title: 16 D

description:
DMSO
Single Cell RNA-Seq (3' V3 Chemistry)

data_processing:
Cellranger.v5.0.1 standard pipeline was used for preprocessing and alignment.
The reads were aligned to the Hybrid genome of Human hg38 and P. falciparum pd37 v3 (PlasmoDB-46_Pfalciparum3D7_Genome.fasta) to remove any human transcript contamination. This was achieved using CellRanger standard pipeline using --nosecondary flag.
Genome_build: hg38, Pf3D7.v3
Supplementary_files_format_and_content: *.tar.gz: Tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; raw counts.

source_name: P. falciparum infected RBCs

extract_protocol:
For 40 h.p.i. time point tight synchronous parasites were enriched using 63% Percol, washed twice with incomplete RPMI media and processed immediately on the 10X Chromium controller (10X Genomics, Pleasanton, CA). For 16 h.p.i. time point parasites were stained with Mitotracker Deep Red FM (Life Technologies, #M22426) for FACS analysis and flow sorting respectively. Briefly, 50 µl of SYBR Green I stained RBC’s were analyzed on BD LSR Fortessa Flow Cytometer with High Throughput sampler (BD Biosciences, San Jose, CA, USA) using BD FACS Diva Software v6.2 and 488 laser excitation / 530 emission filter to determine concentration of SYBR Green I positive cells per microliter. A BD Influx Cell Sorter (BD Biosciences, San Jose, CA, USA) with BD FACS Software v1.0.01 software was used to sort ~40,000 MitoTracker Deep Red FM - positive RBC’s using a 70 µm nozzle, a 640 nm laser excitation / 670 nm emission filter and a pressure setting of 30 psi. Post-sorted cell concentration and quality were checked using a Countess® II Automated Cell Counter (Invitrogen) and FLoid™ Cell Imaging Station (ThermoFisher). Finally, labelled cells (i.e. SYBR Green I or MitoTracker Deep Red FM positive cells) were then loaded onto a 10X chip (Chip G) and processed immediately on the 10X Chromium controller (10X Genomics, Pleasanton, CA).
Single cell libraries were constructed using the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Single Index Kit T Set A. Due to the extremely low RNA content of single cell malaria parasite’s and the AT rich genome (~70% AT), modifications to the cDNA amplification and library preparation workflow were made accordingly. These modifications included - 30x cDNA amplification cycles; taking 50% cDNA as input into library generation; reducing fragmentation time to 2 minutes; and changing the extension time to 65 oC during index PCR. Individual library Qc was performed using the BioAnalyzer HS DNA Assay kit (Agilent).

treatment_protocol: For 40 h.p.i. parasites, DMSO (control) or Rapamycin (to induce PfAP2-MRP knockout) was added to culture at 16 h.p.i. in the same cycle of sample collection. For 16 h.p.i. parasites, DMSO (control) or Rapamycin (to induce PfAP2-MRP knockout) was added to cultures at 35 h.p.i. in cycle 0 and parasites were collected at 16 h.p.i. in cycle 1.

value: Parasites

tag: time point

value: 16 hours post infection


title: 40 D

status: Public on Aug 07 2023

type: SRA

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

library_source: transcriptomic

molecule: total RNA

organism: Plasmodium falciparum

tag: cell type

tag: genotype

value: Control

value: 40 hours post infection


title: 40 R

description:
Rapamycin
Single Cell RNA-Seq (3' V3 Chemistry)

value: PfAP2-MRP knockout


title: Caco-2 cells, differentiated, Carmine treated. 24h, sample B

city: Linz

first: Marlene

last: Rezk

address: Krankenhausstraße 7A

country: Austria

institute: Johannes Kepler Universität

data_processing:
Quality check was performed by FastQC
Data was aligned to hg38 genome by Hisat package
Data was counted by featureCount package
Assembly: hg38
Supplementary files format and content: tab-delimited text files with raw counts
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Homo sapiens

growth_protocol: Caco-2 cells were differentiated in 6-well plates in DMEM supplmented with 10% FBS, 1% Penicillin-streptomycin and 1% glutamine in a humidified atmosphere at 37°C with 5% CO2

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen, Heidelberg, Germany).
22 µL of RNA extracts were provided for library preparation and library was prepared by manufacturer

treatment_protocol: Cells were treated with medium supplemented with 10 µM Carmine, 20 µM Carminic acid or regular cell culture medium as control for 24h (each treatment in triplicate)

tag: cell line

value: WT

tag: treatment

value: Carmine 10 uM


title: Caco-2 cells, differentiated, Carminic acid treated, 24, sample C

value: Carminic acid 20 uM


title: Caco-2 cells, differentiated, Carminic acid treated, 24h, sample B


title: Caco-2 cells, differentiated, Carminic acid treated, 24h, sample A


title: Caco-2 cells, differentiated, Carmine treated, 24h, sample C


title: Caco-2 cells, differentiated, Carmine treated, 24h, sample A


title: A18

city: Brussels

first: Lila

last: Gannoun

address: Avenue Hippocrate 75

department: Institut de Duve

country: Belgium

institute: Université Catholique de Louvain

description: Transgenic mice

data_processing:
RNA sequencing using Illumina HiSeq 2x150bp configuration with estimated data output ≥350M raw paired-end reads per lane
The reads quality control was performed using FastQC software v0.11.7 (Babraham Institute, Cambridge, UK).
Paired-end reads were aligned by HISAT2 software v2.1.0 (Johns Hopkins University School of Medicine, Center for Computational Biology, Baltimore, MD, USA) against the mm10 genome build using the bowtie1 aligner24 option.
Gene counts were generated using HTSeq-count (v0.5.4p3) software and gencode.vM15.annotation.gtf annotation file and raw counts were further converted in transcripts per million (TPM)
Assembly: mm10
Supplementary files format and content: The text file includes TPM values for each sample

organism: Mus musculus

source_name: Mesenchyme

growth_protocol: Mus musculus CD-1 model: Sm22-Cre/ROSA26RYFP

extract_protocol:
RNA extraction of embryonic mesenchyme : The supernatant was removed and RNA from cells pellets was extracted using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol.
RNA libraries were generated using the TruSeq total stranded RNA-seq kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Purification of embryonic mesenchyme (E16 and E18): livers were dissociated using collagenase IV and Dispase. Then, eYFP positive cells were selected using a cell sorter (FACSAria II, BD, Franklin Lakes, USA), harvested in an individual microtube and centrifugated at 1000 rpm during 5 min

tag: strain

tag: tissue

value: Liver

tag: age

value: Embryonic day 18


title: Caco-2 cells, differentiated, untreated. 24h, sample C

value: untreated


title: Caco-2 cells, differentiated, untreated, 24h, sample B


title: A16

description: Transgenic mice

value: Embryonic day 16


title: Caco-2 cells, differentiated, untreated, 24h, sample A


title: B18

description: Transgenic mice


title: C18

description: Transgenic mice


title: TAMR Decitabine Day 7 2 [EPIC]

type: genomic

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw intensity data (IDAT) files were imported and quality controlled using minfi package (v.1.34.0) (Aryee et al., 2014). Data was then normalised with background correction. To reduce the risk of false discoveries, we removed probes affected for cross-hybridization to multiple locations on the genome or overlapped SNPs, as previously described (Pidsley et al., 2016). Beta (β) values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation). β values of loci whose detection P values were > 0.01 were assigned NA in the output file. To map EPIC arrays to hg38/GRCh38 assembly, all probes were annotated with the EPIC.hg38.manifest.tsv.gz files as described in (Zhou et al., 2017).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: TAMR cell line

label_protocol: Standard Illumina Protocol

growth_protocol: Tamoxifen-resistant MCF7 cells (TAMR) were previously generated by the long-term culture of MCF7 cells in phenol red-free RPMI medium containing 10% charcoal-stripped FBS (Gibco) and 4-OH-tamoxifen (1 × 10−7 M; TAM).

extract_protocol: Gernomic DNA from cells was isolated using the  QIAamp DNA Mini Kit (Qiagen).

treatment_protocol: Cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control Early”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35. Matched control cells were cultured for 35 days in normal media and harvested at day 35 for “Control Late”.

value: Tamoxifen-resistant (TAMR) MCF7 cells

value: Decitabine Day 7

tag: replicate


title: TAMR Control Early 1 [EPIC]

value: Control Early


title: 20R_H3K4ME3_rep1

library_source: genomic

data_processing:
bcl2fastq2 Conversion Software
Low-quality reads and Illumina adaptor sequences from the read ends were removed using Trimmomatic (Bolger et al., 2014).    Quality trimmed reads were aligned to the P. falciparum genome (plasmodb.org, v3, release v32) using HiSat2.  Duplicate reads were removed using samtools (markdup) (Li et al., 2009). GC bias was corrected using deeptool’s correctGCBias tool (Ramirez et al., 2014). For coverage plots of Api2EI 40 h.p.i. and 20 h.p.i. ChIP-seq experiments, deeptool’s bamCompare tool was used to normalize the read coverage per base of the genome position ( option  ‘-bs 1’) in the respective input and ChIP samples to the total number of reads in each library (-- nomarmalizeUsing RPKM). Normalized input coverage  per bin was subtracted from the ChIP values (option – operation subtract). Coverage plots were visualized using IGV genome browser (Thorvaldsdottir et al., 2013).
ChIP-Peaks  (q-value cutoff < 0.05) were identified using macs2 (Zhang et al., 2008) by comparing the input with ChIP  with default settings but without prior peak modelling (option ‘-nomodel’), the fragment size set to 200 bp (option ‘-extsize 200’) and the genome size  (option ‘-g’) set to 233332839. Robust common peaks between replicates were identified using bedtools ‘intersect’ (option –f 0.30 –r) (Quinlan and Hall, 2010). Peak annotation was carried out using Homer’s annotatePeaks.pl that assigned each peak with the nearest downstream gene. Enrichment heatmaps and profile plots were generated using the deepTools computeMatrix and plotHeatmap tools.
Assembly: Plasmodium falciparum build version 3
Supplementary files format and content: Bam files were converted to bigwig files using bamCoverage from the deeptools suite

source_name: P. falciparum

growth_protocol: Parasites were maintained in human A+ erythrocytes at 37 °C in RPMI 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM L-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using 70% (v/v) isotonic Percoll (GE Healthcare Life Sciences) before allowing reinvasion to occur, followed by sorbitol treatment.

