title: DSP-1001660002549-A-C06_R2_C4

description: Library name: DSP-1001660002549-A-C06


title: DSP-1001660002549-A-C04_R2_C3

status: Public on Dec 31 2025

type: SRA

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

country: USA

institute: Yale University

description: Library name: DSP-1001660002549-A-C04

library_source: transcriptomic

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Lung Cancer

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5-666 nm, excitation 645-19 nm, emission 683-30 nm), CD45 for lymphocyte compartment (Texas Red-615 nm, excitation 588-19 nm, emission 623-30 nm), S100B (Cy3-568 nm, excitation 538-19 nm, emission 564-15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

tag: tissue

value: Lung Cancer

tag: treatment

value: immunotherapy

tag: batch


title: leaf_fer-4_15m_C

city: Durham

first: Sheng Yang

last: He

address: 124 Science Drive

institute: Duke University

description: Library name: leaf_fer-4_15m_C_S46_

data_processing:
The pool was loaded onto two (2) lanes of an Illumina flow cell and sequencing was performed in a PAIRED end read format using a NovaSeq v1.5, 100 cycle reagent kit. Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. A summary of the run output is attached below. Basic QC information about  sequence data is provided by FastQC reports. Reads were mapped with TAIR genome using STAR and DEseq2 was used to identifiy  differntially expressed genes.
Assembly: TAIR v10
Supplementary files format and content: A CSV file contain Read counts.

organism: Arabidopsis thaliana

source_name: Leaf blade

growth_protocol: Arabidopsis  plants were grown in mix soil (1:1:1 SureMix perlite:vermiculite:perilite) in air-circulating growth chambers at 60% relative humidity, a temperature range of 20 °C to 22 °C, and light intensity of 100 µmol m-2 s-1 with a 12-hour light, 12-hour dark photoperiod for 4-4.5 weeks.

extract_protocol:
Total RNA was extracted using QIAGEN  RNeasy Plant mini kit.
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina RNA UD Indexes, following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar amounts and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Arabidopsis plants were placed under 60% or 100% relative humidity at the setuo temperature range of 20 °C to 22 °C, and light intensity of 100 µmol m-2 s-1 with a 12-hour light, 12-hour dark photoperiod.

value: Leaf blade

tag: cell line

tag: cell type

tag: genotype

value: high humidity


title: leaf_fer-4_60m_C

description: Library name: leaf_fer-4_60m_C_S47_


title: leaf_fer-4_0m_C

description: Library name: leaf_fer-4_0m_C_S45_


title: DSP-1001660013460-E-B09

city: Novato

first: Fei

last: Wu

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: FFPE GeoMx DSP profiling

data_processing:
Geomx sequencing data was analyzed with the standR (version 1.5.3), edge R (version 3.40.2), and limma (version 3.54.2) packages.
Assembly: mm10
Supplementary files format and content: .dcc files
Library strategy: GEOMx Spatial Transcriptomics

organism: Mus musculus

source_name: Spleen

extract_protocol:
Formalin-fixed paraffin embedded (FFPE) spleen tissue from two cohorts of WT mice was used to construct a tissue-micro array (TMA)
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep user guide (MAN-10153-01).

value: Spleen

value: Young


title: DSP-1001660002549-A-D08_R2_C7

description: Library name: DSP-1001660002549-A-D08


title: DSP-1001660013460-E-A05

description: FFPE GeoMx DSP profiling


title: Liver, 24 Months, Rep 9

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

country: Germany

institute: Christian-Albrechts-University Kiel

description:
Library name: sample_24M_N9_L
24M.N9

data_processing:
RNA was isolated using the QIAzol/chloroform extraction method. RNA quality was determined via an Agilent Bioanalyzer 2100 using the RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). An RNA Integrity Number (RIN) value of greater than 7 was considered to be the minimum quality for sequencing.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions. All libraries were sequenced on an NovaSeq 6000 machine (Illumina, San Diego, CA, USA) with an average of 36 million paired-end reads (2x100 bp) at Competence Centre for Genomic Analysis (CCGA, Kiel, Germany) .
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (2.8) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a two-color-chemistry aware, 3’-end quality trimming for a phred-score >= 25 (nextseq-trim=25).
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim from both end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using the tool featureCounts from the subread package (2.0.1) with reverse stranded information, while ignoring chimeric fragments and allowing only properly mapped read pairs with feature sizes in between 50 bp to 600 bp.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Comma separated matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

molecule: polyA RNA

source_name: Liver

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
RNA was isolated using the QIAzol/chloroform extraction method.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions.

value: Liver

tag: age

value: 24 Months

tag: strain

value: Prep 3


title: DSP-1001660002549-A-C03_R2_C3

description: Library name: DSP-1001660002549-A-C03


title: Brain, 9 Months, Rep 11

description:
Library name: sample_9M_N11_B
9M.N11

source_name: Brain

value: Brain

value: 9 Months


title: DSP-1001660013460-E-A03

description: FFPE GeoMx DSP profiling

value: Old


title: DSP-1001660002549-A-C02_R2_C2

description: Library name: DSP-1001660002549-A-C02


title: leaf_Col-0_24h_C

description: Library name: leaf_Col-0_24h_C_S44_


title: leaf_Col-0_0m_C

description: Library name: leaf_Col-0_0m_C_S41_


title: Liver, 9 Months, Rep 11

description:
Library name: sample_9M_N11_L
9M.N11


title: Brain, 28 Months, Rep 12

description:
Library name: sample_28M_N12_B
28M.N12

value: 28 Months


title: DSP-1001660002549-A-C01_R2_C2

description: Library name: DSP-1001660002549-A-C01


title: DSP-1001660013460-E-B08

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-A04

description: FFPE GeoMx DSP profiling


title: DSP-1001660013460-E-A02

description: FFPE GeoMx DSP profiling


title: DSP-1001660002549-A-B12_R2_C2

description: Library name: DSP-1001660002549-A-B12


title: leaf_Col-0_15m_C

description: Library name: leaf_Col-0_15m_C_S42_


title: leaf_fer-4_15m_B

description: Library name: leaf_fer-4_15m_B_S38_


title: leaf_Col-0_60m_C

description: Library name: leaf_Col-0_60m_C_S43_


title: Liver, 28 Months, Rep 12

description:
Library name: sample_28M_N12_L
28M.N12


title: DSP-1001660002549-A-B09_R2_C1

description: Library name: DSP-1001660002549-A-B09


title: DSP-1001660002549-A-B08_R1_C6

description: Library name: DSP-1001660002549-A-B08


title: Liver, 3 Months, Rep 10

description:
Library name: sample_3M_N10_L
3M.N10

value: 3 Months


title: DSP-1001660002549-A-B10_R2_C1

description: Library name: DSP-1001660002549-A-B10


title: leaf_fer-4_60m_B

description: Library name: leaf_fer-4_60m_B_S39_


title: DSP-1001660002549-A-B11_R2_C2

description: Library name: DSP-1001660002549-A-B11


title: Brain, 3 Months, Rep 10

description:
Library name: sample_3M_N10_B
3M.N10


title: L929 cells with HT-DNA+AOA+Asp stimulation for 6h_2

city: Shanghai

first: YH

last: Liao

address: Dongan road 131

country: China

institute: Fudan university

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: cell line

growth_protocol: Cell lines were grown in DMEM (Meilunbio) containing 10% FBS (Gibco), penicillin (100 U/ml) and streptomycin (100 g/ml). All cells were maintained at 37 °C and 5% CO2 and were tested for mycoplasma.

extract_protocol:
RNA were harvest using TRIzol.
Both quality and concentration of RNA samples were detected with a NanoDrop 2000 and Agilent2100 Nano. Qualified RNA samples were used for RNA-seq (Majorbio).

treatment_protocol: Cells were seeded in 6-well plate and HT-DNA was transfected into cells using Lipofectamine 2000 (Thermo Fisher) at a concentration of 0.5/μg ml.

