title: C2C12 cells, iMyoD1, 120 h serum starvation, <40 um myoblast-enriched fraction, untreated, RNA-seq biol rep 3

description:
Library name: C2C12_iMyoD1_120h_lt40um_noDox_RNAseq_biorep3
<40 um myoblast-enriched fraction

value: 120 h vehicle


title: VP-006-01, perilesional skin biopsy

status: Public on Jun 03 2026

type: SRA

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Library name: 16_VP_006_01_perilesioneel_H11

library_source: transcriptomic

data_processing:
Raw read QC was done using FastQC (v0.12.1)
Adapter and quality trimming was done using cutadapt (v5.0)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.11b)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.6)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1)
Assembly: Homo sapiens  GRCh38 (Ensembl release 112)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

molecule: total RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
The sampled tissue was lysed mechanically using a 1000 µL pipette tip, followed by shearing through a syringe (Terumo Corporation, Tokyo, Japan) fitted with a 20Gx1½ needle (Terumo Corporation). Total RNA was extracted using the conventional TriReagent/chloroform method and subsequently purified with the Direct-zol Microprep RNA Kit (Zymo Research), including on-column DNase I treatment, according to the manufacturer’s instructions. As residual genomic DNA was detected in some samples, an additional DNase treatment was performed using the TURBO DNA-free™ Kit (Invitrogen, Thermo Fisher Scientific) on all RNA extracts.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen)

tag: tissue

value: skin


title: Female_FCL_VEH_Adolescent c152

city: Binghamton

first: Anny

last: Gano

state: NY

address: 4400 Vestal Parkway East

country: USA

institute: SUNY Binghamton

description:
Library name: c152
column names are library name - c#, etc

data_processing:
Raw fastq files processed with fastp to remove adapter and low-quality reads, index built using Hisat2 v2.0.5, paired-end clean reads aligned to the genome.
Assembly: Rattus norvegicus, PPI Taxid: 10116, KEGG rno, ncbi_rattus_norvegicus_gcf_036323735_1_grc8
Supplementary files format and content: text file includes gene counts per sample
Supplementary files format and content: text file includes FPKM per sample as well

organism: Rattus norvegicus

source_name: brain (anterior cingulate cortex)

extract_protocol:
RNA was extracted using high-lipid extraction and RNA integrity was assessed using Bioanalyzer 2100 (Agilent Technologies, CA, USA) and purity via the Nanodrop, with all RIN values > 6.3 (except one 5.8), average = 7.2.
cDNA was synthesized using random hexamer primers, second strand synthesis using dTTP for non-strand-specific library construction.

value: brain (anterior cingulate cortex)

tag: genotype

value: Long Evans rat

tag: treatment

value: described in sample name

tag: batch


title: Male_PAE_VEH_Adolescent c151

description:
Library name: c151
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, <40 um myoblast-enriched fraction, untreated, RNA-seq biol rep 2

city: Berkeley

first: Oscar

last: Whitney

address: 1951 Oxford St

institute: UC Berkeley

description:
Library name: C2C12_iMyoD1_120h_lt40um_noDox_RNAseq_biorep2
<40 um myoblast-enriched fraction

data_processing:
core/RNAseq pipeline version 3.14.0
Assembly: mm10
Supplementary files format and content: tab-separated transcript-level estimated count matrices generated from Salmon quantification

molecule: polyA RNA

organism: Mus musculus

source_name: skeletal muscle

growth_protocol: C2C12 skeletal muscle myoblasts were maintained in DMEM supplemented with 20% fetal bovine serum, penicillin streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using TriZol following manufacturer protocols
polyA-mRNA enrichment was performed on extracted RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S). Extracted RNA was reverse transcribed following NEBNext Ultra II RNA Library Prep kit, following manufacturer protocol. Libraries were prepared following NEBNext Ultra II RNA Library Prep kit protocol

value: skeletal muscle

tag: cell line

tag: cell type

value: skeletal muscle myoblast-enriched fraction

value: endogenous MyoD1 + dox-inducible Halo-MyoD1


title: Female_FCL_AAE_Adolescent c150

description:
Library name: c150
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, <40 um myoblast-enriched fraction, untreated, RNA-seq biol rep 1

description:
Library name: C2C12_iMyoD1_120h_lt40um_noDox_RNAseq_biorep1
<40 um myoblast-enriched fraction


title: Male_PAE_AAE_Adolescent c149

description:
Library name: c149
column names are library name - c#, etc


title: Male_FCL_VEH_Adult c148

description:
Library name: c148
column names are library name - c#, etc


title: VP-005-01, healthy skin biopsy

description: Library name: 14_VP_005_01_gezond_F11


title: VP-007-01, lesional skin biopsy

description: Library name: 18_VP_007_01_lesioneel_B10


title: VP-005-01, perilesional skin biopsy

description: Library name: 13_VP_005_01_perilesioneel_E11


title: Female_PAE_VEH_Adult c147

description:
Library name: c147
column names are library name - c#, etc


title: Male_PF_AAE_Adult c145

description:
Library name: c145
column names are library name - c#, etc


title: VP-005-01, lesional skin biopsy

description: Library name: 12_VP_005_01_lesioneel_D11


title: Male_FCL_AAE_Adult c146

description:
Library name: c146
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, >40 um myotube-enriched fraction, dox treatment, RNA-seq biol rep 3

description:
Library name: C2C12_iMyoD1_120h_gt40um_plusDox_RNAseq_biorep3
>40 um myotube-enriched fraction

value: skeletal muscle myotube-enriched fraction

value: 120 h dox


title: C2C12 cells, iMyoD1, 120 h serum starvation, >40 um myotube-enriched fraction, dox treatment, RNA-seq biol rep 2

description:
Library name: C2C12_iMyoD1_120h_gt40um_plusDox_RNAseq_biorep2
>40 um myotube-enriched fraction


title: Female_PAE_VEH_Adolescent c144

description:
Library name: c144
column names are library name - c#, etc


title: VP-004-01, healthy skin biopsy

description: Library name: 11_VP_004_01_gezond_C11


title: Female_PAE_VEH_Adolescent c143

description:
Library name: c143
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, >40 um myotube-enriched fraction, dox treatment, RNA-seq biol rep 1

description:
Library name: C2C12_iMyoD1_120h_gt40um_plusDox_RNAseq_biorep1
>40 um myotube-enriched fraction


title: VP-004-01, perilesional skin biopsy

description: Library name: 10_VP_004_01_perilesioneel_B11


title: Male_PF_AAE_Adolescent c141

description:
Library name: c141
column names are library name - c#, etc


title: Male_FCL_VEH_Adolescent c140

description:
Library name: c140
column names are library name - c#, etc


title: VP-004-01, lesional skin biopsy

description: Library name: 9_VP_004_01_lesioneel_A11


title: C2C12 cells, iMyoD1, 120 h serum starvation, >40 um myotube-enriched fraction, untreated, RNA-seq biol rep 3

description:
Library name: C2C12_iMyoD1_120h_gt40um_noDox_RNAseq_biorep3
>40 um myotube-enriched fraction


title: Female_PAE_AAE_Adolescent c137

description:
Library name: c137
column names are library name - c#, etc


title: Male_PF_VEH_Adolescent c139

description:
Library name: c139
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, >40 um myotube-enriched fraction, untreated, RNA-seq biol rep 2

description:
Library name: C2C12_iMyoD1_120h_gt40um_noDox_RNAseq_biorep2
>40 um myotube-enriched fraction


title: VP-003-01, healthy skin biopsy

description: Library name: 8_VP_003_01_gezond_H12


title: Female_PAE_VEH_Adult c136

description:
Library name: c136
column names are library name - c#, etc


title: Male_FCL_AAE_Adult c165

description:
Library name: c165
column names are library name - c#, etc


title: Female_PF_VEH_Adult c135

description:
Library name: c135
column names are library name - c#, etc


title: C2C12 cells, iMyoD1, 120 h serum starvation, >40 um myotube-enriched fraction, untreated, RNA-seq biol rep 1

description:
Library name: C2C12_iMyoD1_120h_gt40um_noDox_RNAseq_biorep1
>40 um myotube-enriched fraction


title: VP-003-01, perilesional skin biopsy

description: Library name: 7_VP_003_01_perilesioneel_G12


title: Female_FCL_AAE_Adult c134

description:
Library name: c134
column names are library name - c#, etc


title: Male_FCL_AAE_Adult c133

description:
Library name: c133
column names are library name - c#, etc


title: C2C12 cells, iMcam, 48 h serum starvation, dox treatment, RNA-seq biol rep 3

description: Library name: C2C12_iMcam_48h_diff_plusDox_RNAseq_biorep3

value: skeletal muscle myoblast

value: inducible Mcam

value: 48 h dox


title: Male_PF_VEH_Adult c131

description:
Library name: c131
column names are library name - c#, etc


title: C2C12 cells, iMcam, 48 h serum starvation, dox treatment, RNA-seq biol rep 2

description: Library name: C2C12_iMcam_48h_diff_plusDox_RNAseq_biorep2


title: Female_PAE_AAE_Adult c129

description:
Library name: c129
column names are library name - c#, etc


title: VP-003-01, lesional skin biopsy

description: Library name: 6_VP_003_01_lesioneel_F12


title: VP-002-01, healthy skin biopsy

description: Library name: 5_VP_002_01_gezond_E12


title: Male_PF_AAE_Adult c128

description:
Library name: c128
column names are library name - c#, etc


title: Male_FCL_VEH_Adult c126

description:
Library name: c126
column names are library name - c#, etc


title: C2C12 cells, iMcam, 48 h serum starvation, dox treatment, RNA-seq biol rep 1

description: Library name: C2C12_iMcam_48h_diff_plusDox_RNAseq_biorep1


title: VP-002-01, perilesional skin biopsy

description: Library name: 4_VP_002_01_perilesioneel__D12


title: Female_FCL_VEH_Adult c127

description:
Library name: c127
column names are library name - c#, etc


title: Male_PF_VEH_Adult c120

description:
Library name: c120
column names are library name - c#, etc


title: VP-002-01, lesional skin biopsy

description: Library name: 3_VP_002_01_lesioneel__C12


title: Female_PAE_AAE_Adult c119

description:
Library name: c119
column names are library name - c#, etc


title: C2C12 cells, iMcam, 48 h serum starvation, untreated, RNA-seq biol rep 3

description: Library name: C2C12_iMcam_48h_diff_noDox_RNAseq_biorep3

value: 48 h vehicle


title: C2C12 cells, iMcam, 48 h serum starvation, untreated, RNA-seq biol rep 2

description: Library name: C2C12_iMcam_48h_diff_noDox_RNAseq_biorep2


title: Male_PF_VEH_Adolescent c116

description:
Library name: c116
column names are library name - c#, etc


title: Male_PF_VEH_Adult c118

description:
Library name: c118
column names are library name - c#, etc


title: VP-001, healthy skin biopsy

description: Library name: 2_VP_001_gezond_huid_B12


title: C2C12 cells, iMcam, 48 h serum starvation, untreated, RNA-seq biol rep 1

description: Library name: C2C12_iMcam_48h_diff_noDox_RNAseq_biorep1


title: Female_PF_VEH_Adolescent c115

description:
Library name: c115
column names are library name - c#, etc


title: VP-001, perilesional skin biopsy

description: Library name: 1_VP_001_perilesioneel_huid_A12


title: Female_PAE_AAE_Adolescent c114

description:
Library name: c114
column names are library name - c#, etc


title: Male_FCL_AAE_Adolescent c113

description:
Library name: c113
column names are library name - c#, etc


title: C2C12 cells, iCdh23, 48 h serum starvation, dox treatment, RNA-seq biol rep 3

