BBmap (v. 36.59; parameters: k = 13, ktrim = n, useshortkmers = t, mink = 5, qtrim = t, trimq = 10, minlength = 20). Processed reads were aligned to the human reference genome (hg38) using HISAT (v.2.0.4; in addition to default parameters, “–no-mixed” and “–no-discordant” were applied. Uniquely aligned reads were quantified using the featureCounts function from the RSubread R/Bioconductor package (v.2.6.4; in addition to default parameters, “strandSpecific=2”) against the RefSeq annotation GCF_000001405.40, filtered to include only protein-coding genes.
Ribosome profiling: Sequencing reads were preprocessed using cutadapt (v. 1.18; parameters: --nextseq-trim=20 --minimum-length 20 -a TCTCCTTGCATAATCACCAACC --discard-untrimmed). UMI were extracted using umi_tools extract (v. 1.1.2 ; parameters: --bc-pattern='^(?P<umi_1>.{4}).+(?P<umi_2>.{4})\$'). Remaining 'T' was removed using cutadapt (parameters: -g ^T). In addition, BBmap [REF] was used to remove reads matching ribosomal RNA sequences obtained from the SILVA ribosomal RNA database. The remaining reads were aligned to the hg38 genome assembly using Bowtie (v.1.2.2; parameters: -a -m 1 --best --strata -n 2 -l 20). Reads that uniquely aligned or failed to align to the genome were subsequently aligned to RefSeq transcript sequences (GCF_000001405.40) using Bowtie (parameters: -a --best –strata -n 2 -l 20). Umi_tools dedup was used to remove duplicated sequences. To extract the genuine ribosome footprints, only reads with lengths between 25 and 34 nucleotides (inclusive) were retained for further analysis. P-site positions were determined using Ribowaltz. P-sites counts were then summarised at the gene-level across coding sequences defined by RefSeq annotations GCF_000001405.40. When multiple transcript isoforms were present, one isoform was selected at random for quantification.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample
Library strategy: Ribo-Seq

molecule: other

growth_protocol: T3M4 cells were serum straved for 18hours and then stimulated with 10%FBS for 2 hours

extract_protocol:
Cells were washed three times with PBS and harvested by flash-freezing the plate in liquid nitrogen and scrapping the cells with polysome lysis buffer (50mM Tris pH7.5, 100mM KoAc, 15mM Mg(oAc)2, 5% Glycerol and 1%triton). Lysate were centrifuged (8 min at 20,000g) and supernatants were collected for RNA and Riboseq.
For RNA-seq, total RNA was used to prepare stranded poly(A) mRNA libraries. Briefly, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5′-phosphorylated, with a protruding 'A' at the 3′ end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3′ end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing quality control. The library was amplified with phi29 to make DNA nanoballs (DNBs), each containing more than 300 copies of one molecule. The DNBs were loaded onto a patterned nanoarray, and paired-end 150 bp reads were generated by sequencing-by-synthesis. Libraries were sequenced by BGI and adapter sequences used were: adapter3 = AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA; adapter5 = AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG.  For ribosome profiling, active ribosome-protected mRNA fragments (RPFs) were isolated using the ALL-IN-ONE RiboLace Gel Free kit (Immagina BioTechnology). Briefly, lysate collected was subjected to nuclease digestion to generate RPFs. Magnetic beads functionalized with a biotinylated puromycin analog (3P, RiboLace Smart Probe) were used to selectively pull down active ribosome complexes via affinity purification, and RPF-containing RNA was extracted from the captured ribosomes. For library construction, the purified RPFs were 5′-phosphorylated, followed by ligation of the LaceSeq Linker MC+ to the 3′-phosphate end of the RPFs. The ligated products were then circularized, followed by reverse transcription using a primer annealing to the linker sequence to generate single-stranded cDNA. The cDNA was PCR amplified in two sequential rounds (PCR1 and PCR2), with Illumina-compatible Unique Dual Indexes (iUDIs) added during PCR2. Library quality was assessed using an Agilent 2100 Bioanalyzer with the High Sensitivity DNA Kit. Libraries were sequenced by TB-Seq, Inc. on an Illumina NovaSeq platform, single-end, 1x150 cycles. The 3′ adapter sequence used was: TCTCCTTGCATAATCACCAACC (LaceSeq 3′ linker).


title: Thal_SIR_M_8

description: Library name: 403_T

value: Maternal housing SIR

value: Male


title: GSC4121 shDCPS339_1


title: Thal_SIR_M_14

description: Library name: 430_T


title: GSC4121 shCONT_1


title: Thal_SIR_F_7

description: Library name: 399_T

value: Female


title: 7hr in meiosis plus bEST (inducer)

description:
Library name: Sample6
bEST 7hr

data_processing:
First files were clipped for any polyA regions remaining with fastx_clipper
bowtie2 was used to align to rRNA reference file and unaligned files were taken for further processing
tophat was used to align with the SK1 reference genome
Used samtools index to index the bam files outputted from tophat
feature counts command used to assemble raw counts numbers for all files
Assembly: GCA_000766265.2
Supplementary files format and content: .csv files contain qexpression values

organism: Saccharomyces cerevisiae

source_name: meiosis

growth_protocol: Meiotic: Strains were grown in YPD at 30 degrees until saturation before back dilution and growth in BYTA. Strains were grown at 30 degrees in BYTA until saturation before washing with water and resuspention in sporulation media.

extract_protocol:
Cells were harvested via pelleting liquid culture at 6000 RCF then aspirating media before snap freezing in liquid nitrogen. Cells were thawed on ice and resuspended in 625ul TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). An equal volume of citrate-buffered acid phenol (pH 4.3, P4682, Sigma-Aldrich) was added to cells, and they were incubated at 65C for 1 hour in a Thermomixer C (Eppendorf) shaking at 1400 RPM. After microcentrifugation (20,000 g for 10 min) the aqueous phase was transferred to a second tube with 600ul acid phenol. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and transferred to a third tube with 600ul chloroform. The aqueous phase was separated by microcentrifugation (20,000 g for 10 min) and RNA was precipitated in 100% isopropanol with 350 mM sodium acetate (pH 5.2) overnight at –20C. Pellets were washed with 80% ethanol and resuspended in DEPC water
RNA-seq libraries were generated with the NEXTflex Rapid Directional mRNA-Seq Bundle with poly(A) beads (NOVA-5138, Bioo Scientific) according to manufacturer’s instructions. 10 mg of total RNA was used as input for all libraries. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp. Libraries were quantified using the Agilent 4200 TapeStation (Agilent Technologies, Inc). Samples were submitted for 50 bp single-end sequencing by the Vincent J. Coates Genomics Sequencing Laboratory with a HiSeq 2500.

