title: 25L007993 | neuron Reference TP2

description: Library name: 25L007993

value: Supernatant


title: 25L007992 | neuron Reference TP2

status: Public on Mar 27 2026

type: SRA

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description: Library name: 25L007992

library_source: transcriptomic

data_processing:
Deduplication via czid-dedup (paired-end mode)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

molecule: polyA RNA

organism: Mus musculus

source_name: brain

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

tag: tissue

value: brain

tag: cell line

value: murine primary neurons

tag: cell type

value: primary neuron

tag: genotype

value: primary mouse cortical neurons

tag: rna origin

tag: treatment

tag: batch


title: P14 hippocampus H3K27ac ChIP-seq N-bc2S1P rep3

city: GuangZhou

first: Hao

last: Liu

state: Guangdong

address: No. 1023-1063 Shatai South Road, Baiyun District

country: China

institute: Southern Medical University

description:
Library name: N-bc2S1P_3
H3K27ac ChIP DNA; NEBNext Ultra II DNA kit

library_source: genomic

data_processing:
Reads were trimmed with Trim Galore and aligned to mm10 with Bowtie2. Alignments were filtered (MAPQ >= 30) and PCR duplicates were removed. Broad peaks were called with MACS2 in broad mode without a matched input control. A consensus peak set and peak-by-sample count matrix were generated, and differential occupancy was analyzed using DiffBind/DESeq2 with Benjamini-Hochberg FDR control. Replicate concordance was assessed by IDR.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited consensus peak count matrix with genomic coordinates and read counts per sample: CA1_P14_H3K27ac_consensus_peak_counts.tsv.

molecule: genomic DNA

source_name: hippocampus

extract_protocol:
Hippocampal tissue (~60 mg) was fixed in 1% formaldehyde at 4C for 10 min, quenched with 125 mM glycine, lysed and sonicated on a Bioruptor Pico for 30 cycles (30 s ON/30 s OFF) to 200-500 bp. Chromatin (50 ug) was immunoprecipitated overnight with 5 ug anti-H3K27ac (Cell Signaling) and Dynabeads Protein A. After washes, crosslinks were reversed at 65C for 4 h and DNA was purified.
Libraries were built with the NEBNext Ultra II DNA Kit (10 PCR cycles) and sequenced as single-end reads on a NovaSeq 6000.

value: hippocampus


title: P14 hippocampus H3K27ac ChIP-seq Sal rep1

description:
Library name: Sal_1
H3K27ac ChIP DNA; NEBNext Ultra II DNA kit

value: Sal


title: CD4 T cell, REV-Erbβ-H565F overexpression, 48hr, Replicate 1

city: Jupiter

first: Jonathan

last: Chuck

state: FL

address: 130 Scripps Way, C275

department: Immunology

country: USA

institute: UF Scripps

description:
Library name: 48hr_β_H565F_OE_Rep1
normalized_counts_DEseq2.csv

data_processing:
Raw counts were transformed into "Relative Log Expression” normalization (RLE) implemented in the DESeq2 package that was used to assess differential expression and perform gene set testing.
Assembly: M.musculus UCSC mm10 build
Supplementary files format and content: Normalized counts

molecule: total RNA

source_name: T Cells

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits (WT vs KO) of in vitro differentiated Th17 cells.  rRNA-depleted RNA was processed using the TruSeq Stranded Total RNA sample prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: T Cells

value: Primary

value: Th17 cell differentiation with retroviral transduction


title: 25L007990 | neuron Reference TP2

description: Library name: 25L007990


title: HEK293T, OMM-Lantern, omitting-Light control, rep1

city: Beijing

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

institute: Peking University

description:
Library name: OMM-Lantern_NoLight_rep1
Column name in OMM_all_counts.xlsx: NoLight_rep1
OMM_all_counts.xlsx

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (For subcellular transcriptome data, adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; for cancer cell migration study, adaptor1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, adaptor2=CTGTCTCTTATACACATCTGACGCTGCCGACGA; other parameters: -q 20 -O 3 -m 20).
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38), Rnor_6.0, GRCm39
Supplementary files format and content: Excel tables include raw counts for each sample.

organism: Homo sapiens

growth_protocol: HEK293T and MC38 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cortical neurons were dissected from neonatal Sprague Dawley rats (within 24 hours post-birth), plated onto 10-cm dishes, and cultured with GPM for 3-6 h before switching to neural cell culture medium (Neurobasal medium with 2% (v/v) B-27 supplement, 1% (v/v) GlutaMAX supplement, penicillin and streptomycin). Petri dishes were pre-incubated overnight with 50-100 μg/mL PDL at 37°C. The day of rat dissection was designated as DIV 0 (0 days in vitro), and thereafter, half of the spent culture medium was replaced with fresh neural cell culture medium every 3 days.

extract_protocol:
For the profiling of subcellular transcriptomes, cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. For identifying G3BP1-proximal and OMM-proximal RNAs in the HEK293T cells, rRNAs were removed with Ribo-off rRNA Depletion Kit (Vazyme) following the manufacturer’s protocol. The purified RNAs were dissolved in 5 μL nuclease-free water. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. For the study of cancer cell migration, the sorted cells were used for pseudo-bulk RNA-sequencing library construction following the previously published Sherry2 protocol. Libraries constructed from polyA RNAs (OMM-proximal and G3BP1-proximal RNAs of HEK293T cells, and mRNAs of MC38 cells) were sequenced to a depth of 3 G raw base. And libraries constructed from total RNAs (ERM-proximal RNAs of HEK293T cells and G3BP1-proximal RNAs of rat cortical neurons) were sequenced to a depth of 15 G raw base.

treatment_protocol: For general CAP-seq labeling experiments, HEK293T cells were cultured until the confluence reached 90%, incubated with 10 mM propargylamine (PA) in HBSS for 5 min, and irradiated with blue light for 1-120 seconds. For the induction of stress granules, HEK293T cells were incubated with 0.5 mM sodium arsenite for 5-60 minutes. Primary cultures of rat cortical neurons were transduced with a lentivirus expressing G3BP1-Lantern or Lantern-NES at 3 days in vitro (DIV3). At DIV8, neurons were stimulated with 0.25 mM sodium arsenite for 3 hours, and conducted with the CAP-seq labeling procedure. For the cancer cell migration assay, MC38 cells were seeded on coverslips with a culture-insert to create a 500-μm cell-free gap. 24 hours after removing the culture-insert, migrating cells near the gap and remaining cells far from the gap were selectively labeled with DMD-controlled 450-nm laser and 2 mM Bio-NH2 probe.

value: embryonic kidney cells

value: Lantern-MAVS


title: CD4 T cell, REV-Erbβ-ΔDBD overexpression, 48hr, Replicate 1

description:
Library name: 48hr_β_ΔDBD_OE_Rep1
normalized_counts_DEseq2.csv


title: 25L007991 | neuron Reference TP2

description: Library name: 25L007991


title: HEK293T, OMM-Lantern, Input, rep3

description:
Library name: OMM-Lantern_IN_rep3
Column name in OMM_all_counts.xlsx: IN_rep3
OMM_all_counts.xlsx


title: P14 hippocampus H3K27ac ChIP-seq N-bc2S1P rep1

description:
Library name: N-bc2S1P_1
H3K27ac ChIP DNA; NEBNext Ultra II DNA kit


title: 25L007994 | neuron Reference TP2

description: Library name: 25L007994


title: 25L007989 | AAV1P5 hSyn TetOn V9I + AAV1P5 Tre3G NTVE

description: Library name: 25L007989


title: HEK293T, OMM-Lantern, Input, rep2

description:
Library name: OMM-Lantern_IN_rep2
Column name in OMM_all_counts.xlsx: IN_rep2
OMM_all_counts.xlsx


title: 25L007988 | AAV1P5 hSyn TetOn V9I + AAV1P5 Tre3G NTVE

description:
Library name: 25L007988
Primary mouse cortical neuron, AAV1P5 hSyn TetOn V9I + AAV1P5 Tre3G NTVE


title: B6_P60_04

city: New York

first: Revathi

last: Balasubramanian

state: NY

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

description:
Library name: Sample 17
SN81_P60

library_source: transcriptomic single cell

data_processing:
Demultiplexed data was processed using the CellRanger count pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Anterior segment limbal tissue

extract_protocol:
Tissues were digested enzymatically using Papain and Deoxyribonuclease I (Worthington Biochemical Corporation, Cat. no. LK003153) for 20-30 min at 37°C and stopped using Earl’s balanced salt solution (EBSS, Thermo Fisher Scientific, Cat no. 24010-043). Cells were triturated using an 18-gauge needle, centrifuged at 300g at 4 °C, washed with cold DMEM, and filtered using a 100 μm Flowmi Cell Strainer (H13680-0040, Bel-Art. Cells were resuspended in cold DMEM and placed on ice immediately.
Single-cell and single-nucleus RNA-seq was performed at the single-cell sequencing core in Columbia University Genome Center. Single cells or nuclei were loaded into chromium microfluidic chips with v3 chemistry and barcoded with a 10x chromium controller (10x Genomics). RNA from the barcoded cells was reverse-transcribed, and sequencing libraries were constructed with a Chromium Single Cell v3 reagent kit (10x Genomics). Sequencing was performed on NovaSeq 6000 (Illumina).

value: Anterior segment limbal tissue

value: Wild-type


title: HEK293T, OMM-Lantern, Input, rep1

description:
Library name: OMM-Lantern_IN_rep1
Column name in OMM_all_counts.xlsx: IN_rep1
OMM_all_counts.xlsx


title: B6_P60_03

description:
Library name: Sample 16
SN73_P60


title: CD4 T cell, REV-Erbβ overexpression, 48hr, Replicate 1

description:
Library name: 48hr_β_OE_Rep1
normalized_counts_DEseq2.csv


title: 25L007987 | AAV1P5 hSyn TetOn V9I + AAV1P5 Tre3G NTVE

description: Library name: 25L007987


title: HEK293T, OMM-Lantern, Enrich, rep3

description:
Library name: OMM-Lantern_EN_rep3
Column name in OMM_all_counts.xlsx: EN_rep3
OMM_all_counts.xlsx


title: 25L007986 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVEdeltaMyrist

description: Library name: 25L007986


title: P14 hippocampus H3K27ac ChIP-seq N-bc2S1P rep2

description:
Library name: N-bc2S1P_2
H3K27ac ChIP DNA; NEBNext Ultra II DNA kit


title: B6_P60_02

description:
Library name: Sample 15
SN59_P60


title: CD4 T cell, empty vector, 48hr, Replicate 1

description:
Library name: 48hr_EV_Rep1
normalized_counts_DEseq2.csv


title: CD4 T cell, REV-Erbβ overexpression, 48hr, Replicate 2

description:
Library name: 48hr_β_OE_Rep2
normalized_counts_DEseq2.csv


title: HEK293T, OMM-Lantern, Enrich, rep1

description:
Library name: OMM-Lantern_EN_rep1
Column name in OMM_all_counts.xlsx: EN_rep1
OMM_all_counts.xlsx


title: B6_P21_03

description:
Library name: Sample 13
SN79_P21


title: CD4 T cell, REV-Erbα KO, 24hr, Replicate 2

description:
Library name: 24hr_ αKO_Rep2
a_b_normalized_counts_DEseq2.csv

value: REV-ERBa-/- (KO)

value: Th17 cell differentiation


title: HEK293T, OMM-Lantern, Enrich, rep2

description:
Library name: OMM-Lantern_EN_rep2
Column name in OMM_all_counts.xlsx: EN_rep2
OMM_all_counts.xlsx


title: B6_P60_01

description:
Library name: Sample 14
SN39_P60


title: 25L007985 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVEdeltaMyrist

description: Library name: 25L007985


title: 25L007983 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE

description: Library name: 25L007983

value: AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE


title: B6_P21_02

description:
Library name: Sample 12
SN49_P21


title: CD4 T cell, REV-Erbα WT, 24hr, Replicate 2

description:
Library name: 24hr_ αWT_Rep2
a_b_normalized_counts_DEseq2.csv

value: REV-ERBa+/+ (WT)