extract_protocol:
The ChIP assay was performed as described (Pandey et al., 2020) with a few modifications. Parasite culture (50 ml) containing synchronized late-stage schizonts (~ 40 h.p.i.) at ~5% parasitemia was centrifuged at 900 g for 4 min and the cells washed once with PBS. To the cell pellet, 25 ml of 0.15% saponin in PBS was added and incubated on ice for 10 min followed by washing twice with cold PBS. Parasites were crosslinked for 10 min by adding methanol-free formaldehyde at 1% final concentration and incubated for 10 min at 37 °C with occasional shaking. The crosslinking reaction was quenched by adding 1.25 M glycine to achieve a final concentration of 0.125 M and incubated at 37 °C for another 5 min. Parasites were centrifuged for 10 min at 3250 g at 4 °C, washed three times with DPBS, snap frozen in liquid nitrogen and stored at -80 °C until further use. Frozen formaldehyde fixed parasites were thawed on ice for chromatin immunoprecipitation. One ml of nuclear extraction buffer (10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1mM DTT, 1x EDTA-free protease inhibitor cocktail [Roche]) was added to the tubes containing thawed parasites and incubated on ice for 30 min. After the incubation, 10% NP-40 was added to reach a final concentration of 0.25% and the parasites were lysed by passing through a 261/2 G needle seven times. Parasite nuclei were collected by centrifuging at 2500g for 10 min at 4 °C. Shearing of chromatin was carried out using the Covaris Ultra Sonicator (E220) for 14 min with the following settings; 5% duty cycle, 140 intensity peak incident power, 200 cycle per burst to obtain fragment size of 200 to 600 bp. Insoluble materials were removed by centrifuging the sheared chromatin for 10 min at 13500 g at 4 °C. 30 µl of fragmented chromatin were stored as input at -80°C.    Fragmented chromatin was diluted 1:1 in ChIP dilution buffer (30 mM Tris-HCl pH 8.0, 0.1% SDS, 3 mM EDTA, 300 mM NaCl, 1% Triton X-100, EDTA-free protease inhibitor cocktail).  Chromatin was incubated overnight with 6 µg of mentioned antibodies. The antibody-protein complex was recovered with protein A coupled to magnetic beads (Dynabeads, Invitrogen, Cat No. 10002D), followed by extensive washes with low salt immune complex wash buffer, high salt immune complex wash buffer (washes done at 4 °C) and TE buffer (washes done at RT). Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3) at 45 °C for 30 min with shaking. Immunoprecipitated chromatin and input were reverse crosslinked overnight at 45 °C by adding 5 M NaCl to a final concentration of 0.5 M. Samples were treated with RNaseA for 30 min at 37 °C followed by a 2 h incubation at 45 °C with proteinase K (final concentration 66 µg/ml). DNA was purified using ChIP DNA clean & concentrator (Zymo Research, Cat. No. D5205).
Libraries were prepared using NEBNext Ultra II DNA library kit following the manufacturer’s instructions until the step of adapter ligation (Adapters were diluted at 1: 20 ratio). Adapter ligated libraries were purified using AmpureXP beads. The libraries were amplified for a total of 6 PCR cycles (2 min at 98 °C initial denaturation; 6 cycles of 30 s at 98 °C, 50 s at 62 °C, final extension 5 min at 62 °C) using the KAPA HiFi HotStart Ready Mix (Kapa Biosystems).  Amplified libraries were purified and size selected for 350 bp inserts using AmpureXP beads and sequenced on the Illumina HiSeqX platform with 150 bp paired-end read layouts.

tag: chip antibody

value: Rabbit polyclonal anti H3K4me3 antibody (Cat no. ab8580, Abcam, RRID:AB_306649)


title: C16

description: Transgenic mice


title: B16

description: Transgenic mice


title: TAMR Decitabine Recovery 2 [EPIC]

value: Decitabine Recovery


title: TAMR Control Late 1 [EPIC]

value: Control Late


title: TAMR Decitabine Recovery 1 [EPIC]


title: TAMR Control Late 2 [EPIC]


title: 263F

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description:
mouse metagenome
processed data file: tabdin.taxon.txt
processed data file: cnts.protein.txt

data_processing:
Library strategy: DNA-seq
tabdin.taxon.txt: Reads were aligned to the mm10 genome using STAR 2.7.0a with default parameters. DNA contaminated reads were filtered out from the analysis. The first and final 10 bases of the non-contaminated reads were trimmed using DADA2 1.10.1. Taxonomic assignments were carried out through Kaiju 1.7.0 using the microbial subset of the NCBI BLAST non-redundant protein database (nr). Resulting sequencing counts were aggregated at genus level. Reads that could not be assigned to any specific genus were assigned to the nearest known taxonomic rank (these are marked by the term _un). Full taxonomic path could be recovered using the Kaiju names ID.
cnts.protein.txt: Decontamination from host and trimming were done following the same routines as for the taxonomic analysis. Cleaned sequences for all samples were assembled into contigs using megahit 1.2.4 and prodigal 2.6.3 was then used to predict the open reading frames inside the obtained contigs. Protein mapping as well as Kegg and COG annotations were obtained using the eggnog mapper 2.0.0. The abundance of the annotated genes was finally measured by counting aligned reads to them via Bowtie2, version 2.2.2, under default parameters. Resulting counts data were aggregated at protein level.
Genome_build: mm10 (GRCm38); NCBI BLAST non-redundant protein database.
Supplementary_files_format_and_content: tabdin.taxon.txt: Raw counts per Kaiju ID; tab-separated text file.
Supplementary_files_format_and_content: cnts.protein.txt: Raw counts per protein; tab-separated text file.

organism: feces metagenome

source_name: mouse fecal sample

growth_protocol: Transgenic (I4F; ubiquitous doxycycline-inducible expression of Oct4 Sox2 Klf4 c-Myc cassette) or wild type (WT) mice were housed in an SPF facility; fresh stool was harvested and frozen (-80C) before treatment initiation (Start) and 7 days after treatment initiation (finish).

extract_protocol:
Genomic DNA was isolated from mouse stool samples using Qiagen stool kit CAT#51504 as per manufacturer's protocols.
Libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit (ref. E7370L) according to the manufacturer's protocol. Briefly, 50 ng of DNA was fragmented to approximately 400 bp and subjected to end repair plus “A”-tailing, ligation of NEB adapter and Uracil excision by USER enzyme. Then, adapter-ligated DNA was amplified 8 cycles by PCR using indexed primers. All purification steps were performed using AMPure XP Beads (ref. A63881). Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot. Libraries were sequenced 2 x 125 on Illumina’s HiSeq 2500.

treatment_protocol: Mice were given doxycycline (1mg/ml) in their drinking water with 7.5% (w/v) sucrose for a duration of 7 days.

value: Feces

tag: timepoint

value: Finish

tag: mouse


title: TAMR Decitabine Day 7 1 [EPIC]


title: TAMR Control Early 2 [EPIC]


title: 251S

value: Start


title: 263S


title: 261F


title: 262S


title: 202S


title: 201F


title: 200S


title: 225S


title: 200F


title: 225F


title: Xag24h-2

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Calculated manually based on the method in the following paper. (Lee, J., Jang, H., Kang, W. H., & Yeom, S. I. (2023). Transcriptome analysis of pepper-phytophthora infestans interaction based on a pipeline of a simplified and effective RNA-seq analysis (PoRAS).)
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of FPKM/RPKM for each sample

molecule: polyA RNA

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves


title: 202F

value: WT


title: 201S


title: Xag24h-1


title: SWI3_DTT

city: Berkeley

first: Elçin

last: Ünal

state: CA

address: 628 Barker Hall

country: USA

institute: UC Berkeley

data_processing:
raw fast5 files were basecalled with Guppy
fastq files were aligned to the sacCer3 reference genome using the EPI2ME Desktop Agent
bigwig files were generated using deeptools bamCoverage
Assembly: sacCer3 (R64)
Supplementary files format and content: BAM file which can be viewed directly in IGV

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: Cells were grown in YPD to late-log phase and treated with 5 mM DTT. Samples were collected 1 hour post treatment

extract_protocol:
Cells were collected by vacuum filtration and then flash frozen in liquid nitrogen. RNA was extracted by acid phenol chloroform exctration and precipitated in isopropanol.
Libraries were generated with the Oxford Nanopore Direct RNA-Seq kit (SQK-RNA002)

value: cells

value: swi3[delta]; SWI3::LEU2

value: Cells were grown in YPD to mid-log phase, treated with 5 mM DTT, and collected after one hour by vacuum filtration


title: Xag12h-3


title: Xag12h-1


title: Xag12h-2


title: 262F


title: 16 R

value: Parasites

value: PfAP2-MRP knockout

value: 16 hours post infection


title: Xag6h-2


title: Xag3h-1


title: Xag3h-2


title: 261S


title: Xag8ra_Mock_24h-1


title: Xag6h-3


title: Xag8ra_Mock_24h-3


title: Xag6h-1


title: 251F


title: Xag8ra_Mock_12h-1


title: Xag3h-3


title: Xag1h-2


title: Xag1h-1


title: Xag8ra_Mock_3h-3


title: Xag8ra_Mock_6h-2


title: Xag8ra_Mock_12h-3


title: Xag8ra_Mock_12h-2


title: Xag8ra_Mock_3h-2


title: Xag8ra_Mock_6h-1


title: Xag8ra_Mock_3h-1


title: hESCs cells, D60, replicate 3

city: Hong Kong

first: Ellen

middle: Ngar-Yun

last: Poon

state: Hong Kong

address: Shatin

department: School of Biomedical Sciences

country: China

institute: The Chinese University of Hong Kong

data_processing:
Raw reads were aligned to hs37d5 using Tophat
Read count extraction and normalization were performed using htseq-count and Deseq-2
Assembly: hs37d5
Supplementary files format and content: tab-delimited files include raw counts for each sample
Supplementary files format and content: tab-delimited files include FPKMs for each sample

source_name: hESCs

growth_protocol: Undifferentiated H7 ESCs were maintained on Matrigel (Thermo Scientific)-coated surfaces at 37°C and 5% CO2 in E8 medium plus supplements (Thermo Scientific)

extract_protocol:
Total RNA was extracted using an RNeasy micro kit (Qiagen), according to the manufacturer’s protocol.
cDNA libraries were prepared by KAPA Stranded mRNA-Seq Kit

treatment_protocol: To initiate differentiation, the E8 medium was changed to RPMI/B27 medium lacking insulin. CHIR99021 (6 μM; Selleckchem) was added to the cells from days 0 to 2, followed by the addition of IWR-1 (10 μM; Selleckchem) from days 3 to 5 for H7 cells. After day 7, cultures were maintained in RPMI/B27 medium containing insulin (Thermo Scientific), which was changed twice a week.

value: hESCs

value: Human embryonic stem cells

tag: time


title: hESCs cells, D45, replicate 1


title: hESCs cells, D45, replicate 3


title: Bukang0-1


title: Xag8ra_Mock_1h-3


title: Xag8ra_Mock_1h-2


title: Xag1h-3


title: Xag8ra_Mock_1h-1


title: Bukang0-3


title: hESCs cells, D30, replicate 3


title: hESCs cells, D15, replicate 3


title: hESCs cells, D15, replicate 2


title: hESCs cells, D30, replicate 1


title: hESCs cells, D15, replicate 1


title: hESCs cells, D60, replicate 1


title: Xag8ra_Mock_24h-2


title: hESCs cells, D60, replicate 2


title: hESCs cells, D45, replicate 2


title: Female_Cocaine_1

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

description: snATAC-seq

data_processing:
snATAC-seq data was aligned to the mRatBN7.2/Rn7 reference assembly using cellranger-atac v2.1.0 and the procedure outlined by 10X Genomics.
Analysis of the cellranger-atac output was analyzed using Signac v1.9.068 and Seurat v4.3.063. Counts, fragments, and barcode information for each treatment group were loaded and combined into Seurat objects as outlined by the Stuart lab website (https://stuartlab.org/signac/).
Using Signac and Suerat functions, samples were merged into one object based on a common set of features and the standard Signac dimensionality reduction and clustering workflow was performed using 2:30 dimensions and a resolution value of 0.2. Data was then integrated with the snRNA-seq data from the same samples (available at GSE222418). Common anchors between the two were used to predict and label the cell types present in the snATAC-seq data.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger Arc outputs including  matrices for barcodes (.tsv), ATAC matrix (.mtx), and peak locations (.bed) are provided for each sample.

organism: Rattus norvegicus

source_name: Sprague-Dawley

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
Flash-frozen NAc tissue was added to a tube containing 500µl lysis buffer (1mM Tris-HCl pH 7.4, 1mM NAc, 0.3 mM MgCl2, 0.01% Tween-20, 0.01% Igepal in nuclease free water, 0.001% Digitonin, 0.1% BSA), homogenized using a motorized homogenizer and RNase free pestle, and incubated on ice for 5 minutes. Samples were then pipette mixed 15x and incubated on ice for an additional 10 minutes. Following lysis, 4 samples from same sex and treatment were grouped into a single sample, and 2mL chilled wash buffer (10mM Tris-HCl pH 7.4, 10mM NACl, 3mM MgCl2, 1% BSA, 0.1% Tween-20) was added. Samples were then passed through 70µM and 40µM Scienceware Flowmi Cell Strainers. Samples were then centrifuged at 250 rcf for 5 min at 4°C. Supernatant was removed and the pellet was resuspended in 1mL of chilled wash buffer (10mM Tris-HCl pH 7.4, 10mM NACl, 3mM MgCl2, 1% BSA, 0.1% Tween-20). 100µL of sample was then stained with 7-aminoactinomycin D and used to set a representative gate for fluorescence activated cell sorting (FACs). This gate was then used to purify nuclei further. Following FACs, samples were spun at 250 rcf for 10 min at 4°C to remove any remaining debris. Samples were then loaded into individual wells of the Chromium NextGem Single Cell Chip using 4 of the 8 available wells.
FACS-sorted nuclei were subject to 10X GEM generation, transposase barcoding, and library construction using a Chromium Next GEM Single Cell ATAC Kit v2. Libraries were quantified and underwent sequencing on an Illumina sequencing platform (NextSeq 500) using a dual-indexed, paired-end strategy (Read 1N, 50 cycles; i7 index, 8 cycles; i5 index, 16 cycles; Read 2N, 50 cycles).