description: Library name: C2C12_iCdh23_48h_diff_plusDox_RNAseq_biorep3

value: inducible Cdh23


title: Male_PF_VEH_Adult c112

description:
Library name: c112
column names are library name - c#, etc


title: U138 42C RF plus RT 24h replicate 3

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description:
Library name: U_RFRT_7_11_24
U138 glioblastoma cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

data_processing:
RNA-Seq reads were mapped to human reference genome GRCh38.p7 (GENCODE release 25 genome annotation) with STAR (version 2.7.3a) using the following parameters --outFileNamePrefix mapping/star/all_mates/U_AMRF_03_08_0/out/ --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Reads were assigned to genes with FeatureCounts (v2.0.6) using the following parameters  -t exon -g gene_id   -s 2 -p (with GENCODE relase 25, GRCh38 annotation gft file)
Assembly: GRCh38.p7
Supplementary files format and content: Comma separated count matrix with Featurecounts output for all samples

source_name: brain

extract_protocol:
Total RNA was isolated using the RNA extraction kit from Roboklon (Berlin, Germany) according to the manufacturer's instructions. For 0 h samples, cells were pelleted immediately after treatment, washed with PBS, and stored at -80°C. For 24 h samples, cells were re-seeded in 10 cm petri dishes and incubated for 24 hours at 37°C with 5% CO2 before RNA extraction. RNA quality and quantity were assessed using a NanoDrop 2000/2000c spectrophotometer (Peqlab).
RNA-seq libraries were prepared from extracted total RNA using a stranded poly(A)-selected library preparation protocol. Briefly, poly(A)+ RNA was enriched, fragmented, reverse-transcribed into cDNA, adapter-ligated, PCR-amplified, and quality controlled prior to sequencing.

value: brain

value: glioblastoma

value: wild type

value: 42C radiofrequency plus 8Gy gamma-radiation 24h


title: Female_PAE_VEH_Adult c111

description:
Library name: c111
column names are library name - c#, etc

value: brain (anterior cingulate cortex)


title: C2C12 cells, iCdh23, 48 h serum starvation, dox treatment, RNA-seq biol rep 2

description: Library name: C2C12_iCdh23_48h_diff_plusDox_RNAseq_biorep2


title: U138 42C RF plus RT 0h replicate 3

description:
Library name: U_RFRT_7_11_0
U138 glioblastoma cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: 42C radiofrequency plus 8Gy gamma-radiation 0h


title: Male_PF_AAE_Adult c110

description:
Library name: c110
column names are library name - c#, etc

value: Long Evans rat

value: described in sample name


title: Male_PAE_AAE_Adult c109

description:
Library name: c109
column names are library name - c#, etc


title: Male_PAE_VEH_Adolescent c108

description:
Library name: c108
column names are library name - c#, etc


title: C2C12 cells, iCdh23, 48 h serum starvation, dox treatment, RNA-seq biol rep 1

description: Library name: C2C12_iCdh23_48h_diff_plusDox_RNAseq_biorep1

value: skeletal muscle


title: Male_PAE_VEH_Adolescent c107

description:
Library name: c107
column names are library name - c#, etc


title: U138 42C RF plus RT 24h replicate 2

description:
Library name: U_RFRT_23_01_24
U138 glioblastoma cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2


title: U138 42C RF plus RT 0h replicate 2

description:
Library name: U_RFRT_23_01_0
U138 glioblastoma cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2


title: C2C12 cells, iCdh23, 48 h serum starvation, untreated, RNA-seq biol rep 3

description: Library name: C2C12_iCdh23_48h_diff_noDox_RNAseq_biorep3


title: Female_FCL_AAE_Adolescent c106

description:
Library name: c106
column names are library name - c#, etc


title: Female_PF_AAE_Adolescent c105

description:
Library name: c105
column names are library name - c#, etc


title: Female_FCL_VEH_Adult c104

description:
Library name: c104
column names are library name - c#, etc


title: Female_PF_VEH_Adult c103

description:
Library name: c103
column names are library name - c#, etc


title: C2C12 cells, iCdh23, 48 h serum starvation, untreated, RNA-seq biol rep 1

description: Library name: C2C12_iCdh23_48h_diff_noDox_RNAseq_biorep1


title: U138 42C RF plus RT 24h replicate 1

description:
Library name: U_RFRT_22_01_24
U138 glioblastoma cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: Female_PF_AAE_Adult c102

description:
Library name: c102
column names are library name - c#, etc


title: C2C12 cells, iCdh23, 48 h serum starvation, untreated, RNA-seq biol rep 2

description: Library name: C2C12_iCdh23_48h_diff_noDox_RNAseq_biorep2


title: U138 42C RF plus RT 0h replicate 1

description:
Library name: U_RFRT_22_01_0
U138 glioblastoma cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: Female_PAE_AAE_Adult c101

description:
Library name: c101
column names are library name - c#, etc


title: CD36-NK-3

city: Jinzhou

first: wang

last: wenya

address: Sanjeon Songpa-ro

country: China

institute: JZMU

description: Library name: CD36- NK-2

data_processing:
Raw reads obtained from sequencing may contain unqualified reads, such as those with low overall quality, presence of sequencing primers, or low-quality ends. These unqualified reads are likely to affect the quality of downstream analysis and therefore must be filtered to obtain clean reads suitable for data analysis. Seqtk was used for filtering.
The pre-processed reads were aligned to the genome using the spliced mapping algorithm of Hisat2 (version 2.0.4). This algorithm allows reads that cannot be mapped in full length to be split and mapped, making it particularly suitable for eukaryotic transcriptome sequencing data (which contain intronic regions). Default parameters were used. The resulting alignments were output as BAM files.
In transcriptome sequencing, the number of reads mapped to gene regions can be used to estimate gene expression levels. However, the read count is not only proportional to the gene expression level but also related to the gene length and the amount of sequencing data. To make gene expression levels comparable across different genes and samples, the read counts are converted to FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for normalization of gene expression levels.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimted text tile includes raw counts tor each Sample
Supplementary files format and content: csv files include FPKMvalues for each Sample

source_name: primary NK cells

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorivd) following the manufacturer’s standard protocol, and purified using the RNAClean XP Kit (Beckman Coulter) and the RNase-Free DNase Set (QIAGEN). RNA integrity was assessed using the Agilent 2100 Bioanalyzer/Agilent 4200 TapeStation (Agilent Technologies), while total RNA yield and purity were determined using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and the NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific).
The purified total RNA was subjected to mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3′ end A-tailing, adapter ligation, and enrichment to complete mRNA sequencing library construction. The library concentration was measured using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and the library fragment size distribution was assessed using the Agilent 4200 TapeStation (Agilent Technologies).

value: primary NK cells


title: Female_PAE_VEH_Adolescent c99

description:
Library name: c99
column names are library name - c#, etc


title: Female_FCL_AAE_Adult c95

description:
Library name: c95
column names are library name - c#, etc


title: CD36-NK-2

description: Library name: CD36-NK-1


title: U138 42C RF 24h replicate 3

description:
Library name: U_RF_27_11_24
U138 glioblastoma cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

value: 42C radiofrequency 24h


title: Female_PF_AAE_Adult c96

description:
Library name: c96
column names are library name - c#, etc


title: Female_FCL_VEH_Adolescent c88

description:
Library name: c88
column names are library name - c#, etc


title: U138 42C RF 0h replicate 3

description:
Library name: U_RF_27_11_0
U138 glioblastoma cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: 42C radiofrequency 0h


title: CD36+NK-3

description: Library name: CD36--NK-3


title: CD36-NK-1

description: Library name: 6-cd36-nk


title: U138 42C RF 24h replicate 2

description:
Library name: U_RF_26_10_24
U138 glioblastoma cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2


title: Male_FCL_VEH_Adolescent c87

description:
Library name: c87
column names are library name - c#, etc


title: U138 42C RF 0h replicate 2

description:
Library name: U_RF_26_10_0
U138 glioblastoma cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2


title: Male_PAE_VEH_Adult c83

description:
Library name: c83
column names are library name - c#, etc


title: Male_FCL_VEH_Adult c84

description:
Library name: c84
column names are library name - c#, etc


title: CD36+NK-2

description: Library name: CD36--NK-2


title: Female_PF_AAE_Adult c82

description:
Library name: c82
column names are library name - c#, etc


title: Male_PAE_AAE_Adult c81

description:
Library name: c81
column names are library name - c#, etc


title: U138 42C RF 24h replicate 1

description:
Library name: U_RF_27_07_24
U138 glioblastoma cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: CD36+NK-1

description: Library name: 1-cd36--nk


title: Female_FCL_VEH_Adolescent c80

description:
Library name: c80
column names are library name - c#, etc


title: Male_PF_VEH_Adolescent c79

description:
Library name: c79
column names are library name - c#, etc


title: U138 42C RF 0h replicate 1

description:
Library name: U_RF_27_07_0
U138 glioblastoma cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: Male_PF_AAE_Adolescent c78

description:
Library name: c78
column names are library name - c#, etc


title: Female_PF_AAE_Adolescent c77

description:
Library name: c77
column names are library name - c#, etc


title: Male_PAE_VEH_Adult c75

description:
Library name: c75
column names are library name - c#, etc


title: U138 42C AMRF plus RT 24h replicate 3

description:
Library name: U_AMRF-RT_10_10_24
U138 glioblastoma cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

value: 42C amplitude-modulated radiofrequency plus 8Gy gamma-radiation 24h


title: UHRF2_VSV

city: 上海

first: Qian

last: Zhang

state: 上海市

address: 盘山路7号

institute: Naval Medical University

description: Library name: UHRF2

library_source: genomic

data_processing:
Illumina pair-end sequencing reads were trimmed and quality filtered,
and aligned to the mouse mm10 assembly using the Trim Galore and bowtie2 program with default parameters.
DeepTools was used to perform coverage analysis of signals in intragenic regions .
Coverages were peresented in processed data in bigwig files.
Assembly: mm10
Supplementary files format and content: bigwig for reads coverage
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: macrophage

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were perforated for primary and secondory antibody binding, and then cut and adaptor ligated by hyperactive PA/PG-Tn5 transposase from Vazyme. DNA was extracted using DNA extraction beads from Vazyme.
CUT&Tag-seq libraries were prepared using  extracted DNA as starting material. Libraries were amplified using 15-20 cycles on the thermocycler using indexing system of Vazyme. Post amplification libraries were size selected at 150-450bp in length using DNA extraction beads from Vazyme. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Macrophages were infected with Vesicular Stomatitis Virus (1 M.O.I)

value: macrophage

value: primary mouse bone marrow derived macrophage

tag: chip antibody

value: anti-UHRF2 (Santa Cruz)


title: Female_PF_AAE_Adolescent c74

description:
Library name: c74
column names are library name - c#, etc


title: IRF3_VSV

description: Library name: IRF3

value: anti-IRF3 (CST)


title: U138 42C AMRF plus RT 0h replicate 3

description:
Library name: U_AMRF-RT_10_10_0
U138 glioblastoma cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: brain

value: 42C amplitude-modulated radiofrequency plus 8Gy gamma-radiation 0h


title: Female_FCL_VEH_Adult c72

description:
Library name: c72
column names are library name - c#, etc


title: Male_PAE_AAE_Adult c73

description:
Library name: c73
column names are library name - c#, etc


title: WT_PF4_5

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA80714

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (GRCm38.p4) reference genome using HISAT2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted from cells using TRIsure reagent and a miRNeasy Micro Kit (QIAGEN) following the manufacturer’s instructions.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Japan), and sequencing libraries were prepared using a Nextera XT DNA Library Prep Kit (Illumina, USA).