title: CD4 T cell, empty vector, 48hr, Replicate 2

description:
Library name: 48hr_EV_Rep2
normalized_counts_DEseq2.csv


title: HEK293T, Lantern-NES, 60min stress, Enrich, rep1

description:
Library name: Lantern-NES_60min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 60 min-NES_EN_rep1
HEK293T_SG_all_counts.xlsx

value: Lantern-HaloTag-NES

value: stimulation with 0.5 mM sodium arsenite for 60 min


title: 25L007984 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVEdeltaMyrist

description: Library name: 25L007984

value: brain

value: murine primary neurons

value: primary neuron

value: Supernatant


title: CD4 T cell, REV-Erbα KO, 24hr, Replicate 1

description:
Library name: 24hr_ αKO_Rep1
a_b_normalized_counts_DEseq2.csv

value: T Cells


title: HEK293T, Lantern-NES, 30min stress, Enrich, rep2

description:
Library name: Lantern-NES_30min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 30 min-NES_EN_rep2
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 30 min


title: HEK293T, Lantern-NES, 60min stress, Enrich, rep2

description:
Library name: Lantern-NES_60min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 60 min-NES_EN_rep2
HEK293T_SG_all_counts.xlsx


title: 25L007982 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE

description: Library name: 25L007982

value: primary mouse cortical neurons


title: CD4 T cell, REV-Erbα WT, 24hr, Replicate 1

description:
Library name: 24hr_ αWT_Rep1
a_b_normalized_counts_DEseq2.csv

value: Primary


title: B6_P21_01

description:
Library name: Sample 11
SN41_P21


title: CD4 T cell, REV-Erbα KO, 0hr, Replicate 2

description:
Library name: Naïve_αKO_Rep2
a_b_normalized_counts_DEseq2.csv


title: B6_P14_02

description:
Library name: Sample 10
SN43_P14


title: HEK293T, Lantern-NES, 30min stress, Enrich, rep1

description:
Library name: Lantern-NES_30min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 30 min-NES_EN_rep1
HEK293T_SG_all_counts.xlsx

value: embryonic kidney cells


title: B6_P14_01

description:
Library name: Sample 9
SN37_P14

value: Anterior segment limbal tissue


title: CD4 T cell, REV-Erbα KO, 0hr, Replicate 1

description:
Library name: Naïve_αKO_Rep1
a_b_normalized_counts_DEseq2.csv


title: 25L007980 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE

description: Library name: 25L007980


title: HEK293T, Lantern-NES, 15min stress, Enrich, rep1

description:
Library name: Lantern-NES_15min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 15 min-NES_EN_rep1
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 15 min


title: HEK293T, Lantern-NES, 15min stress, Enrich, rep2

description:
Library name: Lantern-NES_15min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 15 min-NES_EN_rep2
HEK293T_SG_all_counts.xlsx


title: B6_P10_02

description:
Library name: Sample 8
SN35_P10

value: Wild-type


title: 25L007979 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE

description: Library name: 25L007979


title: CD4 T cell, REV-Erbα WT, 0hr, Replicate 2

description:
Library name: Naïve_αWT_Rep2
a_b_normalized_counts_DEseq2.csv

value: Th17 cell differentiation


title: B6_P10_01

description:
Library name: Sample 7
SN27_P10


title: 25L007981 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE

description: Library name: 25L007981

value: AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE


title: CD4 T cell, REV-Erbβ KO, 24hr, Replicate 2

description:
Library name: 24hr_ βKO_Rep2
a_b_normalized_counts_DEseq2.csv

value: REV-ERBb-/- (KO)


title: HEK293T, Lantern-NES, 10min stress, Enrich, rep2

description:
Library name: Lantern-NES_10min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 10 min-NES_EN_rep2
HEK293T_SG_all_counts.xlsx

value: Lantern-HaloTag-NES

value: stimulation with 0.5 mM sodium arsenite for 10 min


title: CD4 T cell, REV-Erbα WT, 0hr, Replicate 1

description:
Library name: Naïve_αWT_Rep1
a_b_normalized_counts_DEseq2.csv

value: REV-ERBa+/+ (WT)


title: B6_P6_02

description:
Library name: Sample 6
SN69_P6.5


title: HEK293T, Lantern-NES, 10min stress, Enrich, rep1

description:
Library name: Lantern-NES_10min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 10 min-NES_EN_rep1
HEK293T_SG_all_counts.xlsx


city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: Library name: Mouse_NeuronalCells_ufm1_KO_CTRL_Neuron_Rep2

data_processing:
Raw FASTQ files were preprocessed using Trim Galore with default settings to remove adapter sequences and low-quality bases. Trimmed reads were aligned using STAR in two-pass mode to improve splice junction detection. Transcript-level quantification was performed using Salmon with strand-specific settings, using the aligned BAM files as input.   Aligned BAM files were sorted and indexed using samtools75, and splice junction files from STAR were used as input for rMATS to identify differential alternative splicing events between control and anisomycin-treated samples. rMATS was run in paired-end mode for Arabidopsis and human samples and in single-end mode for mouse samples, with strand-specific orientation and the variable read length option enabled.
Assembly: For Arabidopsis, alignments were performed against a genome index generated using the TAIR10 primary assembly and the Ensembl Plants Release 56 GTF annotation. For human RKO, reads were aligned to the GRCh38 primary assembly using the GENCODE v45 annotation. For mouse, reads were aligned to the GRCm39 primary assembly using the Ensembl Release 112 annotation.
Supplementary files format and content: Bigwigs , normalised Bins per million  obtained from deeptools bamCoverage function with binsize set to 5 (similar to Transcripts per million)

source_name: Neuronal cell lines

extract_protocol:
Cytosolic and nuclear fractions from Arabidopsis and human RKO cells were homogenized and stored in TRIzol at −80 °C until further processing. RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research) according to the manufacturer’s instructions. Neuronal cell samples stored in 300 µL of DNA/RNA Shield were also kept at −80 °C until use. RNA from total cells of these samples was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research), following the recommended protocol. DNase I (NEB) treatment was performed during RNA isolation.
Polyadenylated mRNA was enriched from total RNA using oligo(dT) magnetic beads (NEBNext Poly(A) mRNA Magnetic Isolation Module), followed by strand-specific library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. All steps, including mRNA capture, first- and second-strand synthesis, end repair, adaptor ligation, and library amplification, were performed according to the manufacturer’s instructions. Library quality and fragment size distribution were assessed using an Agilent Fragment Analyzer.

value: Neuronal cell lines

value: ufm1 KO

value: DMSO


title: B6_P6_01

description:
Library name: Sample 5
SN17_P6.5


description: Library name: Mouse_NeuronalCells_ufm1_KO_CTRL_Neuron_Rep1


description: Library name: Mouse_NeuronalCells_ufm1_KO_ANS_Neuron_Rep2

value: Anisomycin


title: HEK293T, Lantern-NES, 5min stress, Enrich, rep2

description:
Library name: Lantern-NES_5min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 5 min-NES_EN_rep2
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 5 min


title: CD4 T cell, REV-Erbβ KO, 24hr, Replicate 1

description:
Library name: 24hr_ βKO_Rep1
a_b_normalized_counts_DEseq2.csv

value: T Cells


title: B6_P4_02

description:
Library name: Sample 4
SN25_P4.5


title: B6_P4_01

description:
Library name: Sample 3
SN21_P4.5


title: 25L007978 | AAV1 hSyn TetOn V9I + AAV1 Tre3G NTVE

description: Library name: 25L007978

value: brain

value: murine primary neurons

value: primary neuron

value: primary mouse cortical neurons

value: Supernatant


title: HEK293T, Lantern-NES, 5min stress, Enrich, rep1

description:
Library name: Lantern-NES_5min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 5 min-NES_EN_rep1
HEK293T_SG_all_counts.xlsx

value: embryonic kidney cells


title: HEK293T, Lantern-NES, unstressed, Enrich, rep2

description:
Library name: Lantern-NES_0min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 0 min-NES_EN_rep2
HEK293T_SG_all_counts.xlsx


description: Library name: Mouse_NeuronalCells_ufm1_KO_ANS_Neuron_Rep1


title: CD4 T cell, REV-Erbβ WT, 24hr, Replicate 2

description:
Library name: 24hr_ βWT_Rep2
a_b_normalized_counts_DEseq2.csv

value: Primary

value: REV-ERBb+/+ (WT)

value: Th17 cell differentiation


title: B6_P2_01

description:
Library name: Sample 1
SN57_P2.5

value: Anterior segment limbal tissue

value: Wild-type


title: CD4 T cell, REV-Erbβ KO, 0hr, Replicate 2

description:
Library name: Naïve_βKO_Rep2
a_b_normalized_counts_DEseq2.csv

value: REV-ERBb-/- (KO)


title: CD4 T cell, REV-Erbβ KO, 0hr, Replicate 1

description:
Library name: Naïve_βKO_Rep1
a_b_normalized_counts_DEseq2.csv


title: HEK293T, Lantern-NES, unstressed, Enrich, rep1

description:
Library name: Lantern-NES_0min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 0 min-NES_EN_rep1
HEK293T_SG_all_counts.xlsx

value: Lantern-HaloTag-NES


title: HEK293T, G3BP1-Lantern, 60min stress, Input, rep2

description:
Library name: G3BP1-Lantern_60min_IN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 60 min-G3BP1_IN_rep2
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 60 min


title: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep4

description: Library name: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep4

value: Neuronal cell lines

value: Wild type

value: DMSO


title: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep3

description: Library name: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep3


title: CD4 T cell, REV-Erbβ WT, 24hr, Replicate 1

description:
Library name: 24hr_ βWT_Rep1
a_b_normalized_counts_DEseq2.csv

value: T Cells


title: B6_P2_02

description:
Library name: Sample 2
SN63_P2.5


title: Aorta, OE_Pdk4_Saline, R3

city: Suzhou

first: You

last: Yu

state: Jiangsu province

address: No.178 Ganjiang Rd

department: Institute for Cardiovascular Science

institute: Soochow University

description:
Library name: Aorta_OE_Pdk4_Saline_R3
AAV_OE_Pdk4_Saline

data_processing:
High quality clean reads, reads were further filtered by fastp and aliged with the reference genome followed by standard pepline. Read count extraction and normalization were performed using default benchwork.
Assembly: GRCm39 (Genome Reference Consortium Mouse Reference 39), INSDC Assembly GCA_000001635.9, Jun 2020
Supplementary files format and content: Table.xlsx files include raw FPKM and Count values for each sample

source_name: Aorta

extract_protocol:
Total RNA was isolated from aorta tissues, and HAECs using RNA isolation reagent (Takara, 9108) according to the manufacturer’s protocol as described. 1 μg total RNA from every sample was subjected to library preparation.
The library was constructed by PolyA method according to the manufacturor's ptotocols.

value: Aorta

value: Saline


title: HEK293T, G3BP1-Lantern, 60min stress, Input, rep1

description:
Library name: G3BP1-Lantern_60min_IN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 60 min-G3BP1_IN_rep1
HEK293T_SG_all_counts.xlsx


title: CD4 T cell, REV-Erbβ WT, 0hr, Replicate 2

description:
Library name: Naïve_βWT_Rep2
a_b_normalized_counts_DEseq2.csv


title: Aorta, OE_Pdk4_Saline, R2

description:
Library name: Aorta_OE_Pdk4_Saline_R2
AAV_OE_Pdk4_Saline


title: CD4 T cell, REV-Erbβ WT, 0hr, Replicate 1

description:
Library name: Naïve_βWT_Rep1
a_b_normalized_counts_DEseq2.csv


title: TUBO cells (replicate 2)