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. Injections occured daily across 7 consecutive days. Tissue was harvested 1hr after the final (7th) injection, when rats were sacrificed, the brain was blocked into 1mm sections, abd the NAc was harvested and flash frozen. A total of 16 rats (8 male, 8 female, 4 per GEMwell) were used for this experiment.

value: Sprague-Dawley

tag: source

value: Nucleus accumbens

value: Cocaine

tag: Sex

value: Female


title: RNA K3

data_processing:
Paired-end FASTQ files were analyzed using a custom bioinformatics pipeline built with Snakemake (v6.1.0). Read quality was assessed using FastQC before and after trimming with Trim_Galore! (v0.6.7). Splice-aware alignment to the mRatBn7.2/Rn7 reference assembly for cultured embryonic rat striatal neurons was performed using Ensembl gene transfer format (gtf) file (version 105) with STAR (v2.7.9a).
Binary alignment map (BAM) files were indexed with SAMtools (v1.13)
Gene-level counts were generated using the featureCounts function within the Rsubread package (v2.6.1) in R (v4.1.1)
QC metrics were collected and reviewed with MultiQC(v1.11).
Differential expression testing was conducted using DeSeq2 (v1.38.3). DEG testing p-values were adjusted with the Benjamini-Hochberg method. DEGs were designated as those genes with an adjusted p-value < 0.05 and a |log2FoldChange| > 0.5.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Str_4h_KCl_count_matrix.txt contains RNA-seq count values for annotated gene for each sample

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to RNA-seq. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for total RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. RNA-seq libraries underwent sequencing (75 bp paired-end directional reads) on an Illumina sequencing platform (NextSeq500).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 10mM) for 4 hours on DIV 11.

value: Embryonic day 18, 11 DIV

value: Striatum

value: KCl (10mM)


title: RNA K4


title: Male_Cocaine_1

description: snATAC-seq

value: Male


title: Male_Saline_1

description: snATAC-seq

value: Saline


title: Female_Saline_1

description: snATAC-seq


title: RNA K1


title: RNA K2


title: hESCs cells, D30, replicate 2


title: RNA V4

value: Vehicle


title: RNA V3


title: RNA V1


title: AK2

description: ATAC-seq

data_processing:
Low-quality bases (Phred <20) and Nextera adapters (5’-CTGTCTCTTATA-3’) were identified and trimmed using FastQC and TrimGalore (v0.6.7).
FASTQ files containing trimmed sequences were then aligned to Rn7 Ensembl genome assembly (v105) to generate binary alignment map (BAM) files with Bowtie2 (v.2.4.4).
PCR duplicates and reads mapping to the mitochondrial genome were removed using SAMtools52 (v1.13)
BigWig files were generated with deeptools v3.5.1. QC metrics were collected and reviewed with MultiQC54 (v1.11)
ATAC peaks were called using MACS2 (v 2.1.1.20160309) callpeak with options - -qvalue  0.01 - -gsize 2626580772 - -format BAMPE.
Differential accessibility analysis was performed with Diffbind (v3.8.4). DARs were defined as regions with an adjusted p-value < 0.05. Reads within peaks were counted using the dba.count() function with options bParallel=TRUE, summits=250, bUseSummarizeOverlaps=TRUE, and score = DBA_SCORE_TMM_READS_FULL_CPM.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: 4_Hour_ATAC_Counts.txt contains ATAC count values for defined peaks for each sample
Supplementary files format and content: 4_Hour_Aniso_ATAC_Counts.txt contains ATAC count values for defined peaks for each sample

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to ATAC-seq. Each culture well contained ~250,000 cells.

extract_protocol:
Following treatment, media was aspirated, and cells were washed with 1x cold PBS. Then, 600 µl of Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, Molecular Grade H2O) was added to cell culture wells and incubated for 5 mins on ice. Lysed cells were then transferred to a 1.5 ml Eppendorf tube and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge. Following removal of supernatant containing lysis buffer and cell debris, 500 µl of 1x cold PBS was added to each tube, and nuclei were counted using the Countess II (Life Technologies). The approximate volume needed to achieve 50,000 nuclei was then placed in new Eppendorf tube, and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge.
The nuclei pellet was then resuspended in 22.5 µl of tagmentation reaction mix containing Molecular Grade H2O, 2x Tagment DNA Buffer (Illumina), 0.011% Digitonin, 0.1% Tween-20, followed by the addition of 2.5 µl TDE1 (Illumina) and incubated at 37°C for 1 hr. Following tagmentation, libraries were PCR amplified and purified using the Qiagen Minelute PCR purification kit (Qiagen). To remove primer dimers, libraries were bead purified using one round of 1.0X Ampure XP beads with 80% ethanol, followed by a second round of 0.8X Ampure beads with 80% ethanol. Libraries were sequenced (75-bp paired end reads) on the NextSeq500 platform (Illumina).

treatment_protocol: Neurons from experiment 1 were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 10mM) for 4 hours on DIV 11. Neurons from experiment 2 were treated with DMSO or anisomycin (40µM) for 30 minutes prior to a second treatment with either vehicle or 10mM KCl. 50,000 cells per sample were harvested for ATAC-seq.

tag: experiment id

tag: treatment 1

value: Anisomycin (40microM)

tag: treatment 2


title: AK3

description: ATAC-seq


title: AK4

description: ATAC-seq


title: DK3

description: ATAC-seq

value: DMSO


title: AK1

description: ATAC-seq


title: DK2

description: ATAC-seq


title: DV4

description: ATAC-seq


title: DK1

description: ATAC-seq


title: DV2

description: ATAC-seq


title: DV1

description: ATAC-seq


title: DV3

description: ATAC-seq


title: K4

description: ATAC-seq


title: K3

description: ATAC-seq


title: K2

description: ATAC-seq


title: V4

description: ATAC-seq


title: V3

description: ATAC-seq


title: V1

description: ATAC-seq


title: Wild-type pollen RNA, Unbound fraction, replicate 5

city: Dunedin

first: Rowan

middle: Paul

last: Herridge

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Adapter trimming (Fastx clipper, v0.0.14)
De-multiplexing (Fastx collapser v0.0.14)
Mapping (Bowtie2 v2.3.4.1)
feature counts (bedtools v2.29.0)
Assembly: TAIR10
Supplementary files format and content: Gene/TE name, sequence length, and RPM
Supplementary files format and content: Sequence, readcount (for pus7 and pus10 samples)

organism: Arabidopsis thaliana

source_name: pollen

extract_protocol:
tissue ground in liquid nitrogen, Trizol total RNA extraction, 15% urea PAGE fractionation, 17-40nt cut and eluted ON
NEBNext small RNA sequencing kit (CMC samples); Perkin Elmer Nextflex v3 (IP samples)

treatment_protocol: N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)

value: pollen

value: unbound (IP)


title: Wild-type pollen RNA, Unbound fraction, replicate 4


title: Wild-type pollen RNA, IP fraction, replicate 5

value: IP


title: RNA V2


title: Wild-type pollen RNA, IP fraction, replicate 4


title: Wild-type pollen RNA, Unbound fraction, replicate 1


title: Wild-type pollen RNA, Unbound fraction, replicate 3


title: Wild-type pollen RNA, Unbound fraction, replicate 2


title: Wild-type pollen RNA, IP fraction, replicate 3


title: Wild-type pollen RNA, IP fraction, replicate 2


title: DK4

description: ATAC-seq


title: Wild-type pollen RNA, IP fraction, replicate 1


title: Wild-type inflorescence RNA, Unbound fraction, replicate 4

source_name: inflorescence

value: inflorescence


title: Wild-type inflorescence RNA, Unbound fraction, replicate 3


title: Wild-type inflorescence RNA, Unbound fraction, replicate 5


title: Wild-type inflorescence RNA, Unbound fraction, replicate 1


title: Wild-type inflorescence RNA, IP fraction, replicate 4


title: Wild-type inflorescence RNA, IP fraction, replicate 3


title: Wild-type inflorescence RNA, IP fraction, replicate 5


title: Wild-type inflorescence RNA, Unbound fraction, replicate 2


title: Wild-type inflorescence RNA, IP fraction, replicate 2


title: Wild-type inflorescence RNA, IP fraction, replicate 1


title: Wild-type inflorescence RNA, CMC-treated, replicate 8

value: CMC


title: Wild-type inflorescence RNA, CMC-treated, replicate 7


title: Wild-type inflorescence RNA, CMC-treated, replicate 6


title: Wild-type inflorescence RNA, CMC-treated, replicate 4


title: Wild-type inflorescence RNA, CMC-treated, replicate 5


title: Wild-type inflorescence RNA, CMC-treated, replicate 3


title: Wild-type inflorescence RNA, CMC-treated, replicate 2


title: Wild-type inflorescence RNA, CMC-treated, replicate 1


title: Wild-type inflorescence RNA, mock-treated, replicate 8

value: mock (CMC)


title: Wild-type inflorescence RNA, mock-treated, replicate 5


title: Wild-type inflorescence RNA, mock-treated, replicate 6


title: Wild-type inflorescence RNA, mock-treated, replicate 3


title: Wild-type inflorescence RNA, mock-treated, replicate 4


title: Wild-type inflorescence RNA, mock-treated, replicate 2


title: pus7 inflorescence RNA, mock-treated, replicate2

data_processing:
Adapter trimming (Fastx clipper, v0.0.14)
De-multiplexing (Fastx collapser v0.0.14)
Mapping (Bowtie2 v2.3.4.1)
Assembly: TAIR10
Supplementary files format and content: Gene/TE name, sequence length, and RPM
Supplementary files format and content: Sequence, readcount (for pus7 and pus10 samples)


title: pus7 inflorescence RNA, mock-treated, replicate1


title: pus7 inflorescence RNA, CMC-treated, replicate1


title: pus10 inflorescence RNA, CMC-treated, replicate2


title: pus10 inflorescence RNA, CMC-treated, replicate1


title: pus10 inflorescence RNA, mock-treated, replicate2


title: pus10 inflorescence RNA, mock-treated, replicate1


title: psd-13 pollen RNA, unbound fraction, replicate 1


title: psd-13 pollen RNA, IP fraction, replicate 3


title: psd-13 pollen RNA, IP fraction, replicate 1


title: psd-13 pollen RNA, unbound fraction, replicate 3


title: psd-13 pollen RNA, unbound fraction, replicate 2


title: psd-13 pollen, input RNA, replicate 1

value: Input (IP)


