title: nPOD_6236_multiome_MM_666_RNA_MM_657_ATAC

data_processing:
Cellranger arc (v2.0.0) was used to demultiplex, barcode processing, and ffeature counting. Hg38 genome assembly was used.
Assembly: hg38
Supplementary files format and content: raw_feature_bc_matrix.h5 contains barcode level counts (gene and peak features) for all detected UMIs
Library strategy: paired snRNA-seq & snATAC-seq

extract_protocol:
Roughly 40 mg ground tissue was resuspended. Nuclei were resuspended in 400 µl of sort buffer, 1 U µl−1 RNasin and stained with 7-aminoactinomycin D. A total of 120,000 nuclei were sorted using an SH800 sorter into 87.5 μl of collection buffer. Supernatant was gently removed, and ~10 µl were left behind to increase nuclei recovery. A total of 650 µl of wash buffer, 1% fatty acid-free BSA, 1 mM DTT , 1x protease inhibitors (Thermo Fisher Scientific, PIA32965), 1 U µl−1 RNasin (Promega, N2515) in molecular biology-grade water) was added with minimal disturbance of the pellet, and samples were centrifuged again with a swinging-bucket centrifuge (500 × g, 5 min, 4 °C; Eppendorf, 5920 R). Supernatant was gently removed without disturbing the pellet, leaving ~2–3 µl behind. Approximately 7–10 µl of 1x Nuclei Buffer (10x Genomics) were added, and nuclei were gently resuspended. Nuclei were counted using a hemocytometer, and 18,300 nuclei were used as input for tagmentation.
Single-cell multiome ATAC and gene expression libraries were generated following manufacturer instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 10x Genomics, 1000283; Chromium Next GEM Chip J Single Cell Kit, 10x Genomics, 1000234; Dual Index Kit TT Set A, 10x Genomics, 1000215; Single Index Kit N Set A, 10x Genomics, 1000212) with the following PCR cycles: 7 cycles for pre-amplification, 8 cycles for ATAC index PCR, 7 cycles for complementary DNA (cDNA) amplification, and 12 cycles for RNA index PCR. Final libraries were quantified using a Qubit fluorometer (Life Technologies), and the size distribution was checked using a TapeStation (High Sensitivity D1000, Agilent). Libraries were sequenced on NovaSeq 6000 sequencers (Illumina) with the following read lengths (Read1 + Index1 + Index2 + Read2): ATAC (NovaSeq 6000), 50 + 8 + 16 + 50; RNA ( NovaSeq 6000), 28 + 10 + 10 + 90


title: nPOD_6267_multiome_MM_667_RNA_MM_659_ATAC

status: Public on Sep 17 2025

type: SRA

city: La Jolla

first: Rebecca

last: Melton

address: 9500 Gilman Dr

country: USA

institute: University of California, San Diego

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: pancreas

tag: tissue

value: pancreas


title: ATF5_WT_ChIP_seq_rep_1

city: Shanghai

first: Yalei

last: Kong

address: No. 280, Chongqing South Road

country: China

institute: Shanghai Jiao Tong University

data_processing:
Data were mapped to the mouse reference genome mm10 with bwa 0.7.15 (mem with default parameters), samtools 1.3.1, and sambamba 0.6.3.
ChIP-Seq peaks were called with macs2 2.1.0.20140616 with “-B” to generate read pileups
Overlaps between peaks were identified with bedtools 2.26.0
DNA motifs were identified (findMotifsGenome.pl: “-size 200 -mask”) and visualized (motif2Logo.pl: “-pdf -ns 1000 -bit”) with homer 4.8.3
GO analysis was conducted with ClusterProfiler 4.8.1 (after removing peaks that are not on reference chromosomes).
Assembly: mm10
Supplementary files format and content: bigWig files

organism: Mus musculus

source_name: Main Olfactory Epithelium (MOE)

extract_protocol:
Dissected MOE was dissociated by the Papain Dissociation System (Worthington) at 37 °C for 15 min and trituration for 5-15 times with a cut P1000 pipette tip. Cells were filtered by a 40-μm strainer (Falcon). After spinning at 400 g for 2 min, cells were resuspended in DMEM (Gibco). ChIP-Seq was performed on dissociated MOE cells with a ChIP-IT High Sensitivity Kit (Active Motif) and an S2 focused-ultrasonicator (Covaris) (settings: frequency sweeping, intensity = 3, duty cycle = 2%, cycles per burst = 200, 15 cycles of 1 min on and 1 min off). Final DNA product was eluted into ~60 mL.
Libraries were prepared with an NEBNext Ultra DNA Library Prep Kit (New England Biolabs) and 11–18 cycles of PCR amplification, and then sized-selected with PCRClean DX magnetic beads (Aline Biosciences) (0.55´ to remove long fragments, and 0.9´ to remove short fragments). Libraries were quantified by a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and a High Sensitivity DNA Analysis Kit on a Bioanalyzer 2100 (Agilent)

value: Main Olfactory Epithelium (MOE)


title: Liver tumor, 4 weeks post AAV8-YFP injection, mouse 5

city: Hamilton

first: Gregory

last: Steinberg

state: Ontario

address: 1280 Main Street

country: Canada

institute: McMaster University

description: Library name: ACLY WT 5

library_source: transcriptomic

data_processing:
Sequence quality was assessed using FastQC followed by the removal of low-quality reads and adapter sequences using Cutadapt. Genome alignment was performed using HISAT2 and the Mus musculus mm10 reference genome. Quantification of reads was performed using featureCounts. Differential gene expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: All processed data files are in the format of a two column table with Entrez ID and featureCounts output.

molecule: polyA RNA

source_name: Liver Tumor

growth_protocol: At 2 wks. of age, C57BL-6/ Aclyf/f mice, obtained from JAX were injected with diethyl nitrosamine (DEN) at 25 mg/kg body weight. After weaning mice were housed with littermates and fed a normal chow diet (Teklad 8640 22/5). At 10 weeks of age, mice were switched to a high fat and high fructose diet (Western Diet (WD): 40 kcal% fat (mostly palm oil), 20 kcal% fructose and 0.02% cholesterol) (Research Diets, Inc., Code: D19101102). When the mice reached 7.5 months, mice were bled from the tail vein, and plasma alpha-fetoprotein (AFP) levels were determined.

extract_protocol:
After 4 (early time point) or 8 (late time point) weeks following AAV injection mice were anesthetized using ketamine/xylazine and liver tumor tissues were collected, flash frozen in liquid nitrogen, and stored for molecular analysis. For RNA-sequencing, frozen tumor tissue (~30 mg) was homogenized with Buffer RLT (RNeasy Mini Kit, Qiagen # 74106), and RNA isolation was performed using RNeasy kit (Qiagen, ID: 74106) following the manufacturer’s instructions. Sample quality was assessed using the Agilent 2100 Bioanalyzer G2938C with the Aligent RNA 6000 Nano Kit (Agilent; Santa Clara, CA, USA).
Only samples passing the RNA integrity number threshold of 7.0 were used for sequencing. mRNA was enriched using NEBNext Poly(A) mRNA Isolation Module (NEB, Ipswich, MA, USA) followed by library preparation using NEBNext® Ultra™ II Directional RNA library kit (NEB, Ipswich, MA, USA). Next-generation sequencing was conducted at the McMaster Genomics Facility, Farncombe Institute, McMaster University, using Illumina HiSeq 1500 (Illumina; San Diego, CA, USA). Samples were randomly distributed across lanes of a HiSeq Rapid v2 flow cell to eliminate lane-specific effects and single-end 50 bp reads were generated at 12.5 million clusters per sample.

treatment_protocol: Animals were grouped based on their AFP levels so there were no differences between groups and were then injected with AAV intravenously (AAV8-YFP or AAV8-TTR-Cre).

value: Liver Tumor

tag: strain

tag: genetic modification

value: Acly tm1.1Welk

tag: timepoint

value: 4 weeks

tag: treatment


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and TIGIT, biol rep 3

city: Saarbruecken

first: Nils

last: Piernitzki

state: Saarland

address: Campus D2 2

country: Germany

institute: INM - Leibniz Institute for New Materials

description: Library name: PANC1_TIGIT_PD1_3_countMatrix

data_processing:
Data was quality checked with FastQC Version 0.11.2
Reads were demultiplexed with samtools (v1.3.1)
Sequence reads were adaptor-trimmed (Q < 20) with Cutadapt (Version 1.4.132) using Trim Galore! (Version 0.3.3)
Reads were aligned to hg38 assembly with the grape-nf pipeline wrapping STAR (Version 2.4.0j33) and RSEM (Version 1.2.2134)
Assembly: hg38
Supplementary files format and content: tab-delimited text file include TPM and FPKM values for each sample

molecule: total RNA

growth_protocol: Cultivation of PANC-1 epithelial cells was carried out in flasks treated for cell culture at 37°C, 5% CO2 and 100% humidity. The cell line was grown in RPMI 1640 w/ L-Glutamine medium supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using the Direct-zol RNA Miniprep Kits (Zymo Research) according to the manufacturers instructions.
RNAseq libraries were prepared using 150 ng of total RNA per sample with the NEBnext Ultra II Directional RNA library kit for Illumina according to the manufacturer's recommendations.

treatment_protocol: PANC-1 cultures with a confluence of 80-90% were washed twice with PBS and detached from their respective flasks using Trypsin 0,25% - EDTA in HBSS. The cell suspension was washed with medium, pelleted and resuspended in RPMI 1640 w/ L-Glutamine medium supplemented with 1% penicillin/streptomycin and 1% fetal bovine serum (FBS). To generate hybrid tumoroids, 50,000 to 100,000 cells were mixed with untreated or protein-labelled DSLBs in untreated 96-Well Flat Bottom plates.

tag: cell line

tag: cell type

value: epithelial cells

tag: genotype

value: WT

value: synthetic cell + protein stimulation


title: Liver tumor, 4 weeks post AAV8-YFP injection, mouse 4

description: Library name: ACLY WT 4


title: nPOD_6228_multiome_MM_665_RNA_MM_657_ATAC


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_early_stg12_carpels, 21d+ (rep. 2)

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

organism: Arabidopsis thaliana

source_name: carpels

growth_protocol: All plants were grown on soil, except those used for the collection of early-stage root samples, which were grown on 0.8% plant agar plates, pH 5.8, containing ½ MS and vitamins (Duchefa M0222).

