title: GIA3857A20

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

description: High VitD3 biovailability

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using RSEM v1.3.0  and STAR v2.5.2 with the “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Raw counts were processed using the bioconductor package DESeq2 v1.18.1 in R v3.4.3, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Assembly: Ensembl GRCm38 (release 86)
Supplementary files format and content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: colon

extract_protocol:
RNA extraction kit (QIAGEN) - mouse colon
Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina Novaseq 6000 platform

treatment_protocol: Male mice (8 ½ weeks old) were fed with the following diets 3 ½ weeks :1)C57BL/6J/WT mice that were fed with standard VitD3 diet (2 IU/g) for 3 ½ weeks, 2) C57BL/6J/WT mice that were fed with high VitD3 diet (10 IU/g) for 3 ½ weeks, 3) Gc KO mice that were fed with standard VitD3 diet (2 IU/g) for 3 ½ weeks, 4) Gc KO mice that were fed with VitD3 deficient diet (10 IU/g) for 3 ½ weeks

value: colon

value: GCKO

value: standard VitD3 diet (2 IU/g)


title: RNA-seq_PRDM1beta-OE-Ctrl-2

status: Public on Nov 29 2024

type: SRA

city: Shanghai

first: Liping

last: Wang

address: 1239 Siping Road

country: China

institute: Tongji University

library_source: transcriptomic

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC hg19) using Hisat2 (v2.1.0) with the parameters: --dta-cufflinks --no-unal.
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20.
The retained reads were subsequently assembled into transcripts guided by the UCSC gtf annotation files using Stringtie (v1.3.4).
The expression level of each gene was quantified as FPKM (fragments per kilobase per million mapped reads).
Assembly: hg19
Supplementary files format and content: tab-delimited  files include FPKM values for all genes.

molecule: polyA RNA

organism: Homo sapiens

source_name: ESC

growth_protocol: hiF-T cells were seeded on feeder cells, then cultured in hESM + Doxycycline (Dox, 1 ng/mL) for 6 days, followed by either culturing as before to generate primed iPSCs or switching to 5iLAF medium to generate naive iPSCs. Naïve hESCs were cultured in 5iLAF medium

extract_protocol:
RNA was extracted by RNAiso Plus (Takara) following the manufacturer’s instructions.
Bulk mRNA-seq libraries were prepared by KAPA mRNA HyperPrep Kit (Kapa Biosystems) following the manufacturer’s instructions. Libraries were submitted to paired-end sequencing on the NovaSeq 6000 platform (Illumina) according to the manufacturer’s instructions at Berry Genomics Corporation.

treatment_protocol: Reprogramming intermediate population was collected by magnetic-activated cell sorting (MACS) through Pluripotent Stem Cell MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions. Naïve hESCs(knockdown and overexpression cell lines) were harvested directly for RNA extraction.

tag: cell line

value: ESC

tag: genotype

value: wild type


title: human tumor cells from mice 974, tested group, ISRIB treament

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

data_processing:
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed reads are mapped to GRCh38  with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Known genes and transcripts are assembled with StringTie based on reference genome model. After assembly, the abundance of gene/transcript is calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Assembly: hg38
Supplementary files format and content: Text files including counts for each sample

molecule: total RNA

growth_protocol: After mice sacrifice and human tumor cells sorted, cells were immediately pelleted and frozen.

extract_protocol:
RNA was harvested using NucleoSpin RNA isolation Kit (Macherey Nagel), by remplaced B-mercaptoethanol with DTT. Minimal of 1.0ug of total RNA was used for construction of sequencing librairies, except for samples m968-T for which only 0.658ug was used. The sequencing was performed by Macrogen, Inc. using the Novaseq 6000
RNA librairies for RNAseq were prepared using Truseq stranded mRNA kit following manufacturer's protocol.

treatment_protocol:
XG7 cells were injected directly in NSG femelle mice femur. Two week after engraftment, mice were randomized into 2 groups. One group of mice was pretreated with high dose (charge dose) of ISRIB for 3 days, and futher maintened at lower dose (maintenance) of ISRIB every two day. All mice receiving the combinaison of two inhibitors AZD1208 and AZD5991.
AZD1208 (from MedChem dissolved in 10% DMSO, 45% PEG300, 5% Tween80, and 40% NaCl 0.9) : 30 mg/kg, daily by oral gavage; AZD5991 (from AstraZeneca dissolved in 10% DMSO and 90% vehicle (20% HPBCD)) : 10 mg/kg, once a week by IV; ISRIB (from Sigma; dissolved in 5% DMSO, 2% Tween20, 20% PEG400, and 73% Dextrose5%) (maintenance dose) : 2mg/kg, every two day by IP ; ISRIB (charge dose) : 3x maintenance dose three succesive day by IP.

tag: cell type

value: myeloma

tag: treatment

value: AZD1208 + AZD5991 + ISRIB


title: GIA3857A19

country: United Kingdom

description: High VitD3 biovailability

organism: Mus musculus

tag: strain

tag: tissue


title: RNA-seq_PRDM1beta-OE-3


title: XY Z-Del 11.5 dpc repilcate 3

city: Oxford

first: Michelle

last: Simon

state: Oxfordshire

address: Harwell

department: Bioinformatics

institute: MRC

library_source: transcriptomic single cell

data_processing:
CellRanger 4 – Alignment and counting
Scrublet - Doublet Identification
Seurat – Cell level QC
Monocle3 – Clustering and downstream analysis
Assembly: mm10/
Supplementary files format and content: Matrix Market (mtx) format and tab-separated values.

source_name: Gonadal

extract_protocol:
Noon on the day that the copulatory plug was detected was counted as 0.5 dpc. Mice were killed by dislocation of the neck, which was confirmed by palpation, and then embryos were decapitated in ice-cold, phosphate - buffered saline solution. Embryos collected at 11.5 and 12.5 dpc were staged accurately based on the number of tail somites (ts), here 18-19 ts (11.5 dpc) and 25-32 ts (12.5 dpc). Gonads at all three stages were carefully dissected away from the mesonephros. Dissected gonads were dissociated in trypsin for 10 to 15 min, at 37°C, depending on stage. The reaction was quenched with fetal bovine serum and, following centrifugation, cells were resuspended in phosphate-buffered saline/0.4% bovine serum albumin. Cell viability was assessed with Trypan Blue and haemocytometer analysis. Most gonads were then immediately fixed with 100% ice-cold methanol to allow sample preservation before cell capture. The fixation had no adverse effects on the samples. Fixed and unfixed 12.5 dpc gonads were used in subsequent analyses. All 11.5 and 14.5 dpc gonads were fixed. Samples were genotyped for sex chromosomes and presence of Znrf3 mutation before being brought to the Wellcome Centre for Human Genetics(Oxford,UK) for rehydation in saline-sodium citrate buffer and library construction.
Samples were transported to the Oxford Genomics Centre, Wellcome Centre for Human Genetics (Oxford, UK), for cell capture on the 10x Chromium System. scRNA-seq libraries were generated using the Chromium Single Cell 3′ v.2 assay (10x Genomics). Libraries were sequenced using the X platform (Illumina) to a depth of ∼50,000 reads per cell.

value: Gonadal

value: XY Z-Del


title: human tumor cells from mice 968, control group


title: RNA-seq_PRDM1beta-KD-1


title: RNA-seq_PRDM1beta-OE-1


title: GIA3857A17

description: High VitD3 biovailability


title: GIA3857A13

description: Low VitD3 biovailability

value: deficient VitD3 diet (0 IU/g)


title: GIA3857A16

description: High VitD3 biovailability


title: RNA-seq_PRDM1beta-OE-2


title: RNA-seq_PRDM1beta-KD-2


title: RNA-seq_PRDM1alpha-OE-Ctrl-3


title: RNA-seq_PRDM1alpha-OE-Ctrl-2


title: RNA-seq_PRDM1alpha-OE-Ctrl-1


title: RNA-seq_PRDM1alpha-OE-3


title: GIA3857A15

description: Low VitD3 biovailability


title: GIA3857A14

description: Low VitD3 biovailability


title: GIA3857A10

description: High VitD3 biovailability

value: wildtype

value: high VitD3 diet (10 IU/g)


title: GIA3857A11

description: Low VitD3 biovailability


title: GIA3857A12

description: Low VitD3 biovailability


title: GIA3857A9

description: High VitD3 biovailability


title: RNA-seq_PRDM1alpha-OE-2


title: GIA3857A18

description: High VitD3 biovailability


title: GIA3857A8

description: High VitD3 biovailability


title: RNA-seq_PRDM1alpha-OE-1


title: GIA3857A7

description: High VitD3 biovailability


title: RNA-seq_PRDM1alpha-KD-3


title: GIA3857A6

description: High VitD3 biovailability


title: GIA3857A5

description: Low VitD3 biovailability


title: RNA-seq_PRDM1alpha-KD-2


title: GIA3857A3

description: Low VitD3 biovailability


title: RNA-seq_PRDM1alpha-KD-1


title: RNA-seq_PRDM1-KD-2


title: GIA3857A2

description: Low VitD3 biovailability


title: RNA-seq_PRDM1-KD-1


title: RNA-seq_control-KD-2


title: GIA3857A1

description: Low VitD3 biovailability


title: RNA-seq_control-KD-1


title: Fibroblasts from prostate, Castration at 10th week, rep5

city: Beijing

first: Zhenpeng

last: Wu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
The bulk RNAseq reads were trimmed for adaptor and filtered using trim_galore (v0.6.7) and Cutadapt (v3.4)  (-q 25 --length 30).
The STAR (v2.7.4a) was used to align the reads to the GRCm39 genome reference(GENCODE Release M29).  The sorted BAM file was generated by STAR after alignment, and samtools (v1.7) was used to index the sorted BAM file.
Reads counts were quantified using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: raw counts for bulk RNAseq

source_name: prostate

extract_protocol:
RNA was extracted using RNAeasy mini kit (Qiagen). 1 ug RNA was used for library construction.
Libraries were constructed with TruePrep DNA Library Prep Kit (Vazyme) according to the manufacturer’s recommendations.

value: prostate

value: Fibroblast cells

value: WT

value: Castration at 10th week


title: Fibroblasts from prostate, Castration at 10th week, rep3


title: CUT&Tag_PRDM1beta-2

library_source: genomic

data_processing:
*library strategy: CUT&Tag
Sequencing reads were first trimmed to remove adapters and then mapped to the annotated human transcripts (UCSC hg19) using bowtie2 (v2.3.5.1) with the parameters:-q --no-mixed --no-discordant --no-unal.
High confidence reads were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 30. PCR duplicate reads removed using sambamba (v0.7.0).
Genome-wide signals were calculated using a 25-bp window and normalized to the uniquely mapped fragments using ‘bamCoverage’ from deepTools (v2.5.7)
Peak calling was performed using macs2 (v2.1.2).
Assembly: hg19
Supplementary files format and content: tab-delimited peak files include protein binding sites

molecule: genomic DNA

source_name: cell line

growth_protocol: hiF-T cells were seeded on feeder cells, then cultured in hESM + Doxycycline (Dox, 1 ng/mL) for 6 days, followed by either culturing as before to generate primed iPSCs or switching to 5iLAF medium to generate naive iPSCs.

extract_protocol:
CUT&Tag was performed by Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme). Briefly, a total of 50,000 cells were harvested, washed by Wash Buffer, and centrifuged for 5 min at 300 × g at room temperature.
10 μL pre-activated ConA beads were added to per sample and incubated at room temperature for 10 min. The supernatant was discarded and the cell-beads complex was resuspended with 50 μL Antibody Buffer with 1 μg primary antibody (Anti-HA, Cell Signaling Technology #3724S; Anti-H3K9me3, Active Motif #39161) and incubated at 4 °C overnight. Then the primary antibody was removed, added 50 μL Dig-wash Buffer with 0.5 μg secondary antibody (Anti-Rb IgG, antibodies-online #ABIN101961), and rotated at room temperature for 1 h. After washing 3 times with 200 μL Dig-wash buffer, 2 μL PA/G–Tnp was added with 98 μL Dig-300 buffer and rotated at room temperature for 1 h, then washed 3 times with 200 μL Dig-wash buffer. 40 μL Dig-300 Buffer was mixed with 10 μL 5 × TTBL, then added and incubated at 37 °C for 1 h. The fragmented DNA was extracted with DNA Extract Beads and then amplified upon the appropriate cycles. Libraries were purified with 2 × AMPure XP (Beckman Coulter). Library concentration was determined by Qubit dsDNA HS Kit (Invitrogen). The resultant CUT&Tag libraries were performed paired-end sequencing on the NovaSeq 6000 platform (Illumina) according to the manufacturer’s instructions at Nanjing Jiangbei New Area.