title: psd-13 inflorescence RNA, unbound fraction, replicate 2


title: psd-13 pollen RNA, IP fraction, replicate 2


title: psd-13 pollen, input RNA, replicate 2


title: psd-13 pollen, input RNA, replicate 3


title: Wild-type inflorescence RNA, mock-treated, replicate 7


title: Wild-type inflorescence RNA, mock-treated, replicate 1


title: psd-13 inflorescence RNA, IP fraction, replicate 1


title: Col-0 pollen RNA, unbound fraction, replicate 3


title: psd-13 inflorescence RNA, IP fraction, replicate 2


title: psd-13 inflorescence RNA, unbound fraction, replicate 1


title: Col-0 pollen RNA, IP fraction, replicate 3


title: pus7 inflorescence RNA, CMC-treated, replicate2


title: Col-0 pollen RNA, IP fraction, replicate 2


title: Col-0 pollen RNA, unbound fraction, replicate 2


title: Col-0 pollen RNA, IP fraction, replicate 1


title: Col-0 pollen RNA, unbound fraction, replicate 1


title: Col-0 pollen, input RNA, replicate 2


title: Col-0 pollen, input RNA, replicate 3


title: Col-0 pollen, input RNA, replicate 1


title: wt_pollen_input_rep1

city: Poznan

first: Jakub

middle: Jacek

last: Dolata

address: Uniwersytetu Poznanskiego 6

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

data_processing:
For small RNA studies, adapters were removed (cutadapt),PCR duplciates were removed (prinseq-lite), reads were trimmed and size selected (cutadapt). Reads corresponding to miRNAs were selected using ‘mirnasoft’ package and counted, number of reads corresponding to TE-siRNA were obtained using bedtools package. Analysis was performed using 'DESeq2'
Assembly: tair10

growth_protocol: temp 22C, long day, 14 days old seedlings were grown on ½ MS plates, older plants were grown on soil

extract_protocol:
NEXTFLEX Small RNA-seq v3 Kit (PerkinElmer)
RNA was extracted with Trizol and using the Direct-zol kit (Zymo Research)

value: WT

value: input sample for small RNA AGO9 IP (WT)


title: wt_pollen_input_rep2


title: psd_pollen_AGO9_Unb_rep1

value: unbound fraction for small RNA AGO9 IP (psd-13)


title: psd_pollen_input_rep2

value: input sample for small RNA AGO9 IP (psd-13)


title: psd_pollen_AGO9_Unb_rep2


title: psd_pollen_AGO9_IP_rep2

value: small RNA AGO9 IP (psd-13)


title: wt_pollen_AGO9_IP_rep2

value: small RNA AGO9 IP (WT)


title: wt_pollen_AGO9_IP_rep1


title: wt_pollen_AGO9_Unb_rep2

value: unbound fraction for small RNA AGO9 IP (WT)


title: psd_pollen_input_rep1


title: IgG control for RNA IP seq from WT Col-0 seedlings

data_processing:
For long RNA IP studies, reads were trimmed (fastx_trimmer), and adapters were removed (Trimmomatic). Transcripts were counted using the Salmon package. Reads were mapped with Hisat2.
txt file containing TPM values for each transcript
Assembly: tair10

source_name: seedlings

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit (NEB)
RNA was extracted with Trizol and using the Direct-zol kit (Zymo Research)

value: seedlings

value: IgG control sample for pseudouridine RNA IP (WT)


title: GFP RNA IP seq from WT Col-0 seedlings rep1

molecule: nuclear RNA

value: GFP RNA IP (WT) rep1


title: Pseudouridine RNA IP seq from WT Col-0 seedlings

value: pseudouridine RNA IP seq from (WT)


title: wt_pollen_AGO9_Unb_rep1

value: pollen


title: GFP RNA IP seq from pNHP2:GFP-NHP2 line 4 seedlings

value: pNHP2:GFP-NHP2 line 4

value: GFP-NHP2 RNA IP (pNHP2:GFP-NHP2 line 4)


title: GFP RNA IP seq from pNHP2:GFP-NHP2 line 7 seedlings

value: pNHP2:GFP-NHP2 line 7

value: GFP-NHP2 RNA IP (pNHP2:GFP-NHP2 line 7)


title: GFP RNA IP seq from pNHP2:GFP-NHP2 line 16 seedlings

value: pNHP2:GFP-NHP2 line 16

value: GFP-NHP2 RNA IP (pNHP2:GFP-NHP2 line 16)


title: RNAseq from WT Col-0 seedlings (input sample)

value: WT

value: input sample for pseudouridine RNA IP (WT)


title: RNAseq from pNHP2:GFP-NHP2 line 4 seedlings (input sample)

value: input sample for RNA IP (pNHP2:GFP-NHP2 line 4)


title: GFP RNA IP seq from WT Col-0 seedlings rep2

value: GFP RNA IP (WT) rep2


title: RNAseq from pNHP2:GFP-NHP2 line 16 seedlings (input sample)

value: input sample for RNA IP (pNHP2:GFP-NHP2 line 16)


title: Unbound fraction for pseudouridine small RNA IP seq from dkc1-10 leaves rep2

data_processing:
For small RNA studies, adapters were removed (cutadapt),PCR duplciates were removed (prinseq-lite), reads were trimmed and size selected (cutadapt). Reads corresponding to miRNAs were selected using ‘mirnasoft’ package and counted, number of reads corresponding to TE-siRNA were obtained using bedtools package. Analysis was performed using 'DESeq2'
BED file
Assembly: tair10

source_name: leaves

value: leaves

value: pABI3:DKC1 line 10 in SALK_031065 background

value: unbound fraction for small RNA pseudouridine IP (dkc1-10)


title: Unbound fraction for pseudouridine small RNA IP seq from dkc1-10 leaves rep1


title: RNAseq from pNHP2:GFP-NHP2 line 7 seedlings (input sample)

value: seedlings

value: input sample for RNA IP (pNHP2:GFP-NHP2 line 7)


title: Unbound fraction for pseudouridine small RNA IP seq from dkc1-7 leaves rep1

value: pABI3:DKC1 line 7 in SALK_031065 background

value: unbound fraction for small RNA pseudouridine IP (dkc1-7)


title: Unbound fraction for pseudouridine small RNA IP seq from WT Col-0 leaves rep3

value: unbound fraction for small RNA pseudouridine IP (WT)


title: Unbound fraction for pseudouridine small RNA IP seq from dkc1-7 leaves rep2


title: Unbound fraction for pseudouridine small RNA IP seq from WT Col-0 leaves rep2


title: Unbound fraction for pseudouridine small RNA IP seq from WT Col-0 leaves rep1


title: psd_pollen_AGO9_IP_rep1

value: pollen

value: small RNA AGO9 IP (psd-13)


title: Pseudouridine small RNA IP seq from WT Col-0 leaves rep3

value: small RNA pseudouridine IP (WT)


title: Pseudouridine small RNA IP seq from dkc1-7 leaves rep2

value: small RNA pseudouridine IP (dkc1-7)


title: Pseudouridine small RNA IP seq from WT Col-0 leaves rep2

value: WT


title: small RNAseq from dkc1-10 leaves (input sample) rep2

value: input sample for small RNA pseudouridine IP (dkc1-10)


title: Pseudouridine small RNA IP seq from WT Col-0 leaves rep1


title: Pseudouridine small RNA IP seq from dkc1-7 leaves rep1


title: RNAseq from WT Col-0 seedlings (input sample) rep2

value: input sample for RNA IP (WT) rep2


title: Pseudouridine small RNA IP seq from dkc1-10 leaves rep1

value: small RNA pseudouridine IP (dkc1-10)


title: small RNAseq from WT Col-0 leaves (input sample) rep3

value: input sample for small RNA pseudouridine IP (WT)


title: small RNAseq from dkc1-7 leaves (input sample) rep2

value: leaves

value: input sample for small RNA pseudouridine IP (dkc1-7)


title: small RNAseq from WT Col-0 leaves (input sample) rep2


title: small RNAseq from WT Col-0 leaves (input sample) rep1


title: psd_sc_IgG

source_name: sperm cells

value: sperm cells

value: IgG control sample for small RNA pseudouridine IP (psd-13)


title: hst_sc_IgG

value: IgG control sample for small RNA pseudouridine IP (hst-6)


title: small RNAseq from dkc1-10 leaves (input sample) rep1

value: pABI3:DKC1 line 10 in SALK_031065 background


title: WT_sc_IgG

value: IgG control sample for small RNA pseudouridine IP (WT)


title: RNAseq from WT Col-0 seedlings (input sample) rep1

value: seedlings

value: input sample for RNA IP (WT) rep1


title: hst_sc_pU

value: small RNA pseudouridine IP (hst-6)


title: psd_sc_pU

value: small RNA pseudouridine IP (psd-13)


title: hst_sc_input

value: input sample for small RNA pseudouridine IP (hst-6)


title: psd_sc_input

value: input sample for small RNA pseudouridine IP (psd-13)


title: WT_sc_input

value: WT


title: Pseudouridine small RNA IP seq from dkc1-10 leaves rep2


title: psd_sc_rep1


title: hst_sc_rep1


title: WT_sc_rep1


title: WT_pollen_rep1

data_processing:
For small RNA studies, adapters were removed (cutadapt), reads were trimmed and size selected (cutadapt). Reads corresponding to miRNAs were selected using ‘mirnasoft’ package and counted, number of reads corresponding to TE-siRNA were obtained using bedtools package.
txt file  containing a number of reads for a particular miRNA
Assembly: tair10

value: pollen


title: WT_pollen_CMC-_Mn_rep1

data_processing:
For miRNA mismatch analysis, adapters sequences were removed and reads were trimmed (cutadapt). Reads were aligned to the genome using BWA and processed with SAMtools. Final files were obtained using ‘bam-readcount’ and AWK scripts
txt file  containing mapping information for each position in the miRNA sequence
Assembly: tair10

value: control for RNA treted with CMC, RT performed using Mn ions


title: small RNAseq from dkc1-7 leaves (input sample) rep1

value: pABI3:DKC1 line 7 in SALK_031065 background


title: WT_pollen_CMC+_Mn_rep1

value: RNA treated with CMC, RT performed using Mn ions


title: WT_pollen_CMC-_Mg_rep1

value: control for RNA treted with CMC, RT performed using Mg ions


title: WT_inflorescence_rep1

value: inflorescence


title: WT_inflorescence_CMC-_Mg_rep1


title: WT_inflorescence_CMC+_Mg_rep1

value: RNA treated with CMC, RT performed using Mg ions


title: WT_inflorescence_CMC-_Mn_rep1


title: WT_inflorescence_CMC+_Mn_rep1


title: snRNA-seq P. miniata 40 hpf

city: PITTSBURGH

first: Hinman

last: Veronica

state: PA

address: 587 S Negley Ave, Apt 17

department: Biological Sciences

institute: Carnegie Mellon University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger V4.0.0 (Zheng et al., 2017) was used to create  aligned to a pre- mRNA indexes for P. miniatagenome V3.0 (GenBank assembly accession: GCA_015706575.1) andS. purpuratusgenome V5.0 (GenBank assembly accession: GCA_000002235.4). The pre-mRNA indices were constructed using gene annotation files modified by an in-house script to remove intron annotations. Read were aligned using the cellranger count command. The raw, unfiltered count files are presented in this GEO entry. In the P. miniata entries, note that when applicable, the gene names are consistant with the names of their 1:1 othologs in S. purpuratus, as is consistant with the gene page naming system of echinobase.org
A Standard Seurat processing pipeline (V4.2.0 ) was used to prepare the final .RDS atlases provided in this entry.
Assembly: S. purpuratusgenome V5.0 (GenBank assembly accession: GCA_000002235.4)
Supplementary files format and content: annotated and processed P.miniata developmental atlas in .RDS format ( note that when applicable, the gene names are consistant with the names of their 1:1 othologs in S. purpuratus, as is consistant with the gene page naming system of echinobase.org)

