title: Case1_Ery_H3K27ac

value: affected

value: ATR-X syndrome

value: Erythroid

value: sample spiked in with Fixed Drosophila melanogaster S2 cells


title: 9perACSH Xylose Rep 2

status: Public on Apr 24 2022

type: SRA

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

country: USA

institute: University of Wisconsin - Madison

library_source: transcriptomic

data_processing:
For RNA-seq analysis, the paired-end FASTQ files were were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3,  SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming the reads were aligned to the Z. mobilis (ZM4, 8b) genome using BWA-mem version 0.7.12-r1039 with default settings. Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings. Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Assembly: GCA_003052025.1
Supplementary files format and content: Zhang_RPKM_data.txt - RPKM normalized read count values from RNA-seq, linear format
Supplementary files format and content: Zhang_RawCounts_data.txt - Raw read count values from RNA-seq, linear format

molecule: total RNA

organism: Zymomonas mobilis

source_name: bacteria

growth_protocol: Z. mobilis was grown in bioreactors as described in Yang, S., et al., Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnol Biofuels, 2018. 11: p. 125.

extract_protocol:
RNA was extracted from cultures using a phenol-chloroform method as described in Rhodius, V.A. and C.A. Gross, Using DNA microarrays to assay part function. Methods Enzymol, 2011. 497: p. 75-113.
Illumina Low Input RNASeq w/rRNA Depletion: rRNA was removed from 100 ng of total RNA using Ribo-Zero rRNA Removal Kit (Illumina). Stranded cDNA libraries were generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. The prepared library was quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified library was then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v4, and Illumina’s cBot instrument to generate a clustered flow cell for sequencing. Sequencing of the flow cell was performed on the Illumina HiSeq 2500 sequencer using HiSeq TruSeq SBS sequencing kits, v4, following a 2x100 indexed run recipe.

treatment_protocol: Samples for RNA-seq were collected by mixing 10 mL of culture with 1.25 mL ice-cold unbuffered phenol and ethanol mixture (5:95, vol/vol) as described in chwalbach, M.S., et al., Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol, 2012. 78(9): p. 3442-57.

tag: strain

value: Z. mobilis 2032

tag: cell type

value: bacteria

tag: treatment

value: 9perACSH Xylose


title: Ctr4_Ery_H33

city: Oxford

first: Julia

last: Truch

address: John Radcliffe Hospital, Headley Way, Headington

department: RDM - WIMM

country: United Kingdom

institute: University of Oxford

description: Genome-wide library of Immunoprecipitated fragments

library_source: genomic

data_processing:
Mapping : bowtie2, hg19
For un-mapping reads : trimming adaptors trim_galore, combining overlapping R1-R2 reads : flash
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie2, hg19
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of filtered fragments

molecule: genomic DNA

organism: Homo sapiens

source_name: CD34 Culture

growth_protocol: CD34+ cells were isolated from either 50mL of donor peripheral blood or leucocyte reduction filters (obtained from the NHSBT) using Ficoll-Histopaque (Sigma) density centrifugation and positive bead selection (Miltenyi).  The CD34+ fraction was cryopreserved in freezing media consisting of 90% FBS (Gibco) and 10% DMSO.  Frozen CD34+ cells were recovered into base medium (IMDM Source BioScience UK Limited) containing 3% (v/v) AB Serum, 10 μg/mL insulin, 3 U/mL heparin (all from Sigma-Aldrich, Poole, UK), 2% (v/v) fetal bovine serum (Gibco), 200 μg/mL Human holo-transferrin (R&D Systems Minneapolis, MN, USA). For the expansion phase of the three-stage erythroid culture system the media was supplemented with 3 U/mL EPO (Eprex Janssen Cilag UK), 10 ng/mL stem cell factor (SCF) and 1 ng/mL IL-3 (Peprotech, London UK). Cells were maintained at a density of 2x105 cells until day 7 when they were transferred to phase 2 differentiation media consisting of base media with 3 U/mL EPO and 10 ng/mL SCF. From this point cells were staged using cytospins and FACS using a panel of 6 flurophore-conjugated monoclonal antibodies. Staining was conducted in FACS buffer containing 10% FBS and 90% PBS (both from Gibco, UK) and samples analysed using the Attune NxT (Life Technologies, California USA). Gates were set using fluorescence-minus-one controls run for each differentiation and data analysed using FlowJo software v 10.0.8r1. Cells were collected at day 10.

extract_protocol:
isolation protocol:  For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 107 cells were lysed by incubation on ice with lysis buffer for 15 minutes. In samples noted as spiked in, fixed Drosophila melanogaster S2 cells  were added. Lysed cells were sonicated on the Covaris S220. Insoluble material was removed by centrifugation and soluble material was diluted with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for H3.3 (09-838, Millipore), H3K27me3 (ab6002, lot: GR275911-6-1, Abcam), H3K27ac (ab4729, lot: GR276932-1, Abcam), H3K4me3 (07-473, lot: 2664283, Millipore), H3K4me1 (ab195391, lot: GR304893-2, Abcam) overnight. Chromatin binding to Protein A and or G/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 2 µl GlycoBlue.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: phenotype

value: unaffected

tag: disease state

value: control

tag: chip antibody

tag: crosslinking

value: single step cross-linking


title: 9perACSH Xylose Rep 3


title: Ctr1_Ery_H33


title: Ctr4_Ery_H3K27me3


title: Arid1a KO ATAC-seq replicate 2

city: Memphis

first: Douglas

middle: R

last: Green

state: United States

address: 262 Danny Thomas Pl

department: Immunology

institute: St Jude Children's Research Hospital

description: First division

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid genome of reference mouse mm10 assembly and drosophila Ensembl r97 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive -X 2000.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions; only reads mapped in proper pair were kept (-F 1804 -f 2 -q 30).
Peaks were called using MACS (version 2.1.2) with narrowPeak setting, --extsize 200, and recommended mappable genome size (default value for other parameters).
Chromatin accessibility signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters. For Myc KO vs wild type (WT replicate 4-6), it was scaled to 1 million reads mapped to spike-in drosophila genome.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads or 1 million mapped reads of spike-in genome.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division Myc high and Myc low cells were sorted.