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.

tag: cultivar

value: Arabidopsis thaliana (Col-0)

value: carpels


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and TIGIT, biol rep 2

description: Library name: PANC1_TIGIT_PD1_2_countMatrix


title: Liver tumor, 4 weeks post AAV8-YFP injection, mouse 3

description: Library name: ACLY WT 3


title: nPOD_6234_multiome_MM_664_RNA_MM_656_ATAC


title: nPOD_6220_multiome_MM_662_RNA_MM_654_ATAC


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_early_stg12_carpels, 21d+ (rep. 1)


title: Liver tumor, 4 weeks post AAV8-YFP injection, mouse 2

description: Library name: ACLY WT 2


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_mature_pollen, 28d (rep. 3)

source_name: pollen

value: pollen


title: nPOD_6362_multiome_MM_661_RNA_MM_653_ATAC


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and LAG3, biol rep 3

description: Library name: PANC1_LAG3_PD1_3_countMatrix


title: Liver tumor, 4 weeks post AAV8-YFP injection, mouse 1

description: Library name: ACLY WT 1


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_mature_pollen, 28d (rep. 2)


title: Foxg1_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_4

data_processing:
Trimmomatic (version 0.39) was used to filter out low-quality reads
Reads were mapped to the mouse reference genome (mm10) with Hisat2 (version 2.1.0).
Raw read counts mapped to genes were calculated using featureCounts from Subread package (version 2.0.1).
DEG analyses were performed using DESeq2 (version 1.40.1) package with the default settings.
Significantly changed genes were identified with adjusted p value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: csv files containing normalized counts and TPM value obtained from DESeq2 package

extract_protocol:
mRNAs from the whole MOE tissues were extracted and purified with a Cell/Tissue total RNA isolation kit V2 (Vazyme, RC112-01).
Libraries were prepared with Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604-02).


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_mature_pollen, 28d (rep. 1)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and LAG3, biol rep 2

description: Library name: PANC1_LAG3_PD1_2_countMatrix


title: nPOD_6375_multiome_MM_660_RNA_MM_652_ATAC


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and LAG3, biol rep 1

description: Library name: PANC1_LAG3_PD1_1_countMatrix


title: nPOD_6229_multiome_MM_510_RNA_MM_505_ATAC


title: Foxg1_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_3


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_early_stg12_carpels, 21d+ (rep. 3)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and ICOS, biol rep 3

description: Library name: PANC1_ICOS_PD1_3_countMatrix


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_stamens, 21d+ (rep. 3)

source_name: stamens

value: stamens


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_stamens, 21d+ (rep. 2)


title: BT40X, REP2

city: San Antonio

first: Hanzhou

last: Wang

state: TX

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg38) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: hg38
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. Merged HTSeq file is similar to individual HTSeq file, first column is gene symbol, and first row is sample name, and each column with read counts from each sample.

source_name: PDX

extract_protocol:
Tumors were collected when tumor volume was 0.3~0.6 cm3.Tumor bearing mice were euthanized with CO2, tumor tissue was collected from three mice and put in 2ml cryogenic vial and flash frozen in liquid nitrogen. Tumor tissue was ground to a fine powder under liquid nitrogen in a cooled mortar and pestle. Tissue powder was transferred to dry ice-cooled cryogenic tube. Twenty to ~50mg tissue powder was measured and transferred to a precooled 1.5ml eppendorf tube, and RNA isolated by adding 1ml Trizol solution (ThermoFisher), and mixing immediately.  300l chloroform was added to the lysate mixture, and vortexed vigorously for 1min, and then left at room temperature for 5 minutes. The following procedure was performed as instructed in the manual of RNeasy Kit (QIAGEN).
The quality of total RNAs was checked by Agilent Fragment Analyzer (Agilent Technologies, Santa Clara, CA), and only samples with RQN >7 were used for subsequent mRNA-seq library preparation and sequencing. Approximately 500ng total RNA was used for stranded mRNA-seq library preparation by following the NEB Directional mRNA-seq sample preparation guide (New England Biolabs, Ipswich, MA). The first step in the workflow involved purifying poly-A containing mRNA using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched by PCR amplification to create the final RNA-seq library. RNA-seq libraries were subjected to quantification process and subsequent 100bp paired read sequencing run with Illumina NovaSeq 6000 platform at 100 bp paired-end module (Greehey Children’s Cancer Research Institute’s Genome Sequencing Facility at UTHSCSA).

value: PDX

tag: tissue type

value: X-radiation therapy resistant


title: Foxg1_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_1


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and ICOS, biol rep 2

description: Library name: PANC1_ICOS_PD1_2_countMatrix


title: BT40X, REP3


title: BT40X, REP1


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and TIGIT, biol rep 1

description: Library name: PANC1_TIGIT_PD1_1_countMatrix


title: Foxg1_Cre_Trim66_flox_homo_bulk_RNA_seq_rep_2


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_stamens, 21d+ (rep. 1)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and ICOS, biol rep 1

description: Library name: PANC1_ICOS_PD1_1_countMatrix


title: Foxg1_Cre_Trim66_flox_het_bulk_RNA_seq_rep_4


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_stamens, 21d+ (rep. 3)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CTLA4, biol rep 3

description: Library name: PANC1_CTLA4_PD1_3_countMatrix


title: BT40, REP3

value: primary model of pediatric glioma without any treatment


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_stamens, 21d+ (rep. 2)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CTLA4, biol rep 2

description: Library name: PANC1_CTLA4_PD1_2_countMatrix


title: Foxg1_Cre_Trim66_flox_het_bulk_RNA_seq_rep_2


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_stamens, 21d+ (rep. 1)


title: Foxg1_Cre_Trim66_flox_het_bulk_RNA_seq_rep_1


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_petals, 21d+ (rep. 3)

source_name: petals

value: petals


title: BT40, REP1


title: BLEO/P-03

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
PE150 high throughout data
BP_vs_BLE.deseq2.annot
Sample 9 (BLEO/PQQ)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome (UCSC GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Human prostate

growth_protocol: Human primary prostate stromal cell line (PSC27) was routinely cultured in PSCC media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) at 50 ug/ml and/or PQQ at 100 uM.

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

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Cells were allowed to stay in culture with appropriate media change until 7-10 days later when they were exposed to PQQ at 100 uM for 2-3 days, then lysed or immediately collected for lysis.

value: Human prostate

value: human primary prostate stromal cell line

value: Wild type

value: Bleomycin/PQQ


title: Trim66_KO_homo_bulk_RNA_seq_rep_5

value: Main Olfactory Epithelium (MOE)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD40L, biol rep 3

description: Library name: PANC1_CD40L_PD1_3_countMatrix


title: BLEO/P-02

description:
PE150 high throughout data
BP_vs_BLE.deseq2.annot
Sample 8 (BLEO/PQQ)


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_petals, 21d+ (rep. 2)


title: BLEO/P-01

description:
PE150 high throughout data
BP_vs_BLE.deseq2.annot
Sample 7 (BLEO/PQQ)


title: Trim66_KO_homo_bulk_RNA_seq_rep_3


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD40L, biol rep 1

description: Library name: PANC1_CD40L_PD1_1_countMatrix


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_petals, 21d+ (rep. 3)


title: BLEO-3

description:
PE150 high throughout data
BLE_vs_CTR.deseq2.annot
Sample 6 (BLEO)

value: Bleomycin


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_petals, 21d+ (rep. 1)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD27, biol rep 3

description: Library name: PANC1_CD27_PD1_3_countMatrix

value: epithelial cells


title: Trim66_KO_homo_bulk_RNA_seq_rep_2


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD27, biol rep 2

description: Library name: PANC1_CD27_PD1_2_countMatrix

value: WT


title: Trim66_KO_homo_bulk_RNA_seq_rep_1


title: BT40, REP2


title: BLEO-2

description:
PE150 high throughout data
BLE_vs_CTR.deseq2.annot
Sample 5 (BLEO)


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_petals, 21d+ (rep. 1)


title: BLEO-1

description:
PE150 high throughout data
BLE_vs_CTR.deseq2.annot
Sample 4 (BLEO)


title: Foxg1_Cre_Trim66_flox_het_bulk_RNA_seq_rep_3


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CTLA4, biol rep 1

description: Library name: PANC1_CTLA4_PD1_1_countMatrix

value: synthetic cell + protein stimulation


title: Trim66_KO_het_bulk_RNA_seq_rep_5


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD2, biol rep 3

description: Library name: PANC1_CD2_PD1_3_countMatrix


title: Trim66_KO_het_bulk_RNA_seq_rep_4


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_sepals, 21d+ (rep. 2)

source_name: sepals

value: Arabidopsis thaliana (Col-0)

value: sepals


title: CTRL-3

description:
PE150 high throughout data
BLE_vs_CTR.deseq2.annot
Sample 3 (Control)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD40L, biol rep 2

description: Library name: PANC1_CD40L_PD1_2_countMatrix


title: Trim66_KO_homo_bulk_RNA_seq_rep_4


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_sepals, 21d+ (rep. 1)


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_petals, 21d+ (rep. 2)


title: CTRL-1

description:
PE150 high throughout data
BLE_vs_CTR.deseq2.annot
Sample 1 (Control)


title: Trim66_KO_het_bulk_RNA_seq_rep_2


title: cocu_dyn, cDNA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
counts_cDNA.tsv.gz
coldata.tsv.gz
cocu_dyn

library_source: transcriptomic single cell

data_processing:
cDNA reads were aligned to ‘hg38’ genome using Ensembl 104 gene models using the STARsolo tool (v2.7.10a).
Merged samples were demultiplexed based on present single nucleotide polymorphisms (SNPs). For this purpose tools cellsnp-lite and vireo were applied.
Further analysis steps were performed using R (v4.2.0). Multiple Bioconductor (v3.15) packages including DropletUtils (v1.16.0), scDblFinder (v1.10.0), scran (v1.24.1), scater (v1.24.0), scuttle (1.6.2) and batchelor (v1.12.3) were applied for the further analysis of the gene expression of remaining cells, mostly following the steps of the workflow presented at https://bioconductor.org/books/release/OSCA/.
Assembly: hg38
Supplementary files format and content: Tab-separated values files: counts_cDNA.tsv.gz with cDNA read counts, coldata.tsv.gz with sample assignment, corrected coordinates of principal components, UMAP coordinates, sample demultiplexing, cluster assignment.

