title: C2061, rep3

city: Bethesda

first: Sujiraphong

last: Pharkjaksu

state: MD

address: 10 Center Dr

department: NIAID

institute: NIH

description: Library name: YC5582-12_S12

data_processing:
The RNA-seq data were analyzed by Partek Flow software, version 12.3.0, 2025 (Partek Inc., St. Louis, MO). Illumina reads were aligned to the reference genome of WM276 (ASM18594v1) using STAR. DESeq2 was used to calculate the differentially expressed genes. Differential expression deemed significant if the changes are at least 2-fold and p-adj is, 0.05.
Assembly: WM276 (ASM18594v1)
Supplementary files format and content: Normalized_data_DESeq2.xlsx

organism: Cryptococcus gattii

growth_protocol: Yeast cultures were initiated in 20 mL YPD medium and maintained at 30°C for 16-18 hours. Subsequently, the overnight culture approximately 5 mL was transferred to fresh 100 mL YPD medium to achieve an initial optical density at OD600 of 0.4. The culture was further incubated at 30°C for 4-5 hours until reaching mid-logarithmic phase at OD600 of 0.8-1.0. Cells were harvested via centrifugation at 3,500 rpm 5 minutes and flash-frozen in ethanol/dry ice prior to overnight lyophilization.

extract_protocol:
Total RNA extraction was performed using a dual-method approach combining Trizol reagent (Invitrogen, Carlsbad, CA) and RNeasy mini kit (Qiagen, Germany). Genomic DNA contamination was eliminated through treatment with Turbo RNase-free DNase (Invitrogen, Carlsbad, CA).
PolyA-RNA was purified from total RNA, processed, and paired-end directional libraries (150 bp) were prepared and sequenced using an Illumina HiSeq 4000 platform (Novogene, Davis, CA).

value: VGII

value: NT


title: SV20, HE rep 1

status: Public on Apr 08 2025

type: SRA

city: Vancouver

first: Tabea

middle: L

last: Stephan

state: BC

address: 2329 West Mall

country: Canada

institute: University of British Columbia

description: Library name: HE rep 1

library_source: transcriptomic

data_processing:
aligned to hg19/GRCH37 using DRAGEN
TPM values were calculated in DRAGEN and differential gene expression was calculated using DESeq2
Assembly: hg19
Supplementary files format and content: TPM values
Supplementary files format and content: excel sheet with all TPM values from all samples

molecule: total RNA

organism: Homo sapiens

source_name: Hepatic endodderm stage

growth_protocol: SV20 iPSCs were differentiated as previously described (Teng Ang et al., 2018). Briefly, cells were grown on Geltrex-coated plates to 100% confluency and subsequently differentiated into definitive endoderm using the StemDiff Endoderm kit from Stemcell Technologies.Cells were then differentiation into posterior foregut cells, hepatic endoderm and subsequently into hepatoblasts as described in Teng Ang et al., 2018.

extract_protocol:
RNA was extracted from collected cell pellets using TRIzol (Thermo Fisher Scientific).
samples were library prepped at the BRC Sequencing core

tag: tissue

value: Hepatic endodderm stage

tag: cell line

tag: cell type

value: differentiated iPSC

tag: genotype

value: WT


title: SV20, HE rep 2

description: Library name: HE rep 2


title: CT-treated and costimulated_donor7

type: RNA

city: Heidelberg

first: Yvonne

last: Samstag

address: INF 305

department: Institute of Immunology

country: Germany

institute: Heidelberg University Hospital

description: total RNA was isolated from T cells pretreated with CT for 1 h  and costimulated for 4 h

hyb_protocol: hybridization of the sample mixed with reporter codeset and capture probeset was done at 65°C for 20 h (according to manufacture's protocol)

scan_protocol: samples were purified, immobilized on cartridges and scanned on the nCounter® SPRINT Profiler (nanoString Technologies)

data_processing: the raw RCC files were uploaded onto the nSolver software, raw counts were measured, stable houskeeping genes for normalization was identified using NormFinder, an excel plug-in software, and data were subsequently normalized to obtain normalized counts. The normalized counts were used for the final evaluations.

label: nCounter® Reporter Codeset and Capture Probeset

source_name: T cells, CD3x28 costimulated, 4 h

label_protocol: for each sample, 5uL of total RNA was mixed with 3uL of reporter codeset and 2uL of capture probeset (according to manufacture's protocol)

extract_protocol: total RNA was extracted using Direct-zol RNA isolation following manufacture's protocol

tag: cells

value: T cells

tag: donor id

value: Donor 7

tag: treatment

value: CT-treated and costimulated


title: untreated and costimulated_donor8

description: total RNA was isolated from T cells kept untreated and costimulated for 4 h

value: Donor 8

value: untreated and costimulated


title: SV20, PFG rep 3

description: Library name: PFG rep 3

source_name: Posterior Foregut stage

value: Posterior Foregut stage


title: Cortex, Q84Pfs/+ P1 rep3

city: Buffalo

first: Soo-Kyung

last: Lee

state: NY

address: 109 Cooke Hall, University at Buffalo, North Campus

department: Biological Sciences

country: USA

institute: University at Buffalo

data_processing:
The paired-end RNA-seq reads were mapped to the mouse reference genome using STAR (v2.6.1d) with the default settings.
Then RSEM (v1.3.3) was used to quantify the gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes expected_count values for each Sample

organism: Mus musculus

source_name: Cortex

extract_protocol:
RNA was extracted from a single hemisphere of the cortex using Rneasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using Illumina Truseq Stranded RNA library prep kit following manufacturer's protocols.

value: Cortex

value: whole cortical cells


title: SV20, PFG rep 2

description: Library name: PFG rep 2


title: C2061, rep1

description: Library name: YC5582-10_S10

treatment_protocol: No treatment


title: untreated and costimulated_donor7


title: SV20, PFG rep 1

description: Library name: PFG rep 1


title: Cortex, Q84Pfs/+ P1 rep1


title: Cortex, Q84Pfs/+ P1 rep2


title: C2104, rep3

description: Library name: YC5582-9_S9


title: C2104, rep2

description: Library name: YC5582-8_S8


title: SV20, DE rep 2

description: Library name: DE rep 2

source_name: Definitive endoderm stage

value: Definitive endoderm stage


title: C2104, rep1

description: Library name: YC5582-7_S7


title: Ap-treated and costimulated_donor6

description: total RNA was isolated from T cells pretreated with Ap for 1 h and costimulated for 4 h

value: Donor 6

value: Ap-treated and costimulated


title: untreated and unstimulated_donor7

description: total RNA was isolated from T cells kept untreated and unstimulated for 4 h

value: untreated and unstimulated


title: DMSO-treated and costimulated_donor6

description: total RNA was isolated from T cells pretreated with DMSO for 1 h and costimulated for 4 h

value: DMSO-treated and costimulated


title: Wildtype Sample 2

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

institute: University of Delaware

description:
WT_2
WT2

data_processing:
Aggregate individual lane files (4 per sample) into a single file for each sample
Remove reads aligning to the Rn45s prespliced transcript using HISAT2
Aligned non Ribosomal reads using HISAT2 ( -fr --rna-strandedness F, default otherwise)
Quantified genes using htseq-count -m union
Normalized counts using TMM (in edgeR)
Tested for differential expression using edgeR's Exact test
Assembly: GRCm39 / Ensembl v104
Supplementary files format and content: Gene level counts and Differential Expression analysis results in an excel spreadsheet

source_name: whole lens

extract_protocol:
Promega SV Total RNA Isolation System
Takara SMARTer Stranded Pico v1; Single end, ribodepletion

value: whole lens

tag: strain

value: lens cells

tag: age

value: 8 weeks

value: wildtype


title: SV20, DE rep 1

description: Library name: DE rep 1

value: differentiated iPSC

value: WT


title: SV20, DE rep 3

description: Library name: DE rep 3


title: Wildtype Sample 1

description:
WT_1
WT1


title: DMSO-treated and costimulated_donor7

value: T cells

value: Donor 7


title: Cd24a Germline Knockout Sample 3

description:
C4_3
Cd24a-3

value: Cd24a Germline knockout


title: CT-treated and costimulated_donor6

value: CT-treated and costimulated


title: C2053, rep3

description: Library name: YC5582-6_S6

value: VGII

value: NT


title: untreated and costimulated_donor6

value: untreated and costimulated


title: SV20, iPSC rep 3

description: Library name: iPSC rep 3

source_name: pluripotent stage

value: pluripotent stage


title: Cd24a Germline Knockout Sample 2

description:
C4_2
Cd24a-2


title: C2053, rep2

description: Library name: YC5582-5_S5


title: untreated and unstimulated_donor6

value: Donor 6


title: C2061, rep2

description: Library name: YC5582-11_S11


title: SV20, iPSC rep 2

description: Library name: iPSC rep 2


title: Wildtype Sample 3

description:
WT_3
WT3


title: Cd24a Germline Knockout Sample 1

description:
C4_1
Cd24a-1


title: C2053, rep1

description: Library name: YC5582-4_S4


title: WM276, rep3

description: Library name: YC5582-3_S3


title: Cz-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with Cz for 1 h and costimulated for 4 h

value: Donor 5

value: Cz-treated and costimulated


title: SV20, HEP rep 3, TBX3 OE

description: Library name: HEP rep 3, TBX3 OE

source_name: Hepatoblast stage

value: Hepatoblast stage

value: TBX3 OE


title: SV20, HEP rep 2, TBX3 OE

description: Library name: HEP rep 2, TBX3 OE


title: DMSO-treated and costimulated_donor5

value: DMSO-treated and costimulated


title: pfnsun3_S_GlcN+_rep2

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

country: China

institute: Central South University

data_processing:
RNA-seq reads were trimmed by trim-galore.
The resulting data was aligned to genome using Hisat2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Read counts  were obtained using FeatureCounts.
Assembly: Pf 3D7 v45
Supplementary files format and content: The raw counts were calculated by FeatureCounts. Then FPKM of each gene was calculated in RStudio.

organism: Plasmodium falciparum 3D7

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax I with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
Total RNA was extracted with the kit (Zymo Research) according to a standardized procedure.
Libraries were carried out by poly(A) selection with the KAPA mRNA Capture Beads (KAPA) and fragmentation to about 300–400 nucleotides (nt) in length according to the KAPA Stranded mRNA-Seq Kit (KK8421).

treatment_protocol: Pfnsun3-ty1-glmS parasites were tightly synchronized by percoll and sorbitol to a 5-hour window with or without 5 mM GlcN treatment. Samples were collected in TRIzol at ring (10-15 hpi), trophozoite (25-30 hpi) and schizont (40-45 hpi) stages of the next cycle, respectively.

tag: developmental stage

value: schizont

value: pfnsun3 knockdown

value: GlcN(+)


title: WM276, rep1

description: Library name: YC5582-1_S1


title: SV20, HEP rep 1, TBX3 OE

description: Library name: HEP rep 1, TBX3 OE

value: differentiated iPSC


title: pfnsun3_T_GlcN+_rep2

value: trophozoite


title: WM276, rep2

description: Library name: YC5582-2_S2


title: CT-treated and costimulated_donor8

value: T cells

value: Donor 8


title: CF-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with CF for 1 h and costimulated for 4 h

value: CF-treated and costimulated


title: pfnsun3_T_GlcN-_rep2

value: normal

value: GlcN(-)


title: ETOH-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with ETOH for 1 h  and costimulated for 4 h

value: ETOH-treated and costimulated


title: SV20, HE rep 3, TBX3 OE

description: Library name: HE rep 3, TBX3 OE

value: Hepatic endodderm stage


title: Experiment_C,Strain_Empy_Vector,Condition_8mM_H2O2,rep2

city: Chapel Hill

first: Christopher

middle: K

last: Cummins

state: NC

address: 120 Mason Farm road

department: BCBP

institute: UNC Chapel Hill

description: Library name: C14982

data_processing:
Sequencing read and base-calling quality were assessed by FastQC v0.11.9
fastq files aligned to the sacCer3 reference genome with Bowtie2
Files were triple filtered from duplicate SAMtools
Gene FPKM were computed with Homer v4.11
To improve the statistical power of differential gene expression analyses, technical and biological replicates were combined by EdgeR v3.34.0
Assembly: SacSer3
Supplementary files format and content: BigWig

