title: Full 3'UTR, DMS treated, Rep1

description:
3UTR_plusDMS_Rep1
In vitro transcribed RNA
3UTR_DMS_Rep1_normalized_reactivities.txt


title: Mouse visual cortex cell mRNA, PBS-Light treatment, Sample 1vc

status: Public on Mar 26 2025

type: SRA

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

description: Library name: 1vc

library_source: transcriptomic

data_processing:
Quality and adaptor trimming with cutadapt
Read mapping with STAR
Read counting with HTSeq
Assembly: mm10
Supplementary files format and content: TSV matrix raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Qiagen RNAeasy minikit according to the manufacturer's protocol
RNA-seq using illumina kit and protocol for library construction

tag: tissue

value: Brain

tag: cell type

value: visual cortex

tag: treatment

value: PBS-Light


title: Full 3'UTR, DMS noMod control , Rep1

city: Aurora

first: Matthew

last: Szucs

state: CO

country: USA

institute: University of Colorado Denver Anschutz Medical Campus

description:
3UTR_minusDMS_Rep1
In vitro transcribed RNA
3UTR_DMS_Rep1_normalized_reactivities.txt

library_source: other

data_processing:
Raw reads were processed using shapemapper2 v2.1.5. args:  --overwrite --verbose --name --out  --temp  --target --min-depth 5000 --modified --folder plus --untreated --folder minus
Assembly: HM440560.1
Supplementary files format and content: Textfile output of normalized reactivity and counts from Shapemapper2

molecule: other

organism: Powassan virus

source_name: in vitro transcribed RNA

extract_protocol:
Modified RNAs were cleaned up with the RNEasy Micro Kit
Reverse transcription, second strand synthesis, and library prep of modified RNA. The following protocol was applied to the full length 3′UTR, sfRNA1 and sfRNA2 RNA species. Approximately 400 ng of modified or control RNA was incubated with of 200 ng/μL random nonamer primer (NEB; S1254S) and 1.0 μL of POWV_SHAPEMAP_RT_Primer (Supplemental Table S2) at 65°C for 5 minutes and then cooled on ice. To each of the reactions 8.0 μL of MAP buffer (125mM Tris pH 8.0, 187.5mM KCl, 15mM MnCl2, 25mM DTT, 1.25mM equimolar dNTP mix, and 200U Superscript III) was added to the reaction and incubated at 25°C for 2 minutes. The reaction was then incubated at 25°C for 10 minutes, 42°C for 3 hours, 70°C for 15 minutes, and cooled to 4°C. The RNA/cDNA hybrids were then purified on the G25 (Cyteva) spin column following the manufacturers protocol. Second strand synthesis of the cDNA was carried out using the NEBNext second strand synthesis kit (NEB) following the manufacturer’s instructions. The resultant cDNA was purified using the DNA Clean & Concentrator-5 kit (Zymo) eluting in 10 μL of DEPC-treated H2O and quantified fluorometrically with the Qubit (Thermo) using the dsDNA HS Assay Kit (Thermo). Next generation sequencing library prep was performed with the Nextera XT DNA library preparation kit (Illumina) using the Nextera XT Index Kit v2 Set B (Illumina). Samples were normalized and pooled together using a combination of the Qubit (Thermo) and the 4200 TapeStation System (Agilent Technologies) with the High Sensitivity D1000 Screen Tape (Agilent Technologies). Final libraries were sequenced on the NovaSeq 6000 platform (Illumina).

treatment_protocol: 1m7 and DMS probing of the POWV 3’UTR: 1.0 μg of in vitro transcribed full length POWV 3′UTR was heat denatured in 12 μLDEPC treated H2O at 95°C for two minutes and then immediately cooled on ice. To this 8.0 μLof concentrated RNA folding buffer was added to a final concentration of 100 mM NaCl, 50 mM Tris pH 7.5, 4 mM MgCl2, and folded for 20 minutes at 55°C. The folded RNA was slow cooled to room temperature. After cooling the reaction was split into two, and 0.5 μg of the RNA was labeled with 10mM 1m7 (Sigma) or DMSO (Sigma) at 37°C for 75 seconds (five 1m7 hydrolysishalf-lives). In parallel, 0.5 μg of folded RNA was modified with 0.5% DMS (Sigma) or an equal mount of EtOH as a negative control for 5 minutes at 37°C, and then quenched with 2-Mercaptoethanol (Sigma). All conditions were purified and concentrated using the Qiagen RNeasy micro kit.1m7 and DMS probing of the POWV sfRNA1 and sfRNA2: 2 μg of folded in vitro transcribed POWV 3′UTR was treated with Xrn1 for two hours. After incubation, DMS, 1m7, or their appropriate controls was added to the reaction at the same final concentrations as the 3’UTR probing outlined above. The reactions were cleaned up using the RNeasy Micro Kit (Qiagen) and separated on a 6% denaturing PAGE gel. The sfRNA1 and sfRNA2 bands were visualized by UV shadowing and cut from the gel. The RNA was eluted from the gel using the crush soak method at 4°C overnight in ~ 5 mL 50 mM Sodium cacodylate pH 6.5, 0.1 mM EDTA, and 50mM NaCl. The RNA was concentrated with a 30K molecular weight cut off Amicon Ultra spin Concentrators (Millipore-Sigma) and buffer exchanged into DEPC water.

value: in vitro transcribed RNA

value: no Mod (DMSO)


title: Mouse visual cortex cell mRNA, Psi-Dark treatment, Sample 20vc

description: Library name: 20vc

value: Psi-Dark


title: Mouse visual cortex cell mRNA, PBS-Dark treatment, Sample 18vc

description: Library name: 18vc

value: PBS-Dark


title: SCA32_MeWo Young replicate 2

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

country: United Kingdom

institute: Cancer Research UK

description: Library name: Sample 5

data_processing:
RNA sequencing was analysed using DESEq2.For cells, GFold (v1.1.4) was used to carry out for differential analysis.
Assembly: chr38
Supplementary files format and content: text with raw files

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: MeWo cells were seeded at 70-80% confluence a day prior to the treatment. Prior to treatment, cells were washed twice with PBS.

extract_protocol:
RNA from cells were extracted using Qiagen RNA extraction kit (Qiagen, Cat no. 74104) as per manual instructions. 1ug RNA used per condition.
PolyA RNASeq libraries were prepared using the SureSelect Automated Strand-Specific RNA Library Prep for Illumina (Agilent, G9691B). An input of 200ng of total RNA was used with 14 cycles of amplification.

treatment_protocol: Cells were treated with adipocyte secretomes for 24-48 hours and serum free DMEM was used as a control.

tag: cell line

value: MeWo

value: human melanoma cell

value: Young adipocyte secretome


title: F36 Placenta Pup3, MNR, Nanoparticle

city: Gainesville

first: Rebecca

last: Wilson

address: 1345 Center Dr

institute: University of Florida

data_processing:
Short reads were trimmed using trimmomatic (v 0.36), and QC on the original and trimmed reads was performed using FastQC (v 0.11.4) and MultiQC.
The reads were aligned to the transcriptome using STAR version 2.7.9a
Transcript abundance was quantified using RSEM (RSEM v1.3.1)
Assembly: Cavpor3.0
Supplementary files format and content: comma-separated values containing fastq counts in all samples
Supplementary files format and content: comma-separated values containing raw FPKM values for all genes in all samples

organism: Cavia porcellus

source_name: Placenta

extract_protocol:
Total RNA was extracted from frozen placenta using Qiagen RNeasy Midi extraction kit
RNA libraries were prepared from 1.5 ug RNA using Illumina Stranded mRNA Prep Kit following manufacturers instructions

value: Placenta

tag: breed

value: Dunkin-Hartley

tag: diet

value: Maternal Nutrient Restriction

value: Nanoparticle


title: F33 Placenta Pup4, MNR, Sham

value: Sham


title: WT bam, unmated three-day old_1

city: Ithaca

first: Catherine

middle: Herminia

last: Kagemann

state: NY

address: 215 Tower Rd, Ithaca, NY, Room 233

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
No reads were trimmed as FastQC scores were high and adapter content was low. Sample alignment of one seample was below 70% and was thus removed (WT three-day old infected with wMel3). DESeq2 was used for differential expression analysis
Assembly: dmel-all-chromosome-r6.39.fasta (Flybase.org)
Supplementary files format and content: WT_All_ReadCounts.txt: processed WT read count matrix, WT_All_Sample.txt: metadata file for processed WT readcount matrix, 10E7_Null_All_ReadCounts.txt: processed bam hypomorph read count matrix, 10E7_Null_All_Sample.txt: metadata for processed bam hypomorph read count matrix

organism: Drosophila melanogaster

source_name: Ovaries

extract_protocol:
We used the Zymo’s Quick-RNA 96 kit to extra total RNA from D. melanogaster ovaries
3' RNA-seq library

value: Ovaries

value: Tissue

tag: genotype

value: WT bam w1118

value: Unmated three-day old


title: F36 Placenta Pup1, MNR, Nanoparticle


title: Mouse visual cortex cell mRNA, PBS-Dark treatment, Sample 17vc

description: Library name: 17vc

value: Brain

value: visual cortex


title: SCA30_ MeWo control replicate 2

description: Library name: Sample 4

value: serum free media


title: CDAC1

city: Shenyang

first: qiu

middle: zhong

last: pang

address: 195 Chuangxin Road, Baita Street

country: China

institute: Northeastern University

data_processing:
The raw data in fastq format is processed using Perl scripts to remove connector sequences, filter out low-quality and unidentifiable base information reads, and obtain clean reads that can be used for subsequent analysis.
HISAT2 software is used to compare clean reads with the reference genome (GRCm39) to obtain mapped reads for subsequent analysis.
Assembly: GRCm39
Supplementary files format and content: FPKM values for each Sample

source_name: liver

growth_protocol: Mice were maintained in a temperature-controlled (23 ± 2°C) and humidity (40–60%) environment with 12hrs light/dark cycles

extract_protocol:
murine livers were obtained, flash frozen on dry ice, and RNA was harvested using Trizol reagent,1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: unrestricted access to food and water

value: liver

tag: strain

tag: Sex

value: male

tag: age


title: AV4_04_SG-RNA-3 - A375 Old

description: Library name: Sample 3

data_processing:
Fastq files were aligned to hg38 (ensembl release 85) using Star aligner (version 2.5.1b). BAM alignments were quantified in R (version 3.6.1) using featureCounts from the Rsubread library (version 2.0.1).
Assembly: hg38
Supplementary files format and content: text file with raw data

growth_protocol: A375 cells were seeded at 70-80% confluence a day prior to the treatment. Prior to treatment, cells were washed twice with PBS.

extract_protocol:
RNA from cells were extracted using Qiagen RNA extraction kit (Qiagen, Cat no. 74104) as per manual instructions. 1ug RNA used per condition.
Samples were received and Poly-A sequencing (SureSelect; Agilent) libraries prepared for sequencing. Libraries were sequenced using the Novaseq (Illumina) platform. Basecalls were converted to fastq files using bcl2fastq (Illumina).

value: Old adipocyte secretome


title: Mouse visual cortex cell mRNA, Psi-Light treatment, Sample 12vc

description: Library name: 12vc

value: Psi-Light


title: F33 Placenta Pup3, MNR, Sham


title: Mouse visual cortex cell mRNA, PBS-Dark treatment, Sample 16vc

description: Library name: 16vc

value: PBS-Dark


title: Ler, bio rep 1

type: RNA

city: East Lansing

first: Hideki

last: Takahashi

state: Michigan

address: 1066 Bogue Street

department: Biochemistry and Molecular Biology

institute: Michigan State University

description: Gene expression data from wild-type Ler roots

hyb_protocol: Samples were hybridized with GeneChip ATH1-121501.1 Array (Affymetrix) according to the manufacturer’s protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using the affy R packgage to determine normalized expression values, ABS calls, and detection p-values for each probe

label: biotin

organism: Arabidopsis thaliana

source_name: Root tissue of wild-type Ler

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Plants were grown for 10 days under a 16 hr day/8 hr night light cycle at 22°C. Plants were grown on MGRL media supplemented with 0.1 mM KNO3 and containing 1% sucrose, 0.05% MES, and 1 % agar.