extract_protocol: 50,000 cells were pelleted at 500 x g for 5 min at 4°C. Samples were washed in 1 ml cold PBS and resuspended in 50 ul cold cell lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei were pelleted at 1000 x g for 10 min and resuspended in 50 ml transposition reaction mixture (25 ml TD buffer, 2.5 ml TDE1, 22.5 ml ddH2O) (20034197, Illumina). Samples were incubated at 42°C for 45 min. DNA was then purified using MiniElute PCR Purification Kit (28004, Qiagen). Libraries were barcoded and amplified with Q5 High-Fidelity 2x Master Mix (M0492S, NEB).

treatment_protocol: For c-Myc KO samples, Naïve CD8 T cells were treated with 4OHT for 24hr., and then activated by anti-CD3/28 with ICAM for 36hr. For Arid1a KO samples, Naïve CD8 T cells were activated by anti-CD3/28 with ICAM for 36hr., and then first-division CD8 T cells were sorted.

value: CD8+ T cells

tag: genotype

value: Arid1a KO


title: Arid1a KO ATAC-seq replicate 3

description: First division


title: Arid1a KO ATAC-seq replicate 1

description: First division


title: Activated - IgG control

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid reference of mouse mm10 and E. coli ASM584v2 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq6 to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions, or have more than 4 mismatches (-F 0x004 -F 0x008 -F 0x0100 -F 0x0400 -f 0x001 -q 1).
MACS (version 2.1.2) was used to call peaks from the BAM file with IgG control and recommended mappable genome size (default value for other parameters). NarrowPeak mode was used for Myc, broadPeak mode for Arid1a and Brg1.
Signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2.

growth_protocol: Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division CD 8 T cells were sorted.

extract_protocol:
CUT&RUN ChIP-seq experiments were performed as previously described (Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019)) with slight modifications.
CUT&RUN

treatment_protocol: For c-Myc KO samples, Naïve CD8 T cells were treated with 4OHT for 24hr before activation.

value: Wild type


title: WT ATAC-seq replicate 3

description: First division


title: WT ATAC-seq replicate 2

description: First division


title: 9perACSH Glucose Rep 5

value: 9perACSH Glucose


title: Case2_Ery_GATA1

extract_protocol:
108 cells were crosslinked with 2 mM EGS for 45 minuntes and 1% FA for 20 minutes (ATRX) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (GATA1). Cells were lysed and sonicated on the Covaris to give fragments of 100-300bp. Immunoprecipitation was performed by incubation of diluted chromatin overnight.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: two steps cross-linking


title: 9perACSH Glucose Rep 4


title: Case1_Ery_GATA1


title: 9perACSH Glucose Rep 3


title: Ctr2_Ery_GATA1


title: Ctr3_Ery_GATA1


title: Myc WT - Myc binding replicate 2


title: 9perACSH Glucose Rep 2


title: Myc WT - Brg1 binding replicate 1


title: Myc WT - Brg1 binding replicate 2


title: Myc WT - Myc binding replicate 1


title: WT ATAC-seq replicate 1

description: First division


title: Myc WT - Arid1a binding replicate 2


title: 9perACSH Xylose Rep 1


title: Myc WT - Arid1a binding replicate 1


title: 9perACSH Glucose Rep 1


title: Ctr4_Ery_InputDC

description: Genome-wide library of sonicated fragments


title: 1st division Arid1a KO - IgG control


title: 7perASGH Xylose Rep 3

value: 7perASGH Xylose


title: Myc KO - Myc binding replicate 2

value: Myc KO


title: Myc KO - Myc binding replicate 1


title: Myc KO - Brg1 binding replicate 1


title: Ctr2_Ery_InputDC


title: 1st division Arid1a WT - IgG control


title: Myc KO - Brg1 binding replicate 2


title: 7perASGH Xylose Rep 2


title: 7perASGH Xylose Rep 1


title: Ctr1_Ery_InputDC


title: Myc KO - Arid1a binding replicate 1


title: Ctr4_Ery_ATRX

value: ATRX (Abcam ab97508)


title: 7perASGH Glucose Rep 3

value: 7perASGH Glucose


title: Arid1a WT - Myc binding replicate 1


title: 7perASGH Glucose Rep 2


title: Arid1a WT - Myc binding replicate 2


title: Arid1a WT - Brg1 binding replicate 2


title: Ctr1_rep2_Ery_ATRX

value: Erythroid


title: Arid1a WT - Arid1a binding replicate 2


title: Arid1a WT - Brg1 binding replicate 1


title: 7perASGH Glucose Rep 1


title: Arid1a WT - Arid1a binding replicate 1


title: Ctr1_rep1_Ery_ATRX


title: Arid1a KO - Myc binding replicate 1


title: Arid1a KO - Brg1 binding replicate 2


title: Myc KO - Arid1a binding replicate 2


title: Arid1a KO - Brg1 binding replicate 1


title: Capture_Ery_ATRX_Case1

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg19
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

tag: day of differentiation

value: Day 10

value: affected

value: ATR-X syndrome


title: Arid1a KO - Arid1a binding replicate 2


title: Ctr1_rep2_LCL_Runx3

source_name: human lymphoblastoid cell line

growth_protocol: LCLs derived from ATR-X patients and healthy controls were incubated with RPMI medium supplemented with 15% FCS, 1% PenStrep and 1% glutamine at 37°C and 5% CO2.