treatment_protocol: Reprogramming intermediate population was collected by magnetic-activated cell sorting (MACS) through Pluripotent Stem Cell MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions.

value: cell line

value: reprogramming

tag: time

tag: antibody


title: Fibroblasts from prostate, Castration at 10th week, rep4


title: CUT&Tag_PRDM1beta-1


title: Fibroblasts from prostate, Castration at 10th week, rep2


title: CUT&Tag_PRDM1alpha-2


title: Fibroblasts from prostate, Castration at 10th week, rep1


title: CUT&Tag_PRDM1alpha-1


title: Epithelial cells from prostate, Castration at 10th week, rep5

value: Epithelial cells

value: Pb-cre+;PtenLoxP/LoxP


title: RNA-seq_control-KD-3

value: ESC


title: CUT&Tag_EGFP-2

value: wild type

value: anti-EGFP


title: CUT&Tag_EGFP-1


title: RNA-seq_PRDM1beta-OE-Ctrl-1


title: Epithelial cells from prostate, Castration at 10th week, rep4


title: ATAC-seq_piPSC-T-2

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to the annotated human transcripts (UCSC hg19) using bowtie2 (v2.3.5.1) with the parameters:-N 0 -X 2000 -q -t --no-mixed --no-discordant --no-unal --very-sensitive.
Reads mapped to mitochondrial DNA were removed, and high confidence reads were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 30. PCR duplicate reads removed using sambamba (v0.7.0).
Genome-wide signals were calculated using a 25-bp window and normalized to the uniquely mapped fragments using ‘bamCoverage’ from deepTools (v2.5.7)
Peak calling was performed using macs2 (v2.1.2)  and the program "multiBigwigSummary" from deepTools was used to calculate the chromatin signals on the peaks.
A peak with a signal (FPKM) greater than 18.57 is considered to be open chromatin.
Peaks for all time points were merged into a  set of genomic open chromatin coordinates using bedtools (v2.28.0).
Assembly: hg19
Supplementary files format and content: Bigwig files indicating chromatin opening signals
Supplementary files format and content: tab-delimited peak files include open chromatin regions

source_name: hiF-T

extract_protocol:
ATAC-seq was performed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). Briefly, a total of 50,000-10,000 cells were resuspended in 200 μL lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.15% NP-40) and placed on the ice for 10-12 min lysis. The suspension was centrifuged for 5 min at 500 g at 4 ℃.
40 μL transposition reaction mix (8 μL 5 × TTBL, 10 μL TTEmix V5, and 22 μL nuclease-free H2O) was added to the pellet. Samples were mixed well and incubated at 37 ℃ for 30 min. After adding 10 μL 5 × TS to stop the reaction,  ATAC-seq libraries were PCR amplified upon the appropriate cycles and submitted to gel electrophoresis. Libraries were purified with NucleoSpin Gel and PCR Clean-Up (MN). Library concentration was determined by Qubit dsDNA HS Kit (Invitrogen). ATAC-seq libraries were performed paired-end sequencing on the NovaSeq 6000 platform (Illumina) according to the manufacturer’s instructions at Berry Genomics Corporation.

value: hiF-T


title: GIA3857A4

description: Low VitD3 biovailability

value: colon

value: standard VitD3 diet (2 IU/g)


title: brain,rAAV2-retro injection,rep1

city: Wuhan

first: Hu

last: Zheng

state: Hubei

address: shizishan street No.1

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

data_processing:
Raw data were processed using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) pipeline (v1.11)
Assembly: mm10
Supplementary files format and content: Comma-separated values cell-gene matrix files

source_name: brain

extract_protocol:
Single-cell suspensions were collected from prefrontal cortex of 12-week c57bl/6 mouse brains. The tissues were digested with 3mg protease XXIII and 30U/ml papin, and single cells were suspended with 0.5% BSA.
Single-cell mRNA library was performed by the BD Rhapsody Single-Cell Analysis System (BD Biosciences, USA). Firstly，single-cell suspension in BSA was loaded into a BD Rhapsody cartridge with >200,000 microwells. Secondly, single-cell mRNA was captured by magnetic beads with barcoded capture oligos.Then, magnetic beads were collected for cDNA synthesis and library construction following the BD Rhapsody single cell 3’ whole transcriptome amplification (WTA) workflow. Finally, the libraries were sequenced on Illumina NovaSeq 6000 (Illumina, USA) with 300-bp reads (150-bp paired-end reads).

value: brain


title: Epithelial cells from prostate, Castration at 10th week, rep1


title: Fibroblasts from prostate, Control, rep3

value: control


title: ATAC-seq_p24d+dox-2


title: ATAC-seq_p24d+dox-1


title: Sorted NK cells from PBMCs P1_NKG2C+_NKG2A+ (NKA)

city: Barcelona

first: Maria

middle: José

last: Buzón

state: Barcelona

address: Passeig Vall d'Hebron 119-129

department: Infectious Diseases

country: Spain

institute: Vall d'Hebron Research Institute

description: 10x Genomics

data_processing:
Quality control of raw reads (Nextflow v23.10.0 for workflow execution, and FASTQC v0.11.9 was used for quality control of the raw data)
Alignment and quantification of reads to described mRNAs (cellranger_count v7.1.0 was used to perform the alignment, filtering, barcode counting, and UMI counting for each library)
Quality control of count data (MultiQC v1.15 was used to group and summarize the analysis results from FastQC and cellranger, Seurat v4.3 ecosystem was used for single cell count data quality control, analysis and exploration)
Data preprocessing, filtering, and normalization (Based on quality control results, a mild filtering was performed on the number of features per cell and mitochondrial/ribosomal counts. A threshold of < 20% mitochondrial counts, > 5% ribosomal reads and > 250 features per cell was used to discard low-quality cells. To filter against possible doublets, cells with > 30000 UMI counts were filtered out.)
Reduction of dimensionality (t-stochastic neighbor embedding (t-SNE) method)
Unsupervised clustering analysis (using a shared nearest neighbor (SNN) modularity optimization based clustering algorithm)
Identification of cluster marker genes (using FindAllMarkers function from Seurat package)
Automatic cell type annotation (SingleR v1.10 was used for reference-based single-cell RNA-seq annotation)
Trajectory analysis (slingshot v2.4 was used for trajectory analysis)
Assembly: Human reference GRCh38 - 2020- A was obtained from Cell Ranger pre-built references (https://www.10xgenomics.com/ support/software/cell-ranger/downloads#reference-downloads)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
For cell sorting, NK cells from EC were isolated from PBMCs using a commercial kit (MagniSortTM Human NK cell Enrichment; eBioscience). After enrichment, NK cells were stained with a viability dye (LIVE/DEAD Fixable Aqua Dead Cell stain; Thermo Fisher) for 20 min at RT in the dark. After, cells were washed with 1X PBS and stained with anti-CXCR3-BV650 (G025H7; Biolegend) for 30 min at 37ºC. Then, cells were washed with staining buffer and stained with anti-CD57-PerCP-Cy5.5 (HNK-1; Biolegend), anti-CD56-FITC (B159; Becton Dickinson), anti-CD3-PE-Cy7 (SK7; Becton Dickinson), anti-NKG2C-PE (134591; R&D Systems), anti-CD4-AF700 (RPA-T4; Becton Dickinson), anti-NKG2A-APC (Z199; Beckman Coulter), and anti-CD16-BV786 (3G8; Becton Dickinson) for 20 min at RT. Cells were then washed with staining buffer and immediately sorted using the Cytek Aurora Cell Sorter. Cells were collected on PBS+ 0.04% BSA.
Libraries were prepared at Josep Carreras Institute using Chromium scRNAseq 3' protocol. Briefly, cells were resuspended in a master mix and loaded together with partitioning oil and geal beads to generate droplets containing gel beads embedded with unique barcodes. This method facilitated the individual capture of mRNA from each cell, enabling transcript differentiation during sequencing. The mRNA was then retrotranscribed into cDNA, incorporating the gel bead barcodes into the cDNA and thus linking each transcript to its originating cell. Subsequently, the cDNA was amplified, and the prepared cDNA libraries were sequenced using Illumina sequencing technology.

value: Blood

value: NK cells

value: FACS sorting


title: Sorted NK cells from PBMCs P2_NKG2C+_NKG2A- (NKB)

description: 10x Genomics


title: Epithelial cells from prostate, Castration at 10th week, rep2

value: prostate


title: Sorted NK cells from PBMCs P3 NKG2C-_NKG2A+ (NKC)

description: 10x Genomics


title: Total_RNA_HeLa_eIF2A-KO_TM_replica_2

city: Heidelberg

first: Mykola

last: Roiuk

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

description: Library name: Total_RNA_HeLa_eIF2A-KO_TM_replica_2

data_processing:
for footprints only: removal of of adaptors and randomized nucleotides.
The reads aligning to tRNA or rRNA were removed using bowtie2.
Remaining reads were mapped to the human transcriptome (Ensemble transcript assembly 94) and genome (hg38) using BBMap software, with multiple mapping allowed
The reads mapping to the coding sequences were quantified with lab-based software written in C (https://github.com/aurelioteleman/Teleman-Lab).
To enable to comparison between samples reads were normalised to the library depth, and rpkm values were quantified.
Assembly: hg38
Supplementary files format and content: The processed data file contains raw reads for each of the samples. The reads are not normalised to the library depth. Reads mapped to the coding sequence were counted in Ribosome profiling libraries and total RNA for ribosome profiling samples.

source_name: HeLa

growth_protocol: DMEM (Gibco 41965039) +10% fetal bovine serum (FBS) (Sigma, S0615) +100 U/ml Penicillin/Streptomycin (Gibco 15140122).

extract_protocol:
Total RNA was extracted with Qiagene Rneasy Kit. Ribosomal footprints were extracted from the monosomal fraction after RNaseI digestion via the size selection.
Libraries from total RNA samples were prepared using the Illumina TruSeq Stranded library preparation kit. Ribosomal footprints were converted into libraries with the use of Next-Flex small RNA v.4 kit protocol.

treatment_protocol: treatment either with DMSO or 1µg/ml tunicamycin for 16 hours

value: HeLa

value: an immortal human epithelial cell line

value: Tunicamycin 1µg/ml 16 hours


description: Library name: Total_RNA_HeLa_control_cells_TM_replica_1

value: wt


title: Total_RNA_HeLa_eIF2A-KO_TM_replica_1

description: Library name: Total_RNA_HeLa_eIF2A-KO_TM_replica_1


title: ATAC-seq_p24d-2


title: Total_RNA_HeLa_eIF2A-KO_dmso_replica_3

description: Library name: Total_RNA_HeLa_eIF2A-KO_dmso_replica_3

value: DMSO


title: Fibroblasts from prostate, Control, rep1

value: Fibroblast cells

value: WT


title: XY Z-Del 11.5 dpc repilcate 2

value: Gonadal

value: XY Z-Del


title: ATAC-seq_p24d-1

value: hiF-T

value: wild type


description: Library name: Total_RNA_HeLa_control_cells_dmso_replica_3


title: Epithelial cells from prostate, Castration at 10th week, rep3

value: Epithelial cells

value: Pb-cre+;PtenLoxP/LoxP

value: Castration at 10th week


title: Total_RNA_HeLa_eIF2A-KO_dmso_replica_1

description: Library name: Total_RNA_HeLa_eIF2A-KO_dmso_replica_1


title: Total_RNA_HeLa_eIF2A-KO_dmso_replica_2

description: Library name: Total_RNA_HeLa_eIF2A-KO_dmso_replica_2


title: ATAC-seq_piPSC-T-1


description: Library name: Total_RNA_HeLa_control_cells_TM_replica_2


title: ATAC-seq_p20d-2


description: Library name: Total_RNA_HeLa_control_cells_dmso_replica_1


title: Epithelial cells from prostate, Control, rep3

value: control


description: Library name: Total_RNA_HeLa_control_cells_dmso_replica_2


title: Riboseq_HeLa_eIF2A-KO_TM_replica_2

description:
Library name: Riboseq_HeLa_eIF2A-KO_TM_replica_2
ribosome footprints were used to generate this library