extract_protocol: Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) according to manufacturer's protocols.

treatment_protocol: Whole root tissue was harvested and flash frozen with liquid nitrogen for RNA extraction.

value: whole root

value: wild-type

tag: ecotype

value: Ler


title: Mouse visual cortex cell mRNA, PBS-Dark treatment, Sample 15vc

description: Library name: 15vc


title: SCA26 MeWo Old replicate 1

description: Library name: Sample 2

value: MeWo

value: human melanoma cell

value: Old adipoycte secretome


title: clv1-15, bio rep 2

description: Gene expression data from roots of a mutant in CLV1

source_name: Root tissue of a mutant in CLV1

value: CLV1 mutant


title: Mouse visual cortex cell mRNA, Psi-Light treatment, Sample 11vc

description: Library name: 11vc


title: Mouse visual cortex cell mRNA, PBS-Dark treatment, Sample 14vc

description: Library name: 14vc


title: CDFF2

value: wild type


title: CDAC2


title: Mouse visual cortex cell mRNA, PBS-Dark treatment, Sample 13vc

description: Library name: 13vc


title: CDFF1


title: Col-0, bio rep 2

description: Gene expression data from wild-type Col-0 roots

source_name: Root tissue of wild-type Col-0


title: Ler, bio rep 2


title: SCA27_MeWo Young replicate 1

description: Library name: Sample 3

value: Young adipocyte secretome


title: CDFF3


title: P5_scRNAseq

status: Public on Mar 25 2025

city: Ikoma

first: Taito

last: Matsuda

country: Japan

institute: Nara Institute of Science and Technology

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files from sequencing were demultiplexed and then used as input for Cell Ranger (v2.2.0), and aligned to the mm10 reference genome for assignment of reads to single cells. To detect age-related gene expression changes, we conducted an integrated analysis using the IntegrateData function of the Seurat package (v4.1.0). Two datasets were confirmed as anchors using the FindIntegrationAnchors function, after which the anchors were used to integrate the three datasets using the IntegrateData function. We then performed a PCA analysis on the integrated dataset36. Using Seurat’s non-linear dimensional reduction algorithm RunUMAP, we clustered cells using variable genes. Differential gene expression analysis was performed using the FindAllMarkers function in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matirix files

source_name: Hippocampus

extract_protocol:
P5, 12w, and 24w Nestin-EGFP mice were euthanized, and each brain was promptly harvested. The DG was quickly microdissected under a dissection scope and minced with a scalpel. The dissociated DG was transferred into prewarmed papain (25 U/mL) solution and incubated at 33 ℃ for 45 min. The suspension was then washed with 2 mL Minimum Essential Medium α (Gibco) containing 5% BSA to stop enzyme activity, mechanically dissociated by gentle pipetting with a fire-polished Pasteur pipette, and centrifuged at 130 × g for 5 min. The cell pellet was then resuspended in 2 mL of Hanks’ balanced salt solution (HBSS) containing 250 U/mL DNase and centrifuged at 130 × g for 5 min, after which the cells were suspended in HBSS. The cells were sorted on a FACS Aria II (BD Biosciences), with 7-AAD (559925, BD Pharmingen) added to exclude nonviable cells from the analysis. Cells dissociated from the DG of WT mice were used to draw gates for EGFP+ and EGFP− cell populations. The EGFP+ cells were sorted into N2 medium and centrifuged at 200 × g at 4 ℃ for 10 min. The supernatant was carefully removed, leaving 30 µL to resuspend the cell pellet. One microliter of cells was mixed with 10 µL Trypan Blue to determine cell viability. For scRNA-seq and scATAC-seq analyses, 700–1200 cells/µL were used.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics).

value: Hippocampus

value: EGFP-positive cells


title: Col-0, bio rep 3


title: SCA25_ MeWo control replicate 1

description: Library name: Sample 1

value: serum free media


title: CDAC3

value: liver


title: AV4_02_SG-RNA-2 -A375 Young

description: Library name: Sample 2

value: Yound adipoycte secretome


title: clv1-15, bio rep 3


title: AV4_05_SG-RNA-1 - A375 control

description: Library name: Sample 1


title: Mouse visual cortex cell mRNA, Psi-Light treatment, Sample 10vc

description: Library name: 10vc

value: Brain

value: visual cortex


title: 12W_scRNAseq

description: 10X Genomics


title: clv1-15, bio rep 1


title: WT bam infected with wMel2a W. pipientis, unmated three-day old_1

value: Ovaries

value: Tissue

value: WT bam w1118 + wMel2a W. pipientis

value: Unmated three-day old


title: 24W_scRNAseq

description: 10X Genomics


title: Mouse Spinal Cord 9, 3 months, M337V transgenic

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

description: Library name: TDP_7

data_processing:
For data analysis, pipelines available from www.cgat.org were used. In brief, data was checked for contamination and read quality using FastQC (v0.11.2) and FastQ Screen (v0.4.4).  Poor quality reads were trimmed using Trimmomatic (v0.32).
Reads were mapped against a custom genome containing the BAC sequence, which was based on Ensembl release 78 for Mus musculus.
Mapping was done using STAR (v2.4.2a) and mapping quality was ascertained using Picard tools (v2.6.0) and other metrics.
Gene level read counts from coding exons were tallied using FeatureCounts from the Subread package (v1.4.6). Pseudocounts were also obtained using Salmon (v.0.8.2) and processed using tximport (v1.2.0). Expression analysis was carried out using DESeq2 (v1.14.1; R v3.3.0).
Assembly: custom genome containing the BAC sequence, which was based on Ensembl release 78 for Mus musculus.
Supplementary files format and content: Counts Table generated using featurecounts

source_name: lumbar spinal cord

growth_protocol: Mice were sacrificed at 3 months of age, following laboratory procedures. Spinal cords were dissected and lumbar regions were isolated and frozen at -80 C in RNALater.

extract_protocol:
RNA was subsequently extracted using Trizol reagent (Life Technologies) and Qiagen miRNeasy kit. RNA integrity was validated using a Bioanalyser (Agilent), with RIN values for all extractions above 8.
Samples were prepared with Illumina TruSeq RNA Stranded Sample Prep Kit v2. All sequencing was performed on the Illumina HiSeq HiSeq2000 platform to a read depth of at least 26 million. Paired-end sequencing was performed over 100 cycles.

value: lumbar spinal cord

value: female


title: Mouse Spinal Cord 10, 3 months, WT transgenic

description: Library name: TDP_8

value: WT


title: Mouse Spinal Cord 8, 3 months, WT transgenic

description: Library name: TDP_6


title: Mouse Spinal Cord 3, 3 months, M337V transgenic

description: Library name: TDP_12


title: Mouse Spinal Cord 6, 3 months, nontransgenic

description: Library name: TDP_4

value: NTg


title: Mouse Spinal Cord 4, 3 months, nontransgenic

description: Library name: TDP_2


title: Ler, bio rep 3

value: whole root

value: wild-type

value: Ler


title: CLE3ox 17-3, bio rep 2

description: Gene expression data from roots of a CLE3 overexpressing line

source_name: Root tissue of a CLE3 overexpressing line

value: CLE3 overexpressing


title: Col-0, bio rep 1


title: CLE3ox 17-3, bio rep 1


title: CLE3ox 12-1, bio rep 2


title: Mouse Spinal Cord 7, 3 months, M337V transgenic

description: Library name: TDP_5


title: CLE3ox 12-1, bio rep 1


title: Mouse Spinal Cord 2, 3 months, M337V transgeni

description: Library name: TDP_11


title: Control_3 N-3

city: Chang Sha

first: He

last: Cailin

state: Hu Nan

address: Kaifu district

institute: xiangya hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

organism: Rattus norvegicus

source_name: synovial tissue

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: synovial tissue

value: Male

value: Control


title: Glyphosate+2,4-D-exposed C3A cells replicate 3

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

description:
Library name: G_24D3
Column name in G_24D_FPKM.csv: G_24D3

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads from raw data (Bolger et al., 2014). All the downstream analyses were based on clean data with high quality. Reference genome (GRCh38/hg38) and gene model annotation files were downloaded from the genome website directly. The index of the reference genome was built, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. The abundance of each transcript was quantified using feature Counts v1.5.0-p3.
Assembly: GRCh38/hg38
Supplementary files format and content: csv. files contain fpkm data for each sample

source_name: Liver

growth_protocol: The human hepatoma C3A/HepG2 (HB-8065, ATCC, USA, https://www.atcc.org/products/crl-3581) cell line was cultured in Eagle's Minimum Essential Medium (MEM) (Vitrocell, Brazil) with low glucose, 1 mM sodium pyruvate, 2 mM L-glutamine, 1% non-essential amino acids, supplemented with 10% fetal bovine serum (FBS) (Gibco, USA), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco, USA) in T75 flasks in a humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
After exposure, the medium was removed, cells were washed in phosphate buffer, harvested with a cell scraper and total RNA was isolated using QIAzol lysis reagent and RNeasy column-based system (Qiagen, UK) according to the manufacturer's instructions.
SMARTer Prep Kit according to the manufacturer's instructions

treatment_protocol: Cells were seeded in 6-well plates and exposed to glyphosate, AMPA, or 2,4-D individually; or to glyphosate + 2,4-D and AMPA + 2,4-D mixtures at concentrations 1000-fold lower than the IC50 (glyphosate: 5.6 µM or 0.95 µg/mL; AMPA: 34 µM or 3.7 µg/mL; 2,4-D: 2.5 µM or 0.56 µg/mL) for 48h.

value: Liver

value: Hepatoma cells


title: Mouse Spinal Cord 1, 3 months, M337V transgenic

description: Library name: TDP_10


title: Control_1 N-1


title: CIA_1 C-7

value: CIA


title: Glyphosate+2,4-D-exposed C3A cells replicate 1

description:
Library name: G_24D1
Column name in G_24D_FPKM.csv: G_24D1


title: BZXD_2 B-9

value: BZXD


title: Control_4 N-13


title: Control_2 N-2


title: Mouse Spinal Cord 5, 3 months, nontransgenic

description: Library name: TDP_3


title: AMPA+2,4-D-exposed C3A cells replicate 1

description:
Library name: A_24D1
Column name in A_24D_FPKM.csv: A_24D1


title: CIA_2 C-8


title: AMPA+2,4-D-exposed C3A cells replicate 3

description:
Library name: A_24D3
Column name in A_24D_FPKM.csv: A_24D3


title: CIA_4 C-16


title: BZXD_4 B-17


title: CIA_3 C-10


title: BZXD_3 B-11


title: BZXD_1 B-5


title: AMPA-exposed C3A cells replicate 2

description:
Library name: A2
Column name in A_FPKM.csv: A2

value: AMPA


title: 2,4-D-exposed C3A cells replicate 2

description:
Library name: D242
Column name in D24_FPKM.csv: D242


title: Glyphosate+2,4-D-exposed C3A cells replicate 2

description:
Library name: G_24D2
Column name in G_24D_FPKM.csv: G_24D2


title: AMPA-exposed C3A cells replicate 3

description:
Library name: A3
Column name in A_FPKM.csv: A3


title: Glyphosate-exposed C3A cells replicate 3

description:
Library name: G3
Column name in GA_FPKM.csv: G3

value: Glyphosate


title: 2,4-D-exposed C3A cells replicate 1

description:
Library name: D241
Column name in D24_FPKM.csv: D241


title: AMPA-exposed C3A cells replicate 1

description:
Library name: A1
Column name in A_FPKM.csv: A1


title: 2,4-D-exposed C3A cells replicate 3

description:
Library name: D243
Column name in D24_FPKM.csv: D243


title: Unexposed C3A cells replicate 5

description:
Library name: M_C3A5
Column name in M_C3A_FPKM.csv: M_C3A5


title: Glyphosate-exposed C3A cells replicate 1

description:
Library name: G1
Column name in GA_FPKM.csv: G1


title: Unexposed C3A cells replicate 6

description:
Library name: M_C3A6
Column name in M_C3A_FPKM.csv: M_C3A6


title: Unexposed C3A cells replicate 4

description:
Library name: M_C3A4
Column name in M_C3A_FPKM.csv: M_C3A4


title: Glyphosate-exposed C3A cells replicate 2

description:
Library name: G2
Column name in GA_FPKM.csv: G2


title: Unexposed C3A cells replicate 1

description:
Library name: M_C3A1
Column name in M_C3A_FPKM.csv: M_C3A1


title: Unexposed C3A cells replicate 2

description:
Library name: M_C3A2
Column name in M_C3A_FPKM.csv: M_C3A2


title: IMR90_Control6_rep2(RNA-seq)