value: spleen

value: treated with PF4 (platelet factor 4)


title: Female_PF_VEH_Adult c71

description:
Library name: c71
column names are library name - c#, etc

value: brain (anterior cingulate cortex)


title: U138 42C AMRF plus RT 24h replicate 2

description:
Library name: U_AMRF-RT_20_11B_24
U138 glioblastoma cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2

value: glioblastoma

value: wild type


title: Female_PF_AAE_Adult c70

description:
Library name: c70
column names are library name - c#, etc

value: Long Evans rat

value: described in sample name


title: WT_PF4_4

description: Library name: GA80713


title: WT_PF4_3

description: Library name: GA80712


title: Male_PAE_AAE_Adult c69

description:
Library name: c69
column names are library name - c#, etc


title: U138 42C AMRF plus RT 0h replicate 2

description:
Library name: U_AMRF-RT_20_11B_0
U138 glioblastoma cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2


title: Male_FCL_VEH_Adolescent c68

description:
Library name: c68
column names are library name - c#, etc


title: U138 42C AMRF plus RT 24h replicate 1

description:
Library name: U_AMRF-RT_22_01_24
U138 glioblastoma cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: Female_FCL_VEH_Adult c64

description:
Library name: c64
column names are library name - c#, etc


title: U138 42C AMRF plus RT 0h replicate 1

description:
Library name: U_AMRF-RT_22_01_0
U138 glioblastoma cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: WT_PF4_2

description: Library name: GA80711


title: Male_PAE_VEH_Adolescent c67

description:
Library name: c67
column names are library name - c#, etc


title: WT_PF4_1

description: Library name: GA80710


title: U138 42C AMRF 24h replicate 3

description:
Library name: U_AMRF_31_07_24
U138 glioblastoma cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

value: 42C amplitude-modulated radiofrequency 24h


title: Male_PAE_AAE_Adolescent c65

description:
Library name: c65
column names are library name - c#, etc


title: Female_PF_VEH_Adult c63

description:
Library name: c63
column names are library name - c#, etc


title: Female_FCL_AAE_Adult c62

description:
Library name: c62
column names are library name - c#, etc


title: WT_m_5

description: Library name: GA80709

value: mock


title: U138 42C AMRF 24h replicate 2

description:
Library name: U_AMRF_18_01_24
U138 glioblastoma cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2


title: Female_PAE_VEH_Adolescent c60

description:
Library name: c60
column names are library name - c#, etc


title: Male_PAE_AAE_Adult c61

description:
Library name: c61
column names are library name - c#, etc


title: WT_m_4

description: Library name: GA80708


title: Male_PAE_AAE_Adolescent c57

description:
Library name: c57
column names are library name - c#, etc


title: Male_FCL_AAE_Adolescent c58

description:
Library name: c58
column names are library name - c#, etc


title: Male_FCL_VEH_Adolescent c56

description:
Library name: c56
column names are library name - c#, etc


title: U138 42C AMRF 0h replicate 3

description:
Library name: U_AMRF_03_08_0
U138 glioblastoma cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: 42C amplitude-modulated radiofrequency 0h


title: WT_m_3

description: Library name: GA80707


title: U138 42C AMRF 24h replicate 1

description:
Library name: U_AMRF_16_01_24
U138 glioblastoma cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: WT_m_2

description: Library name: GA80706


title: Male_PF_AAE_Adult c55

description:
Library name: c55
column names are library name - c#, etc


title: Female_PAE_VEH_Adult c54

description:
Library name: c54
column names are library name - c#, etc


title: U138 42C AMRF 0h replicate 2

description:
Library name: U_AMRF_18_01_0
U138 glioblastoma cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2


title: Female_PF_AAE_Adolescent c52

description:
Library name: c52
column names are library name - c#, etc


title: WT_m_1

description: Library name: GA80705


title: U138 42C AMRF 0h replicate 1

description:
Library name: U_AMRF_16_01_0
U138 glioblastoma cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: Male_FCL_VEH_Adult c51

description:
Library name: c51
column names are library name - c#, etc


title: Male_PAE_AAE_Adolescent c49

description:
Library name: c49
column names are library name - c#, etc


title: Female_FCL_VEH_Adolescent c48

description:
Library name: c48
column names are library name - c#, etc


title: B4galt1 Vav-Cre WT ATAC, scMultiome

city: Milwaukee

first: Karin

last: Hoffmeister

state: WI

address: 8727 Watertown Plank Road

institute: Versiti Blood Research Institute

description: Library name: WT 3620 ATAC

library_source: genomic single cell

data_processing:
Fastqs processed with 10x Genomics Cell Ranger v7.0.0 which yielded feature barcode matrices (HDF5 format)
Matrices read into the R environment using the Seurat version 5.1.0 suite of tools
Assembly: mm10
Supplementary files format and content: output from cellranger: feature barocode matrices and atac fragments files.

source_name: Bone Marrow

extract_protocol:
LSK cells from B4HSC-/- and control specimens were sorted using antibody cocktails described above (Bone marrow isolation, flow cytometry, and fluorescence-activated cell sorting (FACS)), rinsed with 0.04% BSA PBS, and 10,000 cells underwent the manufacturer’s nuclei preparation procedure. Then, about 4,000 nuclei were placed into a 10x Chromium X instrument. The remainder of the library preparation steps were conducted in accordance with the manufacturer’s protocol. Libraries were evaluated using an Agilent Bioanalyzer, quantified utilizing a KAPA Library Quantification Kit, and sequenced on an Illumina Novaseq platform.
Single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) libraries were prepared employing the 10X Genomics Single Cell Multiome assay kit (10X Genomics; 1000230, 1000283, 1000494, 1000215, 1000212) following the manufacturer’s guidelines

value: Bone Marrow

value: LSK


title: U138 44C water bath 24h replicate 3

description:
Library name: U_44_7c_24
U138 glioblastoma cells incubated in 44C water bath (positive HT control) and harvested after 24h re-incubation; biological replicate 3

value: 44C water bath 24h


title: B4galt1 Vav-Cre KO ATAC, scMultiome

description: Library name: VAV-KO 3702 ATAC


title: Male_PF_VEH_Adult c47

description:
Library name: c47
column names are library name - c#, etc


title: Male_PF_AAE_Adult c46

description:
Library name: c46
column names are library name - c#, etc


title: U138 44C water bath 24h replicate 2

description:
Library name: U_44_7b_24
U138 glioblastoma cells incubated in 44C water bath (positive HT control) and harvested after 24h re-incubation; biological replicate 2


title: Male_PAE_AAE_Adolescent c45

description:
Library name: c45
column names are library name - c#, etc


title: B4galt1 Vav-Cre WT RNA, scMultiome

description: Library name: WT 3620 RNA

library_source: transcriptomic single cell


title: U138 44C water bath 0h replicate 3

description:
Library name: U_44_03_08_0
U138 glioblastoma cells incubated in 44C water bath (positive HT control) and harvested immediately (0h); biological replicate 3

value: 44C water bath 0h


title: Female_PF_VEH_Adult c44

description:
Library name: c44
column names are library name - c#, etc


title: Male_FCL_AAE_Adult c43

description:
Library name: c43
column names are library name - c#, etc


title: B4galt1 Vav-Cre KO RNA, scMultiome

description: Library name: VAV-KO 3702 RNA


title: Male_FCL_AAE_Adolescent c41

description:
Library name: c41
column names are library name - c#, etc


title: U138 44C water bath 0h replicate 2

description:
Library name: U_44_7b_0
U138 glioblastoma cells incubated in 44C water bath (positive HT control) and harvested immediately (0h); biological replicate 2


title: Female_FCL_AAE_Adolescent c40

description:
Library name: c40
column names are library name - c#, etc


title: Female_FCL_VEH_Adolescent c38

description:
Library name: c38
column names are library name - c#, etc


title: Liver, MASH, Cxcl5 KO #12

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: Library name: Sample 12

data_processing:
Raw sequencing reads generated on the Illumina NovaSeq 6000 platform were quality checked and trimmed prior to downstream analysis.
Initial quality assessment of raw RNA-seq FASTQ files was performed using FastQC.
Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.6) with parameters: --phred33, --quality 20, --length 50, --paired.
Trimmed reads were aligned to the mouse reference genome (Mus musculus, GRCm39) using STAR aligner (v2.7.9a).
Trimmed reads were aligned to the mouse reference genome (Mus musculus, GRCm39) using STAR aligner (v2.7.9a).
Assembly: Mus musculus genome assembly GRCm39
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: Liver

growth_protocol: Male C57BL/6J mice were housed under standard laboratory conditions with a 12 h light/dark cycle and ad libitum access to food and water. Mice were maintained on either a high-fat diet (HFD) or an AMLN diet to induce metabolic dysfunction-associated steatohepatitis (MASH).

extract_protocol:
Total RNA was extracted from mouse liver tissues using standard RNA isolation procedures according to the manufacturer’s instructions. RNA quality and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using an Illumina-compatible library preparation kit according to the manufacturer’s instructions and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Wild-type and Cxcl5-deficient mice were fed an AMLN diet to induce MASH or maintained on a high-fat diet (HFD). Liver tissues were collected at the experimental endpoint for transcriptomic analysis.