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: All yeast strains were grown SC _URA medium

extract_protocol:
RNA extraction was performed with the MasterPure Yeast RNA Purification Kit (Epicentre MPY03010) using the standard protocol including DNA removal step. RNA quality, concentration and purity was determined by Tapestation (Agilent 5067-5576) and nanodrop (Fisher Scientific), and material stored at -80oC until library preparation.
For each biological replicate, three technical replicates of non-strand specific libraries were prepared from 200ng mRNA (Fast RNA-seq Lib Prep Kit v2; Abclonal RK20306)

treatment_protocol: Overnight cultures of yeast strains -/+ Dsup (RAY149 and RGY002 respectively were grown at 30C in SC-URA medium. Cultures were diluted to OD600 0.2 in 30ml SC-URA media, grown to mid-log (OD600 0.6-0.8), standardized to OD600 0.5 and split to 12x 2mL aliquots. An untreated triplicate (T0) was collected by centrifugation, washed in water and flash frozen in liquid nitrogen. To the remaining aliquots in triplicate H2O2 (Fisher Scientific BP2633-500) was added (0, 4, or 8 mM) and cultures incubated at 30oC for 30 min. Cells were collected by centrifugation, washed in water, and flash frozen.

tag: batch

value: C


title: pfnsun3_R_GlcN+_rep2

value: ring


title: pfnsun3_R_GlcN-_rep2


title: untreated and unstimulated_donor5

value: Donor 5

value: untreated and unstimulated


title: SV20, HE rep 2, TBX3 OE

description: Library name: HE rep 2, TBX3 OE

value: TBX3 OE


title: Experiment_C,Strain_Empy_Vector,Condition_8mM_H2O2,rep1

description: Library name: C14981


title: Experiment_C,Strain_Empy_Vector,Condition_8mM_H2O2,rep3

description: Library name: C14983


title: SV20, iPSC rep 1

description: Library name: iPSC rep 1

value: pluripotent stage

value: WT


title: SV20, HE rep 1, TBX3 OE

description: Library name: HE rep 1, TBX3 OE


title: Experiment_C,Strain_Dsup,Condition_8mM_H2O2,rep3

description: Library name: C00283

source_name: Dsup

value: Dsup


title: SV20, PFG rep 3, TBX3 OE

description: Library name: PFG rep 3, TBX3 OE

value: Posterior Foregut stage

value: differentiated iPSC


title: pfnsun3_S_GlcN+_rep1

value: schizont

value: pfnsun3 knockdown

value: GlcN(+)


title: DMSO-treated and costimulated_donor4

value: T cells

value: Donor 4

value: DMSO-treated and costimulated


title: Cz-treated and costimulated_donor4

value: Cz-treated and costimulated


title: pfnsun3_S_GlcN-_rep2

value: normal

value: GlcN(-)


title: Experiment_C,Strain_Dsup,Condition_8mM_H2O2,rep2

description: Library name: C00282

value: C


title: pfnsun3_S_GlcN-_rep1


title: SV20, PFG rep 2, TBX3 OE

description: Library name: PFG rep 2, TBX3 OE


title: Experiment_C,Strain_Dsup,Condition_8mM_H2O2,rep1

description: Library name: C00281


title: CF-treated and costimulated_donor4

value: CF-treated and costimulated


title: pfnsun3_T_GlcN+_rep1

value: trophozoite


title: SV20, PFG rep 1, TBX3 OE

description: Library name: PFG rep 1, TBX3 OE

value: TBX3 OE


title: Experiment_C,Strain_Empy_Vector,Condition_4mM_H2O2,rep3

description: Library name: C14943


title: SV20, DE rep 3, TBX3 OE

description: Library name: DE rep 3, TBX3 OE

value: Definitive endoderm stage


title: untreated and costimulated_donor5

value: Donor 5

value: untreated and costimulated


title: pfnsun3_T_GlcN-_rep1


title: pfnsun3_R_GlcN+_rep1

value: ring


title: ETOH-treated and costimulated_donor4

value: ETOH-treated and costimulated


title: CR-treated and costimulated_donor4

description: total RNA was isolated from T cells pretreated with CR for 1 h  and costimulated for 4 h

value: CR-treated and costimulated


title: Experiment_C,Strain_Empy_Vector,Condition_4mM_H2O2,rep1

description: Library name: C14941


title: Experiment_C,Strain_Empy_Vector,Condition_4mM_H2O2,rep2

description: Library name: C14942


title: SV20, DE rep 1, TBX3 OE

description: Library name: DE rep 1, TBX3 OE

value: differentiated iPSC


title: SV20, DE rep 2, TBX3 OE

description: Library name: DE rep 2, TBX3 OE


title: Experiment_C,Strain_Dsup,Condition_4mM_H2O2,rep3

description: Library name: C00243

value: Dsup


title: Cz-treated and costimulated_donor3

value: T cells

value: Donor 3


title: pfnsun3-R-RIP

description: PfNSUN3 binding RNA

data_processing:
Reads were trimmed by trim-galore.
The resulting data was aligned to the genome using Hisat2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
The bam files were converted to bigwig files using bamCoverage from the deeptools.
Assembly: Pf 3D7 v45
Supplementary files format and content: Bw files for enrichment ratio

extract_protocol:
The RNA was extracted by phenol-chloroform method.
Libraries were carried out by the KAPA mRNA Capture Beads (KAPA) and fragmentation to about 300–400 nucleotides (nt) in length according to the KAPA Stranded mRNA-Seq Kit (KK8421).

treatment_protocol: 5 x 109 synchronized ring-stage parasites were collected and treated by the saponin. The parasite pellets were lysed under non-denaturing condition. The supernatant was collected and incubated with mouse anti-ty1 and protein G magnetic beads. RNA was eluted by TRIzol reagent and extracted by phenol-chloroform. The eluted RNA was directly used to prepare strand-specific RNA-seq libraries without poly (A) enrichment. Libraries were sequenced on an Illumina NovaSeq 6000 system using 150 bp pair-end reads.

tag: rip antibody


title: SV20, iPSC rep 3, TBX3 OE

description: Library name: iPSC rep 3, TBX3 OE

value: pluripotent stage


title: untreated and unstimulated_donor4

value: Donor 4

value: untreated and unstimulated


title: Experiment_C,Strain_Dsup,Condition_4mM_H2O2,rep2

description: Library name: C00242

value: C


title: SV20, iPSC rep 2, TBX3 OE

description: Library name: iPSC rep 2, TBX3 OE


title: Input-R-RIP


title: CF-treated and costimulated_donor3

value: CF-treated and costimulated


title: SV20, iPSC, rep 1, TBX3 OE

description: Library name: iPSC, rep 1, TBX3 OE


title: Experiment_C,Strain_Dsup,Condition_4mM_H2O2,rep1

description: Library name: C00241


title: 346

city: Hong Kong

first: Yimeng

last: Li

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

description:
Library name: Sample 4
Column name in Counts_normalized.txt: 346-FPKM

data_processing:
Low-quality reads were removed by fastp with default parameters.
Remaining clean reads were align to GRCh38 by hisat2 with default parameters.
Raw counts were generated using featureCounts and then normalized by DEseq2.
Assembly: GRCh38
Supplementary files format and content: Matrix tables with raw gene counts or normalized gene counts for every gene and every sample.

source_name: human endometrial organoid

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA). Samples were frozen in a 2mL tube using liquid nitrogen, homogenized in 1.5ml of TRIZOL reagent for 2 min, and then allowed to rest horizontally for 5 min. After centrifugation at 12000g for 5 min at 4°C, the supernatant was collected and mixed with 0.3 mL chloroform/isoamyl alcohol (24:1). The mixture was vigorously shaken for 15 s and then centrifuged at 12000g for 10 min at 4°C. After centrifugation, the upper aqueous phase was mixed with an equal volume of isopropyl alcohol and was centrifuged at 13600g for 20 min at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL of 75% ethanol and air-dried for 5-10 min. RNA samples were dissolved in 25-100μL of DEPC-treated water. Total RNA was qualified and quantified using a NanoDrop (Thermo Fisher Scientific, MA, USA) and Agilent 2100 bioanalyzer (Agilent, CA, US).
Oligo (dT)-attached magnetic beads were utilized to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer (75mM KCl, 6mM MgCl2, 50mM Tris-HCl, pH 8.3). First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis. Afterward, a-Tailing Mix and RNA Index Adapters were added for end repair. The cDNA fragments were amplified by PCR and the resulting PCR products were purified by Ampure XP Beads. The purified products were dissolved in EB (10mM Tris-HCl, pH8.5) solution and were validated on the Agilent 2100 bioanalyzer for quality control. The double-stranded PCR products from the previous step were heat-denatured and circularized by the splint oligo sequence to generate the final library as single-strand circular DNA. The final library was amplified with phi29 to produce DNA nanoballs (DNB), each containing more than 300 copies of single molecule. The DNBs were then loaded into the patterned nanoarray, and paired-end 150 base reads were generated by BGISEQ-500.

value: human endometrial organoid

tag: tubular gland development capacity

value: no


title: CR-treated and costimulated_donor3


title: untreated and costimulated_donor4


title: SV20, HCL, rep 3

data_processing:
aligned to hg19/GRCH37 using STAR (v2.5.0)
FPKM and differential gene expression was calculated using the Cufflinks suite (V2.2.1)
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: csv file with FPKM values
Supplementary files format and content: csv file with FPKM values, separated by NCBI Refseq isoforms

source_name: Hepatocyte-like stage

growth_protocol: SV20 iPSCs were differentiated as previously described (Si-Tayeb et al., 2010 and Teng Ang et al., 2018). Briefly, cells were grown on Geltrex-coated plates to 100% confluency and subsequently differentiated into mesendodermal progenitors using RPMI media supplemented with 1x B27 minus insulin, Activin A (100ng/ml), FGF2 (20ng/ml) and BMP4 (10ng/ml) for 48h. Definitive endodermal cells were further differentiated with Activin A (100 ng/ml) and 1x B27 minus insulin only for additional 48h. Alternatively, definitive endodermal cells were generated using STEMdiff definitive Endoderm Kit (Stemcell Technologies). Subsequently, cells were specified to hepatic endodermal cells for 96h in RPMI supplemented with 1x B27 with insulin, BMP4 (20ng/ml) and FGF2 (10ng/ml) at 4% O2 or for 24h in IMDM/F12 supplemented with A8301 (1uM), BMP4 (30ng/ml), FGF2 (10ng/ml) and TTNPB (75nM) for 24h followed by Activin A (10ng/ml), BMP4 (30ng/ml), 8-bromo-cAMP (1mM) and C-59 (1µM, first 24h)/CHIR99201(1µM, next 48h) for 96h in atmospheric O2. Hepatoblasts were generated with BMP4 (10ng/ml), OSM (10ng/ml), Dexamethasone (10µM), RO4929097 (2µM), Forskolin (10µM), insulin (10µg/ml), transferrin (15µg/ml), AAP (200µg/ml) and SB505124 (1µM, just first 48h) in full IMDM/F12 media for 6 days in atmospheric O2 or by incubation at 4% O2 and in RPMI supplemented with 1x B27 with insulin and HGF (20ng/ml) only.

value: Hepatocyte-like stage


title: SV20, HCL, rep 2


title: Experiment_C,Strain_Empy_Vector,Condition_0mM_H2O2,rep2

description: Library name: C14902


title: 345

description:
Library name: Sample 3
Column name in Counts_normalized.txt: 345-FPKM


title: 375

description:
Library name: Sample 2
Column name in Counts_normalized.txt: 375-FPKM

value: yes


title: pfnsun3_R_GlcN-_rep1

value: normal

value: GlcN(-)


title: Experiment_C,Strain_Dsup,Condition_0mM_H2O2,rep3

description: Library name: C00203


title: SV20, HEP, rep 3

value: Hepatoblast stage


title: 374

description:
Library name: Sample 1
Column name in Counts_normalized.txt: 374-FPKM


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, DMSO, biological replicate 4

first: Austin

middle: J

last: Hepperla

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Library name: 20241205_SN4

data_processing:
On-board Illumina NextSeq 1k BCL Convert
The fastq files were assessed for quality using fastQC (v.0.12.1).
Adapter sequences were removed and reads less than 40 bp in length were discarded using Cutadapt (v.4.10) with setting -m 40.
To obtain read counts, Salmon (v.1.10.2) was used in mapping mode. First, transcriptome indices were prepared with the Salmon index tool using -k 31 and the custom hg38-AAV genome as the decoy sequence. Next, read abundances were quantified using the Salmon quant tool with the automatic library type detection setting -l A.
Differential expression analysis was performed using DESeq2 (v.1.42.1). Results from the differential expression analysis were then shrunk using DESeq2 and the R package apeglm (v.1.24.0).
Assembly: hg38-AAV/SRW039
Supplementary files format and content: sf files contain the transcript abundance output from salmon

extract_protocol:
RNA was harvested using the RNeasy plus mini kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the Illumina Stranded mRNA Prep kit standard protocol.