data_processing:
for footprints only: removal of of adaptors and randomized nucleotides.
The reads aligning to tRNA or rRNA were removed using bowtie2.
Remaining reads were mapped to the human transcriptome (Ensemble transcript assembly 94) and genome (hg38) using BBMap software, with multiple mapping allowed
The reads mapping to the coding sequences were quantified with lab-based software written in C (https://github.com/aurelioteleman/Teleman-Lab).
To enable to comparison between samples reads were normalised to the library depth, and rpkm values were quantified.
Assembly: hg38
Supplementary files format and content: The processed data file contains raw reads for each of the samples. The reads are not normalised to the library depth. Reads mapped to the coding sequence were counted in Ribosome profiling libraries and total RNA for ribosome profiling samples.
Library strategy: Ribo-Seq


title: Fibroblasts from prostate, Control, rep2


title: ATAC-seq_p20d-1


title: ATAC-seq_p14d-2


title: Epithelial cells from prostate, Control, rep1


title: Riboseq_HeLa_control_cells_TM_replica_2

description:
Library name: Riboseq_HeLa_control_cells_TM_replica_2
ribosome footprints were used to generate this library


title: Riboseq_HeLa_eIF2A-KO_TM_replica_1

description:
Library name: Riboseq_HeLa_eIF2A-KO_TM_replica_1
ribosome footprints were used to generate this library


title: Riboseq_HeLa_control_cells_TM_replica_1

description:
Library name: Riboseq_HeLa_control_cells_TM_replica_1
ribosome footprints were used to generate this library


title: CaP8 cells, Control, rep3

value: Pten-null

value: Vehicle


title: Epithelial cells from prostate, Control, rep2

value: prostate


title: ATAC-seq_p14d-1


title: Riboseq_HeLa_eIF2A-KO_dmso_replica_3

description:
Library name: Riboseq_HeLa_eIF2A-KO_dmso_replica_3
ribosome footprints were used to generate this library

value: HeLa

value: an immortal human epithelial cell line


title: CaP8 cells, Control, rep4


title: XX WT 11.5 dpc repilcate 2

value: XX WT


title: ATAC-seq_p8d-2


title: Riboseq_HeLa_eIF2A-KO_dmso_replica_2

description:
Library name: Riboseq_HeLa_eIF2A-KO_dmso_replica_2
ribosome footprints were used to generate this library

value: DMSO


title: CaP8 cells, Control, rep2


description:
Library name: Riboseq_HeLa_control_cells_dmso_replica_2
ribosome footprints were used to generate this library

value: wt


description:
Library name: Riboseq_HeLa_control_cells_dmso_replica_1
ribosome footprints were used to generate this library


title: ATAC-seq_niPSC-T-2


title: CaP8 cells, Control, rep1


title: primcoln23pinv2

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

description: Primary culture of human colon on INV497 coat 2

data_processing:
Reads were mapped using STAR mapping software
Readcounts were assigned using the subreads package
Assembly: hg38
Supplementary files format and content: raw readcounts

source_name: Colon

extract_protocol:
RNA purification was performed with the RNeasy Mini kit with DNase treatment (Qiagen). RNA integrity was measured using the Agilent RNA 6000 pico kit and concentrations were determined with Qubit RNA HS analyzer (ThermoFisher).
Truseq stranded mRNA

treatment_protocol: Epithelial cells from primary colon biopsies grown on Invasin or BME® coats were collected using Dispase, as described before, and washed with DMEM/F12 medium.

value: Colon

value: various


title: CaP8 cells, TGFβ, rep3

value: TGFbeta 1 hr


title: ATAC-seq_niPSC-T-1

value: hiF-T


title: primcoln23pbme1

description: Primary culture of human colon on BME coat 1

value: BME


title: primcoln23pinv1

description: Primary culture of human colon on INV497 coat 1


title: DMSO-treated tumorspheroid immune cells

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the reference transcriptome Homo sapiens hg38 (including mitochondrial genes) with BWA-MEM (Anders et al. Genome Biol. 2010).
Data was demultiplexed as described in Grün et al. Nat Methods. 2014.
Mapping and generation of count tables were automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Unsupervised clustering and differential gene expression analysis was performed in R with Seurat 3.2.27 (Butler et al. Cell 2019).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic ductal adenocarcinoma tumorspheroids

growth_protocol: Patient-derived tumorspheroids were generated from patient adenocarcinoma pancreatic tissues undergoing surgical resection using a protocol published in33. Tissue was dissociated using gentleMACS™ Octo Dissociator with Heaters and Human tumor dissociation kit (Miltenyi Biotec). Total cell populations including cancer cells and microenvironment was used to generated multicellular tumorspheroids in Corning® 96-well Black/Clear Bottom Low Flange Ultra-Low Attachment Microplate (Corning). Cells were cultured in complete Mammocult medium (STEMCELL) supplemented with patient serum.

extract_protocol:
Tumorspheroids were harvested after treatment and dissociated using accutase. CD45+ cells were sorted by flow cytometry into 384 well cell capture plates (Single Cell Discovery, https://www.scdiscoveries.com) using SH800 cell sorter (Sony).
SORT-seq (partially robotized version of the CEL-seq2 protocol).

treatment_protocol: After 24 h, tumorspheroids were treated with TAK1 inhibitor (25 µM) or DMSO as a control overnight. Medium was then refreshed, and cell viability was assessed after 24h using CellTiter-Glo® (Luminescent Cell Viability Assay), according to manufacturer’s instruction.

value: CD45+ immune cells


title: primcoln23pbme2

description: Primary culture of human colon on BME coat 2


title: ATAC-seq_n24d+dox-1

value: wild type


title: ATAC-seq_n24d-2


title: CaP8 cells, TGFβ, rep1

value: Epithelial cells


title: ATAC-seq_n24d+dox-2


title: Riboseq_HeLa_eIF2A-KO_dmso_replica_1

description:
Library name: Riboseq_HeLa_eIF2A-KO_dmso_replica_1
ribosome footprints were used to generate this library


title: CaP8 cells, TGFβi + TGFβ, rep2

value: SB431542 2 hrs + TGFbeta 1hr


description:
Library name: Riboseq_HeLa_control_cells_dmso_replica_3
ribosome footprints were used to generate this library


title: ATAC-seq_n24d-1


title: ATAC-seq_p8d-1


title: Panc-1 2

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Total RNA was isolated from cells and analyzed miRNA expression by microarray.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: pancreatic ductal adenocarcinoma

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Cells were obtained and cultured as recommended by the supplier.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).


title: CaP8 cells, TGFβi + TGFβ, rep1

value: Pten-null


title: Panc-1 3


title: TAK1 inhibitor-treated tumorspheroid immune cells

value: Pancreatic ductal adenocarcinoma tumorspheroids

value: 5Z-7-oxozeaenol (25 uM for 24 h)


title: ATAC-seq_n20d-2


title: PiwiKDy, Input, rep3

city: New Haven

first: Jiaying

last: Chen

state: CT

address: 10 Amistad St Rm 220

department: Genetics

country: USA

institute: Yale University

data_processing:
Adapters were removed from ChIP-seq reads using Trimmomatic, and subsequent reads shorter than 20 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm6) using Bowtie 2 allowing 1 mismatch in the seed sequence. Bigwig files of Ssrp were generated using the bamCompare command of deepTools. The bamCoverage command used sorted bam files as input and with parameters of binSize 20, BPM for normalization, smoothlength of 60, extendReads 150, and centerReads.
Assembly: dm6
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
50-100 pairs of ovaries were dissected in 1x PBS, then fixed in 1% Formaldehyde solution for 10 min at room temperature with rotation. Then, ovaries were quenched with 1/16th volume of 2.5M Glycine for 5 min with rotation, washed in 0.2% TritonX-100 in PBS x3 for 5 min each, supernatants were removed, and samples were stored at -80°C freezer or proceeded for next steps. The fixed ovaries were gently homogenized in 1x PBS with polypropylene pestle and spun down at 800 g for 1 min. Supernatants were removed and ovaries were resuspended in 200 µl ChIP lysis buffer [10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-laurolysarcosine, 1mM  DTT, 1x protease inhibitor] and transferred to 1.5 ml TPX Plastic Micro Tube (Diagenode) for 10 min sonication using Bioruptor at 30 s ON and 45 s OFF intervals. Sonication was completed when majority of DNA smears were at 200-500 bp sizes. Sonicated chromatins were incubated with 30 µl of Dynabeads Protein G (Dynabeads) for 1 hr at 4°C with rotation to pre-clean the sample. Then, tubes were placed on the magnet and supernatants were transferred to new 1.5 ml tubes. Appropriate antibodies were added into tubes with pre-cleaned chromatin (4 µg of rabbit IgG, or rabbit anti-Pol II Ser5P (ab5131), or rabbit anti-Pol II Ser2P (ab5095)) and incubated overnight at 4°C with rotation. 5% of chromatins were saved as input samples and remaining samples were incubated with 60 µl of Dynabeads for three hr at 4°C with rotation. Beads were washed four times with 0.2% TritonX-100 in PBS for five min each and washed once with TE buffer (10 mM Tris, 0.1 mM EDTA). Tubes were placed on the magnet, supernatants were removed, and chromatin were eluted with 200 µl of Elution Buffer [50 mM Tris-HCl, pH8.0, 10 mM EDTA, 1% SDS] by incubating at 65°C for 15 min. Beads were captured by the magnet and the supernatant from each sample was collected as the immunoprecipitated chromatin. Reverse crosslinking of chromatins was performed by incubating samples at 65°C overnight with 20 µg RNaseA (ThermoFisher) and 40 µg Proteinase K (ThermoFisher). The DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo).
ChIP-seq library was prepared by the Yale Stem Cell Center Genomics and Bioinformatics Core

value: ovary

tag: condition

value: germline Piwi knockdown


title: CaP8 cells, FGF9 + TGFβ, rep3

value: FGF9 0.5 hr + TGFbeta 1 hr


title: PiwiKDy, Input, rep2


title: Panc-1 1


title: CaP8 cells, TGFβ, rep2


title: ATAC-seq_n20d-1


title: HPNE 3

source_name: normal pancreatic ductal epithelial

value: HPNE


title: GFPKDy, Input, rep3

value: germline GFP knockdown


title: CaP8 cells, FGF9 + TGFβ, rep2


title: CaP8 cells, TGFβi + TGFβ, rep3


title: HPNE 2


title: HPNE 1


title: CaP8 cells, FGF9 + TGFβ, rep1


title: GFPKDy, Input, rep2


title: GFPKDy, Input, rep1


title: ATAC-seq_n14d-1


title: CaP8 cells, FGF9, rep3

value: FGF9 0.5 hr


title: ATAC-seq_n8d-2


title: PiwiKD, Ssrp, rep1

tag: chip antibody

value: Ssrp (Cosmo Bio NIG-L1-SHA1)


title: CaP8 cells, FGF9, rep2


title: GFPKD, Ssrp, rep3


title: ATAC-seq_n8d-1


title: Lambayeque1_low-temperature-2

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

institute: Hokkaido University

data_processing:
We obtained expression levels for each gene using kallisto (0.46.2) (Bray et al., 2016). The bootstrap was specified as 100, and the expression levels were corrected to TPM (transcripts per million).
The comparisons of expression levels between cold-treated and control plants of each line and between rice lines were performed sleuth (0.30.0) (Pimentel et al., 2017). Differences in expression levels between treatments in each line were statistically tested using the likelihood ratio test.
Assembly: IRGSP-1.0 (2021-05-10)
Supplementary files format and content: Tab-delimited text file containing TPM values for each sample.

organism: Oryza sativa

source_name: anther

growth_protocol: Materials were grown with 20 individuals sown in one Wagener pot (1/5000 100 m2) and grown in a greenhouse at 25/19℃ (day/night cycle) with only the main stem maintained by cutting off the offshoots.