organism: Patiria miniata

source_name: whole embryo nuclar extract

extract_protocol:
Nuclear isolation protocol adapted from Omni-ATAC-seq protocol (Corces et al., 2017). Full protocol in Meyer et al 2021, biorxiv
Single nuclei libraries were created using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 RevD (10X Genomics) and the Chromium X instrument (10X Genomics) using manufacturer protocols

value: whole embryo nuclar extract

tag: developmental stage

value: 40 hpf


title: snRNA-seq P. miniata 16 hpf

description: 10X Genomics

value: 16 hpf


title: WT_sc_pU

value: sperm cells

tag: genotype

value: small RNA pseudouridine IP (WT)


title: snRNA-seq P. miniata 26 hpf

description: 10X Genomics

value: 26 hpf


title: XCV3-24h-1

value: Leaves


title: XCV3-12h-2


title: XCV3-24h-3


title: XCV3-12h-1


title: XCV3-6h-1


title: XCV3-6h-2


title: XCV3-48h-2


title: XCV3-48h-1


title: XCV3-12h-3


title: XCV3-3h-2


title: XCV3-6h-3


title: XCV3-3h-3


title: XCV1-48h-2


title: XCV1-48h-3


title: WT_pollen_CMC+_Mg_rep1


title: XCV1-48h-1


title: XCV3-48h-3


title: XCV3-24h-2


title: XCV1-24h-3


title: XCV1-24h-2


title: XCV1-24h-1


title: XCV1-12h-3


title: XCV1-12h-1


title: XCV1-6h-1


title: XCV1-6h-3


title: XCV1-6h-2


title: XCV3-3h-1


title: XCV1-3h-3


title: XCV1-3h-2


title: XCV1-3h-1


title: mock-48h-3


title: mock-48h-1


title: mock-12h-2


title: mock-24h-2


title: mock-24h-3


title: mock-6h-2


title: mock-6h-1


title: mock-3h-2


title: mock-3h-1


title: mock-0h-2


title: mock-6h-3


title: mock-0h-3


title: mock-48h-2


title: mock-24h-1


title: mock-12h-3


title: XCV1-12h-2


title: mock-12h-1


title: mock-3h-3


title: KBTRE, normal, replicate S2

city: Santiago

first: Carmen

middle: Gloria

last: Feijoo

state: Region metropolitana

address: Republica 330

department: Facultad de Ciencias de la vida

country: Chile

institute: Universidad Andres Bello

description:
10X Genomics
Dre_KBTREnormal_raw_bc_barcodes.tsv.gz
Dre_KBTREnormal_features.tsv.gz
Dre_KBTREnormal_matrix.mtx.gz

data_processing:
Reads from the four separate conditions (flowcells) were preprocessed using Seurat in R (https://satijalab.org/seurat/)
Assembly: GRCz11
Supplementary files format and content: tab-separated values files

organism: Danio rerio

source_name: whole embryo

extract_protocol:
For tissue disaggregation, whole embryos were incubated with a digestion cocktail (10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L-15 medium was added to stop the digestion process. Isolated cells were pelleted, resuspended in L-15 medium and processed by FACS.
Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion (GEMs). GEM-RT was performed in a C1000 Touch Thermal cycler. After reverse transcription, GEMs were broken, and the single-strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single-Cell 3’ Library Kit following these steps: 1) end repair and A-tailing, 2) adapter ligation, 3) postligation cleanup with SPRIselect, 4) sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.

value: whole embryo

tag: cell type

value: neutrophils


title: KBTRE, cut, replicate S9

description:
10X Genomics
Dre_KBTREcut_raw_bc_barcodes.tsv.gz
Dre_KBTREcut_features.tsv.gz
Dre_KBTREcut_matrix.mtx.gz


title: KBTRE, normal, replicate S3


title: KBTRE, normal, replicate S4


title: KBTRE, normal, replicate S1


title: KBTRE, cut, replicate S11


title: KBTRE, cut, replicate S10


title: mock-0h-1

value: WT

tag: treatment


title: KBTGR, normal, replicate S8

description:
10X Genomics
Dre_KBTGRnormal_raw_bc_barcodes.tsv.gz
Dre_KBTGRnormal_features.tsv.gz
Dre_KBTGRnormal_matrix.mtx.gz


title: KBTGR, normal, replicate S7


title: KBTRE, cut, replicate S12


title: KBTGR, normal, replicate S6


title: KBTGR, cut, replicate S15

description:
10X Genomics
Dre_KBTGRcut_raw_bc_barcodes.tsv.gz
Dre_KBTGRcut_features.tsv.gz
Dre_KBTGRcut_matrix.mtx.gz


title: KBTGR, cut, replicate S14


title: 10cycles, replicate 1, scRNAseq

city: ITHACA

first: Carolyn

last: Adler

state: NY

address: 930 Campus road

institute: Cornell University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: Smed_chr_ref_v1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Schmidtea mediterranea

source_name: Whole animal dissociation

extract_protocol:
For each biological replicate, 10 animals were dissociated into single-cell suspension by dicing in CMFB buffer [calcium-magnesium-free solution with 1% BSA (400 mg/L NaH2PO4, 800 mg/L NaCl, 1200 mg/L KCl, 800 mg/L NaHCO3, 240 mg/L glucose, 1% BSA, 15 mM HEPES, pH7.3)] and nutating for 2 hours at room temperature. The cells were centrifuged at 500g for 5 min, resuspended, and filtered through a 30µm cell strainer (BD Biosciences, cat.no 340628) to remove debris. The concentration of filtered cells was calculated with a TC20 automated cell counter (Bio-Rad). After centrifugation, cell concentration was adjusted to 100,000 cells/mL with staining buffer [CMFB containing DRAQ5 (5 µM) and Calcein-AM (0.4 µM)] and nutated at room temperature for 5 min. X1 cells were gated for vital 4N cells (DRAQ5+ Calcein-AM+) on a Sony MA900 Cell Sorter. 100,000 cells were sorted and diluted to a concentration of 1000 cells/µL for subsequent library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) for untreated samples. For DASH-treated samples, 30 sgRNAs targeting 16S sequences were generated by in vitro transcrption. 1 ng of the cDNA was incubated with 30nM of Cas9 and 300nM of sgRNAs for overnight digestion. Digested cDNA were PCR-clean up by Ampure beads, and followed by 10 cycles of PCR using R1 and TSO primers. The subsequent library preparation for DASH-treated samples were according to manufacter’s instructions for end repair and indexing.

value: Stem cells

value: Whole animal dissociation

tag: strain


title: KBTGR, cut, replicate S13

tag: tissue


title: KBTGR, normal, replicate S5


title: KBTGR, cut, replicate S16


title: 5cycles, replicate 1, scRNAseq

description: 10x Genomics

tag: age


title: noPCR, replicate 1, scRNAseq

description: 10x Genomics


title: DASHed, replicate 1, scRNAseq

description: 10x Genomics


title: untreated, replicate 3, scRNAseq

description: 10x Genomics


title: DASHed, replicate 3, scRNAseq

description: 10x Genomics


title: DASHed, replicate 2, scRNAseq

description: 10x Genomics


title: untreated, replicate 2, scRNAseq

description: 10x Genomics


title: P31.Dataset, 206535570106_R01C02

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to the the Beadchip HorvathMammalMethylChip using standard Illumina protocol

data_processing: Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.

label: Cy3 and Cy5

extract_protocol: genomic DNA was extracted

tag: confidenceinageestimate

value: Tail

tag: female

tag: tissuedetailed

value: Tail skin

tag: specieslatinname

value: Mus musculus


title: P31.Dataset, 206535570091_R03C01

value: Blood

value: Whole blood


title: P31.Dataset, 206535570091_R05C01


title: P31.Dataset, 206535570091_R04C02


title: P31.Dataset, 206535570091_R01C02


title: P31.Dataset, 206535570091_R03C02


title: P31.Dataset, 206535570091_R02C01


title: untreated, replicate 1, scRNAseq

description: 10x Genomics


title: P31.Dataset, 206535570106_R03C02


title: P31.Dataset, 206535570106_R04C02


title: P31.Dataset, 206535570091_R06C02


title: P31.Dataset, 206535570091_R01C01


title: P31.Dataset, 206535570091_R02C02


title: P31.Dataset, 206535570106_R05C02


title: P31.Dataset, 206535570091_R05C02


title: P31.Dataset, 206535570106_R03C01


title: P31.Dataset, 206535570106_R06C01


title: H81 healthy control6

city: Xi'an

first: Xueshan

last: Du

state: Shannxi Province

address: Xiwu Road, Xi’an, Shaanxi, China

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

description: healthy control6

data_processing:
The quality of the raw sequence reads was assessed using Trimmomatic v0.33 was used to trim sequencing adapters, reads with a quality score <20 over a sliding window size of 50 bp, and reads with a sequence length <100 bp
Reads were aligned to the human genome by bowtie2 (version 2.2.4) and any hit associated with the reads and their mated reads were removed.
After trimming the adaptors and filtering low-quality reads, the clean sequence data were used for further bioinformatics analyses.
Metagenomics data were assembled using MEGAHIT , which makes use of succinct de Bruijn graphs.Assembly summary statistics were determined using QUAST software version 2.3 .Contigs with the length being or over 300 bp were selected as the final assembling result, and then the contigs were used for further gene prediction and annotation.
Assembly: MEGAHIT

organism: human feces metagenome

source_name: feces

extract_protocol:
Total genomic DNA was extracted from fecal samples using the PowerSoil® DNA Isolation kit((Mo Bio Laboratories) according to manufacturer’s instructions. The quality and quantity of the extracted DNA were examined using Qubit dsDNA HS Assay Kit on a Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and electrophoresis on a 1% agarose gel, respectively.
Paired-end libraries (insert size, ~350 bp) were prepared using a VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazyme Biotech). The library was sequenced on an Illumina NovaSeq 6000 platform (Biomarker Technologies Co., Ltd., Beijing, China) using the 150-bp paired-end sequencing mode

value: feces

tag: cell line

value: gut microbiome

value: healthy


title: P31.Dataset, 206535570106_R05C01


title: P31.Dataset, 206535570014_R06C02


title: P31.Dataset, 206535570106_R04C01


title: P31.Dataset, 206535570091_R06C01


title: H92 healthy control7

description: healthy control7


title: H72 healthy control5

description: healthy control5


title: H93 healthy control8

description: healthy control8


title: P31.Dataset, 206535570106_R02C02


title: P31.Dataset, 206535570091_R04C01


title: H71 healthy control4

description: healthy control4


title: P31.Dataset, 206535570014_R05C02


title: H111 healthy control2

description: healthy control2


title: P31.Dataset, 206535570106_R01C01


title: H42 healthy control3

description: healthy control3


title: H101 healthy control1

description: healthy control1


title: BT93 untreated8

value: untreated


title: P31.Dataset, 206535570106_R06C02


title: P31.Dataset, 206535570106_R02C01


title: BT92 untreated7


title: BT82 untreated6


title: BT63 untreated5


title: BT53 untreated4


title: P31.Dataset, 206535570014_R04C02


title: BT13 untreated3


title: BT103 untreated2


title: BT102 untreated1


title: AT9 treated8


title: P31.Dataset, 206535570014_R02C02


title: AT8 treated7

value: secukinumab


title: AT7 treated6


title: P31.Dataset, 206535570014_R03C02


title: AT5 treated5


title: AT3 treated4


title: P31.Dataset, 206535570014_R05C01


title: AT2 treated3


title: P31.Dataset, 206535570014_R01C02


title: AT1 treated1


title: P31.Dataset, 206535570026_R06C02

value: Cortex


title: AT10 treated2


title: healthy control35

data_processing:
Paired-end reads ere merged using FLASH v1.2.11, and tags ith more than six mismatches were discarded. The merged tags with an average quality score <20 in a 50 bp sliding window were determined using Trimmomatic and those shorter than 350 bps were removed.
Possible chimeras were further removed and the denoised sequences were clustered into operational taxonomic units (OTUs) with 97% similarity using USEARCH (version 10.0)
Taxonomy was assigned to all OTUs by searching against the Silva databases (Release138) using QIIME software
Assembly: silva
Supplementary files format and content: TXT files include abundance of microbe for all Sample

growth_protocol: Fresh fecal samples were collected in a specimen collection kit and stored at -80 °C before further manipulation in the laboratory.