treatment_protocol: Meiotic cells were harvested at times indicated, with 0 hr being the time that the cells were transferred into sporulation media. Either EtOH or bEST was added 5 hours after switch to sporulation media

tag: strain

value: WT

value: meiosis


title: GSC387 shDCPS657_2


title: sgControl_Ribo_rep2

description: Library name: sgControl_Ribo_rep2

value: sgControl


title: sgMETTL13_Ribo_rep1

description: Library name: sgMETTL13_Ribo_rep1


title: 6.5hr in meiosis plus bEST (inducer)

description:
Library name: Sample5
bEST 6.5hr


title: Thal_SIR_M_6

description: Library name: 393_T

value: Brain - Thalamus


title: GSC387 shDCPS657_1


title: Thal_SIR_M_13

description: Library name: 429_T


title: GSC387 shDCPS339_2


title: sgControl_Ribo_rep1

description: Library name: sgControl_Ribo_rep1


title: 7hr in meiosis plus EtOH (vehicle)

description:
Library name: Sample3
EtOH 7hr


title: GSC387 shDCPS339_1


title: 6hr in meiosis plus bEST (inducer)

description:
Library name: Sample4
bEST 6hr


title: BV-173 cells, 1 nM rapamycin, 48 hours, replicate 1

city: Łódź

first: Zuzanna

last: Nowicka

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Łódź

description: Library name: BV173_RAPA_1nM_1

data_processing:
Raw sequencing reads were evaluated for quality using FastQC (v0.12.1) with default parameters.
Adapter sequences, primers, poly-A tails, and low-quality bases were removed using Cutadapt (v4.9).
Trimmed reads were aligned to the GRCh38 (hg38) human reference genome using STAR (v2.6.1d, default nf-core/rnaseq parameters, two-pass mode).
Transcript-level quantification was performed using Salmon (v1.10.3)
Assembly: GRCh38 (hg38)/Ensembl
Supplementary files format and content: tab-delimited text file containing a gene-level raw count matrix. Values are estimated read counts as reported by Salmon and aggregated across transcripts to gene level using tximeta.
Supplementary files format and content: tab-delimited text file containing a gene-level length-scaled count matrix. Values are length-scaled counts generated by tximeta/tximport, where Salmon transcript-level estimated counts are scaled by the average transcript length (weighted by transcript abundance) and then library size.

growth_protocol: BV-173 human B-cell precursor acute lymphoblastic leukemia cells were cultured according to the supplier’s recommendations under standard humidified conditions at 37°C with 5% CO2 in complete growth medium (RPMI +10% FBS /pen-strep)

extract_protocol:
Total RNA from 1×107 of leukemic cells was extracted using QIAMP RNAeasy mini kit (QIAGEN, Hilden, Germany). RNA quantity was evaluated using NanoDrop 8000 Microvolume UV-Vis spectrophotometer (Thermo Scientific, USA). The quality was verified on TapeStation (Agilent, Technologies, California, USA).
The RNAseq procedure was performed using SureSelect XT RNA Direct Human All Exon V6+UTR (Agilent Technologies, USA) in accordance with the manufacturer protocol. Libraries were sequenced on a Next Seq 550 system (Illumina, San Diego, CA) using NextSeq™ 500/550 High Output Kit v2.5 (300 Cycles; Illumina, USA)  with a PE NextSeq Flow Cell.

treatment_protocol: BV-173 cells were incubated with 1 nM rapamycin (RAPA) or vehicle control (DMSO) for 48 h. Two biological replicates were analyzed per condition.

value: B-cell precursor acute lymphoblastic leukemia (BCP-ALL)

value: 1nM rapamycin


title: 6.5hr in meiosis plus EtOH (vehicle)

description:
Library name: Sample2
EtOH 6.5hr


title: GSC387 shCONT_2

value: patient-derived cells


title: Thal_SIR_M_4

description: Library name: 385_T


title: Thal_SIR_F_5

description: Library name: 388_T


title: RNA-seq, THP1 Marophages, DMSO, 1 ng/mL IFNa 2hr, replicate 2

description: Library name: RS_IFN_2

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

tag: treatment -_stm2457

value: DMSO

value: 1 ng/mL IFNa, 4 hr


title: Thal_SIR_F_2

description: Library name: 322_T


title: BV-173 cells, 1 nM rapamycin, 48 hours, replicate 2

description: Library name: BV173_RAPA_1nM_2


title: BV-173 cells, vehicle control, 48 hours, replicate 2

description: Library name: BV173_CTRL_2


title: GSC387 shCONT_1

value: glioblastoma stem cells

value: shCONT


title: Case_9, ACT

description: Sample ID: 206644410047_R04C01

value: ACT

value: low-grade

value: NL

value: MUT

value: Femur

value: female

value: alive

value: KRYO


title: BV-173 cells, vehicle control, 48 hours, replicate 1

description: Library name: BV173_CTRL_1

value: B-cell precursor acute lymphoblastic leukemia (BCP-ALL)


title: Thal_SIR_F_3

description: Library name: 323_T

value: Brain - Thalamus

value: Maternal housing SIR

value: Female


title: GSC4121 shDCPS657_2

value: patient-derived cells


title: SH control for TRIM28 knockdown rep1

status: Public on Aug 13 2026

city: Nanchang

first: Bin

last: Fu

address: The First Affiliated Hospital of Nanchang University

description:
Library name: Sample 10
TRIM28 knockdown

data_processing:
Raw sequencing reads were first subjected to quality control to remove low-quality reads and adaptor sequences. Clean reads were aligned to the human reference genome using a splice-aware aligner. Gene-level read counts were generated based on genome annotation files. Differential gene expression analysis was performed by comparing FOXA1 knockdown or TRIM28 knockdown samples with their corresponding negative control samples. Genes with significant expression changes were identified for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file containing gene-level expression values for all samples. Rows represent genes and columns represent RNA-seq samples. Values are raw read counts or normalized expression values generated from RNA-seq data processing.

source_name: LACAP cell

extract_protocol:
Total RNA was extracted from LNCaP cells using TRIzol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed using a spectrophotometer, and RNA integrity was evaluated prior to library preparation. Qualified RNA samples were used for subsequent RNA-seq library construction.
RNA-seq libraries were prepared from qualified total RNA samples using a standard mRNA-seq library preparation protocol. Briefly, mRNA was enriched from total RNA using poly(A) selection, fragmented, and reverse-transcribed into cDNA. After second-strand cDNA synthesis, end repair, adaptor ligation, and PCR amplification were performed to generate sequencing libraries. Library quality and concentration were assessed prior to high-throughput sequencing.

value: LACAP cell

value: prostate cancer cells

value: TRIM28 knockdown

tag: batch


title: NOA2

city: hangzhou

first: Huimei

last: Zheng

address: yuhangtang roda866

institute: ZheJiang Univerisity

description:
Library name: NOA-2
Column name in raw_counts_All_Samples.txt: NOA2

data_processing:
The quality of fastq files was assessed using FASTQC (v 0.11.9)
Reads were trimmed using Fastp (v 0.21.0)
Trimmed reads were mapped to human GRCh38 reference genome using STAR (v 2.7.9a). Raw read counts were generated using RSEM (v 1.3.3).
Read counts were used as input and normalized using built-in algorithms in DESeq2.
Differential expression in RNA-Seq was analyzed using the R DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: seminiferous tubules

extract_protocol:
RNA was harvested using R6834 Total RNA Kit I (OMEGA). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: seminiferous tubules

value: spermatogenic cells

value: TDRD9 variants


title: NOA1

description:
Library name: NOA-1
Column name in raw_counts_All_Samples.txt: NOA1


title: SH control for TRIM28 knockdown rep3

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: Sample 12
TRIM28 knockdown