value: AAV2 infected

value: DMSO


title: SV20, HEP, rep 2

value: differentiated iPSC


title: SV20, HEP, rep 1


title: untreated and unstimulated_donor3

value: T cells


title: untreated and costimulated_donor3

value: Donor 3

value: untreated and costimulated


title: ETOH-treated and costimulated_donor3

value: ETOH-treated and costimulated


title: Experiment_C,Strain_Dsup,Condition_0mM_H2O2,rep2

description: Library name: C00202

value: Dsup


title: Cz-treated and costimulated_donor2

value: Donor 2

value: Cz-treated and costimulated


title: Experiment_C,Strain_Dsup,Condition_0mM_H2O2,rep1

description: Library name: C00201

value: C


title: Experiment_C,Strain_Empy_Vector,Condition_0mM_H2O2,rep3

description: Library name: C14903


title: DMSO-treated and costimulated_donor3

value: DMSO-treated and costimulated


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, DMSO, biological replicate 2

description: Library name: 20241205_SN2


title: SV20, HE, rep 3

source_name: Hepatic endoderm stage

value: Hepatic endoderm stage


title: DMSO-treated and costimulated_donor2


title: Experiment_C,Strain_Empy_Vector,Condition_0mM_H2O2,rep1

description: Library name: C14901


title: Experiment_C,Strain_Empy_Vector,Condition_T0,rep3

description: Library name: C149T03


title: CF-treated and costimulated_donor2

value: CF-treated and costimulated


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, DMSO, biological replicate 1

description: Library name: 20241205_SN1


title: SV20, HE, rep 2


title: CR-treated and costimulated_donor2

value: CR-treated and costimulated


title: Experiment_C,Strain_Empy_Vector,Condition_T0,rep2

description: Library name: C149T02


title: Experiment_C,Strain_Empy_Vector,Condition_T0,rep1

description: Library name: C149T01


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, DMSO, biological replicate 3

description: Library name: 20241205_SN3


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, 300 nM C207, biological replicate 4

description: Library name: 20241205_S24


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, 300 nM C207, biological replicate 3

description: Library name: 20241205_S23


title: SV20, HE, rep 1


title: ETOH-treated and costimulated_donor2


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, 300 nM C207, biological replicate 2

description: Library name: 20241205_S22


title: Experiment_C,Strain_Dsup,Condition_T0,rep3

description: Library name: C002T03


title: SV20, iPSC, rep 1

source_name: pluripotent

value: pluripotent


title: SV20, DE, rep 3

value: Definitive endoderm stage


title: Experiment_C,Strain_Dsup,Condition_T0,rep1

description: Library name: C002T01


title: untreated and costimulated_donor2


title: SV20 HE, input

library_source: genomic

data_processing:
aligned to hg19/GRCH37 using STAR (v2.5.0)
Bam files filtered using encode_task_filter.py from the ENCODE chip-seq-pipeline2, dublicate reads mapped using Picard (v2.1.1.1), unmapped, unpaired, low quality (MAPQ<5), non-primary alignment reads removed using SAM flag filter '-F 1804' using SAMtools (v1.3)
peaks were called using MACS2
Bigwig files were generated using MACS2 and deeptools
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
1 million (histone modification ChIP-seq) to 10 million (transcription factor ChIP-seq) cells were cross-linked with 1 % fresh methanol-free formaldehyde for 10 min at room temperature (RT). The cross-linking was stopped with the addition of fresh glycine to a final concentration of 0.125M and incubation for 5 min at RT. Cells were subsequently washed twice with cold PBS, pelleted and resuspended in cold ChIP lysis buffer and lysed for 15 min on ice while dounce homogenizing 20x during the incubation. After re-pelleting, nuclei were resuspended in ChIP nuclear lysis buffer for 30-60 min on ice. Chromatin was sheared by sonication for 20 cycles at 60 hz for 30 sec on/30 sec off. Cellular debris was removed by centrifugation. Chromatin was pre-cleared by rotating at 4 °C for 1h with Protein A/G Ultralink beads (Thermo Fisher Scientific, Pierce) in ChIP dilution buffer. Chromatin was incubated with primary antibodies overnight at 4°C while rotating. Protein A/G Ultralink beads (Thermo Fisher Scientific, Pierce) were added to the immunoprecipitation (chromatin + antibody) mix and incubated at 4°C for further 4 hours. Unbound fraction of the IgG chromatin solution was kept as input DNA. Beads were subsequently washed for 5 min at 4°C once each in low salt buffer, high salt buffer, lithium chloride buffer, followed by two washes in TE buffer, before eluting the DNA by incubating the beads in 125µl-250µl fresh elution buffer for 15 min at RT while vortexing/rotating. To reverse the cross-linking, samples were incubated overnight at 65°C in 0.192M NaCl, 40mM Tris-Cl, pH6.5, 10mM EDTA, 0.08mg/ml Proteinase K and 0.1 mg/ml RNaseA. DNA was subsequently extracted and purified by phenol-chloroform extraction and precipitated in Ethanol at -80°C before being resuspended in 50µl of H2O.
samples were library prepped using the NEBNext Ultra II DNA library Prep Kit for Illumina following manufacturer’s recommendations

value: Hepatic endodderm stage

tag: chip antibody


title: SV20 DE, input


title: U2OS cells, no infection, 300 nM C207, biological replicate 3

description: Library name: 20241205_N23

value: WT


title: Experiment_C,Strain_Dsup,Condition_T0,rep2

description: Library name: C002T02


title: U2OS cells, no infection, 300 nM C207, biological replicate 4

description: Library name: 20241205_N24


title: DMSO-treated and costimulated_donor1

value: Donor 1


title: CF-treated and costimulated_donor1

value: T cells


title: Cz-treated and costimulated_donor1


title: Experiment_B,Strain_Empy_Vector,Condition_8mM_H2O2,rep2

description: Library name: B14982

value: B


title: SV20 ME, input

source_name: Mesendoderm stage

value: Mesendoderm stage

value: differentiated iPSC


title: Experiment_B,Strain_Empy_Vector,Condition_8mM_H2O2,rep3

description: Library name: B14983


title: untreated and unstimulated_donor2

value: untreated and unstimulated


title: SV20 HEP, H3K36me3, ChIP

value: Hepatoblast stage

value: ab9050, abcam


title: U2OS cells, no infection, 300 nM C207, biological replicate 2

description: Library name: 20241205_N22


title: Experiment_B,Strain_Empy_Vector,Condition_8mM_H2O2,rep1

description: Library name: B14981


title: U2OS cells, no infection, DMSO, biological replicate 4

description: Library name: 20241205_N4

value: DMSO


title: U2OS cells, 10k vg/cell AAV2 Jet-FKBP*, 300 nM C207, biological replicate 1

description: Library name: 20241205_S21

value: AAV2 infected


title: U2OS cells, no infection, 300 nM C207, biological replicate 1

description: Library name: 20241205_N21


title: SV20 HE, H3K36me3, ChIP


title: Experiment_B,Strain_Dsup,Condition_8mM_H2O2,rep2

description: Library name: B00282

value: Dsup


title: U2OS cells, no infection, DMSO, biological replicate 3

description: Library name: 20241205_N3


title: Experiment_B,Strain_Dsup,Condition_8mM_H2O2,rep3

description: Library name: B00283


title: SV20 ME, H3K36me3, ChIP


title: U2OS cells, no infection, DMSO, biological replicate 2

description: Library name: 20241205_N2


title: ETOH-treated and costimulated_donor1

value: ETOH-treated and costimulated


title: SV20 HEP, H3K27me3, ChIP

value: C154410096, Diagenode


title: untreated and costimulated_donor1

value: untreated and costimulated


title: Experiment_B,Strain_Dsup,Condition_8mM_H2O2,rep1

description: Library name: B00281


title: Experiment_B,Strain_Empy_Vector,Condition_4mM_H2O2,rep2

description: Library name: B14942


title: untreated and unstimulated_donor1


title: Infected potato 3

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: small RNA

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite applying the Sanger / phred33 / Illumina 1.8+ quality scale
The function SamToFastq, included in the Picard tool package, was used to convert the original BAM format to FASTQ format (for the raw data which was not already in FASTQ format), on which a quality control was performed, using FastQC.
Cutadapt was used for quality trimming with a cutoff of 20 using 18 nt and 38 nt as minimum and maximum read lengths
Bowtie2 in combination with SAMtools view were used for tRNA and rRNA trimming, allowing 0 mismatches per seed against each filtered dataset
The same tools were used to separate potato and P. infestans sRNA by first mapping the sRNA to the individual genomes
Next, the St-sRNA pool was trimmed against the P. infestans genome and the Pi-sRNA pool was trimmed against the potato genome to exclude potential false positives
SamToFastq (Picard Tools) converted the files to FASTQ format. Seqtk was applied to convert the FASTQ files to FASTA.
Assembly: Solanum Tuberosum PGSC v4.04 | Phytophthora infestans T30-4 (ASM14294v1.33)
Supplementary files format and content: rpm

organism: Solanum tuberosum

source_name: Leaf

growth_protocol: Leaves with lesion sizes between 8 and 12 mm from a potato line harboring p35S:StAgo15-GFP inoculated with P. infestans (Pi) strain 3928A were collected 5 days post inoculation (dpi). In parallel, leaf materials from water inoculated potato Desirée were prepared.

extract_protocol:
Three replicates for each sample consisting of 2 g of pooled leaf material were used for co-immunoprecipitation as earlier described (Åsman et al., 2016).
Six libraries were prepared at the SciLifeLab (Solna, Sweden).
The libraries were designed for Illumina NextSeq 2000 P2 (2x50bp), with a 51nt (Read1, R1)-6nt (Index1)-51nt (Read2, R2) setup using Illumina TrueSeq small RNA Kit.

value: Leaf

tag: cultivar

value: Desiree

tag: agent

value: Inoculated with Phytophthora infestans 3928A


title: U2OS cells, no infection, DMSO, biological replicate 1

description: Library name: 20241205_N1

value: WT


title: SV20 HE, H3K27me3, ChIP

value: Hepatic endodderm stage


title: Experiment_B,Strain_Empy_Vector,Condition_4mM_H2O2,rep3

description: Library name: B14943

value: B


title: Experiment_B,Strain_Empy_Vector,Condition_4mM_H2O2,rep1

description: Library name: B14941


title: Infected potato 1

description: small RNA


title: Infected potato 2

description: small RNA


title: SV20 DE, H3K27me3, ChIP

value: Definitive endoderm stage


title: FunGeST MESO cell lines methylation, MPM_41 (HumanMethylation450)

type: genomic

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

hyb_protocol: Methylation analysis was performed either on the Infinium HumanMethylation450 Beadchip (Illumina) or on the Infinium MethylationEPIC BeadChip Kit (Illumina), following the supplier’s recommendations. Briefly, samples were denatured, neutralised, and incubated in an Illumina hybridisation oven for 20-24 hours at 37°C to uniformly amplify genomic DNA and then enzymatically fragmented. Following the fragmentation step, the samples were hybridised to BeadChip and incubated at 48°C for 16-24 hours in an Illumina hybridisation oven. Finally, non-hybridised and non-specific hybridised DNA samples were washed from BeadChip, and labelled nucleotides were added to extend and stain the primers hybridised to the samples.

scan_protocol: The Illumina iScan system (with iScan Control Software) was used to scan Illumina HumanMethylation450 and MethylationEPIC BeadChips

data_processing:
Raw data were analysed using GenomeStudio software according to Illumina’s recommendations to generate result files with beta values.
Processed value definition: Average Beta

label: Cy3 and Cy5

source_name: Pleural Mesothelioma

label_protocol: Standard Illumina protocol

growth_protocol: Patient-derived PM cell lines were cultured in RPMI 1640 medium (Gibco Life Technologies) supplemented with 10% foetal bovine serum (Gibco Life Technologies) and 1% penicillin/streptomycin (Gibco Life Technologies), in a 37°C incubator with 5% CO2.

extract_protocol: Genomic DNA from cell pellets obtained from cultures of PM primary cell lines at low passages were extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol.