extract_protocol:
The bacterial DNA was extracted from fecal samples with a the PowerSoil® DNA Isolation kit((Mo Bio Laboratories) according to manufacturer’s instructions. DNA concentration and purity were determined using NanoDrop 2000 (Thermo Scientific, USA)
Construction of sequencing libraries and paired-_x0002_end sequencing was performed on an Illumina NovaSeq6000 platform at Biomarker Technologies Co, Ltd. (Beijing, China) according to standard protocols


title: healthy control34


title: healthy control33


title: P31.Dataset, 206535570014_R06C01


title: P31.Dataset, 206535570014_R01C01


title: P31.Dataset, 206535570014_R02C01


title: healthy control32


title: healthy control31


title: healthy control30


title: P31.Dataset, 206535570026_R02C02


title: healthy control29


title: P31.Dataset, 206535570026_R04C02


title: P31.Dataset, 206535570026_R03C02


title: healthy control28


title: P31.Dataset, 206535570026_R04C01


title: healthy control27


title: P31.Dataset, 206535570026_R02C01


title: P31.Dataset, 206535570026_R06C01


title: P31.Dataset, 206535570026_R05C02


title: P31.Dataset, 206535570014_R03C01


title: P31.Dataset, 206535570026_R05C01


title: P31.Dataset, 206535570026_R01C02


title: healthy control26


title: healthy control25


title: P31.Dataset, 206535570001_R04C02

value: Liver


title: P31.Dataset, 206535570001_R06C02


title: P31.Dataset, 206535570001_R05C02


title: healthy control24


title: healthy control23


title: P31.Dataset, 206535570026_R01C01


title: healthy control22


title: P31.Dataset, 206535570001_R06C01


title: P31.Dataset, 206535570001_R05C01


title: P31.Dataset, 206535570001_R03C02


title: healthy control21


title: healthy control20


title: healthy control19


title: healthy control18


title: P31.Dataset, 206535570001_R02C02


title: P31.Dataset, 206535570001_R03C01


title: healthy control17


title: healthy control16


title: healthy control14


title: P31.Dataset, 206535570001_R02C01


title: healthy control13


title: healthy control15


title: P31.Dataset, 206535570001_R01C01


title: healthy control12


title: healthy control11


title: P31.Dataset, 206535570001_R04C01


title: P31.Dataset, 206535570001_R01C02


title: P31.Dataset, 206535570026_R03C01


title: P31.Dataset, 206535570014_R04C01


title: P31.Dataset, 206535570002_R06C02


title: P31.Dataset, 206535570002_R02C02

value: Spleen


title: healthy control9


title: healthy control8


title: P31.Dataset, 206535570002_R04C02


title: healthy control6


title: healthy control7


title: healthy control5


title: P31.Dataset, 206535570002_R05C02


title: P31.Dataset, 206535570002_R03C02


title: healthy control4


title: healthy control3


title: healthy control2


title: healthy control1


title: untreated32


title: P31.Dataset, 206535570002_R01C01


title: untreated31


title: P31.Dataset, 206535570002_R04C01


title: P31.Dataset, 206535570002_R06C01


title: P31.Dataset, 206535570002_R03C01


title: healthy control10


title: P31.Dataset, 206535570004_R06C02


title: P31.Dataset, 206535570002_R01C02


title: P31.Dataset, 206535570002_R02C01


title: P31.Dataset, 206535570004_R03C02


title: untreated28


title: P31.Dataset, 206535570002_R05C01


title: P31.Dataset, 206535570004_R04C02


title: untreated25


title: untreated29


title: P31.Dataset, 206535570004_R05C02


title: P31.Dataset, 206535570004_R01C02


title: P31.Dataset, 206535570004_R02C02


title: untreated24


title: untreated27


title: P31.Dataset, 206535570004_R04C01

value: Kidney


title: P31.Dataset, 206535570004_R02C01


title: untreated30


title: untreated23


title: P31.Dataset, 206535570004_R06C01


title: P31.Dataset, 206535570004_R03C01


title: untreated21


title: P31.Dataset, 206535570006_R06C02


title: P31.Dataset, 206535570004_R01C01


title: untreated26


title: untreated22


title: untreated20


title: P31.Dataset, 206535570004_R05C01


title: P31.Dataset, 206535570006_R05C02


title: untreated17


title: P31.Dataset, 206535570006_R03C02


title: P31.Dataset, 206535570006_R02C02


title: untreated18


title: untreated16


title: untreated15


title: P31.Dataset, 206535570006_R04C02


title: untreated13


title: P31.Dataset, 206535570006_R05C01


title: untreated12


title: untreated11


title: P31.Dataset, 206535570006_R01C01


title: untreated10


title: P31.Dataset, 206535570006_R01C02


title: P31.Dataset, 206535570006_R02C01


title: untreated9


title: P30.Dataset, 206535570058_R05C02


title: untreated7


title: untreated8


title: P31.Dataset, 206535570006_R03C01


title: untreated5


title: untreated6


title: P31.Dataset, 206535570006_R04C01


title: untreated14


title: untreated19


title: untreated4


title: untreated3


title: P31.Dataset, 206535570006_R06C01


title: untreated2


title: untreated1


title: P30.Dataset, 206535570058_R06C02


title: treated11


title: treated10


title: treated9


title: treated8


title: P30.Dataset, 206535570058_R06C01


title: P30.Dataset, 206535570058_R03C02


title: treated6


title: treated7


title: treated5


title: P30.Dataset, 206535570058_R02C02


title: P30.Dataset, 206535570058_R01C02


title: P30.Dataset, 206535570058_R04C02


title: treated4


title: treated2


title: treated1


title: P30.Dataset, 206535570033_R06C01


title: P30.Dataset, 206535570058_R05C01


title: treated3


title: P30.Dataset, 206535570058_R02C01


title: P30.Dataset, 206535570058_R03C01


title: P30.Dataset, 206535570112_R06C02


title: P30.Dataset, 206535570033_R03C02


title: P30.Dataset, 206535570058_R01C01


title: P30.Dataset, 206535570112_R05C02


title: E_coli_total_RNA_ModSeq_Mg

city: New Haven

first: Rafael

middle: de Cesaris

last: Araujo Tavares

state: Connecticut

address: 260 Whitney Ave

department: Chemistry

institute: Yale University

data_processing:
ShapeMapper2 (Busan et al.2018)
Mg libraries = untreated samples; Mn libraries = modified samples; use ‘--output-counted-mutations’ flag to output counted mutations
Assembly: human 18S rRNA (NCBI ID: 100008588), human 28S rRNA (NCBI ID: 100008589), human 5.8S rRNA (NCBI ID: 100008587), E. coli 16S rRNA (GeneBank ID: J01859.1), E coli 23S rRNA (GeneBank ID: V00331.1), S cerevisiae 18S rRNA (RNAcentral ID: URS00005F2C2D_4932), S cerevisiae 25S rRNA (RNAcentral ID: URS000061F377_4932)
Supplementary files format and content: profile.txt files = csv containing calculated mutation rates for each nucleotide position in the reference sequence; mutation_counts.txt files = csv containing mutation rate compositions for each nucleotide position in the reference sequence

organism: Escherichia coli

source_name: Bacterial cells (DH5-alpha)

growth_protocol: Human cell lines were grown in DMEM supplemented with 10% fetal bovine serum and 1X antimycotic-antibiotic at 37 deg C; E coli cells were grown in Luria Broth media at 37 deg C; Saccaramyces cerevisiae were grown in YPD at 30 deg C

extract_protocol:
Trizol
cDNA was prepared from total RNA from each source using random nonamer primers and MarathonRT enzyme in the presence of either Mg or Mn as enzymatic cofactors; second-strand synthesis was carried out from each cDNA sample using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module; library preparation was carried out from the resulting dsDNA sample using the Nextera XT DNA kit
Illumina Nextera XT DNA

value: K12 strain


title: CK_WT3

city: Beijing

first: lei

last: zhang

address: Yuanmingyuan West Rd. No.2, Beijing, China

department: College of Horticulture

institute: China Agricultural University

data_processing:
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Genome_build: SL 3.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome
Supplementary_files_format_and_content: text files include FPKM values for each Sample

organism: Solanum lycopersicum

extract_protocol: Total RNA was extracted from 20 days old wild-type tomato and slstop1 mutant plants treated with 0 and 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced.

value: root

value: 20 days after germination

value: wild type

value: 0 microM Al (pH 4.7)


title: P30.Dataset, 206535570112_R03C02

value: Tail

value: Tail skin

value: Mus musculus


title: P30.Dataset, 206535570033_R04C01


title: P30.Dataset, 206535570112_R04C02


title: P30.Dataset, 206535570033_R01C01


title: P30.Dataset, 206535570033_R05C01


title: CK_WT2


title: E_coli_total_RNA_ModSeq_Mn


title: P30.Dataset, 206535570058_R04C01

value: Blood


title: P30.Dataset, 206535570112_R06C01


title: P30.Dataset, 206535570033_R03C01


title: P30.Dataset, 206535570112_R04C01


title: P30.Dataset, 206535570033_R05C02


title: P30.Dataset, 206535570033_R02C02


title: P30.Dataset, 206535570033_R01C02


title: CK_KO2

value: slstop1 mutant


title: P30.Dataset, 206535570112_R05C01


title: P30.Dataset, 206535570112_R01C02


title: CK_KO1


title: CK_KO3


title: P30.Dataset, 206535570033_R04C02


title: P30.Dataset, 206535570033_R02C01


title: P30.Dataset, 206535570112_R02C02


title: P30.Dataset, 206535570033_R06C02


title: Al_WT3

value: 60 microM Al (pH 4.7)


title: Al_WT2


title: Al_KO3


title: P30.Dataset, 206535570112_R02C01


title: CK_WT1


title: Al_KO2


title: P30.Dataset, 206535570112_R03C01


title: △AP2-MRPKO_40hpi_rep2

city: Thuwal

first: AMIT

last: SUBUDHI

address: Level4, Builiding, 2, KAUST

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
The quality of the raw reads was assessed using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Low-quality reads and Illumina adaptor sequences from the read ends were removed using TrimmomaticR  (Bolger et al., 2014). Processed reads were mapped to the P. falciparum 3D7 reference genome (release 40 in PlasmoDB- http://www.plasmoddb.org) using Hisat2 (Kim et al., 2015) (V 2.1.0) with parameter “—rna-strandness FR”. Counts per feature were estimated using FeatureCounts (Liao et al., 2014). Raw read counts data were converted to counts per million (cpm) and genes were excluded if they failed to achieve a cpm value of 1 in at least one of the three replicates performed. Library sizes were scale-normalized by the TMM method using EdgeR software (McCarthy et al., 2012) and further subjected to linear model analysis using the voom function in the limma package (Ritchie et al., 2015). Differential expression analysis was performed using DeSeq2 (Love et al., 2014).  Genes with a fold-change greater than two and a false discovery rate corrected p-value (Benjamini-Hochberg procedure) < 0.05 were considered to be differentially expressed.
Genome_build: Plasmodium falciparum
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Plasmodium falciparum II3 strain

extract_protocol:
Parasite cultures (~0.5-2 ml depending on the asexual developmental stage) were pelleted at 2400 rpm for 3 min, lysed by adding 1ml of Trizol (Sigma), then immediately stored at -80°C until further use. Total RNA was isolated from Trizol lysed parasites according to manufacturer’s instructions (Life Technologies).
Strand-specific mRNA libraries were prepared from total RNA using TruSeq Stranded mRNA Sample Prep Kit LS (Illumina) according to the manufacturer’s instructions. Briefly, for each sample 100-300 ng of total RNA was used to prepare the libraries. PolyA+ mRNA was captured from total RNA using oligo-T attached to magnetic beads. First strand synthesis was performed using random primers followed by second strand synthesis where dUTP was incorporated in place of dTTP to achieve strand-specificity. Double stranded cDNA ends were ligated with adaptors and the libraries were amplified by PCR for 15 cycles, before sequencing the libraries on Illumina HiSeq-4000 platform with paired-end 150 bp read chemistry according to manufacturer’s instructions (Illumina).