value: TRIM30 knockdown

tag: treatment


title: SH control for TRIM28 knockdown rep2

description:
Library name: Sample 11
TRIM28 knockdown

tag: genotype

value: TRIM29 knockdown


title: OA2

description:
Library name: OA-2
Column name in raw_counts_All_Samples.txt: OA2

value: WT


title: NOA3

description:
Library name: NOA-3
Column name in raw_counts_All_Samples.txt: NOA3


title: OA3

description:
Library name: OA-3
Column name in raw_counts_All_Samples.txt: OA3


title: SH control for FOXA1 knockdown rep1

description:
Library name: Sample 4
FOXA1 knockdown

value: FOXA1 knockdown


title: SH control for FOXA1 knockdown rep3

description:
Library name: Sample 6
FOXA1 knockdown


title: 6hr in meiosis plus EtOH (vehicle)

description:
Library name: Sample1
EtOH 6hr

value: meiosis


title: RNA-seq, THP1 Marophages, DMSO, 1 ng/mL IFNa 2hr, replicate 1

description: Library name: RS_IFN_1

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

value: DMSO

tag: treatment -_ifna

value: 1 ng/mL IFNa, 4 hr


title: NC control for TRIM28 knockdown rep3

description:
Library name: Sample 9
control-TRIM28

value: control shRNA


title: NC control for TRIM28 knockdown rep1

description:
Library name: Sample 7
control-TRIM28


title: NC control for FOXA1 knockdown rep2

description:
Library name: Sample 2
control-FOXA1


title: RSA replicate 3, m7G MeRIP library

city: fuzhou

first: Jianping

last: Tang

state: fujian

address: No. 18 Daoshan Road, Gulou District

institute: fujian women and child health hospital

description: Library name: RSA 3.IP

data_processing:
Raw reads were trimmed to remove adapter sequences and low-quality bases using fastp/Trimmomatic.
Clean reads were aligned to the human reference genome GRCh38 using HISAT2 (v2.1.0) or STAR.
m7G peaks were called using MACS2 (with input as control) or exomePeak2, with FDR < 0.05.
Differential methylation analysis was performed using DESeq2/edgeR (FDR < 0.05, |log2FC| > 0.5).
Functional enrichment analysis (GO and KEGG) was conducted on m7G-modified genes using clusterProfiler.
Assembly: GRCh38
Supplementary files format and content: Gene Expression Profiling.xlsx: Microsoft Excel workbook containing gene expression matrix.
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx: Microsoft Excel workbook listing all identified m7G methylation peak sites located on mRNA transcripts.
Library strategy: MeRIP-Seq

source_name: decidual tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer's instructions. RNA integrity was assessed using a Bioanalyzer (RIN ≥ 7.0)
Total RNA was subjected to immunoprecipitation with the GenSeq® m7G MeRIP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was decapping with Decapping Enzyme, and then randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m7G antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in sequencer .

value: decidual tissue

value: m7G antibody immunoprecipitation


title: NC control for FOXA1 knockdown rep1

description:
Library name: Sample 1
control-FOXA1

value: LACAP cell

value: prostate cancer cells


title: RSA replicate 3, input library

description: Library name: RSA 3.Input

value: input total RNA control


title: RSA replicate 2, m7G MeRIP library

description: Library name: RSA 2.IP


title: RSA replicate 2, input library

description: Library name: RSA 2.Input


title: HC replicate 3, m7G MeRIP library

description: Library name: HC 3.IP


title: HC replicate 2, input library

description: Library name: HC 2.Input


title: HC replicate 3, input library

description: Library name: HC 3.Input


title: HC replicate 2, m7G MeRIP library

description: Library name: HC 2.IP


title: PBMCs, sepsis-MDR Enterobacterales, sample 2

city: Rome

first: Claudia

last: Rotondo

address: Via Portuense, 292

country: Italy

institute: National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS

description:
Library name: SEPSIS_02
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, alignment, UMI counting, and generation of raw/unfiltered and filtered feature-barcode matrices were performed using Cell Ranger v9.0.1 (10x Genomics; https://www.10xgenomics.com/support/software/cell-ranger/9.0).
Assembly: GRCh38; 10x Genomics GRCh38-2024-A human reference transcriptome
Supplementary files format and content: Tab-separated values files and matrix files containing Cell Ranger raw/unfiltered and filtered feature-barcode matrices in MEX format
Supplementary files format and content: CSV files containing Cell Ranger sequencing and cell recovery summary metrics

source_name: peripheral blood

growth_protocol: Peripheral whole blood was collected in EDTA tubes and processed within two hours of venipuncture. Peripheral blood mononuclear cells (PBMCs) were isolated by density-gradient centrifugation using Pancoll Human separation medium, washed in RPMI, counted by Trypan blue exclusion, and cryopreserved in FBS with 10% DMSO before downstream processing.

extract_protocol:
Cryopreserved PBMCs were thawed and processed according to the 10x Genomics Chromium Next GEM Single Cell 3′ Gene Expression workflow v3.1. For septic samples showing evidence of haemolysis, the washing step before Chromium loading was intensified by using twice the recommended wash volume and twice as many washes to reduce potential haemoglobin carryover.
Single-cell gene expression libraries were prepared from thawed PBMCs using the Chromium Next GEM Single Cell 3′ Gene Expression workflow v3.1 according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: peripheral blood

value: peripheral blood mononuclear cells

value: female

value: sepsis with MDR Enterobacterales bloodstream infection


title: PBMCs, sepsis-MDR Enterobacterales, sample 1

description:
Library name: SEPSIS_01
10x Genomics


title: PBMCs, healthy control, sample 2

description:
Library name: HC_02
10x Genomics

value: male

value: none (healthy control)


title: T47D_ESR1_DMSO_rep3

city: Basel

first: Fabian

last: Wu

department: Biomedical Research

institute: Novartis Pharma

description: Library name: T47D_ESR1_DMSO_rep3

library_source: genomic

data_processing:
Raw sequencing reads were quality controlled and trimmed for adapter sequences.
Reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.4.3) with parameters recommended by Skene et al. (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700).
Aligned reads were filtered to remove duplicates, mitochondrial reads, and low-quality mappings.
Peak calling was performed using the ENCODE ChIP-seq pipeline2 (v2.1.2), which applies MACS2 for enrichment detection.
Reproducible peaks across replicates were determined using overlap and IDR-based filtering implemented in the ENCODE pipeline.
Assembly: hg38
Supplementary files format and content: narrowPeak files (overlap optimal set): BED6+4 format containing genomic coordinates of peaks identified by MACS2 and reproducibly observed across replicates.
Supplementary files format and content: narrowPeak files (IDR optimal set): BED6+4 format containing high-confidence peaks passing IDR filtering (threshold ≤ 0.05) across biological replicates.
Supplementary files format and content: bigWig files (per replicate): genome-wide normalized coverage tracks generated from aligned reads using genomeCoverageBed (bedtools v2.30.0).
Library strategy: CUT&Run

growth_protocol: T47D cells were cultured in phenol-red-free RPMI medium supplemented with 10% charcoal-stripped fetal bovine serum under standard conditions.