extract_protocol:
108 cells were crosslinked with 2 mM EGS for 45 minuntes and 1% FA for 20 minutes (ATRX) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (Runx3). Cells were lysed and sonicated on the Covaris to give fragments of 100-300bp. Immunoprecipitation was performed by incubation of diluted chromatin overnight.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: antibody

value: Runx3 (39301Active motif + 653604 BioLegend)


title: Capture_Ery_ATRX_Case2


title: Capture_Ery_Control3

value: unaffected


title: Arid1a KO - Arid1a binding replicate 1


title: Naïve replicate 1

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to the reference mouse mm10 assembly using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive -X 2000.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions; only reads mapped in proper pair were kept (-F 1804 -f 2 -q 30).
Peaks were called using MACS (version 2.1.2) with narrowPeak setting, --extsize 200, and recommended mappable genome size (default value for other parameters).
Chromatin accessibility signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2


title: Ctr2_Ery_ATRX

value: control


title: Naïve replicate 3


title: 6perACSH Glucose Rep 5

value: Z. mobilis 2032

value: bacteria

value: 6perACSH Glucose


title: Capture_Ery_Control2


title: Myc low replicate 3

value: CD8+ T cells


title: Case2_Ery_ATAC

description: Genome-wide library of tagmented fragments

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-100000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013.

tag: time

value: differentiation day 10


title: 6perACSH Glucose Rep 4


title: Case1_Ery_ATAC


title: Myc low replicate 1


title: 6perACSH Glucose Rep 3


title: Arid1a KO - Myc binding replicate 2

value: Arid1a KO


title: Myc low replicate 2


title: Ctr3_Ery_ATAC


title: 6perACSH Glucose Rep 2


title: Myc high replicate 1


title: Ctr2_Ery_ATAC


title: Naïve replicate 2


title: 6perACSH Glucose Rep 1


title: Arid1a KO - rep 3, technical rep 3

description: First-division CD8 T cells

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample
Supplementary_files_format_and_content: Raw read counts of feature-sample in csv file

extract_protocol:
Low input
RNA were isolated by using Direct-zol RNA Microprep Kits (R2061, Zymo Research)
Libraries were prepared using KAP RNA HyperPrep Kit with RiboErase (HMR) (08098131702, Roche) and purified by AMPure SPRI beads (B23318, Beckman-Coulter).


title: Don002_Rep1_Ery_ATAC


title: Arid1a KO - rep 3, technical rep 2

description: First-division CD8 T cells


title: Myc high replicate 3


title: Ctr1_Rep2_Ery_ATAC


title: Arid1a KO - rep 3, technical rep 1

description: First-division CD8 T cells


title: Ctr1_Rep1_Ery_ATAC


title: Cotyledonary zygotic embryos sample 3

city: Malaga

first: Vanessa

middle: Viviana

last: Castro Rodriguez

state: Malaga

address: Universidad de Malaga

country: Spain

institute: Universidad de Malaga

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The reads were assembled using Trinity 2.11.0 (Haas et al., 2013, Nature Protocols 8:1494-512). Contigs lower than 400 pb were eliminated, for the rest of contigs the redundancy was reduced using CD-HIT-EST software (Fu et al., 2012, Bioinformatics 28: 3150-3152).
The final transcriptome was used as the reference for the read mapping that was performed with BWA using the MEM option (Li and Durbin, 2009, Bioinformatics 25: 1754-1760). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The transcript expression was normalised by cpm. Finally the transcripts were filtered; 2 cpm in at least 2 samples (Robinson et al., 2010, Bioinformatics 26: 139-140).
Genome_build: Assembled reference transcriptome
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.The column ID is the sequence identifier.

organism: Pinus pinaster

source_name: Cotyledonary zygotic embryos collected from early August to early September

growth_protocol: Somatic embryos samples were collected during maturation of embryogenic cell line PN519 of maritime pine (Pinus pinaster Ait.). The maturation MLV medium was modified with higher content of sucrose (68 g L-1), gellan gum (Phytagel, 9 g L-1), and abcisic acid (ABA, 80 μM) instead of plant growth regulators. Maturation was conducted at 24 ºC in darkness inside a culture chamber. Samples were collected at three different stages of maturation: early-stage translucent SE (ES1, after 4-6 weeks), pre-cotyledonary opaque SE (ES2, after 6-10 weeks) and cotyledonary SE (ES3, after 12-14 weeks). Zygotic embryos (ZE) were excised from seeds collected from a single maritime pine (Pinus pinaster Ait.) seed orchard (Picard, Saint-Laurent-Médoc, France) from July to November 2015. ZE were sampled at different developmental stages according to de Vega-Bartol et al. (2013): pre-cotyledonary ZE (PC, early to mid-July), early cotyledonary ZE (EC, mid to late-July) and cotyledonary immature ZE (C, from early August to early September).

extract_protocol:
Total RNA of embryo samples was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology 34: 209–214) and modified by Canales et al. (2012, Frontiers in Plant Science 3: 100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK). Samples with a RIN value > 7 were selected to mRNA isolation.
RNA-seq was carried out by Novogen (UK). mRNA was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads (Illumina, San Diego, CA, USA). The samples were sequenced producing paired-end reads of 150 bp length.

treatment_protocol: Samples were frozen in liquid nitrogen and stored at -80 ºC until use.