extract_protocol:
Total RNA was extracted using TRIzol® Plus RNA Purification kit (Invitrogen). The extracted RNA was quantified using NanoDrop ND-2000 UV-VIS spectrophotometer (Thermo Scientific) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was performed by Rhelixa (Tokyo, Japan) by dUTP methods using NEBNext® Ultra™ ll Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: The low-temperature treatment was applied for 4 days during the booting stage, which can be estimated by AD. The plants at AD = ± 1 cm, corresponding to the early microspore stage (late tetrad to uninucleate pollen), were exposed to the low temperature of 12℃ for 4 days.

value: anther

tag: growth stage

value: booting stage

value: cold treatment (12℃ four days)


title: ATAC-seq_6d-2

value: hiF-T


title: GFPKD, Ssrp, rep2


title: ATAC-seq_6d-1

value: wild type


title: Lambayeque1_low-temperature-1


title: CaP2 cells, Control, rep4

value: Epithelial cells

value: Vehicle


title: ATAC-seq_2d-3


title: ATAC-seq_n14d-2


title: GFPKD, Ssrp, rep1


title: Nos-PiwiKD,ovary,rep3

description: biological replicate 3

data_processing:
RNA-seq reads were aligned to dm6 genome by STAR (v.2.7.9; settings: -- outSAMattributes All --outSAMtype BAM SortedByCoordinate). HTSeq was used to quantify transcript level and gene expression for each sample with sorted alignment bam files as input and Drosophila_melanogaster.BDGP6.32.104.gtf as the reference annotation file. The package DEseq2 was used to perform differential expression analysis with different cutoffs (p-value or adjusted p-value and fold change) to obtain differentially expressed genes that are statistically significant
Assembly: dm6
Supplementary files format and content: bigWig

extract_protocol:
Total RNA from mature ovaries were extracted, purified following standard phenol-chloroform extraction steps
RNA library preparation was conducted by the Yale Stem Cell Center Genomics Core Facility and sequencing were performed by Yale Center for Genome Analysis.


title: Lambayeque1_control-3

value: non treatment


title: PiwiKDy, Input, rep1


title: Lambayeque1_control-2


title: ATAC-seq_2d-2


title: CaP2 cells, Control, rep1

value: Pten-null


title: Nos-PiwiKD,ovary,rep2

description: biological replicate 2


title: Lambayeque1_low-temperature-3


title: PiwiKD, Ssrp, rep2


title: Lambayeque1_control-1


title: PiwiKD, Ssrp, rep3


title: Nos-PiwiKD,ovary,rep1

description: biological replicate 1


title: ATAC-seq_2d-1


title: CaP2 cells, Control, rep2


title: PL9_low-temperature-3


title: RNA-seq_PRDM1beta-OE-Ctrl-3

value: ESC


title: ATAC-seq_hiF-T-2


title: CaP2 cells, Control, rep3


title: Nos-GFPKD,ovary,rep3

description: biological replicate 3

value: ovary

value: germline GFP knockdown control


title: CaP2 cells, TGFβ, rep2

value: TGFbeta 1 hr


title: CaP2 cells, TGFβ, rep3


title: ATAC-seq_hiF-T-1


title: PL9_low-temperature-2


title: PL9_low-temperature-1


title: Nos-GFPKD,ovary,rep2

description: biological replicate 2


title: PL9_control-3


title: Panc1 shRBM42-2 MYC 5UTR DMS bio rep 2

city: San Francisco

first: Joanna

last: Kovalski

state: CA

institute: University of California San Francisco

library_source: other

data_processing:
Reads were trimmed using trim galore (default parameters), and then aligned to the reference MYC 5’UTR sequence using bowtie, using the parameters -local --no-unal --no-discordant --no-mixed -X 1000 -L 12.
Bam files were then input into the perl-based rnaframework toolkit. Mutations were counted using rf-count -m and normalized using rf-norm (parameters -sm 4 -nm 2 -rb AC).
Normalized replicate xml files were combined using rf-combine.
Assembly: hg38
Supplementary files format and content: tsv file with per-sample normalized bp reactivities
Library strategy: DMS-Seq

molecule: other

extract_protocol:
RNA was purified using Trizol-chloroform as described above. To remove any contaminating genomic DNA, the RNA was treated with TurboDNAse per the manufacturer’s instructions and repurified.
Reverse transcription of the endogenous MYC 5’UTR was done with Induro Reverse Transcriptase (NEB) and a reverse primer targeting the coding sequence proximal to the ATG. The cDNA was purified was SPRI select beads (2x volume). The cDNA was amplified using 5’UTR Myc specific forward and reverse primers using PrimeStar Max (Takara) for 35 cycles using ~20% of purified cDNA product. The resulting DNA product was gel purified. Sequencing libraries were generated using the NEBNext Ultra II Kit following the manufacturer’s instructions.

treatment_protocol: DMS treatment, cells were resuspended in 2.8mL warm cell culture media, followed by 0.8mL 1M bicine buffer (pH 8.57 at room temperature). DMS was added to 1.6% final concentration and incubated at 37C for 5mins. The reaction was quenched with ice cold 2mL BME and cells were pelleted. Cells were washed once with 30% BME in PBS

value: PDAC


title: Panc1 shRBM42-2 MYC 5UTR DMS bio rep 1


title: CaP2 cells, TGFβi + TGFβ, rep2

value: SB431542 2 hrs + TGFbeta 1hr


title: PL9_control-2


title: Panc1 shRBM42-1 MYC 5UTR DMS bio rep 2


title: CaP2 cells, TGFβi + TGFβ, rep1


title: OSC,PiwiKD,IgG,rep3

data_processing:
*library strategy: CUT&RUN
Adapters were removed from CUT&RUN reads using Trimmomatic, and subsequent reads shorter than 20 nt were discarded. CUT&RUN reads were mapped to the Drosophila genome (dm6) using Bowtie 2 allowing 1 mismatch in the seed sequence. Bigwig files of Pol II Ser5P and Pol II Ser2P were generated using the bamCompare command of deepTools. The bamCoverage command used sorted bam files as input and with parameters of binSize 20, BPM for normalization, smoothlength of 60, extendReads 150, and centerReads.
Assembly: dm6
Supplementary files format and content: bigWig

source_name: ovarian somatic cells (OSC)

extract_protocol:
The CUT&RUN experiments were performed using the EpiCypher CUTANA ChIC/CUT&RUN Kit (SKU: 14-1048) following manufacture’s protocol with 500K cells per condition.
CUT&RUN library was prepared using Epicypher library preparation kit following manufacture's protocol.
CUT&RUN libraries were prepare using the EpiCypher CUTANA CUT&RUN Library Prep Kit (SKU: 14-1001) following manufacture's protocol and sequenced at the Yale Center for Genome Analysis with about 10M reads per sample.

value: ovarian somatic cells (OSC)

value: si-Piwi

tag: cutrun antibody

value: rabbit IgG (Epicypher 13-0042k)


title: Panc1 shRBM42-1 MYC 5UTR DMS bio rep 1


title: PL9_control-1

value: anther

value: booting stage


title: Sasanishiki_low-temperature-3

value: Sasanishiki

value: cold treatment (12℃ four days)


title: OSC,GFPKD,IgG,rep3

value: si-EGFP


title: CaP2 cells, FGF9 + TGFβ, rep2

value: Epithelial cells

value: FGF9 0.5 hr + TGFbeta 1 hr


title: CaP2 cells, FGF9 + TGFβ, rep3

value: Pten-null


title: Nos-GFPKD,ovary,rep1

description: biological replicate 1


title: CaP2 cells, TGFβ, rep1


title: Panc1 shSCR MYC 5UTR DMS bio rep 1


title: RBM42 Cytoplasmic CLIP bio rep 2

data_processing:
Adaptor sequences were trimmed using Cutadapt
Reads were then aligned to the human genome (hg38) using bwa and the following parameters: -n 0.06 -q 20. PCR duplicates were collapsed from sorted bam files using umitools.
Peak calling and CIMS calling was performed using the CTK package. Bed file outputs of clip peaks were then annotated to genomic features using bedtools intersect.
Assembly: hg38
Supplementary files format and content: bed file with CLIP peaks from both replicates

molecule: cytoplasmic RNA

extract_protocol:
Protein-bound RNAs were dephosphorylated on bead using T4 PNK (NEB) with modified PNK Buffer (10mM Tris pH 6.5, 50mM MgCl2, 50mM DTT) followed by PolyA tailing with yeast poly(A) polymerase (Jena). This was followed by 3′-end labelled with azide-dUTP, using yeast poly(A) polymerase (Jena) and labelled with IRDye800-DBCO conjugates (LiCor). The protein–RNA complexes were then eluted from beads, resolved on a 4–15% gel, transferred to nitrocellulose and imaged using an Odyssey CLx instrument (LiCor). Regions of interest were excised from the membrane, and the RNA was isolated by Proteinase K digestion and oligo-dT dynabead purified in high salt (500mM NaCl) buffer to promote capture. RNA was eluted into TE buffer (20mM Tris pH 7.5, 1mM EDTA).
Library preparation using SMARTer smRNA-Seq Kit (Takara) with custom primer for reverse transcription (custom RT primer:CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTT, Ns = UMI).

treatment_protocol: Panc1 cells were crosslinked 400mJ/cm2 254nm. After crosslinking, the cells were scraped into ice cold PBS and cytoplasmic/nuclear fractionation was carried out. The cytoplasmic lysate (at 3mg/mL) was digested with RnaseI (Ambion) diluted 1:5000 for 5min, 37C, mixing 15s 1000rpm and 45sec rest. Digestion was stopped with the addition of 2x volumes of cold lysis buffer. RBM42 was precipitated for 4.5hrs rotating at 4C with 1mg of protein with ~2.3ug of antibody per IP pre-coupled to Protein G dynabeads.


title: CaP2 cells, FGF9 + TGFβ, rep1


title: CaP2 cells, TGFβi + TGFβ, rep3


title: Sasanishiki_low-temperature-1


title: OSC,GFPKD,IgG,rep1


title: OSC,PiwiKD,IgG,rep2


title: CaP2 cells, FGF9, rep3

value: FGF9 0.5 hr


title: RBM42 Cytoplasmic CLIP bio rep 1


title: CaP2 cells, FGF9, rep2


title: OSC,PiwiKD,H3,rep3

value: H3 (abcam ab1791)


title: Sasanishiki_control-2

value: non treatment


title: Sasanishiki_control-1


title: OSC,PiwiKD,H3,rep2


title: OSC,PiwiKD,H3,rep1


title: Panc1 shSCR MYC 5UTR DMS bio rep 2


title: CaP2 cells, FGF9, rep1


title: Panc1 shRBM42 Poly RNA 7-10 bio rep 3

data_processing:
Gencode V28 transcripts, and ERCC control RNAs were separately quantified in the paired end samples using salmon quant (default parameters)
Counts were normalized to the ERRC in the untranslated fraction (pooled fractions 3-6) within their respective samples. In particular, the lm() function in R was used to model the slope of the low translated (7-10) and high translated (11-14) fractions against the untranslated fraction (low/high ~ untranslated).
The slope of the line of best fit was then used to scale and normalize the low/high fractions to the untranslated fraction.
Assembly: hg38
Supplementary files format and content: ERCC normalized reads

extract_protocol:
For each sample, equal volumes per polysome fraction were pooled as follows fractions 3-6 for untranslated, fractions 7-10 for low translation and fractions 11-14 for high translation. The RNA from each pool was purified using Trizol-chloroform followed by isopropanol precipitation. Then 1 or 2μl of 1:200 ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added to each fraction pool, depending upon the RNA amount. DNase treatment was performed with TURBO DNase (Ambion, AM2238) for 30 min at 37°C and samples underwent acid phenol extraction and were resuspended in 15μl of Ultra Pure DNase/RNase-Free Distilled Water.
10ng was used as input into the SMARTer Stranded Total RNA-Seq Kit v3-Pico (Takara)

value: RBM42 knockdown


title: Panc1 shRBM42 Poly RNA 11-14 bio rep 3

value: PDAC


title: Sasanishiki_low-temperature-2


title: CaP8 cells, FGF9, rep1

data_processing:
The bulk RNAseq reads were trimmed for adaptor and filtered using trim_galore (v0.6.7) and Cutadapt (v3.4)  (-q 25 --length 30).
The STAR (v2.7.4a) was used to align the reads to the GRCm39 genome reference(GENCODE Release M29).  The sorted BAM file was generated by STAR after alignment, and samtools (v1.7) was used to index the sorted BAM file.
Reads counts were quantified using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: raw counts for bulk RNAseq


title: Nipponbare_low-temperature-3

value: Nipponbare


title: sample_12_Combo_poly_rep2

city: Moscow

first: Alexander

last: Tyurin

address: Botanicheskaya st., 35, building 1

country: Russia

institute: Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

description: Library name: sample_12_rep2

data_processing:
FASTQ files were obtained using bcl2fastq v2.20 Conversion Software (Illumina). The format of the quality data line recording is Phred 33.
Pseudoalignment of raw reads was performed with kallisto program using bootstrap (100 iterations)
Assembly: SL3.1
Supplementary files format and content: Tab-delimited text file includes normalized reads in TPM values for each sample