value: Pleural Mesothelioma

value: primary

tag: Sex

value: male


title: CR-treated and costimulated_donor1

value: T cells

value: Donor 1

value: CR-treated and costimulated


title: SV20 DE, H3K36me3, ChIP

tag: tissue

value: differentiated iPSC

value: ab9050, abcam


title: Experiment_B,Strain_Dsup,Condition_4mM_H2O2,rep3

description: Library name: B00243

value: Dsup


title: Experiment_B,Strain_Dsup,Condition_4mM_H2O2,rep2

description: Library name: B00242


title: FunGeST MESO cell lines methylation, MPM_60 (HumanMethylation450)

tag: cell line

value: female


title: FunGeST MESO cell lines methylation, MPM_10 (HumanMethylation450)

tag: cell type


title: SV20 HEP, H3K27ac, ChIP

value: Hepatoblast stage

value: ab4729, abcam


title: Potato (control) 1

description: small RNA

value: Leaf

value: Desiree

value: Inoculated with water


title: Potato (control) 2

description: small RNA


title: SV20 HE, H3K27ac, ChIP

value: Hepatic endodderm stage


title: Experiment_B,Strain_Dsup,Condition_4mM_H2O2,rep1

description: Library name: B00241

value: B


title: SV20 DE, H3K27ac, ChIP

value: Definitive endoderm stage


title: FunGeST MESO cell lines methylation, MPM_16 (HumanMethylation450)

value: Pleural Mesothelioma

value: primary


title: SV20 ME, H3K27ac, ChIP

value: Mesendoderm stage


title: Experiment_B,Strain_Empy_Vector,Condition_0mM_H2O2,rep3

description: Library name: B14903


title: SV20 HEP, H3K4me1, ChIP

value: C15410037, Diagenode


title: HEK293T, NLS-dCas13-NLS-edNAT10 transfection, nuclear fraction, rep2

city: Daejeon

first: Won Do

last: Heo

address: 291, Daehak-ro, Yuseong-gu

department: Department of Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology (KAIST)

description:
Library name: Fractionation-seq sample 8
Nuc_dN2

data_processing:
Raw reads were trimmed using Trimmomatic v0.40 (settings: 3 LEADING/TRAILING; 4:15 SLIDINGWINDOW; 36 MINLEN).
Trimmed reads were aligned and quantified to the RefSeq GRCh38 human transcriptome or RefSeq GRCm39 mouse transcriptome using Kallisto (v.0.43.1).
Expression matrix was obtained, and transcript ID was matched with each annotated gene name using tximport (v.1.22.0), with RefSeq GFF as a reference. TPM values were extracted for each gene.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Xlsx file including TPM values for each sample

molecule: nuclear RNA

growth_protocol: HEK293T cells (ATCC) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin (Gibco). Cells were maintained in T75 flasks (SPL) at 37℃ in a humidified 10% CO2 incubator and subcultured every other day.

extract_protocol:
Total RNA was isolated and purified using a PureLink RNA Mini Kit (Invitrogen). For acRIP-seq, one day before immunoprecipitation, Protein G Dynabeads (Invitrogen) was mixed with antibody and incubated overnight at 4℃ with rotation. 1.5 ug of rabbit anti-ac4C (Abcam, ab252215) and 1.5 ug of rabbit isotype IgG (CST, #3900) was used for each sample. In both cases (anti-ac4C and isotype controls), 35 ug of isolated total RNA was mixed with antibody-conjugated beads. Samples were incubated for 4 hours at 4℃ with rotation. After incubation, beads were washed three times with RIP buffer, and bound RNA was eluted using lysis buffer provided in the PureLink RNA Mini Kit, supplemented with 1% beta-mercaptoethanol (Sigma). Eluted RNA was purified using an RNA Clean & Concentrator kit (Zymo Research). For ac4C-seq, total RNA was split into two reactions: the first half (10 ug) was incubated with 10 ul of 1 M NaCNBH3 (Sigma) and 10 ul of 1 M HCl (Sigma), and the reaction volume was adjusted to 100 ul with nuclease-free distilled water; the second half (NaCNBH3-untreated controls) was the same except that NaCNBH3 was replaced with 10 ul of distilled water. Reactions were carried out for 20 minutes at room temperature, then were terminated by addition of 30 ul of Tris-HCl pH 8.0 (LPS solution). RNA was precipitated with 3 M sodium acetate (Invitrogen) and 70% ethanol. For fractionation-seq, transfected cells grown in 6-well cell culture plate were harvested and resuspended with 200 µl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 in DPBS). Cells were lysed on ice for exactly 2 minutes and the lysis was terminated by adding 500 ul resuspension buffer (1% bovine serum albumin, 0.2 U/ul murine RNase inhibitor in DPBS). Samples were centrifuged at 500g for 10 minutes at 4℃, and supernatant was carefully harvested for cytoplasmic fraction. Pallets were washed two more times with 500 ul resuspension buffer, and resulting pallet was harvested for nuclear fraction. Cytoplasmic fraction and nuclear fraction were subjected to RNA isolation
Sequencing library was constructed from RNA samples using SureSelect RNA Direct kit (Agilent).

tag: genotype

value: WT


title: HEK293T, NLS-dCas13-NLS-edNAT10 transfection, nuclear fraction, rep1

description:
Library name: Fractionation-seq sample 7
Nuc_dN1


title: FunGeST MESO cell lines methylation, MPM_14 (HumanMethylation450)

value: male


title: FunGeST MESO cell lines methylation, MPM_57 (HumanMethylation450)


title: Experiment_B,Strain_Empy_Vector,Condition_0mM_H2O2,rep2

description: Library name: B14902


title: FunGeST MESO cell lines methylation, MPM_12 (HumanMethylation450)


title: HEK293T, NLS-dCas13-NLS-eNAT10 transfection, nuclear fraction, rep2

description:
Library name: Fractionation-seq sample 6
Nuc_N2


title: HEK293T, NLS-dCas13-NLS-eNAT10 transfection, nuclear fraction, rep1

description:
Library name: Fractionation-seq sample 5
Nuc_N1


title: SV20 HE, H3K4me1, ChIP

value: differentiated iPSC


title: SV20 ME, H3K27me3, ChIP

value: C154410096, Diagenode


title: Experiment_B,Strain_Empy_Vector,Condition_0mM_H2O2,rep1

description: Library name: B14901


title: Potato (control) 3

description: small RNA


title: Experiment_B,Strain_Dsup,Condition_0mM_H2O2,rep3

description: Library name: B00203

value: Dsup


title: FunGeST MESO cell lines methylation, MPM_37 (HumanMethylation450)


title: FunGeST MESO cell lines methylation, MPM_30 (HumanMethylation450)


title: HEK293T, NLS-dCas13-NLS-edNAT10 transfection, cytoplasmic fraction, rep2

description:
Library name: Fractionation-seq sample 4
Cyt_dN2

molecule: cytoplasmic RNA


title: HEK293T, NLS-dCas13-NLS-edNAT10 transfection, cytoplasmic fraction, rep1

description:
Library name: Fractionation-seq sample 3
Cyt_dN1


title: Experiment_B,Strain_Dsup,Condition_0mM_H2O2,rep2

description: Library name: B00202


title: SV20 DE, H3K4me1, ChIP


title: SV20 HEP, H3K4me3, ChIP

value: Hepatoblast stage

value: clone C42D8, Cell Signalling


title: FunGeST MESO cell lines methylation, MPM_08 (HumanMethylation450)


title: HEK293T, NLS-dCas13-NLS-eNAT10 transfection, cytoplasmic fraction, rep2

description:
Library name: Fractionation-seq sample 2
Cyt_N2


title: Experiment_B,Strain_Empy_Vector,Condition_T0,rep3

description: Library name: B149T03


title: FunGeST MESO cell lines methylation, MPM_27 (HumanMethylation450)

value: female


title: FunGeST MESO cell lines methylation, MPM_09 (HumanMethylation450)


title: Experiment_B,Strain_Empy_Vector,Condition_T0,rep2

description: Library name: B149T02


title: HEK293T, dCas13-NES-edNAT10 transfection, rep3

description:
Library name: RNA-seq sample 6
dN3


title: SV20 HE, H3K4me3, ChIP


title: FunGeST MESO cell lines methylation, MPM_31 (HumanMethylation450)


title: FunGeST MESO cell lines methylation, MPM_11 (HumanMethylation450)


title: HEK293T, dCas13-NES-edNAT10 transfection, rep1

description:
Library name: RNA-seq sample 4
dN1


title: FunGeST MESO cell lines methylation, MPM_19 (HumanMethylation450)


title: SV20 ME, H3K4me3, ChIP


title: Experiment_B,Strain_Dsup,Condition_T0,rep2

description: Library name: B002T02


title: HEK293T, dCas13-NES-edNAT10 transfection, rep2

description:
Library name: RNA-seq sample 5
dN2


title: HEK293T, dCas13-NES-eNAT10 transfection, rep3

description:
Library name: RNA-seq sample 3
N3


title: Experiment_B,Strain_Dsup,Condition_0mM_H2O2,rep1

description: Library name: B00201


title: FunGeST MESO cell lines methylation, MPM_28 (HumanMethylation450)


title: Experiment_B,Strain_Dsup,Condition_T0,rep1

description: Library name: B002T01


title: FunGeST MESO cell lines methylation, MPM_23 (HumanMethylation450)


title: SV20 ME, H3K4me1, ChIP


title: HEK293T, dCas13-NES-eNAT10 transfection, rep2

description:
Library name: RNA-seq sample 2
N2


title: FunGeST MESO cell lines methylation, MPM_40 (HumanMethylation450)


title: Experiment_A,Strain_Empy_Vector,Condition_8mM_H2O2,rep3

description: Library name: A14983

value: A


title: HEK293T, dCas13-NES-eNAT10 transfection, rep1

description:
Library name: RNA-seq sample 1
N1


title: HEK293T, NLS-dCas13-NLS-eNAT10 transfection, cytoplasmic fraction, rep1

description:
Library name: Fractionation-seq sample 1
Cyt_N1


title: Experiment_A,Strain_Empy_Vector,Condition_8mM_H2O2,rep2

description: Library name: A14982


title: Experiment_B,Strain_Empy_Vector,Condition_T0,rep1

description: Library name: B149T01


title: SV20 DE, H3K4me3, ChIP


title: FunGeST MESO cell lines methylation, MPM_25 (HumanMethylation450)


title: HEK293T, dCas13-NES-edNAT10 transfection, untreat, rep2

description:
Library name: ac4C-seq sample 8
Un_dN2

value: HCl


title: FunGeST MESO cell lines methylation, MPM_07 (HumanMethylation450)


title: Experiment_A,Strain_Empy_Vector,Condition_8mM_H2O2,rep1

description: Library name: A14981


title: Experiment_B,Strain_Dsup,Condition_T0,rep3

description: Library name: B002T03


title: K1808Mt6

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Tumor ID: K1808Mt6

hyb_protocol: Labeled RNA was hybridized to DNA microarrays using the Gene Expression Hybridization Kit (Agilent Technologies, Inc.) at 65°C for 17 h

scan_protocol: Microarrays were scanned with DNA Microarray Scanner, Model G2565BA (Agilent Technologies, Inc.). The image data were processed with the Feature Extraction 10.7.3.1 software (Agilent Technologies, Inc.).

data_processing: On the GeneSpring GX 11.5.1 software (Agilent Technologies, Inc.), data from different microarrays were normalized to the seventy-fifth percentile of raw signal values. Values for each probe were then transformed to log2-fold differences from the median value of all samples.

organism: Rattus norvegicus

source_name: mammary cancer

label_protocol: Cyanine 3-labeled complementary RNA was generated from total RNA samples using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA).

growth_protocol: Female Sprague-Dawley rats (Jcl:SD; Clea Japan, Tokyo, Japan) were housed in autoclaved cages and maintained in rooms with controlled temperature and humidity under a regular 12-hour light/12-hour dark cycle with a standard laboratory diet (CE-2; Clea Japan) and water provided ad libitum.

extract_protocol: Total RNA was extracted from frozen carcinomas and frozen tissues with AllPrep Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer protocol.

treatment_protocol: Postnatal rats (weeks 1, 3, or 7 after birth) were whole-body irradiated with gamma rays at 2.0 Gy under pentobarbital-mediated anesthesia.