value: cell line

value: L929 cells

value: Fibroblasts

value: WT

value: HT-DNA+AOA+Asp


title: Liver, 9 Months, Rep 6

description:
Library name: sample_9M_N6_L
9M.N6


title: Brain, 9 Months, Rep 6

description:
Library name: sample_9M_N6_B
9M.N6


title: L929 cells with HT-DNA+AOA+Asp stimulation for 6h_3


title: DSP-1001660002549-A-B07_R1_C6

description: Library name: DSP-1001660002549-A-B07

value: Lung Cancer

value: immunotherapy


title: leaf_fer-4_0m_B

description: Library name: leaf_fer-4_0m_B_S37_

value: Leaf blade

value: high humidity


title: Brain, 15 Months, Rep 5

description:
Library name: sample_15M_N5_B
15M.N5

value: 15 Months


title: leaf_fer-4_24h_B

description: Library name: leaf_fer-4_24h_B_S40_


title: Liver, 15 Months, Rep 5

description:
Library name: sample_15M_N5_L
15M.N5

value: Liver


title: L929 cells with HT-DNA+AOA stimulation for 6h_3

value: HT-DNA+AOA


title: leaf_Col-0_24h_B

description: Library name: leaf_Col-0_24h_B_S36_


title: L929 cells with HT-DNA+AOA stimulation for 6h_2


title: DSP-1001660002549-A-B05_R1_C6

description: Library name: DSP-1001660002549-A-B05


title: DSP-1001660002549-A-B06_R1_C6

description: Library name: DSP-1001660002549-A-B06


title: L929 cells with HT-DNA+AOA stimulation for 6h_1


title: L929 cells with HT-DNA+AOA+Asp stimulation for 6h_1


title: DSP-1001660002549-A-B04_R1_C4

description: Library name: DSP-1001660002549-A-B04


title: Brain, 24 Months, Rep 11

description:
Library name: sample_24M_N11_B
24M.N11

value: Brain

value: 24 Months

value: Prep 3


title: leaf_Col-0_15m_B

description: Library name: leaf_Col-0_15m_B_S34_


title: Liver, 24 Months, Rep 11

description:
Library name: sample_24M_N11_L
24M.N11


title: L929 cells with HT-DNA stimulation for 6h_3

value: HT-DNA


title: DSP-1001660002549-A-B02_R1_C4

description: Library name: DSP-1001660002549-A-B02


title: Brain, 9 Months, Rep 10

description:
Library name: sample_9M_N10_B
9M.N10

value: 9 Months


title: leaf_Col-0_0m_B

description: Library name: leaf_Col-0_0m_B_S33_


title: leaf_fer-4_24h_A

description: Library name: leaf_fer-4_24h_A_S80_


title: L929 cells with HT-DNA stimulation for 6h_1

value: cell line


title: DSP-1001660002549-A-B03_R1_C4

description: Library name: DSP-1001660002549-A-B03


title: Brain, 3 Months, Rep 3

description:
Library name: sample_3M_N3_B
3M.N3

value: 3 Months


title: leaf_fer-4_60m_A

description: Library name: leaf_fer-4_60m_A_S79_


title: DSP-1001660002549-A-B01_R1_C3

description: Library name: DSP-1001660002549-A-B01


title: DSP-1001660002549-A-A12_R1_C3

description: Library name: DSP-1001660002549-A-A12


title: Liver, 3 Months, Rep 3

description:
Library name: sample_3M_N3_L
3M.N3


title: L929 cells control_3

value: L929 cells

value: Fibroblasts

value: Mock


title: L929 cells control_1

value: WT


title: L929 cells control_2


title: leaf_fer-4_15m_A

description: Library name: leaf_fer-4_15m_A_S78_


title: leaf_fer-4_0m_A

description: Library name: leaf_fer-4_0m_A_S77_


title: DSP-1001660002549-A-A10_R1_C3

description: Library name: DSP-1001660002549-A-A10

value: Lung Cancer

value: immunotherapy


title: DSP-1001660002549-A-A11_R1_C3

description: Library name: DSP-1001660002549-A-A11


title: leaf_Col-0_24h_A

description: Library name: leaf_Col-0_24h_A_S76_

value: Leaf blade

value: high humidity


title: Liver, 28 Months, Rep 15

description:
Library name: sample_28M_N15_L
28M.N15

value: Liver

value: 28 Months


title: Brain, 28 Months, Rep 15

description:
Library name: sample_28M_N15_B
28M.N15

value: Brain


title: leaf_Col-0_60m_A

description: Library name: leaf_Col-0_60m_A_S75_


title: leaf_Col-0_60m_B

description: Library name: leaf_Col-0_60m_B_S35_


title: YOUNG3

city: Harbin

first: sijia

last: li

address: 157 Health Road, Nangang District, Harbin City, Heilongjiang Province

institute: Harbin Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: mm10
Supplementary files format and content: tab-delimited  text files includ RPKM  values for each Sample

source_name: retina

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using  SMARTER mRNA-seq Library Prep Kit following manufacture's protocols.

value: retina


title: L929 cells with HT-DNA stimulation for 6h_2


title: Brain, 9 Months, Rep 13

description:
Library name: sample_9M_N13_B
9M.N13

value: Prep 3


title: Liver, 9 Months, Rep 10

description:
Library name: sample_9M_N10_L
9M.N10


title: YOUNG2


title: DSP-1001660002549-A-A08_R1_C2

description: Library name: DSP-1001660002549-A-A08


title: leaf_Col-0_15m_A

description: Library name: leaf_Col-0_15m_A_S74_


title: Liver, 9 Months, Rep 13

description:
Library name: sample_9M_N13_L
9M.N13


title: DSP-1001660002549-A-A07_R1_C2

description: Library name: DSP-1001660002549-A-A07


title: leaf_Col-0_0m_A

description: Library name: leaf_Col-0_0m_A_S73_


title: YOUNG1


title: EGCG3


title: DSP-1001660002549-A-A06_R1_C2

description: Library name: DSP-1001660002549-A-A06


title: Liver, 24 Months, Rep 6

description:
Library name: sample_24M_N6_L
24M.N6

value: 24 Months


title: DSP-1001660002549-A-A04_R1_C1

description: Library name: DSP-1001660002549-A-A04


title: DSP-1001660002549-A-A05_R1_C1

description: Library name: DSP-1001660002549-A-A05


title: Brain, 15 Months, Rep 10

description:
Library name: sample_15M_N10_B
15M.N10

value: 15 Months


title: EGCG1


title: DSP-1001660002549-A-A09_R1_C2

description: Library name: DSP-1001660002549-A-A09


title: Liver, 15 Months, Rep 10

description:
Library name: sample_15M_N10_L
15M.N10


title: Pet_fer-4_15m_D

description: Library name: Pet_fer-4_15m_D_S30

source_name: Petiole

value: Petiole


title: Pet_fer-4_60m_D

description: Library name: Pet_fer-4_60m_D_S31


title: AGED3


title: Brain, 28 Months, Rep 1

description:
Library name: sample_28M_N1_B
28M.N1


title: AGED2


title: DSP-1001660002549-A-A02_R1_C1

description: Library name: DSP-1001660002549-A-A02


title: Pet_Col-0_24h_D

description: Library name: Pet_Col-0_24h_D_S28


title: DSP-1001660002549-A-A03_R1_C1

description: Library name: DSP-1001660002549-A-A03


title: Pet_fer-4_0m_D

description: Library name: Pet_fer-4_0m_D_S29


title: AGED1


title: Brain, 24 Months, Rep 6

description:
Library name: sample_24M_N6_B
24M.N6


title: scRNA-seq, iMGLs polyIC XP2, GDO

city: New York

first: Andrew

last: Sproul

state: NY

department: Pathology and Cell Biology

institute: Columbia University

description: Library name: AS002F

library_source: transcriptomic single cell

data_processing:
cellranger-7.1.0 count function used with feature_ref4.csv to generate counts for mRNA and GDO contained within barcodes.tsv, features.tsv, and matrix.mtx files.
Followed 10x genomics pipeline for CRISPR guide capture.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv, features.tsv, and matrix.mtx containing counts for mRNA GEX and guide counts GDO.

growth_protocol: Differentiation of human iPSC into microglia-like cells using protocol described previously (McQuade et al.). iPSCs were transfected to create a CRISPRi permanent line.

extract_protocol:
Total RNA was used for GEM generation and barcoding. Single-cell 3' v3.1 gel beads contain poly(dT) primers and additional primers (capture sequences). Followed manufacturer's protocol for Chromium Next GEM single cell 3' reagent kit v3.1 (dual index).
cDNA amplification and cleanup followed by gene expression library construction and CRISPR screening library construction.

treatment_protocol: Treatment with lentivirus containing sgRNA against target (top hit from CRISPRi screen) on day 21. Treatment with either vehicle of 10 ug/mL poly(I:C) for 2 hours.

value: microglia


title: Pet_Col-0_60m_D

description: Library name: Pet_Col-0_60m_D_S27


title: Liver, 9 Months, Rep 9

description:
Library name: sample_9M_N9_L
9M.N9

value: 9 Months


title: Pet_Col-0_15m_D

description: Library name: Pet_Col-0_15m_D_S26


title: Pet_fer-4_24h_D

description: Library name: Pet_fer-4_24h_D_S32


title: mir499_3

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

description:
Mouse HSPC were transfected with control miR499
mir499_6_S6

data_processing:
CLC Genomics Workbench v 11.0.1
The RNA-Seq analysis is done in several steps using CLC Genomics Workbench: First, all genes are extracted from the reference genome (using annotations of type gene). Other annotations on the gene sequences are preserved (e.g. CDS information about coding sequences etc). Next, all annotated transcripts (using annotations of type mRNA) are extracted. If there are several annotated splice variants, they are all extracted. Note that the mRNA annotation type is used for extracting the exon-exon boundaries.
Next, the reads are mapped against all the transcripts plus the entire gene
From this mapping, the reads are categorized and assigned to the genes, and expression values for each gene and each transcript are calculated. After that, putative exons are identified.
Fold change in gene expression was calculated
Assembly: mm10
Supplementary files format and content: The excel file includes RPKM values for each Sample.

source_name: bone marrow

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: hematopoietic stem and progenitor cells


title: scRNA-seq, iMGLs polyIC XP2, GEX

description: Library name: AS002


title: Brain, 9 Months, Rep 9

description:
Library name: sample_9M_N9_B
9M.N9


title: EGCG2


title: Pet_Col-0_0m_D

description: Library name: Pet_Col-0_0m_D_S25


title: mir499_2

description:
Mouse HSPC were transfected with control miR499
mir499_4_S5

value: WT


title: scRNA-seq, iMGLs vehicle XP2, GDO

description: Library name: AS001F

value: vehicle


title: scRNA-seq, iMGLs polyIC XP1, GDO

description: Library name: SS002F


title: Brain, 3 Months, Rep 16

description:
Library name: sample_3M_N16_B
3M.N16

value: 3 Months


title: scRNA-seq, iMGLs vehicle XP2, GEX

description: Library name: AS001


title: Liver, 3 Months, Rep 16

description:
Library name: sample_3M_N16_L
3M.N16


title: Pet_fer-4_60m_C

description: Library name: Pet_fer-4_60m_C_S23


title: Brain, 28 Months, Rep 6

description:
Library name: sample_28M_N6_B
28M.N6


title: Pet_fer-4_24h_C

description: Library name: Pet_fer-4_24h_C_S24


title: Liver, 28 Months, Rep 1

description:
Library name: sample_28M_N1_L
28M.N1


title: Control_5

description:
Mouse HSPC were transfected with control miR
Control_4_3_8_21_S2

value: control miR


title: Pet_fer-4_15m_C

description: Library name: Pet_fer-4_15m_C_S22

value: high humidity


title: Liver, 28 Months, Rep 6

description:
Library name: sample_28M_N6_L
28M.N6

value: Liver


title: scRNA-seq, iMGLs vehicle XP1, GDO

description: Library name: SS001F


title: scRNA-seq, iMGLs polyIC XP1, GEX

description: Library name: SS002


title: Pet_fer-4_0m_C

description: Library name: Pet_fer-4_0m_C_S21


title: Brain, 24 Months, Rep 1

description:
Library name: sample_24M_N1_B
24M.N1


title: scRNA-seq, iMGLs vehicle XP1, GEX

description: Library name: SS001


title: Liver, 24 Months, Rep 1

description:
Library name: sample_24M_N1_L
24M.N1


title: mir184_2

description:
Mouse HSPC were transfected with control miR184
mir184_2_S11


title: Pet_Col-0_60m_C

description: Library name: Pet_Col-0_60m_C_S19


title: Pet_Col-0_24h_C

description: Library name: Pet_Col-0_24h_C_S20


title: mir184_1

description:
Mouse HSPC were transfected with control miR184
mir184_1_S10


title: Brain, 15 Months, Rep 16

description:
Library name: sample_15M_N16_B
15M.N16


title: mir499_1

description:
Mouse HSPC were transfected with control miR499
mir499_1_S4


title: shTOP2A-2 rep1

city: Chongqing

first: Yanfei

last: Liu

address: No.1 Yixueyuan Road, Yuzhong District,

department: Institute of Life Sciences

institute: Chongqing Medical University

description: Library name: Sample 5

data_processing:
Illumina Casava2.19 software used for basecalling.
Assembly: gencode, hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample.