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Library name: TUBO_rep2

data_processing:
Read quality was assessed using FastQC (version 0.11.9). Adapter sequences and low-quality bases (Q < 20) were trimmed from raw reads with BBDuk (version 38.92) and reads shorter than 35 bp post-trimming were discarded.
Trimmed reads were then aligned using STAR (version 2.7.9a) to the mouse reference genome (mm10).
Raw gene counts were generated in R 4.1.1 using the featureCounts function from the Rsubread package (version 2.8.1) and the Cell Ranger v3.0.0 gene annotation for mm10 mouse genome.
Assembly: mm10
Supplementary files format and content: Raw gene counts

source_name: TUBO

growth_protocol: Cells were cultured in DMEM/F12 with 10%FBS, 2% PS and 1% L-glutamine.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen); DNA was removed by DNase treatment.
RNA-seq libraries for deep-sequencing were prepared with TruSeq Stranded mRNA (Illumina)

value: TUBO

value: Breast cancer cells

value: None, 2D cultures on plastics


title: Aorta, OE_Pdk4_Saline, R1

description:
Library name: Aorta_OE_Pdk4_Saline_R1
AAV_OE_Pdk4_Saline


title: HEK293T, G3BP1-Lantern, 60min stress, Enrich, rep2

description:
Library name: G3BP1-Lantern_60min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 60 min-G3BP1_EN_rep2
HEK293T_SG_all_counts.xlsx

value: embryonic kidney cells


title: Mouse_NeuronalCells_WT_ANS_Neuron_Rep4

description: Library name: Mouse_NeuronalCells_WT_ANS_Neuron_Rep4

value: Anisomycin


title: HEK293T, G3BP1-Lantern, 60min stress, Enrich, rep1

description:
Library name: G3BP1-Lantern_60min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 60 min-G3BP1_EN_rep1
HEK293T_SG_all_counts.xlsx


title: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep1

description: Library name: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep1


title: TUBO cells (replicate 1)

description: Library name: TUBO_rep1


title: HEK293T, G3BP1-Lantern, 30min stress, Input, rep1

description:
Library name: G3BP1-Lantern_30min_IN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 30 min-G3BP1_IN_rep1
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 30 min


title: Aorta, OE_Pdk4_BAPN, R2

description:
Library name: Aorta_OE_Pdk4_BAPN_R2
AAV_OE_Pdk4_BAPN

value: BAPN


title: Aorta, OE_Pdk4_BAPN, R3

description:
Library name: Aorta_OE_Pdk4_BAPN_R3
AAV_OE_Pdk4_BAPN


title: HEK293T, G3BP1-Lantern, 30min stress, Input, rep2

description:
Library name: G3BP1-Lantern_30min_IN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 30 min-G3BP1_IN_rep2
HEK293T_SG_all_counts.xlsx


title: Mouse_NeuronalCells_WT_ANS_Neuron_Rep2

description: Library name: Mouse_NeuronalCells_WT_ANS_Neuron_Rep2


title: Aorta, OE_Pdk4_BAPN, R1

description:
Library name: Aorta_OE_Pdk4_BAPN_R1
AAV_OE_Pdk4_BAPN


title: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep2

description: Library name: Mouse_NeuronalCells_WT_CTRL_Neuron_Rep2


title: Mouse_NeuronalCells_WT_ANS_Neuron_Rep3

description: Library name: Mouse_NeuronalCells_WT_ANS_Neuron_Rep3


title: Aorta, OE_CTR_BAPN, R3

description:
Library name: Aorta_OE_CTR_BAPN_R3
AAV_OE_Control_BAPN

value: CTR


title: 4T1 ETV4 KO + FGF (rep 3)

description: Library name: 4T1-3D-sgETV4-C39-+FGF-n3

data_processing:
Read quality was assessed using FastQC (version 0.11.9). Adapter sequences and low-quality bases (Q < 20) were trimmed from raw reads with BBDuk (version 38.92) and reads shorter than 35 bp post-trimming were discarded.
Trimmed reads were then aligned using STAR (version 2.7.9a) to the human reference genome (hg38).
Raw gene counts were generated in R 4.1.1 using the featureCounts function from the Rsubread package (version 2.8.1) with gene annotation provided by GENCODE v44 for hg38 human genome.
Assembly: mm10
Supplementary files format and content: Raw gene counts

growth_protocol: Cells were cultured in DMEM/F12 with 2%FBS, 2% PS and 1% L-glutamine.

extract_protocol:
For harvesting of the 3D cultures, collagen 1 gels were washed once with HBSS and digested with 1ml collagenase I at 300U/ml for 10 minutes at 37°C. After 10 minutes, mechanical disruption of the gels was performed by pipetting. Additional 5 minutes incubation at 37°C was performed. The suspension was then washed with HBSS by centrifugation and cell pellet was frozen at -80°C. RNA extraction was performed using RNeasy Mini Kit (Qiagen); DNA was removed by DNase treatment.
RNA-seq libraries for deep-sequencing were prepared with TruSeq Stranded mRNA (Illumina)

treatment_protocol: Nucleofection was carried out  with the SE-kit (Lonza) using Nucleofector (Lonza) following manufacturer’s instructions. For 3D cell cultures, cells  were resuspended at 100,000 cells/ml in collagen1 at 1.2 or 2.4 mg/ml. 80 ul droplets were let to jellify for 30 minutes at 37°C in 24 well Ultra Low Attachment plates. Culture media was then added to the wells. For FGF experiments, after seeding, cells were cultured in 10% FBS containing FGF10 at 25ng/ml (Peprotech, 100-26) and basic FGF (FGF2) at 40ng/ml (Peprotech, 100-18). The next day, cells were washed twice in FBS free medium and grown in 2% FBS containing FGF10 and FGF2 for 4 days. Medium change with fresh FGF supplementation was performed every 2 days.

value: Knockout of ETV4 nucleofected with Cas9 and gene-specific sgRNA sequences, 2% serum 3D Collagen I cultures, plusFGF


title: salmonella exposed to tyramine 10 minutes rep 3

city: Rehovot

first: Erez

last: Mills

address: Hertzel 229

country: Israel

institute: The Hebrew University

description: Library name: pool3_TYRAMINE.fastq.gz

library_source: other

data_processing:
quality check using fastqc
Cutadapt v4.7 (py-cutadapt) (Martin, 2011) for adapter removal and quality filtering — trimming reads with Phred scores < 30 and lengths < 80 bp in pool1 and pool3 samples including combining R1 and r2 reads. For batch2 samples, R1 and R2 were not combined and are in seperated files as submitted.
Assembly: ASM2216v1
Supplementary files format and content: raw gene-level read counts

molecule: other

organism: Salmonella enterica

source_name: Salmonella enterica serovar Typhimurium stain SL14028

growth_protocol: Mills, E., Petersen, E., Kulasekara, B.R., Miller, S.I., 2015. A direct screen for c-di-GMP modulators reveals a Salmonella Typhimurium periplasmic ʟ-arginine–sensing pathway. Sci Signal 8, ra57–ra57. https://doi.org/10.1126/scisignal.aaa1796

extract_protocol:
Total RNA purification was performed using Norgen kits for the rapid purification of total RNA, including microRNA without the use of phenol (Norgen Biotek, Cat no. SKU 17200). Chemical and mechanical lysis was performed using 1mg/ml of lysozyme and vertexing as described in section 1E of the kit protocol, suitable for gram negative bacteria.
Avraham, R., Haseley, N., Fan, A., Bloom-Ackermann, Z., Livny, J., Hung, D.T., 2016. A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. Nat. Protoc. 11, 1477–1491. https://doi.org/10.1038/nprot.2016.090

treatment_protocol: Bacterial cultures were treated with one of the following compounds, each added at a final concentration as specified: Acetic acid (1 mM), propionic acid (400 µM), isobutyric acid (100 µM), glycine (20 µM), gamma aminobutyric acid (GABA, 25 µM), taurine (50 µM), cysteine (5 µg/mL or 41.3 µM), proline (20 µM), 5-oxoproline (10 mM), D-arabinose (50 µM), L-arabinose (50 µM), salicylic acid (400 µM), p-aminobenzoic acid (PABA, 4 µM), tyramine (100 µM), dopamine (500 µM), tyrosine (200 µM), tryptophan (100 µM), melatonin (2 µg/mL or 8.61 µM), and α-tocopherol (8 µM). Concentrations were chosen according to the literature to represent physiological concentrations. Double-distilled water (DDW) was used as the control treatment. Each treatment had 3 biological replicates. Compounds were administered in a 1:4 ratio (compound to bacterial culture), with a total final volume of 1 mL per sample. The exposure time for all treatments was 10 minutes. Exposure was done in a shaker incubator at 37C.


title: Mouse_NeuronalCells_WT_ANS_Neuron_Rep1

description: Library name: Mouse_NeuronalCells_WT_ANS_Neuron_Rep1


title: HEK293T, G3BP1-Lantern, 15min stress, Input, rep2

description:
Library name: G3BP1-Lantern_15min_IN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 15 min-G3BP1_IN_rep2
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 15 min


title: HEK293T, G3BP1-Lantern, 30min stress, Enrich, rep1

description:
Library name: G3BP1-Lantern_30min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 30 min-G3BP1_EN_rep1
HEK293T_SG_all_counts.xlsx


title: 4T1 ETV4 KO + FGF (rep 1)

description: Library name: 4T1-3D-sgETV4-C39-+FGF-n1


title: Aorta, OE_CTR_BAPN, R2

description:
Library name: Aorta_OE_CTR_BAPN_R2
AAV_OE_Control_BAPN


title: salmonella exposed to tyrosine 10 minutes rep 3

description: Library name: pool3_TYR.fastq.gz

value: Salmonella enterica serovar Typhimurium stain SL14028


title: HEK293T, G3BP1-Lantern, 30min stress, Enrich, rep2

description:
Library name: G3BP1-Lantern_30min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 30 min-G3BP1_EN_rep2
HEK293T_SG_all_counts.xlsx


title: 4T1 ETV4 KO + FGF (rep 2)

description: Library name: 4T1-3D-sgETV4-C39-+FGF-n2


title: 4T1 control + FGF (control, rep 3)

description: Library name: 4T1-3D-sgCTRL-+FGF-n3

value: Nucleofected with Cas9 and Control sgRNA sequences, 2% serum 3D Collagen I cultures, plus FGF


title: Aorta, OE_CTR_BAPN, R1

description:
Library name: Aorta_OE_CTR_BAPN_R1
AAV_OE_Control_BAPN


title: salmonella exposed to tryptophan 10 minutes rep 3

description: Library name: pool3_TRP.fastq.gz


title: HEK293T, G3BP1-Lantern, 15min stress, Input, rep1

description:
Library name: G3BP1-Lantern_15min_IN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 15 min-G3BP1_IN_rep1
HEK293T_SG_all_counts.xlsx


title: 4T1 control + FGF (control, rep 2)

description: Library name: 4T1-3D-sgCTRL-+FGF-n2


title: HEK293T, G3BP1-Lantern, 15min stress, Enrich, rep2

description:
Library name: G3BP1-Lantern_15min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 15 min-G3BP1_EN_rep2
HEK293T_SG_all_counts.xlsx


title: Aorta, OE_CTR_Saline, R3

description:
Library name: Aorta_OE_CTR_Saline_R3
AAV_OE_Control_Saline


title: 4T1 control + FGF (control, rep 1)

description: Library name: 4T1-3D-sgCTRL-+FGF-n1


title: Aorta, OE_CTR_Saline, R2

description:
Library name: Aorta_OE_CTR_Saline_R2
AAV_OE_Control_Saline


title: 4T1 ETV4 KO (rep 3)

description: Library name: 4T1-3D-sgETV4-C39-n3

value: Knockout of ETV4 nucleofected with Cas9 and gene-specific sgRNA sequences, 2% serum 3D Collagen I cultures


title: salmonella exposed to salicylic acid 10 minutes rep 3

description: Library name: pool3_SA.fastq.gz


title: Aorta, KD_CTR_BAPN, R3

description:
Library name: Aorta_KD_CTR_BAPN_R3
AAV_KD_Control_BAPN


title: salmonella exposed to proline 10 minutes rep 3

description: Library name: pool3_PRO.fastq.gz


title: Aorta, OE_CTR_Saline, R1

description:
Library name: Aorta_OE_CTR_Saline_R1
AAV_OE_Control_Saline


title: 4T1 ETV4 KO (rep 2)