value: Liver

value: Cxcl5 deficient

value: MASH+Cxcl5 KO


title: Female_PAE_VEH_Adult c35

description:
Library name: c35
column names are library name - c#, etc


title: Liver, MASH, Cxcl5 KO #11

description: Library name: Sample 11


title: U138 44C water bath 24h replicate 1

description:
Library name: U_44_03_08_24
U138 glioblastoma cells incubated in 44C water bath (positive HT control) and harvested after 24h re-incubation; biological replicate 1

value: brain


title: Male_FCL_AAE_Adult c34

description:
Library name: c34
column names are library name - c#, etc


title: U138 44C water bath 0h replicate 1

description:
Library name: U_44_7_0
U138 glioblastoma cells incubated in 44C water bath (positive HT control) and harvested immediately (0h); biological replicate 1


title: Female_PF_VEH_Adolescent c32

description:
Library name: c32
column names are library name - c#, etc


title: Female_FCL_VEH_Adult c29

description:
Library name: c29
column names are library name - c#, etc


title: Liver, MASH, Cxcl5 KO #10

description: Library name: Sample 10


title: Male_PF_AAE_Adult c27

description:
Library name: c27
column names are library name - c#, etc


title: Liver, MASH, Cxcl5 KO #9

description: Library name: Sample 9


title: Female_PF_VEH_Adolescent c26

description:
Library name: c26
column names are library name - c#, etc


title: U138 42C water bath plus RT 24h replicate 3

description:
Library name: U_42RT_2_24
U138 glioblastoma cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested after 24h re-incubation; biological replicate 3

value: 42C water bath plus 8Gy gamma-radiation 24h


title: Female_PF_AAE_Adolescent c25

description:
Library name: c25
column names are library name - c#, etc

value: brain (anterior cingulate cortex)


title: U138 42C water bath plus RT 0h replicate 3

description:
Library name: U_42RT_2_0
U138 glioblastoma cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested immediately (0h); biological replicate 3

value: glioblastoma

value: 42C water bath plus 8Gy gamma-radiation 0h


title: Liver, MASH, Wildtype #8

description: Library name: Sample 8

value: Wildtype

value: MASH


title: Male_PAE_VEH_Adult c24

description:
Library name: c24
column names are library name - c#, etc

value: Long Evans rat

value: described in sample name


title: Male_PF_AAE_Adult c22

description:
Library name: c22
column names are library name - c#, etc


title: U138 42C water bath plus RT 24h replicate 2

description:
Library name: U_42RT_7_11_24
U138 glioblastoma cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested after 24h re-incubation; biological replicate 2

value: wild type


title: Female_FCL_AAE_Adolescent c23

description:
Library name: c23
column names are library name - c#, etc


title: Liver, MASH, Wildtype #7

description: Library name: Sample 7


title: U138 42C water bath plus RT 24h replicate 1

description:
Library name: U_42RT_20_09_24
U138 glioblastoma cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested after 24h re-incubation; biological replicate 1


title: Male_FCL_VEH_Adolescent c21

description:
Library name: c21
column names are library name - c#, etc


title: Liver, MASH, Wildtype #6

description: Library name: Sample 6


title: U138 42C water bath plus RT 0h replicate 2

description:
Library name: U_42RT_7_11_0
U138 glioblastoma cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested immediately (0h); biological replicate 2


title: Male_PAE_AAE_Adult c20

description:
Library name: c20
column names are library name - c#, etc


title: Male_PAE_VEH_Adult c19

description:
Library name: c19
column names are library name - c#, etc


title: Liver, MASH, Wildtype #5

description: Library name: Sample 5


title: Male_PAE_VEH_Adolescent c18

description:
Library name: c18
column names are library name - c#, etc


title: U138 42C water bath plus RT 0h replicate 1

description:
Library name: U_42RT_20_09_0
U138 glioblastoma cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested immediately (0h); biological replicate 1


title: U138 42C water bath 24h replicate 3

description:
Library name: U_42_7_11_24
U138 glioblastoma cells incubated in 42C water bath (HT control) and harvested after 24h re-incubation; biological replicate 3

value: 42C water bath 24h


title: Male_PF_AAE_Adolescent c17

description:
Library name: c17
column names are library name - c#, etc


title: Liver, HFD, Wildtype #4

description: Library name: Sample 4

value: HFD


title: Female_FCL_VEH_Adult c15

description:
Library name: c15
column names are library name - c#, etc


title: Male_FCL_VEH_Adolescent c16

description:
Library name: c16
column names are library name - c#, etc


title: Female_FCL_AAE_Adult c13

description:
Library name: c13
column names are library name - c#, etc


title: Liver, HFD, Wildtype #3

description: Library name: Sample 3


title: Male_FCL_AAE_Adolescent c12

description:
Library name: c12
column names are library name - c#, etc


title: U138 42C water bath 0h replicate 3

description:
Library name: U_42_7_11_0
U138 glioblastoma cells incubated in 42C water bath (HT control) and harvested immediately (0h); biological replicate 3

value: 42C water bath 0h


title: Female_PAE_AAE_Adult c11

description:
Library name: c11
column names are library name - c#, etc


title: Liver, HFD, Wildtype #2

description: Library name: Sample 2


title: U138 42C water bath 24h replicate 2

description:
Library name: U_42_26_10_24
U138 glioblastoma cells incubated in 42C water bath (HT control) and harvested after 24h re-incubation; biological replicate 2


title: Liver, HFD, Wildtype #1

description: Library name: Sample 1


title: Male_PF_VEH_Adolescent c10

description:
Library name: c10
column names are library name - c#, etc


title: Male_FCL_VEH_Adolescent c8

description:
Library name: c8
column names are library name - c#, etc


title: Male_PF_VEH_Adolescent c7

description:
Library name: c7
column names are library name - c#, etc


title: retina, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 13

city: Mannheim

first: Lucas

last: Schirmer

address: Theodor-Kutzer-Ufer 1-3

institute: University of Heidelberg

description:
Library name: Sample 13
6 retinae pooled, FACS sorted for RGCs

data_processing:
The expression count matrices were generated by aligning the sequencing data to the GRCm39-2024-A reference transcriptome with Cell Ranger Count (v.7.0.0).
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated value files and matrix files

molecule: nuclear RNA

source_name: retina

extract_protocol:
After nuclei isolation using Dounce homogenizers and ultracentrifugation at 500g for 5 min,  pelleted nuclei were resuspended in staining buffer containing primary antibodies targeting NeuN and RBPMS to detect RGCs for 15 minutes at 4 °C. Nuclei were washed, centrifuged at 500 × g for 5 minutes, stained with secondary antibodies and sorted using a BD FACSDiva device. Sorted NeuN+/RBPMS+ nuclei were pelleted at 500 × g for 5 minutes at 4 °C, resuspended, counted in a Neubauer chamber and adjusted to a concentration of ~600 nuclei µl–1. Nuclei were then loaded onto a microfluidic platform (Chromium X Series controller) aiming for 8,000 nuclei per reaction.
Libararies were generated according to the 10x Next GEM 3' Kit v.3.1 protocol.

value: retina


title: Female_FCL_AAE_Adult c6

description:
Library name: c6
column names are library name - c#, etc


title: U138 42C water bath 0h replicate 2

description:
Library name: U_42_26_10_0
U138 glioblastoma cells incubated in 42C water bath (HT control) and harvested immediately (0h); biological replicate 2


title: U138 42C water bath 24h replicate 1

description:
Library name: U_42_27_07_24
U138 glioblastoma cells incubated in 42C water bath (HT control) and harvested after 24h re-incubation; biological replicate 1


title: Female_PF_AAE_Adult c5

description:
Library name: c5
column names are library name - c#, etc


title: Female_PF_VEH_Adult c4

description:
Library name: c4
column names are library name - c#, etc


title: U138 42C water bath 0h replicate 1

description:
Library name: U_42_27_07_0
U138 glioblastoma cells incubated in 42C water bath (HT control) and harvested immediately (0h); biological replicate 1


title: retina, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 12

description:
Library name: Sample 12
6 retinae pooled, FACS sorted for RGCs


title: Male_PF_AAE_Adolescent c1

description:
Library name: c1
column names are library name - c#, etc


title: retina, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 11

description:
Library name: Sample 11
6 retinae pooled, FACS sorted for RGCs


title: U138 37C water bath plus RT 24h replicate 3

description:
Library name: U_37RT_3c_24
U138 glioblastoma cells irradiated with 8Gy and incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 3

value: 37C water bath plus 8Gy gamma-radiation 24h


title: Veh2

city: Beijing

first: mao yang

last: Zhou

address: No. 27 Courtyard, Taiping Road, Haidian District, Beijing

institute: Academy of Military Medical Sciences

description: Library name: sample5

data_processing:
Quality control and preprocessing Raw reads were processed using fastp. Adapter sequences, reads containing poly-N (N > 10% of read length), and low-quality reads (Q ≤ 5 for > 50% of bases) were removed to obtain clean reads. Quality metrics including Q20, Q30, and GC content were calculated for the clean data. All downstream analyses were based on these high-quality clean reads.
Alignment to reference genome The reference genome and gene annotation files were downloaded from the genome database. HISAT2 (version 2.2.1) was used to build the reference genome index and to align paired-end clean reads to the reference genome. HISAT2 leverages splice junction information derived from the gene annotation file for improved alignment accuracy compared to non-splice-aware aligners.
Novel transcript prediction StringTie (version 2.2.3) was used for transcript assembly and novel transcript prediction. StringTie applies a network flow algorithm and optional de novo assembly to reconstruct transcripts, offering advantages in transcript completeness, accuracy, expression estimation, and computational efficiency compared to methods such as Cufflinks.
Gene expression quantification featureCounts (version 2.0.6) was used to quantify reads mapped to each gene. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated to normalize for sequencing depth and gene length, providing a commonly used metric for gene expression estimation.
Differential expression analysis Differential expression analysis between treatment groups was performed using the DESeq2 R package (version 1.42.0), which models count data using a negative binomial distribution. The Benjamini–Hochberg method was applied to adjust p-values for multiple testing, controlling the false discovery rate (FDR). Differentially expressed genes were defined as those with adjusted p-value ≤ 0.05 and |log₂(fold change)| ≥ 1.
Assembly: mRatBN7.2 (rn7)
Supplementary files format and content: gene_count.txt：Tab-delimited text file containing raw read counts per gene for each sample.A column: Entrez Gene ID, B-G column: samples,  H columns: Gene name. HcyvsVeh_deg.txt: Tab-delimited text file containing differential expression analysis results between Hcy-treated and control groups. A column: Entrez Gene ID, B-G column: samples, H column: log2FoldChange,  I column: pvalue, J column: padj,  K column: gene_name.

source_name: Brain

growth_protocol: Primary rat brain microvascular endothelial cells (rBMECs) were isolated from the cerebral cortex of 18–22-day-old SD rats using a rat brain microvascular endothelial cell isolation kit (Procell, P-CA-601) following the manufacturer's instructions. Briefly, the cerebral cortex was dissected and minced, then digested with the provided specialized digestive solutions.The tissue homogenate was filtered through a 100 μm cell filter, and the isolated microvessels were collected by centrifugation using the specialized isolation solution. The obtained cells were resuspended in planting solution and seeded into T25 culture flasks. After 48 h of culture, the cells were purified using the screening solution to eliminate contaminating cells. Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO₂ and subjected to interventions and subsequent experiments after one passage. rBMECs were maintained in complete medium containing endothelial cell growth supplements (Procell, CM-R108).

extract_protocol:
1. Sample Lysis Rat cells were harvested and lysed directly in TRIzol Reagent. The homogenized samples were incubated at room temperature to allow complete dissociation of nucleoprotein complexes. 2. Phase Separation Chloroform was added to the homogenate. The mixture was vigorously shaken and centrifuged at 12,000 × g for 15 minutes at 4°C. This step separates the mixture into a lower organic phase, an interphase, and an upper aqueous phase containing the RNA. 3. RNA Precipitation The upper aqueous phase was transferred to a fresh tube. Isopropanol was added to precipitate the RNA. The samples were incubated at room temperature and then centrifuged at 12,000 × g for 10 minutes at 4°C to pellet the RNA. 4. RNA Wash and Dissolution The supernatant was removed, and the RNA pellet was washed twice with 75% ethanol. The pellet was air-dried briefly and then dissolved in RNase-free water. 5. DNase I Digestion (Optional but recommended) To eliminate residual genomic DNA, the RNA sample was treated with DNase I according to the manufacturer's instructions.6. Quality ControlRNA concentration was measured using a NanoDrop spectrophotometer. RNA integrity was precisely assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano kit. Only samples with an RNA Integrity Number (RIN) ≥ 7.0 were used for subsequent library preparation.
Total RNA was used as input material. Poly(A) mRNA was enriched using Oligo dT magnetic beads. Following enrichment, the mRNA was fragmented under controlled conditions. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis.  The resulting double-stranded cDNA underwent end repair, A-tailing, and adapter ligation. Fragments of appropriate size were selected, followed by PCR amplification and purification to generate the final library.  Library quantification was performed using a Qubit fluorometer and real-time quantitative PCR (qPCR). Fragment size distribution was assessed using a bioanalyzer system.