tag: tissue

value: Zygotic embryo

tag: provenance

value: Seeds collected from a single seed orchard from July to November 2015

tag: collection time

value: from early August to early September


title: Don002_Rep2_Ery_ATAC


title: Arid1a WT - rep 3, technical rep 3

description: First-division CD8 T cells

value: Wild type


title: Arid1a WT - rep 3, technical rep 2

description: First-division CD8 T cells


title: Arid1a WT - rep 3, technical rep 1

description: First-division CD8 T cells


title: Cotyledonary zygotic embryos sample 1


title: Arid1a KO - rep 2

description: First-division CD8 T cells


title: Myc high replicate 2


title: TPEN and Zn treatment_rep2

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

country: China

institute: Yangzhou University

description: The transcriptome of V. parahaemolyticus grown under Zn-replete conditions

data_processing:
The clean reads were mapped to the V. parahaemolyticus RIMD2210633 genome (GenBank accession:  NC_004603.1, NC_004605.1) using Bowtie2.
Gene expression levels were evaluated using featureCounts and differentially expressed genes (DEGs) were identified using DESeq2.
Those genes with a fold change greater than 3 and an adjusted P value less than 0.05 were defined as DEGs.
Assembly: V. parahaemolyticus RIMD2210633 , complete genome (NC_004603.1, NC_004605.1)
Supplementary files format and content: read counts for each gene.
Supplementary files format and content: TPM values for each gene.

organism: Vibrio parahaemolyticus

growth_protocol: The RIMD2210633 strain was grown in LB broth to the early-exponential phase (OD600 of ~0.7).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were analyzed by gel electrophoresis and spectrophotometric analysis using a Nanodrop 200, respectively.
The ribosomal RNA was removed using a rRNA Removal Kit. Then, the mRNA was fragmented into short fragments (300-500 bp) and used as template for cDNA synthesis. The cDNA was added with sequencing adapters and enriched by PCR amplification.

treatment_protocol: Subsequently, two aliquots (1 mL) of the culture were removed and bacterial cells were collected by centrifugation at 6 000 rpm for 5 min. The two bacterial pellets were resuspended with 1 mL LB pretreated with eiher 35 μM TPEN alone or 35 μM TPEN along with 500 μM Zn. The cultures were incubated for 15 min at 37°C.

tag: medium

value: LB

value: Grown in LB pretreated with 35 μM TPEN alone with 500 μM Zn

tag: phase

value: mid-exponential phase


title: TPEN treatment_rep3

description: The transcriptome of V. parahaemolyticus grown under Zn-deficient conditions

value: Grown in LB pretreated with 35 μM TPEN


title: Early-cotyledonary zygotic embryos sample 1

source_name: Early-cotyledonary zygotic embryos collected mid to late-July

value: mid to late-July


title: Arid1a WT - rep 2

description: First-division CD8 T cells


title: TPEN and Zn treatment_rep3

source_name: V. parahaemolyticus grown under Zn-replete conditions


title: TPEN and Zn treatment_rep1


title: Early-cotyledonary zygotic embryos sample 3


title: SU-DIPG-XIII-WT_ATAC-seq rep2

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: untreated ATAC-seq

data_processing:
Grooming: Adaptors were removed from raw paired-end sequencing files using bbduk (BBMap version 38.70 BBDUK).
Mapping: Reads were aligned to the hg19 genome using Bowtie2 default parameters (version 1.1.2). The resultant Sequence Alignment Map (SAM) files were compressed to the Binary Alignment Map (BAM) files on which mitochondrial reads were removed using samtools (samtools 1.4).
Peak Calling: Peaks were called using HOMER default parameters (v4.11). Unique peaks in each cell line were identified using the R package DiffBind (R version 3.6.3, DiffBind version 2.12.0).
Assembly: hg19
Supplementary files format and content: peaks.bed

source_name: brain

growth_protocol: Isogenic H3 wild-type cell lines were made by Dr. Kuang-Yui Chen as previously described (Chen et al., 2020). All cell lines were cultured in Tumor Stem Media as described in Nagaraja et al., 2017. Briefly, the media contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10 mM HEPES (Invitrogen), 1x MEM sodium pyruvate (Invitrogen), human basic fibroblast growth factor and human epidermal growth factor (20 ng/mL each) (Shenandoah), human platelet-derived growth factor (PDGF)-A and PDGF-B (20 ng/mL) (Shendandoah), heparin (10 ng/mL) (StemCell Technologies), and B27 without Vitamin A (Invitrogen).

extract_protocol:
ATAC-seq for cell lines was performed similarly to previously published protocols (Buenrostro et al., 2015 and Corces et al., 2017) with some modifications. Cells were dissociated and 100,000 cells were washed twice with cold PBS at 4°C. Cells were resuspended in 50 uL of ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal, 0.1% Tween-20, and 0.01% Digitonin) and triturated until cells were lysed. Samples were incubated on ice for 3 minutes, washed with 1 mL of the buffer (excluding 0.1% Igepal), and centrifuged at 500 RCF for 10 minutes at 4°C. The pellet was resuspended in 50 uL of transposition mixture containing 25 uL of 2x TD Buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 5 uL Transposase (Illumina Nextera Kit), 0.5 uL 0.1% digitonin, 0.5 uL 10% Tween-20, and PBS, and incubated at 37°C for 60 minutes, and DNA recovered using Zymo DNA Clean and Concentrator-5 Kit.
Libraries were generated by PCR in 50 uL reactions (20 uL of samples, 25 uL 2x NEBNext Master Mix, and 2.5 uL of each custom primers made by Integrated DNA Technologies (IDT) (for sequences see Buensostro et al., 2013). The PCR reaction was as follows: 72°C for 5 minutes, 98°C for 30 sec, and 5 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 minute. DNA was recovered using Zymo DNA Clean and Concentrator-5 Kit. Libraries were sequenced on Illumina HiSeq.

treatment_protocol: None of the cell lines were treated prior to sample collection.