extract_protocol:
Cells were fixed with formaldehyde, quenched with glycine, and immobilized on Concanavalin A beads. After permeabilization, cells were incubated with an anti-ESR1 antibody followed by pAG-MNase. Targeted chromatin digestion was performed, and released DNA fragments were purified after proteinase K treatment and DNA extraction.
Sequencing libraries were prepared from CUT&RUN DNA fragments using the NEBNext Ultra II DNA Library Prep Kit with Illumina-compatible adapters, followed by PCR amplification and size selection using AMPure XP beads.

treatment_protocol: Cells were seeded 24 h prior to treatment and then treated with DMSO for 24 h.

value: breast cancer cell line

tag: antibody

value: Epicypher, #13-2011


title: Subject ZA0010882, Visit 3

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

description: Library name: ZA0010882.Visit.3

data_processing:
Sequencing data were aligned to a composite reference of GRCh38 with Ensemble annotation version 100 and SARS-CoV-2 reference assembly MN985325.1 using STAR v2.7.3a. Transcript abundance estimates were calculated by using the
STAR “quantMode GeneCounts” option using the algorithm of htseq-count.
Assembly: GRCh38-100, MN985325.1
Supplementary files format and content: Tab delimited text with counts for each sample in columns and transcript in rows.

source_name: Whole blood

growth_protocol: Whole blood collected in Paxgene tubes. No growth

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific). RNA quality was assessed using a TapeStation 4200 and one microgram of total RNA was subjected to globin transcript depletion using the human GLOBINclear Kit (ThermoFisher Scientific).
Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent)

treatment_protocol: Whole blood collected 1, 2, 3 or 7 days after primary, secondary or tertiary vaccinations

value: Whole blood

tag: subject

tag: visit

tag: day post_prior_vaccition

tag: prior vaccition

value: Tertiary

tag: infection status

value: Infected

tag: infection category

value: Prior

tag: study

value: NX


title: Subject ZA0010882, Visit 2

description: Library name: ZA0010882.Visit.2

tag: tissue


title: T47D_ESR1_DMSO_rep1

description: Library name: T47D_ESR1_DMSO_rep1

tag: cell line

tag: cell type

value: DMSO


title: Subject ZA0010882, Visit 1

description: Library name: ZA0010882.Visit.1


title: Subject ZA0010999, Visit 2

description: Library name: ZA0010999.Visit.2

tag: day post_primary

value: Primary


title: Subject ZA0010999, Visit 1

description: Library name: ZA0010999.Visit.1


title: Subject ZA0010998, Visit 3

description: Library name: ZA0010998.Visit.3


title: Subject ZA0010802, Visit 3

description: Library name: ZA0010802.Visit.3

value: Uninfected

value: Healthy


title: Subject ZA0010855, Visit 3

description: Library name: ZA0010855.Visit.3


title: Subject ZA0010763, Visit 3

description: Library name: ZA0010763.Visit.3


title: Subject ZA0010855, Visit 1

description: Library name: ZA0010855.Visit.1


title: Subject ZA0010954, Visit 3

description: Library name: ZA0010954.Visit.3


title: Subject ZA0010954, Visit 2

description: Library name: ZA0010954.Visit.2


title: Subject ZA0010837, Visit 7

description: Library name: ZA0010837.Visit.7

value: Secondary


title: Subject ZA0010837, Visit 6

description: Library name: ZA0010837.Visit.6


title: Subject ZA0010740, Visit 3

description: Library name: ZA0010740.Visit.3


title: Subject ZA0010837, Visit 5

description: Library name: ZA0010837.Visit.5


title: Subject ZA0010676, Visit 7

description: Library name: ZA0010676.Visit.7


title: Subject ZA0010676, Visit 6

description: Library name: ZA0010676.Visit.6


title: Subject ZA0010676, Visit 5

description: Library name: ZA0010676.Visit.5


title: HC replicate 1, m7G MeRIP library

description: Library name: HC 1.IP

value: decidual tissue

value: m7G antibody immunoprecipitation


title: Subject ZA0010994, Visit 6

description: Library name: ZA0010994.Visit.6


title: T47D_ESR1_DMSO_rep2

description: Library name: T47D_ESR1_DMSO_rep2


title: Subject ZA0010911, Visit 7

description: Library name: ZA0010911.Visit.7


title: PBMCs, healthy control, sample 1

description:
Library name: HC_01
10x Genomics

value: peripheral blood

value: peripheral blood mononuclear cells

tag: Sex

value: female


title: Subject ZA0010998, Visit 5

description: Library name: ZA0010998.Visit.5


title: Subject ZA0010911, Visit 5

description: Library name: ZA0010911.Visit.5


title: Subject ZA0010911, Visit 6

description: Library name: ZA0010911.Visit.6


title: Subject ZA0010802, Visit 1

description: Library name: ZA0010802.Visit.1


title: Subject ZA0010998, Visit 2

description: Library name: ZA0010998.Visit.2


title: Subject ZA0010911, Visit 2

description: Library name: ZA0010911.Visit.2


title: Subject ZA0010763, Visit 2

description: Library name: ZA0010763.Visit.2


title: Subject ZA0010681, Visit 6

description: Library name: ZA0010681.Visit.6


title: Subject ZA0010911, Visit 1

description: Library name: ZA0010911.Visit.1


title: M55 line with Dox-inducible CXCR2 transgene, Dox_1000ng/mL, P12, Rep2

status: Public on Aug 15 2026

first: Alex

last: Plesa

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: A32
Donor age 55, Passage 12

data_processing:
To minimize variability arising from differences in sequencing depth, FASTQ files for all libraries (except LIB058979, LIB092645, and LIB083102) were downsampled to 20 million reads using Seqtk-1.3.
Raw RNA-seq reads were aligned to the GRCh38/GRCm39 reference genome using STAR v2.5.2b and checked for quality control using FastQC v0.11.5
Alignment files were indexed using SAMtools v1.3.154 and gene-level counts were obtained using featureCounts from the Subread v2.0.1 package
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: NHDFs were maintained in low-glucose DMEM supplemented with 15% fetal bovine serum (FBS) and 1% Pen-strep (P/S) in humidified atmosphere with 5% CO2 and 5% O2, at 37C. iPSCs were maintained in mTESR+supplement in humidified atmosphre with 5% CO2 at 37C.

extract_protocol:
Cells were lysed using the Monarch DNA/RNA Protection Reagent (NEB T2011) and stored at -80°C until RNA extraction. Total RNA was extrqacted using the Monarch Total RNA Miniprep kit (NEB T2010). Mouse tissues were processed by Novogene.
Libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the polyA mRNA workflow according to manufacturer's instructions. LIB058979 was genereated using the Tecan MagicPrepRevelo mRNA-seq kit acoording to manufacturare's instructions. LIB083102 was generated by Novogene using a directional mRNA library preparation method.

treatment_protocol: Transgene was induced using doxycycline at the specified concentration for the specified amount of time. Similarly, rapamycin was added to the media at the 100nM for the specified amount of time.