source_name: skin

growth_protocol: HaCaT cells were maintained in MEM supplement with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: cell line

value: keratinocyte

value: TOP2A knockdown


title: Pet_Col-0_15m_C

description: Library name: Pet_Col-0_15m_C_S18


title: Control_6

description:
Mouse HSPC were transfected with control miR
Control_5_3_8_21_S3


title: Liver, 15 Months, Rep 16

description:
Library name: sample_15M_N16_L
15M.N16

value: Prep 3


title: Control_3

description:
Mouse HSPC were transfected with control miR
Control_4_S9


title: shTOP2A-1 rep2

description: Library name: Sample 4


title: Pet_Col-0_0m_C

description: Library name: Pet_Col-0_0m_C_S17


title: Brain, 9 Months, Rep 2

description:
Library name: sample_9M_N2_B
9M.N2

value: Brain

value: Prep 2


title: Control_2

description:
Mouse HSPC were transfected with control miR
Control_3_S8


title: Control_4

description:
Mouse HSPC were transfected with control miR
Control_1_3_8_21_S1


title: Liver, 9 Months, Rep 2

description:
Library name: sample_9M_N2_L
9M.N2


title: TRC rep2

description: Library name: Sample 2

value: wild type


title: Control_1

description:
Mouse HSPC were transfected with control miR
Control_1_S7


title: Pet_fer-4_60m_B

description: Library name: Pet_fer-4_60m_B_S15

value: Petiole


title: Liver, 3 Months, Rep 6

description:
Library name: sample_3M_N6_L
3M.N6


title: mir184_3

description:
Mouse HSPC were transfected with control miR184
mir184_5_S12

value: bone marrow


title: TRC rep1

description: Library name: Sample 1


title: Primed replicate 3

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt -1.9.1
Reads were aligned and quantified using RSEM-1.3.0/STAR-2.5.2
Assembly: GRCm38
Supplementary files format and content: Comma-delimited file containing matrix table with raw gene counts for every gene and every sample

source_name: Embryonic stem cells

growth_protocol: mES cells were grown in 2iLIF media

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit as per manufacturer's instructions
Libraries were constructed using a KAPA mRNA HyperPrep Kit.

treatment_protocol: mES cells were stimulated with NB27+100ng/ml FGF2 for 24hrs or 48hrs

value: R1 mouse embryonic stem cells

value: Primed

tag: treatment length


title: Pet_fer-4_15m_B

description: Library name: Pet_fer-4_15m_B_S14


title: shTOP2A-2 rep2

description: Library name: Sample 6


title: Primed replicate 2


title: Primed replicate 1


title: AML_12

city: Guiyang

first: Dan

last: Ma

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

description:
Library name: Samples 12
Column name in genes_fpkm_expression.txt: S13

data_processing:
Sequence was trimmed using Fastp v0.20 to remove adaptor and low quality reads
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: GRCh_38
Supplementary files format and content: Supplementary files format and content: genes_fpkm_expressiont.txt: Tab-delimited text file contains FPKM for each sample.

source_name: human bone marrow

growth_protocol: Bone marrow samples were obtained from newly diagnosed, treatment-naïve acute myeloid leukemia (AML) patients under sterile conditions.  Mononuclear cells were isolated using Ficoll density gradient centrifugation, washed with phosphate-buffered saline (PBS), and immediately treated with TRIzol before storage at -80°C for subsequent RNA extraction.

extract_protocol:
Total RNA was extracted and purified from bone marrow mononuclear cells using TRIzol reagent according to the manufacturer’s instructions.
cDNA

treatment_protocol: No treatments were applied to the biological material prior to RNA extraction.  Bone marrow mononuclear cells were collected from treatment-naïve AML patients.

value: human bone marrow

value: Acute myeloid leukemia


title: Brain, 24 Months, Rep 8

description:
Library name: sample_24M_N8_B
24M.N8

value: 24 Months


title: AML_13

description:
Library name: Samples 13
Column name in genes_fpkm_expression.txt: S14


title: Brain, 15 Months, Rep 3

description:
Library name: sample_15M_N3_B
15M.N3

value: 15 Months


title: shTOP2A-1 rep1

description: Library name: Sample 3


title: AML_11

description:
Library name: Samples 11
Column name in genes_fpkm_expression.txt: S3


title: 2iLIF replicate 3

value: 2i LIF


title: Pet_Col-0_24h_B

description: Library name: Pet_Col-0_24h_B_S12

value: high humidity


title: Liver, 15 Months, Rep 3

description:
Library name: sample_15M_N3_L
15M.N3

value: Liver


title: Pet_Col-0_60m_B

description: Library name: Pet_Col-0_60m_B_S11


title: AML_9

description:
Library name: Samples 9
Column name in genes_fpkm_expression.txt: S25


title: Pet_fer-4_24h_B

description: Library name: Pet_fer-4_24h_B_S16


title: 2iLIF replicate 2


title: Pet_Col-0_15m_B

description: Library name: Pet_Col-0_15m_B_S10


title: Pet_fer-4_24h_A

description: Library name: Pet_fer-4_24h_A_S8


title: FGF4 48h replicate 3


title: Brain, 3 Months, Rep 9

description:
Library name: sample_3M_N9_B
3M.N9

value: 3 Months


title: Pet_fer-4_60m_A

description: Library name: Pet_fer-4_60m_A_S7


title: FGF4 48h replicate 2


title: Liver, 24 Months, Rep 8

description:
Library name: sample_24M_N8_L
24M.N8


title: FGF4 48h replicate 1


title: Liver, 3 Months, Rep 9

description:
Library name: sample_3M_N9_L
3M.N9


title: AML_6

description:
Library name: Samples 6
Column name in genes_fpkm_expression.txt: S20


title: Brain, 15 Months, Rep 2

description:
Library name: sample_15M_N2_B
15M.N2


title: Pet_fer-4_15m_A

description: Library name: Pet_fer-4_15m_A_S6


title: Pet_fer-4_0m_A

description: Library name: Pet_fer-4_0m_A_S5


title: AML_5

description:
Library name: Samples 5
Column name in genes_fpkm_expression.txt: S38


title: AML_10

description:
Library name: Samples 10
Column name in genes_fpkm_expression.txt: S26


title: Liver, 15 Months, Rep 2

description:
Library name: sample_15M_N2_L
15M.N2


title: Brain, 9 Months, Rep 5

description:
Library name: sample_9M_N5_B
9M.N5

value: 9 Months


title: FGF4 24h replicate 3


title: AML_4

description:
Library name: Samples 4
Column name in genes_fpkm_expression.txt: S37


title: FGF4 24h replicate 2


title: Pet_Col-0_24h_A

description: Library name: Pet_Col-0_24h_A_S4


title: Brain, 28 Months, Rep 8

description:
Library name: sample_28M_N8_B
28M.N8

value: 28 Months


title: Liver, 9 Months, Rep 5

description:
Library name: sample_9M_N5_L
9M.N5


title: FGF4 24h replicate 1


title: AML_3

description:
Library name: Samples 3
Column name in genes_fpkm_expression.txt: S36


title: Pet_Col-0_60m_A

description: Library name: Pet_Col-0_60m_A_S3


title: Liver, 28 Months, Rep 8

description:
Library name: sample_28M_N8_L
28M.N8


title: FGF4 1h replicate 3


title: AML_2

description:
Library name: Samples 2
Column name in genes_fpkm_expression.txt: S33


title: Pet_Col-0_15m_A

description: Library name: Pet_Col-0_15m_A_S2


title: FGF4 1h replicate 2


title: Brain, 24 Months, Rep 17

description:
Library name: sample_24M_N17_B
24M.N17

value: Brain


title: AML_1

description:
Library name: Samples 1
Column name in genes_fpkm_expression.txt: S31


title: Liver, 24 Months, Rep 17

description:
Library name: sample_24M_N17_L
24M.N17

value: Prep 2


title: Pet_Col-0_0m_A

description: Library name: Pet_Col-0_0m_A_S1


title: AML_8

description:
Library name: Samples 8
Column name in genes_fpkm_expression.txt: S22


title: FGF4 1h replicate 1


title: T41

city: Houston

first: Han

last: Liang

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Library name: T41

data_processing:
FASTQ files were mapped to the mouse reference genome using STAR (v2.7.10a) and gene expression was quantified by RSEM (v1.3.3)
CLC Genomics Workbench v 11.0.1
Assembly: GRCh38
Supplementary files format and content: Comma separated text file includes log2 TPM for each sample

extract_protocol:
Total RNA was extracted from FFPE slides containing tissue sections from these blocks using a Purigen Biosystems Ionic Purification System, and the DV200 values (representing the percentage of fragments >200 nucleotides) exceeded 15%.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library prep kit following manufacturer's protocol

value: HCC tumor

value: sorafenib


title: FGF2 1h replicate 3


title: non4N_Arabi-flower-rep3

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description:
Library name: F4R17
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: absolute quantification of miRNA expression for each Sample

source_name: flower

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

value: flower

tag: libtype

value: Salt-seq


title: Liver, 15 Months, Rep 12

description:
Library name: sample_15M_N12_L
15M.N12


title: T39

description: Library name: T39


title: Brain, 15 Months, Rep 12

description:
Library name: sample_15M_N12_B
15M.N12


title: FGF2 1h replicate 2

value: R1 mouse embryonic stem cells


title: non4N_Arabi-flower-rep4

description:
Library name: F4R18
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Liver, 9 Months, Rep 14

description:
Library name: sample_9M_N14_L
9M.N14


title: non4N_Arabi-flower-rep2

description:
Library name: F4R16
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: T38

description: Library name: T38


title: Brain, 9 Months, Rep 14

description:
Library name: sample_9M_N14_B
9M.N14


title: T37

description: Library name: T37


title: hCOs, mock-inoculated, 3 days post-inoculation

city: Hamilton

first: Emmie

last: de Wit

state: MT

address: 903 S 4th St

institute: NIAID

description: Library name: S10

data_processing:
Illumina bcl2fastq was used for demultiplexing. Reads were aligned to a combined human influenza A virus reference genome and unique molecular identifier counts were generated using PIPseeker v3.3 software (Fluent Biosciences).
Assembly: hg38
Supplementary files format and content: tab-separated matrix, genes, and barcodes files
Supplementary files format and content: h5ad AnnData file