treatment_protocol: A pre prepared 50 μmol/L Hcy solution (Sigma Aldrich, H4628) dissolved in ddH₂O was used for interventions, with ddH₂O serving as the vehicle control. Cells were treated with 100 µM homocysteine (Hcy) for 24 h.

value: Brain

value: Brain Microvascular Endothelial Cells

value: Vehicle( sterile water)


title: Veh3

description: Library name: sample6


title: retina, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 10

description:
Library name: Sample 10
6 retinae pooled, FACS sorted for RGCs


title: U138 37C water bath plus RT 0h replicate 3

description:
Library name: U_37RT_3c_0
U138 glioblastoma cells irradiated with 8Gy and incubated in 37C water bath and harvested immediately (0h); biological replicate 3

value: brain

value: 37C water bath plus 8Gy gamma-radiation 0h


title: histone acetylation 12h

description: Library name: H3K27ac_vsv_12h

data_processing:
Illumina pair-end sequencing reads were trimmed and quality filtered,
and aligned to the mouse mm10 assembly using the Trim Galore and bowtie2 program with default parameters.
DeepTools was used to perform coverage analysis of signals in intragenic regions and TADs regions .
Coverages were peresented in processed data in bigwig files.
Assembly: mm10
Supplementary files format and content: bigwig for reads coverage
Library strategy: CUT&Tag

treatment_protocol: Macrophages were infected with Vesicular Stomatitis Virus (1 M.O.I) for 12h

value: macrophage

value: primary mouse bone marrow derived macrophage

value: anti-H3K27ac (cst)


title: mPASMC_Normoxia_2

city: Daqing

first: Hao

last: Yuan

address: 39 Xinyang Rd

institute: Harbin Medical University

description:
Library name: Nor2_tsRNA_from_tRNA
Column name in matrix: Nor2_tsRNA_from_tRNA

library_source: other

data_processing:
Raw sequencing reads were quality-controlled and adapter sequences were trimmed to obtain clean reads.
The clean reads were aligned and annotated using the SPORTS1.1 software pipeline. For this submission, only sequences mapping to the GtRNAdb database were extracted to specifically identify and quantify tRNA-derived small RNAs (tsRNAs).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing raw read counts exclusively for annotated tsRNAs across all samples

molecule: other

source_name: pulmonary artery smooth muscle cells

growth_protocol: Primary mouse pulmonary artery smooth muscle cells (mPASMCs) were cultured under standard normoxic conditions. For the hypoxia group, cells were exposed to 3% O2 for 24 hours

extract_protocol:
Total RNA was extracted from the mPASMCs using TRIzol reagent according to the manufacturer's instructions.
Small RNA libraries were prepared using the Pandora-seq strategy. Briefly, RNA samples were enzymatically treated to remove RNA modifications that interfere with adapter ligation and reverse transcription, followed by standard small RNA library construction procedures.

value: pulmonary artery smooth muscle cells

value: Wild type

value: Normoxia


title: mPASMC_Normoxia_3

description:
Library name: Nor3_tsRNA_from_tRNA
Column name in matrix: Nor3_tsRNA_from_tRNA


title: Veh1

description: Library name: sample4


title: U138 37C water bath plus RT 24h replicate 2

description:
Library name: U_37RT_3b_24
U138 glioblastoma cells irradiated with 8Gy and incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 2

value: glioblastoma

value: wild type


title: Hcy3

description: Library name: sample3

value: 100 μM Hcy 24h


title: mPASMC_Normoxia_1

description:
Library name: Nor1_tsRNA_from_tRNA
Column name in matrix: Nor1_tsRNA_from_tRNA


title: histone acetylation 0h

description: Library name: H3K27ac_vsv_0h


title: U138 37C water bath plus RT 0h replicate 2

description:
Library name: U_37RT_3b_0
U138 glioblastoma cells irradiated with 8Gy and incubated in 37C water bath and harvested immediately (0h); biological replicate 2


title: Hcy2

description: Library name: sample2


title: U138 37C water bath plus RT 24h replicate 1

description:
Library name: U_37RT_7_11_24
U138 glioblastoma cells irradiated with 8Gy and incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 1


title: mPASMC_Hypoxia_3

description:
Library name: Hyp3_tsRNA_from_tRNA
Column name in matrix: Hyp3_tsRNA_from_tRNA

value: Hypoxia (3% O2, 24h)


title: histone lactylation 12h

description: Library name: H4K12la_vsv_12h

value: anti-H4k12la (.ptm-biolab)


title: Hcy1

description: Library name: sample1


title: mPASMC_Hypoxia_2

description:
Library name: Hyp2_tsRNA_from_tRNA
Column name in matrix: Hyp2_tsRNA_from_tRNA


title: mBMSCs, Ni, rep3

city: Guangzhou

first: Xi

last: Huang

state: Guangdong Province

address: Lingyuan West Road

department: Department of Periodontology

institute: Hospital of Stomatology, Sun Yat-sen University

description:
Library name: Sample 6
Column name in Ni_vs_Control_raw_counts_All_samples.txt: Ni3

data_processing:
Raw sequencing reads were subjected to quality control (QC), including assessment of error rate distribution and GC-content distribution. Adapter sequences and low-quality reads were removed to generate high-quality clean reads.
Clean reads were aligned to the reference genome, followed by gene-level expression quantification to obtain a normalized expression matrix for downstream analyses. Based on the quantified expression matrix, correlation analysis was performed where appropriate to evaluate gene–gene or gene–phenotype associations. In parallel, gene set enrichment analysis (GSEA) was conducted using the ranked expression matrix to identify coordinately altered pathways and biological processes.
Differential expression analysis was subsequently performed to identify significantly differentially expressed genes (DEGs) between experimental groups under predefined statistical thresholds (e.g., adjusted P value and |log₂ fold change| criteria).
Functional analysis was then carried out based on the DEG list. Enrichment analyses were performed using Gene Ontology (GO), KEGG, and Reactome databases.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample
Supplementary files format and content: excel file includes gene annotation

source_name: bone

growth_protocol: mBMSCs were maintained in MEM α supplemented with 10% fetal bovine serum(FBS) and 1% antibiotic in humandified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested through standard wordflow. Quality control was conducted by Agilent 2100 bioanalyzer.
Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA is synthesised within the M-MuLV reverse transcriptase system. Subsequently, the RNA strand is degraded by RNase H, and the second strand of cDNA is synthesised using dNTPs as substrates within the DNA polymerase I system. The purified double-stranded cDNA undergoes end repair, A-tailing, and sequencing adapter ligation. AMPure XP beads are employed to enrich cDNA fragments of approximately 250–300 bp, which are then amplified via PCR. The PCR products are further purified using AMPure XP beads to yield the final library. The library preparation was performed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Following library construction, an initial quantification was performed using the Qubit 2.0 Fluorometer. The library was diluted to 1.5 ng/μl, after which the insert size was assessed using the Agilent 2100 Bioanalyzer. Once the insert size met expectations, qRT-PCR was employed to accurately quantify the effective library concentration (above 2 nM), thereby ensuring library quality.

treatment_protocol: Osteogenic differentiation was induced by treatment of 70% confluent primary mouse bone marrow–derived mesenchymal stem cells (mBMSCs) with osteogenic induction medium containing 100 nM dexamethasone, 50 μg/mL ascorbic acid, and 10 mM β-glycerophosphate for 7 days.

value: bone

value: mesenchymal stem cells

value: 0.1 μM nickel ion, osteogenic differentiation


title: U138 37C water bath plus RT 0h replicate 1

description:
Library name: U_37RT_7_11_0
U138 glioblastoma cells irradiated with 8Gy and incubated in 37C water bath and harvested immediately (0h); biological replicate 1


title: histone lactylation 0h

description: Library name: H4K12la_vsv_0h


title: RNA-seq_HLF_R1064K_3

city: Chapel Hill

first: Jesse

last: Raab

state: NC

address: Rm 5028 Genetic Medicine Building

institute: UNC Chapel Hill - Raab Lab

description:
Library name: R1064K_3
RNA-seq

data_processing:
raw data was processed through github.com/raab-lab/rnaseq
STAR alignment or Salmon pseudoquant
STAR alighnment was then passed to bamCoverage to generate coverage tracks on forward and reverse strand
Salmon quantification was imported into R using tximeta and processed using DESeq2
Assembly: hg38
Supplementary files format and content: processed data are strand specific bigwig files or WT vs BAF155-R1064K differentially expressed genes.

source_name: HLF

growth_protocol: DMEM + 10% FBS + penicillin/streptomycin

extract_protocol:
Monarch Total RNA kit
Strand specific RNA-seq service provider (Admera)

treatment_protocol: CRISPR/CAS9 Knockout with re-expression of BAF155 WT or R1064K Mutant by Lentivirus

value: HLF

value: Liver Cancer

value: BAF155-KO; re-expressing R1064K BAF155


title: mPASMC_Hypoxia_1

description:
Library name: Hyp1_tsRNA_from_tRNA
Column name in matrix: Hyp1_tsRNA_from_tRNA


title: mBMSCs, Ni, rep2

description:
Library name: Sample 5
Column name in Ni_vs_Control_raw_counts_All_samples.txt: Ni2


title: RNA-seq_HLF_R1064K_2

description:
Library name: R1064K_2
RNA-seq


title: U138 37C water bath 24h replicate 3

description:
Library name: U_37_6c_24
U138 glioblastoma cells incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 3

value: brain

value: 37C water bath 24h


title: w10 control blastocyst

city: Napoli

first: Francesco

last: Cecere

state: Napoli

address: Via Posillipo 226

department: UOC Ricerca Clinica e Traslazionale

country: Italy

institute: AORN Santobono-Pausilipon

description: Library name: w10

data_processing:
The first 6 bp containing the N portion of the random primers, adapters, and bases called with poor quality (Phred score <20) were removed using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) in single-end mode. Only the good quality reads were used for alignment to the Genome Reference Consortium mouse genome build 39 (GRCm39) using Bismark version 0.18.2 with single-end and nondirectional mode followed by deduplication and methylation calling using Bismark functions. The global methylation were obtained as median methylation of all the CpGs site covered in the experiment.
Assembly: mm39
Supplementary files format and content: Promoter methylation

source_name: Blastocist

growth_protocol: Blastocysts were cultured in a medium supplemented with 15% FBS in 0.5% gelatin-coated plates and incubated at 37°C in a humidified atmosphere with 5% CO2 for 72 h. Trophoblast outgrowth was evaluated by measuring the area occupied (mm²) using ZEN 3.9 software. To evaluate ICM expansion, blastocysts were further cultured for one week in 2i medium.