value: Fibroblast

value: Dox_1000ng/mL, 3days

tag: batch


title: Subject ZA0010681, Visit 2

institute: Stanford University

description: Library name: ZA0010681.Visit.2

value: Whole blood


title: Subject ZA0010681, Visit 5

description: Library name: ZA0010681.Visit.5


title: Subject ZA0010954, Visit 1

description: Library name: ZA0010954.Visit.1

value: Tertiary


title: Subject ZA0011006, Visit 7

description: Library name: ZA0011006.Visit.7


title: Subject ZA0011006, Visit 1

description: Library name: ZA0011006.Visit.1


title: Subject ZA0011006, Visit 5

description: Library name: ZA0011006.Visit.5


title: Subject ZA0011006, Visit 2

description: Library name: ZA0011006.Visit.2


title: Subject ZA0010740, Visit 2

description: Library name: ZA0010740.Visit.2


title: Subject ZA0010850, Visit 2

description: Library name: ZA0010850.Visit.2

value: Infected


title: Subject ZA0010850, Visit 1

description: Library name: ZA0010850.Visit.1

value: Prior


title: Subject ZA0010841, Visit 3

description: Library name: ZA0010841.Visit.3

value: NX


title: Subject ZA0010841, Visit 1

description: Library name: ZA0010841.Visit.1


title: Subject ZA0010938, Visit 3

description: Library name: ZA0010938.Visit.3


title: Subject ZA0010938, Visit 1

description: Library name: ZA0010938.Visit.1


title: Subject ZA0010841, Visit 2

description: Library name: ZA0010841.Visit.2


title: Subject ZA0010893, Visit 1

description: Library name: ZA0010893.Visit.1


title: Subject ZA0010938, Visit 2

description: Library name: ZA0010938.Visit.2


title: Subject ZA0010863, Visit 5

description: Library name: ZA0010863.Visit.5


title: Subject ZA0010863, Visit 2

description: Library name: ZA0010863.Visit.2


title: Subject ZA0010893, Visit 2

description: Library name: ZA0010893.Visit.2


title: Subject ZA0010879, Visit 3

description: Library name: ZA0010879.Visit.3


title: Subject ZA0010863, Visit 1

description: Library name: ZA0010863.Visit.1


title: Subject ZA0010994, Visit 5

description: Library name: ZA0010994.Visit.5


title: Subject ZA0010879, Visit 5

description: Library name: ZA0010879.Visit.5


title: Subject ZA0010753, Visit 7

description: Library name: ZA0010753.Visit.7


title: Subject ZA0010914, Visit 1

description: Library name: ZA0010914.Visit.1


title: Subject ZA0010879, Visit 2

description: Library name: ZA0010879.Visit.2


title: Subject ZA0010879, Visit 1

description: Library name: ZA0010879.Visit.1


title: Subject ZA0010753, Visit 5

description: Library name: ZA0010753.Visit.5


title: Subject ZA0010898, Visit 5

description: Library name: ZA0010898.Visit.5


title: Subject ZA0010914, Visit 2

description: Library name: ZA0010914.Visit.2


title: Subject ZA0010753, Visit 6

description: Library name: ZA0010753.Visit.6


title: Subject ZA0010898, Visit 3

description: Library name: ZA0010898.Visit.3


title: Subject ZA0010898, Visit 2

description: Library name: ZA0010898.Visit.2


title: Subject ZA0010681, Visit 1

description: Library name: ZA0010681.Visit.1


title: Subject ZA0010838, Visit 5

description: Library name: ZA0010838.Visit.5


title: Subject ZA0010898, Visit 1

description: Library name: ZA0010898.Visit.1


title: Subject ZA0011006, Visit 3

description: Library name: ZA0011006.Visit.3


title: Thal_SIR_M_1

description: Library name: 320_T

value: Brain - Thalamus

tag: treatment

value: Maternal housing SIR

value: Male


title: Subject ZA0010838, Visit 3

description: Library name: ZA0010838.Visit.3

value: Uninfected

value: Healthy


title: Subject ZA0010838, Visit 1

description: Library name: ZA0010838.Visit.1


title: Subject ZA0010767, Visit 6

description: Library name: ZA0010767.Visit.6

value: Secondary


title: Subject ZA0010850, Visit 3

description: Library name: ZA0010850.Visit.3

value: Primary


title: OA1

description:
Library name: OA-1
Column name in raw_counts_All_Samples.txt: OA1

value: seminiferous tubules

value: spermatogenic cells

tag: genotype

value: WT


title: Subject ZA0010767, Visit 5

description: Library name: ZA0010767.Visit.5


title: Subject ZA0010767, Visit 7

description: Library name: ZA0010767.Visit.7


title: Subject ZA0010767, Visit 2

description: Library name: ZA0010767.Visit.2


title: Subject ZA0010767, Visit 3

description: Library name: ZA0010767.Visit.3


title: Subject ZA0010767, Visit 1

description: Library name: ZA0010767.Visit.1


title: Subject ZA0010808, Visit 1

description: Library name: ZA0010808.Visit.1


title: Subject ZA0010808, Visit 2

description: Library name: ZA0010808.Visit.2


title: Subject ZA0010123, Visit 1

description: Library name: ZA0010123.Visit.1


title: SH control for FOXA1 knockdown rep2

description:
Library name: Sample 5
FOXA1 knockdown

value: LACAP cell

value: prostate cancer cells

value: FOXA1 knockdown


title: NC control for FOXA1 knockdown rep3

description:
Library name: Sample 3
control-FOXA1

value: control shRNA


title: Subject ZA0010821, Visit 3

description: Library name: ZA0010821.Visit.3

value: Whole blood

value: Tertiary

value: Infected


title: Subject ZA0010123, Visit 7

description: Library name: ZA0010123.Visit.7

value: NX


title: Subject ZA0010821, Visit 1

description: Library name: ZA0010821.Visit.1

value: Prior


title: NC control for TRIM28 knockdown rep2

description:
Library name: Sample 8
control-TRIM28


title: Subject ZA0010821, Visit 2

description: Library name: ZA0010821.Visit.2


title: Subject ZA0010781, Visit 6

description: Library name: ZA0010781.Visit.6


title: Subject ZA0010123, Visit 5

description: Library name: ZA0010123.Visit.5


title: Subject ZA0010893, Visit 3

description: Library name: ZA0010893.Visit.3


title: Subject ZA0010123, Visit 2

description: Library name: ZA0010123.Visit.2


title: Subject ZA0010781, Visit 5

description: Library name: ZA0010781.Visit.5


title: Subject ZA0010781, Visit 3

description: Library name: ZA0010781.Visit.3


title: Subject ZA0010781, Visit 1

description: Library name: ZA0010781.Visit.1


title: Subject ZA0010781, Visit 7

description: Library name: ZA0010781.Visit.7


title: RSA replicate 1, input library

description: Library name: RSA 1.Input

value: decidual tissue

value: input total RNA control


title: Subject ZA0010703, Visit 1

description: Library name: ZA0010703.Visit.1


title: RSA replicate 1, m7G MeRIP library

description: Library name: RSA 1.IP

value: m7G antibody immunoprecipitation


title: Subject ZA0010703, Visit 2

description: Library name: ZA0010703.Visit.2


title: HC replicate 1, input library

description: Library name: HC 1.Input


title: Subject ZA0010632, Visit 3

description: Library name: ZA0010632.Visit.3


title: Subject ZA0010632, Visit 1

description: Library name: ZA0010632.Visit.1


title: Subject ZA0010632, Visit 2

description: Library name: ZA0010632.Visit.2


title: Subject ZA0010945, Visit 7

description: Library name: ZA0010945.Visit.7

value: Secondary

value: Uninfected

value: Healthy


title: Subject ZA0010945, Visit 2

description: Library name: ZA0010945.Visit.2

value: Primary


title: Subject ZA0010945, Visit 5

description: Library name: ZA0010945.Visit.5


title: Subject ZA0010945, Visit 6

description: Library name: ZA0010945.Visit.6


title: Subject ZA0010836, Visit 3

description: Library name: ZA0010836.Visit.3


title: Subject ZA0010836, Visit 5

description: Library name: ZA0010836.Visit.5


title: Subject ZA0010945, Visit 1

description: Library name: ZA0010945.Visit.1