city: Beijing

first: Wei

last: Tao

address: No.5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

description: Library name: Sample8

data_processing:
The raw sequencing data were processed using trim_galore (version  0.6.10) to remove adapters and low-quality reads
The trimmed reads were then mapped to the hg38 or mm10 reference genome using hisat2 (version 2.2.1), and the SAM files were converted to sorted BAM files using samtools (version 1.7)
The gene expression count matrix was obtained using featureCounts (version 2.0.6) and normalized with DESeq2 (version 1.34.0)
Assembly: hg38, mm10
Supplementary files format and content: Tab-delimited text files include normalized values for each sample

source_name: lung

extract_protocol:
Total RNA was extracted from cells for the construction of sequencing libraries using TRIzol® (Invitrogen, 15596018)
RNA libraries were prepared for sequencing using Illumina protocols

value: lung

value: Fibroblast


title: Full 3'UTR, DMS treated, Rep3

description:
3UTR_plusDMS_Rep3
In vitro transcribed RNA
3UTR_DMS_Rep3_normalized_reactivities.txt

value: in vitro transcribed RNA

value: DMS


title: IMR90_Control6_rep1(RNA-seq)

description: Library name: Sample7

value: WT


title: IMR90_Pyruvate_rep2(RNA-seq)

description: Library name: Sample6

value: Pyruvate


title: IMR90_Pyruvate_rep1(RNA-seq)

description: Library name: Sample5


title: IMR90_Control_ace(CUT&Tag)

description: Library name: Sample16

data_processing:
Clean data were mapped to the hg38 or mm10 reference genome using bowtie2 (version 2.2.5).The sorted bam files were converted to bigwig format using bamCoverage (version 3.5.1)
The normalized signal was visualized in Integrative Genomics Viewer (IGV, version 2.11.3). deepTools (version 3.5.1) was used to calculate signal scores between ±3 kb from the transcriptional start site and create profiles
Peak calling was performed using MACS2 (version 2.2.7.1). DESeq2 (version 1.34.0) and MACS2 (version 2.2.7.1) were used to identify altered peaks
Peaks distribution and annotation were analyzed using ChIPseeker (version 1.30.3)
Assembly: hg38, mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag experiments were performed according to the CUT&Tag Assay Kit manual (Vazyme, TD903). Briefly, cell pellets were collected at 600 × g for 5 min, washed with wash buffer, and incubated with ConA beads for 10 min at room temperature in 8-strip tubes. Subsequently, the cell–ConA bead complexes were incubated with anti-H3K9la (PTM BIOLABS, PTM1419RM) at 4℃ overnight and a secondary antibody for 1 h at room temperature. The pA/G-Tnp transposon mediated the transposition reaction, and TTBL mediated DNA fragmentation. DNA extraction beads were used to extract CUT&Tag-enriched DNA
CUT&Tag libraries were prepared for sequencing using established protocols


title: IMR90_A485_ace(CUT&Tag)

description: Library name: Sample14


title: IMR90_Control_lac(CUT&Tag)

description: Library name: Sample13


title: IMR90_A485_lac(CUT&Tag)

description: Library name: Sample11


title: IMR90_Pyruvate(CUT&Tag)

description: Library name: Sample9


title: IMR90_MS-275_lac(CUT&Tag)

description: Library name: Sample12


title: IMR90_Control6(CUT&Tag)

description: Library name: Sample10


title: THP-1 cells,Day 1-3

city: chongqing

first: yusheng

last: yang

address: Department of Orthopedic, Southwest Hospital, Army Medical University

institute: 陆军军医大学第一附属医院

description: Library name: Sample6

data_processing:
The products were then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using a Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the molar concentration. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Assembly: Conducting bioinformatics analysis through R language
Supplementary files format and content: All processed files are ultimately presented in xls format

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, GER,74106).
Paired-end libraries were synthesized using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA, RS-122-2001) following the TruSeq™ RNA Sample Preparation Guide. In brief, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Subsequently, the mRNA was fragmented into small pieces using divalent cations at 94℃ for 8 min. The cleaved RNA fragments were then used to generate first-strand cDNA with reverse transcriptase and random primers. This was followed by the synthesis of second-strand cDNA using DNA Polymerase I and RNase H. The resulting cDNA fragments underwent an end repair process, the addition of a single ‘A’ base, and ligation of the adapters.

value: Peripheral blood

value: Human Acute Monocytic Leukemia Cells


title: THP-1 cells,Day 1-2

institute: 陆军军医大学第一附属医院

description: Library name: Sample5


title: THP-1 cells,infected with H37Rv,Day1-1_C1

institute: 陆军军医大学第一附属医院

description: Library name: SAMPLE-1


title: THP-1 cells,Day 1-1

institute: 陆军军医大学第一附属医院

description: Library name: Sample4


title: THP-1 cells,infected with H37Rv,Day1, treated with 1,25(OH)2D3-2

institute: 陆军军医大学第一附属医院

description: Library name: SAMPLE-4


title: Unexposed C3A cells replicate 3

description:
Library name: M_C3A3
Column name in M_C3A_FPKM.csv: M_C3A3


title: THP-1 cells,infected with H37Rv,Day1-2

institute: 陆军军医大学第一附属医院

description: Library name: Sample2


title: THP-1 cells,infected with H37Rv,Day1-3

institute: 陆军军医大学第一附属医院

description: Library name: Sample3


title: THP-1 cells,infected with H37Rv,Day1-2_C3

institute: 陆军军医大学第一附属医院

description: Library name: SAMPLE-2


title: IMR90_MS-275_ace(CUT&Tag)

description: Library name: Sample15


title: THP-1 cells,infected with H37Rv,Day1, treated with 1,25(OH)2D3-1

institute: 陆军军医大学第一附属医院

description: Library name: SAMPLE-3


title: THP-1 cells,infected with H37Rv,Day1-1

institute: 陆军军医大学第一附属医院

description: Library name: Sample1


title: PC9 NKX2-1-dTag dTagV-1NEG 2hr TT-seq Rep1

city: Boston

last: Meyerson

state: MA

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: JLP-T009
PC9_NKX2-1-dTag_dTagV-1NEG_2hr_Rep1

data_processing:
Paired-end RNA-seq reads were trimmed using Trimmomatic (v. 0.36) for properly paired reads and to remove any TruSeq adapter sequences. RNA-seq reads were mapped to the human reference genome (hg38) using STAR (Dobin et al., 2013) version 2.3.1 with default parameters.
Raw read counts were generated with Rsubread featureCounts against the hg38 refFlat annotation from UCSC—reads were allowed to map to multiple annotations (allowMultiOverlap=T) but we only counted the primary alignment of each read (primaryOnly=T). Significance was assessed using the R package DESeq2. Significantly changing genes were assessed with a Bonferri-corrected p value≤1e-3 and a fold change≥1.5 to determine set of significantly changing genes. Transcripts per million (TPM) were determined from featureCounts raw counts normalized per million total reads.
TT-seq data was aligned and analyzed similarly to RNA-seq data above with the following modifications. Raw read counts were generated with Rsubread featureCounts against a modified hg38 refFlat annotation to count all nascent reads from TSS to TTS for each transcript.
Log2 fold change values were generated as above for RNA-seq using a pseudocount of 1. For genes identified as significantly changed in overexpression experiments by RNA-seq, the analogous fold changes in overexpression by RNA-seq was plotted against the fold change by TT-seq. Genes with a 1.25 fold change by TT-seq in the same direction as the significant change by RNA-seq were considered “direct”targets, and others were considered “secondary” targets of NKX2-1 regulation.
Assembly: GRCh38
Supplementary files format and content: Transcripts per million normalized reads for the hg38 refFlat annotation.

growth_protocol: Cell lines were cultured in RPMI + 10% Fetal Bovine Serum + 1X PenStrep

extract_protocol:
Cells were immediately lysed on plate with Trisol, scraped, and harvested for TT-seq.
TT-Seq library construction was performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA. TT-seq libraries were sequenced at 2x60bp on a NovaSeq SP.

treatment_protocol: Cells were spinfected with constructs at day 0, changed over to hard selection (1µg/mL puromycin) on day 1, then reduced to low selection (0.5µg/mL puromycin) on day 4. Cells were plated for TT-seq on day -1, on day 0 cells were treated with 500nM dTagV-1 or dTagV-1NEG for 1 hour 45 minutes, then treated with 500nM dTagV-1 or dTagV-1NEG + 500μM 4-Thiouridine (4sU) for 15 minutes.

value: lung adenocarcinoma


title: HCC364 Hi-C Rep2

description:
Library name: JLP-H008
HCC364_Hi-C_Rep2

library_source: genomic

data_processing:
Hi-C libraries were analyzed using Juicer (v. 2.0) with Arima flag, for analyses the fastqs of the two technical replicates were merged after confirmation of similar observed results.
Hi-C contact maps were visualized using the R package plotgardener (v. 1.8.3).
Assembly: GRCh38
Supplementary files format and content: hic - Juicer HiC contact map of Hi-C reads

molecule: genomic DNA

extract_protocol:
Hi-C libraries were prepared using the Arima Genome-Wide Hi-C+ kit. DNA from two pellets of each cell line were titred for DNA content and prepared according to the Arima protocol. DNA was sheared in an 8 tube microtube strip (Covaris) in Covaris Shearing Buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.1% SDS) on a Covaris LE220sc at PIP 450/DF 15/CBP 200 for 90 seconds total.
Hi-C libraries were prepared using the Arima Genome-Wide Hi-C+ kit and sequenced as 2x60bp on a NovaSeq SP.

treatment_protocol: Naïve cells of NCI-H2087, NCI-H358, NCI-H441, and HCC364 were trypsinized, counted, and fixed in culture media at 1% formaldehyde at room temperature for 10min, quenched in 0.125M glycine for 5min at room temperature. Cells were pelleted, PBS washed, pelleted, resuspended and aliquoted, pelleted again, aspirated, and stored at -80°C.