extract_protocol:
DNA and RNA were separated using the G&T protocol [59]. Magnetic beads (MyOne C1, Life Technologies) were washed and annealed to oligo dTs and then used to capture polyadenylated mRNA from individual cell lysates. The supernatant containing the DNA was transferred to a new tube, and the beads washed three times in 1× FSS buffer (SuperScript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma), and 0.4 U/μl RNasin (Promega) to remove all DNA residues. Each washing solution was added to the DNA tube to maximize recovery.
The single blastocyst BS-seq libraries were generated as described [60]. The DNA was purified from the lysate using a 0.9:1 ratio of Ampure XP beads (Beckman Coulter) and eluted into 10 μl of water. DNA purified from single blastocysts was treated with the EZ Methylation Direct kit (Zymo) for bisulfite conversion following the manufacturer's instructions. For the first-strand synthesis, the bisulfite-treated DNA was mixed with 40 μl of first-strand synthesis master mix (1× blue buffer [Enzymatics], 0.4 mM dNTP mix [Roche], 0.4 μM 6NF oligo), heated for 2 min to 65°C, and cooled on ice, followed by the addition of 50 U of exo− Klenow fragment DNA polymerase (Enzymatics) and incubation for 90 min at 37°C after slowly ramping up from 4°C. Exonuclease digestion was carried out by adding 20 U of exonuclease I (NEB) in a total volume of 100 μl for 1 h at 37°C. The resulting samples were purified using AMPure XP beads with a 0.8:1 ratio. The beads were mixed with 50 μl of second-strand master mix (1× blue buffer [Enzymatics], 0.4 mM dNTP mix [Roche], 0.4 μM 6NR oligo). The mixture was heated for 1 min to 98°C and then cooled on ice. Next, 50 U of exo− Klenow was added. The mixture was incubated on a thermocycler for 90 min at 37°C after slowly ramping up from 4°C. The resulting samples were purified using a 0.8:1 ratio of AMPure XP beads, and libraries were amplified using 50 μl of PCR master mix (1× KAPA HiFi Readymix, 0.2 μM PE1.0 primer, 0.2 μM iTAG index primer). The amplification process involved a 2-min step at 95°C, followed by 20 cycles of 80 sec at 94°C, 30 sec at 65°C, and 30 sec at 72°C, with a final extension of 3 min at 72°C. Finally, the libraries were subjected to purification using a 0.7:1 ratio of AMPure XP beads. After purification, the libraries were eluted in 15 µl of water, pooled together, and sequenced. The sequencing process involved the generation of pools of 20 libraries, which were sequenced on an Illumina NextSeq 500 platform. On average, the libraries were sequenced to generate 13.0 million paired-end reads with a read length of 75 bp.

value: Blastocist

value: Control


title: U138 37C water bath 0h replicate 3

description:
Library name: U_37_6c_0
U138 glioblastoma cells incubated in 37C water bath and harvested immediately (0h); biological replicate 3

value: 37C water bath 0h


title: RNA-seq_HLF_R1064K_1

description:
Library name: R1064K_1
RNA-seq


title: mBMSCs, Ni, rep1

description:
Library name: Sample 4
Column name in Ni_vs_Control_raw_counts_All_samples.txt: Ni1


title: w9 control blastocyst

description: Library name: w9


title: mBMSCs, Con, rep3

description:
Library name: Sample 3
Column name in Ni_vs_Control_raw_counts_All_samples.txt: Con3

value: osteogenic differentiation


title: RNA-seq_HLF_WT_3

description:
Library name: WT_3
RNA-seq

value: BAF155-KO; re-expressing WT BAF155


title: w8 control blastocyst

description: Library name: w8


title: U138 37C water bath 0h replicate 2

description:
Library name: U_37_6b_0
U138 glioblastoma cells incubated in 37C water bath and harvested immediately (0h); biological replicate 2

value: glioblastoma

value: wild type


title: U138 37C water bath 24h replicate 2

description:
Library name: U_37_6b_24
U138 glioblastoma cells incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 2


title: RNA-seq_HLF_WT_2

description:
Library name: WT_2
RNA-seq


title: mBMSCs, Con, rep2

description:
Library name: Sample 2
Column name in Ni_vs_Control_raw_counts_All_samples.txt: Con2


title: w7 control blastocyst

description: Library name: w7


title: RNA-seq_HLF_WT_1

description:
Library name: WT_1
RNA-seq


title: U138 37C water bath 24h replicate 1

description:
Library name: U_37_7_11_24
U138 glioblastoma cells incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 1


title: mBMSCs, Con, rep1

description:
Library name: Sample 1
Column name in Ni_vs_Control_raw_counts_All_samples.txt: Con1


title: w6 control blastocyst

description: Library name: w6


title: U138 37C water bath 0h replicate 1

description:
Library name: U_37_7_11_0
U138 glioblastoma cells incubated in 37C water bath and harvested immediately (0h); biological replicate 1


title: TT-seq_HLF_BAF155-WT-3

description:
Library name: BAF155-WT-3
TT-seq (4sU nascent RNA labeling)

data_processing:
TT-seq data were aligned to human genome version “hg38” and gencode v32 using STAR with the following parameters: --runMode alignReads --outSamunmapped None --twoPassMode --none.
A second pass aligning reads to the yeast genome using bowtie2 and the sacCer3 UCSC genome index was performed to derived normalization factors as the sum of properly mapped reads to yeast genome from `samtools flagstat` with parameters --very-sensitive --no-unal.
Bigwig files were computed using deeptool bamCoverage with --scaleFactor 1/[(# of correct pairs of yeast reads)/median(# correct pairs of yeast reads) ] --filterStrand [reverse|forward] --binSize 10.
Metaplots and coverage over regions of interest were calculated in R.
Assembly: hg38
Supplementary files format and content: bigwig files of forward or reverse strand signal normalized to yeast spik-in

extract_protocol:
TT-seq was performed as previously described (Gregersen et al., 2020). In short, cells were seeded at ~80% confluency in 3, 15 cm dishes 24 hours prior to labeling. Cells were pulse-labeled with 1 mM of 4-thiouridine (4SU) for 15 minutes with labeling being quenched with the removal of the media and the addition of 2 mL of TRIzol (ThermoFisher, 15596026). RNA was extracted using phenol/chloroform and quantified on a TapeStation 4200 (Agilent, G2991BA). Incorporation of 4SU in extracted RNA was validated using dot blot and imaged with an Odyssey CLx machine (LI-COR). Labeled RNA was fragmented using 1 M NaOH and isolated using Micro Bio-Gel spin columns (BioRad, 7326250). Fragmented RNA was then biotinylated with biotin buffer and 0.1 mg/mL MTSEA biotin-XX linker (Biotium, BT90066) for 30 minutes. RNA was harvested using phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)) followed by precipitation with 5 M NaCl and isopropanol. Biotinylated RNA was extracted from the unlabeled RNA by incubation with μMACS streptavidin MicroBeads (Miltenyi, 130-074-101) and subsequent pull-down with μColumns (Miltenyi, 130-042-701) and warmed pull down wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% (vol/vol) Tween 20). After pull-down, 4SU-RNA was cleaned and concentrated using the RNeasy MinElute Cleanup Kit (Qiagen, 74204). Size and quality of the isolated RNA was checked on a TapeStation 4200.
Library prep was performed using the Hyperprep Kit (KAPA, 08098093702) for degraded RNA (1 minute fragmentation step) with Kapa Dual Index Adapters (KAPA, 08278555702). Size and concentration of libraries were verified using TapeStation 4200 and Qubit (Invitrogen, Q32857). Libraries were pooled and sequenced at 2x150 bp on a Novaseq X Plus 10B.


title: mouse, control, WT,  bone marrow, erythroblast, rep1

city: Baltimore

first: Iqbal

last: Hamza

state: MD

address: 670 W Baltimore St

department: Pediatrics

institute: University of Maryland Baltimore

description: Library name: BM_WT

data_processing:
The resulting sequence data were demultiplexed using Illuminas bcl2fastq2 Conversion Software v2.20. Each sample was analyzed using 10x Genomics Cell Ranger v8.0.0. The reference for gene expression was refdata-gex-GRCh38-2024-A, available at https://www.10xgenomics.com/support/software/cell-ranger/downloads.
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: h5
Supplementary files format and content: h5

source_name: bone marrow

extract_protocol:
Cells were counted and viability assessed using a Countess 3 (Invitrogen, Carlsbad,CA). Cell suspensions were loaded onto a 10x Genomics Chromium X (Pleasanton,CA) using the NextGEM 3 V3.1 Gel bead kit. Cell capture, GEM generation, cDNA amplification, and library preparation were performed according to manufacturer protocol.
The resulting 3 gene expression libraries were assessed for concentration and fragment size using the DNA High Sensitivity Assay on a GX Touch (Revity, Waltham, MA). The libraries were pooled, assessed by qPCR using the KAPA Library Quantification Kit (Complete, Universal) (Kapa Biosystems, Woburn, MA), and sequenced on an Illumina NovaSeq 6000 using 100bp PE reads (Illumina, San Diego, CA).

value: bone marrow

value: erythroblasts

value: WT

value: control


title: w5 control blastocyst

description: Library name: w5


title: SW620 42C RF plus RT 24h replicate 3

description:
Library name: SW_RFRT_24_10_24
SW620 colorectal cancer cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

source_name: colon

value: colon

value: colorectal adenocarcinoma

value: 42C radiofrequency plus 8Gy gamma-radiation 24h


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, RNA-seq biol rep 3

description: Library name: c2d1c_dmcntrlr3

data_processing:
core/RNAseq pipeline version 3.14.0
Assembly: mm10
Supplementary files format and content: tab-separated text files including tpm-scaled counts for all samples

value: skeletal muscle

value: skeletal muscle myoblast

value: endogenous MyoD1 + dox-inducible Halo-MyoD1

value: 24 h vehicle


title: TT-seq_HLF_BAF155-R1064K-3

description:
Library name: BAF155-R1064K-3
TT-seq (4sU nascent RNA labeling)

value: HLF

value: Liver Cancer


title: w4 control blastocyst

description: Library name: w4

value: Blastocist

value: Control


title: SW620 42C RF plus RT 0h replicate 3

description:
Library name: SW_RFRT_24_10_0
SW620 colorectal cancer cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: 42C radiofrequency plus 8Gy gamma-radiation 0h


title: TT-seq_HLF_BAF155-WT-2

description:
Library name: BAF155-WT-2
TT-seq (4sU nascent RNA labeling)


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, RNA-seq biol rep 2

description: Library name: c2d1c_dmcntrlr2


title: w3 control blastocyst

description: Library name: w3


title: SW620 42C RF plus RT 24h replicate 2

description:
Library name: SW_RFRT_21_09_24
SW620 colorectal cancer cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2

value: wild type


title: TT-seq_HLF_BAF155-R1064K-2

description:
Library name: BAF155-R1064K-2
TT-seq (4sU nascent RNA labeling)


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, RNA-seq biol rep 1

description: Library name: c2d1c_dmcntrlr1


title: w2 control blastocyst

description: Library name: w2


title: SW620 42C RF plus RT 0h replicate 2

description:
Library name: SW_RFRT_21_09_0
SW620 colorectal cancer cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2


title: w1 control blastocyst

description: Library name: w1


title: TT-seq_HLF_BAF155-WT-1

description:
Library name: BAF155-WT-1
TT-seq (4sU nascent RNA labeling)