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Growing of tomato plants (Solanum lycopersicum L., selection line YaLF) was carried out under normal conditions of life (at 25 ± 1 °C, 16-hour photoperiod, illumination of 100 μmol quanta/(m2s). Plants with 5-7 true leaves (28 days) were used for the experiments.

extract_protocol:
Polysome profiling was performed according to [Lecampion et al., 2016 (https://doi.org/10.3791/54231)]. Briefly:  - 4-layer gradient (50%, 35% and 2 layers of 20% sucrose) - saline buffer (400 mM Tris-HCl pH 8.4; 200 mM KCl; 100 mM MgCl2) - polysome buffer (saline buffer 4x; EGTA 5.26 mM; Triton x100 0.5%; cycloheximide 50 μg/ml; chloramphenicol 50 μg/ml) - refrigerated centrifugation (4°C) for 2 hours 45 minutes at 175,000 g - precipitation with isopropanol  Total RNA from plants was isolated by phenol-chloroform extraction using ExtractRNA reagent (Eurogen, Russia, cat. no. BC032) according to the manufacturer's protocol. The obtained samples of total RNA were treated with DNaseI (Thermo scientific, USA, cat. no. EN0521) according to the manufacturer's protocol. Quantitative assessment and purification quality of the isolated RNA samples were determined by spectrophotometric method using a photometer for Synergy H1 microplates (BioTek, USA) and by electrophoresis in 1% agarose gel containing formaldehyde.
TruSeq mRNA Stranded (Illumina) total RNA samples were enriched for the poly(A+) fraction, and then cDNA was synthesized from the stranded primer. The resulting cDNA was used to prepare libraries compatible with Illumina sequencing technology. The quality of the obtained libraries was checked using the Fragment Analyzer. Quantitative analysis was performed using qPCR. After quality control and DNA quantity assessment, the library pool was sequenced on an Illumina NovaSeq 6000 (read length - 150 bp on both sides of the fragments).

treatment_protocol: For a comprehensive assessment of the resistance of S. lycopersicum to low temperatures, hardening and damaging cold exposures were used in the work. Hardening of plants was carried out for 5 days in a KBW-240 climate chamber (“Binder”, Germany) at a temperature of +6ºС, a 16-hour photoperiod and illumination of 200 μmol/(m2s). Damaging cold exposures had the following parameters: cooling of plants at a temperature of 0°С for 2 hours.

value: leaf

value: YaLF

value: Combo

tag: fraction

value: poly


title: OSC,GFPKD,H3,rep3

value: ovarian somatic cells (OSC)


title: Panc1 shRBM42 Poly RNA 3-6 bio rep 3


title: OSC,GFPKD,IgG,rep2

value: rabbit IgG (Epicypher 13-0042k)


title: Nipponbare_low-temperature-2

value: anther

value: booting stage

value: cold treatment (12℃ four days)


title: Panc1 shRBM42 Poly RNA 11-14 bio rep 2


title: sample_10_Hardening_poly_rep2

description: Library name: sample_10_rep2

value: Hardening


title: Nipponbare_low-temperature-1


title: sample_11_Stress_poly_rep2

description: Library name: sample_11_rep2

value: Stress


title: OSC,GFPKD,H3,rep2

value: si-EGFP


title: OSC,GFPKD,H3,rep1

value: H3 (abcam ab1791)


title: Panc1 shRBM42 Poly RNA 7-10 bio rep 2


title: Nipponbare_control-3

value: non treatment


title: sample_9_Control_poly_rep2

description: Library name: sample_9_rep2

value: Control


title: Panc1 shRBM42 Poly RNA 3-6 bio rep 2

value: PDAC

value: RBM42 knockdown


title: OSC,PiwiKD, Pol2s2p,rep3

value: si-Piwi

value: Pol II Ser2P (abcam ab5095)


title: sample_8_Combo_mono_rep2

description: Library name: sample_8_rep2

value: leaf

value: YaLF

value: Combo

value: mono


title: Panc1 shRBM42 Poly RNA 11-14 bio rep 1


title: Nipponbare_control-2

value: anther

value: Nipponbare


title: sample_7_Stress_mono_rep2

description: Library name: sample_7_rep2


title: Panc1 shRBM42 Poly RNA 7-10 bio rep 1


title: Nipponbare_control-1

value: booting stage


title: OSC,PiwiKD, Pol2s2p,rep1

value: ovarian somatic cells (OSC)


title: Panc1 shRBM42 Poly RNA 3-6 bio rep 1


title: Panc1 shSCR Poly RNA 11-14 bio rep 3

value: WT


title: OSC,GFPKD,Pol2s2p,rep3

value: si-EGFP


title: OSC,GFPKD,Pol2s2p,rep2


title: sample_5_Control_mono_rep2

description: Library name: sample_5_rep2


title: Panc1 shSCR Poly RNA 7-10 bio rep 3


title: OSC,GFPKD,Pol2s2p,rep1


title: Panc1 shSCR Poly RNA 3-6 bio rep 3


title: sample_3_Stress_total_rep2

description: Library name: sample_3_rep2

value: Stress

value: total


title: sample_2_Hardening_total_rep2

description: Library name: sample_2_rep2

value: Hardening


title: OSC,PiwiKD, Pol2s5p,rep3

value: Pol II Ser5P (abcam ab5131)


title: sample_1_Control_total_rep2

description: Library name: sample_1_rep2

value: Control


title: OSC,PiwiKD, Pol2s5p,rep2

value: si-Piwi


title: Panc1 shSCR Poly RNA 7-10 bio rep 2

value: PDAC


title: OSC,PiwiKD, Pol2s5p,rep1


title: OSC,PiwiKD, Pol2s2p,rep2

value: Pol II Ser2P (abcam ab5095)


title: sample_12_Combo_poly_rep1

description: Library name: sample_12_rep1

value: leaf

value: YaLF

value: poly


title: OSC,GFPKD,Pol2s5p,rep3


title: sample_6_Hardening_mono_rep2

description: Library name: sample_6_rep2

value: mono


title: Panc1 shSCR Poly RNA 3-6 bio rep 2


title: OSC,PiwiKD,IgG,rep1

value: rabbit IgG (Epicypher 13-0042k)


title: Panc1 shSCR Poly RNA 11-14 bio rep 1


title: sample_11_Stress_poly_rep1

description: Library name: sample_11_rep1


title: sample_4_Combo_total_rep2

description: Library name: sample_4_rep2

value: Combo


title: sample_10_Hardening_poly_rep1

description: Library name: sample_10_rep1


title: Panc1 shSCR Poly RNA 7-10 bio rep 1


title: D21.C_S11

city: La Jolla

first: David

last: Brenner

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys

data_processing:
Quality control of the raw fastq files was performed using the software tool FastQC v0.11.8. Sequencing reads were trimmed with Trimmomaticand aligned to the human genome (GRCh38.p13 ) using the STAR aligner . Read quantification was performed with RSEM and the Gencode release 43 annotation.
Assembly: hg38
Supplementary files format and content: raw counts

source_name: bioprinted liver

growth_protocol: 3D liver tissues comprising of cryopreserved primary human hepatocytes, hepatic stellate cells, liver endothelial cells, and Kupffer cells, were fabricated by Organovo, Inc. (San Diego, CA, USA) with a NovoGen Bioprinter onto 24-well transwell culture inserts using patented protocols as previously described.

extract_protocol:
Prior to RNA extraction, media was removed and bioprinted liver tissues were frozen in liquid nitrogen and stored at −80 °C until ready for RNA extraction. Tissues were homogenized using a homogenizer, and total RNA was isolated from homogenized tissue with RNeasy Mini Kit (QIAGEN, Valencia, CA).
Strand-specific mRNA-sequencing libraries (polyA+) were generated and barcoded using Illumina’s TruSeq stranded mRNA library prep kits. Each RNA-Seq library was sequenced on an Illumina HISEQ.

treatment_protocol: MASH phenotype was induced by adding unsaturated fatty acid – Oleic acid, saturated fatty acid – Palmitic acid  and bacterial endotoxin – LPS in 10% BSA to the liver tissue maintenance media consisting of Williams E hepatocyte media with maintenance supplements (CM 4000, Life Technologies, Carlsbad, CA) and EGM-2 (Lonza, Basel, Switzerland), for a final fatty acid concentration of 3mM and LPS concentration of 10 µg/mL.  Tissues were allowed to mature in culture for three days following fabrication prior to initiation of the experiment.

value: bioprinted liver

tag: timepoint

tag: disease stage

value: MASH


title: D21.B_S10


title: D14.C_S8


title: D14.B_S7


title: D21.A_S9


title: sample_9_Control_poly_rep1

description: Library name: sample_9_rep1


title: sample_8_Combo_mono_rep1

description: Library name: sample_8_rep1


title: OSC,GFPKD,Pol2s5p,rep1

value: ovarian somatic cells (OSC)

value: si-EGFP


title: Panc1 shSCR Poly RNA 11-14 bio rep 2

value: WT


title: Panc1 shSCR Poly RNA 3-6 bio rep 1


title: Panc1 shRBM42-1 total RNA bio rep 3

data_processing:
Salmon quant with default parameters was used to quantify paired end RNA-Seq reads
Pairwise comparisons were performed using default DESeq2 parameters
Assembly: hg38
Supplementary files format and content: featureCounts RNA count matrix

extract_protocol:
RNA was purified using RNeasy Plus Mini Kit.
10ng was used as input into the SMARTer Stranded Total RNA-Seq Kit v3-Pico (Takara)

value: RBM42 knockdown


title: D7.C_S5


title: PiwiKD,IgG, rep2

data_processing:
Adapters were removed from ChIP-seq reads using Trimmomatic, and subsequent reads shorter than 20 nt were discarded. CUT&RUN reads were mapped to the Drosophila genome (dm6) using Bowtie 2 allowing 1 mismatch in the seed sequence. Bigwig files of Pol II Ser5P and Pol II Ser2P were generated using the bamCompare command of deepTools. The bamCoverage command used sorted bam files as input and with parameters of binSize 20, BPM for normalization, smoothlength of 60, extendReads 150, and centerReads.
Assembly: dm6
Supplementary files format and content: bigWig

value: ovary

value: germline Piwi knockdown

value: rabbit IgG (cell signaling#2729)


title: D14.A_S6


title: sample_7_Stress_mono_rep1

description: Library name: sample_7_rep1

value: Stress


title: Panc1 shRBM42-1 total RNA bio rep 2

value: PDAC


title: PiwiKD,IgG, rep1


title: D7.B_S4


title: OSC,GFPKD,Pol2s5p,rep2

value: Pol II Ser5P (abcam ab5131)