description: Library name: 4T1-3D-sgETV4-C39-n2


title: HEK293T, G3BP1-Lantern, 10min stress, Input, rep2

description:
Library name: G3BP1-Lantern_10min_IN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 10 min-G3BP1_IN_rep2
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 10 min


title: HEK293T, G3BP1-Lantern, 10min stress, Input, rep1

description:
Library name: G3BP1-Lantern_10min_IN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 10 min-G3BP1_IN_rep1
HEK293T_SG_all_counts.xlsx


title: Aorta, KD_CTR_BAPN, R2

description:
Library name: Aorta_KD_CTR_BAPN_R2
AAV_KD_Control_BAPN


title: 4T1 control (control, rep 3)

description: Library name: 4T1-3D-sgCTRL-n3

value: Nucleofected with Cas9 and Control sgRNA sequences, 2% serum 3D Collagen I cultures


title: 4T1 ETV4 KO (rep 1)

description: Library name: 4T1-3D-sgETV4-C39-n1


title: salmonella exposed to propionic acid 10 minutes rep 3

description: Library name: pool3_poropionicacid.fastq.gz


title: HEK293T, G3BP1-Lantern, 10min stress, Enrich, rep2

description:
Library name: G3BP1-Lantern_10min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 10 min-G3BP1_EN_rep2
HEK293T_SG_all_counts.xlsx


title: salmonella exposed to PABA 10 minutes rep 3

description: Library name: pool3_PAMINOBENZOICACID.fastq.gz


title: HEK293T, G3BP1-Lantern, 10min stress, Enrich, rep1

description:
Library name: G3BP1-Lantern_10min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 10 min-G3BP1_EN_rep1
HEK293T_SG_all_counts.xlsx


title: salmonella exposed to l-arabinose  10 minutes rep 3

description: Library name: pool3_LARABINOSE.fastq.gz


title: salmonella exposed to melatonine  10 minutes rep 3

description: Library name: pool3_Melatonine.fastq.gz


title: salmonella exposed to tairine 10 minutes rep 3

description: Library name: pool3_TAURINE.fastq.gz


title: 4T1 control (control, rep 1)

description: Library name: 4T1-3D-sgCTRL-n1


title: Aorta, KD_CTR_Saline, R2

description:
Library name: Aorta_KD_CTR_Saline_R2
AAV_KD_Control_Saline

value: Aorta


title: 4T1 ETV4 KO (replicate 3)

description: Library name: 4T1-3D_c39_n3

treatment_protocol: Nucleofection was carried out  with the SE-kit (Lonza) using Nucleofector (Lonza) following manufacturer’s instructions. For 3D cell cultures, cells  were resuspended at 100,000 cells/ml in collagen1 at 1.2 or 2.4 mg/ml. 80 ul droplets were let to jellify for 30 minutes at 37°C in 24 well Ultra Low Attachment plates. Complete media was then added to the wells.

value: Knockout of ETV4 after nucleofection with Cas9 and gene-specific sgRNA sequences, 3D Collagen I cultures


title: Aorta, KD_CTR_Saline, R3

description:
Library name: Aorta_KD_CTR_Saline_R3
AAV_KD_Control_Saline

value: Saline


title: HEK293T, G3BP1-Lantern, 5min stress, Input, rep2

description:
Library name: G3BP1-Lantern_5min_IN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 5 min-G3BP1_IN_rep2
HEK293T_SG_all_counts.xlsx

value: stimulation with 0.5 mM sodium arsenite for 5 min


title: Aorta, KD_CTR_Saline, R1

description:
Library name: Aorta_KD_CTR_Saline_R1
AAV_KD_Control_Saline


title: HEK293T, G3BP1-Lantern, 15min stress, Enrich, rep1

description:
Library name: G3BP1-Lantern_15min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 15 min-G3BP1_EN_rep1
HEK293T_SG_all_counts.xlsx


title: HEK293T, G3BP1-Lantern, 5min stress, Enrich, rep2

description:
Library name: G3BP1-Lantern_5min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 5 min-G3BP1_EN_rep2
HEK293T_SG_all_counts.xlsx


title: 4T1 control (control, rep 2)

description: Library name: 4T1-3D-sgCTRL-n2

value: Breast cancer cells


title: Aorta, KD_CTR_BAPN, R1

description:
Library name: Aorta_KD_CTR_BAPN_R1
AAV_KD_Control_BAPN


title: salmonella exposed to glycine 10 minutes rep 3

description: Library name: pool3_glycine.fastq.gz


title: 4T1 ETV4 KO (replicate 1)

description: Library name: 4T1-3D_c39_n1


title: salmonella exposed to GABA  10 minutes rep 3

description: Library name: pool3_GABA.fastq.gz


title: Aorta, KD_Pdk4_BAPN, R3

description:
Library name: Aorta_KD_Pdk4_BAPN_R3
AAV_KD_Pdk4_BAPN


title: HEK293T, G3BP1-Lantern, 5min stress, Enrich, rep1

description:
Library name: G3BP1-Lantern_5min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 5 min-G3BP1_EN_rep1
HEK293T_SG_all_counts.xlsx

value: embryonic kidney cells


title: salmonella exposed to dopamine  10 minutes rep 3

description: Library name: pool3_dopamin.fastq.gz


title: HEK293T, G3BP1-Lantern, unstressed, Input, rep2

description:
Library name: G3BP1-Lantern_0min_IN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 0 min-G3BP1_IN_rep2
HEK293T_SG_all_counts.xlsx


title: 4T1 control (replicate 2)

description: Library name: 4T1-3D_sgCTRL_n2

value: Nucleofected with Cas9 and Control sgRNA sequences, 3D Collagen I cultures


title: HEK293T, G3BP1-Lantern, unstressed, Input, rep1

description:
Library name: G3BP1-Lantern_0min_IN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 0 min-G3BP1_IN_rep1
HEK293T_SG_all_counts.xlsx


title: 4T1 control (replicate 3)

description: Library name: 4T1-3D_sgCTRL_n3


title: Aorta, KD_Pdk4_BAPN, R1

description:
Library name: Aorta_KD_Pdk4_BAPN_R1
AAV_KD_Pdk4_BAPN


title: salmonella exposed to isobutyric  acid 10 minutes rep 3

description: Library name: pool3_isobutyricacid.fastq.gz


title: HEK293T, G3BP1-Lantern, unstressed, Enrich, rep2

description:
Library name: G3BP1-Lantern_0min_EN_rep2
Column name in HEK293T_SG_all_counts.xlsx: 0 min-G3BP1_EN_rep2
HEK293T_SG_all_counts.xlsx


title: salmonella exposed to d-arabinose  10 minutes rep 3

description: Library name: pool3_DARABINOSE.fastq.gz


title: 4T1 control (replicate 1)

description: Library name: 4T1-3D_sgCTRL_n1


title: salmonella exposed to cysteiene 10 minutes rep 3

description: Library name: pool3_CYS.fastq.gz


title: HEK293T, G3BP1-Lantern, unstressed, Enrich, rep1

description:
Library name: G3BP1-Lantern_0min_EN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 0 min-G3BP1_EN_rep1
HEK293T_SG_all_counts.xlsx


title: HEK293T, G3BP1-Lantern, 5min stress, Input, rep1

description:
Library name: G3BP1-Lantern_5min_IN_rep1
Column name in HEK293T_SG_all_counts.xlsx: 5 min-G3BP1_IN_rep1
HEK293T_SG_all_counts.xlsx


title: Aorta, KD_Pdk4_Saline, R2

description:
Library name: Aorta_KD_Pdk4_Saline_R2
AAV_KD_Pdk4_Saline


title: Aorta, KD_Pdk4_Saline, R3

description:
Library name: Aorta_KD_Pdk4_Saline_R3
AAV_KD_Pdk4_Saline


title: Aorta, KD_Pdk4_BAPN, R2

description:
Library name: Aorta_KD_Pdk4_BAPN_R2
AAV_KD_Pdk4_BAPN


title: 4T1 FGFR2 KO (replicate 3)

description: Library name: 4T1-3D-sgFGFR2-n3

value: Knockout of FGFR2 after nucleofection with Cas9 and gene-specific sgRNA sequences, 3D Collagen I cultures


title: 4T1 FGFR2 KO (replicate 2)

description: Library name: 4T1-3D-sgFGFR2-n2


title: salmonella exposed to ddw  10 minutes rep 3

description: Library name: pool3_ddw.fastq.gz


title: 4T1 ETV4 KO (replicate 2)

description: Library name: 4T1-3D_c39_n2


title: salmonella exposed to a-tocopherol  10 minutes rep 3

description: Library name: pool3_atocopherol.fastq.gz


title: salmonella exposed to acetic acid 10 minutes rep 3

description: Library name: pool3_ACETICACID.fastq.gz


title: HEK293T, ERM-Lantern, 1s irradiation, Input, rep2

description:
Library name: ERM-Lantern_1s_irradiation_IN_rep2
Column name in ERM_all_counts.xlsx: IN_rep2
ERM_all_counts.xlsx


title: 4T1 FGFR2 KO (replicate 1)

description: Library name: 4T1-3D-sgFGFR2-n1


title: Aorta, BAPN_Week4, R2

description:
Library name: Aorta_BAPN_Week4_R2
4-weeks of BAPN

value: BAPN

tag: time point


title: 4T1 control (control, replicate 3)

description: Library name: 4T1-3D-sgCTRL-n3


title: Aorta, BAPN_Week4, R3

description:
Library name: Aorta_BAPN_Week4_R3
4-weeks of BAPN


title: HEK293T, ERM-Lantern, 1s irradiation, Input, rep1

description:
Library name: ERM-Lantern_1s_irradiation_IN_rep1
Column name in ERM_all_counts.xlsx: IN_rep1
ERM_all_counts.xlsx


title: salmonella exposed to 5oxoproline 10 minutes rep 3

description: Library name: pool3_5oxoproline.fastq.gz


title: Aorta, BAPN_Week4, R1

description:
Library name: Aorta_BAPN_Week4_R1
4-weeks of BAPN


title: HEK293T, ERM-Lantern, 1s irradiation, Enrich, rep2

description:
Library name: ERM-Lantern_1s_irradiation_EN_rep2
Column name in ERM_all_counts.xlsx: EN_rep2
ERM_all_counts.xlsx


title: HEK293T, ERM-Lantern, 1s irradiation, Enrich, rep1

description:
Library name: ERM-Lantern_1s_irradiation_EN_rep1
Column name in ERM_all_counts.xlsx: EN_rep1
ERM_all_counts.xlsx


title: 4T1 control (control, replicate 2)

description: Library name: 4T1-3D-sgCTRL-n2


title: Aorta, KD_Pdk4_Saline, R1

description:
Library name: Aorta_KD_Pdk4_Saline_R1
AAV_KD_Pdk4_Saline


title: Aorta, BAPN_Week2, R3

description:
Library name: Aorta_BAPN_Week2_R3
2-weeks of BAPN


title: Aorta, BAPN_Week2, R2

description:
Library name: Aorta_BAPN_Week2_R2
2-weeks of BAPN


title: 4T1 control (control, replicate 1)

description: Library name: 4T1-3D-sgCTRL-n1


title: salmonella exposed to tryptophan 10 minutes

description: Library name: pool1_TRP.fastq.gz


title: Aorta, BAPN_Week2, R1

description:
Library name: Aorta_BAPN_Week2_R1
2-weeks of BAPN


title: HEK293T, ERM-Lantern, 1min irradiation, Input, rep2

description:
Library name: ERM-Lantern_1min_irradiation_IN_rep2
Column name in ERM_all_counts.xlsx: IN_rep2
ERM_all_counts.xlsx


title: salmonella exposed to tyrosine 10 minutes

description: Library name: pool1_TYR.fastq.gz


title: HEK293T, ERM-Lantern, 1min irradiation, Input, rep1

description:
Library name: ERM-Lantern_1min_irradiation_IN_rep1
Column name in ERM_all_counts.xlsx: IN_rep1
ERM_all_counts.xlsx


title: 4T1 ETV4 KO C2 3D rep2

data_processing:
Read quality was assessed using FastQC (version 0.11.9). Adapter sequences and low-quality bases (Q < 20) were trimmed from raw reads with BBDuk (version 38.92) and reads shorter than 35 bp post-trimming were discarded.
Trimmed reads were then aligned using STAR (version 2.7.9a) to the mouse reference (mm10).
Raw gene counts were generated in R 4.1.1 using the featureCounts function from the Rsubread package (version 2.8.1) and the Cell Ranger v3.0.0 gene annotation for mm10 mouse genome.
Assembly: mm10
Supplementary files format and content: Raw gene counts

extract_protocol:
2D cell cultures were collected using the RNeasy Mini Kit (Qiagen) for total RNA extraction. For harvesting of the 3D cultures, collagen 1 gels were washed once with HBSS and digested with 1ml collagenase I at 300U/ml for 10 minutes at 37°C. After 10 minutes, mechanical disruption of the gels was performed by pipetting. Additional 5 minutes incubation at 37°C was performed. The suspension was then washed with HBSS by centrifugation and cell pellet was frozen at -80°C. RNA extraction was performed using RNeasy Mini Kit (Qiagen); DNA was removed by DNase treatment.
RNA-seq libraries for deep-sequencing were prepared with TruSeq Stranded mRNA (Illumina)

treatment_protocol: Nucleofection was carried out  with the SE-kit (Lonza) using Nucleofector (Lonza) following manufacturer’s instructions.  2D cell cultures were carried out on cell-culture plastic wells. For 3D cell cultures, cells  were resuspended at 100,000 cells/ml in collagen1 at 1.2 or 2.4 mg/ml. 80 ul droplets were let to jellify for 30 minutes at 37°C in 24 well Ultra Low Attachment plates. Complete media was then added to the wells.