value: naive


title: NCI-H1975 NKX2-1-dTag dTagV-1 2hr TT-seq Rep1

description:
Library name: JLP-T015
NCI-H1975_NKX2-1-dTag_dTagV-1_2hr_Rep1


title: NCI-H1975 NKX2-1-dTag dTagV-1 2hr TT-seq Rep2

description:
Library name: JLP-T016
NCI-H1975_NKX2-1-dTag_dTagV-1_2hr_Rep2


title: NCI-H358 Hi-C Rep1

description:
Library name: JLP-H003
NCI-H358_Hi-C_Rep1


title: NCI-H2087 Hi-C Rep1

description:
Library name: JLP-H001
NCI-H2087_Hi-C_Rep1


title: NCI-H2087 Hi-C Rep2

description:
Library name: JLP-H002
NCI-H2087_Hi-C_Rep2


title: NCI-H1975 NKX2-1-dTag dTagV-1NEG 2hr TT-seq Rep1

description:
Library name: JLP-T013
NCI-H1975_NKX2-1-dTag_dTagV-1NEG_2hr_Rep1


title: NCI-H441 Hi-C Rep1

description:
Library name: JLP-H005
NCI-H441_Hi-C_Rep1


title: PC9 NKX2-1-dTag dTagV-1 2hr TT-seq Rep1

description:
Library name: JLP-T011
PC9_NKX2-1-dTag_dTagV-1_2hr_Rep1


title: NCI-H441 Hi-C Rep2

description:
Library name: JLP-H006
NCI-H441_Hi-C_Rep2


title: NCI-H1975 NKX2-1-dTag dTagV-1NEG 2hr TT-seq Rep2

description:
Library name: JLP-T014
NCI-H1975_NKX2-1-dTag_dTagV-1NEG_2hr_Rep2


title: HCC364 Hi-C Rep1

description:
Library name: JLP-H007
HCC364_Hi-C_Rep1


title: PC9 NKX2-1-dTag dTagV-1 2hr TT-seq Rep2

description:
Library name: JLP-T012
PC9_NKX2-1-dTag_dTagV-1_2hr_Rep2


title: NCI-H358 Hi-C Rep2

description:
Library name: JLP-H004
NCI-H358_Hi-C_Rep2


title: ABE8e(V106W),RNF2,mcf7,rep1

city: Wuhan

first: qi

last: wei

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

description:
Library name: sample17
Mutation_raw_counts_20samples.xlsx

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After adapter trimming and filtering out low-quality reads, all fastq files were aligned to the human reference genome hg38, using bowtie2 v2.4.5.
PCR duplicates were removed using Picard MarkDuplicates v.2.0.1
A custom python script was used to parse the pileup format into a tabular format summarizing the mutation at each position.
Assembly: hg38
Supplementary files format and content: The XLSX files contain raw count values for each site

growth_protocol: HEK293T (ATCC, CRL-11268) and MCF7 (ATCC, HTB-22) cells were separately maintained in DMEM and MEM supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C under 5% CO2

extract_protocol:
Genomic DNA was freshly extracted using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme, DC112) and stored in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) at −80 °C
2μL 100μM Ad1-F and 2μL 200μM Ad1-R were annealed in 1× T4 RNA ligation buffer in a thermos cycler. Similarly, hybridize 20μL Ad2-F and 20μL Ad2-R in 50mM NaCl. Afterwards, eluted DNA were incubated in a 100 ul mixture (1ul annealed Ad1-F/Ad1-R (10μM/20μM), 20% PEG-8000, 0.5mM ATP, 0.375 U/μL T4 DNA ligase high conc (NEB, M0437M) in 1× T4 RNA ligation buffer ) at 37°C for 1h and at 95°C for 2min.  The ligation products were immobilized on Streptavidin C1 beads according to the manufacturer’s instruction. Free adapters were removed by washing once with 1× B&W buffer, once with 100μL stringency wash buffer (0.1% SDS, 0.1× SSC buffer) at 45°C for 3min and another once with 1× B&W buffer. To synthesize the second strand, the beads were resuspended with 48μL mixture containing 2μM Primer , 200μM each dNTP, 0.05% Tween-20 in 1× Klenow reaction buffer. After 2min at 65°C, 2μL Klenow fragment was added and the beads were incubated for 2min at 25°C and for 25min at 35°C with gentle shaking. After a second bead wash, the beads were resuspended with 100μL mixture containing 2μM each Ad2-F/Ad2-R, 5% PEG-4000, 0.05% Tween-20, 0.1U/μL T4 DNA ligase in 1×T4 DNA ligase buffer. After incubating for 1h at 22°C in a thermomixer (800 r.p.m), another bead wash was performed with B&W buffer, stringency wash buffer and B&W buffer as described above. The DNA was eluted from C1 beads using TET buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5% Tween-20) after heating at 95°C for 1min. Eluted DNA was finally subjected to PCR amplification. Sequencing was performed by Illumina Novaseq (Azenda Life Science).
Library construction was performed according to the ssDNA library construction protocol with some modifications.(PMID: 32612278)

value: Michigan Cancer Foundation-7


title: Input,mcf7,rep1

description:
Library name: sample19
Mutation_raw_counts_20samples.xlsx


title: Input,mcf7,rep2

description:
Library name: sample20
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),RNF2,mcf7,rep2

description:
Library name: sample18
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),EMX1,mcf7,rep2

description:
Library name: sample14
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),mcf7,rep1

description:
Library name: sample15
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),HBG,rep2

description:
Library name: sample12
Mutation_raw_counts_20samples.xlsx

value: Human embryonic kidney


title: ABE8e(V106W),EMX1,mcf7,rep1

description:
Library name: sample13
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),VEGFA3,rep2

description:
Library name: sample10
Mutation_raw_counts_20samples.xlsx


title: ABE7.10, VEGFA3, rep2

description:
Library name: sample8
Mutation_raw_counts_20samples.xlsx


title: SMA20

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

description: Library name: IGS_MLI_231rCAP

data_processing:
Reads were mapped to the human genome Hg38 using HISAT2(v2.0.4),
Counts were obtained using the Python library HTseq82.
Assembly: Hg38
Supplementary files format and content: tsv of counts of each sample

source_name: whole blood

extract_protocol:
A total of 2.5 mL of venous blood was collected from each study participant during acute illness and before initiation of antimalarial treatment. Blood was collected into PreAnalytiX PAXgene Blood RNA collection tubes (Qiagen). RNA extractions were performed with the PreAnalytiX PAXgene Blood RNA extraction kit in accordance with the manufacturer’s instructions.
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used for cDNA synthesis and library preparation

value: whole blood

tag: match group

value: SMA

value: Male

value: 16 months

tag: ethnicity

value: Senoufo

tag: blantyre coma_scale

tag: hemoglobin g_dl

tag: parasitemia

tag: age years

tag: age months

tag: blood type

value: A

tag: rh factor

tag: type cat

value: case

tag: blantyre coma_scale_2

tag: cm sma


title: ABE7.10, RNF2, rep2

description:
Library name: sample6
Mutation_raw_counts_20samples.xlsx

tag: cell line

tag: cell type


title: ABE7.10, HBG, rep2

description:
Library name: sample4
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),VEGFA3,rep1

description:
Library name: sample9
Mutation_raw_counts_20samples.xlsx


title: ABE7.10, VEGFA3, rep1

description:
Library name: sample7
Mutation_raw_counts_20samples.xlsx


title: SMA19

description: Library name: IGS_MLI_230rCAP

tag: tissue

tag: Sex

value: 19 months

value: Bambara

value: O


title: SMA18

description: Library name: IGS_MLI_228rCAP

value: Female

tag: age

value: 1 year


title: ABE7.10, HBG, rep1

description:
Library name: sample3
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),HBG,rep1

description:
Library name: sample11
Mutation_raw_counts_20samples.xlsx


title: ABE8e(V106W),mcf7,rep2

description:
Library name: sample16
Mutation_raw_counts_20samples.xlsx


title: ABE7.10, EMX1, rep2

description:
Library name: sample2
Mutation_raw_counts_20samples.xlsx


title: ABE7.10, RNF2, rep1

description:
Library name: sample5
Mutation_raw_counts_20samples.xlsx


title: ABE7.10, EMX1, rep1

description:
Library name: sample1
Mutation_raw_counts_20samples.xlsx


title: Both9

description: Library name: IGS_MLI_222rCAP

tag: match group

value: CM + SMA

value: 3 years

value: Bozo

value: B

value: both


title: CM21

description: Library name: IGS_MLI_223rCAP

value: whole blood

value: CM

value: 5 years

tag: ethnicity

value: Sonrhaï


title: CM20

description: Library name: IGS_MLI_220rCAP

value: Bobo

tag: blantyre coma_scale


title: SMA16

description: Library name: IGS_MLI_219rCAP

value: SMA

value: Male

tag: hemoglobin g_dl


title: SMA17

description: Library name: IGS_MLI_221rCAP

value: Dogon

tag: parasitemia

value: case


title: SMA15

description: Library name: IGS_MLI_217rCAP

value: 5 ans

tag: age years

value: A


title: CS10

description: Library name: IGS_MLI_216rCAP

value: 2 ans

value: Bambara


title: CM18

description: Library name: IGS_MLI_207rCAP

value: Female

value: 4 years


title: SMA12

description: Library name: IGS_MLI_212rCAP

value: 1 year

value: O


title: SMA14

description: Library name: IGS_MLI_215rCAP

value: whole blood

value: 11 months

value: Senoufo

tag: age months


title: SMA13

description: Library name: IGS_MLI_213rCAP

tag: blood type

value: B


title: SMA11

description: Library name: IGS_MLI_211rCAP

value: 18 months

value: Peulh

tag: rh factor


title: CM17

description: Library name: IGS_MLI_206rCAP

value: CM

value: 3 years

tag: type cat


title: CM15

description: Library name: IGS_MLI_201rCAP

value: Male

value: Dogon

value: case

tag: blantyre coma_scale_2


title: CM16

description: Library name: IGS_MLI_205rCAP

value: AB

tag: cm sma


title: shRNF25#2

city: Shaanxi

first: Li

last: Lei

state: Xi 'an

address: 277 Yanta West Road, Xi 'an, Shaanxi

institute: The First Affiliated Hospital of Xi'an Jiaotong University

description:
Library name: shRNF25B-2
Bulk RNA-seq shRNF25-2

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: The gene expression data file (.txt) contains normalized expression values for each gene across control and RNF25 knockdown samples.

growth_protocol: SW839 cell line was grown in their respective media supplemented with 10% fetal bovine serum, 1000 U/ml penicillin and 100 μg/ml streptomycin, in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA from cells was extracted with Trizol reagent.
RNA-Seq

treatment_protocol: SW839 cell line was transfection with shRNF25 plasmid to decrease the expression of RNF25.