source_name: Cartilage

growth_protocol: Cartilage and subchondral tissue microconstructs were achieved embedding hACs or bmMSCs into an enzymatically crosslinkable and degradable PEG based hydrogel. Appropriate differentiation medium was injected into the dedicated channels. Osteochondral medium (OCM) was constituted by DMEM (Sigma–Aldrich) containing, 4.5 mg ml−1 d-glucose, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 mM HEPES buffer,100 U ml−1 penicillin, 100 μg ml−1 streptomycin, 0.29 mg ml−1 l-glutamine, 1.0 mg/ml insulin, 0.55 mg/ml human transferrin, 0.5 μg/ml sodium selenite, 50 mg/ml bovine serum albumin, 470 μg/ml linoleic acid, and 1.25 % of human serum albumin and supplemented with 0.1 mM ascorbic acid 2-phosphate, 10-4 mM dexamethasone, 10 ng ml-1 TGF-β3.  And beta-Glycerophosphate 10 mM (β-Gly, Sigma Aldrich).

extract_protocol:
hACs from single cultures and osteochondral constructs (i.e. constructs comprehensive of both hACs and bmMSCs) were retrieved from microfluidic devices and enzymatically digested on a shaker in a solution of 0.15% type II collagenase (Worthington Biochemical Corporation) in DMEM (300 µl per construct) for 30-45 minutes.
Cells from each sample were loaded on a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA, USA). Single-cell capture, and cDNA and library preparation were performed with a Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein and Cell Multiplexing from 10x Genomics (User Guide CG000390, Rev B) according to the manufacturer’s instructions.

treatment_protocol: After 14 days of maturation, constructs were subjected to mechanical loading for further 7 days. Two 2-hours stimulation cycles (1Hz, 50% duty cycle) were applicated each day with four hours stop period in-between. Culture medium was changed every second day. Static constructs were adopted as controls.

value: Cartilage

value: articular chondrocytes

tag: culture type

value: co-culture with mineralized tissue (bmMSCs)

tag: mechnaical loading

value: yes


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD2, biol rep 1

description: Library name: PANC1_CD2_PD1_1_countMatrix


title: Trim66_KO_het_bulk_RNA_seq_rep_1


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_sepals, 21d+ (rep. 2)


title: cocu_st, cDNA

description:
counts_cDNA.tsv.gz
coldata.tsv.gz
cocu_st

value: no


title: PANC-1 hybrid tumoroids, dsLBs with PD1, biol rep 2

description: Library name: PANC1_PD1_2_countMatrix


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_sepals, 21d+ (rep. 1)


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg15_sepals, 21d+ (rep. 3)


title: E14.5

city: Hong Kong

first: Wai-Yee

last: Chan

address: Rm 123, LKS integrated Biomedical Sciences Building

department: School of Biomedical Sciences

institute: The Chinese University of Hong Kong

data_processing:
The raw data were processed with the Seqsense Analysis Toolkit which was packed into a Docker container: bioraddbg/2d-complete-all:latest.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts, RPKM and TPM of each library.

source_name: Embryonic gonad

growth_protocol: Animal experiments followed protocols approved by the Animal Experiment Ethics Committee (AEEC) of The Chinese University of Hong Kong (CUHK) and the guidelines of Animals (Control of Experiments) Ordinance (Cap. 340) licensed by the Department of Health of HK SAR. Mice were housed at CUHK Laboratory Animal Services Centre with a 12-hour light and dark cycle, temperature range of 22-24°C, and ad libitum access to food

extract_protocol:
total RNAs were extracted with Trizol reagent (Invitrogen)
Libraries were prepared with SEQuoia Complete Stranded RNA Library Prep Kit (BioRad #17005726) and SEQuoia Dual Indexed Primers Set (BioRad #12011928) and rRNA Depletion Kit (Human/Mouse/Rat) with RNA Sample Purification Beads (NEB #E6350S) according to the manufacturer's manual.

value: Embryonic gonad

value: mixed XX and XY


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD27, biol rep 1

description: Library name: PANC1_CD27_PD1_1_countMatrix


title: ch_dyn, cDNA

description:
counts_cDNA.tsv.gz
coldata.tsv.gz
ch_dyn

value: single culture


title: ch_st, cDNA

description:
counts_cDNA.tsv.gz
coldata.tsv.gz
ch_st


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg15, 21d+ (rep. 3)

source_name: flowers

value: flowers


title: PANC-1 hybrid tumoroids, dsLBs with PD1, biol rep 1

description: Library name: PANC1_PD1_1_countMatrix


title: E13.5


title: CTRL-2

description:
PE150 high throughout data
BLE_vs_CTR.deseq2.annot
Sample 2 (Control)

value: Human prostate

value: human primary prostate stromal cell line

value: Wild type


title: PANC-1 hybrid tumoroids, non-functionalized dsLBs, biol rep 3

description: Library name: PANC1_plain_dsLB_3_countMatrix

value: epithelial cells

value: synthetic cell stimulation


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg15, 21d+ (rep. 2)


title: PANC-1 hybrid tumoroids, dsLBs with PD1 and CD2, biol rep 2

description: Library name: PANC1_CD2_PD1_2_countMatrix

value: WT

value: synthetic cell + protein stimulation


title: E12.5


title: Trim66_KO_het_bulk_RNA_seq_rep_3

value: Main Olfactory Epithelium (MOE)


title: F19B2.5.2

city: Boston

first: Long-Wen

last: Zhao

state: Massachusetts

address: 77 Avenue  Louis Pasteur, NRB Room 266

department: Genetics

institute: Harvard Medical School

description:
Library name: S5
cDNA (RT-PCR amplicon)

data_processing:
Reads were mapped using Minimap2 (V 2.22 --r1109dirty), and isoform identification was performed using IsoQuant (V 3.5.0).
Assembly: The reference FASTA files were provided as supplementary files.
Supplementary files format and content: IsoQuant output (.bed.gz, transcript isoforms).

organism: Caenorhabditis elegans

source_name: C. elegans animals

growth_protocol: C. elegans strains were maintained at 20 °C on nematode growth medium (NGM) plates seeded with Escherichia coli (E. coli) OP50. HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, 11995-065) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10437-028). All cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNAs were extracted using RNA Clean & Concentrator-5 (Zymo, R1014), followed by DNase treatment to eliminate genomic DNA contamination.
Total RNA was reverse transcribed using Induro® Reverse Transcriptase (NEB, M0681L) with Random Primer Mix. cDNA was amplified using primers covering the SOS splicing events.

value: C. elegans animals


title: PANC-1 hybrid tumoroids, non-functionalized dsLBs, biol rep 2

description: Library name: PANC1_plain_dsLB_2_countMatrix


title: E11.5


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg15, 21d+ (rep. 1)

value: Arabidopsis thaliana (Col-0)


title: RNA-Seq of Arabidopsis thaliana (Col-0): floral_organ_stg12_sepals, 21d+ (rep. 3)

value: sepals


title: PANC-1 hybrid tumoroids, dsLBs with PD1, biol rep 3

description: Library name: PANC1_PD1_3_countMatrix


title: wago_2

description:
Library name: S4
cDNA (RT-PCR amplicon)


title: PANC-1 hybrid tumoroids, non-functionalized dsLBs, biol rep 1

description: Library name: PANC1_plain_dsLB_1_countMatrix


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg12, 21d+ (rep. 3)


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg12, 21d+ (rep. 2)


title: H3

first: Youqin

last: Zhang

institute: NewsMORE+  Shanghai Institute of Immunology

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were aligned to the mouse reference genome (version mm10) by using Hisat2 RNASeq alignment software.
Quantitated relative mRNA expression levels (FPKM) were calculated based on exon regions using Cufflinks and the mm10 reference genome annotations.
Assembly: mm10
Supplementary files format and content: comma-separated values files include readcounts (column J-M) and FPKM values (column N-Q) for each Sample and every gene

source_name: VAT ILC2

extract_protocol:
Total RNA from sorted VAT ILC2s of wild-type mice fed with normal-diet and high-fat-diet was extracted by Trizol reagent.  RNA quality was examined with an Agilent Bioanalyzer 2100 (Agilent). The SMART-Seq HT Kit (Takara Bio USA, Inc) was used to generate high-quality, full-length cDNA.
Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol.

tag: Sex

value: male

tag: age

value: 14-week old

value: epididymal visceral adipose tissue

value: high-fat-diet

value: wild-type


title: unc-22_r750

description:
Library name: S2
cDNA (RT-PCR amplicon)


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg12, 21d+ (rep. 1)

value: flowers


title: H2


title: PANC-1 tumoroids, no dsLBs, biol rep 2

description: Library name: PANC1_dsLB_free_2_countMatrix

value: untreated


title: H1


title: W07G4.3

description:
Library name: S1
cDNA (RT-PCR amplicon)


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg10_11, 21d+ (rep. 3)


title: Y37D8A.6_pkP516

description:
Library name: S23
cDNA (RT-PCR amplicon)

source_name: WT C. elegans animals

value: WT C. elegans animals


title: PANC-1 tumoroids, no dsLBs, biol rep 1

description: Library name: PANC1_dsLB_free_1_countMatrix


title: N4

value: normal-diet


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg10_11, 21d+ (rep. 2)


title: ChIP_RNAPIISer2P_ETOP

city: Seville

first: Silvia

last: Jimeno-González

address: Avda. Américo Vespucio 24

department: Genética

country: Spain

institute: Universidad de Sevilla

description: Library name: ChIP_RNAPIISer2P_ETOP

data_processing:
NextSeq Control Software v4.2.0 was used for basecalling
FastQ files from libraries were de-multiplexed and trimmed using Illumina FastQ Generation (version 1.0.0) from BaseSpace using default parameters.
Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) and the April 2006 D. melanogaster genome assembly (BDGP R5/dm3) using Bowtie (v.1.2.0) with parameters -m1--best.
PCR duplicates were removed with RmDup (v.12.0.1) with default parameters.
Assembly: Genome coverage was calculated with ‘Genome Coverage’ (v.2.30.0) from bedtools using default parameters but normalizing reads to Counts per million (CPM).
Supplementary files format and content: hg38
Supplementary files format and content: Bedgraph files include RPE1 CPM values for each sample.

source_name: h-TERT RPE-1

growth_protocol: RPE-1 cels were grown in Dubelcco’s Modified Eagle’s Medium (DMEM) F-12 supplemented with 50 units ml-1 penicillin, 50 units ml-1 streptomycin and 10% Fetal Bovine Serum (FBS). Cells were cultured at 37ºC in 5% CO2 atmosphere.

extract_protocol:
RPE-1 cells were crosslinked with 1% formaldehyde for 10 minutes at 37ºC. Crosslinking reaction was quenched with 0.136 M glycine for 5 minutes at RT. Chromatin was sonicated using Bioruptor Pico (Diagenode) to obtain chromatin fragment size of 250-500 bp. Chromatin associated to each RNAPII Ser2P was obtained by incubating sonicated chromatin with the corresponding antibody. DNA was purified using QIAquick® PCR Purification Kit (QIAGEN).
ChIPmentation was carried out using Tn5A Enzyme during the  and libraries were amplified using NEBNext® High-Fidelity 2X PCR Master Mix (NEB). Libraries were purified with Sera-Mag Select Beads (CYTIVA).