value: Etv4 knockout clone 2, obtained after selection of cells nucleofected with Cas9 and gene-specific sgRNA sequences, 3D Collagen I cultures


title: HEK293T, ERM-Lantern, 1min irradiation, Enrich, rep2

description:
Library name: ERM-Lantern_1min_irradiation_EN_rep2
Column name in ERM_all_counts.xlsx: EN_rep2
ERM_all_counts.xlsx


title: 4T1 ETV4 KO C2 3D rep1


title: Aorta, BAPN_Control, R3

description:
Library name: Aorta_BAPN_Control_R3
Control of BAPN groups

value: Control


title: salmonella exposed to tairine 10 minutes

description: Library name: pool1_TAURINE.fastq.gz


title: salmonella exposed to salicylic acid 10 minutes

description: Library name: pool1_SA.fastq.gz


title: 4T1 ETV4 KO C1 3D rep2

value: Etv4 knockout clone 1, obtained after selection of cells nucleofected with Cas9 and gene-specific sgRNA sequences, 3D Collagen I cultures


title: Aorta, BAPN_Control, R2

description:
Library name: Aorta_BAPN_Control_R2
Control of BAPN groups


title: salmonella exposed to proline 10 minutes

description: Library name: pool1_PRO.fastq.gz

value: Salmonella enterica serovar Typhimurium stain SL14028


title: Aorta, BAPN_Control, R1

description:
Library name: Aorta_BAPN_Control_R1
Control of BAPN groups


title: MCF7 MALAT1 ASO hypoxia input [TSA-seq]

city: Urbana

first: Prasanth

last: Kannanganattu

state: IL

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

description: Library name: Sample_12

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Assembly: hg38
Supplementary files format and content: BigWig format of SON TSA-DNA-seq data in 20 kb bins.
Library strategy: TSA-seq

growth_protocol: Cells were cultured at 37 degrees Celsius with 5% carbon dioxide.

extract_protocol:
DNA was extracted using phenol-chloroform-isoamyl alcohol.
Libraries were constructed using Illumina TruSeq ChIP Sample Prep Kit.

treatment_protocol: Hypoxia treatment was done by incubating the cells in 0.2% oxygen, 5% carbon dioxide chamber for 24 hours. Transient knockdown of MALAT1 was done using ASO.

value: Breast epithelial cell

value: MALAT1 ASO

value: Hypoxia

tag: antibody


title: 4T1 ETV4 KO C1 3D rep1


title: HEK293T, ERM-Lantern, 1min irradiation, Enrich, rep1

description:
Library name: ERM-Lantern_1min_irradiation_EN_rep1
Column name in ERM_all_counts.xlsx: EN_rep1
ERM_all_counts.xlsx


title: salmonella exposed to propionic acid 10 minutes

description: Library name: pool1_poropionicacid.fastq.gz


title: salmonella exposed to tyramine 10 minutes

description: Library name: pool1_TYRAMINE.fastq.gz


title: MCF7 MALAT1 ASO normoxia input [TSA-seq]

description: Library name: Sample_11

value: Normoxia


title: 4T1 CTRL 3D rep2

value: Pools of clones of cells nucleofected with Control sgRNA sequences, 3D Collagen I cultures


title: MCF7 Scramble ASO hypoxia input [TSA-seq]

description: Library name: Sample_10

value: Scramble ASO


title: salmonella exposed to PABA 10 minutes

description: Library name: pool1_PAMINOBENZOICACID.fastq.gz


title: Visium_P60_Brain_WT_rep2

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description: Library name: Sample 6

data_processing:
Generated libraries were sequenced on Illumina NovaSeq 6000
Sequenced reads were de-multiplexed and mapped to the mouse genome (mm10-2020-A) SpaceRanger (v1.3.1, 10x Genomics)
Outputs SpaceRanger were analyzed using Seurat.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 = filtered gene count matrix
Supplementary files format and content: .tif = visium image in tif used as input for space ranger
Supplementary files format and content: .png = high resolution visium image in png output of space ranger
Supplementary files format and content: Integrated_brain.rds = seurat object of integrated visium data
Library strategy: Spatial Transcriptomics

source_name: Brain

growth_protocol: Sample were obtained from P6, P12 and P60 mouse brain. The Comité Institutionnel des Bonnes Pratiques Animales en Recherche (CIBPAR) approved all the breeding colonies and experimental protocols.

extract_protocol:
Brains were simultaneously frozen and embedded in OCT for cryo-sectioning at 10uM thickness
Visium libraries were prepared with the Visium Spatial Gene Expression (GEX) and Tissue Optimization (TO) Slide & Rea-gent Kits according to the manufacturer’s protocol with recommended reagents (10X Genomics, 1000193 and 1000187).

value: Brain

tag: genetic modification

value: WT

tag: age


title: MCF7 Scramble ASO normoxia input [TSA-seq]

description: Library name: Sample_9


title: Visium_P60_Brain_WT_rep1

description: Library name: Sample 5


title: 4T1 ETV4 KO C2 2D rep2

value: Breast cancer cells

value: Etv4 knockout clone 2, obtained after selection of cells nucleofected with Cas9 and gene-specific sgRNA sequences, 2D cultures in plastics


title: Visium_P12_Brain_WT_rep2

description: Library name: Sample 4


title: salmonella exposed to l-arabinose  10 minutes

description: Library name: pool1_LARABINOSE.fastq.gz


title: MCF7 MALAT1 ASO hypoxia rep2 [TSA-seq]

description: Library name: Sample_8

value: SON


title: 4T1 ETV4 KO C2 2D rep1


title: FLEX-Pool2-Adult

description: Library name: FLEX-Pool2-Adult

data_processing:
Generated FLEX libraries were sequenced on an Illumina NovaSeq6000 S4, followed by de-multiplexing and mapping to the mouse transcriptome probe set (Chromium_Mouse_Transcriptome_Probe_Set_v1.1.1_GRCm39-2024-A) using CellRanger multi (pipeline version 9.0.1) (10x Genomics).
Further processing and analysis of the 12 scRNAseq dataset were performed using R (version 4.4.0).
Assembly: Chromium_Mouse_Transcriptome_Probe_Set_v1.1.1_GRCm39-2024-A
Supplementary files format and content: sample_filtered_feature_bc_matrix.h5 = filtered gene count matrix for specific sample in the pool
Supplementary files format and content: Multiplex_config.csv = description of samples in the pool
Supplementary files format and content: raw_feature_bc_matrix.h5 = raw unfiltered gene count matrix for all samples in the pool

growth_protocol: Sample were obtained from thalamus and cortical region of P6, P12 and P40 mouse brain. The Comité Institutionnel des Bonnes Pratiques Animales en Recherche (CIBPAR) approved all the breeding colonies and experimental protocols.

extract_protocol:
Brains were placed in a chilled brain slicer (WPI; rodent brain matrices acrylic) to obtain 1mm thickness of coronal brain sections. According to Allen brain atlas reference, isocortex and thalamic area were microdissected using microscalpel (WPI, 500250) under microscope in ice cold dissociation medium solution (DM; Hank’s balanced salt solution without calcium and magnesium (Thermofisher, 14175095), 10mM HEPES (Thermofisher, 15630080), 9mM MgCl2 (Fisher Scientific, AAJ61014EQE), 35mM D-glucose (Fisher Scientific, AAJ60067AK), pH=7,35). After slicing in little pieces, brains were enzymatically digested using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130-092-628) for 15 min in mix 1 and 10 min in mix 2 at 33°C. During the digestion process, tissues were homogenized two times by up and down pipetting. At the end of the digestion process, samples were put in the ice with DM solution and cell clusters were removed by filtration through prewetted 70um and centrifuge at 200g for 8 min at 4°C. To stop the enzymatic reactions, the pellet is resuspended in DM solution with 3mg of ovomucoid protease (Worthington, LK003182, resuspended in DM solution) and 300 units of DNAse1 (Worthington, LK003172, resuspended in DM solution). The myelin and the cell debris were removed by using the debris removal solution (Miltenyi Biotec, 130-109-398). After 10 min blocking at RT with 5ug/mL of CD16/CD32 Fc Block (eBiosciences, 16-0161-82), the cells were stained at RT for 20 min with APC anti mouse CD31 (BD Biosciences, 551262) and live/dead fixable Aqua dead (ThermoFisher Scientific, L34957) allowing the staining of dead cells. After staining process, the cell pellet is fixed between 16h and 20 hours at 4°C according to the manufacturer’s instructions (10x Genomics, Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit). After a washing step, the stained cells were resuspended with 2mM of EDTA and 0,04 % of BSA. The setting up of the gates and compensations were allowed with the unstained cells, the single positive staining, the Fluorescence Minus One (FMO) and the isotype control staining (APC Rat IgG2a, κ (BD Biosciences, 551139). After removing the dead cells and doublets, endothelial cells (CD31+) were sorted using a BD FACS Aria Fusion from 26 P6, 19 P12 and 39 2-month-old mice and stored at -80C in buffer.
Single-cell suspensions of fixed and sorted brain cells from P6, P12 and adult Thalamus and Cortex regions (12 datasets in total) were resuspended in PBS containing 0.04% ultra-pure BSA. Multiplexed libraries were prepared using the Chromium Next GEM Single Cell Fixed RNA Kit, Mouse Transcriptome, 4rxns x 4 BC (# 1000496, 10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. The target recovery for each sample was 10,000 cells.

tag: strain

value: Brain cells


title: MCF7 MALAT1 ASO hypoxia rep1 [TSA-seq]

description: Library name: Sample_7


title: MCF7 MALAT1 ASO normoxia rep2 [TSA-seq]

description: Library name: Sample_6


title: 4T1 CTRL 3D rep1


title: salmonella exposed to isobutyric  acid 10 minutes

description: Library name: pool1_isobutyricacid.fastq.gz


title: salmonella exposed to glycine 10 minutes

description: Library name: pool1_glycine.fastq.gz


title: 4T1 CTRL 2D rep2

value: Pools of clones of cells nucleofected with Control sgRNA sequences, 2D cultures in plastics


title: salmonella exposed to GABA  10 minutes

description: Library name: pool1_GABA.fastq.gz


title: salmonella exposed to melatonine  10 minutes

description: Library name: pool1_Melatonine.fastq.gz


title: MCF7 MALAT1 ASO normoxia rep1 [TSA-seq]

description: Library name: Sample_5


title: 4T1 ETV4 KO C1 2D rep1

value: Etv4 knockout clone 1, obtained after selection of cells nucleofected with Cas9 and gene-specific sgRNA sequences, 2D cultures in plastics


title: MCF7 Scramble ASO hypoxia rep2 [TSA-seq]

description: Library name: Sample_4


title: salmonella exposed to ddw  10 minutes

description: Library name: pool1_ddw.fastq.gz


title: FLEX-Pool1-P6

description: Library name: FLEX-Pool1-P6


title: FLEX-Pool1-P12

description: Library name: Pool3-CTX-THAL


title: salmonella exposed to dopamine  10 minutes

description: Library name: pool1_dopamin.fastq.gz


title: 4T1 ETV4 KO C1 2D rep2


title: Visium_P6_Brain_WT_rep2

description: Library name: Sample 3


title: HLCS4

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description: Library name: Sample 24