extract_protocol:
Human cerebral organoids (hCOs) were dissociated into a single cell suspension as follows: one organoid per well was placed in a 24-well plate. hCOs were washed with Dulbecco’s Modified Eagle Medium/F-12 (Gibco). hCOs were incubated with 500 µl trypsin EDTA (Gibco), 500µl Accutase (MilliporeSigma), and 200 units of RNase inhibitor (Applied Biosystems) for 20 minutes at 37°C and 5% CO2. Every ten minutes, hCOs were gently agitated using a wide-bore P1000 pipette tip. If hCOs were not dissociated after twenty minutes, they were incubated for a further 5 minutes. Cells were filtered through a pre-wet 70 µm filter (pluriSelect) into stop solution (PBS + 20% FBS) and centrifuged at 200 x g for 5 minutes at 4°C. The cell pellet was resuspended in Cell Suspension Buffer (Fluent Biosciences), and filtered through a pre-wet 40 µm filter (pluriSelect). Cell concentration was determined using trypan blue and a manual hemocytometer.
The recommended 5,000 cell input was used for the PIPseq T2 protocol (Fluent Biosciences). Cells derived from 3 organoids per sample were pooled for scRNA-seq library construction. Libraries were prepared using PIPseq T2 3’ Single Cell RNA kit v4.0 PLUS (Fluent Biosciences) according to the manufacturer’s instructions. Samples were indexed using the PIPseq UDI-96 kit (Fluent Biosciences)

treatment_protocol: influenza A virus inoculation

value: human cerebral organoid

value: mock


title: non4N_Arabi-flower-rep1

description:
Library name: F4R15
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Brain, 3 Months, Rep 1

description:
Library name: sample_3M_N1_B
3M.N1


title: T36

description: Library name: T36


title: non4N_Arabi-leaf-rep4

description:
Library name: F4R14
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

source_name: leaf

value: leaf


title: T40

description: Library name: T40


title: non4N_Arabi-leaf-rep3

description:
Library name: F4R13
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: hCOs, mock-inoculated, 1 day post-inoculation

description: Library name: S4


title: FGF2 1h replicate 1


title: Liver, 3 Months, Rep 1

description:
Library name: sample_3M_N1_L
3M.N1


title: RiboSeq, HeLa, Whole Cell, Recover 2h, RiboSeq, biological replicate 3

city: Singapore

first: Jovi

last: Lim

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description:
Library name: RiboSeq_Recover2h_RiboSeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 2h. The column names are corresponding to the prefix of the raw fastq files
Recover2h_tpm_te.csv

library_source: other

data_processing:
Briefly, icSHAPE libraries were de-duplicated and adapter-trimmed. Remaining reads were mapped to genome. RT stops and base coverage were called out for each nucleotide. Genomic coordinates were converted to transcript coordinate for downstream analysis.
Assembly: ENSEMBL GRCh38 release 98
Supplementary files format and content: Processed data consists of icSHAPE reactivity for all detected transcripts in each sample i.e. files ending with "shape.txn.txt". Each row in the files represent one transcript. Each entry (tab delimited) in each row represent the reactivity of each nucleotide. SPLASH txt files contain the information of all detected chimeras in each sample. eCLIP txt.gz files contain the enriched windows for each sample (refer to software Skipper for details https://doi.org/10.1016/j.xgen.2023.100317). Translation Efficiency data are recorded in "tpm_te.csv"  files. Transcript per million (TPM) was quantified for each gene. Translation efficiency was quantified by dividing TPM of Ribo-seq samples with that of RNA-seq.
Library strategy: Ribo-Seq

molecule: other

source_name: Cervix

extract_protocol:
RNA was harvested using TRIzol/TRIzol LS reagent following manufacturer's instructions. The amount of 500ng and 1,500ng RNA were used for generating icSHAPE and SPLASH libraries, repectively. For SRSF1 eCLIP libraries, cells were fixed with UV (254nm, 400mJ/cm^2) in prior to proceeding to immunoprecipitation and library preparation.
icSHAPE library preparation was carried out according to the protocol described before (Flynn, et al, 2016); SPLASH library preparation was performed according to the protocol described before (Aw, et al, 2016); eCLIP library preparation was performed according to the protocol described before (Blue, et al, 2022).

value: Cervix

value: HeLa

value: Cervical adenocarcinoma

value: wt

value: Ribosome

tag: group


title: non4N_Arabi-leaf-rep2

description:
Library name: F4R12
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Brain, 28 Months, Rep 10

description:
Library name: sample_28M_N10_B
28M.N10


title: Liver, 28 Months, Rep 10

description:
Library name: sample_28M_N10_L
28M.N10

value: Liver


title: T34

description: Library name: T34


title: RiboSeq, HeLa, Whole Cell, Recover 2h, RNASeq, biological replicate 3

description:
Library name: RiboSeq_Recover2h_RNASeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 2h. The column names are corresponding to the prefix of the raw fastq files
Recover2h_tpm_te.csv

data_processing:
Briefly, icSHAPE libraries were de-duplicated and adapter-trimmed. Remaining reads were mapped to genome. RT stops and base coverage were called out for each nucleotide. Genomic coordinates were converted to transcript coordinate for downstream analysis.
Assembly: ENSEMBL GRCh38 release 98
Supplementary files format and content: Processed data consists of icSHAPE reactivity for all detected transcripts in each sample i.e. files ending with "shape.txn.txt". Each row in the files represent one transcript. Each entry (tab delimited) in each row represent the reactivity of each nucleotide. SPLASH txt files contain the information of all detected chimeras in each sample. eCLIP txt.gz files contain the enriched windows for each sample (refer to software Skipper for details https://doi.org/10.1016/j.xgen.2023.100317). Translation Efficiency data are recorded in "tpm_te.csv"  files. Transcript per million (TPM) was quantified for each gene. Translation efficiency was quantified by dividing TPM of Ribo-seq samples with that of RNA-seq.

value: Input


title: non4N_Arabi-stem-rep4

description:
Library name: F4R10
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

source_name: stem

value: stem


title: T33

description: Library name: T33


title: Brain, 24 Months, Rep 3

description:
Library name: sample_24M_N3_B
24M.N3

value: Brain

value: 24 Months

value: Prep 2


title: non4N_Arabi-stem-rep3

description:
Library name: F4R9
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: RiboSeq, HeLa, Whole Cell, Recover 2h, RiboSeq, biological replicate 2

description:
Library name: RiboSeq_Recover2h_RiboSeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 2h. The column names are corresponding to the prefix of the raw fastq files
Recover2h_tpm_te.csv


title: RiboSeq, HeLa, Whole Cell, Recover 2h, RNASeq, biological replicate 2

description:
Library name: RiboSeq_Recover2h_RNASeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 2h. The column names are corresponding to the prefix of the raw fastq files
Recover2h_tpm_te.csv


title: T32

description: Library name: T32

value: HCC tumor

value: sorafenib


title: Liver, 24 Months, Rep 3

description:
Library name: sample_24M_N3_L
24M.N3


title: non4N_Arabi-stem-rep2

description:
Library name: F4R8
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: Salt-seq


title: RiboSeq, HeLa, Whole Cell, Recover 2h, RNASeq, biological replicate 1

description:
Library name: RiboSeq_Recover2h_RNASeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 2h. The column names are corresponding to the prefix of the raw fastq files
Recover2h_tpm_te.csv


title: Brain, 15 Months, Rep 14

description:
Library name: sample_15M_N14_B
15M.N14

value: 15 Months


title: RiboSeq, HeLa, Whole Cell, Recover 2h, RiboSeq, biological replicate 1

description:
Library name: RiboSeq_Recover2h_RiboSeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 2h. The column names are corresponding to the prefix of the raw fastq files
Recover2h_tpm_te.csv


title: T30

description: Library name: T30


title: non4N_Arabi-stem-rep1

description:
Library name: F4R7
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Liver, 15 Months, Rep 14

description:
Library name: sample_15M_N14_L
15M.N14


title: T35

description: Library name: T35


title: RiboSeq, HeLa, Whole Cell, Recover 1h, RiboSeq, biological replicate 3

description:
Library name: RiboSeq_Recover1h_RiboSeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 1h. The column names are corresponding to the prefix of the raw fastq files
Recover1h_tpm_te.csv


title: T29

description: Library name: T29


title: non4N_Arabi-root-rep3

description:
Library name: F4R6
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

source_name: root

value: root


title: Brain, 28 Months, Rep 5

description:
Library name: sample_28M_N5_B
28M.N5

value: 28 Months


title: RiboSeq, HeLa, Whole Cell, Recover 1h, RNASeq, biological replicate 3

description:
Library name: RiboSeq_Recover1h_RNASeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 1h. The column names are corresponding to the prefix of the raw fastq files
Recover1h_tpm_te.csv

value: Cervix


title: T28

description: Library name: T28


title: non4N_Arabi-root-rep2

description:
Library name: F4R5
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Liver, 28 Months, Rep 5

description:
Library name: sample_28M_N5_L
28M.N5


title: RiboSeq, HeLa, Whole Cell, Recover 1h, RiboSeq, biological replicate 2

description:
Library name: RiboSeq_Recover1h_RiboSeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 1h. The column names are corresponding to the prefix of the raw fastq files
Recover1h_tpm_te.csv

value: HeLa


title: 4N_Arabi-flower-rep4

description:
Library name: F4R35
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: flower

value: qMap-seq


title: Brain, 3 Months, Rep 13

description:
Library name: sample_3M_N13_B
3M.N13

value: 3 Months


title: Liver, 3 Months, Rep 13

description:
Library name: sample_3M_N13_L
3M.N13

value: Liver


title: non4N_Arabi-root-rep1

description:
Library name: F4R4
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: T31

description: Library name: T31


title: 4N_Arabi-flower-rep3

description:
Library name: F4R34
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: T25

description: Library name: T25


title: RiboSeq, HeLa, Whole Cell, Recover 1h, RiboSeq, biological replicate 1

description:
Library name: RiboSeq_Recover1h_RiboSeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 1h. The column names are corresponding to the prefix of the raw fastq files
Recover1h_tpm_te.csv