treatment_protocol: RPE-1 cells were serum starved by 48h incubation in the same medium, but with reduced 0.1% FBS content. Then, cells were treated with 50µM etoposide for 30 minutes.

value: h-TERT RPE-1

value: Immortalized retinal pigment epithelial cells

tag: chip antibody

value: RNA polymerase II B1 subunit (phospho-CTD Ser2) (Sigma Aldrich, 04-1571)

tag: cell cycle

tag: etoposide treatment

value: Yes


title: ChIP_RNAPIISer2P_DMSO

description: Library name: ChIP_RNAPIISer2P_DMSO

value: No


title: N3

tag: tissue


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg10_11, 21d+ (rep. 1)


title: Tc1_Ngfp_invitro

description:
Library name: S17
cDNA (RT-PCR amplicon)

source_name: in vitro RNA control

value: in vitro RNA control


title: Tc1_NmScarlet

description:
Library name: S22
cDNA (RT-PCR amplicon)

source_name: WT C. elegans animals with a Tc1::NmScarlet reporter plasmid


title: N2

tag: strain


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg9, 21d+ (rep. 3)

value: Arabidopsis thaliana (Col-0)


title: H4


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg9, 21d+ (rep. 2)


title: AD-MSC, Electrically stimulated, 100 Hz, 2h, rep3

city: Gwangju

first: Seungjun

last: Lee

address: 123 cheomgan gwagiro

department: MSE

country: South Korea

institute: Gwangju institute of science and technology

description: Library name: TEST3

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Adipose

growth_protocol: hAD-MSCs (PromoCell, Heidelberg, Germany) were maintained in MEM-α (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% antibiotic-antimycotic (100×, Gibco) in an incubator with 5% CO2 at 37ºC used at passage number 6. HUVECs (Gibco) were cultured in endothelial culture medium (ECM, SceinCell, CA, USA) supplemented with 5% FBS, 1% penicillin-streptomycin, and 1% endothelial cell growth supplement in an incubator with 5% CO2 at 37ºC and used at passage number 6.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: hAD-MSCs were seeded onto sterile stainless-steel plates (3.8 × 2.8 × 0.7 cm) at a density of 2×104 cells/cm2 and incubated for 24 h at 37ºC with 5% CO2. The cells were randomly divided into control (unstimulated) and two ES groups. A two-electrode system was employed, in which a platinum mesh (5 × 10 mm) and the cell-seeded stainless-steel plate served as the counter and working electrodes, respectively, using a multichannel potentiostat (VersaSTAT3, Princeton Applied Research, Oakridge, TN, USA). Stimulation was applied at 0.3 V, 5 ms pulse duration, and frequencies of 1 Hz (LF) or 100 Hz (HF) for 2 h, according to previous studies with some modifications 44–47.

value: Adipose

value: hAD-MSC

value: Mesenchymal stem  cell

value: WT

value: Electrical stim. (100 Hz)

tag: batch


title: ced-4_n1416

description:
Library name: S3
cDNA (RT-PCR amplicon)


title: AD-MSC, Electrically stimulated, 100 Hz, 2h, rep2

description: Library name: TEST2


title: Tc1_Ngfp_WT

description:
Library name: S16
cDNA (RT-PCR amplicon)


title: N1

value: male

value: 14-week old

value: epididymal visceral adipose tissue

value: wild-type


title: RNA-Seq of Arabidopsis thaliana (Col-0): flower_stg9, 21d+ (rep. 1)

value: flowers


title: PANC-1 tumoroids, no dsLBs, biol rep 3

description: Library name: PANC1_dsLB_free_3_countMatrix

value: epithelial cells

value: untreated


title: AD-MSC, rep3

description: Library name: CTL3


title: glc-1_pk54

description:
Library name: S14
cDNA (RT-PCR amplicon)


title: msh-2_ev679

description:
Library name: S15
cDNA (RT-PCR amplicon)


title: AD-MSC, Electrically stimulated, 100 Hz, 2h, rep1

description: Library name: TEST1


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence, 28d (rep. 3)

source_name: inflorescence apex

value: inflorescence apex


title: AD-MSC, rep2

description: Library name: CTL2


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence, 28d (rep. 2)


title: akap-17(-)_replicate3

description: Library name: S6

data_processing:
Nextflow (V24.04.4)-based nf-core/rnasplice pipeline (V1.0.4)
Read quality was assessed using FastQC (V0.12.1), and low-quality reads were trimmed or removed using Trim Galore (V0.6.7).
Clean reads were aligned to the C. elegans genome (WBcel235) using STAR (V2.7.9a).
Aligned reads were analyzed for alternative splicing events using rMATS (V4.1.2).
Assembly: WBcel235
Supplementary files format and content: rMATS output (alternative splicing events in TXT format, including JC and JCEC counts for A3SS, A5SS, MXE, RI, and SE events).

growth_protocol: C. elegans strains were maintained at 20 °C on nematode growth medium (NGM) plates seeded with Escherichia coli (E. coli) OP50.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen, 15596026), and rRNA-depleted total RNA was used for library construction.
Libraries were prepared using the KAPA mRNA HyperPrep Kit (KR1352-v4.17) following the manufacturer's protocol.


title: cct-1_pk58

description:
Library name: S13
cDNA (RT-PCR amplicon)


title: AD-MSC, rep1

description: Library name: CTL1


title: akap-17(-)_replicate1

description: Library name: S4


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence_clv1, 21d+ (rep. 3)


title: Tc1-traD_ITRscr_rsd-3_invitro

description:
Library name: S12
cDNA (RT-PCR amplicon)


title: Tc1-traD_rsd-3_invitro

description:
Library name: S11
cDNA (RT-PCR amplicon)


title: WT_replicate2

description: Library name: S2


title: WT_replicate3

description: Library name: S3


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence, 28d (rep. 1)


title: WT_replicate1

description: Library name: S1


title: Tc1-traD_ITRscr_rsd-3_WT

description:
Library name: S10
cDNA (RT-PCR amplicon)


title: hRPC_Female2

city: Firenze

first: Giulia

last: Carangelo

address: Viale Pieraccini 6

country: Italy

institute: University of Florence

description: Library name: hRPC_female 2

data_processing:
Basecall performed with cellranger mkfastq v8.0.1
Single cell feature counts performed with cellranger count v8.0.1
Reference genome alignment performed with STAR v2.7.11b
Assembly: GRCh38
Supplementary files format and content: All tab separated value files

source_name: kidney

growth_protocol: Human progenitor cells were isolated from human kidney tissues, cultured in conventional medium, and processed before reaching 70% confluency

extract_protocol:
The single cell suspension with 95% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions

value: kidney

value: hRPC

value: Primary cell culture of renal progenitor from kidney


title: hRPC_Female1

description: Library name: hRPC_female 1


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence_clv1, 21d+ (rep. 2)

value: Arabidopsis thaliana (Col-0)


title: Tc1-traD_rsd-3_WT

description:
Library name: S9
cDNA (RT-PCR amplicon)


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence_clv1, 21d+ (rep. 1)


title: mRNAseq_grh1::degron_Auxin_31h_Rep2

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: 3610F23

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR package in R with splicedAlignement = TRUE, using the aligner HISAT2including an exon-exon junction database. Gene expression levels were quantified using the qCount() function. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

source_name: Whole animal

growth_protocol: Synchronized L1 animals were grownat at 20oC and at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Following the addition of treatments, animals were collected every hour (over 12-13 hours), and washed 3 times with M9, then resuspended in Trizol and flash frozen in liquid N2.  Samples were stored at -80 until further processing. Note that in replicate Rep1 ethanol and auxin were added at 21h of development while in Rep2 this was done at 20h.

extract_protocol:
For RNA extraction, samples were submitted to 4 rounds of freeze-thawing, and then RNA was purified using the Direct-zol RNA microcprep kit (R2062, Zymo Research) according to manufacturers instructions.
Libraries were prepared using the Illumina Stranded mRNA-seq protocol.

value: Whole animal

value: Auxin

tag: time of_treatment

tag: time of_larval_development


title: lin-41_ma104

description:
Library name: S8
cDNA (RT-PCR amplicon)


title: hRPC_Male

description: Library name: hRPC_male

tag: cell line


title: akap-17(-)_replicate2

description: Library name: S5


title: mRNAseq_grh1::degron_Auxin_30h_Rep2

description: Library name: 3610F22

tag: treatment


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence, 21d (rep. 3)


title: R3_RNAseq_ETOP_T20

data_processing:
NextSeq Control Software v4.2.0 was used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQ Generation based on bcl2fastq with default parameters. Mapping and subsequent analysis of the data were done using Europe Reads were mapped to human genome assembly (GRCh38/hg38) using ‘HISAT2’ with default parameters but specifying --rna-strandness RF and paired end parameters --fr. To calculate reads in each gene, “feature counts” tool was used with the Ensembl gene table (Version 108).
Assembly: hg38
Supplementary files format and content: featureCounts files with exon counts were uploaded for each sample.

source_name: h-TERT RPE-1 cells

growth_protocol: RPE-1 cells were grown in Dubelcco’s Modified Eagle’s Medium (DMEM) F-12 supplemented with 50 units ml-1 penicillin, 50 units ml-1 streptomycin and 10% Fetal Bovine Serum (FBS). Cells were cultured at 37ºC in 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using RNAeasy Mini KIT (QIAGEN) and then treated with TURBO DNA-free kit (INVITROGEN).
Libraries were constructed using TrueSeq Stranded mRNA (Illumina)

treatment_protocol: RPE-1 cells were serum starved by 48h incubation in the same medium, but with reduced 0.1% FBS content. Then, cells were treated with 50µM etoposide for 30 minutes. Using 10µM  triptolide, transcription was repressed and RNA was collected at different times. Three independient replicates were performed.