title: GFPKD, IgG, rep3

value: germline GFP knockdown


title: Panc1 shRBM42-1 total RNA bio rep 1


title: Panc1 shSCR total RNA bio rep 3


title: sample_5_Control_mono_rep1

description: Library name: sample_5_rep1

value: leaf

value: YaLF

value: Control


title: D7.A_S3


title: GFPKD, IgG, rep2


title: D1.B_S2


title: PiwiKD,IgG, rep3


title: sample_4_Combo_total_rep1

description: Library name: sample_4_rep1

value: Combo

value: total


title: GFPKD, IgG, rep1


title: Panc1 shSCR total RNA bio rep 1


title: PiwiKD, Input, rep3


title: Panc1 shSCR total RNA bio rep 2


title: sample_2_Hardening_total_rep1

description: Library name: sample_2_rep1

value: Hardening


title: D1.A_S1

value: bioprinted liver

value: MASH


title: sample_1_Control_total_rep1

description: Library name: sample_1_rep1


title: sample_3_Stress_total_rep1

description: Library name: sample_3_rep1


title: D21.N.231127


title: PiwiKD, Input, rep2


title: D21.H1.231127

value: healthy


title: PiwiKD, Input, rep1


title: GFPKD, Input, rep3


title: sample_6_Hardening_mono_rep1

description: Library name: sample_6_rep1

value: mono


title: D14.H3.231127


title: GFPKD, Input, rep2

value: ovary


title: D14.H2.231127


title: aPD-1

city: Seongbuk-gu

first: In-San

last: KIM

address: 5, Hwarang-ro 14-gil

country: South Korea

institute: Korea Institute of Science and Technology

description: 10X Genomics

data_processing:
The resulting reads were aligned with the mouse genome reference (GRCm38) using the Cell Ranger pipeline (version 3.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissues were harvested from the tumor-bearing mice. Tumor tissues were digested using a tumor dissociation kit and dissociated into single cells using a gentleMACSTM Octo Dissociator. Red blood cells (RBCs) in a single-cell suspension derived from tumor tissues were lysed using RBC lysis buffer, and debris and dead cells were removed using a debris removal solution and dead cell removal kit.
Viable cells were counted and processed to generate an RNA library following the 10X Chromium Single Cell V(D)J User Guide (CG000086). Briefly, cell suspensions were diluted in nuclease-free water to achieve a target cell count of 10,000 cells. The suspension was combined with a master mix and loaded onto a Single-Cell-A-Chip together with Single-Cell 5′ Gel Beads and Partitioning Oil. Within individual droplets, the RNA transcripts from single cells were uniquely barcoded and reverse-transcribed. The resulting cDNA molecules were pooled and PCR-enriched. For the V(D)J Enriched Library, the cDNA pool was first amplified using the T Cell Mix1 or B Cell Mix1 primer, followed by a second amplification using the T Cell Mix2 or B Cell Mix2 primer. For the 5′ Gene Expression Library, the cDNA pool underwent an end repair process, the addition of a single A base, and subsequent adapter ligation. The resulting products were purified and PCR-enriched to create the 5′ Gene Expression Library. The purified libraries were quantified using qPCR according to the KAPA qPCR Quantification Protocol Guide, and the quality was checked using an Agilent Technologies 4200 TapeStation. Sequencing was performed on a HiSeq X Ten (Illumina) following the recommended read-length guidelines.

value: Tumor

value: Melanoma


title: D+F

description: 10X Genomics


title: GFPKD, Input, rep1


title: D14.H1.231127


title: Control

description: 10X Genomics


title: PiwiKD, Pol2s2p, rep3

value: germline Piwi knockdown

value: Pol II Ser2P (abcam ab5095)


title: D7.H3.231127


title: piwi,ovary,rep3

description: biological replicate 3

data_processing:
CAGE-seq reads were aligned to dm6 genome by STAR 2.7.7. rRNA reads were removed and only reads that are uniquely aligned with zero or one mismatch were used for downstream analysis. The TSS coordinates were based on the gene annotation file BDGP6.28. 101.gff3. For transcripts that share the same starting site, one representative transcript was randomly chosen for the TSS coordinate pool to get rid of the redundancy. To calculate the usage of a TSS of a gene, the reads whose very 5’ end fell within the +15bp and -100bp region of the very 5’ end of the TSS were summed and divided by the total reads fell within all non-redundant TSSs for the gene. We only consider the genes who have at least one TSS with >= 10 reads. The usage change was measured by the ratio of the usage in piwi mutant against the usage in wild type.
Assembly: dm6
Supplementary files format and content: bedGraph

extract_protocol:
Total RNA from young wildtype (w1118) and piwi1/piwi2 mutant fly ovaries were extracted, purified following standard phenol-chloroform extraction steps.
CAGE library preparation and sequencing were performed by DNAFORM. Qualities of total RNA were assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0. The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument.

value: piwi mutant


title: piwi,ovary,rep1

description: biological replicate 1


title: PiwiKD, Pol2s2p, rep1


title: GFPKD, Pol2s2p, rep3

value: germline GFP knockdown


title: piwi,ovary,rep2

description: biological replicate 2


title: WT,ovary,rep3

description: biological replicate 3

value: wild type (w1118)


title: D7.H2.231127


title: PiwiKD, Pol2s2p, rep2


title: WT,ovary,rep2

description: biological replicate 2


title: GFPKD, Pol2s2p, rep1


title: WT,ovary,rep1

description: biological replicate 1


title: 77-Treated

type: protein

city: Indianapolis

first: Xavier

last: Taylor

state: Indiana

address: 307 E Merrill St

institute: Eli Lilly and Company

description:
20221208_P1001660003206A_RCC
1-12 (Leptomeninges) 13-24 (penetrating vessels)
3D6 treated

hyb_protocol: Once all ROIs were processed, pools of released indexing oligos were hybridized to NanoString optical barcodes for digital counting and subsequently analyzed with a nCounter Analysis System. nCounter hybridization assay for photocleaved oligo counting Hybridization of cleaved indexing oligonucleotides to fluorescent barcodes was performed using the nCounter Protein PlexSet reagents based on the manufacturer's directions. Hybridizations were performed at 65 °C overnight in a thermocycler.

scan_protocol: For each mouse, 12 CAA containing leptomeningeal and 12 CAA containing penetrating vessels were selected as ROIs for high-resolution multiplex profiling, comprising a total of 24 ROIs per animal. A 100-μm in diameter circle was selected as the center ROI surrounding each blood vessel with β-amyloid deposition.

data_processing:
After hybridization, samples were processed using the nCounter Prep Station and Digital Analyzer as per manufacturer instructions. Data were normalized to technical controls and areas.
Digital counts were normalized with negative controls (Rt IgG2b, Rb IgG, and Rt IgG2a)

label: Unique Multiplex Barcodes

molecule: protein

source_name: Brain 3D6 treatment

label_protocol: Slides were removed from the BOND RXm and were incubated overnight at 4°C with a multiplexed cocktail of primary antibodies each of which are conjugated to unique ultraviolent-photocleavable oligonucleotide tags (GeoMx Immune Profile Core and Immune Cell Typing modules containing 31 targets, including three housekeeper and three background probes). Additional fluorescently labeled antibodies were used as morphology markers to select regions of interest (ROIs). In the current study, the morphology markers included β-amyloid (MOAB-2, Novus Biologicals, NBP2-13075AF594), and laminin (Novus Biologicals, NB300-144AF532) to visualize β-amyloid deposition and neuro-vasculature, respectively.

extract_protocol: Assay was performed on 5 μm thick FFPE (Formalin-fixed paraffin-embedded) coronal brain sections from IgG- and 3D6-treated PDAPP mice. Sections were mounted onto charged slides and underwent baking at 65°C in a drying oven for 2 hours prior to deparaffinization. Slides were deparaffinized and rehydrated by incubating in CitriSolv (Decon Labs) 3 times for 5min each followed by 2 washes of 100% ethanol for 5 min and 2 washes of 95% Ethanol for 5min and 2 washes of distilled water for 5 min each.

treatment_protocol: PDAPP mice received weekly subcutaneous injections of 3D6 (anti-Aβ1-x,IgG2b) (25mg/kg) or twice-weekly subcutaneous injections of IgG (IgG2a isotype) (50mg/kg) for three months

value: Brain


title: D+F+P

description: 10X Genomics


title: D1.H2.231127


title: GFPKD, Pol2s2p, rep2


title: PiwiKD, Pol2s5p, rep3

value: Pol II Ser5P (abcam ab5131)


title: 72-Treated

description:
20221212_P1001660003206E_RCC
1-12 (Leptomeninges) 13-24 (penetrating vessels)
3D6 treated


title: 81-Treated

description:
20221207_P1001660003205A_RCC
1-12 (Leptomeninges) 13-24 (penetrating vessels)
3D6 treated


title: EEO3

city: Hangzhou

first: Xiaona

last: Lin

address: No.3 Qingchun East Road

institute: Sir Run Run Shaw Hospital Affiliated to Zhejiang University School of Medicine

data_processing:
The purified RNA underwent 150-bp single-end RNA-sequencing (RNA-seq) using the BGISEQ platform (China, BGI).
Raw RNA-seq data underwent quality control using TrimGalore to obtain clean data.
The cleaned sequence reads were aligned against the Rattus norvegicus genome using Bowtie2 (version 2.2.5)
Assembly: GCF 000001895.5 Rnor 6.0
Supplementary files format and content: fpkm and tpm

organism: Rattus norvegicus

source_name: Endometrial epithelial  organoids

extract_protocol:
Total RNA was extracted from rEEOs (n = 3) and rBMSCs (n = 3) using the RNA-Quick Purification Kit (ES Science, Shanghai, China, RN001) following the manufacturer's instructions.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.3 mRNA Fragmentation the reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.4 cDNA Synthesis prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.5 End Repair, Add A and Adaptor Ligation after the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.6 PCR the PCR reaction system and program are configured and set up to amplify the product.7 Library QC the corresponding library quality control protocol will be selected depending upon product requirements.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Endometrial epithelial  organoids


title: EEO2


title: PiwiKD, Pol2s5p, rep2


title: PiwiKD, Pol2s5p, rep1


title: EEO1


title: 83-Treated


title: GFPKD, Pol2s5p, rep3


title: 49-Untreated

description:
20221207_P1001660003205A_RCC
1-12 (Leptomeninges) 13-24 (penetrating vessels)
IgG treated

source_name: Brain IgG treatment


title: D1.H1.231127


title: D7.H1.231127


title: BMSC3

source_name: BMSCs

value: BMSCs


title: GFPKD, Pol2s5p, rep2


title: D21.H2.231127


title: Panc1 JUN 5UTR DMS bio rep 2

value: PDAC


title: Panc1 JUN 5UTR DMS bio rep 1


title: 29-Untreated

description:
20221212_P1001660003206E_RCC
1-12 (Leptomeninges) 13-24 (penetrating vessels)
IgG treated


title: Panc1 EGFR 5UTR DMS bio rep 2


title: BMSC1


title: BMSC2


title: GFPKD, Pol2s5p, rep1


title: Panc1 EGFR 5UTR DMS bio rep 1


title: 37-Untreated

description:
20221208_P1001660003206A_RCC
1-12 (Leptomeninges) 13-24 (penetrating vessels)
IgG treated


title: DNA from FFPE adjacent normal tissue WT complete reponse patient 10

status: Public on Nov 28 2024

type: genomic

city: Cairo

first: Deena

last: Jalal

address: 1 Seket Al-Emam Street, El-Madbah El-Kadeem Yard,El-Saida Zenab

country: Egypt

institute: Children Cancer Hospital Egypt 57357

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human infinium MethylationEPIC Beadchip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan microarray scanner according to the manufacturer’s recommendations (Illumina Inc.)

data_processing:
minfi package (v1.44.0) in R environment (v4.3.1)
Average Beta

label: Cy3, Cy5

source_name: FFPE adjacent normal tissue

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from FFPE tumor and normal tissue samples using QIAamp DNA FFPE tissue kit (Qiagen) according to the manufacturer’s instructions.