title: Subject ZA0010945, Visit 3

description: Library name: ZA0010945.Visit.3


title: Subject ZA0010836, Visit 1

description: Library name: ZA0010836.Visit.1


title: Subject ZA0010752, Visit 3

description: Library name: ZA0010752.Visit.3


title: Subject ZA0010322, Visit 5

description: Library name: ZA0010322.Visit.5


title: Subject ZA0010777, Visit 7

description: Library name: ZA0010777.Visit.7


title: Subject ZA0010322, Visit 6

description: Library name: ZA0010322.Visit.6


title: Subject ZA0010777, Visit 5

description: Library name: ZA0010777.Visit.5


title: Subject ZA0010777, Visit 6

description: Library name: ZA0010777.Visit.6


title: Subject ZA0010729, Visit 6

description: Library name: ZA0010729.Visit.6


title: Subject ZA0010705, Visit 7

description: Library name: ZA0010705.Visit.7


title: Subject ZA0010729, Visit 7

description: Library name: ZA0010729.Visit.7


title: Subject ZA0010705, Visit 5

description: Library name: ZA0010705.Visit.5


title: Subject ZA0010839, Visit 5

description: Library name: ZA0010839.Visit.5


title: Subject ZA0010729, Visit 5

description: Library name: ZA0010729.Visit.5


title: Subject ZA0010705, Visit 6

description: Library name: ZA0010705.Visit.6


title: Subject ZA0010839, Visit 1

description: Library name: ZA0010839.Visit.1


title: Subject ZA0010839, Visit 3

description: Library name: ZA0010839.Visit.3


title: Subject ZA0010822, Visit 2

description: Library name: ZA0010822.Visit.2


title: Subject ZA0010895, Visit 3

description: Library name: ZA0010895.Visit.3


title: Subject ZA0010822, Visit 5

description: Library name: ZA0010822.Visit.5


title: Subject ZA0010895, Visit 5

description: Library name: ZA0010895.Visit.5


title: Subject ZA0010822, Visit 3

description: Library name: ZA0010822.Visit.3


title: Subject ZA0010720, Visit 3

description: Library name: ZA0010720.Visit.3


title: Subject ZA0010839, Visit 2

description: Library name: ZA0010839.Visit.2


title: Subject ZA0010895, Visit 1

description: Library name: ZA0010895.Visit.1


title: Subject ZA0010720, Visit 2

description: Library name: ZA0010720.Visit.2


title: Subject ZA0010822, Visit 1

description: Library name: ZA0010822.Visit.1


title: Subject ZA0010720, Visit 1

description: Library name: ZA0010720.Visit.1


title: Subject 1.30097, Visit 8

description: Library name: 1.30097.Visit.8

value: AZ


title: Subject 1.30097, Visit 7

description: Library name: 1.30097.Visit.7


title: Subject 1.30097, Visit 2

description: Library name: 1.30097.Visit.2


title: Subject 1.30037, Visit 8

description: Library name: 1.30037.Visit.8

value: Report says after


title: Subject 1.30097, Visit 1

description: Library name: 1.30097.Visit.1


title: Subject 1.30097, Visit 3

description: Library name: 1.30097.Visit.3


title: Subject 1.30037, Visit 7

description: Library name: 1.30037.Visit.7


title: Subject 1.30037, Visit 3

description: Library name: 1.30037.Visit.3


title: Subject 1.30011, Visit 7

description: Library name: 1.30011.Visit.7

value: Report says infected


title: Subject 1.30037, Visit 1

description: Library name: 1.30037.Visit.1


title: Subject 1.30011, Visit 6

description: Library name: 1.30011.Visit.6


title: Subject 1.30011, Visit 2

description: Library name: 1.30011.Visit.2


title: Subject 1.30011, Visit 1

description: Library name: 1.30011.Visit.1


title: Subject 1.3001, Visit 7

description: Library name: 1.30010.Visit.7


title: Subject 1.3001, Visit 2

description: Library name: 1.30010.Visit.2


title: Subject 1.3001, Visit 6

description: Library name: 1.30010.Visit.6


title: Subject 1.3001, Visit 1

description: Library name: 1.30010.Visit.1


title: HuCCT1 NC biological replicate 2

first: Yingbin

last: Liu

state: Shanghai

address: Dongfang Road1630

institute: Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: HuCCT1_NC_Rep2
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after vehicle control for 72 h, biological replicate 2.

data_processing:
Illumina base-call files were demultiplexed into lane- and library-specific paired-end FASTQ files using bcl2fastq. The resulting gzip-compressed, unfiltered FASTQ files were deposited as raw sequencing data.
For OCUG-1-S10-2, OCUG-1-S125-2, OCUG-1-S125-3, and OCUG-1-S125-I-2, the corresponding L2 and L3 paired-end FASTQ files were combined by read direction before alignment and expression quantification. All original lane-specific FASTQ files are deposited.
Raw RNA-seq data were subjected to quality control and filtering using fastp (v1.3.2) to remove adapter sequences and low-quality reads. Reads with low-quality bases (quality score < Q20) exceeding 30% of total bases were removed, and reads shorter than 36 bp after trimming were discarded. Basic sequencing metrics, including base quality profiles, Q30, and GC content, were assessed. Clean high-quality reads were aligned to the human reference genome GRCh38 using HISAT2 (v2.2.2) with Ensembl release 113 annotation. Gene-level quantification was performed using featureCounts (Subread v2.1.1) based on exon annotations to generate raw count matrices. Sequencing quality, alignment performance, and read assignment statistics were summarized using MultiQC (v1.33).
All downstream analyses were performed in R (v4.4.1). To minimize the impact of lowly expressed genes, only genes with non-zero expression in at least 75% of samples were retained for subsequent analyses. Principal component analysis (PCA) was used to evaluate overall sample relationships and data quality. Differential expression analysis was conducted on raw counts using DESeq2 (v1.42.1). Differentially expressed genes (DEGs) were defined as |log2 fold change| > 1 and Benjamini-Hochberg-adjusted P value (FDR) < 0.05 and were visualized using volcano plots and heatmaps. Heatmaps were generated from DESeq2 size-factor-normalized counts with row-wise Z-score scaling; displayed genes met FDR < 0.05 and |log2 fold change| > 1 in at least one relevant contrast.
GO Biological Process (BP) enrichment analysis was performed on DEGs using clusterProfiler (v4.10.1); multiple-testing-adjusted P values were calculated, and representative terms with P value < 0.05 were selected for display. Gene set enrichment analysis was performed using the GSEA() function in clusterProfiler (v4.10.1). Before GSEA, genes were not filtered by P value, adjusted P value, or absolute log2 fold change. All genes with non-missing gene symbols and available log2 fold change values from the differential expression analysis were included. For duplicated gene symbols, one representative record was retained. Genes were ranked by log2 fold change in decreasing order to generate a preranked gene list. Gene sets were obtained from the MSigDB C5 collection, version 2025.1, using human gene symbols, and gene sets containing 10 to 500 genes were retained. Enrichment score, normalized enrichment score, P value, and Benjamini-Hochberg-adjusted P value were calculated for each pathway, and the complete GSEA results were retained; representative pathways with P value < 0.05 were selected for display.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts generated by featureCounts based on Ensembl release 113 annotation for the GRCh38 human reference genome. Rows represent Ensembl gene IDs and columns represent individual RNA-seq samples. Count values are unnormalized integer read counts and were used as input for downstream differential expression analysis with DESeq2.