value: exposure to gamma rays (2 Gy, 1 weeks of age)

tag: diet

value: CE2 diet


title: K1821Mt1

description: Tumor ID: K1821Mt1


title: HEK293T, dCas13-NES-edNAT10 transfection, untreat, rep1

description:
Library name: ac4C-seq sample 7
Un_dN1


title: Experiment_A,Strain_Dsup,Condition_8mM_H2O2,rep3

description: Library name: A00283


title: FunGeST MESO cell lines methylation, MPM_33 (HumanMethylation450)


title: K1808Mt1

description: Tumor ID: K1808Mt1


title: Experiment_A,Strain_Dsup,Condition_8mM_H2O2,rep1

description: Library name: A00281


title: HEK293T, dCas13-NES-edNAT10 transfection, NaCNBH3-treated, rep2

description:
Library name: ac4C-seq sample 4
Red_dN2

value: NaCNBH3, HCl


title: FunGeST MESO cell lines methylation, MPM_17 (HumanMethylation450)

value: Pleural Mesothelioma


title: HEK293T, dCas13-NES-eNAT10 transfection, untreat, rep2

description:
Library name: ac4C-seq sample 6
Un_N2


title: Experiment_A,Strain_Dsup,Condition_8mM_H2O2,rep2

description: Library name: A00282


title: K1753Mt1

description: Tumor ID: K1753Mt1

value: exposure to gamma rays (2 Gy, 3 weeks of age)


title: FunGeST MESO cell lines methylation, MPM_59 (HumanMethylation450)

value: primary


title: Experiment_A,Strain_Empy_Vector,Condition_4mM_H2O2,rep3

description: Library name: A14943


title: FunGeST MESO cell lines methylation, MPM_02 (HumanMethylation450)


title: Experiment_A,Strain_Empy_Vector,Condition_4mM_H2O2,rep2

description: Library name: A14942


title: HEK293T, dCas13-NES-edNAT10 transfection, NaCNBH3-treated, rep1

description:
Library name: ac4C-seq sample 3
Red_dN1


title: HEK293T, dCas13-NES-eNAT10 transfection, untreat, rep1

description:
Library name: ac4C-seq sample 5
Un_N1


title: K1784Mt2

description: Tumor ID: K1784Mt2


title: FunGeST MESO cell lines methylation, MPM_04 (HumanMethylation450)


title: K1797Mt4

description: Tumor ID: K1797Mt4


title: K1692Mt5

description: Tumor ID: K1692Mt5


title: HEK293T, dCas13-NES-eNAT10 transfection, NaCNBH3-treated, rep2

description:
Library name: ac4C-seq sample 2
Red_N2


title: Experiment_A,Strain_Empy_Vector,Condition_4mM_H2O2,rep1

description: Library name: A14941


title: FunGeST MESO cell lines methylation, MPM_32 (HumanMethylation450)


title: Experiment_A,Strain_Dsup,Condition_4mM_H2O2,rep3

description: Library name: A00243


title: HEK293T, dCas13-NES-eNAT10 transfection, NaCNBH3-treated, rep1

description:
Library name: ac4C-seq sample 1
Red_N1


title: K1667Mt1

description: Tumor ID: K1667Mt1


title: FunGeST MESO cell lines methylation, MPM_45 (HumanMethylation450)


title: K1667Mt4

description: Tumor ID: K1667Mt4


title: K1618Mt1

description: Tumor ID: K1618Mt1


title: HEK293T, NLS-dCas13-NLS-edNAT10 and T gRNA transfection, isotype control IP, rep2

description:
Library name: acRIP-seq sample 26
IgG_dN2L

value: isotype control IP


title: K1662Mt1

description: Tumor ID: K1662Mt1

value: exposure to gamma rays (2 Gy, 7 weeks of age)


title: FunGeST MESO cell lines methylation, MPM_22 (HumanMethylation450)

value: male


title: FunGeST MESO cell lines methylation, MPM_53 (HumanMethylation450)


title: HEK293T, NLS-dCas13-NLS-edNAT10 and T gRNA transfection, isotype control IP, rep1

description:
Library name: acRIP-seq sample 25
IgG_dN1L

value: WT


title: Experiment_A,Strain_Dsup,Condition_4mM_H2O2,rep2

description: Library name: A00242


title: Experiment_A,Strain_Dsup,Condition_4mM_H2O2,rep1

description: Library name: A00241


title: FunGeST MESO cell lines methylation, MPM_18 (HumanMethylation450)


title: HEK293T, NLS-dCas13-NLS-eNAT10 and T gRNA transfection, isotype control IP, rep2

description:
Library name: acRIP-seq sample 24
IgG_N2L


title: FunGeST MESO cell lines methylation, MPM_05 (HumanMethylation450)


title: K1600Mt1

description: Tumor ID: K1600Mt1


title: HEK293T, NLS-dCas13-NLS-eNAT10 and T gRNA transfection, isotype control IP, rep1

description:
Library name: acRIP-seq sample 23
IgG_N1L


title: HEK293T, NLS-dCas13-NLS-edNAT10 and T gRNA transfection, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 22
ac4C_dN2L

value: anti-ac4C IP


title: FunGeST MESO cell lines methylation, MPM_15 (HumanMethylation450)


title: Experiment_A,Strain_Empy_Vector,Condition_0mM_H2O2,rep2

description: Library name: A14902


title: Experiment_A,Strain_Empy_Vector,Condition_0mM_H2O2,rep1

description: Library name: A14901


title: HEK293T, NLS-dCas13-NLS-edNAT10 and T gRNA transfection, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 21
ac4C_dN1L


title: FunGeST MESO cell lines methylation, MPM_64 (HumanMethylation450)


title: HEK293T, NLS-dCas13-NLS-eNAT10 and T gRNA transfection, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 20
ac4C_N2L


title: Experiment_A,Strain_Dsup,Condition_0mM_H2O2,rep3

description: Library name: A00203

value: Dsup


title: FunGeST MESO cell lines methylation, MPM_01 (HumanMethylation450)


title: K1596Mt1

description: Tumor ID: K1596Mt1


title: K1539Mt2

description: Tumor ID: K1539Mt2


title: K1635Mt1

description: Tumor ID: K1635Mt1

value: spontaneous


title: HEK293T, NLS-dCas13-NLS-eNAT10 and T gRNA transfection, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 19
ac4C_N1L


title: Experiment_A,Strain_Dsup,Condition_0mM_H2O2,rep2

description: Library name: A00202


title: Experiment_A,Strain_Empy_Vector,Condition_0mM_H2O2,rep3

description: Library name: A14903


title: K1506Mt3

description: Tumor ID: K1506Mt3


title: Experiment_A,Strain_Dsup,Condition_0mM_H2O2,rep1

description: Library name: A00201


title: FunGeST MESO cell lines methylation, MPM_43 (HumanMethylation450)


title: HEK293T, dCas13-NES-edNAT10 and T gRNA transfection, isotype control IP, rep3

description:
Library name: acRIP-seq sample 18
IgG_dN3E


title: Experiment_A,Strain_Empy_Vector,Condition_T0,rep3

description: Library name: A149T03


title: K1516Mt3

description: Tumor ID: K1516Mt3


title: K1165Mt1

description: Tumor ID: K1165Mt1


title: FunGeST MESO cell lines methylation, MPM_29 (HumanMethylation450)


title: K1154Mt1

description: Tumor ID: K1154Mt1


title: K1439Mt1

description: Tumor ID: K1439Mt1


title: HEK293T, dCas13-NES-edNAT10 and T gRNA transfection, isotype control IP, rep2

description:
Library name: acRIP-seq sample 17
IgG_dN2E


title: Experiment_A,Strain_Empy_Vector,Condition_T0,rep2

description: Library name: A149T02


title: FunGeST MESO cell lines methylation, MPM_35 (HumanMethylation450)


title: Experiment_A,Strain_Empy_Vector,Condition_T0,rep1

description: Library name: A149T01


title: FunGeST MESO cell lines methylation, MPM_67 (HumanMethylation450)


title: K1113Mt1

description: Tumor ID: K1113Mt1


title: K1051Mt1

description: Tumor ID: K1051Mt1


title: HEK293T, dCas13-NES-eNAT10 and T gRNA transfection, isotype control IP, rep3

description:
Library name: acRIP-seq sample 15
IgG_T3E


title: HEK293T cells, SA3

city: Beijing

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

description: Library name: sample6

data_processing:
The Bowtie2 software was used to compare the high-quality Reads obtained from the sequencing of each sample with the reference genome to obtain the alignment efficiency of the sample Reads and the position information of the Reads on the genome.
Assembly: Homo_sapiens.GRCh38.dna.alt.fa
Supplementary files format and content: xlsx files include peaks for each Sample

extract_protocol:
DNA was harvested using  DNA QIAGEN Acube HT Kit.
50000 cells were centrifuged using 4℃,5 min and 500 g centrifuging parameters, and then the supernatant was removed. The cells were washed with cold PBS once. Using 4℃,5min and 500 g centrifuging parameters the supernatant was removed.The cells were suspended with cold lysis buffer. Using 4℃,10 min and 500 g centrifuging parameters the supernatant was removed. The transposing reaction system was configured with the Tn5 Transposase. The cell nucleus were suspended with the transposing reaction system, and the DNA were purified after incubating at 37℃ for 30 minutes. The PCR reaction system was configured with the purified DNA ,and then the PCR amplification reaction was performed. The final DNA libraries were runned on sequencing platform after the DNA were purified.

value: Epithelial Cell

value: SA

value: Adavosertib


title: HEK293T, dCas13-NES-eNAT10 and T gRNA transfection, isotype control IP, rep2

description:
Library name: acRIP-seq sample 14
IgG_T2E


title: HEK293T cells, SA2

description: Library name: sample5


title: K0244Mt1

description: Tumor ID: K0244Mt1


title: Experiment_A,Strain_Dsup,Condition_T0,rep2

description: Library name: A002T02

value: A


title: HEK293T, dCas13-NES-eNAT10 and NT gRNA transfection, isotype control IP, rep3

description:
Library name: acRIP-seq sample 12
IgG_NT3E


title: HEK293T, dCas13-NES-eNAT10 and T gRNA transfection, isotype control IP, rep1

description:
Library name: acRIP-seq sample 13
IgG_T1E


title: HEK293T cells, SA1

description: Library name: sample4


title: HEK293T, dCas13-NES-edNAT10 and T gRNA transfection, isotype control IP, rep1

description:
Library name: acRIP-seq sample 16
IgG_dN1E


title: Experiment_A,Strain_Dsup,Condition_T0,rep1

description: Library name: A002T01


title: Infected

city: Manhattan

first: Gagandeep

last: Singh

state: KS

address: 1800 Denison Ave

institute: Kansas State Univeristy

description:
Library name: Sample 2
10X genomics

library_source: transcriptomic single cell

data_processing:
The sequencing process yielded raw fastq files which were used for input for cellranger package v9.0.0 (10X genomics) using 10x genomics cloud.
Assembly: Bovine reference and annotation (ARS-UCD1.2/bosTau9)
Supplementary files format and content: cloupe file (10x genomics Loupe brower file)

organism: Bos taurus

source_name: raw milk

extract_protocol:
The cells and viruses were then incubated together for 24 hrs at 37oC supplemented with 5% CO2. After 24 hrs incubation, cells were centrifuged at 400xg for 5 mins at 4oC to remove debris and ambient host and viral DNA/RNA. The cells were again subjected to Dead Cell Removal Kit (Miltenyi Biotec) for removing dead cells and debris and to reach the viable cell target of more than 70% live cells for scRNA-seq experiments.
The library was constructed using Chromium Next GEM Single Cell 5' Reagent Kits v2 (10X genomics) following manufacturer’s instructions. Briefly, single-cells suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10000 individual cells per sample using Chromium Controller (10x Genomics).

treatment_protocol: Pooled bMSCs plated at density of 1x106 cells/well in low Ultra-Low attachment 6-well plate (Corning) were infected with 0.01 multiplicity of infection (MOI) with either bovine-H5N1 or infection media.

value: raw milk

value: Female

value: milk somatic cells

value: Holstein-Friesian

value: H5N1 infection

tag: virus isolate

value: A/dairy cattle/Kansas/5/2024


title: HEK293T cells, WT3

description: Library name: sample3

tag: treatment


title: HEK293T cells, WT2

description: Library name: sample2


title: HEK293T, dCas13-NES-eNAT10 and NT gRNA transfection, isotype control IP, rep1

description:
Library name: acRIP-seq sample 10
IgG_NT1E

value: isotype control IP


title: Control

description:
Library name: Sample 1
10X genomics

value: uninfected


title: HEK293T, dCas13-NES-eNAT10 and NT gRNA transfection, isotype control IP, rep2

description:
Library name: acRIP-seq sample 11
IgG_NT2E


title: Experiment_A,Strain_Dsup,Condition_T0,rep3

description: Library name: A002T03

tag: strain


title: HEK293T, dCas13-NES-edNAT10 and T gRNA transfection, anti-ac4C IP, rep3

description:
Library name: acRIP-seq sample 9
ac4C_dN3E


title: PP2C 2.5mM Rep 3

city: New delhi

first: Pushkar

last: Sharma

address: Aruna Asaf Ali marg

country: India

institute: National Institute of Immunology

data_processing:
FASTQ analysis for quality check and adapter trimmed
Hisat2 Ver 53 used for mapping to Plasmodium falciparum genome
Stringtie used for generation of TPM
DESeq2 used for finding deregulated genes in PP2C vs Control NF54
Assembly: Done using Hisat2 ver. 53
Supplementary files format and content: Individual sample TPM present as .tab files
Supplementary files format and content: Deregulated genes of PP2C are present as .txt file

organism: Plasmodium falciparum

source_name: PP2C/PPM2  (treated)

extract_protocol:
RNA was harvested using phenol-chloroform extraction method. 1 μg of whole RNA taken as an input for all samples sequenced
mRNA enrichment was done using NEBNext (polyA)mRNA isolation kit (E7490S). Library prepration was done using NEBNext Ultra II RNA library prep kit for Illumina (E7770S) as per manufacturer's instructions

value: whole organism (schizonts, cycle 1)

value: Glucosamine treated (2.5mM)


title: Jurkat clone E6-1 cells from laboratory 3

city: Wellington

first: Andrew

middle: David

last: Wilson

address: Gate 7 Kelburn Parade, Victoria University of Wellington

country: New Zealand

institute: Malaghan Institute of Medical Research

hyb_protocol: Labelled experimental and control gDNA samples (Agilent Euro Male control DNA) were hybridized to Agilent GenetiSure Cyto CGH+SNP 4x180k microarray slides contained within a SureHyb enabled hybridization chamber. Slides were washed according to the manufacturer's protocol.