tag: cell line

value: RCC cell line

tag: genotype

tag: treatment

value: shRNA


title: shControl#2

description:
Library name: PLKOseq48
Bulk RNA-seq PLKO-2

tag: cell type

value: shControl


title: shRNF25#3

description:
Library name: shRNF25B-3
Bulk RNA-seq shRNF25-3


title: shRNF25#1

description:
Library name: shRNF25B-1
Bulk RNA-seq shRNF25-1


title: shControl#1

description:
Library name: PLKOseq422
Bulk RNA-seq PLKO-1


title: shControl#3

description:
Library name: PLKO
Bulk RNA-seq PLKO-3


title: CS2

description: Library name: IGS_MLI_147rCap

tag: tissue

value: CM + SMA

tag: Sex

tag: age

value: both


title: UMC1

description: Library name: IGS_MLI_151rCap

value: whole blood

tag: match group

value: 4 years

tag: ethnicity

tag: blantyre coma_scale

value: A

value: control

value: neither


title: SMA1

description: Library name: IGS_MLI_148rCap

value: SMA

value: Female

tag: hemoglobin g_dl

tag: parasitemia

tag: age years

value: B


title: CM4

description: Library name: IGS_MLI_144rCap

value: CM

value: Male

value: 16 months

tag: age months

tag: blood type

value: O

tag: rh factor


title: CS1

description: Library name: IGS_MLI_145rCap

value: 3 years

value: Dogon

tag: type cat

value: case

tag: blantyre coma_scale_2

tag: cm sma


title: CM2

description: Library name: IGS_MLI_142rCap


title: CM19

description: Library name: IGS_MLI_214rCAP

value: 5 years

value: Malinké


title: CM1

description: Library name: IGS_MLI_141rCap

value: whole blood


title: CM3

description: Library name: IGS_MLI_143rCap

value: 18 months


title: CM14

description: Library name: IGS_MLI_200rCAP

value: 2 years


title: PC9 NKX2-1-dTag dTagV-1NEG 2hr TT-seq Rep2

description:
Library name: JLP-T010
PC9_NKX2-1-dTag_dTagV-1NEG_2hr_Rep2

tag: cell line

value: lung adenocarcinoma

tag: genotype


title: UMS7

description: Library name: IGS_MLI_137rCap

tag: tissue

value: Bambara

value: control

value: neither


title: UMC11

description: Library name: IGS_MLI_136rCap

tag: Sex

value: Female

value: 15 months


title: SMA7

description: Library name: IGS_MLI_131rCap

value: SMA

value: Male

tag: age

value: B


title: SMA10

description: Library name: IGS_MLI_127rCap

tag: match group

value: 3 years

value: AB


title: SMA8

description: Library name: IGS_MLI_134rCap

tag: ethnicity

value: Peulh

value: case


title: UMCS8

description: Library name: IGS_MLI_103rCap

value: CM + SMA

value: 4 years

value: Dogon

tag: blantyre coma_scale

value: A


title: CM11

description: Library name: IGS_MLI_126rCap

value: whole blood

value: CM

value: 9 months

tag: hemoglobin g_dl

value: O


title: UMC10

description: Library name: IGS_MLI_104rCap

tag: parasitemia

value: control

value: neither


title: UMCS7

description: Library name: IGS_MLI_102rCap

value: 4 ans

value: Bambara

tag: age years


title: UMC12

description: Library name: IGS_MLI_105rCap

value: Male


title: UMC9

description: Library name: IGS_MLI_100rCap

value: 3 years


title: UMS8

description: Library name: IGS_MLI_138rCap

value: SMA

value: Female


title: UMCS5

description: Library name: IGS_MLI_098rCap


title: UMC7

description: Library name: IGS_MLI_094rCap


title: UMCS3

description: Library name: IGS_MLI_089rCap

value: B


title: UMS6

description: Library name: IGS_MLI_097rCap

value: 1 year


title: UMCS4

description: Library name: IGS_MLI_092rCap

value: CM + SMA

value: 5 years


title: UMC8

description: Library name: IGS_MLI_095rCap

value: 2 years

value: Dogon


title: UMS5

description: Library name: IGS_MLI_090rCap

value: whole blood

value: A


title: UMC6

description: Library name: IGS_MLI_091rCap

value: CM

value: O


title: AMPA+2,4-D-exposed C3A cells replicate 2

description:
Library name: A_24D2
Column name in A_24D_FPKM.csv: A_24D2

value: Liver

tag: cell type

value: Hepatoma cells

value: WT

tag: treatment


title: UMCS6

description: Library name: IGS_MLI_099rCap

value: Male

value: Malinke

tag: blood type

tag: rh factor

value: control

value: neither


title: UMC5

description: Library name: IGS_MLI_088rCap

value: Female

value: 1 years

tag: type cat

tag: blantyre coma_scale_2


title: UMS2

description: Library name: IGS_MLI_085rCap

value: SMA

value: 3 years

value: AB

tag: cm sma


title: UMS3

description: Library name: IGS_MLI_086rCap

value: Dogon


title: UMCS2

description: Library name: IGS_MLI_083rCap

value: whole blood

value: CM + SMA

value: 4 years


title: UMS4

description: Library name: IGS_MLI_087rCap

value: A


title: UMS1

description: Library name: IGS_MLI_084rCap

value: B


title: UMCS1

description: Library name: IGS_MLI_082rCap


title: UMC3

description: Library name: IGS_MLI_080rCap

value: CM

value: 21 Months

tag: age months


title: CM12

description: Library name: IGS_MLI_076rCap

tag: tissue

value: Male

value: O

value: case


title: UMC2

description: Library name: IGS_MLI_079rCap

tag: Sex

value: control

value: neither


title: CM10

description: Library name: IGS_MLI_075rCap

tag: age

value: 5 years


title: CS7

description: Library name: IGS_MLI_073rCap

tag: match group

value: Bambara

value: both


title: CS5

description: Library name: IGS_MLI_067rCap

value: Female

value: 3 years

tag: ethnicity


title: CM13

description: Library name: IGS_MLI_071rCap

value: whole blood

value: Dogon

tag: blantyre coma_scale

value: AB


title: CM7

description: Library name: IGS_MLI_063rCap

tag: hemoglobin g_dl


title: SMA9

description: Library name: IGS_MLI_061rCap

value: SMA

tag: parasitemia


title: CS3

description: Library name: IGS_MLI_050rCap

value: CM + SMA

value: 1 year

tag: age years

value: B


title: CM5

description: Library name: IGS_MLI_049rCap

value: CM

value: A


title: SMA4

description: Library name: IGS_MLI_048rCap

value: Male

value: case


title: SMA5

description: Library name: IGS_MLI_053rCap

value: 2 years


title: CS4

description: Library name: IGS_MLI_059rCap

value: 5 years


title: CM6

description: Library name: IGS_MLI_057rCap


title: SMA2

description: Library name: IGS_MLI_046rCap

value: O


title: SMA3

description: Library name: IGS_MLI_047rCap


title: UMC4

description: Library name: IGS_MLI_081rCap

value: 16 Months

value: control

value: neither


title: Homo sapiens, HUVEC Cells, control Hep3B-vector/Evs, biol rep3

city: Harbin

first: Ye

last: Han

state: Heilongjiang

address: No. 157, baojian Road

institute: The second Affiliated Hospital of Harbin Medical University

description:
Library name: A4
Column name gene_count.txt: A4

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters. The expression count matrix was obtained by FeatureCounts.
Assembly: hg38
Supplementary files format and content: Tab separated table count values of genes for each sample

source_name: HUVEC

extract_protocol:
RNA was harvested using TRIzol Reagent (Thermo Fisher, Cat#15596018CN). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA extracted according to the manufacturer’s instructions. RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

tag: cell type

value: HUVEC

value: control Hep3B-vector/Evs


title: Homo sapiens, HUVEC Cells, experiment Hep3B-miR-183-5p mimics/EVs, biol rep3

description:
Library name: B4
Column name gene_count.txt: B4

tag: treatment

value: experiment Hep3B-miR-183-5p mimics/EVs


title: Homo sapiens, HUVEC Cells, experiment Hep3B-miR-183-5p mimics/EVs, biol rep1

description:
Library name: B2
Column name gene_count.txt: B2


title: Homo sapiens, HUVEC Cells, control Hep3B-vector/Evs, biol rep2

description:
Library name: A3
Column name gene_count.txt: A3


title: Homo sapiens, HUVEC Cells, control Hep3B-vector/Evs, biol rep1

description:
Library name: A2
Column name gene_count.txt: A2


title: Homo sapiens, HUVEC Cells, experiment Hep3B-miR-183-5p mimics/EVs, biol rep2

description:
Library name: B3
Column name gene_count.txt: B3


title: A11, Normoxia, Rep1

city: Cambridge

first: Ashley

middle: David

last: Sawle

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: Library name: A11_N_1

data_processing:
Quality of raw sequence data was assessed using FastQC (version 0.11.8)
Quantification of gene expression was performed using Salmon (v 1.6.0) in mapping-based mode versus the Ensembl release 102 transcriptome
Assembly: GRCh38.p5
Supplementary files format and content: Tar archive file containing full Salmon output

source_name: Glioblastoma Neurosphere Organoid

growth_protocol: Neurospheres in Matrigel domes were grown on two 24 well plates at 37ºC. Medium was refreshed every 48 h and on day 10 it was removed, the plates placed on ice and the wells washed with 1 mL of ice-cold PBS, followed by the addition of 1 mL Corning Cell Recovery Solution (Corning, New York, USA).

extract_protocol:
The plates were incubated at 4ºC for 1 h and then washed four times with ice-cold PBS to give a pellet of neurospheres. RNA was isolated using a QIAshredder spin column (Qiagen). RNA was further isolated using AllPrep DNA/RNA Mini Kit (Qiagen).
For library preparation, the Illumina Truseq stranded mRNA kit was used, and paired end read sequencing was performed on a NovaSeq 6000 machine

treatment_protocol: One plate was incubated in atmospheric O2 while the other was grown in 0.5% O2, 0.5 Pa (Avatar, XCellbio, CA).

value: Glioblastoma Neurosphere Organoid

tag: cell line

value: Normoxia


title: AT3, Normoxia, Rep1

description: Library name: AT3_N_1


title: CM9

description: Library name: IGS_MLI_069rCap

value: whole blood

value: 3 years

value: Dogon

tag: blood type

tag: rh factor


title: A11, Hypoxia, Rep4b

description: Library name: A11_H_4b

value: Hypoxia


title: CS6

description: Library name: IGS_MLI_068rCap

value: CM + SMA

value: Male

value: Sarakolé

tag: type cat

tag: blantyre coma_scale_2

value: both


title: SMA6

description: Library name: IGS_MLI_066rCap

value: SMA

value: Female

value: 1 year

value: O

value: case

tag: cm sma


title: CM8

description: Library name: IGS_MLI_064rCap

tag: tissue

value: CM

value: 2 years


title: S2, Hypoxia, Rep2

description: Library name: S2_H_2

value: Glioblastoma Neurosphere Organoid


title: AT8C1, Hypoxia, Rep4

description: Library name: AT8C1_H_4


title: A11, Hypoxia, Rep2

description: Library name: A11_H_2


title: AT3, Normoxia, Rep2

description: Library name: AT3_N_2

value: Normoxia


title: AT8C1, Normoxia, Rep3

description: Library name: AT8C1_N_3


title: A11, Normoxia, Rep2

description: Library name: A11_N_2


title: SP20, Normoxia, Rep1

description: Library name: SP20_N_1


title: AT5C1, Normoxia, Rep2

description: Library name: AT5C1_N_2


title: AT5C1, Normoxia, Rep1

description: Library name: AT5C1_N_1


title: AT3, Normoxia, Rep3

description: Library name: AT3_N_3


title: AT8C1, Hypoxia, Rep1

description: Library name: AT8C1_H_1


title: AT5C1, Normoxia, Rep3

description: Library name: AT5C1_N_3


title: SP20, Normoxia, Rep3

description: Library name: SP20_N_3


title: A11, Hypoxia, Rep3

description: Library name: A11_H_3


title: AT2, Hypoxia, Rep1

description: Library name: AT2_H_1


title: AT2, Hypoxia, Rep4

description: Library name: AT2_H_4


title: S2, Normoxia, Rep3

description: Library name: S2_N_3


title: SP20, Normoxia, Rep4

description: Library name: SP20_N_4


title: S2, Hypoxia, Rep3

description: Library name: S2_H_3


title: S2, Normoxia, Rep1

description: Library name: S2_N_1


title: AT8C1, Hypoxia, Rep2

description: Library name: AT8C1_H_2


title: S2, Normoxia, Rep2

description: Library name: S2_N_2


title: AT8C2, Normoxia, Rep1

description: Library name: AT8C2_N_1


title: RPE, G2, EU-RNA-seq

city: Hefei

first: Yan

last: Yang

state: Anhui

address: No.373 Huangshan Road

institute: University of Science and Technology of China

description: Library name: EU-G2

data_processing:
Raw sequencing reads were trimmed for adapters using fastp, and mapped to the human genome (hs1) using Bowtie2. Alignments were converted to bigWig file for visualization using deepTools. Reads of annotated alpha-satellite transcripts in assembly T2T-CHM13v2.0 were counted using bedtools, and RPKM values were calculated for downstream analysis.
Assembly: hs1
Supplementary files format and content: bigWig files including CPM values across the whole genome
Supplementary files format and content: tab-delimited text file including RPKM values of all annotated alpha-satellite transcripts for each sample
Library strategy: EU-RNA-seq

extract_protocol:
EU-RNA-seq was performed according to a commercially available kit (Click-iT™ Nascent RNA Capture Kit, Invitrogen). Briefly, about 2,000,000 cells were labelled with EU, and total RNA were extracted, followed by biotinylation by click reaction. Biotinylated RNA was then precipitated with ammonium acetate, and captured using Streptavidin T1 magnetic beads, followed by cDNA systhesis.
Sequencing of the library was conducted on Illumina Novaseq (PE150) platform (Novogene).