value: h-TERT RPE-1 cells

tag: cell type

value: Immortalized retinal pigment epithelial cells

value: Yes

tag: time point


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence, 21d (rep. 2)

tag: cultivar


title: R3_RNAseq_ETOP_T0


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_inflorescence, 21d (rep. 1)


title: mRNAseq_grh1::degron_Auxin_29h_Rep2

description: Library name: 3610F21

tag: genotype


title: dpy-19_n1347

description:
Library name: S7
cDNA (RT-PCR amplicon)


title: bli-1_gg881

description:
Library name: S6
cDNA (RT-PCR amplicon)


title: Tc1_rsd-3_invitro

description:
Library name: S4
cDNA (RT-PCR amplicon)

value: in vitro RNA control


title: mRNAseq_grh1::degron_Auxin_28h_Rep2

description: Library name: 3610F20


title: R3_RNAseq_DMSO_T20

value: No


title: mRNAseq_grh1::degron_Auxin_26h_Rep2

description: Library name: 3610F18


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 14d (rep. 2)

source_name: vegetative apex

value: vegetative apex


title: rsd-3_invitro

description:
Library name: S5
cDNA (RT-PCR amplicon)


title: R3_RNAseq_DMSO_T40


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 14d (rep. 1)


title: Tc1_rsd-3_smg-2(-)

description:
Library name: S2
cDNA (RT-PCR amplicon)


title: rsd-3_pk2010

description:
Library name: S3
cDNA (RT-PCR amplicon)


title: R2_RNAseq_ETOP_T40


title: R3_RNAseq_DMSO_T0


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 10d (rep. 3)


title: R3_RNAseq_ETOP_T40


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 10d (rep. 2)


title: mRNAseq_grh1::degron_Auxin_27h_Rep2

description: Library name: 3610F19


title: mRNAseq_grh1::degron_Auxin_23h_Rep2

description: Library name: 3610F15


title: mRNAseq_grh1::degron_Auxin_25h_Rep2

description: Library name: 3610F17


title: Tc1_rsd-3_WT

description:
Library name: S1
cDNA (RT-PCR amplicon)


title: R2_RNAseq_ETOP_T0


title: mRNAseq_grh1::degron_Auxin_24h_Rep2

description: Library name: 3610F16


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 14d (rep. 3)


title: Eristalis_tenax_eggs_sRNA_rep2

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: Eristalis_tenax_eggs_sRNA_rep2
Small RNA sequencing from Eristalis tenax eggs replicate 2

library_source: other

data_processing:
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting. The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses. Trimmed reads were first mapped to infrastructural RNAs including ribosomal RNA, small nuclear RNA, small nucleolar RNA, microRNA, and transfer RNA, which are annotated in their respetive genomes or genomes from closely related species using bowtie v1.2.3 allowing up to one mismatch. Reads that did not map to these infrastructural RNAs were subsequently mapped to the corresponding species' genomes. The sam file was further processed to the bam file, then to the bed file using samtools/1.19 and bedtools/2.28.0. The coverage of uniquely mappable reads on 0.5kb genomic tiles was measured using bedtools intersect.
Assembly: GCA_905231855.2_idEriTena2.2 for Eristalis tenax GCF_016617805.1_CSIRO_BtryS06_freeze2 for Bactrocera tryoni GCF_002204515.2_AaegL5.0 for Aedes aegypti GCF_013141755.1_UCI_ANSTEP_V1.0 for Anopheles stephensi GCA_032399595.1_TetCarb_2.0 for Tetragonula carbonaria GCA_031308135.1_ado_dt_MfTpo_fix for Acheta domesticus GCA_964035755.1_iqTelOcea1 for Teleogryllus oceanicus
Supplementary files format and content: *_genomic-tile-coverage.txt: coverage of uniquely mappable piRNA (>22nt) reads on individual 0.5kb genomic tiles <tile position with genomic coodinate and strand> <coverage per 1 million piRNA reads>

molecule: other

organism: Eristalis tenax

source_name: eggs

growth_protocol: Insects were kept at standard conditions at room temperature.

extract_protocol:
Small RNA sequencing was performed on ovaries and eggs collected from a variety of insects. About 10 pairs of ovaries from 1 week to up to 3 months old females and eggs within up to 8 hours of egg laying have been collected per replicate. Total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
Small RNAs were first size-selected from the total RNA by 12% w/v UREA-PAGE using radio-labelled 19mer (5′-CGUACGCGGGUUUAAACGA) and 35mer (5'-CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU) spikes, and oxidised using sodium periodate. The oxidised small RNAs were further size-selected by PAGE. The size-selected oxidised small RNAs were ligated to the 3' adapter 5rApp/NNNNAGATCGGAAGAGCACACGTCT/3ddC, and then to the 5' adapter ACACUCUUUCCCUACACGACGCUCUUCCGAUCUNNNN where Ns are randomised. The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the RT primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT. The library was amplified using KAPA LongRange DNA polymerase (Sigma) with a universal TruSeq forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcode-containing TruSeq reverse primer (e.g. CAAGCAGAAGACGGCATACGAGATxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where xxxxxx were the barcode).

value: eggs

value: mixed

value: wild type

value: oxidized

value: 0 - 1 hour old


title: R2_RNAseq_ETOP_T20


title: R2_RNAseq_DMSO_T40


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 10d (rep. 1)


title: mRNAseq_grh1::degron_Auxin_21h_Rep2

description: Library name: 3610F13


title: Eristalis_tenax_eggs_sRNA_rep1

description:
Library name: Eristalis_tenax_eggs_sRNA_rep1
Small RNA sequencing from Eristalis tenax eggs replicate 1


title: R2_RNAseq_DMSO_T20


title: mRNAseq_grh1::degron_EtOH_31h_Rep2

description: Library name: 3610F11

value: EtOH


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 7d (rep. 3)


title: Eristalis_tenax_ovaries_sRNA_rep2

description:
Library name: Eristalis_tenax_ovaries_sRNA_rep2
Small RNA sequencing from Eristalis tenax ovaries replicate 2

source_name: ovaries

value: ovaries

value: female

value: 3 months old


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 7d (rep. 2)

value: Arabidopsis thaliana (Col-0)


title: R2_RNAseq_DMSO_T0


title: Eristalis_tenax_ovaries_sRNA_rep1

description:
Library name: Eristalis_tenax_ovaries_sRNA_rep1
Small RNA sequencing from Eristalis tenax ovaries replicate 1


title: RNA-Seq of Arabidopsis thaliana (Col-0): apex_vegetative, 7d (rep. 1)


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_stg12_equiv_stamens, 32d (rep. 3)

organism: Brachypodium distachyon

source_name: stamens

value: Brachypodium distachyon (Bd21)

value: stamens


title: R1_RNAseq_ETOP_T40

value: h-TERT RPE-1 cells

value: Immortalized retinal pigment epithelial cells


title: RNA-Seq of Arabidopsis thaliana (Col-0): cauline_leaves, 24d (rep. 3)

source_name: leaf

value: leaf


title: mRNAseq_grh1::degron_EtOH_29h_Rep2

description: Library name: 3610F9

value: Whole animal


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_stg12_equiv_stamens, 32d (rep. 2)


title: R1_RNAseq_ETOP_T20

value: Yes


title: mRNAseq_grh1::degron_Auxin_22h_Rep2

description: Library name: 3610F14

value: Auxin


title: mRNAseq_grh1::degron_EtOH_28h_Rep2

description: Library name: 3610F8


title: RNA-Seq of Arabidopsis thaliana (Col-0): cauline_leaves, 24d (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): cauline_leaves, 24d (rep. 1)


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_stg12_equiv_stamens, 32d (rep. 1)


title: mRNAseq_grh1::degron_EtOH_27h_Rep2

description: Library name: 3610F7


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_stg12_equiv_carpels, 32d (rep. 3)

source_name: carpels

value: carpels


title: R1_RNAseq_DMSO_T40

value: No


title: mRNAseq_grh1::degron_EtOH_26h_Rep2

description: Library name: 3610F6


title: R1_RNAseq_ETOP_T0


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_senescing, 35d (rep. 3)


title: mRNAseq_grh1::degron_EtOH_25h_Rep2

description: Library name: 3610F5


title: R1_RNAseq_DMSO_T20


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_senescing, 35d (rep. 2)


title: R1_RNAseq_DMSO_T0


title: mRNAseq_grh1::degron_EtOH_30h_Rep2

description: Library name: 3610F10


title: mRNAseq_grh1::degron_EtOH_24h_Rep2

description: Library name: 3610F4


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_mature_pollen, 32d (rep. 3)

source_name: pollen

value: pollen


title: meRIP_INPUT_ETOP

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using FASTQ Generation based on bcl2fastq with default parameters. Mapping and subsequent analysis of the data were done using Europe Galaxy Server. Reads were mapped to December 2013 human genome assembly (GRCh38/hg38) and to Saccharomyces cerevisiae genome SacCer3 (GCA_000146045.2) using STAR (Version 2.7.11a) with default parameters for each specie.
Genome Coverage of the ratio of each m6A/INPUT BAM pair was calculated using bamCompare (Version 3.5.4) from deepTools with default parameters but establishing 5bp of bin size and  --skipNAs and --skipZeroOverZero parameters. Mapped reads were scaled using a Spike-In factor based on the number of uniquely mapped reads to S. cerevisiae genome.  The mean of bigwigs from independent replicates were generated using bigwigCompare (Version 3.5.4) from deepTools.
Finally, bigwig files were converted to bedgraph using bigWigtoBedGraph tool (Version 312) from UCSC.
Assembly: hg38
Supplementary files format and content: Bedgraph files with the m6A/INPUT coverage

source_name: hTert RPE-1

extract_protocol:
RNA  was extracted using Trizol (Ambion, 15596926) following the instructions provided by the manufacturer. mRNA was purified using GenElute mRNA Miniprep Kit (Sigma, MRN70-1KT) following the manufacturer’s instructions. Then, mRNA purified was treated with TURBO DNase (Invitrogen, AM2238) following the manufacturer’s protocol. After that, mRNA was precipitated. To perform the meRIP, it was used the EpiQuik ™ CUT&RUN m6A RNA Enrichment (MeRIP) Kit (EpigenTek, P9018-12).
The libraries for meRIP-seq were done following the manufacturer’s protocol of the EpiNext™ CUT&RUN RNA m6A-Seq Kit (EpigenTek, P9016-12) and a spike-in from yeast was used as a control to normalize meRIP sequencing.

treatment_protocol: For meRIPseq, RPE-1 cells were serum starved by 48h incubation in the same medium, but with reduced 0.1% FBS content. Then, cells were treated with 50µM etoposide for 30 minutes.

value: hTert RPE-1

tag: antibody

value: YES


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_mature_pollen, 32d (rep. 2)


title: meRIP_INPUT_DMSO

value: NO


title: mRNAseq_grh1::degron_EtOH_23h_Rep2

description: Library name: 3610F3

value: EtOH


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_9+10, 27d (rep. 3)


title: mRNAseq_grh1::degron_EtOH_22h_Rep2

description: Library name: 3610F2


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_9+10, 27d (rep. 2)