scan_protocol: Microarray slides were scanned using an Agilent SureScan Microarray scanner (Agilent part number G4900DA) according to the manufacturer's protocol.

data_processing: Scanned microarray files were analysed using Cytogenomics v5.2.1.4 (Agilent).

source_name: Laboratory 3

label_protocol: 500 ng gDNA were labelled using the Agilent SureTag Complete Labeling kit (Agilent part number 5190-4240) according to the manufacturer's protocol.

growth_protocol: Jurkat clone E6-1 cells (American Type Culture Collection (ATCC), TIB-152) were cultured according to recommended methods published by the ATCC. Briefly, Jurkat clone E6-1 cells were cultured in T75 cell culture flasks (Corning) using Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco) supplemented with 10% foetal bovine serum and 1% penicillin and streptomycin (Gibco). Suspension cultures were maintained in a 37oC incubator with 5% CO2.

extract_protocol: 5x10^6 Jurkat clone E6-1 cells had gDNA extracted using the NucleoSpin® Tissue gDNA isolation kit (Macherey-Nagel) according to the manufacturer’s protocol.

value: Jurkat clone E6-1 (ATCC:TIB-152)

value: Peripheral blood

value: T lymphoblast

tag: disease

value: Acute T cell leukaemia

source_name: Agilent Euro Male control DNA

tag: gender

value: Male


title: PP2C 0mM Rep 3

source_name: PP2C/PPM2  (untreated)

value: Control/ untreated


title: HEK293T, dCas13-NES-edNAT10 and T gRNA transfection, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 8
ac4C_dN2E

value: WT

value: anti-ac4C IP


title: HEK293T, dCas13-NES-edNAT10 and T gRNA transfection, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 7
ac4C_dN1E


title: Jurkat clone E6-1 cells from laboratory 2

source_name: Laboratory 2


title: NF54 2.5 mM Rep 3

source_name: Parental (treated)

value: Parental


title: NormalMammaryTissue, NonIrradiated, HighCornOil Diet, M1234

hyb_protocol: Labeled RNA was hybridized to DNA microarrays (Whole Rat Genome Microarray Kit, Agilent) using the Gene Expression Hybridization Kit (Agilent) at 65°C for 17 h and washed with Gene Expression Wash Buffers 1 and 2 (Agilent).

scan_protocol: Microarrays were then scanned (DNA Microarray Scanner, Model G2565BA; Agilent) using one color scan setting for 4x44K array slides (scan area, 61x21.6 mm; scan resolution, 5 um; scanning mode, single pass; extended dynamic range, on; dye channel, Green; Green PMT for XDR-Hi, 100%; and Green PMT for XDR-Lo, 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and grid 014879_D_F_20100118) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as not positive and significant or not above background were excluded. The median normalized signal intensity from the three non-irradiated control signals were compared with each hybridized sample and log2 transformed.

label_protocol: Cyanine 3–labeled complementary RNA was generated from total RNA samples of tumors and normal mammary tissues using the Low RNA Input Linear Amplification Kit Plus (Agilent Technologies, Inc., Santa Clara, CA).

growth_protocol: Female Sprague-Dawley rats (Jcl:SD; Clea Japan, Tokyo, Japan) were housed in autoclaved cages and maintained in rooms with controlled temperature and humidity under a regular 12-hour light/12-hour dark cycle with water provided ad libitum.

extract_protocol: Total RNA was extracted from frozen carcinomas and frozen tissues with the Maxwell 16 Total RNA Purification kit (Promega Co., Madison, WI) according to the manufacturer protocol.

treatment_protocol: Postnatal rats (weeks 3 or 7 after birth) were whole-body irradiated with gamma rays at 2.0 Gy.

value: normal

tag: exposure

value: not applicable

value: HCO


title: HEK293T, dCas13-NES-eNAT10 and T gRNA transfection, anti-ac4C IP, rep3

description:
Library name: acRIP-seq sample 6
ac4C_T3E


title: Jurkat clone E6-1 cells from laboratory 1

source_name: Laboratory 1


title: NF54 0mM Rep 3

source_name: Parental (untreated)


title: NormalMammaryTissue, NonIrradiated, HighCornOil Diet, M1183


title: NormalMammaryTissue, NonIrradiated, HighCornOil Diet, M1300

description: Not previously uploaded


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, HighCornOil Diet, M1197Mt2

value: cancer

value: gamma rays, 2 Gy

value: 7 weeks


title: K0813Mt3

description: Tumor ID: K0813Mt3

value: spontaneous

value: CE2 diet


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, HighCornOil Diet, M1222Mt4


title: HEK293T cells, WT1

description: Library name: sample1

value: Epithelial Cell

value: Adavosertib


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, HighCornOil Diet, M1192Mt1


title: PP2C 2.5mM Rep 2

value: whole organism (schizonts, cycle 1)

value: Glucosamine treated (2.5mM)


title: Mouse liver, dCas13-edNAT10 AAV transduction, isotype control IP, rep2

description:
Library name: acRIP-seq sample 34
IgG_dN2m

source_name: liver

value: liver

value: isotype control IP


title: HEK293T, dCas13-NES-eNAT10 and T gRNA transfection, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 4
ac4C_T1E

value: WT


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, HighCornOil Diet, M1113Mt3


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, HighCornOil Diet, M1113Mt2


title: PP2C 0mM Rep 2

value: Control/ untreated


title: HEK293T, dCas13-NES-eNAT10 and NT gRNA transfection, anti-ac4C IP, rep3

description:
Library name: acRIP-seq sample 3
ac4C_NT3E

value: anti-ac4C IP


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, HighCornOil Diet, M1182Mt1


title: HEK293T, dCas13-NES-eNAT10 and NT gRNA transfection, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 2
ac4C_NT2E


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, Standard Diet, K1439Mt1

description: Not previously uploaded


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, HighCornOil Diet, M1501Mt2

value: 3 weeks


title: NF54 0mM Rep 2

value: Parental


title: MammaryCarcinoma, Postpubertal, Irradiation Induced, Standard Diet, K1113Mt1

description: Not previously uploaded


title: NF54 2.5 mM Rep 2


title: HEK293T, dCas13-NES-eNAT10 and NT gRNA transfection, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 1
ac4C_NT1E


title: Mouse liver, dCas13-eNAT10 AAV transduction, isotype control IP, rep2

description:
Library name: acRIP-seq sample 32
IgG_N2m


title: Reference Jurkat clone E6-1 cells

source_name: Reference

value: Jurkat clone E6-1 (ATCC:TIB-152)

value: Peripheral blood

value: T lymphoblast

value: Acute T cell leukaemia

value: Male


title: HEK293T, dCas13-NES-eNAT10 and T gRNA transfection, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 5
ac4C_T2E


title: Mouse liver, dCas13-eNAT10 AAV transduction, isotype control IP, rep1

description:
Library name: acRIP-seq sample 31
IgG_N1m


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, HighCornOil Diet, M1495Mt1

value: cancer

value: gamma rays, 2 Gy

value: HCO


title: skin epidermis, Normal2

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

description:
Library name: N2-ATAC
10XGenomics

library_source: genomic single cell

data_processing:
snATAC-seq data were preprocessed using the 10x Genomics pipeline (Cell Ranger ATAC v2) using the hg38 genome and default parameters. Samples from each individual were preprocessed separately. Using ArchR package, the fragments files were read and combined at the single-nucleus level for dimensionality reduction and clustering. Quality control measurements and filtering were conducted including functions like addDoubletScores, filterDoublets for doblet removal. Then we performed Dimensionality reduction in ArchR using addIterativeLSI function and addHarmony for batch correction in default setting. The top 30 dimensions were selected for cell clustering. We then ran addClusters function to classify the clusters and addUMAP function to run UMAP in ArchR. In the process of identifying differential peaks, pseudo bulk replicates were created using addGroupCoverages function. Peaks were called using findMacs2 function and marker peaks were identified by calling the addMarkerFeatures function. Desired marker peaks list can be retrieved by using the function getMarkers, with option (cutOff = "FDR <= 0.01 & Log2FC >= 1").
Assembly: hg38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz

source_name: skin epidermis

extract_protocol:
HS and healthy skin tissues were cut into small pieces and were digested with 2.5U/ml Dispase-II (Millipores Sigma, Cat#4942078001) in Hanks’ Balanced Salt Solution (HBSS, Corning, Cat#21-022-CM) overnight at 4°C. After digestion, the epidermis was peeled off and minced. The minced epidermis was incubated with 0.05% trypsin-EDTA at 37°C for 40 mins for further digestion. The suspension was then filtered through a 40um cell strainer and spun down at 300g at 4°C for 5 mins. Collected single nucleus were for the application of snATAC  sequence.
The snATAC-seq libraries were constructed according to manufacture's protocol provided by the Chromium Next GEM single cell ATAC v1.1 reagent kit (10X Genomics).

value: skin epidermis

value: female

tag: disease state

value: healthy skin


title: Mouse liver, dCas13-edNAT10 AAV transduction, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 29
ac4C_dN1m

value: liver


title: Mouse liver, dCas13-edNAT10 AAV transduction, isotype control IP, rep1

description:
Library name: acRIP-seq sample 33
IgG_dN1m

value: WT

value: isotype control IP


title: PP2C 2.5mM Rep 1

value: whole organism (schizonts, cycle 1)

value: Glucosamine treated (2.5mM)


title: PP2C 0mM Rep 1

value: Control/ untreated


title: Mouse liver, dCas13-edNAT10 AAV transduction, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 30
ac4C_dN2m

value: anti-ac4C IP


title: NF54 2.5 mM Rep 1

value: Parental


title: skin epidermis, Normal1

description:
Library name: N1-ATAC
10XGenomics


title: Mouse liver, dCas13-eNAT10 AAV transduction, anti-ac4C IP, rep1

description:
Library name: acRIP-seq sample 27
ac4C_N1m


title: skin epidermis, HS2

description:
Library name: HS2-ATAC
10XGenomics

value: male

value: Hurley III


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, Standard Diet, K1506Mt3

description: Not previously uploaded

value: 3 weeks


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, HighCornOil Diet, M1493Mt1

value: cancer


title: Mouse liver, dCas13-eNAT10 AAV transduction, anti-ac4C IP, rep2

description:
Library name: acRIP-seq sample 28
ac4C_N2m


title: NF54 0mM Rep 1


title: PLC/PRF/5 SNDX 12

status: Public on Apr 07 2025

first: Jesse

last: Raab

address: 120 Mason Farm Rd

institute: University of North Carolina Chapel Hill

description: Library name: PLCPRF5_SNDX_2

data_processing:
salmon 1.10.0 was used to generate count tables salmon quant  - l A --gcBias --seqBias --posBias
all processing steps are implemented in github.com/raab-lab/rnaseq
Assembly: hg38
Supplementary files format and content: TSV files of raw count fiels used for DESEq2

source_name: Liver tumor

growth_protocol: HLF and PLC/PRF5 cells are grown in DMEM + 10% FBS + penicillin and streptomycin.