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, RNA-seq biol rep 3

description: Library name: c2d1c_dmplusdoxr3

value: 24h dox


title: SW620 42C RF plus RT 24h replicate 1

description:
Library name: SW_RFRT_30_08_24
SW620 colorectal cancer cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: TT-seq_HLF_BAF155-R1064K-1

description:
Library name: BAF155-R1064K-1
TT-seq (4sU nascent RNA labeling)


title: SW620 42C RF plus RT 0h replicate 1

description:
Library name: SW_RFRT_30_08_0
SW620 colorectal cancer cells irradiated with 8Gy and treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, RNA-seq biol rep 1

description: Library name: c2d1c_dmplusdoxr1


title: CUT&RUN:_HLF_BAF155-R1064K_SCAF4_5

description:
Library name: 1007
SCAF4

data_processing:
all fastq procesed with pipeline at github.com/raab-lab/cut-n-run
bowtie2 for alignment
picard MarkDuplicates
peak calls with macs2
bamCoverage using counts from csaw for normalized coverage bigwig for IGV
Assembly: hg38
Supplementary files format and content: normalized bigwig files
Library strategy: CUT&RUN

source_name: Liver Cancer

growth_protocol: 10% FBS DMEM + p/s

extract_protocol:
CUT&RUN protocol was adapted from Epicypher and Skene and Henikoff 2017]. Briefly, cells were detached from plates and counted for a total of ~500,000 cells per antibody per cell line. Cells were pelleted at RT for 3 minutes at 300 g. Cells were washed 2x with Wash Buffer (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, protease inhibitor (1 tablet/30mL Roche)). 11 μL of Concanavalin beads (Bangs Laboratories) per sample were 2x washed with cold Bead Activation Buffer (20mM HEPES ph7.9, 10mM KCl, 1mM CaCl2, and 1mM MnCl2). Cells were then added to beads and incubated with rotation for 5 minutes at RT. Samples were placed on a magnet to remove the supernatant and resuspended in 50 μL Wash Buffer with 0.05% Digitonin and 2mM EDTA. Corresponding antibodies were added to the samples and were incubated overnight at 4℃ with rotation. The following day, beads were washed on a magnet 3x with Digitonin-Wash Buffer (Wash Buffer, 0.05% Digitonin). Beads were resuspended in 50 μL Digitonin-Wash Buffer with guinea pig anti-rabbit secondary antibody (1:100, Novus, NBP1-72763) and incubated at 4℃ for 1 hour with rotation. Following secondary antibody binding, beads were washed 4x with cold Digitonin-Wash buffer on a magnet and then resuspended in 50 μL pAG Mnase solution (~700 ng/ul pAG-Mnase, Digitonin-Wash Buffer) (purified in-house [47]). Beads were incubated with pAG Mnase solution for 1 hour at 4℃ with rotation. Beads were washed 4x with cold Digitonin-Wash Buffer on a magnet and then resuspended in 50 μL cold Digitonin-Wash Buffer. 1 μL of 100 mM CaCl2 was added to the samples and incubated in a cold metal block in ice at 4℃ for 30 minutes. 50 μL of Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05µg/µL RNAseA (ThermoFisher, EN0531), 0.1% Triton X-100) was added to the samples and then incubated at 37℃ for 30 minutes in a thermocycler. DNA was purified from the samples using the Zymo ChIP Clean and Concentrator kit (Genesee Scientific,  11-379C) following the manufacturer’s protocol.
Libraries were prepared using the KAPA HyperPrep DNA kit with modifications. End-repair/A-tailing was performed in 25 μL volume reactions and performed on a thermocycler with the following protocol: 12℃ for 15 minutes, 37℃ for 15 minutes, 58℃ for 45 minutes, hold at 12℃. For adapter ligation, half volumes were used with 5 μL of 750 nM Kapa Unique Dual-Indexed Adapters (KAPA, 8861919702). Samples were incubated for 1 hour at RT and cleaned with a 1.1X KAPA Pure Bead clean up 2x. A library amplification was performed with KAPA HiFi HotStart ReadyMix with the following program: 98℃ for 45 seconds, 98℃ for 15 seconds, 60℃ for 10 seconds, Cycle to Step 2 13x, 71℃ for 60 seconds, hold at 4℃. A final KAPA Pure Bead 1X clean up was performed on the amplified libraries before being quantified and pooled on TapeStation 4200 and Qubit.


title: m20 Padi6 mutant blastocyst

description: Library name: m20


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, RNA-seq biol rep 2

description: Library name: c2d1c_dmplusdoxr2


title: m19 Padi6 mutant blastocyst

description: Library name: m19


title: SW620 42C RF 24h replicate 3

description:
Library name: SW_RF_23_11_24
SW620 colorectal cancer cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

data_processing:
RNA-Seq reads were mapped to human reference genome GRCh38.p7 (GENCODE release 25 genome annotation) with STAR (version 2.7.3a) using the following parameters --outFileNamePrefix mapping/star/all_mates/U_AMRF_03_08_0/out/ --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Reads were assigned to genes with FeatureCounts (v2.0.6) using the following parameters  -t exon -g gene_id   -s 2 -p (with GENCODE relase 25, GRCh38 annotation gft file)
Assembly: GRCh38.p7
Supplementary files format and content: Comma separated count matrix with Featurecounts output for all samples

value: 42C radiofrequency 24h


title: CUT&RUN:_HLF_BAF155-WT_SCAF4_5

description:
Library name: 1001
SCAF4


title: C2C12 cells, iMyoD1, no differentiation, untreated, RNA-seq biol rep 3

description: Library name: c2d1c_gmcntrlr3


title: m18 Padi6 mutant blastocyst

description: Library name: m18


title: SW620 42C RF 0h replicate 3

description:
Library name: SW_RF_23_11_0
SW620 colorectal cancer cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: 42C radiofrequency 0h


title: C2C12 cells, iMyoD1, no differentiation, untreated, RNA-seq biol rep 2

description: Library name: c2d1c_gmcntrlr2


title: CUT&RUN:_HLF_BAF155-KO_SCAF4_5

description:
Library name: 995
SCAF4


title: m17 Padi6 mutant blastocyst

description: Library name: m17


title: SW620 42C RF 24h replicate 2

description:
Library name: SW_RF_09_11_24
SW620 colorectal cancer cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2


title: CUT&RUN:_HLF_BAF155-WT_SCAF4_4

description:
Library name: 692
SCAF4


title: m16 Padi6 mutant blastocyst

description: Library name: m16


title: C2C12 cells, iMyoD1, no differentiation, untreated, RNA-seq biol rep 1

description: Library name: c2d1c_gmcntrlr1


title: CUT&RUN:_HLF_BAF155-R1064K_SCAF4_4

description:
Library name: 686
SCAF4


title: SW620 42C RF 0h replicate 2

description:
Library name: SW_RF_09_11_0
SW620 colorectal cancer cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, RNA-seq biol rep 3

description: Library name: c2d1c_gmplusdoxr3


title: m15 Padi6 mutant blastocyst

description: Library name: m15


title: SW620 42C RF 24h replicate 1

description:
Library name: SW_RF_01_08_24
SW620 colorectal cancer cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: CUT&RUN:_HLF_BAF155-KO_SCAF4_4

description:
Library name: 680
SCAF4


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, RNA-seq biol rep 2

description: Library name: c2d1c_gmplusdoxr2


title: SW620 42C RF 0h replicate 1

description:
Library name: SW_RF_01_08_0
SW620 colorectal cancer cells treated with continuous radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: m14 Padi6 mutant blastocyst

description: Library name: m14


title: CUT&RUN:_HLF_BAF155-KO_SCAF4_3

description:
Library name: 619
SCAF4


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, RNA-seq biol rep 1

description: Library name: c2d1c_gmplusdoxr1


title: m13 Padi6 mutant blastocyst

description: Library name: m13


title: SW620 42C AMRF plus RT 24h replicate 3

description:
Library name: SW_AMRF-RT_15_11_24
SW620 colorectal cancer cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

value: 42C amplitude-modulated radiofrequency plus 8Gy gamma-radiation 24h


title: CUT&RUN:_HLF_BAF155-WT_SCAF4_3

description:
Library name: 613
SCAF4


title: m12 Padi6 mutant blastocyst

description: Library name: m12


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, biol rep 4

description: Library name: 300k_DM_rep4

data_processing:
nf-core/atacseq v 2.1.2 pipeline
Assembly: mm10
Supplementary files format and content: bigWig generated by deeptools
Supplementary files format and content: NarrowPeak files generated by MACS2 peak calling

growth_protocol: C2C12 skeletal muscle myoblasts were maintained in DMEM supplemented with 20% fetal bovine serum, penicillin streptomycin in a humidified atmosphere with 5% CO2 at 37C. Cells were seeded at 75,000 or 300,000 per well of a 12-well dish for no differentiation and 24 h serum starvation conditions

extract_protocol:
Fragment purification via Zymo DNA clean and concentrator-5.
Library preparation was performed using NEBNext Ultra II DNA library Prep kit for Illumina, following manufacturer protocols, employing custom Nextera primers

treatment_protocol: C2C12 were differentiated via 24 h of serum starvation (DM), and/or treated with doxycycline to induce exogenous MyoD1 expression


title: SW620 42C AMRF plus RT 0h replicate 3

description:
Library name: SW_AMRF-RT_15_11_0
SW620 colorectal cancer cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: colon

value: 42C amplitude-modulated radiofrequency plus 8Gy gamma-radiation 0h


title: CUT&RUN:_HLF_BAF155-R1064K_SCAF4_3

description:
Library name: 607
SCAF4


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, biol rep 3

description: Library name: 300k_DM_rep3


title: m11 Padi6 mutant blastocyst

description: Library name: m11


title: SW620 42C AMRF plus RT 24h replicate 2

description:
Library name: SW_AMRF-RT_11_10_24
SW620 colorectal cancer cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2

value: colorectal adenocarcinoma


title: CUT&RUN:_HLF_BAF155-WT_SCAF4_2

description:
Library name: 418
SCAF4


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, biol rep 2

description: Library name: 300k_DM_rep2

value: skeletal muscle


title: Liver, HuR F/F Tbg Cre+, HFCF Rep. 3

city: Kansas City

first: Yuxia

state: KS

department: Pharmacology, Toxicology, and Therapeutics

institute: The University of Kansas Medical Center

description:
Library name: HFCF HuRHep-/-3
Column name in HuR_HFCF_Liver_Raw_Counts.txt: Raw_Counts_HFCF_HuRHep-/-_3
HuR_HFCF_Liver_Raw_Counts.txt

data_processing:
CLC Genomics Workbench v 24.0.1
Sequenced reads were trimmed for low quality sequences using CLC Genomics Workbench (parameter- quality limit: 0.05)
Trimmed sequence reads were mapped to the Gene track of the  mus_musculus_refseq_GRCm38.p6 (parameters- mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.6, similarity fraction: 0.8, no global alignment, reverse strand, bulk library type, max number of hits per read: 10.
Assembly: mm10
Supplementary files format and content: tab-deliminited text file includes raw counts for each sample

extract_protocol:
Total RNA for sequencing was extracted from mouse liver tissues using a Direct-zol RNA kit (Zymo Research, R2071) according to the manufacturer’s protocol. During RNA isolation, DNA was removed by treating the samples with RNase-free DNase to avoid DNA contamination. The purity, concentration, and integrity of the RNA were examined using a NanoDrop 1000 spectrophotometer (Thermo Fisher) and an Agilent Bioanalyzer 2100 system (Agilent Technologies). The RNA integrity number values of all samples used for RNA-Seq were above 6.0.
cDNA libraries were prepared using the NEBNext stranded RNA Library Prep kit according to the manufacturer’s protocol.