value: Cervical adenocarcinoma

value: wt

value: Ribosome


title: Brain, 15 Months, Rep 6

description:
Library name: sample_15M_N6_B
15M.N6

value: Brain


title: Pet_Col-0_0m_B

description: Library name: Pet_Col-0_0m_B_S9

value: Petiole

value: high humidity


title: T24

description: Library name: T24

value: HCC tumor

value: sorafenib


title: 4N_Arabi-flower-rep2

description:
Library name: F4R33
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: 4N_Arabi-flower-rep1

description:
Library name: F4R32
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: RiboSeq, HeLa, Whole Cell, NaAsO2, RNASeq, biological replicate 3

description:
Library name: RiboSeq_NaAsO2_RNASeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of NaAsO2. The column names are corresponding to the prefix of the raw fastq files
NaAsO2_tpm_te.csv

value: Input


title: Brain, 24 Months, Rep 13

description:
Library name: sample_24M_N13_B
24M.N13

value: 24 Months

value: Prep 2


title: RiboSeq, HeLa, Whole Cell, NaAsO2, RiboSeq, biological replicate 3

description:
Library name: RiboSeq_NaAsO2_RiboSeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of NaAsO2. The column names are corresponding to the prefix of the raw fastq files
NaAsO2_tpm_te.csv

value: Cervix


title: Liver, 15 Months, Rep 6

description:
Library name: sample_15M_N6_L
15M.N6

value: 15 Months


title: 4N_Arabi-leaf-rep4

description:
Library name: F4R31
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: leaf


title: T27

description: Library name: T27


title: T22

description: Library name: T22


title: RiboSeq, HeLa, Whole Cell, NaAsO2, RiboSeq, biological replicate 2

description:
Library name: RiboSeq_NaAsO2_RiboSeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of NaAsO2. The column names are corresponding to the prefix of the raw fastq files
NaAsO2_tpm_te.csv

value: HeLa


title: T26

description: Library name: T26


title: Liver, 24 Months, Rep 13

description:
Library name: sample_24M_N13_L
24M.N13


title: T21

description: Library name: T21


title: 4N_Arabi-leaf-rep3

description:
Library name: F4R30
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: qMap-seq


title: Brain, 9 Months, Rep 15

description:
Library name: sample_9M_N15_B
9M.N15

value: 9 Months


title: T20

description: Library name: T20


title: RiboSeq, HeLa, Whole Cell, Recover 1h, RNASeq, biological replicate 1

description:
Library name: RiboSeq_Recover1h_RNASeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Recover 1h. The column names are corresponding to the prefix of the raw fastq files
Recover1h_tpm_te.csv

value: Cervical adenocarcinoma


title: 4N_Arabi-leaf-rep2

description:
Library name: F4R29
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Liver, 9 Months, Rep 15

description:
Library name: sample_9M_N15_L
9M.N15

value: Liver


title: RiboSeq, HeLa, Whole Cell, NaAsO2, RiboSeq, biological replicate 1

description:
Library name: RiboSeq_NaAsO2_RiboSeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of NaAsO2. The column names are corresponding to the prefix of the raw fastq files
NaAsO2_tpm_te.csv

value: wt

value: Ribosome


title: RiboSeq, HeLa, Whole Cell, NaAsO2, RNASeq, biological replicate 2

description:
Library name: RiboSeq_NaAsO2_RNASeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of NaAsO2. The column names are corresponding to the prefix of the raw fastq files
NaAsO2_tpm_te.csv


title: T18

description: Library name: T18


title: 4N_Arabi-leaf-rep1

description:
Library name: F4R28
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Brain, 3 Months, Rep 5

description:
Library name: sample_3M_N5_B
3M.N5

value: Brain

value: 3 Months


title: T23

description: Library name: T23

value: HCC tumor


title: RiboSeq, HeLa, Whole Cell, NaAsO2, RNASeq, biological replicate 1

description:
Library name: RiboSeq_NaAsO2_RNASeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of NaAsO2. The column names are corresponding to the prefix of the raw fastq files
NaAsO2_tpm_te.csv


title: Liver, 3 Months, Rep 5

description:
Library name: sample_3M_N5_L
3M.N5


title: 4N_Arabi-stem-rep3

description:
Library name: F4R26
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: stem


title: Brain, 28 Months, Rep 17

description:
Library name: sample_28M_N17_B
28M.N17

value: 28 Months


title: RiboSeq, HeLa, Whole Cell, Untreated, RiboSeq, biological replicate 3

description:
Library name: RiboSeq_Untreated_RiboSeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Untreated. The column names are corresponding to the prefix of the raw fastq files
Untreated_tpm_te.csv


title: RiboSeq, HeLa, Whole Cell, Untreated, RNASeq, biological replicate 3

description:
Library name: RiboSeq_Untreated_RNASeq_rep3
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Untreated. The column names are corresponding to the prefix of the raw fastq files
Untreated_tpm_te.csv

value: Input


title: AML_7

description:
Library name: Samples 7
Column name in genes_fpkm_expression.txt: S21

value: human bone marrow

value: Acute myeloid leukemia


title: T11

description: Library name: T11

value: sorafenib


title: Liver, 28 Months, Rep 17

description:
Library name: sample_28M_N17_L
28M.N17

value: Prep 2


title: 4N_Arabi-stem-rep2

description:
Library name: F4R25
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: 4N_Arabi-stem-rep1

description:
Library name: F4R24
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: T10

description: Library name: T10


title: RiboSeq, HeLa, Whole Cell, Untreated, RiboSeq, biological replicate 2

description:
Library name: RiboSeq_Untreated_RiboSeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Untreated. The column names are corresponding to the prefix of the raw fastq files
Untreated_tpm_te.csv

value: Cervix

value: HeLa


title: Brain, 24 Months, Rep 14

description:
Library name: sample_24M_N14_B
24M.N14

value: 24 Months


title: RiboSeq, HeLa, Whole Cell, Untreated, RNASeq, biological replicate 2

description:
Library name: RiboSeq_Untreated_RNASeq_rep2
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Untreated. The column names are corresponding to the prefix of the raw fastq files
Untreated_tpm_te.csv

value: Cervical adenocarcinoma


title: T08

description: Library name: T08


title: T07

description: Library name: T07


title: RiboSeq, HeLa, Whole Cell, Untreated, RiboSeq, biological replicate 1

description:
Library name: RiboSeq_Untreated_RiboSeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Untreated. The column names are corresponding to the prefix of the raw fastq files
Untreated_tpm_te.csv


title: Liver, 24 Months, Rep 14

description:
Library name: sample_24M_N14_L
24M.N14

value: Liver


title: 4N_Arabi-root-rep2

description:
Library name: F4R22
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: root

value: qMap-seq


title: T13

description: Library name: T13


title: RiboSeq, HeLa, Whole Cell, Untreated, RNASeq, biological replicate 1

description:
Library name: RiboSeq_Untreated_RNASeq_rep1
Processed data are produced using 3 biological replicates from RNAseq and Riboseq samples of Untreated. The column names are corresponding to the prefix of the raw fastq files
Untreated_tpm_te.csv

value: wt


title: 4N_Arabi-stem-rep4

description:
Library name: F4R27
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: Brain, 15 Months, Rep 13

description:
Library name: sample_15M_N13_B
15M.N13

value: Brain

value: 15 Months


title: 4N_Arabi-root-rep3

description:
Library name: F4R23
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries


title: T06

description: Library name: T06

value: HCC tumor


title: Liver, 15 Months, Rep 13

description:
Library name: sample_15M_N13_L
15M.N13


title: T05

description: Library name: T05


title: eCLIP, HeLa, SRSF1 NaAsO2, Immuno-precipitation, biological replicate 2

description: Library name: eCLIP_SRSF1_NaAsO2_IP_rep2


title: Brain, 3 Months, Rep 12

description:
Library name: sample_3M_N12_B
3M.N12

value: 3 Months


title: kin10_root_4

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Library name: 1417

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, v.20 101 214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

growth_protocol: For the "shoots" samples plants were cultivated for 4 weeks in soil, at 22`C and 10 h light / 14 h dark conditions. For the  "roots" samples, seedlings were cultivated at half-strength Murashige-Skiig medium without sucrose, for 7 days at 22`C and 16 h light / 8 h dark regime.

extract_protocol:
protocol from RNeasy Plant MiniKit (Qiagen) or Plant Total RNA Mini Kit (Favorgen)
performed by IAB service company (Czech republic)

treatment_protocol: Samples were collected in the middle of light phase of the circadian cycle.


title: eCLIP, HeLa, SRSF1 NaAsO2, Input, biological replicate 2

description: Library name: eCLIP_SRSF1_NaAsO2_IN_rep2

value: Input

value: eCLIP, HeLa, SRSF1 NaAsO2, Input


title: T03

description: Library name: T03


title: T02

description: Library name: T02


title: KIN10-OE_root_3

description: Library name: 1416


title: Brain, 9 Months, Rep 1

description:
Library name: sample_9M_N1_B
9M.N1

value: 9 Months


title: KIN10-OE_root_2

description: Library name: 1414


title: HTN2

first: Qianwan

last: Deng

address: Ruijin 2nd Road 197

institute: Shanghai Institute of Hypertension

description: Library name: SAMPLESCon2

data_processing:
1. Quality Control: Raw sequencing data were processed using fastp to remove low-quality reads and adapter sequences, resulting in clean data.  2. Read Alignment: Clean reads were aligned to the human genome (GRCh38, Ensembl 104) using cellranger v7.1.0 to create feature-barcode matrices.  3. Normalization and Analysis: Gene expression levels were normalized, and the data were analyzed to identify cell populations and perform differential expression analysis between groups.
Assembly: hg38
Supplementary files format and content: Processed data are provided as 10x Genomics format files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) processed with Cell Ranger v7.1.0 using the GRCh38 reference genome.

source_name: blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque PLUS (density 1.077 g/mL) gradient centrifugation.
Single-cell RNA libraries were prepared using the 10X Genomics Chromium Controller and Single Cell 3’ V3.1 Reagent Kits. PBMCs were concentrated to 1000 cells/μL and loaded into the Chromium chip to generate single-cell Gel Bead-In-Emulsions (GEMs). After reverse transcription, the cDNA was amplified, fragmented, and ligated with adapters. Index PCR was performed, and the final libraries were quantified using Qubit and analyzed for size distribution with a Bioanalyzer 2200. Libraries were sequenced using an Illumina sequencer with a 150 bp paired-end run.