value: FFPE adjacent normal tissue

tag: gender

value: Female

value: normal


title: DNA from FFPE adjacent normal tissue WT relapse patient 11

value: Male


title: DNA from FFPE adjacent normal tissue WT complete reponse patient 11


title: DNA from FFPE adjacent normal tissue WT relapse patient 10


title: DNA from FFPE tumour tissue WT relapse patient 12

source_name: FFPE tumour tissue

value: FFPE tumour tissue

value: tumour


title: DNA from FFPE tumour tissue WT relapse patient 11


title: DNA from FFPE tumour tissue WT relapse patient 9


title: DNA from FFPE tumour tissue WT relapse patient 8


title: DNA from FFPE tumour tissue WT relapse patient 10


title: DNA from FFPE tumour tissue WT relapse patient 7


title: DNA from FFPE tumour tissue WT relapse patient 6


title: DNA from FFPE tumour tissue WT relapse patient 5


title: DNA from FFPE tumour tissue WT complete reponse patient 9


title: DNA from FFPE tumour tissue WT complete reponse patient 10


title: DNA from FFPE tumour tissue WT complete reponse patient 12


title: DNA from FFPE tumour tissue WT complete reponse patient 8


title: DNA from FFPE tumour tissue WT complete reponse patient 11


title: DNA from FFPE tumour tissue WT complete reponse patient 3


title: DNA from FFPE tumour tissue WT complete reponse patient 7


title: HK2 cells, shControl, long-term, biol rep 3

city: Cardiff

first: Iain

middle: A

last: Perry

state: South Glamorgan

address: Longwood Drive

department: Wales Gene Park

institute: Cardiff University

description: Library name: M-011

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastP
Trimmed sequence reads were mapped to GrCh38 using STAR 2-Pass)
Read count were identified using FeatureCounts
Reads were normalised using DESeq2 in the SARTools wrapper
Assembly: GrCh38
Supplementary files format and content: tab-delimited text file includes raw and normalised counts for each Sample

growth_protocol: HK2 cells were maintained in DMEM with 10% fetal bovine serum and antibiotics in a humidified atmosphere at 37C with 5% CO2

extract_protocol:
RNA was extracted using the RNeasy plus mini kit (Qiagen)
RNA libraries were prepared using the Illumina TruSeq RNA Library preparation kit v2, following manufacturer's protocols

treatment_protocol: Cells were either harvested at fewer than 30 passages growth (short-term) or after 120 pssages growth (long-term)

value: proximal tubule cells

value: WT

value: >120 passages growth


title: DNA from FFPE tumour tissue WT complete reponse patient 6


title: HK2 cells, shRNA FLCN, long-term, biol rep 3

description: Library name: M-012

value: FLCN knockdown


title: HK2 cells, shRNA FLCN, short-term, biol rep 3

description: Library name: M-010

value: <30 passages growth


title: DNA from FFPE adjacent normal tissue WT relapse patient 12


title: HK2 cells, shControl, short-term, biol rep 3

description: Library name: M-009


title: HK2 cells, shRNA FLCN, long-term, biol rep 2

description: Library name: M-008


title: HK2 cells, shControl, long-term, biol rep 2

description: Library name: M-007


title: HK2 cells, shRNA FLCN, short-term, biol rep 2

description: Library name: M-006


title: DNA from FFPE adjacent normal tissue WT complete reponse patient 9


title: HK2 cells, shRNA FLCN, long-term, biol rep 1

description: Library name: M-004


title: HK2 cells, shRNA FLCN, short-term, biol rep 1

description: Library name: M-002


title: Sasanishiki_control-3

data_processing:
We obtained expression levels for each gene using kallisto (0.46.2) (Bray et al., 2016). The bootstrap was specified as 100, and the expression levels were corrected to TPM (transcripts per million).
The comparisons of expression levels between cold-treated and control plants of each line and between rice lines were performed sleuth (0.30.0) (Pimentel et al., 2017). Differences in expression levels between treatments in each line were statistically tested using the likelihood ratio test.
Assembly: IRGSP-1.0 (2021-05-10)
Supplementary files format and content: Tab-delimited text file containing TPM values for each sample.

value: anther

value: booting stage

value: Sasanishiki

value: non treatment


title: HK2 cells, shControl, long-term, biol rep 1

description: Library name: M-003


title: HK2 cells, shControl, short-term, biol rep 2

description: Library name: M-005


title: DNA from FFPE tumour tissue WT relapse patient 4


title: F_7BAB_042922__Control (long-term)

city: Cambridge

first: Sinisa

last: Hrvatin

state: MA

address: 455 Main Street

department: Whitehead Institute

institute: MIT

hyb_protocol: A Tecan liquid handler was used to automate the process from Hybridization to X-Stain

scan_protocol: Samples were scanned on the Illumina iScan System

data_processing:
The SeSaMe normalization method was used to estimate methylation levels (B-values) for each CpG site.
processed value definition: B-values provide the average methylation levels for each CpG site.  Detection P-values represent the probability of a detected signal being background fluorescence

label: Cy3 and Cy5

source_name: Blood

extract_protocol: Genomic DNA was extracted using Dneasy blood and tissue kit  (QIAGEN #69506). DNA samples were normalized to between 12.5-25 ng/μL in 30 μL. DNA was bisulfite converted using the Zymo EZ DNA methylation kit (D5004).

value: Blood

value: Control (long-term)


title: F_3BBC_042922__Control (long-term)

label_protocol: A Tecan liquid handler was used to automate the process from Hybridization to X-Stain


title: F_756A_042922__Control (long-term)


title: F_7BE9_042922__Control (long-term)


title: F_493A_042922__Control (long-term)


title: HK2 cells, shControl, short-term, biol rep 1

description: Library name: M-001


title: DNA from FFPE tumour tissue WT complete reponse patient 5


title: F_2F05_042922__Control (long-term)


title: C_773F_042922__TLS (long-term)

value: TLS (long-term)


title: C_581C_042922__TLS (long-term)


title: C_4780_042922__TLS (long-term)


title: F_3569_042922__TLS (long-term)


title: C_4108_042922__TLS (long-term)


title: CR_T08__Time 0

value: Time 0


title: CR_T07__Time 0


title: CR_T05__Time 0


title: CR_T04__Time 0


title: CR_T03__Time 0


title: CR_T02__Time 0


title: CR7_3BD5__CR

value: CR


title: CR30_0D73__CR


title: CR4_7708__CR


title: CR_T01__Time 0


title: CR28_3D56__CR


title: CR8_460D__CR


title: C_EC93_042922__TLS (long-term)


title: CR27_EE0F__CR


title: CR25_6084__TLS+CR

value: TLS+CR


title: CR22_542D__TLS+CR


title: CR24_3D41__TLS+CR


title: CR23_E6C0__TLS+CR


title: C_5512_042922__TLS (long-term)


title: CR26_423A__TLS+CR


title: CR20_D804__TLS+CR


title: CR21_41E9__TLS+CR


title: CR1_7855__TLS+CR


title: CR18_F760__Control

value: Control


title: CR_T06__Time 0


title: CR19_A3E7__Control


title: CR17_1F45__Control


title: CR14_76FE__Control


title: CR15_F34D__Control


title: CR13_30ED__Control


title: CR16_F660__Control


title: CR2_2270__CR


title: TC_Liver_T08_Liver_T0

source_name: Liver

value: Liver


title: TC_Liver_T07_Liver_T0


title: CR29_2F29__CR


title: TC_Liver_T04_Liver_T0


title: TC_Liver_T06_Liver_T0


title: TC_Liver_T03_Liver_T0


title: TC_Liver_T01_Liver_T0


title: TC_Liver_T02_Liver_T0


title: TC_Liver_L9_E239_Liver_Con 22c

value: Con 22c


title: TC_Liver_L9_A367_Liver_Con 22c


title: TC_Liver_L7_A5DA_Liver_TLS

value: TLS


title: TC_Liver_L7_E46E_Liver_TLS


title: TC_Liver_L3_D215_Liver_Con 22c


title: TC_Liver_L7_47BE_Liver_TLS


title: TC_Liver_L3_A123_Liver_Con 22c


title: TC_Liver_L3_9916_Liver_Con 22c


title: CR10_DC5A__Control


title: TC_Liver_L1_B4B9_Liver_TLS


title: TC_L9_E239_blood_Con 22c

source_name: blood

value: blood


title: TC_Liver_L1_B23B_Liver_TLS


title: TC_L9_A367_blood_Con 22c


title: TC_L9_9BA4_blood_Con 22c


title: TC_L8_F99D_blood_32c stim

value: 32c stim


title: TC_L8_D63D_blood_32c stim


title: TC_L9_5A66_blood_Con 22c


title: TC_L8_B4CE_blood_32c stim


title: TC_L7_E46E_blood_TLS


title: TC_L7_DDF3_blood_TLS


title: TC_L7_A5DA_blood_TLS


title: TC_L7_47BE_blood_TLS


title: TC_Liver_L9_9BA4_Liver_Con 22c


title: TC_L4_DA7B_blood_32c con

value: 32c con


title: TC_L4_F0CB_blood_32c con


title: TC_Liver_L9_5A66_Liver_Con 22c


title: TC_L3_D123_blood_Con 22c


title: TC_L4_9952_blood_32c con


title: TC_L4_6396_blood_32c con


title: TC_Liver_L3_9388_Liver_Con 22c


title: TC_L3_9916_blood_Con 22c


title: TC_L2_DD39_blood_32c stim


title: TC_L3_9388_blood_Con 22c


title: TC_L3_A123_blood_Con 22c


title: TC_L2_CB2C_blood_32c stim


title: TC_Liver_L1_B03E_Liver_TLS


title: TC_L2_20A6_blood_32c stim


title: TC_L2_B711_blood_32c stim


title: TC_L1_B4B9_blood_TLS


title: TC_L1_B51B_blood_TLS


title: TC_L1_B23B_blood_TLS


title: TC_L10_E247_blood_32c con


title: TC_L10_C570_blood_32c con


title: TC_Liver_L1_B51B_Liver_TLS


title: TC_L10_C03B_blood_32c con


title: TC_L10_60C4_blood_32c con


title: TC_Kidney_T07_kidney_T0

source_name: kidney

value: kidney


title: TC_Kidney_T03_kidney_T0


title: TC_Kidney_T05_kidney_T0


title: TC_Kidney_T02_kidney_T0


title: TC_Kidney_T04_kidney_T0


title: TC_Kidney_T06_kidney_T0


title: TC_Kidney_T01_kidney_T0


title: TC_Kidney_L9_A367_kidney_Con 22c


title: TC_Kidney_L9_9BA4_kidney_Con 22c


title: TC_Kidney_L9_5A66_kidney_Con 22c


title: TC_Kidney_L7_E46E_kidney_TLS


title: TC_Kidney_L7_DDF3_kidney_TLS


title: TC_Kidney_L9_E239_kidney_Con 22c


title: TC_Kidney_L7_47BE_kidney_TLS


title: TC_Kidney_L3_D215_kidney_Con 22c


title: TC_Kidney_L3_9388_kidney_Con 22c


title: TC_L1_B03E_blood_TLS


title: TC_Kidney_L3_9916_kidney_Con 22c


title: TC_Kidney_L1_B4B9_kidney_TLS


title: TC_Kidney_L1_B03E_kidney_TLS


title: TC_Cortex_T08_cortex_T0

source_name: cortex

value: cortex


title: TC_Kidney_L1_B23B_kidney_TLS


title: TC_Cortex_T06_cortex_T0


title: TC_Cortex_T07_cortex_T0


title: TC_Kidney_T08_kidney_T0


title: TC_Cortex_T05_cortex_T0


title: TC_Cortex_T03_cortex_T0


title: TC_Cortex_T02_cortex_T0


title: TC_Cortex_T04_cortex_T0


title: TC_Cortex_T01_cortex_T0


title: TC_Cortex_L9_E239_cortex_Con 22c


title: TC_Cortex_L9_5A66_cortex_Con 22c


title: TC_Cortex_L9_9BA4_cortex_Con 22c


title: TC_Kidney_L7_A5DA_kidney_TLS


title: TC_Cortex_L7_DDF3_cortex_TLS


title: TC_Cortex_L7_E46E_cortex_TLS


title: TC_Cortex_L7_47BE_cortex_TLS


title: TC_Kidney_L3_A123_kidney_Con 22c


title: TC_Cortex_L7_A5DA_cortex_TLS


title: TC_Kidney_L1_B51B_kidney_TLS


title: TC_Cortex_L3_D215_cortex_Con 22c


title: TC_Cortex_L3_A123_cortex_Con 22c


title: TC_Cortex_L3_9916_cortex_Con 22c


title: TC_Cortex_L3_9388_cortex_Con 22c


title: TC_Cortex_L1_B4B9_cortex_TLS


title: TC_Cortex_L1_B03E_cortex_TLS


title: TC_Cortex_L1_B23B_cortex_TLS


title: TC_Blood_T0_8_blood_T0


title: TC_Blood_T0_6_blood_T0


title: TC_Blood_T0_5_blood_T0


title: TC_Blood_T0_3_blood_T0


title: TC_Blood_T0_2_blood_T0


title: TC_Cortex_L9_A367_cortex_Con 22c


title: TC_Blood_T0_1_blood_T0


title: F4_2F05_020422_blood_Control (Long-term)

value: Control (Long-term)


title: F4_2F05_112022_blood_Control (Long-term)


title: F3_41F8_112022_blood_Control (Long-term)


title: F3_7BAB_112022_blood_Control (Long-term)


title: F3_3BBC_112022_blood_Control (Long-term)