growth_protocol: HuCCT1 cells were cultured in RPMI-1640, and OCUG-1 cells were cultured in DMEM, at 37 °C in a humidified incubator with 5% CO2. Media were supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin (Procell). Cells were routinely passaged at a 1:3 ratio, and experiments used cells in logarithmic growth phase.

extract_protocol:
Cells were harvested after 72 h of drug treatment, and total RNA was extracted using the TRIzol method.
RNA-seq libraries were prepared by Berry Genomics using a TruSeq mRNA-seq workflow for eukaryotic RNA samples and sequenced on an Illumina NovaSeq platform as 150-bp paired-end reads.

treatment_protocol: Sorafenib and IACS-010759 were dissolved in DMSO as 10 mM stock solutions and diluted in the corresponding culture medium. Cells were treated for 72 h under four conditions: vehicle control with matched DMSO at no more than 0.1%, 1.25 µM sorafenib, 10 µM sorafenib, or 1.25 µM sorafenib plus 1 µM IACS-010759. Each condition included three independent biological replicates for each cell line.

value: vehicle control (DMSO <= 0.1%), 72 h


title: Subject 1.20384, Visit 2

description: Library name: 1.20384.Visit.2


title: Subject 1.20384, Visit 3

description: Library name: 1.20384.Visit.3


title: Subject 1.20384, Visit 1

description: Library name: 1.20384.Visit.1


title: Subject 1.20369, Visit 1

description: Library name: 1.20369.Visit.1


title: Subject 1.20369, Visit 6

description: Library name: 1.20369.Visit.6


title: Subject 1.20209, Visit 2

description: Library name: 1.20209.Visit.2


title: Subject 1.20209, Visit 7

description: Library name: 1.20209.Visit.7


title: Subject 1.20209, Visit 6

description: Library name: 1.20209.Visit.6


title: Subject 1.20369, Visit 7

description: Library name: 1.20369.Visit.7


title: Subject 1.20369, Visit 2

description: Library name: 1.20369.Visit.2


title: Subject 1.20209, Visit 1

description: Library name: 1.20209.Visit.1


title: Subject 1.20369, Visit 8

description: Library name: 1.20369.Visit.8


title: Subject 1.20081, Visit 7

description: Library name: 1.20081.Visit.7


title: Subject 1.20081, Visit 2

description: Library name: 1.20081.Visit.2


title: Subject 1.20081, Visit 3

description: Library name: 1.20081.Visit.3


title: Subject 1.20209, Visit 8

description: Library name: 1.20209.Visit.8


title: Subject 1.20081, Visit 1

description: Library name: 1.20081.Visit.1


title: Subject 1.20078, Visit 8

description: Library name: 1.20078.Visit.8

value: After


title: Subject 1.20078, Visit 7

description: Library name: 1.20078.Visit.7

value: Whole blood


title: Subject 1.20081, Visit 6

description: Library name: 1.20081.Visit.6


title: Subject 1.20078, Visit 6

description: Library name: 1.20078.Visit.6


title: Subject 1.20078, Visit 2

description: Library name: 1.20078.Visit.2


title: Subject 1.20076, Visit 8

description: Library name: 1.20076.Visit.8


title: Subject 1.20076, Visit 6

description: Library name: 1.20076.Visit.6


title: Subject 1.20078, Visit 1

description: Library name: 1.20078.Visit.1


title: Subject 1.20076, Visit 7

description: Library name: 1.20076.Visit.7


title: Subject 1.20028, Visit 7

description: Library name: 1.20028.Visit.7


title: Subject 1.20076, Visit 2

description: Library name: 1.20076.Visit.2


title: Subject 1.20076, Visit 1

description: Library name: 1.20076.Visit.1


title: Subject 1.20028, Visit 1

description: Library name: 1.20028.Visit.1


title: Subject 1.20027, Visit 6

description: Library name: 1.20027.Visit.6


title: Subject 1.20027, Visit 8

description: Library name: 1.20027.Visit.8


title: Subject 1.20027, Visit 7

description: Library name: 1.20027.Visit.7


title: Subject 1.20028, Visit 8

description: Library name: 1.20028.Visit.8


title: Subject 1.20028, Visit 6

description: Library name: 1.20028.Visit.6


title: Subject 1.20028, Visit 2

description: Library name: 1.20028.Visit.2


title: Subject 1.20027, Visit 2

description: Library name: 1.20027.Visit.2


title: Subject 1.20027, Visit 1

description: Library name: 1.20027.Visit.1


title: Subject 1.20001, Visit 8

description: Library name: 1.20001.Visit.8


title: Subject 1.20001, Visit 7

description: Library name: 1.20001.Visit.7


title: Subject 1.20001, Visit 6

description: Library name: 1.20001.Visit.6


title: Subject 1.3004, Visit 8

description: Library name: 1.30040.Visit.8


title: Subject 1.3004, Visit 6

description: Library name: 1.30040.Visit.6


title: Subject 1.20001, Visit 2

description: Library name: 1.20001.Visit.2


title: Subject 1.3004, Visit 7

description: Library name: 1.30040.Visit.7


title: Subject 1.3004, Visit 3

description: Library name: 1.30040.Visit.3


title: Subject 1.3004, Visit 2

description: Library name: 1.30040.Visit.2


title: Subject 1.3004, Visit 1

description: Library name: 1.30040.Visit.1


title: Mtb, phoT::Tn, lactate, pH 5.7, Rep A

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

description: Library name: Lac_Tn_5A_S5_L001_R1_001.fastq.gz

data_processing:
After the sequencing runs, reads were demultiplexed and converted fastq format using Illumina bcl2fastq (v1.8.4) script.  The reads in the raw files were then subjected to trimming of low quality bases and removal of adapter sequences using Trimmomatic (v0.30) with a 4bp sliding window, cutting when the read quality dropped below 15, or read length was less than 36 bp.  Trimmed reads were aligned to the WT erdman genome using bowtie with the -S option to produce SAM files as output.
SAM files produced by bowtie were converted to BAM files and coverage depth was calculated using SAM tools resulting in 98% coverage.  Aligned reads were then counted gene feature in WT erdman genome using the HTSeq software suite.  Data were normalized by estimating effective library sizes using robust regression within the DEseq package.  Statistical analysis and differential gene expression was performed in R studio by fitting a negative binomial model to each set of conditions and testing for differences utilizing the DESeq package.
Assembly: M. tuberculosis Erdman (ATCC 35801), GCA\_000350205.1
Supplementary files format and content: Processed files are presented as an .xlsx spreadsheet with calculated CPMs of each Rep presented.
Supplementary files format and content: Dataset_GEO.xlsx

organism: Mycobacterium tuberculosis

source_name: Bacterial Cell

growth_protocol: Mtb cultures were cultured for 3 days  in T-75 standing flasks in a 37C incubator (with 5% CO2).