treatment_protocol: To generate hepatoctye-specific HuR deficient male mice, 4-6 month old C57BL/6N male mice with a floxed Elavl1 allele (HuR flox/flox) were injected with AAV8-Tbg-Cre. WT controls were generated by injecting HuR flox/flox mice with AAV8-Tbg-null. For the chow diet feeding group, livers were collected for RNA isolation following normal chow diet feeding. For the High Fat Cholesterol and fructose (HFCF, Research Diet: D09100301, 40 kcal% fat, 2% cholesterol, 20 kcal% fructose) diet feeding group, livers were collected for RNA isolation following 16-weeks HFCF diet feeding.

value: Liver

value: C57BL/6N HuR F/F Tbg Cre Pos.

value: 16-weeks High Fat, Cholesterol, and Fructose Diet


title: SW620 42C AMRF plus RT 0h replicate 2

description:
Library name: SW_AMRF-RT_11_10_0
SW620 colorectal cancer cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2

extract_protocol:
Total RNA was isolated using the RNA extraction kit from Roboklon (Berlin, Germany) according to the manufacturer's instructions. For 0 h samples, cells were pelleted immediately after treatment, washed with PBS, and stored at -80°C. For 24 h samples, cells were re-seeded in 10 cm petri dishes and incubated for 24 hours at 37°C with 5% CO2 before RNA extraction. RNA quality and quantity were assessed using a NanoDrop 2000/2000c spectrophotometer (Peqlab).
RNA-seq libraries were prepared from extracted total RNA using a stranded poly(A)-selected library preparation protocol. Briefly, poly(A)+ RNA was enriched, fragmented, reverse-transcribed into cDNA, adapter-ligated, PCR-amplified, and quality controlled prior to sequencing.


title: CUT&RUN:_HLF_BAF155-R1064K_SCAF4_2

description:
Library name: 410
SCAF4

value: HLF


title: C2C12 cells, iMyoD1, 24 h serum starvation, untreated, biol rep 1

description: Library name: 300k_DM_rep1

value: skeletal muscle myoblast

value: endogenous MyoD1 + dox-inducible Halo-MyoD1

value: 24 h vehicle


title: Liver, HuR F/F Tbg Cre+, HFCF Rep. 2

description:
Library name: HFCF HuRHep-/-2
Column name in HuR_HFCF_Liver_Raw_Counts.txt: Raw_Counts_HFCF_HuRHep-/-_2
HuR_HFCF_Liver_Raw_Counts.txt


title: SW620 42C AMRF plus RT 24h replicate 1

description:
Library name: SW_AMRF-RT_21_11A_24
SW620 colorectal cancer cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, biol rep 4

description: Library name: 300k_DM_plusdox_rep4

value: 24 h dox


title: CUT&RUN:_HLF_BAF155-KO_SCAF4_2

description:
Library name: 402
SCAF4

value: Liver Cancer


title: Liver, HuR F/F Tbg Cre+, HFCF Rep. 1

description:
Library name: HFCF HuRHep-/-1
Column name in HuR_HFCF_Liver_Raw_Counts.txt: Raw_Counts_HFCF_HuRHep-/-_1
HuR_HFCF_Liver_Raw_Counts.txt


title: SW620 42C AMRF plus RT 0h replicate 1

description:
Library name: SW_AMRF-RT_21_11A_0
SW620 colorectal cancer cells irradiated with 8Gy and treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1

value: wild type


title: CUT&RUN:_HLF_BAF155-WT_SCAF4_1

description:
Library name: 394
SCAF4


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, biol rep 3

description: Library name: 300k_DM_plusdox_rep3


title: Liver, HuR F/F, HFCF Rep. 3

description:
Library name: HFCF WT3
Column name in HuR_HFCF_Liver_Raw_Counts.txt: Raw_Counts_HFCF_WT_3
HuR_HFCF_Liver_Raw_Counts.txt

value: C57BL/6N HuR F/F Tbg Cre Neg.


title: SW620 42C AMRF 24h replicate 3

description:
Library name: SW_AMRF_22_11_24
SW620 colorectal cancer cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 3

value: 42C amplitude-modulated radiofrequency 24h


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, biol rep 2

description: Library name: 300k_DM_plusdox_rep2


title: Liver, HuR F/F, HFCF Rep. 2

description:
Library name: HFCF WT2
Column name in HuR_HFCF_Liver_Raw_Counts.txt: Raw_Counts_HFCF_WT_2
HuR_HFCF_Liver_Raw_Counts.txt


title: CUT&RUN:_HLF_BAF155-R1064K_SCAF4_1

description:
Library name: 386
SCAF4


title: SW620 42C AMRF 0h replicate 3

description:
Library name: SW_AMRF_22_11_0
SW620 colorectal cancer cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 3

value: 42C amplitude-modulated radiofrequency 0h


title: CUT&RUN:_HLF_BAF155-KO_SCAF4_1

description:
Library name: 378
SCAF4


title: SW620 42C AMRF 24h replicate 2

description:
Library name: SW_AMRF_02_08_24
SW620 colorectal cancer cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 2

value: colon


title: C2C12 cells, iMyoD1, 24 h serum starvation, dox treatment, biol rep 1

description: Library name: 300k_DM_plusdox_rep1


title: C2C12 cells, iMyoD1, no differentiation, untreated, biol rep 4

description: Library name: 75k_GM_rep4


title: CUT&RUN:_HLF_BAF155-WT_Rfx5_2

description:
Library name: 417
Rfx5


title: Liver, HuR F/F Tbg Cre+, Chow Rep. 3

description:
Library name: Chow HuRHep-/-3
Column name in HuR_Chow_Liver_Raw_Counts.txt: Raw_Counts_Chow_HuRHep-/-_3
HuR_Chow_Liver_Raw_Counts.txt

value: Normal Chow Diet


title: Liver, HuR F/F, HFCF Rep. 1

description:
Library name: HFCF WT1
Column name in HuR_HFCF_Liver_Raw_Counts.txt: Raw_Counts_HFCF_WT_1
HuR_HFCF_Liver_Raw_Counts.txt


title: SW620 42C AMRF 0h replicate 2

description:
Library name: SW_AMRF_02_08_0
SW620 colorectal cancer cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 2

value: colorectal adenocarcinoma


title: CUT&RUN:_HLF_BAF155-R1064K_Rfx5_2

description:
Library name: 409
Rfx5


title: C2C12 cells, iMyoD1, no differentiation, untreated, biol rep 3

description: Library name: 75k_GM_rep3

value: skeletal muscle


title: Liver, HuR F/F Tbg Cre+, Chow Rep. 2

description:
Library name: Chow HuRHep-/-2
Column name in HuR_Chow_Liver_Raw_Counts.txt: Raw_Counts_Chow_HuRHep-/-_2
HuR_Chow_Liver_Raw_Counts.txt

value: Liver


title: SW620 42C AMRF 24h replicate 1

description:
Library name: SW_AMRF_26_07_24
SW620 colorectal cancer cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested after 24h re-incubation; biological replicate 1


title: Liver, HuR F/F Tbg Cre+, Chow Rep. 1

description:
Library name: Chow HuRHep-/-1
Column name in HuR_Chow_Liver_Raw_Counts.txt: Raw_Counts_Chow_HuRHep-/-_1
HuR_Chow_Liver_Raw_Counts.txt

value: C57BL/6N HuR F/F Tbg Cre Pos.


title: CUT&RUN:_HLF_BAF155-KO_Rfx5_2

description:
Library name: 401
Rfx5


title: C2C12 cells, iMyoD1, no differentiation, untreated, biol rep 2

description: Library name: 75k_GM_rep2


title: SW620 42C AMRF 0h replicate 1

description:
Library name: SW_AMRF_26_07_0
SW620 colorectal cancer cells treated with amplitude-modulated radiofrequency at 13.56 MHz and 42C and harvested immediately (0h); biological replicate 1


title: C2C12 cells, iMyoD1, no differentiation, untreated, biol rep 1

description: Library name: 75k_GM_rep1


title: CUT&RUN:_HLF_BAF155-WT_Rfx5_1

description:
Library name: 393
Rfx5


title: CUT&RUN:_HLF_BAF155-R1064K_Rfx5_1

description:
Library name: 385
Rfx5


title: Liver, HuR F/F, Chow Rep. 3

description:
Library name: Chow WT3
Column name in HuR_Chow_Liver_Raw_Counts.txt: Raw_Counts_Chow_WT_3
HuR_Chow_Liver_Raw_Counts.txt


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, biol rep 4

description: Library name: 75k_GM_plusdox_rep4


title: SW620 44C water bath 24h replicate 3

description:
Library name: SW_44_25_10_24
SW620 colorectal cancer cells incubated in 44C water bath (positive HT control) and harvested after 24h re-incubation; biological replicate 3

value: 44C water bath 24h


title: Liver, HuR F/F, Chow Rep. 2

description:
Library name: Chow WT2
Column name in HuR_Chow_Liver_Raw_Counts.txt: Raw_Counts_Chow_WT_2
HuR_Chow_Liver_Raw_Counts.txt


title: CUT&RUN:_HLF_BAF155-KO_Rfx5_1

description:
Library name: 377
Rfx5

value: HLF


title: SW620 44C water bath 0h replicate 3

description:
Library name: SW_44_25_10_0
SW620 colorectal cancer cells incubated in 44C water bath (positive HT control) and harvested immediately (0h); biological replicate 3

value: 44C water bath 0h


title: Liver, HuR F/F, Chow Rep. 1

description:
Library name: Chow WT1
Column name in HuR_Chow_Liver_Raw_Counts.txt: Raw_Counts_Chow_WT_1
HuR_Chow_Liver_Raw_Counts.txt


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, biol rep 3

description: Library name: 75k_GM_plusdox_rep3

value: skeletal muscle myoblast

value: endogenous MyoD1 + dox-inducible Halo-MyoD1


title: SW620 44C water bath 24h replicate 2

description:
Library name: SW_44_4b_24
SW620 colorectal cancer cells incubated in 44C water bath (positive HT control) and harvested after 24h re-incubation; biological replicate 2


title: SW620 44C water bath 24h replicate 1

description:
Library name: SW_44_4_24
SW620 colorectal cancer cells incubated in 44C water bath (positive HT control) and harvested after 24h re-incubation; biological replicate 1


title: SW620 44C water bath 0h replicate 2

description:
Library name: SW_44_4b_0
SW620 colorectal cancer cells incubated in 44C water bath (positive HT control) and harvested immediately (0h); biological replicate 2


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, biol rep 1

description: Library name: 75k_GM_plusdox_rep1

value: 24 h dox