tag: cell cycle

tag: genotype

value: WT


title: AT2, Normoxia, Rep2

description: Library name: AT2_N_2


title: A11, Hypoxia, Rep4a

description: Library name: A11_H_4a


title: AT8C1, Hypoxia, Rep3

description: Library name: AT8C1_H_3


title: AT2, Normoxia, Rep1

description: Library name: AT2_N_1


title: A11, Normoxia, Rep3

description: Library name: A11_N_3


title: AT8C2, Normoxia, Rep3

description: Library name: AT8C2_N_3


title: RPE, S, EU-RNA-seq

description: Library name: EU-S

value: S


title: AT8C1, Normoxia, Rep4

description: Library name: AT8C1_N_4


title: RPE, G1, EU-RNA-seq

description: Library name: EU-G1


title: RPE, Async, EU-RNA-seq

description: Library name: EU-A

value: asynchronous


title: RPE, M, EU-RNA-seq

description: Library name: EU-M

value: M


title: 1210_0048_Healthy - IL2_TGFb1 - LAMP1_hi

city: Biberach

first: Katrin

last: Fundel-Clemens

address: Birkendorfer 65

country: Germany

institute: Boehringer Ingelheim

description:
Library name: 1210_0048
1210_0048

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using mm10/GRCm38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html). Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences. For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25 for human. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Assembly: ENSEMBL hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Natural Killer Cell

extract_protocol:
Samples were transferred to PRIME PhaseLock tubes (QuantaBio, 2302820) and chloroform (Honeywell, C2432-25mL) was added at a 5:1 ratio and vigorously mixed. Samples were centrifuged. The resulting top aqueous layer was mixed with 1.5 volumes of Ethanol 100% (Roth, 9065.3). Samples were then pipetted onto miRNeasy spin columns included in the miRNease Micro Kit (Qiagen, 217084). Next steps were performed as suggested in the protocol provided by the manufacturer. DNase I (Agilent, 600031) was used to digest DNA present in the RNA samples. RNA was eluted with 14 μL UltraPure RNAse-free water in Lo-Bind tubes and stored at -80°C.
Total RNA was quantitatively and qualitatively assessed using the fluorescence Broad Range Quant-iT RNA Assay Kit (Thermo Fisher Scientific) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 96-channel Fragment Analyzer (Agilent), respectively. Total RNA samples had a RIN >7.5 and an input of 25ng was employed for bulk mRNA-seq library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7760), NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490) and NEBNext Multiplex Oligos for Illumina (#E7600) (New England Biolabs) as per manufacturer’s instructions. Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification were used instead of the recommended SPRIselect Beads. Libraries were amplified with 15 PCR cycles and quantified with the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Libraries were assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 96-channel Fragment Analyzer (Agilent). Libraries were normalized on the MicroLab STAR (Hamilton), pooled and sequenced on a NovaSeq 6000 (Illumina) with dual index, paired-end reads (Read Parameter: Rd1:101, Rd2:10, Rd3:10, Rd4:101) with an average sequencing depth of ~28 million Pass-Filter reads per sample.

treatment_protocol: To modulate NK cell activity, NK cells were either stimulated with recombinant Human IL-2 10 ng/mL (BioLegend, 589104), or inhibited with TGF-β (Bio-Techne, 7754-BH-005/CF) at the same concentration, and cells were cultured at 37°C and 5% CO2 for 2 days.

value: Natural Killer Cell

tag: lamp status


title: 1210_0046_Healthy - TGFb1 - LAMP1_hi

description:
Library name: 1210_0046
1210_0046

value: TGFb


title: 1210_0047_Healthy - IL2_TGFb1 - LAMP1_neg

description:
Library name: 1210_0047
1210_0047


title: AT8C2, Normoxia, Rep4

description: Library name: AT8C2_N_4


title: AT8C1, Normoxia, Rep2

description: Library name: AT8C1_N_2


title: 1210_0044_Healthy - IL2 - LAMP1_hi

description:
Library name: 1210_0044
1210_0044


title: 1210_0043_Healthy - IL2 - LAMP1_neg

description:
Library name: 1210_0043
1210_0043


title: 1210_0041_Healthy - Control - LAMP1_neg

description:
Library name: 1210_0041
1210_0041

value: CTRL


title: 1210_0038_Healthy - TGFb1 - LAMP1_hi

description:
Library name: 1210_0038
1210_0038


title: 1210_0042_Healthy - Control - LAMP1_hi

description:
Library name: 1210_0042
1210_0042


title: 1210_0039_Healthy - IL2_TGFb1 - LAMP1_neg

description:
Library name: 1210_0039
1210_0039


title: 1210_0037_Healthy - TGFb1 - LAMP1_neg

description:
Library name: 1210_0037
1210_0037


title: 1210_0036_Healthy - IL2 - LAMP1_hi

description:
Library name: 1210_0036
1210_0036


title: 1210_0035_Healthy - IL2 - LAMP1_neg

description:
Library name: 1210_0035
1210_0035


title: 1210_0040_Healthy - IL2_TGFb1 - LAMP1_hi

description:
Library name: 1210_0040
1210_0040


title: 1210_0033_Healthy - Control - LAMP1_neg

description:
Library name: 1210_0033
1210_0033


title: 1210_0034_Healthy - Control - LAMP1_hi

description:
Library name: 1210_0034
1210_0034


title: 1210_0031_Healthy - IL2_TGFb1 - LAMP1_neg

description:
Library name: 1210_0031
1210_0031


title: 1210_0029_Healthy - TGFb1 - LAMP1_neg

description:
Library name: 1210_0029
1210_0029


title: 1210_0030_Healthy - TGFb1 - LAMP1_hi

description:
Library name: 1210_0030
1210_0030


title: 1210_0027_Healthy - IL2 - LAMP1_neg

description:
Library name: 1210_0027
1210_0027


title: 1210_0026_Healthy - Control - LAMP1_hi

description:
Library name: 1210_0026
1210_0026


title: 1210_0024_Healthy - IL2_TGFb1 - LAMP1_hi

description:
Library name: 1210_0024
1210_0024


title: 1210_0032_Healthy - IL2_TGFb1 - LAMP1_hi

description:
Library name: 1210_0032
1210_0032


title: 1210_0020_Healthy - IL2 - LAMP1_hi

description:
Library name: 1210_0020
1210_0020


title: 1210_0019_Healthy - IL2 - LAMP1_neg

description:
Library name: 1210_0019
1210_0019


title: 1210_0023_Healthy - IL2_TGFb1 - LAMP1_neg

description:
Library name: 1210_0023
1210_0023


title: 1210_0016_Healthy - IL2_TGFb1 - LAMP1_hi

description:
Library name: 1210_0016
1210_0016


title: 1210_0045_Healthy - TGFb1 - LAMP1_neg

description:
Library name: 1210_0045
1210_0045


title: 1210_0025_Healthy - Control - LAMP1_neg

description:
Library name: 1210_0025
1210_0025


title: 1210_0018_Healthy - Control - LAMP1_hi

description:
Library name: 1210_0018
1210_0018


title: 1210_0017_Healthy - Control - LAMP1_neg

description:
Library name: 1210_0017
1210_0017


title: 1210_0022_Healthy - TGFb1 - LAMP1_hi

description:
Library name: 1210_0022
1210_0022


title: 1210_0015_Healthy - IL2_TGFb1 - LAMP1_neg

description:
Library name: 1210_0015
1210_0015


title: 1210_0014_Healthy - TGFb1 - LAMP1_hi

description:
Library name: 1210_0014
1210_0014


title: 1210_0013_Healthy - TGFb1 - LAMP1_neg

description:
Library name: 1210_0013
1210_0013


title: 1210_0012_Healthy - IL2 - LAMP1_hi

description:
Library name: 1210_0012
1210_0012


title: 1210_0008_Healthy - IL2_TGFb1 - LAMP1_hi

description:
Library name: 1210_0008
1210_0008


title: 1210_0009_Healthy - Control - LAMP1_neg

description:
Library name: 1210_0009
1210_0009


title: 1210_0007_Healthy - IL2_TGFb1 - LAMP1_neg

description:
Library name: 1210_0007
1210_0007


title: 1210_0006_Healthy - TGFb1 - LAMP1_hi

description:
Library name: 1210_0006
1210_0006


title: 1210_0005_Healthy - TGFb1 - LAMP1_neg

description:
Library name: 1210_0005
1210_0005


title: 1210_0003_Healthy - IL2 - LAMP1_neg

description:
Library name: 1210_0003
1210_0003


title: 1210_0004_Healthy - IL2 - LAMP1_hi

description:
Library name: 1210_0004
1210_0004


title: 1210_0002_Healthy - Control - LAMP1_hi

description:
Library name: 1210_0002
1210_0002


title: 1210_0001_Healthy - Control - LAMP1_neg

description:
Library name: 1210_0001
1210_0001


title: Caco-2_TotalexRNA_rep4

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Library name: 18

data_processing:
For sRNA libraries we first trimmed the adaptors using Cutadapt version 1.16 using a minimum insert size of 10 nt and no maximum. We assessed sequence quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/). We aligned clean reads to the genome and all subsequent analyses were performed using the software Bowtie2. For miRNA analyses, we used the latest version of miRBase (version 22).
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium
Supplementary files format and content: small RNA seq.: microRNA count files

source_name: Colorectal

growth_protocol: Caco-2 cells were cultured with DMEM supplemented with 20% FBS and 1% Pen/Strep and incubated at 37°C and 5% CO2.

extract_protocol:
For extracellular RNA isolation, media was collected and centrifuged to remove cell debris. Total exRNA was isolated from a portion of the supernatant by nucleic acid precipitation, followed by Trizol. The other portion of supernatant was centrifuged at 40,000xg. P40 exRNA was isolated from the resulting pellet using Trizol. The supernatant was collected and centrifuged at 100,000xg. S100 RNA was isolated from the supernatant by nucleic acid percipitation and subsequent Trizol isolation. P100 exRNA was isolated from the pellet using Trizol. Intracellular RNA was isolated from the Caco-2 cells using Trizol.
sRNA libraries were constructed using the RealSeq-AC kit version 2 (Realseq Biosciences, Santa Cruz, CA, catalog no. 500-00048;) as per the manufacturer’s instructions. We sent all sRNA libraries for sequencing to the University of Delaware Sequencing and Genotyping Center, where they were sequenced on a NovaSeq2000 instrument using 50-bp single-end reads.

treatment_protocol: Once cells reached 80% confluence, the growth media was changed to FBS and antibiotic free media and cells were allowed to incubate for 24 hours prior to isolation.