value: blood

value: primary cell

value: blood cell


title: eCLIP, HeLa, SRSF1 NaAsO2, Immuno-precipitation, biological replicate 1

description: Library name: eCLIP_SRSF1_NaAsO2_IP_rep1

value: Cervix

value: HeLa


title: Ler-0_root_4

description: Library name: 1413


title: Liver, 9 Months, Rep 1

description:
Library name: sample_9M_N1_L
9M.N1

value: Prep 2


title: eCLIP, HeLa, SRSF1 Untreated, Immuno-precipitation, biological replicate 2

description: Library name: eCLIP_SRSF1_Untreated_IP_rep2

value: Cervical adenocarcinoma


title: HTN1

description: Library name: SAMPLESCon1


title: eCLIP, HeLa, SRSF1 Untreated, Input, biological replicate 2

description: Library name: eCLIP_SRSF1_Untreated_IN_rep2

value: eCLIP, HeLa, SRSF1 Untreated, Input


title: Brain, 15 Months, Rep 4

description:
Library name: sample_15M_N4_B
15M.N4


title: Ler-0_root_3

description: Library name: 1412

value: root


title: Liver, 15 Months, Rep 4

description:
Library name: sample_15M_N4_L
15M.N4

value: Liver


title: Ler-0_root_2

description: Library name: 1411


title: eCLIP, HeLa, SRSF1 Untreated, Immuno-precipitation, biological replicate 1

description: Library name: eCLIP_SRSF1_Untreated_IP_rep1

value: wt


title: kin10_root_3

description: Library name: 1410


title: Liver, 3 Months, Rep 12

description:
Library name: sample_3M_N12_L
3M.N12


title: AFHTN3

description: Library name: SAMPLES3


title: Liver, 24 Months, Rep 2

description:
Library name: sample_24M_N2_L
24M.N2

value: 24 Months


title: kin10_root_2

description: Library name: 1409


title: AFHTN2

description: Library name: SAMPLES2


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siDDX3X, NAIN3, biological replicate 2

description: Library name: siDDX3X_NAIN3_rep2

value: DDX3X knockdown


title: AFHTN1

description: Library name: SAMPLES1


title: Brain, 28 Months, Rep 14

description:
Library name: sample_28M_N14_B
28M.N14

value: Brain

value: 28 Months


title: eCLIP, HeLa, SRSF1 NaAsO2, Input, biological replicate 1

description: Library name: eCLIP_SRSF1_NaAsO2_IN_rep1

value: Input

value: eCLIP, HeLa, SRSF1 NaAsO2, Input


title: Col-0_root_3

description: Library name: 1408


title: OE-HDAC5-H3K27ac+TNF

city: shenzhen

first: weihao

last: zhang

address: futian

department: Department of Orthopedics, The Eighth Affiliated Hospital

institute: Sun Yat-sen university

description: Library name: SAMPLES16

library_source: genomic

data_processing:
Basecall were performed by Bcl2Fastq
raw data was filtered to remove low-quality reads and trim adaptors using TrimGalore (v0.6.6) with parameters --phred33 -q 20 -stringency3
Clean reads were then mapped to hg38 genome using Bowtie2 (version 2.5.1) with default parameters.
All peaks were called by MACS2(v2.1.1) with the parameters -p 1e-5 -g hs
DeepTools (v2.3.6.0) was used to normalize the CUT&Tag-seq data in RPKM using the bamCoverage command
Assembly: hg38
Supplementary files format and content: bw file, narrow Peak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Mesenchymal stem cells

extract_protocol:
The CUT&Tag assay was performed using the NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein) according to the manufacturer’s instructions.
Library was constructed using the NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein)

value: Mesenchymal stem cells


title: Liver, 28 Months, Rep 14

description:
Library name: sample_28M_N14_L
28M.N14


title: Col-0_root_2

description: Library name: 1407


title: AFHTN4

description: Library name: SAMPLES4

value: blood

value: primary cell


title: KIN10-OE_root_1

description: Library name: 1405


title: Brain, 28 Months, Rep 11

description:
Library name: sample_28M_N11_B
28M.N11

value: Prep 1


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siDDX3X, DMSO, biological replicate 1

description: Library name: siDDX3X_DMSO_rep1

value: Cervix

value: HeLa

value: DMSO


title: OE-HDAC5-BRD4+TNF

description: Library name: SAMPLES15


title: OE-NC-H3K27ac+TNF

description: Library name: SAMPLES14


title: Ler-0_root_1

description: Library name: 1404


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siControl, NAIN3, biological replicate 2

description: Library name: siCtrl_NAIN3_rep2

value: Cervical adenocarcinoma

value: Mock knockdown


title: Liver, 28 Months, Rep 11

description:
Library name: sample_28M_N11_L
28M.N11

value: Liver


title: OE-NC-BRD4+TNF

description: Library name: SAMPLES13


title: kin10_root_1

description: Library name: 1403

value: root


title: Brain, 9 Months, Rep 8

description:
Library name: sample_9M_N8_B
9M.N8

value: 9 Months


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siDDX3X, DMSO, biological replicate 2

description: Library name: siDDX3X_DMSO_rep2

value: DDX3X knockdown


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siControl, DMSO, biological replicate 2

description: Library name: siCtrl_DMSO_rep2


title: OE-NC-H3K27ac

description: Library name: SAMPLES12


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siDDX3X, NAIN3, biological replicate 1

description: Library name: siDDX3X_NAIN3_rep1


title: Liver, 9 Months, Rep 8

description:
Library name: sample_9M_N8_L
9M.N8


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siControl, NAIN3, biological replicate 1

description: Library name: siCtrl_NAIN3_rep1


title: Brain, 24 Months, Rep 2

description:
Library name: sample_24M_N2_B
24M.N2

value: Brain

value: 24 Months

value: Prep 2


title: OE-NC-BRD4

description: Library name: SAMPLES11


title: kin10_shoot_3

description: Library name: 39

source_name: shoot

value: shoot


title: Brain, 24 Months, Rep 15

description:
Library name: sample_24M_N15_B
24M.N15


title: icSHAPE, HeLa, Whole Cell, NaAsO2 siControl, DMSO, biological replicate 1

description: Library name: siCtrl_DMSO_rep1


title: TNF-H3K27ac

description: Library name: SAMPLES10

value: Mesenchymal stem cells


title: kin10_shoot_2

description: Library name: 38


title: Liver, 24 Months, Rep 15

description:
Library name: sample_24M_N15_L
24M.N15

source_name: Liver


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2 ATP depletion, NAIN3, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_RNAGranule_NAIN3_rep2

value: wt


title: 2iLIF replicate 1

value: R1 mouse embryonic stem cells

value: 2i LIF


title: TNF-BRD4

description: Library name: SAMPLES9


title: kin10_shoot_1

description: Library name: 37


title: Brain, 28 Months, Rep 7

description:
Library name: sample_28M_N7_B
28M.N7

source_name: Brain

value: 28 Months

value: Prep 1


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2 ATP depletion, DMSO, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_RNAGranule_DMSO_rep2

value: Cervix

value: HeLa

value: DMSO


title: Col-0_shoot_3

description: Library name: 28


title: Liver, 28 Months, Rep 7

description:
Library name: sample_28M_N7_L
28M.N7

value: Liver


title: NC-H3K27ac

description: Library name: SAMPLES8


title: Col-0_root_1

description: Library name: 1402

value: root


title: NC-BRD4

description: Library name: SAMPLES7


title: Col-0_shoot_2

description: Library name: 26


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2 ATP depletion, NAIN3, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_RNAGranule_NAIN3_rep1

value: Cervical adenocarcinoma


title: Brain, 3 Months, Rep 2

description:
Library name: sample_3M_N2_B
3M.N2

value: 3 Months


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2 ATP depletion, DMSO, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_RNAGranule_DMSO_rep1


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2 ATP depletion, NAIN3, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_SolubleCytosol_NAIN3_rep2

molecule: cytoplasmic RNA


title: Col-0_shoot_1

description: Library name: 25


title: KIN10-OE_shoot_3

description: Library name: 15


title: non4N_Arabi-leaf-rep1

description:
Library name: F4R11
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: leaf

value: Salt-seq


title: KIN10-OE_shoot_2

description: Library name: 14


title: Brain, 9 Months, Rep 4

description:
Library name: sample_9M_N4_B
9M.N4

value: Brain

value: 9 Months


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2 ATP depletion, DMSO, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_SolubleCytosol_DMSO_rep2


title: organoid microglia, C9-2, biol rep4

city: Utrecht

first: Roland Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

description: Library name: X104700-001-025

data_processing:
Raw sequence reads were trimmed of low-quality bases and adapter sequences with cutadapt v2.10. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters). Trimmed reads were mapped the human GRCh38.p13 using a short read aligner based on Burrows—Wheeler Transform (STAR2 v2.5.4) with default settings. The mapped counts for each gene were determined and summarised in a count table using HTSeq v0.11.0, which served as input for downstream RNA-Seq differential expression analysis.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files

source_name: Cerebral organoids

growth_protocol: iPSC derived cerebral organoids were generated as previously described (Ormel et al., 2018 & Geest et al., 2024). Organoids were grown for 64 days.

extract_protocol:
Total RNA was isolated using QIAzol Lysis reagent (Qiagen) and miRNeasy mini kit (Qiagen) with DNA digestion on-column, according to the manufacturer's instructions. RNA concentration and integrity (RIN) was verified in an Agilent 2100 bioanalyzer and only samples with RIN ≥ 9.0 were used for RNA sequencing.
Sample preparation was performed according to "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Samples were sequenced using the Illumina NovaSeq 6000, following a data quality metrics check for possible sample and barcode contamination, using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.25) quality control tools.