value: brain

tag: cell line

value: SU-DIPG-XIII-WT

value: Diffuse intrinsic pontine gliome (DIPG) cells


title: TPEN treatment_rep2

source_name: V. parahaemolyticus grown under Zn-deficient conditions

tag: strain


title: SU-DIPG-XIII_ATAC-seq rep2

description: untreated ATAC-seq

value: SU-DIPG-XIII

tag: cell type


title: Arid1a WT - rep 1

description: First-division CD8 T cells


title: TPEN treatment_rep1

tag: treatment


title: SU-DIPG-XIII-WT_ATAC-seq rep1

description: untreated ATAC-seq


title: Cotyledonary zygotic embryos sample 2


title: SU-DIPG-XIII_ATAC-seq rep1

description: untreated ATAC-seq


title: Pre-cotyledonary zygotic embryos sample 3

source_name: Pre-cotyledonary zygotic embryos collected early to mid-July

value: early to mid-July


title: SU-DIPG-XVII-WT_ATAC-seq rep2

description: untreated ATAC-seq

value: SU-DIPG-XVII-WT


title: Granta-Vehicle_RNAseq_1

city: Xi’an, China

first: lei

last: zhao

state: Shaanxi

address: Youyixi Road 21

department: School of Ecology and Environment

institute: Northwestern Polytechnical University

description:
Jeko_Granta_Chidmide_VS_Vehicle_all_count.csv
Jeko_Granta_Chidmide_VS_Vehicle_all_tpm.csv

data_processing:
Sequenced reads were mapped to hg19 reference using STAR
Counts were normalized by Transcript per million(TPM)
Genome_build: hg19
Supplementary_files_format_and_content: csv files with gene counts
Supplementary_files_format_and_content: csv files with gene TPM normalized

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: JeKo-1 or Granta-519 lymphoma cell line cultured in RPMI1640 medium supplemented with 10% FBS.

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq of JeKo-1 lymphoma cell line treated with Chidamide or vehicle
RNA-seq of Granta-519 lymphoma cell line treated with Chidamide or vehicle

treatment_protocol: JeKo-1 or Granta-519 lymphoma cell line treated with 4μM Chidamide or vehicle for 12h.

value: Lymphoma

value: Granta

tag: agent

value: Vehicle

tag: replicates

value: replicate 1


title: Granta-Vehicle_RNAseq_2

value: replicate 2


title: Myc KO - rep 5

extract_protocol:
Standard
RNA were isolated by using Direct-zol RNA Microprep Kits (R2061, Zymo Research)
Libraries were prepared using KAP RNA HyperPrep Kit with RiboErase (HMR) (08098131702, Roche) and purified by AMPure SPRI beads (B23318, Beckman-Coulter).

value: CD8+ T cells

value: Myc KO


title: SU-DIPG-XVII-WT_ATAC-seq rep1

description: untreated ATAC-seq


title: Arid1a KO - rep 1

description: First-division CD8 T cells

value: Arid1a KO


title: Pre-cotyledonary zygotic embryos sample 2

value: Zygotic embryo

value: Seeds collected from a single seed orchard from July to November 2015


title: Granta-Chidmide_RNAseq_3

value: Chidmide

value: replicate 3


title: Somatic embryos cotyledonary stage 3 sample  B

source_name: Cotyledonary somatic embryos collected after 12-14 weeks of maturation

value: Somatic embryo

value: Somatic line PN519

value: after 12-14 weeks of maturation


title: Early-cotyledonary zygotic embryos sample 2

value: mid to late-July


title: Granta-Chidmide_RNAseq_1


title: Granta-Vehicle_RNAseq_3


title: Somatic embryos cotyledonary stage 3 sample  C


title: Pre-cotyledonary zygotic embryos sample 1

value: early to mid-July


title: Somatic embryos pre-cotyledonary stage 2 sample  C

source_name: Pre-cotyledonary opaque somatic embryos collected after 6-10 weeks of maturation

value: after 6-10 weeks of maturation


title: Control REP1

city: Roorkee

first: Shri Ram

last: Yadav

state: Uttarakhand

address: Civil Lines

department: Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

data_processing:
The paired-end reads were mapped to the rice reference genome (MSU release 7) using STAR in two-pass mode.
A gene count matrix was generated using quant mode- GeneCounts with rows corresponding to individual genes and columns corresponding to samples.
Genome_build: RGAP V7.0
Supplementary_files_format_and_content: FPKM.txt

organism: Oryza sativa

source_name: Stem base

growth_protocol: Wild-type rice (IR64) seeds were germinated on 1/2 MS media for 6 days under 16/8 h day night condition.

extract_protocol:
RNA was isolated from LCM collected CRP using ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher, Waltham, MA, USA)
RNA sequencing library was prepared using SMARTer universal low input RNA kit (Clontech, Mountain View, CA)

tag: condition/tissue type

value: Ground tissues

value: Control

tag: age

value: 6 days


title: SU-DIPG-XVII_ATAC-seq rep1

description: untreated ATAC-seq

value: brain

value: SU-DIPG-XVII

value: Diffuse intrinsic pontine gliome (DIPG) cells

tag: genotype


title: Granta-Chidmide_RNAseq_2

value: Lymphoma

value: Granta

value: replicate 2


title: Myc KO - rep 3

value: CD8+ T cells

value: Myc KO


title: Myc KO - rep 1


title: Myc KO - rep 2


title: Stage II REP 1

value: Root Primordia

value: CRP outgrowth


title: Stage II REP 2


title: Stage I REP 3

value: CRP initiation


title: Somatic embryos pre-cotyledonary stage 2 sample  B

value: Somatic embryo

value: Somatic line PN519


title: Jeko-1-Vehicle_RNAseq_2

value: Vehicle


title: Somatic embryos early-stage 1 sample  C

source_name: Early-stage translucent somatic embryos collected after 4-6 weeks of maturation