value: Colorectal

value: Epithelial

tag: fraction

value: TotalexRNA

tag: batch


title: 1210_0021_Healthy - TGFb1 - LAMP1_neg

description:
Library name: 1210_0021
1210_0021


title: 21T1_S28

city: Madison

first: Lingxin

last: Cheng

state: WI

address: University of Wisconsin Madison

department: Biomedical Data Science

institute: UW Madison

data_processing:
Quality control of raw sequencing reads was performed using FastQC (version 0.12.1)
reads were aligned to the human reference genome using the STAR aligner (version 2.7.11a)
gene expression levels were quantified using RSEM (version 1.2.7)
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing each sample as a column

source_name: vocal fold

extract_protocol:
Total RNA extracted; purity verified by NanoDrop One Spectrophotometer; integrity verified by Agilent 4200Tapestation
TruSeq® Stranded Library Preparation; 300 ng total RNA input; Poly-A enrichment; RNA fragmentation; cDNA synthesis; purification with AMPure XP beads; Illumina index ligation; PCR amplification (15 cycles)
RNA-Seq, paired-end, 150 base pair sequencing on Illumina NovaSeq6000

value: vocal fold

value: control (healthy) VFF

value: tVFF (scar model)


title: Caco-2_TotalexRNA_rep3

description: Library name: 17


title: ScN3_S26

value: scarred vocal fold fibroblast

value: nVFF (neutralization)


title: ScC3_S25

value: cVFF (untreated)


title: Caco-2_TotalexRNA_rep2

description: Library name: 16


title: 59N3_S35


title: Caco-2_TotalexRNA_rep1

description: Library name: 15


title: 59C3_S33


title: Caco-2_Supernatant_S100_rep4

description: Library name: 13


title: Caco-2_Supernatant_S100_rep3

description: Library name: 11


title: 1210_0010_Healthy - Control - LAMP1_hi

description:
Library name: 1210_0010
1210_0010


title: 1210_0011_Healthy - IL2 - LAMP1_neg

description:
Library name: 1210_0011
1210_0011


title: 58T3_S37


title: Caco-2_Supernatant_S100_rep1

description: Library name: 9


title: Caco-2_Supernatant_S100_rep2

description: Library name: 10


title: 41T3_S31


title: Caco-2_Pellet_P40_rep4

description: Library name: 4


title: 58N2_S38


title: Caco-2_Pellet_P40_rep1

description: Library name: 19


title: Caco-2_Pellet_P40_rep3

description: Library name: 3


title: 41N3_S32


title: 41C1_S30


title: Caco-2_Pellet_P40_rep2

description: Library name: 2


title: 58C2_S36


title: Caco-2_Pellet_P100_rep4

description: Library name: 8


title: 21N3_S29


title: 59T1_S34


title: 1210_0028_Healthy - IL2 - LAMP1_hi

description:
Library name: 1210_0028
1210_0028


title: Caco-2_Pellet_P100_rep2

description: Library name: 6


title: ABE8e(V106W),RNF2,rep2

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After adapter trimming and filtering out low-quality reads, all fastq files were aligned to the human reference genome hg38, using bowtie2 v2.4.5.
PCR duplicates were removed using Picard MarkDuplicates v.2.0.1
A custom python script was used to parse the pileup format into a tabular format summarizing the mutation at each position.
Assembly: hg38
Supplementary files format and content: The XLSX files contain raw count values for each site
Library strategy: DNA-seq

growth_protocol: HEK293T (ATCC, CRL-11268) cells were maintained in DMEM (Corning, 10-013-CVR) supplemented with 10% FBS (Gibco) and 1% penicillin/ streptomycin (Gibco, 10378016) at 37 °C under 5% CO2

value: Human embryonic kidney


title: ABE8e(V106W),RNF2,rep1


title: Caco-2_CellLysate_rep3

description: Library name: 14

value: WT

value: CellLysate


title: ABE8e(V106W),HEK293_site_2,rep2


title: ABE8e(V106W),HEK293_site_2,rep1


title: Caco-2_CellLysate_rep1

description: Library name: 1


title: ABE8e(V106W),rep1


title: ABE8e(V106W),EMX1,rep1


title: HCEC_WT_Input

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
ChIPseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner
ChIPseq fastq samples were downsampled using seqtk 1.4-r122 to get to homogeneous number of reads between samples
After downsamplig, ChIPseq reads were aligned to the hg38 genome using nf-core/chipseq pipeline version 2.0.0 with bwa aligner
BigWig files were generated within the nf-core/chipseq pipeline version 2.0.0 on downsapled files
Peak calling was generated within the nf-core/chipseq pipeline version 2.0.0 on downsapled files
Assembly: hg38
Supplementary files format and content: bigWig for genome browser visualization
Supplementary files format and content: narrowPeak files with peak calling (except for input)

growth_protocol: HCEC-1CT cells were acquired from Evercyte (CHT-039-0229) and cultured in a mix of 4 parts DMEM High Glucose (Euroclone) to 1 part Medium 199 with stable glutamine (Sigma-Aldrich FG0615) containing 2 % Cosmic Calf Serum (GE HyClone SH30087.02), 20 nM hEGF (Sigma-Aldrich E9644), 100 μM Insulin (Sigma-Aldrich I9278), 2 mg/mL Apo-transferrin (Sigma-Aldrich T2036), 5 nM sodium selenite (Sigma-Aldrich S5261), and 1 μg/mL Hydrocortisone (Sigma-Aldrich H0396). Media contained 100 U/ml penicillin and 100 μg/mL streptomycin (Sigma P4333), and cells were cultured in normoxia at 37°C in 5% CO2.

extract_protocol:
Cells were crosslinked by addition of formaldehyde to a final concentration of 1%, and incubation for 10 min at RT. Fixation was stopped by addition of glycine to a final concentration of 0.125 M. Cells were washed in PBS, and harvested in SDS buffer (50 mM Tris pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA and protease inhibitors). Then, cells were pelleted down and resuspended in ice-cold IP buffer (1 vol. SDS buffer, 0,5 vol. Triton Dilution Buffer [100mM Tris-HCl ph 8.6, 100mM NaCl, 5mM EDTA, 5% Triton X-100] and protease inhibitors). Samples were then sonicated to an average length of 500-200 base pairs, using a Bioruptor Pico sonifier. The volume of the samples was adjusted with IP buffer to reach ~1ml per immunoprecipitation (9ug of DNA per IP sample). The sheared chromatin was blocked with Sepharose Protein-A beads. Next, a volume equal to 5% of the lysate used for each IP was removed, to be used later as the input samples. The rest of the lysates were incubated with 4ug primary antibody against H3K27ac (Abcam, Ab4729)followed by overnight incubation at 4C on a rotating wheel. The next day, lysates were centrifuged for 20 minutes at full speed, and the supernatants transferred to clean Eppendorf tubes pre-loaded with Blocked protein A beads followed by incubation for 3 hours at 4C on a rotating wheel. The beads were centrifuged and washed 3 times in Mixed Micelle Washing Buffer (150mM NaCl, 20mM Tris-HCl pH 8.1, 5mM EDTA, 5,2% w/v sucrose, 1% Triton X-100, 0,2% SDS), 3 times in Buffer 500 (0,1% deoxycholic acid, 1mM EDTA, 50mM HEPES, 500mM NaCl, 1% Triton X-100), 3 times in LiCl/detergent solution Buffer (0,5% deoxycholic acid, 1mM EDTA, 250mM LiCl, 0,5% NP-40, 10mM Tris-HCl pH 8) and once more in TE, before final resuspension in TE with 2% SDS and overnight incubation at 65C for decrosslinking. Finally, the beads were discarded by centrifugation and the supernatants moved to clean Eppendorf tubes, followed by DNA purification using a Qiaquick PCR Purification kit (Qiagen 28106).
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit 96 (New England Biolabs BE7645L) according to manufacturer’s instructions. Adapter ligation was carried out using the NEBNext Multiplex Oligos for Illumina (96 Dual Index Pairs) according to manufacturer’s instructions. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 (Illumina) to an average read depth of 30M.

value: colonic epithelial cells

tag: antibody


title: ABE8e(V106W),rep2


title: Caco-2_CellLysate_rep2

description: Library name: 12


title: XP121, NT, input

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: XP121_NT_input

data_processing:
single-end 100 bp read length Fastq files were checked for quality using fastqc (version 0.11.2) and fastq_screen (version 0.4.4)
Reads were aligned to the hg19 reference genome using bowtie2 (version 2.5.1) filtering out alignments with mapping quality less than 10
Duplicate alignments were removed using picard-tools (version 1.127)
The ChIP-seq peaks were called using MACS2 (version 2.1.1.20160309) using the input ChIP samples as controls.
Assembly: hg19
Supplementary files format and content: narrowPeak (except for input sample)

source_name: tRCC

growth_protocol: Engineered XP121 cells were grown in full medium (DMEM FisherScientific 11995) supplemented with 10% FBS (Sigma F0926), 1x GlutaMAX (FisherScientific 35050), 1x Penicillin-Streptomycin (FisherScientific 15140), 1x MEM Non-Essential Amino Acids Solution (Fisher Scientific 11-140-050), 5 ng/mL EGF (Thermo Fisher Scientific PHG0313) and 0.4 µg/mL hydrocortisone (Sigma Aldrich H0396), puromycin (1µg/mL). Cells were grown at 37°C with 5% CO2 in a humidified sterile incubator.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quencing and lysing the cells, the chromatin was sonicated using a Covaris S220 Sonicator.
The library for ChIP-seq was prepared by the Next Generation Sequencing team at McDermott Center in UT Southwestern Medical Center. According to their protocol, libraries from 5–10 ng ChIP DNA are prepared using KAPA HTP Library Preparation Kit. The ChIP DNA is quantified on the Qubit® 2.0 Fluorometer from Invitrogen Samples are end repaired, 3' ends adenylated and barcoded with mµltiplex adapters. PCR amplified libraries are purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer to ensure the library is the expected size. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using 50SR SBS v3 reagents.

treatment_protocol: NT or shRNA cells were treated with dox (5µg/mL) 4 days before IP. The shRNA in XP121 cells targets the 3'UTR of PRCC-TFE3.

value: tRCC

value: translocation renal cell carcinoma cell

value: dox (5µg/mL) 4 days


title: ABE8e(V106W),EMX1,rep2


title: HCEC_CBP_KO3_H3K27ac

value: CBP KO

value: H3K27ac Abcam Ab4729


title: XP121, shRNA, TFE3, ChIP

description: Library name: XP121_shRNA_TFE3


title: XP121, shRNA, RPB1, ChIP

description: Library name: XP121_shRNA_RPB1


title: XP121, NT, RPB1, ChIP

description: Library name: XP121_NT_RPB1


title: 21C2_S27


title: HCEC_CBP_KO2_H3K27ac


title: XP121, shRNA, input

description: Library name: XP121_shRNA_input


title: Caco-2_Pellet_P100_rep3

description: Library name: 7

value: Colorectal

value: Epithelial


title: XP121, NT, TFE3, ChIP

description: Library name: XP121_NT_TFE3


title: HCEC_WT3_H3K27ac


title: HCEC_WT2_H3K27ac


title: XP121, TFE3, ChIP

growth_protocol: ACHN cells were grown in Eagle's MEM supplemented with 10% FBS, and 1% penicillin/streptomycin. XP121 cells were grown in  full medium (DMEM FisherScientific 11995) supplemented with 10% FBS (Sigma F0926), 1x GlutaMAX (FisherScientific 35050), 1x Penicillin-Streptomycin (FisherScientific 15140), 1x MEM Non-Essential Amino Acids Solution (Fisher Scientific 11-140-050), 5 ng/mL EGF (Thermo Fisher Scientific PHG0313) and 0.4 µg/mL hydrocortisone (Sigma Aldrich H0396). Cells were grown at 37°C with 5% CO2 in a humidified sterile incubator.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quencing and lysing the cells, the chromatin was sonicated using a Covaris S220 Sonicator.
Libraries from 5–10 ng ChIP DNA are prepared using KAPA HTP Library Preparation Kit. The ChIP DNA is quantified on the Qubit® 2.0 Fluorometer from Invitrogen Samples are end repaired, 3' ends adenylated and barcoded with mµltiplex adapters. PCR amplified libraries are purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer to ensure the library is the expected size. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using 50SR SBS v3 reagents.


title: HCEC_CBP_KO1_H3K27ac


title: XP121, RPB1, ChIP


title: HCEC_WT1_H3K27ac


title: HCEC_KO_Input


title: ACHN, TFE3, ChIP

source_name: RCC

value: RCC

value: ACHN

value: adenocarcinoma, renal cell

value: WT TFE3


title: XP121, H3K27ac, ChIP


title: PMA Treated, CRISPRi-PPP2R5C-AS1, Rep 1

city: Santa Cruz

first: Susan

last: Carpenter

address: Red Hill Rd, Biomedical Sciences

department: MCD

institute: UC Santa Cruz

data_processing:
Transcript expression was quantified with Salmon with Hg38 as a decoy sequence
Out was imported into R with tximport
Differential gene expression between CRISPRi-<lncRNA replicates> and negative controls (anti-GFP and Negative Control) was analyzd with DESeq2
Assembly: Hg38
Supplementary files format and content: Salmon quantification, transcript per million

source_name: human leukemia monocytic cells

growth_protocol: All THP1 cell lines were cultured in RPMI 1640 supplemented with 10% low-endotoxin fetal bovine serum (ThermoFisher), 1X penicillin/streptomycin, and incubated at 37°C in 5% CO2.