treatment_protocol: DiCre recombinase-mediated excision was induced by adding rapamycin to the culture of ring-stage parasites at a final concentration of 10 nM.

tag: time point


title: Al_WT1


title: △AP2-MRPKO_40hpi_rep3


title: △AP2-MRPKO_40hpi_rep1


title: Control_40hpi_rep3

value: Control


title: Control_40hpi_rep2


title: Control_40hpi_rep1


title: Al_KO1

source_name: Solanum lycopersicum


title: P30.Dataset, 206535570092_R05C02


title: △AP2-MRPKO_16hpi_rep3


title: P30.Dataset, 206535570092_R03C02


title: △AP2-MRPKO_16hpi_rep2


title: Control_16hpi_rep3


title: △AP2-MRPKO_16hpi_rep1


title: P30.Dataset, 206535570092_R02C02


title: Control_16hpi_rep1


title: rpoC H419P M9 glucose with octanoic acid R2

city: La Jolla

first: Christopher

last: Dalldorf

address: 9500 Gilman Dr

department: Bioengineering

institute: UCSD

description:
same as sample name
RPO_HRS_H419P_rpoC_M9_OctanoicA_R2
54

data_processing:
Processed according to https://github.com/avsastry/modulome-workflow
Assembly: GCA_000005845.2
Supplementary files format and content: counts.csv
Supplementary files format and content: log_tpm.csv

organism: Escherichia coli K-12

growth_protocol: M9 4 g/L glucose

extract_protocol:
3 ml of culture was added to 6 ml of Qiagen RNA-protect Bacteria Reagent after sample collection
Sequencing libraries were created using a Kapa Biosystems RNA HyperPrep per vendor protocol.

value: MG1655 substrain BOP27

value: bacterial cell

value: rpoC H419P


title: Control_16hpi_rep2


title: P30.Dataset, 206535570092_R04C02

value: Cortex


title: rpoC H419P M9 glucose with octanoic acid R1

description:
same as sample name
RPO_HRS_H419P_rpoC_M9_OctanoicA_R1
53


title: wt M9 glucose with octanoic acid R2

description:
same as sample name
RPO_HRS_BOP27_M9_OctanoicA_R2
52

source_name: wt M9 glucose with octanoic acid

value: wt

value: wt M9 glucose with octanoic acid


title: P30.Dataset, 206535570092_R01C02


title: P30.Dataset, 206535570092_R06C01


title: P30.Dataset, 206535570092_R05C01


title: wt M9 glucose with octanoic acid R1

description:
same as sample name
RPO_HRS_BOP27_M9_OctanoicA_R1
51


title: P30.Dataset, 206535570092_R02C01


title: P30.Dataset, 206535570092_R04C01


title: AP2-MRP:HA IgG 16 h.p.i.Rep 1

data_processing:
bcl2fastq2 Conversion Software
Low-quality reads and Illumina adaptor sequences from the read ends were removed using Trimmomatic (Bolger et al., 2014).    Quality trimmed reads were aligned to the P. falciparum genome (plasmodb.org, v3, release v32) using HiSat2.  Duplicate reads were removed using samtools (markdup) (Li et al., 2009). GC bias was corrected using deeptool’s correctGCBias tool (Ramirez et al., 2014). For coverage plots of Api2EI 40 h.p.i. and 20 h.p.i. ChIP-seq experiments, deeptool’s bamCompare tool was used to normalize the read coverage per base of the genome position ( option  ‘-bs 1’) in the respective input and ChIP samples or IgG and ChIP samples to the total number of reads in each library (-- nomarmalizeUsing RPKM). Normalized input coverage or IgG coverage per bin was subtracted from the ChIP values (option – operation subtract). Coverage plots were visualized using IGV genome browser (Thorvaldsdottir et al., 2013).
ChIP-Peaks  (q-value cutoff < 0.05) were identified using macs2 (Zhang et al., 2008) by comparing the input with ChIP or IgG with ChIP with default settings but without prior peak modelling (option ‘-nomodel’), the fragment size set to 200 bp (option ‘-extsize 200’) and the genome size  (option ‘-g’) set to 233332839. Robust common peaks between replicates were identified using bedtools ‘intersect’ (option –f 0.30 –r) (Quinlan and Hall, 2010). Peak annotation was carried out using Homer’s annotatePeaks.pl that assigned each peak with the nearest downstream gene. Enrichment heatmaps and profile plots were generated using the deepTools computeMatrix and plotHeatmap tools.
Genome_build: Plasmodium falciparum build version 3
Supplementary_files_format_and_content: Bam files were converted to bigwig files using bamCoverage from the deeptools suite

source_name: P. falciparum

extract_protocol:
The ChIP assay was performed as described (Pandey et al., 2020) with a few modifications. Parasite culture (50 ml) containing synchronized late-stage schizonts (~ 40 h.p.i.) at ~5% parasitemia was centrifuged at 900 g for 4 min and the cells washed once with PBS. To the cell pellet, 25 ml of 0.15% saponin in PBS was added and incubated on ice for 10 min followed by washing twice with cold PBS. Parasites were crosslinked for 10 min by adding methanol-free formaldehyde at 1% final concentration and incubated for 10 min at 37 °C with occasional shaking. The crosslinking reaction was quenched by adding 1.25 M glycine to achieve a final concentration of 0.125 M and incubated at 37 °C for another 5 min. Parasites were centrifuged for 10 min at 3250 g at 4 °C, washed three times with DPBS, snap frozen in liquid nitrogen and stored at -80 °C until further use. Frozen formaldehyde fixed parasites were thawed on ice for chromatin immunoprecipitation. One ml of nuclear extraction buffer (10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1mM DTT, 1x EDTA-free protease inhibitor cocktail [Roche]) was added to the tubes containing thawed parasites and incubated on ice for 30 min. After the incubation, 10% NP-40 was added to reach a final concentration of 0.25% and the parasites were lysed by passing through a 261/2 G needle seven times. Parasite nuclei were collected by centrifuging at 2500g for 10 min at 4 °C. Shearing of chromatin was carried out using the Covaris Ultra Sonicator (E220) for 14 min with the following settings; 5% duty cycle, 140 intensity peak incident power, 200 cycle per burst to obtain fragment size of 200 to 600 bp. Insoluble materials were removed by centrifuging the sheared chromatin for 10 min at 13500 g at 4 °C. 30 µl of fragmented chromatin were stored as input at -80°C.    Fragmented chromatin was diluted 1:1 in ChIP dilution buffer (30 mM Tris-HCl pH 8.0, 0.1% SDS, 3 mM EDTA, 300 mM NaCl, 1% Triton X-100, EDTA-free protease inhibitor cocktail).  Chromatin was incubated overnight with 6 µg of rabbit polyclonal anti-HA antibody (Abcam no. ab9110, RRID:AB_307019)or, as control, the same amount of non-specific Rabbit IgG isotype control (Cat. No. 14-4301-82, Invitrogen, RRID:AB_2532981). The antibody-protein complex was recovered with protein A coupled to magnetic beads (Dynabeads, Invitrogen, Cat No. 10002D), followed by extensive washes with low salt immune complex wash buffer, high salt immune complex wash buffer (washes done at 4 °C) and TE buffer (washes done at RT). Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3) at 45 °C for 30 min with shaking. Immunoprecipitated chromatin and input were reverse crosslinked overnight at 45 °C by adding 5 M NaCl to a final concentration of 0.5 M. Samples were treated with RNaseA for 30 min at 37 °C followed by a 2 h incubation at 45 °C with proteinase K (final concentration 66 µg/ml). DNA was purified using ChIP DNA clean & concentrator (Zymo Research, Cat. No. D5205).
Libraries were prepared using NEBNext Ultra II DNA library kit following the manufacturer’s instructions until the step of adapter ligation (Adapters were diluted at 1: 20 ratio). Adapter ligated libraries were purified using AmpureXP beads. The libraries were amplified for a total of 6 PCR cycles (2 min at 98 °C initial denaturation; 6 cycles of 30 s at 98 °C, 50 s at 62 °C, final extension 5 min at 62 °C) using the KAPA HiFi HotStart Ready Mix (Kapa Biosystems).  Amplified libraries were purified and size selected for 350 bp inserts using AmpureXP beads and sequenced on the Illumina HiSeqX platform with 150 bp paired-end read layouts.

tag: chip antibody


title: rpoB I966S M9 glucose at 42 Celsius R1

description:
same as sample name
RPO_HRS_I966S_rpoB_42C_M9_R1
49

source_name: rpoB I966S M9 glucose at 42 Celsius

value: rpoB I966S

value: rpoB I966S M9 glucose at 42 Celsius


title: P30.Dataset, 206535570110_R03C02

value: Liver


title: AP2-MRP:HA input 16 h.p.i. Rep 2

value: none (input)


title: P30.Dataset, 206535570110_R05C01


title: P30.Dataset, 206535570092_R01C01


title: AP2-MRP:HA input 16 h.p.i. Rep 1


title: P30.Dataset, 206535570110_R03C01


title: P30.Dataset, 206535570112_R01C01


title: P30.Dataset, 206535570092_R03C01


title: P30.Dataset, 206535570110_R02C02


title: rpoB I966S M9 glucose at 42 Celsius R2

description:
same as sample name
RPO_HRS_I966S_rpoB_42C_M9_R2
50


title: P30.Dataset, 206535570110_R04C02


title: P30.Dataset, 206535570110_R05C02


title: P30.Dataset, 206535570110_R02C01


title: wt M9 glucose at 42 Celsius R1

description:
same as sample name
RPO_HRS_BOP27_42C_M9_R1
47

source_name: wt M9 glucose at 42 Celsius

value: wt M9 glucose at 42 Celsius


title: AP2-MRP:HA anti HA 16 h.p.i. Rep 1

value: rabbit polyclonal anti-HA (Abcam no. ab9110, RRID:AB_307019)


title: AP2-MRP:HA IgG 40 h.p.i.Rep 2

value: Rabbit IgG isotype control (Cat. No. 14-4301-82, Invitrogen, RRID:AB_2532981)