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
DNA libraries were constructed using the illumina true seq RNA library preparation kit omiting the polyA selection step.  After library quality control, samples were pooled and sequenced in one lane Illumina HiSeq 2500 Rapid Run flow (v1) in 50 bp, single end read format (SE50).

treatment_protocol: 8 conditions conditions, and three strains,WTERDMAN, phoR::Tn and phoT::Tn were examined with two biological replicates. The conditions examined include: 1)WT, 2mM propionate acidic, pH 7.0; 2) WT, 2mM propionate acidic, pH 5.7, 3) phoR::TN, 2mM propionate, pH 7.0, 4) phoR::TN, 2mM propionate, pH 5.7; 5) WT, 4 mM lacate,  pH7.0, 6) WT, 4 mM lactate, pH 5.7; 7) phoT::Tn 4 mM lactate, pH 7.0, 8) phoT::Tn, 4 mM lacate, pH 5.7.   Following, a 3 day incubation, total bacterial RNA was extracted.

value: Bacterial Cell


title: Mtb, phoT::Tn, lacate, pH 7.0, Rep B

description: Library name: Lac_Tn_7B_S15_L001_R1_001.fastq.gz


title: Subject 1.30023, Visit 8

description: Library name: 1.30023.Visit.8

value: Infected


title: Mtb, phoT::Tn, lactate, pH 7.0, Rep A

description: Library name: Lac_Tn_7A_S13_L001_R1_001.fastq.gz


title: Mtb, WT, lactate, pH 5.7, Rep B

description: Library name: Lac_WT_5B_S3_L001_R1_001.fastq.gz


title: Subject 1.30023, Visit 7

description: Library name: 1.30023.Visit.7


title: Mtb, WT, lactate, pH 5.7, Rep A

description: Library name: Lac_WT_5A_S1_L001_R1_001.fastq.gz


title: Subject 1.30023, Visit 6

description: Library name: 1.30023.Visit.6


title: Mtb, WT, lactate, pH 7.0, Rep B

description: Library name: Lac_WT_7B_S11_L001_R1_001.fastq.gz


title: Subject 1.30023, Visit 1

description: Library name: 1.30023.Visit.1


title: Mtb, phoR::Tn, propionate, pH 5.7, Rep B

description: Library name: Prop_Tn_5B_S8_L001_R1_001.fastq.gz


title: Subject 1.20414, Visit 6

description: Library name: 1.20414.Visit.6


title: Mtb, phoR::Tn, propionate, pH 7.0, Rep B

description: Library name: Prop_Tn_7B_S16_L001_R1_001.fastq.gz


title: Subject 1.20414, Visit 3

description: Library name: 1.20414.Visit.3


title: Subject 1.20414, Visit 2

description: Library name: 1.20414.Visit.2


title: Mtb, WT, propionate, pH 5.7, Rep B

description: Library name: Prop_WT_5B_S4_L001_R1_001.fastq.gz


title: Mtb, WT, propionate, pH 5.7, Rep A

description: Library name: Prop_WT_5A_S2_L001_R1_001.fastq.gz


title: Subject 1.20365, Visit 8

description: Library name: 1.20365.Visit.8


title: Mtb, WT, propionate, pH 7.0, Rep B

description: Library name: Prop_WT_7B_S12_L001_R1_001.fastq.gz


title: Subject 1.20365, Visit 7

description: Library name: 1.20365.Visit.7


title: Mtb, WT, propionate, pH 7.0, Rep A

description: Library name: Prop_WT_7A_S10_L001_R1_001.fastq.gz

value: Erdman


title: Subject 1.20365, Visit 6

description: Library name: 1.20365.Visit.6


title: B3,primary cardiomyocytes,Adv-ABHD11,hypoxia 24h

city: Guangzhou

first: Yu

address: No. 1838, Guangzhou Avenue North

institute: NANFANG HOSPITAL SOUTHERN MEDICAL UNIVERSITY

description: Library name: Sample 6

data_processing:
Transcriptome sequencing and analysis were performed on an Illumina HiSeq X Ten platform by Gene Denovo (Guangzhou, China)
Raw reads (FASTQ files) were preprocessed with Trimmomatic (v0.39) to filter low-quality sequences, aligned to the Mus musculus reference genome (mm10) using HISAT2. The resulting alignment files in BAM format were subsequently processed for transcript quantification using the RSEM (RNA-Seq by Expectation-Maximization) tool, which was employed to estimate gene and transcript expression levels
Differential gene expression was conducted via the DESeq2 R package, with significance thresholds set at a p-value＜0.05 and a foldchange＞1.5 or＜0.66. Gene Ontology (GO) enrichment analysis and Gene Set Enrichment Analysis (GSEA) were performed using the ClusterProfiler package.
Assembly: mm10

source_name: Heart

extract_protocol:
Total RNA was extracted with TRIzol reagent according to the manufacturer’s protocol. RNA purity and concentration were measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), while RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Libraries were constructed using Hieff NGS DNA Selection Beads according to the manufacturer’s instructions.

value: Heart

value: cardiomyocytes

value: primary cardiomyocytes

value: ABHD11 overexpression

value: hypoxia


title: Subject 1.20365, Visit 3

description: Library name: 1.20365.Visit.3

value: Uninfected


title: B2,primary cardiomyocytes,Adv-ABHD11,hypoxia 24h

description: Library name: Sample 5


title: Subject 1.20365, Visit 2

description: Library name: 1.20365.Visit.2

value: Healthy


title: B1,primary cardiomyocytes,Adv-ABHD11,hypoxia 24h

description: Library name: Sample 4


title: Subject 1.30023, Visit 2

description: Library name: 1.30023.Visit.2

value: Primary

value: Prior


title: Mtb, WT, lactate, pH 7.0, Rep A

description: Library name: Lac_WT_7A_S9_L001_R1_001.fastq.gz


title: Subject 1.20414, Visit 8

description: Library name: 1.20414.Visit.8

value: Secondary

value: AZ


title: Subject 1.20414, Visit 7

description: Library name: 1.20414.Visit.7


title: Mtb, phoR::Tn, propionate, pH 5.7, Rep A

description: Library name: Prop_Tn_5A_S6_L001_R1_001.fastq.gz


title: A3,primary cardiomyocytes,Adv-NC,hypoxia 24h

description: Library name: Sample 3

value: WT


title: Subject 1.20365, Visit 1

description: Library name: 1.20365.Visit.1


title: Subject 1.20304, Visit 8

description: Library name: 1.20304.Visit.8


title: A2,primary cardiomyocytes,Adv-NC,hypoxia 24h

description: Library name: Sample 2


title: Subject 1.20304, Visit 7

description: Library name: 1.20304.Visit.7


title: A1,primary cardiomyocytes,Adv-NC,hypoxia 24h

description: Library name: Sample 1