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_mature_pollen, 32d (rep. 1)


title: meRIP_m6A_ETOP

value: m6A antibody


title: mRNAseq_grh1::degron_EtOH_21h_Rep2

description: Library name: 3610F1


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_9+10, 27d (rep. 1)

value: Arabidopsis thaliana (Col-0)


title: RNA-Seq of Brachypodium distachyon (Bd21): floret_w_anthers, 32d (rep. 3)

source_name: flowers

value: Brachypodium distachyon (Bd21)

value: flowers


title: RNA-Seq of Brachypodium distachyon (Bd21): floret_w_anthers, 32d (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_5+6, 17d (rep. 3)


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_stg12_equiv_carpels, 32d (rep. 2)


title: mRNAseq_grh1::degron_Auxin_31h_Rep1

description: Library name: 3535F11


title: meRIP_m6A_DMSO


title: ChIP_METTL3_ETOP

data_processing:
NextSeq Control Software v4.2.0 was used for basecalling
FastQ files from libraries were de-multiplexed and trimmed using Illumina FastQ Generation (version 1.0.0) from BaseSpace using default parameters.
Mapping and subsequent analysis of the data were done using Europe Galaxy Server. For ChIPseq RNAPII , reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) using Bowtie (v.1.2.0) with parameters -m1--best. For ChIPseq METTL3, reads were mapped to the December 2013 human genome assembly (GRCh38/hg38) using Bowtie2 with default parameters.
PCR duplicates were removed with RmDup (v.12.0.1) with default parameters.
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
Assembly: For ChIPseq RNAPII, genome coverage was calculated with ‘Genome Coverage’ (v.2.30.0) from bedtools using default parameters but normalizing reads to Counts per million (CPM). For ChIPseq METTL3, bamCoverage from deepTools by default was used to calculate genome coverage.
Supplementary files format and content: hg38
Supplementary files format and content: Bedgraph files include RPE1 CPM values for each sample.

source_name: h-TERT RPE-1

extract_protocol:
RPE-1 cells were crosslinked with 1% formaldehyde for 10 minutes at 37ºC. In METTL3 ChIPseq, double-crosslinking was performed by also adding DSS (disuccinimidyl suberate) in a final concentration of 5 µM in PBS for 5 minutes at 37ºC before formaldehyde addition. Crosslinking reaction was quenched with 0.136 M glycine for 5 minutes at RT. Chromatin was sonicated using Bioruptor Pico (Diagenode) to obtain chromatin fragment size of 250-500 bp. Chromatin associated to each RNAPII was obtained by incubating sonicated chromatin with the corresponding antibody. DNA was purified using QIAquick® PCR Purification Kit (QIAGEN). Two independient replicates were performed for RNAPII ChIPseq and only one for METTL3 ChIPseq.
ChIPmentation was carried out using Tn5A Enzyme during the  and libraries were amplified using NEBNext® High-Fidelity 2X PCR Master Mix (NEB). Libraries were purified with Sera-Mag Select Beads (CYTIVA).

value: h-TERT RPE-1

value: METTL3/MT-A70 Polyclonal Antibody (Bethyl Laboratories, A301-568A)


title: mRNAseq_grh1::degron_Auxin_30h_Rep1

description: Library name: 3535F10


title: RNA-Seq of Brachypodium distachyon (Bd21): floret_w_anthers, 32d (rep. 1)

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_5+6, 17d (rep. 2)

value: leaf


title: ChIP_METTL3_DMSO

value: Immortalized retinal pigment epithelial cells


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_5+6, 17d (rep. 1)


title: RNA-Seq of Brachypodium distachyon (Bd21): floral_organ_stg12_equiv_carpels, 32d (rep. 1)


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_senescing, 35d (rep. 1)


title: RNA-Seq of Brachypodium distachyon (Bd21): lateral_spikelet_meristem, 18-20d (rep. 3)

value: inflorescence apex


title: ChIP_RNAPII_ETOP

value: Rpb1 NTD (D8L4Y) (Cell Signaling Technology, Cat No. 14958; RRID:AB_2687876)

value: Yes


title: mRNAseq_grh1::degron_Auxin_28h_Rep1

description: Library name: 3535F8

value: Whole animal

value: Auxin


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2_leaf_tip, 10d (rep. 3)


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2_leaf_tip, 10d (rep. 2)


title: plate-based Smartseq2 scRNA-seq

first: Julia

last: Frede

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
For plate-based scRNA-sequencing adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5'.  Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline aligning to the hg19 genome build.
For plate-based scRNA-sequencing adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5'.  Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Assembly: hg19
Supplementary files format and content: Aggregated 10x Genomics output files with raw counts per feature (gene expressoin and feature barcoding) for all individual cells: CITE-seq_GEXFB_raw_count_matrix.csv
Supplementary files format and content: Smartseq2 (plate-based scRNA-Seq): htseq count matrix with raw counts for all individual cells: Unfiltered_count_matrix_Smartseq2.txt

source_name: Bone marrow/peripheral blood

extract_protocol:
Single cells were directly sorted into 96 well plates containing TCL buffer
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.
For plate-based scRNA-Seq, single T cells were directly sorted into 96 well plates containing TCL buffer.
Library was performed according to the manufacter’s instructions (single cell 5’ protocol, 10x Genomics). For plate-based scRNA-Seq, full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

value: Bone marrow/peripheral blood

value: T cells/ CAR-T cells

value: CAR-T

tag: molecule subtype

value: mRNA


title: RNA-Seq of Brachypodium distachyon (Bd21): lateral_spikelet_meristem, 18-20d (rep. 1)


title: mRNAseq_grh1::degron_Auxin_27h_Rep1

description: Library name: 3535F7


title: mRNAseq_grh1::degron_Auxin_26h_Rep1

description: Library name: 3535F6


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2_leaf_tip, 10d (rep. 1)


title: RNA-Seq of Brachypodium distachyon (Bd21): apex_vegetative, 5d (rep. 3)

value: vegetative apex


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2_petiole, 10d (rep. 3)

value: Arabidopsis thaliana (Col-0)


title: 10X_genomics_scRNA-seq

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline aligning to the hg19 genome build. Further processing was performed using Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline aligning to the hg19 genome build.
For plate-based scRNA-sequencing adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5'.  Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Assembly: hg19
Supplementary files format and content: Aggregated 10x Genomics output files with raw counts per feature (gene expressoin and feature barcoding) for all individual cells: CITE-seq_GEXFB_raw_count_matrix.csv
Supplementary files format and content: Smartseq2 (plate-based scRNA-Seq): htseq count matrix with raw counts for all individual cells: Unfiltered_count_matrix_Smartseq2.txt

source_name: Bone marrow

extract_protocol:
Library was performed according to the manufacter’s instructions (single cell 5’ protocol, 10x Genomics)
For plate-based scRNA-Seq, single T cells were directly sorted into 96 well plates containing TCL buffer.
Library was performed according to the manufacter’s instructions (single cell 5’ protocol, 10x Genomics). For plate-based scRNA-Seq, full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

value: Bone marrow

value: CD45+ cells

value: mRNA/ADT/HTO


title: mRNAseq_grh1::degron_Auxin_25h_Rep1

description: Library name: 3535F5


title: RNA-Seq of Brachypodium distachyon (Bd21): apex_vegetative, 5d (rep. 2)

value: Brachypodium distachyon (Bd21)


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2_petiole, 10d (rep. 2)

value: leaf


title: mRNAseq_grh1::degron_Auxin_23h_Rep1

description: Library name: 3535F3


title: RNA-Seq of Brachypodium distachyon (Bd21): apex_vegetative, 5d (rep. 1)


title: mRNAseq_grh1::degron_Auxin_24h_Rep1

description: Library name: 3535F4


title: metastasis Replicate 2

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

institute: Army Medical University (Third Military Medical University)

description: Library name: metastasis Rep2

data_processing:
To guarantee optimal utilization of data, each specimen was divided into two sub-libraries to assess the reliability of experiments. The high correlation of the normalized sgRNA counts between the two sub-libraries of CRISPR-Cas9 screen experiment of tissue from in situ and metastatic focuses respectively. It showed that those experiments had high quality for further analysis.The sequences data were aligned to the sgRNAs using Bowtie2. The correlation of the normalized sgRNA counts between the two sub-libraries were calculated to assess the reliability of experiments. And MAGeCK RRA was implemented to select candidate regulatory genes enriched in metastatic focus compared with the primary sites.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts of targeted genes
Library strategy: CRISPR Screen

source_name: metastatic focuses

extract_protocol:
The CRISPR-Cas9 library used in this study was based on the human genome-scale GeCKO v2.0 library, which contains 123,411 sgRNA sequences targeting  targeting 19,050 human genes, with an average of 6 sgRNAs per gene. The library construction process was carried out using the proprietary CRISPR2 self-balancing library preparation technology and unbiased sgRNA fragment capture technology developed by Shanghai Genechem Co., LTD.
The library construction involved the extraction of genomic DNA from tissue samples, followed by quality control assessments using UV absorbance spectroscopy, Qubit DNA quantification, and capillary electrophoresis. Subsequently, the genomic DNA was processed into libraries through PCR amplification and purification steps. The final libraries were sequenced using the Illumina HiSeq X platform.

value: metastatic focuses

value: Human gastric cancer


title: mRNAseq_grh1::degron_Auxin_29h_Rep1

description: Library name: 3535F9


title: metastasis Replicate 1

description: Library name: metastasis Rep1


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2_petiole, 10d (rep. 1)


title: mRNAseq_grh1::degron_Auxin_22h_Rep1

description: Library name: 3535F2


title: mRNAseq_grh1::degron_EtOH_31h_Rep1

description: Library name: 3535F24

value: EtOH


title: RNA-Seq of Brachypodium distachyon (Bd21): lateral_spikelet_meristem, 18-20d (rep. 2)

source_name: inflorescence apex

value: inflorescence apex


title: RNA-Seq of Brachypodium distachyon (Bd21): leaf_1, 4d (rep. 3)


title: RNA-Seq of Brachypodium distachyon (Bd21): leaf_1, 4d (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2, 10d (rep. 3)


title: ChIP_RNAPII_DMSO

value: h-TERT RPE-1

value: Immortalized retinal pigment epithelial cells

value: Rpb1 NTD (D8L4Y) (Cell Signaling Technology, Cat No. 14958; RRID:AB_2687876)

value: No


title: in situ Replicate 2

description: Library name: in situ Rep2

source_name: inSitu

value: inSitu


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2, 10d (rep. 2)


title: RNA-Seq of Brachypodium distachyon (Bd21): leaf_1, 4d (rep. 1)


title: mRNAseq_grh1::degron_EtOH_30h_Rep1

description: Library name: 3535F23

source_name: Whole animal

value: Whole animal


title: Overexpression_2

city: Changchun

first: Caomeihui

last: Shen

address: No. 5333 Xi'an Road, Lvyuan District

institute: Jilin University

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Rfam,Repbase
Supplementary files format and content: excel
Supplementary files format and content: expression profiles

organism: Sus scrofa

source_name: follicular granulosa cells

growth_protocol: Granulosa cells were cultured in DMEM/F12 culture medium containing 10% fetal bovine serum  in an incubator which has 5%CO2 at 37℃