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm39/mm39) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Assembly: GRCm39/mm39
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: all_compare copy.txt includes the differential analysis results of all genes and all comparisions Tab-delimited text file.

source_name: Liver

growth_protocol: Mice were housed in ventilated racks and fed a standard chow diet (5V75, Labdiets). Before sacrifice, mice were fasted for 4 hours with water provided ad libitum.

extract_protocol:
Tissues were homogenized in Trizol (Invitrogen) and processed according to manufacturer protocol. Total RNA was precipitated with isopropanol, pellet was washed twice in ethanol, and RNA was resuspended in RNAse-free water. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc.
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

treatment_protocol: ERT2 mice were injected with 125mg/kg tamoxifen five times over the course of 7 days at 5 weeks of age to induce full body knockout. iCre mice were retro-orbitally injected with 2×10^11 genome copies of iCre-AAV8 (VB1724, Vector Biolabs) driven by the TBG promoter.

value: Liver

value: Hlcs ff


title: 4T1 CTRL 2D rep1


title: salmonella exposed to d-arabinose  10 minutes

description: Library name: pool1_DARABINOSE.fastq.gz

value: Salmonella enterica serovar Typhimurium stain SL14028


title: MCF7 Scramble ASO normoxia rep2 [TSA-seq]

description: Library name: Sample_2

value: Breast epithelial cell


title: HLCS2

description: Library name: Sample 22


title: HLCS3

description: Library name: Sample 23


title: Frontal cortex, CORT+DFP+LPS, 24 h, CT_24h3

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

institute: University of Toronto Scarborough

description:
Library name: CT_24h3
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_24h_percent_methylation.tsv

data_processing:
Raw RRBS FASTQ files were processed as single-end reads. Adapters and low-quality bases were trimmed with Trim Galore! using RRBS mode (--rrbs), Phred quality cutoff 30, and FastQC was run on trimmed libraries.
After initial trimming, RRBS diversity adapters were removed using trimRRBSdiversityAdaptCustomers.py.
Trimmed single-end reads were aligned to the mouse reference genome GRCm38 (mm10) using Bismark with Bowtie2, and aligned BAM files were sorted with SAMtools.
Methylation levels for each CpG site were estimated in methylKit from the ratio of methylated to total reads at each locus; processed files are tissue-specific CpG-level percent methylation matrices for CORT+DFP+Saline, 6 h baseline controls versus CORT+DFP+LPS comparisons at 6 h, 12 h, and 24 h.
Differential methylation in the study was assessed using methylKit logistic regression with minimum 10x coverage in every sample, at least 5% methylation difference, and FDR-adjusted p < 0.05.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data files are unfiltered TSV tables containing genomic coordinates (chr, start, end, strand) followed by sample-specific percent methylation values. These files are not restricted to statistically significant differentially methylated CpGs.
Supplementary files format and content: Nine processed files are included: Blood_Con_6h_percent_methylation.tsv, Blood_Con_12h_percent_methylation.tsv, Blood_Con_24h_percent_methylation.tsv, HPC_Con_6h_percent_methylation.tsv, HPC_Con_12h_percent_methylation.tsv, HPC_Con_24h_percent_methylation.tsv, CTX_Con_6h_percent_methylation.tsv, CTX_Con_12h_percent_methylation.tsv, and CTX_Con_24h_percent_methylation.tsv.

source_name: Frontal cortex

growth_protocol: Adult male C57BL/6J mice (8-12 weeks old, approximately 30 g) were obtained from Jackson Laboratory and housed individually under controlled temperature and humidity on a 12 h light/12 h dark cycle with ad libitum access to food and water.

extract_protocol:
Genomic DNA was extracted from whole blood and dissected brain tissues using standard column-based purification methods; only high-quality DNA was used for RRBS library preparation.
RRBS libraries were prepared from 100 ng high-quality genomic DNA using the Ovation RRBS Methyl-Seq System (Tecan Genomics/NuGEN) according to the manufacturer's protocol, followed by bisulfite conversion and library amplification.

treatment_protocol: To model Gulf War Illness-related stress and toxicant exposure, mice received corticosterone (CORT; 200 mg/L in 0.6% ethanol) in the drinking water for 7 days, followed on day 8 by a single intraperitoneal injection of diisopropyl fluorophosphate (DFP; 4 mg/kg). Mice then received periodic CORT administration for 7 days every other week to a total of 5 weeks. On the final day, mice received either saline or lipopolysaccharide (LPS; 0.5 mg/kg, subcutaneous). Whole blood, hippocampus, and frontal cortex were collected 6 h, 12 h, or 24 h after challenge, depending on group.

value: Frontal cortex

value: wild type

value: CORT+DFP+LPS, 24 h


title: MCF7 Scramble ASO hypoxia rep1 [TSA-seq]

description: Library name: Sample_3

value: Hypoxia


title: MCF7 Scramble ASO normoxia rep1 [TSA-seq]

description: Library name: Sample_1

value: Scramble ASO

value: Normoxia


title: HLCS1

description: Library name: Sample 21


title: HEK293T MALAT1 ASO hypoxia input [eCLIP-seq]

description: Library name: Sample_24

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
eCLIP-seq reads were processed using the CLIP tool kit (CTK) pipeline.
Assembly: GRCh38
Supplementary files format and content: Annotated peaks in csv format.
Library strategy: eCLIP-seq

extract_protocol:
RNA was extracted using Trizol.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

value: Epithelial-like cell derived from human fetal kidney

value: MALAT1 ASO


title: PCCATAM4

description: Library name: Sample 20

value: PCCA ff; R26-CreERT2

value: Tamoxifen


title: Frontal cortex, CORT+DFP+LPS, 24 h, CT_24h1

description:
Library name: CT_24h1
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_24h_percent_methylation.tsv


title: HEK293T MALAT1 ASO normoxia input [eCLIP-seq]

description: Library name: Sample_23


title: HEK293T Scramble ASO hypoxia input [eCLIP-seq]

description: Library name: Sample_22


title: Frontal cortex, CORT+DFP+LPS, 12 h, CT_12h3

description:
Library name: CT_12h3
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_12h_percent_methylation.tsv

value: CORT+DFP+LPS, 12 h


title: salmonella exposed to cysteiene 10 minutes

description: Library name: pool1_CYS.fastq.gz


title: PCCATAM2

description: Library name: Sample 18


title: PCCATAM3

description: Library name: Sample 19


title: salmonella exposed to a-tocopherol  10 minutes

description: Library name: pool1_atocopherol.fastq.gz


title: PCCATAM1

description: Library name: Sample 17


title: Frontal cortex, CORT+DFP+LPS, 24 h, CT_24h2

description:
Library name: CT_24h2
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_24h_percent_methylation.tsv


title: HEK293T Scramble ASO normoxia input [eCLIP-seq]

description: Library name: Sample_21


title: Control

city: Shanghai

first: Xiangchen

last: Gu

address: 110 Ganhe Rd, Hongkou  Distrcit

department: Department of Nephrology

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

data_processing:
Raw sequencing data were processed using Cell Ranger v7.2.0 (10x Genomics). The steps included:
Demultiplexing: Sequencing reads were demultiplexed based on sample indices.
Alignment: Reads were aligned to the mouse reference genome (GRCm39) using the STAR aligner integrated within Cell Ranger.
Barcode and UMI Processing: Cellular barcodes and unique molecular identifiers (UMIs) were extracted to generate count matrices.
Alignment: Reads were aligned to the mouse reference genome (GRCm39) using the STAR aligner integrated within Cell Ranger.
Barcode and UMI Processing: Cellular barcodes and unique molecular identifiers (UMIs) were extracted to generate count matrices.
Gene Expression Quantification: UMI counts were aggregated to quantify gene expression levels for each cell.
Quality Control: Cells with mitochondrial gene content exceeding 50% or ribosomal gene content exceeding 40% were excluded. Cells expressing fewer than 200 genes and genes expressed in fewer than three cells were also filtered out.
Ambient RNA Correction: SoupX v1.6.0 was used to correct for ambient RNA contamination.
Doublet Detection: Potential doublets were identified and removed using scDblFinder v3.19.
Assembly: The genome build used for read alignment was the GRCm39 (Genome Reference Consortium Mouse Build 39) mouse genome assembly.
Supplementary files format and content: The processed data files are provided in standard formats compatible with common single-cell analysis tools

source_name: Kidney

extract_protocol:
Kidney tissues from control, AKI, and CKD phase mice were harvested and immediately processed to obtain single-cell suspensions. The kidneys were minced into small fragments and enzymatically digested using a cocktail of enzymes, including collagenase type IV and DNase I, at 37°C with gentle agitation for 30 minutes. The resulting cell suspension was filtered through a 40 μm cell strainer to remove debris and obtain a uniform single-cell suspension. Cells were then washed with PBS containing 0.04% BSA and counted using a hemocytometer to ensure viability above 85% before proceeding to library preparation.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics) according to the manufacturer's protocol.
The library strategy employed was single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium platform.

value: Kidney

value: Wild-Type


title: AAI injection induced CKD model sample 2


title: Frontal cortex, CORT+DFP+LPS, 12 h, CT_12h2

description:
Library name: CT_12h2
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_12h_percent_methylation.tsv


title: Frontal cortex, CORT+DFP+LPS, 24 h, CT_24h4

description:
Library name: CT_24h4
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_24h_percent_methylation.tsv


title: HEK293T MALAT1 ASO hypoxia rep2 [eCLIP-seq]

description: Library name: Sample_20


title: ffvill4

description: Library name: Sample 16

value: Liver

value: PCCA ff; Villin-Cre

value: Villin-Cre


title: AAI injection induced CKD model sample 1


title: Frontal cortex, CORT+DFP+LPS, 12 h, CT_12h1

description:
Library name: CT_12h1
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_12h_percent_methylation.tsv


title: HEK293T MALAT1 ASO hypoxia rep1 [eCLIP-seq]

description: Library name: Sample_19


title: salmonella exposed to acetic acid 10 minutes

description: Library name: pool1_ACETICACID.fastq.gz

value: Salmonella enterica serovar Typhimurium stain SL14028


title: ffvill3

description: Library name: Sample 15


title: Frontal cortex, CORT+DFP+LPS, 6 h, CT_6h4

description:
Library name: CT_6h4
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv

value: Frontal cortex

value: CORT+DFP+LPS, 6 h


title: AAI injection induced AKI model sample 2


title: Frontal cortex, CORT+DFP+LPS, 6 h, CT_6h3

description:
Library name: CT_6h3
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv

value: wild type


title: ffvill2

description: Library name: Sample 14


title: HEK293T MALAT1 ASO normoxia rep1 [eCLIP-seq]

description: Library name: Sample_17


title: salmonella exposed to 5oxoproline 10 minutes

description: Library name: pool1_5oxoproline.fastq.gz


title: AKI phase Sample 1


title: HEK293T MALAT1 ASO normoxia rep2 [eCLIP-seq]

description: Library name: Sample_18


title: Frontal cortex, CORT+DFP+LPS, 6 h, CT_6h2

description:
Library name: CT_6h2
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv


title: ffvill1

description: Library name: Sample 13


title: rCN, Wild type, 3h stress, Enrich, rep3

description:
Library name: rCN_WildType_rep3
Column name in rCN_SG_all_counts.xlsx: WildType_EN_rep3
rCN_SG_all_counts.xlsx

organism: Rattus norvegicus

source_name: primary cortical neurons

value: primary cortical neurons

value: WT

value: stimulation with 0.25 mM sodium arsenite for 3 hour


title: Frontal cortex, CORT+DFP+LPS, 6 h, CT_6h1

description:
Library name: CT_6h1
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv


title: rCN, Wild type, 3h stress, Enrich, rep2

description:
Library name: rCN_WildType_rep2
Column name in rCN_SG_all_counts.xlsx: WildType_EN_rep2
rCN_SG_all_counts.xlsx


title: ffffiCre3

description: Library name: Sample 11

value: PCCA ff; Pcx ff


title: HEK293T Scramble ASO hypoxia rep1 [eCLIP-seq]

description: Library name: Sample_15

value: Epithelial-like cell derived from human fetal kidney

value: Scramble ASO

value: Hypoxia


title: HEK293T Scramble ASO normoxia rep2 [eCLIP-seq]

description: Library name: Sample_14

value: Normoxia


title: Frontal cortex, CORT+DFP+Saline, 6 h, CT_Con4

description:
Library name: CT_Con4
Reduced representation bisulfite sequencing of mouse frontal cortex DNA
CTX_Con_6h_percent_methylation.tsv

value: CORT+DFP+Saline, 6 h


title: ffffiCre2

description: Library name: Sample 10


title: T3-4T1

city: 郑州

first: yucheng

last: li

state: 河南省

address: 河南省郑州市金水区博学路街道金水东路156号

institute: Henan University of Chinese Medicine

description: Library name: T3-4T1

data_processing:
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols.
Assembly: GRCH38
Supplementary files format and content: The text arranged in tabular form contains the raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Use TRIzol (thermofisher, 15596018) to isolate and purify total sample RNA according to the manufacturer's protocol.