title: F2_756A_112022_blood_Control (Long-term)


title: F3_41F8_020422_blood_Control (Long-term)


title: TC_Cortex_L1_B51B_cortex_TLS


title: F3_7BAB_020422_blood_Control (Long-term)


title: F1_7BE9_112022_blood_Control (Long-term)


title: F1_7BE9_020422_blood_Control (Long-term)


title: F1_3569_112022_blood_Control (Long-term)


title: F1_493A_112022_blood_Control (Long-term)


title: F1_3569_020422_blood_Control (Long-term)


title: F2_756A_020422_blood_Control (Long-term)


title: TC_Liver_T05_Liver_T0


title: TC_Blood_T0_7_blood_T0


title: C3_6314_112022_blood_TLS (Long-term)

value: TLS (Long-term)


title: C4_773F_020422_blood_TLS (Long-term)


title: C3_581C_112022_blood_TLS (Long-term)


title: F1_493A_020422_blood_Control (Long-term)


title: C3_4108_112022_blood_TLS (Long-term)


title: C3_581C_020422_blood_TLS (Long-term)


title: C3_4108_020422_blood_TLS (Long-term)


title: C2_5512_112022_blood_TLS (Long-term)


title: C2_5512_020422_blood_TLS (Long-term)


title: C1_EC93_112022_blood_TLS (Long-term)


title: C1_4934_112022_blood_TLS (Long-term)


title: F3_3BBC_020422_blood_Control (Long-term)


title: C1_EC93_020422_blood_TLS (Long-term)


title: C1_4780_020422_blood_TLS (Long-term)


title: C1_4780_112022_blood_TLS (Long-term)


title: C1_4934_020422_blood_TLS (Long-term)


title: C4_773F_112022_blood_TLS (Long-term)


title: C_3F44_110121_blood_TLS (long-term)


title: C_773F_110121_blood_TLS (long-term)


title: C_5512_110121_blood_TLS (long-term)


title: C_EC93_110121_blood_TLS (long-term)


title: C_4108_110121_blood_TLS (long-term)


title: C_6314_110121_blood_TLS (long-term)


title: C_3569_110121_blood_TLS (long-term)


title: F_7BE9_110121_blood_Control (long-term)


title: F_7BAB_110121_blood_Control (long-term)


title: C_581C_110121_blood_TLS (long-term)


title: F_6886_110121_blood_Control (long-term)


title: F_756A_110121_blood_Control (long-term)


title: F_493A_110121_blood_Control (long-term)


title: F_627B_110121_blood_Control (long-term)


title: F_2F05_110121_blood_Control (long-term)


title: F_3BBC_110121_blood_Control (long-term)


title: F_46C9_110121_blood_Control (long-term)


title: C_581C_072921_blood_TLS (long-term)


title: C_4934_110121_blood_TLS (long-term)


title: C_4780_110121_blood_TLS (long-term)


title: C_3F44_072921_blood_TLS (long-term)


title: C_6314_072921_blood_TLS (long-term)


title: 1C45 70F8_072921_blood_N/A

description: 1C45 70F8_072921


title: C_773F_072921_blood_TLS (long-term)


title: F_ 6866_072921_blood_Control (long-term)

description: F_ 6866_072921


title: F_3569_072921_blood_Control (long-term)


title: C_66B2_072921_blood_TLS (long-term)


title: F_756A_072921_blood_Control (long-term)


title: C_4780_072921_blood_TLS (long-term)


title: F_41F8_110121_blood_Control (long-term)


title: C_5512_072921_blood_TLS (long-term)


title: C_4108_072921_blood_TLS (long-term)


title: F_3BBC_072921_blood_Control (long-term)


title: F_2F05_072921_blood_Control (long-term)


title: F_7BE9_072921_blood_Control (long-term)


title: C_4934_072921_blood_TLS (long-term)


title: F_41F8_072921_blood_Control (long-term)


title: F_493A_072921_blood_Control (long-term)


title: F_627B_072921_blood_Control (long-term)


title: F_46C9_072921_blood_Control (long-term)


title: C_6314_042821_blood_TLS (long-term)


title: C_4108_042821_blood_TLS (long-term)


title: C_773F_042821_blood_TLS (long-term)


title: C_3F44_042821_blood_TLS (long-term)


title: F_6866_042821_blood_Control (long-term)


title: 1C45 70F8_042821_blood_N/A

description: 1C45 70F8_042821


title: C_5512_042821_blood_TLS (long-term)


title: F_756A_042821_blood_Control (long-term)


title: C_EC93_072921_blood_TLS (long-term)


title: C_EC93_042821_blood_TLS (long-term)


title: C_66B2_042821_blood_TLS (long-term)


title: F_3569_042821_blood_Control (long-term)


title: C_4780_042821_blood_TLS (long-term)


title: C_4934_042821_blood_TLS (long-term)


title: F_7BE9_042821_blood_Control (long-term)


title: F_7BAB_042821_blood_Control (long-term)


title: IBA Subfornical Organ Replicate 4

first: Madeleine

last: Junkins

state: Connecticut

address: 333 Cedar Street

department: Cellular & Molecular Physiology; Neuroscience

data_processing:
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.39 (Bolger et al., 2014) with default parameters.
Filtered high-quality reads from all samples were aligned to Ictidomys tridecemlineatus reference genome using STAR aligner v2.7.7a with default parameters (Dobin et al., 2013).
Aligned reads were counted by the featureCounts module within the Subread package v2.0.1 with default parameters (Liao et al., 2014).
Processing, normalization, and statistical analysis of read counts was performed using the EdgeR v3.38.4 package in R v4.2.1 (Robinson et al., 2010)
Statistical analysis of differential expression of genes between groups was performed using the GLM approach and the quasi-likelihood F-test, as implemented in the EdgeR package.
Assembly: The SpeTri2.0 [GCA_000236235.1] reference genome and the gene annotation were obtained from the Broad Institute through the National Center for Biotechnology Information (Ictidomys tridecemlineatus; assembly SpeTri2.0; NCBI Ictidomys tridecemlineatus Annotation Release 102; all files accessed on 8/17/2020). Reference genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.fna.gz; Gene annotation: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/235/GCF_000236235.1_SpeTri2.0/GCF_000236235.1_SpeTri2.0_genomic.gff.gz; the gene annotation was filtered to include only protein-coding genes.
Supplementary files format and content: Processed data file in Excel format (.xlsx) contains normalized read counts, normalized mean read counts, P-values, adjusted FDR values, and fold change (log2) for statistical comparison of expression values between 2 groups.

organism: Ictidomys tridecemlineatus

source_name: Subfornical organ

growth_protocol: The brain was rapidly dissected and a vibratome (Leica VT1200) was used to cut 300-600 μm coronal slices. The subfornical organ was manually dissected out from the slices using 27G needles and placed immediately into RNA lysis buffer from the Quick-RNA Microprep Kit (Zymo, R1050).

extract_protocol:
Total RNA was isolated from tissue using the Quick-RNA Microprep Kit (Zymo, R1050). RNA concentration and integrity number (RIN) were assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). RNA concentrations were in the range of ~8.5 - 25.8 ng/µL and RIN values were in the range of 6.8 – 9.1.
Sequencing libraries were prepared using the Kapa mRNA Hyper Prep kit (KAPA Biosystems, Wilmington, MA).

value: Subfornical organ


title: IBA Subfornical Organ Replicate 5


title: F_3BBC_042821_blood_Control (long-term)

value: Control (long-term)


title: F_493A_042821_blood_Control (long-term)


title: F_2F05_042821_blood_Control (long-term)


title: TC_Liver_L7_DDF3_Liver_TLS


title: F_41F8_042821_blood_Control (long-term)


title: IBA Subfornical Organ Replicate 1


title: IBA Subfornical Organ Replicate 3


title: Active Subfornical Organ Replicate 5


title: C_581C_042821_blood_TLS (long-term)

value: TLS (long-term)


title: IBA Subfornical Organ Replicate 2


title: F_46C9_042821_blood_Control (long-term)


title: F_627B_042821_blood_Control (long-term)


title: Active Subfornical Organ Replicate 4


title: Active Subfornical Organ Replicate 3


title: Active Subfornical Organ Replicate 2


title: Active Subfornical Organ Replicate 1


title: Human_testis_normal

first: Ivan

last: Milenkovic

state: Catalonia

address: Dr. Aiguader 88

institute: Centre for Genomic Regulation

data_processing:
Basecalling using Guppy.
Demultiplexing using Guppy.
Mapping using graphmap.
Assembly: Mouse and human rRNA fasta.
Supplementary files format and content: CMC scores for the nanoCMC sequencing (they are calculated by comparing the treated vs untreated sample, that is why there is only one processed file per 2 raw files), as well as the EpiNano outputs for the rest of the cDNA runs;  they contain the values for mismatches, insertions and deletions per site for all cytosolic rRNA molecules, which we used to infer the presence/absence of modifications and SNPs.

source_name: Testis

extract_protocol:
RNA was extracted using TRIzol.
cDNAlibraries were done following ONT instruction manuals.

value: Testis

value: WT


title: Human_liver_cancer


title: Human_liver_normal


title: C274_pDC_IgG_Rep2

city: New York

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

institute: Hospital for Special Surgery

description:
Library name: C274_pDC_IgG_D3
CUT&RUN

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and peaks called using MACS2
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes filtered raw counts and merged peaks file
Library strategy: CUT&RUN

source_name: pDC

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. pDCs were isolated using BDCA4+ positive selection (Miltenyi Biotec: 130-090-532). pDCs were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS, penicillin/streptomycin (Invitrogen), and L-glutamine (Invitrogen).

extract_protocol: Epicypher CUT and RUN Protocol was followed

treatment_protocol: pDCs were cultured at 40,000 cells (for HDs) or at 10,000-20,000 cells (for patients with SSc and SLE) per well in a 96-U bottom plate and incubated at 37°C, 5% CO2 and 95% humidity. For TLR7 and TLR9 activation assays, pDCs were stimulated with either heat- inactivated H1N1 VR-95 influenza A virus (ATCC) at a concentration of 2 MOI/cells or with CpG C274 at 0.075μM (Guiducci et al., 2006) respectively

value: pDC


title: C274_pDC_NRF2_Rep1

description:
Library name: C274_pDC_NRF2_D2
CUT&RUN


title: C274_pDC_NRF2_Rep2

description:
Library name: C274_pDC_NRF2_D3
CUT&RUN


title: Dual_pDC_IgG_Rep2

description:
Library name: Dual_pDC_IgG_D3
CUT&RUN


title: Dual_pDC_NRF2_Rep1

description:
Library name: Dual_pDC_NRF2_D2
CUT&RUN


title: C274_pDC_NRF2_Rep3

description:
Library name: C274_pDC_NRF2_D4
CUT&RUN


title: Human_testis_cancer

city: Barcelona


title: Dual_pDC_NRF2_Rep2

description:
Library name: Dual_pDC_NRF2_D3
CUT&RUN


title: Human_lung_normal

source_name: Lung

value: Lung


title: KI696_pDC_IgG_Rep2

description:
Library name: KI696_pDC_IgG_D3
CUT&RUN


title: Dual_pDC_NRF2_Rep3

description:
Library name: Dual_pDC_NRF2_D4
CUT&RUN


title: KI696_pDC_NRF2_Rep1

description:
Library name: KI696_pDC_NRF2_D2
CUT&RUN


title: Human_lung_cancer


title: Human_colon_normal

source_name: Colon

value: Colon


title: KI696_pDC_NRF2_Rep2

description:
Library name: KI696_pDC_NRF2_D3
CUT&RUN


title: KI696_pDC_NRF2_Rep3

description:
Library name: KI696_pDC_NRF2_D4
CUT&RUN


title: Human_colon_cancer


title: Human_lung_normal_19

data_processing:
Basecalling using Guppy.
Demultiplexing using deeplexicon.
Mapping using graphmap.
Assembly: Mouse and human rRNA fasta.
Supplementary files format and content: EpiNano output with basecalling errors per-site, corresponding to the RNA modification levels.

extract_protocol:
RNA was extracted using TRIzol.
dRNA libraries were done following ONT instruction manuals.


title: Media_pDC_IgG__Rep2

description:
Library name: Media_pDC_IgG_D3
CUT&RUN

value: Media


title: Human_lung_normal_18


title: Human_lung_normal_17