value: Cerebral organoids

value: Organoid derived Microglia

value: C9ORF72-HRE patient sample

value: Untreated


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2 ATP depletion, NAIN3, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_SolubleCytosol_NAIN3_rep1

value: wt


title: KIN10-OE_shoot_1

description: Library name: 13

value: shoot


title: organoid microglia, C9-3, biol rep3

description: Library name: X104700-001-023


title: Liver, 9 Months, Rep 4

description:
Library name: sample_9M_N4_L
9M.N4

data_processing:
RNA was isolated using the QIAzol/chloroform extraction method. RNA quality was determined via an Agilent Bioanalyzer 2100 using the RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). An RNA Integrity Number (RIN) value of greater than 7 was considered to be the minimum quality for sequencing.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions. All libraries were sequenced on an NovaSeq 6000 machine (Illumina, San Diego, CA, USA) with an average of 36 million paired-end reads (2x100 bp) at Competence Centre for Genomic Analysis (CCGA, Kiel, Germany) .
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (2.8) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a two-color-chemistry aware, 3’-end quality trimming for a phred-score >= 25 (nextseq-trim=25).
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim from both end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using the tool featureCounts from the subread package (2.0.1) with reverse stranded information, while ignoring chimeric fragments and allowing only properly mapped read pairs with feature sizes in between 50 bp to 600 bp.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Comma separated matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

value: Prep 1


title: Brain, 15 Months, Rep 11

description:
Library name: sample_15M_N11_B
15M.N11

value: 15 Months


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2, NAIN3, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2_RNAGranule_NAIN3_rep2

value: Cervix

value: HeLa


title: organoid microglia, C9-2, biol rep3

description: Library name: X104700-001-022


title: organoid microglia, C9-1, biol rep3

description: Library name: X104700-001-021


title: organoid microglia, C9-3, biol rep4

description: Library name: X104700-001-026


title: Liver, 3 Months, Rep 2

description:
Library name: sample_3M_N2_L
3M.N2

value: Liver


title: Ler-0_shoot_3

description: Library name: 3


title: organoid microglia, C9-4, biol rep2

description: Library name: X104700-001-027


title: Ler-0_shoot_2

description: Library name: 2


title: Liver, 15 Months, Rep 11

description:
Library name: sample_15M_N11_L
15M.N11


title: Liver, 28 Months, Rep 4

description:
Library name: sample_28M_N4_L
28M.N4

value: 28 Months


title: Brain, 28 Months, Rep 4

description:
Library name: sample_28M_N4_B
28M.N4


title: organoid microglia, C9-3, biol rep2

description: Library name: X104700-001-020


title: organoid microglia, C9-2, biol rep2

description: Library name: X104700-001-019


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2, NAIN3, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2_RNAGranule_NAIN3_rep1

value: Cervical adenocarcinoma


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2, DMSO, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2_RNAGranule_DMSO_rep2

value: DMSO


title: prr5_ZT11_3

city: SH

first: chen

last: shi

address: Fenglin Road

institute: CSA Center for Excellence in Molecular Plant Science

description:
prr5 ZTT1 rep3.xlsx
prr5 ZT11 rep3

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Assembly: TAIR10.1_NCBI
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: seedling

growth_protocol: Col-0 and cry1 cry2 grown under continuous blue light (20 μmol/m−2 s−1) for 7 days before harvest or Col-0 and prr5 grown in 1/2 MS under 12/12 white light (80 μmol/m−2 s−1) for 7 days then harvested at ZT11.

extract_protocol:
Total RNA was isolated using RNAiso Plus (Takara). Three biological replicates were prepared independently.
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

value: seedling

value: 7 DAY OLD


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2 ATP depletion, DMSO, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2ATPdepletion_SolubleCytosol_DMSO_rep1


title: organoid microglia, C9-1, biol rep2

description: Library name: X104700-001-018


title: prr5_ZT11_2

description:
prr5 ZTT1 rep2.xlsx
prr5 ZT11 rep2

treatment_protocol: Col-0 and cry1 cry2 grown under continuous blue light (20 μmol/m−2 s−1) for 7 days before harvest or Col-0 and prr5 grown in 1/2 MS under 12/12 white light (80 μmol/m−2 s−1) for 7 days then harvested at ZT11.


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2, NAIN3, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2_SolubleCytosol_NAIN3_rep2


title: Liver, 9 Months, Rep 12

first: Lena

last: Best

institute: Christian-Albrechts-University Kiel

description:
Library name: sample_9M_N12_L
9M.N12

extract_protocol:
RNA was isolated using the QIAzol/chloroform extraction method.
RNA libraries were prepared using TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions.

value: 9 Months


title: Pet_fer-4_0m_B

city: Durham

first: Sheng Yang

last: He

address: 124 Science Drive

institute: Duke University

description: Library name: Pet_fer-4_0m_B_S13

data_processing:
The pool was loaded onto two (2) lanes of an Illumina flow cell and sequencing was performed in a PAIRED end read format using a NovaSeq v1.5, 100 cycle reagent kit. Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. A summary of the run output is attached below. Basic QC information about  sequence data is provided by FastQC reports. Reads were mapped with TAIR genome using STAR and DEseq2 was used to identifiy  differntially expressed genes.
Assembly: TAIR v10
Supplementary files format and content: A CSV file contain Read counts.

source_name: Petiole

extract_protocol:
Total RNA was extracted using QIAGEN  RNeasy Plant mini kit.
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina RNA UD Indexes, following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar amounts and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

value: Petiole

value: high humidity


title: prr5_ZT11_1

description:
prr5 ZTT1 rep1.xlsx
prr5 ZT11 rep1


title: organoid microglia, C9-4, biol rep1

description: Library name: X104700-001-017

value: Cerebral organoids

value: Organoid derived Microglia

value: C9ORF72-HRE patient sample


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2, DMSO, biological replicate 2

description: Library name: FracSHAPE-ATPdep_NaAsO2_SolubleCytosol_DMSO_rep2

value: wt


title: organoid microglia, C9-3, biol rep1

description: Library name: X104700-001-016

value: Untreated


title: Ler-0_shoot_1

description: Library name: 1

value: shoot


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2, NAIN3, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2_SolubleCytosol_NAIN3_rep1

value: Cervix


title: Liver, 24 Months, Rep 7

address: Michaelis-Straße 5

description:
Library name: sample_24M_N7_L
24M.N7

value: 24 Months

value: Prep 1


title: organoid microglia, C9-2, biol rep1

description: Library name: X104700-001-015


title: cry2_ZT11_2

description:
cry2 ZTT1 rep2.xlsx
cry2 ZT11 rep2


title: FracSHAPE-ATPdep, HeLa, Soluble Cytosol, NaAsO2, DMSO, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2_SolubleCytosol_DMSO_rep1

value: HeLa


title: organoid microglia, C9-1, biol rep1

description: Library name: X104700-001-014


title: Brain, 9 Months, Rep 12

description:
Library name: sample_9M_N12_B
9M.N12

value: Brain


title: cry2_ZT11_1

description:
cry2 ZTT1 rep1.xlsx
cry2 ZT11 rep1


title: Brain, 15 Months, Rep 1

description:
Library name: sample_15M_N1_B
15M.N1

value: 15 Months


title: Liver, 15 Months, Rep 1

description:
Library name: sample_15M_N1_L
15M.N1

value: Liver


title: FracSHAPE-ATPdep, HeLa, RNA Granule, NaAsO2, DMSO, biological replicate 1

description: Library name: FracSHAPE-ATPdep_NaAsO2_RNAGranule_DMSO_rep1

value: Cervical adenocarcinoma

value: DMSO


title: FracSHAPE, HeLa, RNA Granule, NaAsO2, NAIN3, biological replicate 3

description: Library name: FracSHAPE_NaAsO2_RNAGranule_NAIN3_rep3


title: WT_ZT11_3

description:
Col ZTT1 rep3.xlsx
Col ZT11 rep3

value: seedling

value: 7 DAY OLD


title: organoid microglia, HC-4, biol rep3

description: Library name: X104700-001-013

value: Cerebral organoids

value: Healthy control


title: organoid microglia, HC-2, biol rep4

description: Library name: X104700-001-011

value: Organoid derived Microglia


title: Liver, 28 Months, Rep 2

description:
Library name: sample_28M_N2_L
28M.N2

value: 28 Months


title: FracSHAPE, HeLa, RNA Granule, NaAsO2, NAIN3, biological replicate 2

description: Library name: FracSHAPE_NaAsO2_RNAGranule_NAIN3_rep2

value: wt


title: Brain, 24 Months, Rep 7

description:
Library name: sample_24M_N7_B
24M.N7


title: FracSHAPE, HeLa, RNA Granule, NaAsO2, NAIN3, biological replicate 1

description: Library name: FracSHAPE_NaAsO2_RNAGranule_NAIN3_rep1


title: organoid microglia, HC-1, biol rep4

description: Library name: X104700-001-010

value: Untreated


title: FracSHAPE, HeLa, RNA Granule, NaAsO2, DMSO, biological replicate 3

description: Library name: FracSHAPE_NaAsO2_RNAGranule_DMSO_rep3

value: Cervix


title: Brain, 3 Months, Rep 11

description:
Library name: sample_3M_N11_B
3M.N11

value: 3 Months


title: organoid microglia, HC-4, biol rep2

description: Library name: X104700-001-009


title: cry1  cry2_Blue_3

description:
cry1 cry2 blue rep3.xlsx
cry1 cry2 Blue rep3

value: cry1 cry2


title: Liver, 3 Months, Rep 11

description:
Library name: sample_3M_N11_L
3M.N11

value: Prep 1


title: WT_ZT11_2

description:
Col ZTT1 rep2.xlsx
Col ZT11 rep2


title: FracSHAPE, HeLa, RNA Granule, NaAsO2, DMSO, biological replicate 2

description: Library name: FracSHAPE_NaAsO2_RNAGranule_DMSO_rep2

value: HeLa


title: organoid microglia, HC-3, biol rep1

description: Library name: X104700-001-008


title: FracSHAPE, HeLa, RNA Granule, NaAsO2, DMSO, biological replicate 1

description: Library name: FracSHAPE_NaAsO2_RNAGranule_DMSO_rep1


title: organoid microglia, HC-2, biol rep3

description: Library name: X104700-001-007


title: Brain, 9 Months, Rep 3

description:
Library name: sample_9M_N3_B
9M.N3

value: Brain

value: 9 Months


title: cry1  cry2_Blue_1

description:
cry1 cry2 blue rep1.xlsx
cry1 cry2 Blue rep1


title: cry1  cry2_Blue_2

description:
cry1 cry2 blue rep2.xlsx
cry1 cry2 Blue rep2


title: cry2_ZT11_3

description:
cry2 ZTT1 rep3.xlsx
cry2 ZT11 rep3


title: Brain, 28 Months, Rep 2

description:
Library name: sample_28M_N2_B
28M.N2


title: FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, NAIN3, biological replicate 3