title: P30.Dataset, 206535570110_R04C01

value: Mus musculus


title: AP2-MRP:HA anti HA 16 h.p.i. Rep 2


title: P30.Dataset, 206535570110_R06C02


title: AP2-MRP:HA input 40 h.p.i. Rep 2


title: P30.Dataset, 206535570110_R01C01


title: rpoB G1189C M9 glucose R2

description:
same as sample name
RPO_HRS_G1189C_rpoB_M9_R2
46

source_name: rpoB G1189C M9 glucose

value: rpoB G1189C

value: rpoB G1189C M9 glucose


title: AP2-MRP:HA IgG 40 h.p.i.Rep 1


title: rpoB G1189C M9 glucose R1

description:
same as sample name
RPO_HRS_G1189C_rpoB_M9_R1
45


title: AP2-MRP:HA input 40 h.p.i. Rep 1


title: P30.Dataset, 206535570108_R04C02


title: AP2-MRP:HA anti HA 40 h.p.i. Rep 2


title: AP2-MRP:HA anti HA 40 h.p.i. Rep 1


title: P30.Dataset, 206535570108_R06C02


title: P30.Dataset, 206535570110_R01C02


title: rpoC G1055V M9 glucose R2

description:
same as sample name
RPO_HRS_G1055V_rpoC_M9_R2
44

source_name: rpoC G1055V M9 glucose

value: rpoC G1055V

value: rpoC G1055V M9 glucose


title: wt M9 glucose at 42 Celsius R2

description:
same as sample name
RPO_HRS_BOP27_42C_M9_R2
48

value: MG1655 substrain BOP27

value: bacterial cell


title: P30.Dataset, 206535570110_R06C01


title: P30.Dataset, 206535570108_R06C01

value: Spleen


title: P30.Dataset, 206535570108_R03C02


title: P30.Dataset, 206535570108_R05C02


title: rpoC G1055V M9 glucose R1

description:
same as sample name
RPO_HRS_G1055V_rpoC_M9_R1
43


title: P30.Dataset, 206535570108_R01C02


title: rpoB T1037P M9 glucose R2

description:
same as sample name
RPO_HRS_T1037P_rpoB_M9_R2
42

source_name: rpoB T1037P M9 glucose

value: rpoB T1037P

value: rpoB T1037P M9 glucose


title: Spike-In_Pseudouridine_100%_Input_rep2

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

library_source: other

data_processing:
The code for sequencing processing and mutation calling has been packaged into one App (docker image), and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: mm10
Assembly: synthetic
Supplementary files format and content: xlsx (excel)

molecule: other

organism: synthetic construct

source_name: synthetic

extract_protocol:
With 10 ng synthetic RNA oligos carrying 0%, 20%, 40%, 60%, 80%, or 100% pseudouridine, 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). To perform 3′-adapter ligation, 10 µl 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNN AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.  The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.  A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

value: synthetic

value: Spike-In Pseudouridine 100%


title: Spike-In_Pseudouridine_40%_Input_rep2

value: Spike-In Pseudouridine 40%


title: Spike-In_Pseudouridine_80%_Input_rep2

value: Spike-In Pseudouridine 80%


title: Spike-In_Pseudouridine_20%_Input_rep2

value: Spike-In Pseudouridine 20%


title: Spike-In_Pseudouridine_60%_Input_rep2

value: Spike-In Pseudouridine 60%


title: P30.Dataset, 206535570108_R02C02


title: rpoA G315V M9 glucose R2

description:
same as sample name
RPO_HRS_G315V_rpoA_M9_R2
40

source_name: rpoA G315V M9 glucose

value: rpoA G315V

value: rpoA G315V M9 glucose


title: Spike-In_Pseudouridine_60%_Input_rep1


title: Spike-In_Pseudouridine_100%_Input_rep1


title: Spike-In_Pseudouridine_80%_Input_rep1


title: rpoA G315V M9 glucose R1

description:
same as sample name
RPO_HRS_G315V_rpoA_M9_R1
39


title: Spike-In_Pseudouridine_0%_Input_rep2

value: Spike-In Pseudouridine 0%


title: Spike-In_Pseudouridine_40%_Input_rep1


title: rpoB T1037P M9 glucose R1

description:
same as sample name
RPO_HRS_T1037P_rpoB_M9_R1
41


title: Spike-In_Pseudouridine_20%_Input_rep1


title: Spike-In_Pseudouridine_0%_Input_rep1


title: rpoB G858D M9 glucose R2

description:
same as sample name
RPO_HRS_G858D_rpoB_M9_R2
38

source_name: rpoB G858D M9 glucose

value: rpoB G858D

value: rpoB G858D M9 glucose


title: P30.Dataset, 206535570108_R05C01

value: Mus musculus


title: rpoB G858D M9 glucose R1

description:
same as sample name
RPO_HRS_G858D_rpoB_M9_R1
37

value: MG1655 substrain BOP27


title: Spike-In_Pseudouridine_40%_Treated_rep2


title: rpoB I966S M9 glucose R2

description:
same as sample name
RPO_HRS_I966S_rpoB_M9_R2
36

source_name: rpoB I966S M9 glucose

value: bacterial cell

value: rpoB I966S

value: rpoB I966S M9 glucose


title: Spike-In_Pseudouridine_20%_Treated_rep2


title: Spike-In_Pseudouridine_0%_Treated_rep2


title: rpoB I966S M9 glucose R1

description:
same as sample name
RPO_HRS_I966S_rpoB_M9_R1
35


title: P30.Dataset, 206535570108_R04C01

value: Spleen


title: P30.Dataset, 206535570108_R03C01


title: Spike-In_Pseudouridine_100%_Treated_rep2

value: synthetic


title: Spike-In_Pseudouridine_100%_Treated_rep1

value: Spike-In Pseudouridine 100%


title: Spike-In_Pseudouridine_60%_Treated_rep1


title: Spike-In_Pseudouridine_80%_Treated_rep2


title: P30.Dataset, 206535570108_R02C01


title: Spike-In_Pseudouridine_60%_Treated_rep2


title: rpoC N720H M9 glucose R1

description:
same as sample name
RPO_HRS_N720H_rpoC_M9_R1
33

source_name: rpoC N720H M9 glucose

value: rpoC N720H

value: rpoC N720H M9 glucose


title: Spike-In_Pseudouridine_40%_Treated_rep1

value: Spike-In Pseudouridine 40%


title: Spike-In_Pseudouridine_20%_Treated_rep1

value: Spike-In Pseudouridine 20%


title: Spike-In_Pseudouridine_80%_Treated_rep1

value: Spike-In Pseudouridine 80%


title: rpoC N720H M9 glucose R2

description:
same as sample name
RPO_HRS_N720H_rpoC_M9_R2
34


title: Spike-In_Pseudouridine_0%_Treated_rep1


title: rpoC H419P M9 glucose R2

description:
same as sample name
RPO_HRS_H419P_rpoC_M9_R2
32

source_name: rpoC H419P M9 glucose

value: rpoC H419P

value: rpoC H419P M9 glucose


title: 61.5 B12 MATi [0798_2023]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

address: Baldiri Reixac 10

institute: IRB Barcelona

data_processing:
Single-end reads were aligned to the mouse genome version mm10 using STAR (v.2.5.2b).
SAM files were converted to BAM files and sorted using sambamba.
The count matrix was generated with Rsubread with the custom annotation downloaded from ENSEMBL GRCm38.102
Assembly: mm10
Supplementary files format and content: count matrix

source_name: MEF

growth_protocol: Cells were seeded in 6-well plates (300 000 cells per well) in DMEM (10% FBS, pen/strep). The following day, media was replaced with iPSC media and cells were treated as described. RNA was harvested 72h after transfer to iPSC media.

extract_protocol:
RNA was harvested using Qiagen RNeasy kit (Cat. 74106) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using the kits Illumina Stranded mRNA Prep, Ligation (20040534) and IDT for Illumina RNA UD Indexes Set A (20040553), following manufacturer's instructions and 10 cycles of amplification

treatment_protocol: Cells were grown in iPSC media treated continuously with 1μg/mL doxycycline. Samples treated with indicated compounds were treated continuously throughout the 72h of growth (starting at the time of transfer to iPSC media)

value: MEF

value: C57BL/6 Rosa26-rtTA , +/T || Tet-O-OSKM , +/T


title: rpoC H419P M9 glucose R1

description:
same as sample name
RPO_HRS_H419P_rpoC_M9_R1
31


title: 61.5 SAM [0796_2023]

value: 100µM SAM


title: P30.Dataset, 206535570108_R01C01

value: Mus musculus


title: P30.Dataset, 206535570103_R06C02


title: rpoB P1100Q M9 glucose R2

description:
same as sample name
RPO_HRS_P1100Q_rpoB_M9_R2
30

source_name: rpoB P1100Q M9 glucose

value: MG1655 substrain BOP27

value: bacterial cell

value: rpoB P1100Q

value: rpoB P1100Q M9 glucose


title: 61.3 B12 MATi [0792_2023]


title: 61.5 B12 [0797_2023]

value: 2µM B12


title: rpoB P1100Q M9 glucose R1

description:
same as sample name
RPO_HRS_P1100Q_rpoB_M9_R1
29


title: 61.3 NSC [0789_2023]


title: 61.3 B12 [0791_2023]


title: rpoC N309Y M9 glucose R2

description:
same as sample name
RPO_HRS_N309Y_rpoC_M9_R2
28

source_name: rpoC N309Y M9 glucose

value: rpoC N309Y

value: rpoC N309Y M9 glucose


title: 61.5 NSC [0795_2023]


title: P30.Dataset, 206535570103_R04C02

value: Spleen


title: doxB12IP [0145_2022]

data_processing:
Reads were aligned to the mm10 reference genome using bowtie (v.0.12.9) with parameters -n 2 and -m 1. Read deduplication was performed using the markdup function from the sambamba package.
Peaks were called using MACS2 (v.2.2.6) with the --broad option considering the corresponding INPUT files as controls (-c option)
Assembly: mm10
Supplementary files format and content: Peak files from MACS2 in excel format

source_name: Mouse Embryo E13.5

growth_protocol: Cells were seeded in 6-well plates (300 000 cells per well) in DMEM (10% FBS, pen/strep). The following day, media was replaced with iPSC media and cells were treated as described. DNA was harvested 72h after transfer to iPSC media.

extract_protocol:
Cells were fixed with 1% (v/v) PFA for 2 minutes and then quenched with 750 mM Tris for 5 minutes. Cells were washed twice with PBS, scraped, and spun down at 1200 x g for 5 minutes. Pellets were lysed with 100 uL (per well) lysis buffer on ice for 10 minutes, the sonicated using a Diagenode BioRuptor Pico for 10 cycles (30’ on, 30’ off) at 4°C. Lysates were clarified for 10 minutes at 8000 x g, 1% input samples were reserved, and supernatant was used for immunoprecipitation with Diagenode Magnetic beads and H3K3me3 mAb (Cell Signaling Technologies #4909). The following day, cells were washed 3 times and eluted. Cross-links were reversed with RNaseA, proteinase K and NaCl, and chromatin fragments were purified using Qiagen PCR cleanup kit .
ChIP libraries were prepared for sequencing using the kit NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Cat#E7645), following manufacturer´s instructions and 11 cycles of amplification.

treatment_protocol: MEFs were grow in iPSC media. Doxy-OSKM were grown in iPSC media treated continuously with 1μg/mL doxycycline. Samples treated with vitamin B12 had 2 µM supplemented continuously throughout the 72h of growth (starting at the time of transfer to iPSC media)

tag: clone

value: Clone 1

tag: condition

value: doxy-OSKM

tag: ip

value: Mouse Embryo E13.5


title: 61.3 SAM [0790_2023]


title: P30.Dataset, 206535570103_R02C02


title: doxnoB12IP [0144_2022]


title: rpoC N309Y M9 glucose R1

description:
same as sample name
RPO_HRS_N309Y_rpoC_M9_R1
27


title: doxB12input [0074_2022]

value: INPUT


title: doxnoB12input [0073_2022]


title: P30.Dataset, 206535570103_R05C01


title: rpoB E672K M9 glucose R2

description:
same as sample name
RPO_HRS_E672K_rpoB_M9_R2
26

source_name: rpoB E672K M9 glucose

value: rpoB E672K

value: rpoB E672K M9 glucose


title: MEFB12IP [0143_2022]

value: MEF


title: P30.Dataset, 206535570103_R01C02


title: P30.Dataset, 206535570103_R03C02


title: MEFnoB12IP [0142_2022]


title: rpoB E672K M9 glucose R1

description:
same as sample name
RPO_HRS_E672K_rpoB_M9_R1
25