value: mouse mammary carcinoma cell line

value: corticosterone-treated


title: T1-4T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: T1-4T1


title: ffffiCre1

description: Library name: Sample 9

value: Liver


title: rCN, Lantern-NES, 3h stress, Enrich, rep1

description:
Library name: rCN_Lantern-NES_rep1
Column name in rCN_SG_all_counts.xlsx: NES_EN_rep1
rCN_SG_all_counts.xlsx

value: Lantern-NES


title: rCN, Lantern-NES, 3h stress, Enrich, rep3

description:
Library name: rCN_Lantern-NES_rep3
Column name in rCN_SG_all_counts.xlsx: NES_EN_rep3
rCN_SG_all_counts.xlsx


title: T2-4T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: T2-4T1


title: ffffiCre4

description: Library name: Sample 12


title: MCF7 MALAT1 ASO hypoxia input [eCLIP-seq]

description: Library name: Sample_12

value: Breast epithelial cell

value: MALAT1 ASO


title: MCF7 MALAT1 ASO normoxia input [eCLIP-seq]

description: Library name: Sample_11


title: ffiCre4

description: Library name: Sample 8

value: PCCA ff


title: HEK293T Scramble ASO normoxia rep1 [eCLIP-seq]

description: Library name: Sample_13


title: HEK293T Scramble ASO hypoxia rep2 [eCLIP-seq]

description: Library name: Sample_16


title: rCN, Wild type, 3h stress, Enrich, rep1

description:
Library name: rCN_WildType_rep1
Column name in rCN_SG_all_counts.xlsx: WildType_EN_rep1
rCN_SG_all_counts.xlsx


title: NC3-4T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: NC3-4T1

value: control


title: ffiCre3

description: Library name: Sample 7


title: rCN, G3BP1-Lantern, 3h stress, Input, rep2

description:
Library name: rCN_G3BP1-Lantern_IN_rep2
Column name in rCN_SG_all_counts.xlsx: G3BP1_IN_rep2
rCN_SG_all_counts.xlsx

value: primary cortical neurons


title: MCF7 Scramble ASO normoxia input [eCLIP-seq]

description: Library name: Sample_9


title: rCN, G3BP1-Lantern, 3h stress, Input, rep1

description:
Library name: rCN_G3BP1-Lantern_IN_rep1
Column name in rCN_SG_all_counts.xlsx: G3BP1_IN_rep1
rCN_SG_all_counts.xlsx


title: MCF7 Scramble ASO hypoxia input [eCLIP-seq]

description: Library name: Sample_10


title: NC1-4T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: NC1-4T1


title: ffiCre1

description: Library name: Sample 5


title: rCN, G3BP1-Lantern, 3h stress, Enrich, rep2

description:
Library name: rCN_G3BP1-Lantern_EN_rep2
Column name in rCN_SG_all_counts.xlsx: G3BP1_EN_rep2
rCN_SG_all_counts.xlsx


title: MCF7 MALAT1 ASO hypoxia rep2 [eCLIP-seq]

description: Library name: Sample_8


title: S2W-Cre-HSC-3

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

description: Library name: SAMPLES6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence / low - quality sequence using CLC genomic benchwork ( parameter - Quality limit :0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork ( parameters - mismath cost :2 insertion cost :3 deletion cost :3 length fraction :0.8 similarity fraction :0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: hg38
Supplementary files format and content: tab - delimited text file includes raw counts for each Sample
Supplementary files format and content: Csv files include FPKM values for each Sample

source_name: Primary hepatic stellate cells

growth_protocol: BucheΔHep mice were housed in a room at 25℃ with a 12-hour lingh/dark cycle and understricted access to chow food and water

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

value: Primary hepatic stellate cells

value: BucheHep

value: CCl4 treatment


title: ffGFP4

description: Library name: Sample 4


title: rCN, Lantern-NES, 3h stress, Enrich, rep2

description:
Library name: rCN_Lantern-NES_rep2
Column name in rCN_SG_all_counts.xlsx: NES_EN_rep2
rCN_SG_all_counts.xlsx

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (For subcellular transcriptome data, adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; for cancer cell migration study, adaptor1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, adaptor2=CTGTCTCTTATACACATCTGACGCTGCCGACGA; other parameters: -q 20 -O 3 -m 20).
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38), Rnor_6.0, GRCm39
Supplementary files format and content: Excel tables include raw counts for each sample.

extract_protocol:
For the profiling of subcellular transcriptomes, cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. For identifying G3BP1-proximal and OMM-proximal RNAs in the HEK293T cells, rRNAs were removed with Ribo-off rRNA Depletion Kit (Vazyme) following the manufacturer’s protocol. The purified RNAs were dissolved in 5 μL nuclease-free water. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. For the study of cancer cell migration, the sorted cells were used for pseudo-bulk RNA-sequencing library construction following the previously published Sherry2 protocol. Libraries constructed from polyA RNAs (OMM-proximal and G3BP1-proximal RNAs of HEK293T cells, and mRNAs of MC38 cells) were sequenced to a depth of 3 G raw base. And libraries constructed from total RNAs (ERM-proximal RNAs of HEK293T cells and G3BP1-proximal RNAs of rat cortical neurons) were sequenced to a depth of 15 G raw base.

value: stimulation with 0.25 mM sodium arsenite for 3 hour


title: NC2-4T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: NC2-4T1


title: rCN, G3BP1-Lantern, 3h stress, Enrich, rep1

description:
Library name: rCN_G3BP1-Lantern_EN_rep1
Column name in rCN_SG_all_counts.xlsx: G3BP1_EN_rep1
rCN_SG_all_counts.xlsx


title: S2W-Cre-HSC-2

description: Library name: SAMPLES5


title: S2W-Cre-HSC-1

description: Library name: SAMPLES4


title: ffiCre2

description: Library name: Sample 6


title: MCF7 MALAT1 ASO hypoxia rep1 [eCLIP-seq]

description: Library name: Sample_7


title: ffGFP1

description: Library name: Sample 1


title: ffGFP3

description: Library name: Sample 3


title: r201203

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl  and python scripts. In this step, clean data (clean reads) were obtained by  removing reads containing ploy-N, with 5’ adapter contaminants, without 3’  adapter or the insert tag, containing ploy A or T or G or C and low quality reads  from raw data.
To remove tags originating from protein-coding genes, repeat sequences, rRNA,  tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker,  Rfam database or those types of datas from the specified species itself.
Bowtie was used to align clean reads to the reference genome (rn6).
Mapped small RNA tags were used to look for known miRNA. miRBase20.0  was used as reference, and the modified software mirdeep2 (Friedlander et al., 2011).
The characteristics of hairpin structure of miRNA precursor can be used to predict  novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2  (Friedlander et al., 2011) were integrated to predict novel miRNA through  exploring the secondary structure, the Dicer cleavage site and the minimum free  energy of the small RNA tags unannotated in the former steps.
Assembly: rn6
Supplementary files format and content: miRNAs expression level was calculated as Transcripts Per Kilobase Million (TPM) to directly compare differences in gene expression between samples.

source_name: orbitofrontal cortex

extract_protocol:
Total RNA was isolated using the miRvana PARIS kit (AM1556) from Invitrogen according to the manufacturer's protocol.
Small-RNA sequencing was performed on three biological replicates per group by Novogene America (Sacramento, CA, USA). Total RNA was assessed for quality before library preparation and RNA Integrity Numbers (RIN) were ≥ 7 with 28S/18S ≥ 1.3. A total amount of 2 μg total RNA per sample was used as input material for the  small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations. PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA  fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: Adult male Sprague Dawley rats underwent a repeated mild injury of controlled cortical impact or sham surgery. Following acclimation to the animal facility, animals underwent three surgeries on days 1, 4 and 7 where they received controlled cortical impact at a velocity of 5m/s and depth of 2mm or sham surgery with no impact. On day 42, animals were euthanized and their brains  frozen in ice cold isopentane. Orbitofrontal cortex tissue was dissected from each animal on dry ice then RNA extraction proceeded.

value: Sprague Dawley

tag: Sex

value: male

value: adult

value: repeated mild controlled cortical impact

value: orbitofrontal cortex


title: ffGFP2

description: Library name: Sample 2


title: r201207


title: S2W-flox-HSC-2

description: Library name: SAMPLES2


title: r201208

value: sham surgery


title: MCF7 MALAT1 ASO normoxia rep1 [eCLIP-seq]

description: Library name: Sample_5

value: Normoxia


title: Sample 6_Cortico_3

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description: Library name: Sample 6

data_processing:
In brief, amplified cDNA samples were subjected to different quality control standards. RNA sample was used for library preparation using NEB Next Ultra RNA Library Prep Kit for Illumina.
Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, the insert size of the library was validated on an Agilent 2100 and quantified using quantitative qPCR.
Assembly: . Libraries were then sequenced on Illumina NovaSeq 6000 S4 flow cell with PE150 according to results from library quality control and expected data volume.
Supplementary files format and content: mm10
Supplementary files format and content: raw counts for each sample

source_name: Bone

growth_protocol: MC3T3-E1 Subclone four mouse preosteoblast cells were maintained in α-Minimum Essential Medium supplemented with nucleosides, 2 mM L-glutamine (Thermo Fisher, Cat. 22571038), and 10% FBS, with 100U/ml penicillin and 100 μg/ml streptomycin. Cells at passages 4 to 10 were seeded onto 12-well plates and cultured for 24 h. Osteogenic differentiation was initiated by culturing the cells in a medium containing 50 μg/ml ascorbic acid and 10 mM β-glycerophosphate for 6 days.

extract_protocol:
RNA was isolated using column method
RNA sample was used for library preparation using NEB Next Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were  subjected to treatment with 100 nM corticosterone for  24 h in the presence of calcitriol (10 nM).

value: Bone

value: differentiated

value: WT

value: Corticosterone

value: passage 6-12


title: r201205


title: MCF7 Scramble ASO hypoxia rep1 [eCLIP-seq]

description: Library name: Sample_3

value: Breast epithelial cell

value: Scramble ASO

value: Hypoxia


title: Sample 5_Cortico_2

description: Library name: Sample 5


title: MCF7 Scramble ASO normoxia rep2 [eCLIP-seq]

description: Library name: Sample_2


title: r201206


title: T786 PDXC, Carboplatin + RP-6306, 3

city: Montreal

first: Mark

last: Basik

address: 3755 Chem. de la Côte-Sainte-Catherine

institute: Lady Davis Institute

description: Library name: Sample 18

data_processing:
Raw RNA-seq reads (FASTQ) were aligned to the human genome hg19 (UCSC) using STAR aligner v2.7.10a with default parameters.
Resulting BAM files were sorted and indexed using samtools v1.17 to prepare for counting.
Assembly: hg19 (UCSC)
Supplementary files format and content: Gene-level counts were generated from sorted BAMs using htseq-count v0.13.5 with hg19 GTF annotation, mode=strict, and stranded=yes.
Supplementary files format and content: Raw counts were used for submission.