description: Library name: FracSHAPE_NaAsO2_SolubleCytosol_NAIN3_rep3

value: Cervical adenocarcinoma


title: Liver, 9 Months, Rep 3

description:
Library name: sample_9M_N3_L
9M.N3

value: Liver


title: T12

description: Library name: T12

value: HCC tumor

value: sorafenib


title: WT_Blue_3

description:
Col blue rep3.xlsx
Col Blue rep3

value: seedling

value: 7 DAY OLD


title: FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, NAIN3, biological replicate 2

description: Library name: FracSHAPE_NaAsO2_SolubleCytosol_NAIN3_rep2


title: organoid microglia, HC-4, biol rep1

description: Library name: X104700-001-005

value: Cerebral organoids

value: Organoid derived Microglia

value: Healthy control


title: Brain, 24 Months, Rep 4

description:
Library name: sample_24M_N4_B
24M.N4

value: 24 Months


title: organoid microglia, HC-1, biol rep3

description: Library name: X104700-001-006

value: Untreated


title: WT_ZT11_1

description:
Col ZTT1 rep1.xlsx
Col ZT11 rep1


title: Liver, 24 Months, Rep 4

description:
Library name: sample_24M_N4_L
24M.N4


title: WT_Blue_2

description:
Col blue rep2.xlsx
Col Blue rep2


title: FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, NAIN3, biological replicate 1

description: Library name: FracSHAPE_NaAsO2_SolubleCytosol_NAIN3_rep1

value: Cervix

value: wt


title: organoid microglia, HC-2, biol rep2

description: Library name: X104700-001-004


title: WT_Blue_1

description:
Col blue rep1.xlsx
Col Blue rep1


title: Brain, 28 Months, Rep 9

description:
Library name: sample_28M_N9_B
28M.N9

value: 28 Months

value: Prep 1


title: Liver, 28 Months, Rep 9

description:
Library name: sample_28M_N9_L
28M.N9


title: FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, DMSO, biological replicate 2

description: Library name: FracSHAPE_NaAsO2_SolubleCytosol_DMSO_rep2

value: HeLa

value: DMSO


title: Synthetic mitochondrial Leu-CNN unmodified

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
After sequencing, reads were basecalled using Guppy basecaller v3.6.1 in high-accuracy (hac) mode. All Us were converted to Ts before mapping using BWA, with the following parameters bwa mem -W13 -k6 -xont2d -T20. Reference contained tRNAs with 5‘ and 3‘ RNA adapter sequences included. Differential tRNA modifications were analysed using various basecalling “errors” such as mismatch, insertion and deletion for each position. The basecalling “error” sum was calculated by substracting the frequency of the reference base from 1. The frequency of the reference base equals the number of reads with a basecalled equivalent to the reference base, divided by the depth of coverage for that position. In order to plot differential tRNA modifications, first, get_sum_err.py script was used to calculated the differential sum “errors”, then plot_heatmap.py was used to plot heatmaps. All the scripts were taken from NanotRNA-seq github repo (https://github.com/novoalab/Nano-tRNAseq).
Assembly: hg38
Supplementary files format and content: Each processed data file contains summed basecalling "error" that are used to analyse modification frequency at each tRNA position
Library strategy: NanotRNA-seq (Adapted Nanopore direct RNA sequencing)

organism: synthetic construct

extract_protocol:
Mitochondria were isolated using a MACS antibody based mitochondria extraction kit (Miltenyi Biotech) to obtain high quality and intact mitochondria for subsequent RNA isolation. Subsequently, small and large RNAs were isolated using the miRNeasy Micro Kit (Qiagen).
In order to perform NanotRNA-seq on tRNAs, small RNA fractions isolated from KO and scrambled were deacylated with the following protocol; 10 µL nuclease-free water and deacylated in 95 µL 100 mM Tris-HCl (pH 9.0) at 37°C for 30 min. Deacylated tRNAs were recovered using Zymo RNA Clean and Concentrator-5 kit (Zymo, R1016), following the manufacturer’s instructions. tRNA libraries were prepared using NanotRNA-seq library protocol with some protocol alterations described here. The 5’ and 3’ splint adapters were mix at a 1:1 molar ratio in a solution of 10 mM Tris-HCl (pH 7.5), 50 mM NaCl and 1 µL RNasin® Ribonuclease Inhibitor (Promega, N251A) to a final concentration of 1 uM. The mix was heated to 75°C for 15 s and cooled to 25°C at a rate of 0.1°C/s to anneal splint adapters. 200 ng deacylated tRNAs were ligated to the pre-annealed splint adapters at a molar ratio of 1.2:1 (with median length of 90 nucleotides. Deacylated tRNAs were ligated to the pre-annealed 5’ and 3’ splint adapters at a molar ratio of 1.2:1 (assuming an average tRNA length of 90 nt). The ligation was carried out at room temperature for 2 hours in 25 µL with 20% PEG PEG 8000 (NEB, B10048), 1X T4 RNA Ligase 2 Buffer (NEB, B0239S), 2 µL 6 mg/mL recombinant E. coli T4 RNA 2 Ligase (made in-house) and 0.5 µL RNasin® Ribonuclease Inhibitor. Ligation reaction was then cleaned up with 2X volume of RNAClean XP beads (Beckman, A63987) following manufacturer’s instructions. The RNA concentration was determined using Qubit™ RNA High Sensitivity (HS) assay kit (Thermo, Q32852). At least 50 ng of 5‘ and 3‘ ligated tRNAs were ligated to the RTA adapter (ONT, SQK-RNA002)  at a molar ratio of 1:2 in the presence of 1X Quick Ligation Reaction buffer (NEB, B6058S), 1.5 μL T4 DNA Ligase (NEB, M0202M, 2,000,000 units/mL) and 0.5 µL RNasin® Ribonuclease Inhibitor in 15 µL reaction at room temperature for 10 minutes. Consequently, the reaction mix was added to a reverse transcription mix of 11 µL nuclease-free water, 2 µL 10 mM dNTPs (NEB, N0447S), 8 µL 5X Maxima H Minus Reverse Transcriptase Buffer, and 2 µL Maxima H Minus Reverse Transcriptase (Life Technologies, EP0751). Reverse transcription mix was then mixed well and incubated at 60°C for 1 hour, 85°C for 5 minutes and then brought to 4°C. The linearized tRNAs were cleaned up using 2X RNAClean XP beads following manufacturer’s instructions. Then, 6 ul ONT RMX sequencing adapters (ONT, SQK-RNA002) were ligated at room temperature for 10 minutes in a total reaction volume of 40 µL with 1X Quick Ligation Reaction buffer, 3 μL T4 DNA Ligase. The ligation mix was cleaned up with 2X volume of RNAClean XP beads  following manufacturer’s instructions with a few adjustments. The sample was washed twice with 150 μL WSB (Wash Buffer), in which the pellet was resuspended by flicking the tube. The sample was eluted in 20 μL ELB (Elution Buffer) and incubated for 10 minutes at room temperature on a Hula mixer. The final library was prepared by adding 17.5 μL of nuclease-free water and 37.5 μL of vortexed RRB and kept on ice until loading. The MinION flow cell (FLO-MIN-106) was quality checked, primed, and loaded following the standard ONT SQK-RNA002 protocol.

value: Synthetic

tag: cell compartment


title: MBNL1 KD-3

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

description: Library name: S12

data_processing:
Quality control of raw sequencing reads was performed using FastQC (v0.11.9) and summarized with MultiQC (v1.14). To standardize coverage, sequencing reads were subsampled to 55 million reads per sample using seqtk (v1.3-r106). Alignment to the rattus norvegicus reference genome (build mRatBN7.2) was performed using STAR (STAR_2.7.11b) with default parameters.
The data was normalised using quantile normalisation and noise was removed using noisyR (v1.0.0) (https://doi.org/10.1093/nar/gkab433).
Downstream quality checks and data analysis was performed using the bulkAnalyseR (v1.1.0) shiny app framework (https://doi.org/10.1101/2021.12.23.473982). Density plots, MA plots, Jaccard similarity index heatmaps and PCA were performed as further quality checks. Differential expression analysis was performed using edgeR (v3.40.2) and DESeq2 (1.38.3).
Alternative splicing analysis was performed using the rMATS software (v4.3.0). Splicing events were filtered to retain those with read counts ≥ 50 per group, FDR < 0.05, and |ΔPSI| ≥ 10%, excluding low-confidence junctions (<0.015 junction-to-expression ratio).
Assembly: mRatBN7.2
Supplementary files format and content: Csv file for raw counts. Rows represent features and columns represent samples.
Supplementary files format and content: Csv file for normalised counts (after noise removal). Rows represent features and columns represent samples.

organism: Rattus norvegicus

growth_protocol: Rat PAC-1 cells were cultured in DMEM + Glutamax medium with 10% Foetal Bovine Serum. For the more differentiated state (PAC1-D), the cells were split once per week at a 1:10 dilution. The more proliferative PAC1 cells (PAC1-P) were split at 1:20 dilution twice per week.

extract_protocol:
Cells were lysed with TRI-reagent and total RNA purified by Direct-zol purification column (Zymo Research). The DNase treatment was performed in column during the total RNA purification.
We have used the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (#E7760L) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (#E6440L) in conjunction with NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490L) for these samples.

treatment_protocol: The siRNA knockdown was performed by reverse transfection in a 6-well plate. The 90 pmols of siRNA from Thermo Fisher Scientific and lipofectamine RNAiMAX (Invitrogen) complexes were prepared inside the wells, then 2X10^5 cells/well PAC1 cells were added to the well. After 24 h, the cells were second treated with the same concentration of siRNAs and lipofectamine RNAiMAX. The PAC1 cells were then assessed 48 hr after the second treatment.

value: condition_MBNL1+2-KD in PAC1-D


title: FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, DMSO, biological replicate 1

description: Library name: FracSHAPE_NaAsO2_SolubleCytosol_DMSO_rep1

value: Cervical adenocarcinoma


title: 4N_Arabi-root-rep1

city: Shanghai

description:
Library name: F4R21
Comparison of ligation efficiency of 3'end-modified RNA in Truseq and qMap-seq libraries

value: root

value: qMap-seq


title: Liver, 15 Months, Rep 15

city: Kiel

description:
Library name: sample_15M_N15_L
15M.N15

value: Liver

value: 15 Months


title: FracSHAPE, HeLa, RNA Granule, Untreated, NAIN3, biological replicate 3

description: Library name: FracSHAPE_Untreated_RNAGranule_NAIN3_rep3


title: MBNL1 KD-2

description: Library name: S11