value: after 4-6 weeks of maturation


title: Somatic embryos early-stage 1 sample  B


title: SU-DIPG-XVII_ATAC-seq rep2

description: untreated ATAC-seq


title: Somatic embryos cotyledonary stage 3 sample  A

value: after 12-14 weeks of maturation


title: Myc WT - rep 2

value: Wild type


title: Somatic embryos early-stage 1 sample  A


title: Myc WT - rep 5


title: Myc WT - rep 3


title: Jeko-1-Chidmide_RNAseq_3

value: Chidmide

value: replicate 3


title: Stage I REP 1

value: 6 days


title: Jeko-1-Vehicle_RNAseq_1

value: Lymphoma

value: replicate 1


title: Jeko-1-Chidmide_RNAseq_1


title: Somatic embryos pre-cotyledonary stage 2 sample  A

value: after 6-10 weeks of maturation


title: Jeko-1-Vehicle_RNAseq_3


title: Jeko-1-Chidmide_RNAseq_2

value: replicate 2


title: Control REP2

value: Ground tissues

value: Control


title: CASC3-EIF4A3_RIPiT_rep2

status: Public on Apr 23 2022

city: Columbus

first: Zhongxia

last: Yi

state: OH

department: Molecular Genetics

institute: The Ohio State University

data_processing:
Library strategy: RIPiT-Seq
For Total RNA-Seq, first 10bp of the read 1 (UMI) is appended to the header line and the rest of the read starting from 13bp position is written to new fastq file using a custom Awk script.
Cutadapt is used to trim reads with adapter sequence of "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
Trimmed reads were aligned to the human genome using STAR aligner.
PCR duplicates are removed using UMI-tools with options [--method=unique --multimapping-detection-method=NH]
Deduplicated reads are extracted from the deduplicated bam files and are used as input for Kallisto quantification at the transcript level
Tximport is used to create count matrices. RUVSeq is used to remove unwanted variation and DESeq2 is used to calculate fold change and adjusted p value.
For RIPiT-Seq, using a custom Awk script, the first 8bp of read 1 is appended to the header line and the rest of the read starting from 9bp position is saved.
Only reads starting with "CC" and ending with adapter sequence are saved to a new fastq file using cutadapt command [--discard-untrimmed -g ^CC --no-indels | --discard-untrimmed -O 12 -a TGGAATTCTCGGGTGCCAAGG -].
Trimmed reads were aligned to the human genome using STAR aligner. Gene level quantification is done using the reads align to the canonical EJC position (-39 to -9bp of 3′ end of non-last exon).
DESeq2 is used to calculate fold change along with adjusted p value for each gene.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: DESeq2 table

source_name: HCT116 colorectal cancer cells

growth_protocol: All HCT116 cells are grown in McCoy 5A media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin solution.

extract_protocol:
For total RNA-Seq are extracted from Trizol using either isopropanol precipitation, or silica column based RNA extraction. Total RNAs are suject to DNase I treatment. For small RNA footprint sequencing (RIPiT-Seq), small RNAs and protein are eluted from the primary antibody conjugated to magnetic protein A beads using SDS containing buffer. The elution is then diluted with nuclease-free water and RNAs are extracted using acid phenol chloroform and ethanol precipitation.
For total RNA-Seq, 800 ng of input RNA are used to make RNA-Seq libraries using Corall Total RNA Prep kit from Lexogen. For RIPiT-Seq, an in-house library prep method as described in PMID: 34183131.

treatment_protocol: For siRNA knockdown, 300000 cells are added to a complex of 60 pmol siRNA, 3.2 μL of RNAiMAX (Thermo Fisher) and 200 μL Opti-MEM (Thermo Fisher). Cells are harvested for RNA extraction after 48 hours of initial transfection.

value: HCT116 colorectal cancer cells

tag: knockout

value: WT

tag: sirna

tag: protein tag

tag: molecule

value: Small RNA footprints


title: UPF3B-EIF4A3_RIPiT_rep2

tag: time


title: UPF3B-EIF4A3_RIPiT_rep3


title: Stage I REP 2

value: Root Primordia

tag: tissue

value: CRP initiation


title: Myc WT - rep 1

value: CD8+ T cells


title: MAGOH-EIF4A3_RIPiT_rep3

value: FLAG-MAGOH


title: MAGOH-EIF4A3_RIPiT_rep2


title: Myc WT - rep 4

value: Wild type


title: CASC3-EIF4A3_RIPiT_rep3


title: 20W_3DKO#2_siUPF2_rep1

data_processing:
For Total RNA-Seq, first 10bp of the read 1 (UMI) is appended to the header line and the rest of the read starting from 13bp position is written to new fastq file using a custom Awk script.
Cutadapt is used to trim reads with adapter sequence of "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
Trimmed reads were aligned to the human genome using STAR aligner.
PCR duplicates are removed using UMI-tools with options [--method=unique --multimapping-detection-method=NH]
Deduplicated reads are extracted from the deduplicated bam files and are used as input for Kallisto quantification at the transcript level
Tximport is used to create count matrices. RUVSeq is used to remove unwanted variation and DESeq2 is used to calculate fold change and adjusted p value.
For RIPiT-Seq, using a custom Awk script, the first 8bp of read 1 is appended to the header line and the rest of the read starting from 9bp position is saved.
Only reads starting with "CC" and ending with adapter sequence are saved to a new fastq file using cutadapt command [--discard-untrimmed -g ^CC --no-indels | --discard-untrimmed -O 12 -a TGGAATTCTCGGGTGCCAAGG -].
Trimmed reads were aligned to the human genome using STAR aligner. Gene level quantification is done using the reads align to the canonical EJC position (-39 to -9bp of 3′ end of non-last exon).
DESeq2 is used to calculate fold change along with adjusted p value for each gene.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: DESeq2 table