extract_protocol: library was generated using Kapa mRNA Hyperprep kit

treatment_protocol: HLF and PLC/PRF5 cells were treated with 5uM SNDX-5613 or DMSO for 24 hours or menin KO cell lines were generated by CRISPR

value: Liver tumor

value: SNDX

tag: batch


title: PLC/PRF/5 menin KO 1

description: Library name: PLCPRF5_MEN1-KO_1

value: menin-ko


title: PLC/PRF/5 DMSO 3

description: Library name: PLCPRF5_DMSO_3

value: DMSO


title: PLC/PRF/5 menin KO 2

description: Library name: PLCPRF5_MEN1-KO_2


title: PLC/PRF/5 nontargeting 1

description: Library name: PLCPRF5_NTC_1


title: PLC/PRF/5 DMSO 1

description: Library name: PLCPRF5_DMSO_1


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, HighCornOil Diet, M1180Mt1

value: gamma rays, 2 Gy

value: HCO


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, Standard Diet, K1165Mt1

description: Not previously uploaded


title: PLC/PRF/5 SNDX 3

description: Library name: PLCPRF5_SNDX_3

value: WT


title: skin epidermis, HS1

description:
Library name: HS1-ATAC
10XGenomics

value: skin epidermis

value: female


title: MammaryCarcinoma, Prepubertal, Irradiation Induced, Standard Diet, K1106Mt1

description: Not previously uploaded


title: PLC/PRF/5 menin KO 3

description: Library name: PLCPRF5_MEN1-KO_3


title: PLC/PRF/5 nontargeting 3

description: Library name: PLCPRF5_NTC_3


title: HLF treated with DMSO IP for IgG replicate 10

description: Library name: 1238_JR989_HLF_IgG_DMSO_2

data_processing:
trim_galore version 0.6.7 --paired
bowtie2 version 2.3.4.1 --very-sensitive-local -X 800
picard version 2.20.0 MarkDuplicates
samtools view -b -q 30
deeptools version 3.5.4  bamCoverage --binSize 30 --smoothLength 60 --extendReads --ignoreDuplicates --efectiveGenomeSize 2701495761
macs version 2.2.7.1 macs2 callpeak -g 2701495761 --call-summits -q .05
individual bigwig files were averaged using wiggle tools from ucsc tools wiggletools mean ${bws} |\\   awk '\$1 ~ /^chr[XY0-9]+\$/' |\\   wigToBigWig stdin ${chrom_sizes} group${group_avg}_mean.bw
individual narrowPeak files were used to generate consensus peaks using RMSPC  version 1.8
all data processing steps are implemented as  Nextflow pipeline at github.com/raab-lab/cut-n-run using the --mode cnr
Assembly: hg38
Supplementary files format and content: peak files produced from Macs2, consensus peak files across all samples generated using RMSPC, and bigwig files for individual replicates as well as average bigwig tracks for each treatment condition.
Library strategy: CUT&RUN

source_name: liver cancer

growth_protocol: HLF cells were grown in DMEM + 10% FBS + penicillin and streptomycin

extract_protocol:
CUT&RUN was performed adapted from PMID: PMC6598765
Kapa Hyperprep DNA kit

treatment_protocol: 5uM SNDX-5613 for 24 hours

value: liver cancer

value: HLF

tag: antibody

value: IgG


title: HLF treated with DMSO IP for TEAD4 replicate 4

description: Library name: 1236_JR987_HLF_TEAD4_DMSO_2


title: HLF treated with SNDX IP for TEAD4 replicate 4

description: Library name: 1242_JR993_HLF_TEAD4_SNDX_2


title: HLF treated with DMSO IP for NFYB replicate 3

description: Library name: 1235_JR986_HLF_NFYB_DMSO_2

value: NFYB


title: HLF treated with SNDX IP for H3K27ac replicate 2

description: Library name: 1240_JR991_HLF_H3K27ac_SNDX_2


title: HLF treated with SNDX IP for NFYB replicate 3

description: Library name: 1241_JR992_HLF_NFYB_SNDX_2


title: PLC/PRF/5 DMSO 2

description: Library name: PLCPRF5_DMSO_2


title: HLF treated with DMSO IP for H3K27ac replicate 3

description: Library name: 1234_JR985_HLF_H3K27ac_DMSO_2


title: HLF treated with SNDX IP for IgG replicate 10

description: Library name: 1245_JR996_HLF_IgG_SNDX_2


title: HLF treated with DMSO IP for TEAD4 replicate 3

description: Library name: 1230_JR981_HLF_TEAD4_DMSO_1


title: HLF treated with DMSO IP for NFYB replicate 2

description: Library name: 1229_JR980_HLF_NFYB_DMSO_1


title: PLC/PRF/5 SNDX 1

description: Library name: PLCPRF5_SNDX_1


title: HLF treated with SNDX IP for H3K27ac replicate 1

description: Library name: 1222_JR973_HLF_H3K27ac_SNDX_1


title: HLF treated with SNDX IP for H3K27me3 replicate 4

description: Library name: 971_JR848_HLF_H3K27me3_SNDX_2


title: HLF treated with SNDX IP for TEAD4 replicate 3

description: Library name: 1224_JR975_HLF_TEAD4_SNDX_1


title: HLF treated with DMSO IP for H3K27ac replicate 2

description: Library name: 1228_JR979_HLF_H3K27ac_DMSO_1


title: PLC/PRF/5 nontargeting 2

description: Library name: PLCPRF5_NTC_2


title: HLF treated with DMSO IP for H3K4me3 replicate 4

description: Library name: 967_JR844_HLF_H3K4me3_DMSO_2


title: HLF treated with Sndx IP for IgG replicate 7

description: Library name: 1108_JR947_HLF_IgG_Sndx_1

value: Sndx


title: HLF treated with DMSO IP for Menin replicate 3

description: Library name: 1103_JR942_HLF_Menin_DMSO_1

value: Menin


title: HLF treated with DMSO IP for IgG replicate 6

description: Library name: 969_JR846_HLF_IgG_DMSO_2


title: HLF treated with SNDX IP for H3K4me3 replicate 4

description: Library name: 970_JR847_HLF_H3K4me3_SNDX_2


title: HLF treated with DMSO IP for IgG replicate 7

description: Library name: 1105_JR944_HLF_IgG_DMSO_1


title: HLF treated with DMSO IP for H3K27me3 replicate 4

description: Library name: 968_JR845_HLF_H3K27me3_DMSO_2


title: HLF treated with SNDX IP for IgG replicate 5

description: Library name: 966_JR843_HLF_IgG_SNDX_1


title: HLF treated with Sndx IP for Menin replicate 3

description: Library name: 1106_JR945_HLF_Menin_Sndx_1


title: HLF treated with SNDX IP for H3K4me3 replicate 3

description: Library name: 964_JR841_HLF_H3K4me3_SNDX_1


title: HLF treated with DMSO IP for H3K4me3 replicate 3

description: Library name: 961_JR838_HLF_H3K4me3_DMSO_1


title: HLF treated with DMSO IP for IgG replicate 5

description: Library name: 963_JR840_HLF_IgG_DMSO_1


title: HLF treated with SNDX IP for H3K27me3 replicate 3

description: Library name: 965_JR842_HLF_H3K27me3_SNDX_1


title: HLF treated with SNDX IP for H3K4me3 replicate 2

description: Library name: 775_MD0036_HLF_H3K4me3_SNDX_2


title: HLF treated with SNDX IP for NFYB replicate 2

description: Library name: 1223_JR974_HLF_NFYB_SNDX_1


title: HLF treated with DMSO IP for IgG replicate 4

description: Library name: 772_MD0033_HLF_IgG_DMSO_2


title: HLF treated with DMSO IP for H3K4me3 replicate 2

description: Library name: 771_MD0032_HLF_H3K4me3_DMSO_2


title: HLF treated with SNDX IP for IgG replicate 3

description: Library name: 768_MD0029_HLF_IgG_SNDX_1


title: HLF treated with SNDX IP for IgG replicate 4

description: Library name: 776_MD0037_HLF_IgG_SNDX_2


title: HLF treated with SNDX IP for Menin replicate 2

description: Library name: 773_MD0034_HLF_Menin_SNDX_2


title: HLF treated with SNDX IP for H3K4me3 replicate 1

description: Library name: 767_MD0028_HLF_H3K4me3_SNDX_1


title: HLF treated with DMSO IP for Menin replicate 2

description: Library name: 769_MD0030_HLF_Menin_DMSO_2


title: HLF treated with SNDX IP for IgG replicate 6

description: Library name: 972_JR849_HLF_IgG_SNDX_2


title: HLF treated with SNDX IP for Menin replicate 1

description: Library name: 765_MD0026_HLF_Menin_SNDX_1


title: HLF treated with DMSO IP for Menin replicate 1

description: Library name: 761_MD0022_HLF_Menin_DMSO_1


title: HLF treated with SNDX IP for IgG replicate 2

description: Library name: 953_MD0061_HLF_IgG_SNDX_2


title: HLF treated with DMSO IP for IgG replicate 3

description: Library name: 764_MD0025_HLF_IgG_DMSO_1


title: HLF treated with SNDX IP for H3K27me3 replicate 2

description: Library name: 952_MD0060_HLF_H3K27me3_SNDX_2


title: HLF treated with DMSO IP for H3K4me3 replicate 1

description: Library name: 763_MD0024_HLF_H3K4me3_DMSO_1


title: HLF treated with SNDX IP for MLL1 replicate 2

description: Library name: 951_MD0059_HLF_MLL1_SNDX_2


title: HLF treated with DMSO IP for IgG replicate 2

description: Library name: 950_MD0058_HLF_IgG_DMSO_2


title: HLF treated with DMSO IP for H3K27me3 replicate 3

description: Library name: 962_JR839_HLF_H3K27me3_DMSO_1


title: HLF treated with SNDX IP for IgG replicate 1

description: Library name: 947_MD0055_HLF_IgG_SNDX_1


title: HLF treated with SNDX IP for MLL1 replicate 1

description: Library name: 945_MD0053_HLF_MLL1_SNDX_1


title: HLF treated with DMSO IP for H3K27me3 replicate 2

description: Library name: 949_MD0057_HLF_H3K27me3_DMSO_2


title: HLF treated with SNDX IP for H3K27me3 replicate 1

description: Library name: 946_MD0054_HLF_H3K27me3_SNDX_1


title: HLF treated with DMSO IP for MLL1 replicate 2

description: Library name: 948_MD0056_HLF_MLL1_DMSO_2


title: HLF treated with DMSO IP for IgG replicate 1

description: Library name: 944_MD0052_HLF_IgG_DMSO_1


title: HLF treated with DMSO IP for H3K27me3 replicate 1

description: Library name: 943_MD0051_HLF_H3K27me3_DMSO_1


title: HLF cells, SNDX-5613 treated, replicate 2

description: Library name: HLF_SNDX_2

data_processing:
trim_galore version 0.6.7 --paired
bowtie2 version 2.3.4.1 --very-sensitive-local -X 800
picard version 2.20.0 MarkDuplicates
samtools view -b -q 30 -e 'rname !=\"chrM\"'" : ""
deeptools version 3.5.4  bamCoverage --binSize 30 --smoothLength 60 --extendReads --ignoreDuplicates --efectiveGenomeSize 2701495761
macs version 2.2.7.1 macs2 callpeak -g 2701495761 --call-summits -q .05
individual bigwig files were averaged using wiggle tools from ucsc tools wiggletools mean ${bws} |\\   awk '\$1 ~ /^chr[XY0-9]+\$/' |\\   wigToBigWig stdin ${chrom_sizes} group${group_avg}_mean.bw
individual narrowPeak files were used to generate consensus peaks using RMSPC  version 1.8
all data processing steps are implemented as  Nextflow pipeline at github.com/raab-lab/cut-n-run using the --mode atac
Assembly: hg38
Supplementary files format and content: peak files produced from Macs2, consensus peak files across all samples generated using RMSPC, and bigwig files for individual replicates as well as average bigwig tracks for each treatment condition.

source_name: liver tumor

growth_protocol: HLF cells are grown in DMEM + 10% FBS + penicillin and streptomycin.

extract_protocol:
ATAC-seq was performed as in  PMCID: PMC5623106.
Library was constructed by PCR as in  PMCID: PMC5623106

treatment_protocol: HLF cells were treated with 5uM SNDX-5613 or DMSO for 24 hours

value: liver tumor

value: 5uM SNDX-5613 24 hours


title: HLF cells, SNDX-5613 treated, replicate 3

description: Library name: HLF_SNDX_3


title: Diseased 4

city: Torrance

first: Michelle

last: Matter

state: CA

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

description: Gene expression data from diseased tissue

hyb_protocol: In a rotating chamber, 5.5 μg of fragmented and labeled ss-cDNA were hybridized to the Clariom D Human Array for 16 h at 45 °C.

scan_protocol: The hybridized arrays were scanned on the Affymetrix GeneChip Array Scanner 3000-7G.

data_processing: Generated CEL files were normalized and differential gene expression was investigated using the TAC software.

label: biotin

source_name: FPPE Heart (left ventricle)

label_protocol: A combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) was used to fragment ssDNA, which was afterwards labelled with biotin (WT Terminal Labelling Kit, Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from FFPE heart (left ventricle) blocks using the RecoverAll Total Nucleic Acid Isolation Kit (Thermo Fisher Scientific). RNA samples were tested for quality control using Qubit.
Samples were prepared for microarray hybridization as described in the Thermo Fisher Scientific GeneChip Whole Transcript (WT) Expression manual using the WT Pico Reagent Kit.