extract_protocol:
Cells were homogenized in Tri-Reagent (Sigma Aldrich, T9424-200 mL). RNA was extracted with Direct-zol RNA miniprep plus RNA extraction Kit (Zymo, R2072). 400 ng were sent out to Novogene
Processed by Novogene

treatment_protocol: Cells were treated with 100nM of PMA for 24hrs

value: human leukemia monocytic cells

value: PPP2R5C-AS1 Knockdown

value: 100nM PMA, 24hrs


title: ACHN, H3K27ac, ChIP


title: XP121, input


title: RPTEC, CUT&RUN, IgG

city: Ediburgh

first: Maximilian

last: Reck

address: 47 Little France Crescent

institute: University of Edinburgh

data_processing:
Libraries were sequenced on a NextSeq 2000 platform (Illumina) with 100bp paired-end reads and a mean read depth of 10M reads per library.
After library demultiplexing remaining Illumina indices were removed using Trim Galore (Cutadapt v2.8) and aligned to the GRCh38 (hg38) reference genome with bowtie2 --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 (v2.5.2). Peak calling was performed using MACS2 (v2.2.7.1)
The BAM files were converted to BigWig format using the bamCoverage command from DeepTools (v3.5.4) with the normalisation option --normalizeUsing CPM.
Assembly: hg38
Supplementary files format and content: .bigWig files contain genome coverage of CUT&RUN signal
Library strategy: CUT&RUN

source_name: Primary Renal Proximal Tubule Epithelial Cells; Normal, Human (RPTEC)

growth_protocol: Primary renal proximal tubule epithelial cells (RPTEC/TERT1, ATCC CRL-4031) were cultured at 37 °C in a 5% CO2 incubator using custom medium containing 25ng/ml hydrocortisone (Merck, H0888), 3.5g/ml ascorbic acid (Sigma-Aldrich, A4403), 1% insulin-transferrin-selenium-ethanolamine (ITS-X) (Thermo-Fisher Scientific, 51500056), 6pM Triiodo-L-Thyronine (Merck, T6397), 25ng/ml Prostaglandin E1 (Merck, P8908), 0.8% v/v of 0.28g/ml N-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid (HEPES, Sigma-Aldrich, H4034) dissolved in 1M sodium hydroxide, 10ng/ml recombinant human Epidermal Growth Factor (Promega, G5021) and 0.1mg/ml  geneticin (Gibco, 10131027) in Dulbecco’s Modified Eagle Medium (GIBCO, 31331093). All experiments were performed with cells between passage 3 and 6.

extract_protocol:
CUT&RUN libraries from TNF-alpha treated RPTECs were generated using the CUTANA ChIC/CUT&RUN kit (EpiCypher) with provided reagents unless indicated. After cell harvest samples nuclei were isolated. For this, cells were resuspended in 500l cold nuclei extraction buffer containing 2mM HEPES pH 7.9, 10mM KCl, 0.1% Triton X-100, 20% glycerol, 1X cOmplete protease inhibitor cocktail, 0.5mM spermidine in PBS. After incubation on ice for 5min, nuclei were centrifuged (500g, 5min, 4°C) and the nuclei pellet was resuspended in nuclei extraction buffer without Triton X-100. Nuclei were counted using a LUNA-FX7 cell counter and 0.5×106 nuclei were used as input for the CUT&RUN assay.
The CUT&RUN assay was then performed following manufacturer instructions. Briefly, activated Concanavalin A (ConA)-conjugated paramagnetic beads were bound to nuclei. Using a magnetic rack bead-bound nuclei were washed and resuspended in antibody buffer. For control reactions 0.5mg IgG negative control antibody (EpiCypher, 13-0042) was used while 0.5mg of NFKB1 (Cell Signalling Technology, 13586S) or JUN (EpiCypher, 13-2019) were added for positive reactions. After overnight incubation and washes pAG-MNase was added and chromatin was digested by addition of CaCl2 solution. Digestion was stopped by addition of the Stop Master Mix and the supernatant was transferred to a DNA clean-up column. After washes DNA was eluted in 12ml of DNA Elution Buffer and quantified using the Qubit dsDNA Quantification kit (Thermo Fisher Scientific, Q32851).
For each reaction 5ng purified DNA were used as input for library preparation using the CUTANA CUT&RUN Library Prep Kit (EpiCypher, 14-100) according to manufacturer instructions. Library was quantified using the Qubit dsDNA Quantification kit and fragment size was assessed using the Bioanalyzer High Sensitivity DNA Analysis kit (Agilent, 5067-4626).

treatment_protocol: The day before harvest,cells were treated with recombinant human TNF-alpha (20 ng/ml, Bio-Techne 210-TA-020). After 24 hours cells were detached using 0.05% Trypsin and 0.02% EDTA in PBS for 8 minutes and resuspended in culture medium before nuclei isolation.

value: Human Renal Proximal Tubule Epithelial

value: TNF-alpha (20 ng/ml) for 24h

tag: chip antibody

value: IgG Control


title: PMA Treated, CRISPRi-PPP2R5C-AS1, Rep 2


title: ACHN, RPB1, ChIP


title: ACHN, input


title: Input,rep2

value: Human embryonic kidney


title: PMA Treated, CRISPRi-LincANXA3, Rep 3

value: LincRNA-ANXA3 Knockdown


title: RPE, Meta, Even

description:
Meta_genome_merged_norm.bw
Meta_genome_merge_true_peaks.bed

data_processing:
Raw sequencing reads were trimmed for adapters using fastp, and mapped to the human genome (hs1) using Bowtie2. Results of Odd and Even probe pools were merged according to the pipline developed by Chang lab (PMID:21963238) and converted to bigWig files for visualization. Peaks were called from merged results using MACS2.
Assembly: hs1
Supplementary files format and content: bigWig files of merged (even and odd probe pools) α-satellite ChIRP-seq read density
Supplementary files format and content: bed files including peaks called from the merged α-satellite ChIRP-seq alignments
Library strategy: ChIRP-seq

extract_protocol:
Biotinylated antisense probes were incubated with the diluted chromatin which was produced from sonicated cells to enrich α-satellite RNAs and the associated genomic DNAs.
Libraries were constructed from the eluted DNA and sequenced on Illumina system.

value: WT


title: WTtestes1

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description:
Library name: WTtestes1
tRNAseq

data_processing:
Reads  were processed using the minm-tRNAseq pipeline.
Assembly: mm10
Supplementary files format and content: Differential expression of tRNA isodecoders

source_name: testes

extract_protocol:
total RNA were extracted and subjected to small RNA enrichment.
tNRAs were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.

value: testes

value: mouse


title: Input,rep1


title: PMA Treated, CRISPRi-LincANXA3, Rep 1


title: RPTEC, CUT&RUN, NFKB1

value: Primary Renal Proximal Tubule Epithelial Cells; Normal, Human (RPTEC)


title: KOcereb1_S1_R1_001

description:
KOcereb1
KOcelebvsWTceleb_diffexpr-results.csv

data_processing:
*library strategy: tRNAseq
Reads  were processed using the minm-tRNAseq pipeline.
Assembly: hg38
Supplementary files format and content: Differential expression of tRNA isodecoders

source_name: mouse

value: cerebellum

value: KO


title: RPE, Meta, Scr


title: PMA Treated, CRISPRi-LincJADE1, Rep 2

value: LincRNA-JADE1 Knockdown


title: RPE, Meta, Input


title: WTcereb2_S4_R1_001

description:
WTcereb2
KOcelebvsWTceleb_diffexpr-results.csv


title: RPE, Async, Even

description:
Async_genome_merged_norm.bw
Async_genome_merge_true_peaks.bed


title: KOtestes2

description:
Library name: KOtestes2
tRNAseq


title: PMA Treated, CRISPRi-LincJADE1, Rep 1


title: PMA Treated, Negative Control, Rep 1

value: Negative Control, Knockdown


title: WTcereb1_S3_R1_001

description:
WTcereb1
KOcelebvsWTceleb_diffexpr-results.csv


title: KOtestes1

description:
Library name: KOtestes1
tRNAseq


title: RPE, Async, Odd


title: PMA Treated, CRISPRi-LincJADE1, Rep 3


title: PMA Treated, Anti-GFP, Rep1

value: Anti-GFP Knockdown


title: PMA Treated, CRISPRi-LincANXA3, Rep 2

value: human leukemia monocytic cells


title: WTtestes2

description:
Library name: WTtestes2
tRNAseq


title: RPTEC, CUT&RUN, JUN

value: JUN


title: RPE, Async, Scr


title: RPE, Meta, Odd


title: Human RPE/choroid scRNA rep16

city: Stanford

first: Sean

middle: K

last: Wang

address: 269 Campus Drive

department: Genetics

institute: Stanford University

description: scRNA-seq

data_processing:
Demultiplexed scRNA- and scATAC-seq fastq files were inputted into the Cell Ranger ARC pipeline (version 2.0.0) from 10x Genomics to generate barcoded count matrices of gene expression and ATAC data. For each sample, count matrices were loaded in ArchR and selected for barcodes that appeared in both the scRNA-seq and scATAC-seq datasets. Samples in ArchR were quality control filtered for nuclei with 200-10,000 RNA transcripts, <1% mitochondrial reads, <5% ribosomal reads, TSS enrichment >4, and >1,000 ATAC fragments. Quality control filtered nuclei subsequently underwent automated removal of doublets using the filterDoublets function in ArchR, which identifies and removes the nearest neighbors of simulated doublets.
scRNA-seq data from nuclei remaining after quality control filtering and automated removal of doublets were analyzed using Seurat (version 3.1.5). After merging all preprocessed samples into a single Seurat object, gene expression counts were normalized using the NormalizeData function, scaled using the ScaleData function, and batch corrected using Harmony. Graph-based clustering was then performed on the Harmony-corrected data using the top 30 principal components at a resolution of 0.3. Cluster identities were manually annotated based on the expression of canonical marker genes. Clusters expressing marker genes from different cell types were designated as putative doublets and excluded, after which re-clustering was performed using the same parameters. Clusters with no detected marker genes were also excluded, after which the dataset was also re-clustered.
scATAC-seq data were analyzed using ArchR (version 1.0.1) based on barcoded cell type identities from scRNA-seq. For each cell type, pseudo-bulk ATAC replicates were created using the addGroupCoverages function with default parameters. Chromatin accessibility peaks on chromosomes 1-22 and X and outside of blacklist regions were then called using the addReproduciblePeakSet function and MACS2.
HiChIP sequencing files were initially processed using the HiC-Pro pipeline (version 2.11.0) to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. Filtered read pairs from HiC-Pro were subsequently converted into .hic files and inputted into HiCCUPS from the Juicer pipeline to call loops.
Assembly: hg38
Supplementary files format and content: tsv and mtx files represent raw gene counts for each barcode in the file scRNA-seq dataset. fragments files represent aggregated scATAC-seq fragments organized by cell type.
Supplementary files format and content: hic files represent all valid interaction pairs detected by HiC-Pro following H3K27ac HiChIP of human RPE/choroid tissue. bedpe files represent H3K27ac HiChIP loops detected by HiCCUPS.

molecule: nuclear RNA

source_name: RPE/choroid

extract_protocol:
Nuclei were isolated from frozen RPE/choroid using a modified Omni-ATAC protocol (doi.org/10.17504/protocols.io.6t8herw)
Joint scRNA- and scATAC-seq libraries were prepared using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions. HiChIP libraries were prepared according to Mumbach et al., 2016.
scRNA-seq, scATAC-seq, and H3K27ac HiChIP

value: RPE/choroid


title: Human RPE/choroid scRNA rep15

description: scRNA-seq


title: KOliver2

description:
KOliver2
KOlivervsWTliver_diffexpr-results.csv

value: liver


title: KOliver1

description:
KOliver1
KOlivervsWTliver_diffexpr-results.csv


title: WTliver1

description:
WTliver1
KOlivervsWTliver_diffexpr-results.csv


title: RPE, Async, Input