value: Total RNA


title: CASC3-EIF4A3_RIPiT_rep4


title: UPF3B-EIF4A3_RIPiT_rep4


title: 20W_3DKO#2_siUPF1_rep3


title: CASC3-EIF4A3_RIPiT_rep1


title: 20W_3DKO#2_siUPF2_rep3


title: 20W_3DKO#2_siUPF1_rep2


title: UPF3B-EIF4A3_RIPiT_rep1


title: MAGOH-EIF4A3_RIPiT_rep1


title: MAGOH-EIF4A3_RIPiT_rep4


title: 20W_3DKO#2_siUPF2_rep2


title: 20W_3DKO#2_siNC_rep2

value: siNC


title: 20W_3DKO#2_siNC_rep1


title: 20W_WT_siUPF2_rep3


title: 20W_WT_siUPF2_rep2


title: 20W_3DKO#2_siNC_rep3


title: 20W_WT_siNC_rep3


title: 20W_WT_siNC_rep2


title: 20W_WT_siUPF2_rep1


title: 20W_WT_siNC_rep1


title: 20S_3BKO#1_siUPF3A_rep2


title: 20S_3BKO#1_siUPF3A_rep3


title: 20W_3DKO#2_siUPF1_rep1


title: 20S_WT_siUPF3A_rep3


title: 20S_3BKO#1_siUPF3A_rep1


title: 20S_WT_siUPF3A_rep2


title: 20S_WT_siUPF3A_rep1


title: 20S_3BKO#1_siNC_rep2


title: 20S_3BKO#1_siNC_rep3


title: 20S_WT_siNC_rep1


title: 19S_WT_siUPF1_rep3


title: 20S_3BKO#1_siNC_rep1


title: 19S_3BKO#1_siUPF1_rep3


title: 19S_3BKO#1_siUPF1_rep2


title: 20S_WT_siNC_rep2


title: 19S_3BKO#1_siUPF1_rep1


title: 19S_3BKO#1_siNC_rep3


title: 19S_WT_siUPF1_rep1


title: 19S_3BKO#1_siNC_rep1


title: 19S_WT_siNC_rep3


title: 19S_WT_siNC_rep1


title: 19S_3BKO#1_siNC_rep2


title: 19S_WT_siNC_rep2


title: OS_10

city: Houston

first: Jing

last: Yang

address: 6550 Fannin St

institute: Houston Methodist Research Institute

data_processing: RNA-seq Fastq files were processed through FastQC (v0.11.5), a quality control tool to evaluate the quality of sequencing reads at both the base and read levels, and RNA-SeQC (v1.1.8) to create quality control metrics. One RNA sample with a low sequencing yield and poor mapping rate was excluded from this study. STAR 2-pass alignment (v2.5.3) was performed with default parameters to generate RNA-seq BAM files.

source_name: Osteocytes

growth_protocol: Briefly, after the removal of bone marrow cells, trabecular bone pieces were dissected and placed into PBS buffer. The bone pieces were washed three times in PBS and then further dissected into small bone pieces. The bone pieces were incubated at 37°C for 20 min with shaking in 2 mg/ml collagenase type II (Sigma). The collagenase solution was then removed and discarded, and this procedure was repeated twice. The bone pieces were transferred into flasks, containing Dulbecco’s modified Eagle’s medium (DMEM). Replace culture medium three times per week. On average the osteoblast growing from the bone fragments will be ready for use after 11-15 days. For osteocytes isolation, the washed bone pieces were digested in PBS containing 5 mM EDTA and 0.1% BSA at 37°C for 20 min and rinsed once with PBS, and cell pellets were collected. The bone pieces were then digested with at 37°C for 20 min with shaking in 2 mg/ml collagenase type II and rinsed once with PBS, and cell pellets were collected.  The bone chips were subjected to another 4 times sequential digestion with collagenase and EDTA solution as above and harvested the cell pellets.

extract_protocol:
In brief, RNAs were isolated from mice osteocytes and then purified with the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). RNA-seq libraries were synthesized according to the manufacturer’s instructions (Illumina).
Pooled libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems), examined for size distribution using the Fragment Analyzer (Advanced Analytical), and using the 76-bp paired-end format, sequenced in four lanes of the Illumina HiSeq 4000 Sequencer.

treatment_protocol: Murine myeloma vk12598 cells were intrafemorally injected into C57BL/6 mice. Osteocytes were isolated from control mice (OS_1, OS_2, OS_3, OS_4, OS_5) or myeloma cell vk12598-bearing mice (OS_6, OS_7, OS_8, OS_9, OS_10).

value: C57BL/6, male, 8 wks

value: Bone

tag: disease state

value: multiple myeloma


title: OS_9


title: OS_8


title: OS_7


title: OS_5

value: normal


title: OS_4


title: 20S_WT_siNC_rep3


title: OS_2


title: 19S_WT_siUPF1_rep2


title: OS_1


title: pRPS3-mCherry-tRPS3_modHNH_1

city: Edinburgh

first: Edward

last: Wallace

address: Waddington 2.18, Max Born Crescent, King’s Buildings

department: School of Biological Sciences

institute: University of Edinburgh

data_processing:
Read quality was checked with fastqc=0.11.9
Adapters were removed with cutadapt=1.18 (Options = --trim-n -O 1 -m 20)
Alignment was completed with hisat2=2.1.0 (Options = --no-spliced-alignment --no-unal --maxins 1500 -k 2)
Reads per gene were counted with featureCounts=2.00 (Options = -p -s 2 -R BAM)
Bed files were created with bedtools=2.30.0
Alignment quality was checked with multiQC=1.9
Bam files were create with samtools=1.11
5'P ends quantified with fivepseq=1.0.0
Assembly: sacCer3 (R64-2)
Supplementary files format and content: Format: csv, Content: quantified reads ending in 3'-UTR region of reporter constructs, per construct
Supplementary files format and content: Format: csv, Content: quantified reads corresponding to decapped 5' ends of mRNA of reporter constructs, per construct
Supplementary files format and content: Format: csv, Content: raw read counts mapped to each gene across the genome, one file per sample.
Supplementary files format and content: Format: csv, Content: quantified reads ending in 3'-UTR region of control gene, per construct
Supplementary files format and content: Format: csv, Content: quantified reads corresponding to decapped 5' ends of mRNA of control genes, per construct
Library strategy: HT-5PSeq