value: heart

value: PPCM


title: HLF cells, SNDX-5613 treated, replicate 1

description: Library name: HLF_SNDX_1


title: HLF cells, DMSO treated, replicate 1

description: Library name: HLF_DMSO_1

value: DMSO 24 hours


title: HLF cells, DMSO treated, replicate 2

description: Library name: HLF_DMSO_2


title: Diseased 5


title: HLF treated with DMSO IP for MLL1 replicate 1

description: Library name: 942_MD0050_HLF_MLL1_DMSO_1

value: DMSO


title: Normal 6

description: Gene expression data from normal tissue

value: normal


title: HLF cells, DMSO treated, replicate 3

description: Library name: HLF_DMSO_3


title: Diseased 3


title: Mus musculus, cardiomyocyte Cells, control blank, biol repl3

city: Guangzhou

first: Jianning

last: Chen

address: No. 12 Minyou Road

institute: The Second Affiliated Hospital of Guangdong Medical University

description:
Library name: NC3
Column name gene_count.txt: NC3

data_processing:
Raw reads were quality-checked with FastQC, trimmed using Trimmomatic, and aligned to the mm10 mouse genome via STAR (PMID: 23104886). Gene counts were quantified with feature Counts
Assembly: mm10
Supplementary files format and content: Tab separated table count values of genes for each sample

source_name: cardiomyocyte

extract_protocol:
Below, we provide a summary of the RNA-seq workflow, which will be expanded in the revised Methods section: Total RNA was extracted from isolated cardiomyocytes (AAV9-Firre 、 AAV9-VC、NC n = 3 per group) using TRIzol, followed by rRNA depletion (NEBNext® rRNA Depletion Kit).
Library preparation (NEBNext® Ultra™ II Directional RNA Library Prep Kit). Sequencing was performed on an Illumina NovaSeq 6000 platform (150-bp paired-end reads, ~40 million reads/sample).

value: cardiomyocyte


title: Mus musculus, cardiomyocyte Cells, control blank, biol repl2

description:
Library name: NC2
Column name gene_count.txt: NC2


title: Mus musculus, cardiomyocyte Cells, control negative, biol repl3

description:
Library name: VC3
Column name gene_count.txt: VC3


title: Mus musculus, cardiomyocyte Cells, LncFirre overexpresssion, biol repl2

description:
Library name: OE-LncFirre2
Column name gene_count.txt: OE_LncFirre2


title: Mus musculus, cardiomyocyte Cells, LncFirre overexpresssion, biol repl3

description:
Library name: OE-LncFirre3
Column name gene_count.txt: OE_LncFirre3


title: Mus musculus, cardiomyocyte Cells, control negative, biol repl2

description:
Library name: VC2
Column name gene_count.txt: VC2


title: Mus musculus, cardiomyocyte Cells, LncFirre overexpresssion, biol repl1

description:
Library name: OE-LncFirre1
Column name gene_count.txt: OE_LncFirre1


title: Mus musculus, cardiomyocyte Cells, control negative, biol repl1

description:
Library name: VC1
Column name gene_count.txt: VC1


title: Mus musculus, cardiomyocyte Cells, control blank, biol repl1

description:
Library name: NC1
Column name gene_count.txt: NC1


title: iMOP-derived neurons, stranded RNA-seq, biol rep 1

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Library name: SG0920_S17_Sample5

data_processing:
Sequence reads were mapped to reference mouse genome (mm10) using HISAT2.
SAM files were converted, sorted, and indexed to generate sorted BAM files using Samtools
The featureCounts command from Rsubread was used to create a count matrix and differential expression was calculated using DEseq2.
To visualize RNA-seq read coverage at forward(+) and reverse(-) strands of the genome separately, employed Deeptools (3.4.3) bamCCoverage function (-normalizeUsing RPKM-filterRNAstrand forward/reverse) with sorted BAN files as input.
Assembly: mm10
Supplementary files format and content: comma separated values text files include raw counts for each sample
Supplementary files format and content: comma separated values text files include differential expression

source_name: iMOPs

growth_protocol: Proliferating iMOPs: DMEM/F12, 1XB27, 25 µg/ml carbenicillin and 20 ng/ml bFGF.iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.

extract_protocol:
Total RNA was extracted from 1-5x106 proliferating or neuronal iMOP cells using TRIzol Reagent following the manufacturer's protocol. Total RNA was treated with Dnase I and phenol-chloroform extraction was used to remove DNaseI. Ribosomal RNA was depleted from 500 ng of Dnase-treated total RNA using the NEBNext rRNA depletion kit.
Yielded RNA was used for stranded RNA-seq library preparation with the Takara SMARTer Stranded RNA-seq kit following the manufacturer's instructions. The average library size, including adaptors was ~300bp. Eight uniquely indexed libraries were normalized by concentration and pooled together. Pooled libraries were sequenced using Illumina Novaseq 6000 S4 platform (2x150bp) and resulted in ~2.5 billion total paired reads.

value: iMOPs

value: iMOP-derived neurons

value: wild-type


title: Proliferating iMOPs, stranded RNA-seq, set 2, biol rep 2

description: Library name: SG0920_S15_Sample3

value: Proliferating iMOPs


title: iMOP-derived neuron_2, RNA-seq

description: Library name: iMOP-derived neuron_2

data_processing:
Paired-end sequence reads were mapped to reference mouse genome (mm10) using HISAT2.
The resulting SAM files were converted, sorted, and indexed to generate sorted BAM files using Samtools.
The featureCounts command from Rsubread was used to create the count matrix, and differential expression was calculated using DEseq2.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file contains raw counts for each sample.
Supplementary files format and content: The tab-delimited text file contains normalized read counts (RPKM) for each sample.

growth_protocol: Proliferating iMOPs: DMEM/F12, 1XN21, 25 µg/ml carbenicillin and 20 ng/ml bFGF. iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.

extract_protocol:
Total RNA was extracted from 1-5x10^6 proliferating or neuronal iMOP cells using 1ml of TRIzol Reagent (Thermo Fisher Scientific). Total RNA was treated with DNaseI, and then DNaseI was removed by phenol-chloroform extraction. Ribosomal RNA was depleted from 500 ng of DNase-treated total RNA using the NEBNext rRNA depletion kit.
Stranded RNA-seq library was prepared with the Takara SMARTer Stranded RNA-seq kit.


title: Proliferating iMOP_1, RNA-seq

description: Library name: Proliferating iMOP_1

value: Poliferating iMOPs


title: iMOP-derived neuron_1, RNA-seq

description: Library name: iMOP-derived neuron_1


title: C57BL/6 mouse, cadmium-exposed, Day90, rep2 [Input]

first: Hao

last: Huang

state: Guangdong

address: No. 1023 Shatai Road

institute: Southern Medical University

description:
Library name: 28-Input
Mouse, Liver, Input, 20 mg/kg/day CdCl2, Gavage, 90 days

data_processing:
*library strategy: MeRIP-seq
Following sequencing, paired-end reads were generated and subjected to quality control in accordance with the Q30 standard.
Adapters and low-quality reads were removed from the raw data using the Cutadapt program (v1.1.8).
The clean reads from all libraries were aligned to the reference genome using STAR (v2.7.1a), and duplicate reads were removed using Samtools (v1.3.1).
The differential m6A methylation peaks and genes were characterized and subjected to analysis utilising the Model-based Analysis of MACS (v2.1.1) and DESeq2 R package (v4.1.0), respectively. The peaks identified by the two software programs were then subjected to screening and annotation, with the objective of identifying those that overlapped with exons of mRNA.
Assembly: mm10
Supplementary files format and content: Each processed data file type is an XLS file, and these include -LOG10(pvalue)/fold_enrichment for each sample.

source_name: Liver

growth_protocol: Male C57BL/6 mice aged between 6 and 8 weeks old were housed in a dedicated pathogen-free facility with controlled environmental conditions (room temperature maintained at 24±2℃, relative humidity between 40-60%, and a 12/12 h light/dark cycles), and the subjects had unlimited accessibility to food and water.

extract_protocol:
Total RNA was extracted from liver tissues using TRIzol reagent (Invitrogen, Grand Island, NY, USA).
After determining RNA concentration with Qubit (4.0) and assessing RNA quality by agarose gel electrophoresis techniques. An adequate quantity of RNA was interrupted to 200-500 bp using metal ions, then purified and solubilised. Next, an anti-m6A antibody (Danvers, MA, USA) was added for immunoprecipitation, which binds to the RNA fragments containing the m6A site. Subsequently, the immunoprecipitated RNA fragments (IP) and the unbound RNA fragments (Input) were subjected to library construction using the Ovation SoLo RNA-Seq System Core Kit (NuGEN, USA). The Illumina NovaSeq 6000 platform (Illumina, USA) was used to sequence the resulting libraries in PE150 sequencing mode.

treatment_protocol: The mice were randomly selected to either the control or the Cd exposure group, with each group comprising six individuals. In the groups exposed to Cd, mice were intragastric injected with 0/20 mg/kg CdCl2 daily for a period of 90 days. Stock solutions of cadmium chloride (CdCl2) were prepared by dissolving CdCl2 (Sigma-Aldrich, 439800) in deionized water for subsequent use.

value: Liver

value: WT

value: 20 mg/kg/day CdCl2, Gavage

tag: time

value: Day 90


title: Proliferating iMOP_2, RNA-seq

description: Library name: Proliferating iMOP_2


title: C57BL/6 mouse, cadmium-exposed, Day90, rep1 [Input]

description:
Library name: 37-Input
Mouse, Liver, Input, 20 mg/kg/day CdCl2, Gavage, 90 days


title: C57BL/6 mouse, cadmium-exposed, Day90, rep3 [Input]

description:
Library name: 88-Input
Mouse, Liver, Input, 20 mg/kg/day CdCl2, Gavage, 90 days


title: C57BL/6 mouse, control, Day90, rep3 [Input]

description:
Library name: 94-Input
Mouse, Liver, Input, Control, Gavage, 90 days

value: 0 mg/kg/day CdCl2, Gavage


title: C57BL/6 mouse, control, Day90, rep2 [Input]

description:
Library name: 1035-Input
Mouse, Liver, Input, Control, Gavage, 90 days


title: C57BL/6 mouse, cadmium-exposed, Day90, rep1 [IP]

description:
Library name: 37-IP
Mouse, Liver, IP, 20 mg/kg/day CdCl2, Gavage, 90 days


title: C57BL/6 mouse, cadmium-exposed, Day90, rep3 [IP]

description:
Library name: 88-IP
Mouse, Liver, IP, 20 mg/kg/day CdCl2, Gavage, 90 days


title: C57BL/6 mouse, control, Day90, rep3 [IP]

description:
Library name: 94-IP
Mouse, Liver, IP, Control, Gavage, 90 days


title: C57BL/6 mouse, control, Day90, rep1 [Input]

description:
Library name: 54-Input
Mouse, Liver, Input, Control, Gavage, 90 days


title: C57BL/6 mouse, cadmium-exposed, Day90, rep3

description:
Library name: Sample6
Mouse, Liver, Input, 20 mg/kg/day CdCl2, Gavage, 90 days
S88

data_processing:
Following sequencing, paired-end reads were generated and subjected to quality control in accordance with the Q30 standard.
Adapters and low-quality reads were removed from the raw data using the Cutadapt program (v1.1.8).
The clean reads from all libraries were aligned to the reference genome using STAR (v2.7.1a), and duplicate reads were removed using Samtools (v1.3.1).
The differential m6A methylation peaks and genes were characterized and subjected to analysis utilising the Model-based Analysis of MACS (v2.1.1) and DESeq2 R package (v4.1.0), respectively. The peaks identified by the two software programs were then subjected to screening and annotation, with the objective of identifying those that overlapped with exons of mRNA.
The construction and sequencing of the RNA-seq libraries were conducted using the MeRIP-seq input libraries and the same methodology.
Assembly: mm10
Supplementary files format and content: Each processed data file type is an XLS file, and these include FPKM for each sample.


title: C57BL/6 mouse, cadmium-exposed, Day90, rep2 [IP]

description:
Library name: 28-IP
Mouse, Liver, IP, 20 mg/kg/day CdCl2, Gavage, 90 days


title: iMOP-derived neurons, stranded RNA-seq, set 2, biol rep 2

description: Library name: SG0920_S18_Sample6


title: C57BL/6 mouse, control, Day90, rep2 [IP]

description:
Library name: 1035-IP
Mouse, Liver, IP, Control, Gavage, 90 days


title: C57BL/6 mouse, control, Day90, rep1 [IP]

description:
Library name: 54-IP
Mouse, Liver, IP, Control, Gavage, 90 days