source_name: Triple-negative breast cancer tumor

extract_protocol:
RNA extraction was done by using the RNeasy Mini Kit (QIAGEN cat#74104) with RNase A (QIAGEN Cat # 19101 ) and DNase (Qiagen Cat # 79254) according to  the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the KAPA mRNA HyperPrep kit following manufacture's protocol

value: Triple-negative breast cancer tumor

value: Patient-derived xenograft cell

value: Carboplatin + RP-6306


title: Sample 4_Cortico_1

description: Library name: Sample 4


title: Sample 3_Ctrl_3

description: Library name: Sample 3

value: Vehicle


title: r201204

value: Sprague Dawley

value: male

value: adult


title: T786 PDXC, Carboplatin + RP-6306, 2

description: Library name: Sample 17


title: MCF7 MALAT1 ASO normoxia rep2 [eCLIP-seq]

description: Library name: Sample_6

value: MALAT1 ASO


title: T786 PDXC, Carboplatin + RP-6306, 1

description: Library name: Sample 16


title: MCF7 Scramble ASO normoxia rep1 [eCLIP-seq]

description: Library name: Sample_1

value: Normoxia


title: Sample 2_Ctrl_2

description: Library name: Sample 2

value: Bone


title: MCF7_T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: MCF7_T1

source_name: Michigan Cancer Foundation-7

value: Michigan Cancer Foundation-7

value: cancer cell

value: corticosterone-treated


title: HEK293T SRSF1 shRNA normoxia rep2

description:
Library name: Sample_38
SRSF1_sh3_nor3

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
RNA-seq reads were aligned to human reference genome GRCh38 assembly using STAR.
Raw gene counts were first analyzed by HTSEQ-Count.
Assembly: GRCh38
Supplementary files format and content: HTSeq gene count information in tab-separated tables for each set of experiments.

extract_protocol:
RNA was extracted using Trizol and cleaned up using Qiagen RNeasy column.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads.

treatment_protocol: Hypoxia treatment was done by incubating the cells in 0.2% oxygen, 5% carbon dioxide chamber for 24 hours. Transient knockdown of MALAT1 was done using ASO. Stable knockdown of SRSF1 was done using shRNA.

value: Epithelial-like cell derived from human fetal kidney

value: SRSF1 shRNA


title: S2W-flox-HSC-1

description: Library name: SAMPLES1

value: Primary hepatic stellate cells

value: BucheHep

value: CCl4 treatment


title: S2W-flox-HSC-3

description: Library name: SAMPLES3


title: T786 PDXC, Carboplatin + BAY1895344, 2

description: Library name: Sample 14

value: Triple-negative breast cancer tumor

value: Patient-derived xenograft cell

value: WT

value: Carboplatin + BAY1895344


title: MCF7_T3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: MCF7_T3


title: T786 PDXC, Carboplatin + BAY1895344, 3

description: Library name: Sample 15


title: Sample 1_Ctrl_1

description: Library name: Sample 1

value: differentiated

value: Vehicle

value: passage 6-12


title: MCF7_T2

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: MCF7_T2


title: HEK293T SRSF1 shRNA normoxia rep1

description:
Library name: Sample_37
SRSF1_sh3_nor2

value: Normoxia


title: dock8_ko4_d1

city: Bethesda

first: Philip

last: Murphy

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: Library name: A52

data_processing:
Reads were trimmed using Cutadapt v5.0
Reads were mapped using STAR 2.7.9a
Raw counts were generated using RSEM v1.3.3
Assembly: GRCm39/Gencode M36
Supplementary files format and content: Tab delimited raw counts

source_name: Tongue

growth_protocol: Wild-type (C57BL/6J) mice were purchased from Jackson Laboratory (Bar Harbor, ME). Dock8–/– mice44 and Dock8fl/fl mice46 were provided by Helen Su (NIAID/NIH). CD45.1 (Jackson stock #002014) and CD45.1/CD45.2 congenic mice were obtained through the NIAID Taconic Contract. LckCre and ItgaxCre (B6.Cg-Tg(Itgax-cre)1-1Reiz) mice were provided by Judith Mandl (McGill University). RorcCre mice were provided by Vanja Lazarevic (NIH/NCI). Dock8–/– mice were crossed with Act1–/– mice [provided by Ulrich Siebenlist (NIAID/NIH)])67 to generate Dock8+/– Act1+/-- mice which were then backcrossed to Dock8–/– mice to generate Dock8–/– Act1+/– mice. For all experiments, sex-matched female or male mice aged 8-14 weeks were used. Mice were maintained in individually ventilated cages under specific pathogen-free conditions at NIH. All experiments were performed according to guidelines set forth by the Guide for the Care and Use of Laboratory Animals under a protocol approved by the NIAID Animal Care and Use Committee (LCIM14E).

extract_protocol:
Qiagen Rneasy
TruSeq Stranded mRNA Prep

value: Tongue

value: KO


title: T786 PDXC, Carboplatin + BAY1895344, 1

description: Library name: Sample 13


title: dock8_ko2_d1

description: Library name: A50


title: dock8_ko1_d1

description: Library name: A49


title: HEK293T SRSF1 shRNA hypoxia rep2

description:
Library name: Sample_40
SRSF1_sh3_hyp3

value: Hypoxia


title: T786 PDXC, RP-6306, 3

description: Library name: Sample 12


title: HEK293T pLKO vector hypoxia rep1

description:
Library name: Sample_35
con_hyp2

value: Empty shRNA lentivirus


title: HEK293T pLKO vector hypoxia rep2

description:
Library name: Sample_36
con_hyp3

value: Epithelial-like cell derived from human fetal kidney


title: MCF7_NC1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: MCF7_NC1

value: Michigan Cancer Foundation-7

value: cancer cell

value: control


title: MCF7 Scramble ASO hypoxia rep2 [eCLIP-seq]

description: Library name: Sample_4

value: Breast epithelial cell

value: Scramble ASO


title: HEK293T pLKO vector normoxia rep2

description:
Library name: Sample_34
con_nor3


title: MCF7_NC2

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: MCF7_NC2


title: T786 PDXC, RP-6306, 1

description: Library name: Sample 10

value: Triple-negative breast cancer tumor

value: Patient-derived xenograft cell


title: dock8_wt3_d1

description: Library name: A47

value: WT


title: T786 PDXC, RP-6306, 2

description: Library name: Sample 11


title: dock8_wt4_d1

description: Library name: A48


title: MCF7_NC3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: MCF7_NC3


title: ID8 cells, T3_AW4, Day14

city: Seoul

first: Mahesh

middle: Chandra

last: Patra

state: 경기도

address: 241 Gangnam-daero

country: South Korea

institute: Arontier Co. Ltd

description:
Library name: Sample48
Column name in mRNA.count_data.txt: T3_AW4

data_processing:
Cutadapt → STAR (2-pass alignment) → HTSeq → TPM normalization → t-test DEG analysis
Assembly: Mus musculus reference genome (GRCm38.p6)
Supplementary files format and content: Tab delimited text files include raw counts and TPM-UQ values for each sample

source_name: Ovary Epithelium

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer's protocol. RNA concentration and purity were measured using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. Samples with RNA integrity number (RIN) ≥ 6.0 were used for library preparation.
RNA-seq libraries were prepared using a poly(A) mRNA enrichment strategy. Polyadenylated mRNA was isolated from total RNA using oligo(dT) magnetic beads. Purified mRNA was fragmented and reverse transcribed using random hexamer primers to generate first-strand cDNA, followed by second-strand synthesis. The resulting cDNA fragments were end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Libraries were amplified by PCR and purified prior to sequencing.

value: Ovary Epithelium

value: Surface epithelial cells

value: Anaesthesia + Wounding

tag: time


title: ID8 cells, T3_AW1, Day14

description:
Library name: Sample46
Column name in mRNA.count_data.txt: T3_AW1


title: T786 PDXC, BAY1895344, 3

description: Library name: Sample 9


title: ID8 cells, T3_AW3, Day14

description:
Library name: Sample47
Column name in mRNA.count_data.txt: T3_AW3


title: HEK293T pLKO vector normoxia rep1

description:
Library name: Sample_33
con_nor2

value: Normoxia


title: HEK293T SRSF1 shRNA hypoxia rep1

description:
Library name: Sample_39
SRSF1_sh3_hyp2

value: SRSF1 shRNA


title: HEK293T MALAT1 ASO hypoxia rep2

description:
Library name: Sample_32
ASO53_hyp3

value: MALAT1 ASO


title: dock8_wt1_d1

description: Library name: A45

value: Tongue


title: T786 PDXC, BAY1895344, 2

description: Library name: Sample 8


title: HEK293T MALAT1 ASO hypoxia rep1

description:
Library name: Sample_31
ASO53_hyp2

value: Hypoxia


title: MC38, "Near" cells, rep5

city: Beijing

first: Yuxin

last: Fang

address: Yiheyuan Road No.5

institute: Peking University

description:
Library name: MC38_Near_rep5
Column name in MC38_migration_all_counts.xlsx:Near5
MC38_migration_all_counts.xlsx

value: colorectal tumor cells

value: Lantern-TM


title: T786 PDXC, BAY1895344, 1

description: Library name: Sample 7


title: ID8 cells, T3_A8, Day14

description:
Library name: Sample45
Column name in mRNA.count_data.txt: T3_A8

value: Anaesthesia


title: T786 PDXC, Carboplatin, 3

description: Library name: Sample 6

value: Carboplatin


title: HEK293T MALAT1 ASO normoxia rep2

description:
Library name: Sample_30
ASO53_nor3

value: Epithelial-like cell derived from human fetal kidney


title: ID8 cells, T3_A6, Day14

description:
Library name: Sample44
Column name in mRNA.count_data.txt: T3_A6


title: ID8 cells, T3_A5, Day14

description:
Library name: Sample43
Column name in mRNA.count_data.txt: T3_A5


title: HEK293T MALAT1 ASO normoxia rep1

description:
Library name: Sample_29
ASO53_nor2


title: MC38, "Near" cells, rep3

description:
Library name: MC38_Near_rep3
Column name in MC38_migration_all_counts.xlsx:Near3
MC38_migration_all_counts.xlsx


title: ID8 cells, T3_A4, Day14

description:
Library name: Sample42
Column name in mRNA.count_data.txt: T3_A4


title: T786 PDXC, Carboplatin, 2

description: Library name: Sample 5


title: MC38, "Near" cells, rep2

description:
Library name: MC38_Near_rep2
Column name in MC38_migration_all_counts.xlsx:Near2
MC38_migration_all_counts.xlsx


title: HEK293T Scramble ASO hypoxia rep2

description:
Library name: Sample_28
con_hyp3

value: Scramble ASO


title: T786 PDXC, Carboplatin, 1

description: Library name: Sample 4

value: Triple-negative breast cancer tumor


title: MC38, "Near" cells, rep1

description:
Library name: MC38_Near_rep1
Column name in MC38_migration_all_counts.xlsx:Near1
MC38_migration_all_counts.xlsx


title: ID8 cells, T3_A3, Day14

description:
Library name: Sample41
Column name in mRNA.count_data.txt: T3_A3


title: ID8 cells, T3_A1, Day14

description:
Library name: Sample40
Column name in mRNA.count_data.txt: T3_A1


title: HEK293T Scramble ASO hypoxia rep1

description:
Library name: Sample_27
con_hyp2


title: MC38, "Far" cells, rep5

description:
Library name: MC38_Far_rep5
Column name in MC38_migration_all_counts.xlsx: Far5
MC38_migration_all_counts.xlsx