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare four small RNA libraries (V_1,V_2, OE_1,OE_2) according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: follicular granulosa cells

value: LOC102163816 overexpression


title: RNA-Seq of Brachypodium distachyon (Bd21): mesocotyl, 7d (rep. 3)

source_name: hypocotyl

value: hypocotyl


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2, 10d (rep. 1)

value: Arabidopsis thaliana (Col-0)


title: Overexpression_1


title: Control_2

value: control


title: mRNAseq_grh1::degron_EtOH_28h_Rep1

description: Library name: 3535F21


title: mRNAseq_grh1::degron_EtOH_29h_Rep1

description: Library name: 3535F22


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2, 7d (rep. 3)


title: RNA-Seq of Brachypodium distachyon (Bd21): mesocotyl, 7d (rep. 1)

value: Brachypodium distachyon (Bd21)


title: in situ Replicate 1

description: Library name: in situ Rep1


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2, 7d (rep. 2)

value: leaf


title: mRNAseq_grh1::degron_EtOH_27h_Rep1

description: Library name: 3535F20


title: RNA-Seq of Brachypodium distachyon (Bd21): root_whole_root, 4d (rep. 3)

source_name: root

value: root


title: RNA-Seq of Arabidopsis thaliana (Col-0): cotyledons, 7d (rep. 3)


title: Dissociated E11.5 somite cells

city: Montreal

first: Jean-Francois

last: Cote

state: Quebec

address: 110 pine avenue

institute: IRCM

description:
Library name: Sample 2
10X Genomics

data_processing:
Sequence alignment was done using Cellranger count (v 3.0.1).
Assembly: reference genome mm10-1.2.0.
Supplementary files format and content: Fastq files and Filtered_feature_bc_matrix files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Embryonic

extract_protocol:
Pregnant C57BL/6 wild type mice were sacrificed at 9.5 days and 11.5 days p.c. Embryos were extracted and interlimb somites were dissected in a PBS, 1% BSA filled plate using Dumont #5SF forceps. Somites from three embryos of each embryonic age were aspirated with a wide-bore p200 pipette tip with the surrounding PBS and pooled together in low-bind 1.5 mL tubes. The pooled somites were centrifuged at 100g, 4°C for 2 min. Supernatant was aspirated and replaced with 50 µL trypsin (325-043-CL, Wisent Bioproducts) and incubated at 37°C for 15 min. 200 µL of fetal bovine serum (FBS, 090150 Wisent Bioproducts) was then added, and cells were dissociated by pipetting up and down. Cells were centrifuged at 200g for 4 min at 4°C. Cells were washed twice with DMEM supplemented with 10% FBS then manually counted (viability >90%) and filtered with a Flowmi 40 µm tip strainer (cat. H13680-0040, Belart) and subsequently re-counted. Cells were adjusted at 1,100 cells/µL and a 150 µL aliquot was sent for analysis
Aliquot was sent for analysis using the 10X Chromium Chip (10X Genomics) for library preparation. Sequencing was performed with a High Output (150 cycles) flowcell using Illumina Nextseq 500. For each sample (E9.5 and E11.5), a total of 10,000 cells were sequenced with approximately 30,000 median reads per cell and 3,500 median genes per cell.

value: Embryonic

tag: age

value: Embryonic somite cells

value: wild type


title: Control_1


title: mRNAseq_grh1::degron_EtOH_25h_Rep1

description: Library name: 3535F18

value: EtOH


title: RNA-Seq of Arabidopsis thaliana (Col-0): leaf_1+2, 7d (rep. 1)


title: Dissociated E9.5 somite cells

description:
Library name: Sample 1
10X Genomics


title: mRNAseq_grh1::degron_EtOH_26h_Rep1

description: Library name: 3535F19


title: RNA-Seq of Brachypodium distachyon (Bd21): root_whole_root, 4d (rep. 1)


title: RNA-Seq of Brachypodium distachyon (Bd21): root_whole_root, 4d (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): cotyledons, 7d (rep. 1)


title: mRNAseq_grh1::degron_EtOH_24h_Rep1

description: Library name: 3535F17


title: 21DIV_Bicuculline_45min_2

city: CABA

first: Damian

last: Refojo

state: CABA

address: Godoy Cruz 2390

country: Argentina

institute: Biomedicine Research Institute of Buenos Aires (IBioBA)

data_processing:
Raw reads were aligned to the Mus musculus genome (version mm10) using STAR(76)
Reads were quantified using End Sequence Analysis Toolkit(77) for 3' RNA libraries.
Differential gene expression analysis was done with edgeR
Libraries were sequenced 2 times to increase coverage. Fastq files were merged and processed together afterwards (we are providing both sequenced runs separately in the each Exp folders)
Assembly: mm10
Supplementary files format and content: ExpA_ESAT_merged.gene.txt and ExpD_ESAT_merged.gene.txt

source_name: forebrain primary neuronal cultures

growth_protocol: Neurons were dissected from embryonic day 16 to 17.5 (E16 - E17.5) CD1 embryos of mixed sex. Culture preparation was performed as previously described (Dotti, Sulluvan, and Banker 1988). Briefly, forebrain (cortex and hippocampal) from CD1 mouse embryos were dissected and a neuronal suspension was prepared through Trypsin digestion and mechanical disruption of the tissue. Neurons were plated in 24 multi-well plates at a density of 80cells/mm2 (150.000 cells per well) and maintained in Neurobasal-A media (ThermoFisher) with 2% B27 and 0.5 mMGlutaMAX-I (ThermoFisher) at 37 °C and 5% CO2. CD1 mice were provided by our Specific Pathogen Free Animal Facility. All procedures were approved by National Department of Animal Care and Health (SENASA, Argentina) and were following the general guidelines of the National Institute of Health (NIH, USA).

extract_protocol:
RNA was extracted using the RNeasy mini kit with in-column DNase treatment
30ng of RNA was used as input for preparing 3' RNA sequencing libraries following CelSeq2 protocol

treatment_protocol: Neurons were used between 19–23 DIV or at DIV7 when indicated. Stimulations were performed in neuronal growing media adding drugs at indicated final concentration.  No previous silencing was performed in any of the stimulation protocols. Massive membrane depolarization was achieved by applying 55 mM extracellular potassium chloride (KCl). To induce synaptic stimulation, we triggered neuronal activity by treating neurons with 50uM Bicuculline (Sigma). As indicated in the DIV7 - 21 DIV comparison, we also added 2.5mM M 4-Aminopyridine (Sigma) to the 50uM Bicuculline treatment. Synaptic rebound was induced performing TTX withdrawal was performed (Rutherford et al., 1997; Saha et al., 2011). Cultures were treated with 1 uM TTX (Tocris) for 48hs, and the TTX was then washed out through seven exchanges of 1 ml of medium with fresh control medium. Control neurons were washed identically and processed in parallel. Results are shown in comparison to TTX control situation (silenced neurons TTX, 48hs). Each stimulation was sustained until indicated time.

value: forebrain primary neuronal cultures

value: CD1 mice

value: BIC 45min


title: Spun_H3K4me3_rep2

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

data_processing:
All ChIP-seq data was analysed using fastp to trim the reads, and these were mapped to the genomes using bowtie2, allowing a maximum insert size of 2000 base pairs (-I 2000). Duplicate reads were removed using Sambamba. DeepTools2 was used to generate bigwig files and to visualise epigenomic data, as well as Integrative Genome Viewer.
Assembly: Creolimax fragrantissima assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Spizellomyces punctatus: GCF_000182565.1, Acanthamoeba castellanii: https://zenodo.org/records/6800059, Naegleria gruberi: GCF_000004985.1
Supplementary files format and content: ChIP-seq bigwig files were generated with DeepTools2 using the bamCoverage tool (bamCoverage -bs 10 --normalizeUsing CPM -p $cores -b "$prefix".dedup.bam -o "$prefix".bigwig)

organism: Spizellomyces punctatus

source_name: microorganism

growth_protocol:
Spizellomyces punctatus cells were grown axenically at 17°C in liquid medium (containing 2.5 g of yeast extract, 0.5 g of K2HPO4, 2.5 ml of ethanol, 15 ml of glycerol and 485 ml of Milli-Q water).
Creolimax fragrantissima cells were grown axenically in marine broth liquid medium (Difco 2216) at 17°C. Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034. Spizellomyces punctatus cells were grown axenically at 17°C in liquid medium (containing 2.5 g of yeast extract, 0.5 g of K2HPO4, 2.5 ml of ethanol, 15 ml of glycerol and 485 ml of Milli-Q water).

extract_protocol:
Fixed cell pellets are treated with 2 ul of 3%SDS, to achieve a final concentration of 0.5% SDS. Cells are thoroughly re-suspended and lysed on ice for 10 min. Lysates are transferred into 0.1 ml Bioruptor Microtubes (Diagenode C30010015, Liège, Belgium) and the chromatin was sheared using an NGS Bioruptor Sonicator (Diagenode) at High Intensity and cycles of 30'' ON/30'' OFF.
100 ng chromatin per species was pooled per ChIP. Pooled chromatin was incubated at 4°C for 12−14 h with rotation with 2.5 µg anti-H3K27ac (Abcam, ab4729) or  2.5 µg anti-H3K4me3 (Millipore, 07-473). Immunoprecipitated complexes were captured using a mix of Protein A (16-661, Sigma-Aldrich) and Protein G magnetic beads (16-662, Sigma-Aldrich), washed, and reverse crosslinked for 30 min at 55°C followed by an hour at 68°C. Immunoprecipitated DNA was purified using SPRI beads (A63881, Beckman Coulter). The NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) was used to produce the resulting ChIP libraries according to the manufacturer's protocol.

treatment_protocol: No treatments were performed.

value: DAOM BR117

value: Axenic culture

tag: library type

value: ChIP-seq with anti-H3K4me3 (Millipore, 07-473)

tag: time

value: 14 days culture

value: microorganism


title: RNA-Seq of Arabidopsis thaliana (Col-0): cotyledons, 7d (rep. 2)

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

source_name: leaf

value: Arabidopsis thaliana (Col-0)


title: 21DIV_Bicuculline_45min_1


title: RNA-Seq of Arabidopsis thaliana (Col-0): first_internode, 28d+ (rep. 3)

source_name: stem

value: stem


title: Spun_H3K4me3_rep1


title: mRNAseq_grh1::degron_EtOH_23h_Rep1

description: Library name: 3535F16

value: Whole animal


title: RNA-Seq of Brachypodium distachyon (Bd21): mesocotyl, 7d (rep. 2)

value: Brachypodium distachyon (Bd21)

value: hypocotyl


title: mRNAseq_grh1::degron_EtOH_22h_Rep1

description: Library name: 3535F15


title: 21DIV_KCl_15min_2

value: KCl 15min


title: Spun_H3K27ac_rep2

value: ChIP-seq with anti-H3K27ac (Abcam, ab4729)


title: RNA-Seq of Arabidopsis thaliana (Col-0): first_internode, 28d+ (rep. 2)


title: mRNAseq_grh1::degron_Untreated_21h_Rep1

description: Library name: 3535F1

value: Untreated


title: RNA-Seq of Arabidopsis thaliana (Col-0): first_internode, 28d+ (rep. 1)


title: Spun_H3K27ac_rep1


title: 21DIV_Bicuculline_15min_3

value: BIC 15min


title: 21DIV_KCl_15min_1

value: forebrain primary neuronal cultures


title: RNA-Seq of Arabidopsis thaliana (Col-0): second_internode, 24d (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): second_internode, 24d (rep. 1)


title: 21DIV_Bicuculline_15min_2

value: CD1 mice


title: ChIPseq_NHR23_input

description: Library name: 3237F1

data_processing:
The ChIP-seq data were mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR package in R
To find peaks, we used MACS2(v 2.2.6) with the parameters “-g ce -f BAMPE"
Assembly: ce11
Supplementary files format and content: bed file with ChIP-seq peaks

source_name: Whole worm

growth_protocol: HW3232 worms (nhr-23(wrd8[nhr-23::GFP::degron::3xFLAG]) I) were synchronised by hatching in the absence of food followed by synchronised plating on NA22-containing and peptone rich XL plates at 25°C for 20 hrs.

extract_protocol:
5 million animals were collected in PBS + PI + PMSF 1mM at 20 hours after plating and popcorn was created from resuspended larvae mix. Lysate was prepared by grinding the popcorn, crosslinking with 1.1% formaldehyde and sonication with a Diagnode Biorupter Pico. For the chromatin immuno-precipitation, 50 uL of protein G Dynabeads (10003D, ThermoFisher Scientific) were incubated with 5 ug of anti-GFP antibody (ab290, Abcam) for 4 hours rotating at 4°C. 100 ug of chromatin was added, and incubated over night at 4°C rotating. Beads were washed and the elute was treated with proteinase K and RNaseA, and DNA was purified using Zymo ChIP Concentrator Kit. Sequencing libraries were prepared using the ChIP-seq NEB Ultra protocol (New England Biolabs) and sequenced using the Nova SP 2x50bp protocol.
ChIP-seq NEB Ultra protocol

value: Whole worm

tag: fraction

value: Input


title: RNA-Seq of Arabidopsis thaliana (Col-0): third_internode, 24d (rep. 3)

tag: tissue


title: AKAP17_ip_replicate2

description: Library name: S8

data_processing:
Snakemake workflow based on the CLAPAnalysis pipeline (Guo et al., 2024, Mol. Cell, PMC10997485).
Read quality was assessed using FastQC (V 0.11.8), and reads were trimmed to remove adaptor sequences using Trim Galore! (V 0.6.2).
Clean reads were aligned to the C. elegans genome (WBcel235) using STAR (V2.7.9a).
PCR duplicates were removed using Picard MarkDuplicates (V 2.18.7). Read coverage was computed in 100-nt windows across each gene body, normalized to total read depth. Gene level enrichment was defined as the sum of normalized counts per gene, and IP enrichment was calculated as the ratio of IP to input signals.
Assembly: WBcel235
Supplementary files format and content: Gene body coverage (100-nt windows, TXT format).

source_name: Caenorhabditis elegans

extract_protocol:
C. elegans were crosslinked with 1.8% formaldehyde and sonicated. Lysates were centrifuged, and the supernatant was incubated with Anti-FLAG® M2 magnetic beads (Millipore Sigma, M8823). Bound RNAs were reverse crosslinked and extracted using TRIzol.
Libraries were prepared following a previously described protocol (Guo et al., 2024, Mol. Cell, PMC10997485).

tag: strain

value: Caenorhabditis elegans


title: ATACseq_grh1::degron_Auxin_31h_Rep2

description: Library name: 3616F23

data_processing:
Paired-end ATAC-seq reads were trimmed with Cutadapt v 1.18 using the parameters “-a NCTGTCTCTTATA -A NCTGTCTCTTATA --minimum-length=10 --overlap=1”. The N in the adapter was used to remove one additional nucleotide in every read in order to ensure correct downstream alignment of adapter reads with Bowtie. Trimmed reads were mapped to the C. elegans genome (ce11) using the qAlign function from the R package QuasR (v 1.42.1) with standard parameters which deploys the aligner Bowtie. The fragment size distributions of the individual libraries showed multiple peaks, the short fraction corresponding to transcription factor footprints (<120bp) and long fraction to nucleosomes (>120bp). We thus considered fragments with a read length of less than 120 bp for further analysis. We quantified the number of reads in all the ATAC-seq peaks (obtained from the N2 timecourse, see other series in the same super series) using the function qCount() in the package QuasR. We further performed quantile normalization to correct for non-linear trends in the data, followed by log2 transformation with a pseudocount of 32 (log2(x+32)). In the first replicate of the GRH-1 degron time course we noticed two outlier samples, EtOH_24h and Auxin_25h showing lower correlation to all other samples but high correlation to the each other. These two samples were simultaneously processed together, suggesting a technical batch effect. We corrected for this batch effect, by first calculating the average ATAC-seq intensity profile of those two samples and then subtracting the average profile of the neighboring 4 samples in the time course. This resulted in a batch correction vector, which we then subtracted from the 2 outlier samples to obtain corrected intensities for those 2 samples.
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw ATAC-seq read counts for all ATAC-seq peaks (obtained from the N2 timecourse)
Supplementary files format and content: tab-delimited text file with normalized log2 ATAC-seq read counts for all ATAC-seq peaks  (obtained from the N2 timecourse)

growth_protocol: Synchronized L1 animals were grownat at 20oC and at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Following the addition of treatments, animals were collected every hour (over 12-13 hours), and washed 3 times with M9 befor flash freezing the pellet in liquid N2. Samples were stored at -80 until further processing. Note that in replicate Rep1 ethanol and auxin were added at 21h of development while in Rep2 this was done at 20h.

extract_protocol:
Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Briefly, 7 rounds of douncing (3 times / round) were performed in Omni-ATAC buffer, and nuclei were seperated from worm debry by slow centrifugation. Isolated nuclei were then tagmented according to the Omni-ATAC protocol (Corces et al., 2017, Nat Methods), and DNA isolated using the MinElute PCR purification kit (28004, Qiagen).
Isolated DNA was amplified using NEB Next High-Fidelity PCR Master Mix (M0541S, NEB), and barcoded illumina sequencing primers before Ampure XP bead purification.

value: Auxin


title: notag_ip_replicate2

description: Library name: S6

value: WT


title: 21DIV_KCl_45min_2

value: KCl 45min


title: notag_ip_replicate1

description: Library name: S5


title: 21DIV_KCl_45min_1


title: 21DIV_Basal_0min_5


title: AKAP17_input_replicate2

description: Library name: S4


title: 21DIV_TTXwithdrawal_15min_3

value: TTXw 15min


title: RNA-Seq of Arabidopsis thaliana (Col-0): third_internode, 24d (rep. 2)

growth_protocol: All plants were grown on soil, except those used for the collection of early-stage root samples, which were grown on 0.8% plant agar plates, pH 5.8, containing ½ MS and vitamins (Duchefa M0222).

value: Arabidopsis thaliana (Col-0)

value: stem


title: RNA-Seq of Arabidopsis thaliana (Col-0): second_internode, 24d (rep. 3)


title: RNA-Seq of Arabidopsis thaliana (Col-0): third_internode, 24d (rep. 1)


title: ATACseq_grh1::degron_Auxin_29h_Rep2

description: Library name: 3616F21

value: Whole animal


title: AKAP17_input_replicate1

description: Library name: S3


title: ATACseq_grh1::degron_Auxin_27h_Rep2

description: Library name: 3616F19


title: 21DIV_TTXwithdrawal_15min_2


title: RNA-Seq of Arabidopsis thaliana (Col-0): hypocotyl, 10d (rep. 3)

value: hypocotyl


title: ATACseq_grh1::degron_Auxin_30h_Rep2

description: Library name: 3616F22


title: AKAP17_ip_replicate1

description: Library name: S7


title: ChIPseq_NHR23_IP

description: Library name: 3237F3

value: IP


title: 21DIV_TTXwithdrawal_15min_1


title: notag_input_replicate2

description: Library name: S2


title: ATACseq_grh1::degron_Auxin_26h_Rep2

description: Library name: 3616F18


title: RNA-Seq of Arabidopsis thaliana (Col-0): hypocotyl, 10d (rep. 2)


title: notag_input_replicate1

description: Library name: S1


title: 21DIV_TTXwithdrawal_3h_3

value: TTXw 180min


title: ATACseq_grh1::degron_Auxin_25h_Rep2

description: Library name: 3616F17


title: RNA-Seq of Arabidopsis thaliana (Col-0): hypocotyl, 10d (rep. 1)


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_mid_stg12_equiv_stamens, 11w (rep. 3)

organism: Tarenaya hassleriana

source_name: stamens

value: Tarenaya hassleriana (ES1100)

value: stamens


title: 21DIV_TTXwithdrawal_3h_2

value: forebrain primary neuronal cultures


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 21d (rep. 3)

value: root


title: RNA-Seq of Tarenaya hassleriana (ES1100): floral_organ_mid_stg12_equiv_stamens, 11w (rep. 2)


title: RNA-Seq of Arabidopsis thaliana (Col-0): root_whole_root, 21d (rep. 2)