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modHNH

growth_protocol: Yeast cultures were grown for 4h at 30degC, 200rpm, in liquid SC-Ura medium up to OD600=0.7

extract_protocol:
RNA extraction protocol: dx.doi.org/10.17504/protocols.io.beetjben
HT-5PSeq: https://doi.org/10.1016/j.crmeth.2021.100001 with following modifications: reverse transcription performed with only oligo(dT) and without random primers

tag: plasmid

value: pRPS3-mCherry-tRPS3_modHNH (pJA0072)


title: OS_6


title: pRPS3-mCherry-tRPS3_modHNH_2


title: pRPS3-mCherry-tRPS3_modHTH_1

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modHTH

value: pRPS3-mCherry-tRPS3_modHTH (pJA0073)


title: pRPS3-mCherry-tRPS3_modHTH_2


title: pRPS3-mCherry-tRPS3_modNAA_1

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNAA

value: pRPS3-mCherry-tRPS3_modNAA (pJA0070)


title: pRPS3-mCherry-tRPS3_modNNN_2

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNNN

value: pRPS3-mCherry-tRPS3_modNNN (pJA0068)


title: pRPS3-mCherry-tRPS3_modNTN_1

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNTN

value: pRPS3-mCherry-tRPS3_modNTN (pJA0069)


title: pRPS3-mCherry-tRPS3_modNTN_2


title: β-elemene treatment -Total RNA(B2）

city: Hefei

first: Heng

last: Deng

address: 300 Shouchun Road, Hefei, Anhui, China

institute: Anhui acupuncture hospital

description:
S20L0600
B_vs_A-group-anno(circRNA).xls/B_vs_A-group-anno(LncRNA).xls/B_vs_A-group-anno(mRNA).xls

data_processing:
Illumina HiSeq 1000 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by Cufflinks
Assembly: mm9
Supplementary files format and content: tab-delimited text files include the expression values of this transcript  for each Sample ...

source_name: CRC cells

growth_protocol: HCT116 cells were grown in high glucose DMEM medium supplemented with 10% fetal bovine serum and antibiotics. Cell cultures were maintained at 37  C with 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor cell

value: colorectal

value: b-elemene


title: β-elemene treatment -Total RNA(B3）


title: pRPS3-mCherry-tRPS3_modNGG_1

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNGG

value: pRPS3-mCherry-tRPS3_modNGG (pJA0071)


title: pRPS3-mCherry-tRPS3_WT_2

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_WT

value: pRPS3-mCherry-tRPS3_WT (pJA0066)


title: β-elemene treatment -Total RNAB1）


title: pRPS3-mCherry-tRPS3_modNGG_2


title: negative control-Total RNA(A3）

description:
S20L0599
B_vs_A-group-anno(circRNA).xls/B_vs_A-group-anno(LncRNA).xls/B_vs_A-group-anno(mRNA).xls

value: control


title: POT1-ccdB_b2

source_name: S.cerevisiae expressing control plasmid without reporter gene

value: POT1-ccdB (pJA0004)


title: pRPS3-mCherry-tRPS3_modNNN_1


title: negative control-Total RNA(A1）


title: pRPS3-mCherry-tRPS3_WT_1


title: OS_3


title: negative control-Total RNA(A2）


title: POT1-ccdB_b1


title: β-elemene treatment-miRNA(B3）

description:
S20L0600
B_vs_A_diff.xls


title: Oslec1 LE-3

city: Hangzhou

first: Fu

last: Guo

address: Yuhangtang Road 866

institute: Zhejiang University

description:
Oslec1_25-DAP embryo_sample3
Rice_S233-01-T06

data_processing:
Illumina HCS 2.2.68 software used for basecalling.
The adapters and low-quality reads were removed by Trimmomatic v0.36.
The clean reads were mapped to the rice reference genome Oryza_sativa. IRGSP-1.0.45 using Hisat2 program v2.1.0. The transcripts were assembly and merged using StringTie v1.3.4d.
Genome_build: Oryza_sativa. IRGSP-1.0.45
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: RNA-seq datasets of Oslec1 25-DAP embryos

growth_protocol: The plants were grown in greenhouse at 16 h light, 28 ℃/8 h dark, 24 ℃ cycle.

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

tag: background ecotype

value: Nipponbare

value: embryo

tag: developmental stage


title: β-elemene treatment-miRNA(B2）

description:
S20L0600
B_vs_A_diff.xls

tag: cell type


title: Oslec1 LE-2

description:
Oslec1_25-DAP embryo_sample2
Rice_S233-01-T05


title: β-elemene treatment-miRNA(B1）

description:
S20L0600
B_vs_A_diff.xls

tag: treatment


title: negative control-miRNA(A2）

description:
S20L0599
B_vs_A_diff.xls


title: pRPS3-mCherry-tRPS3_modNAA_2


title: NIP LE-3

description:
NIP_25-DAP embryo_sample3
Rice_S233-01-T03

source_name: RNA-seq datasets of NIP 25-DAP embryos

value: NIP


title: negative control-miRNA(A1）

description:
S20L0599
B_vs_A_diff.xls


title: NIP LE-2

description:
NIP_25-DAP embryo_sample2
Rice_S233-01-T02


title: NIP LE-1

description:
NIP_25-DAP embryo_sample1
Rice_S233-01-T01


title: Myc KO - rep 4

source_name: CD8+ T cells

value: CD8+ T cells

value: Myc KO


title: Oslec1 EE-2

description:
Oslec1_7-DAP embryo_sample2
Rice_R814-02-T05

source_name: RNA-seq datasets of Oslec1 7-DAP embryos


title: Oslec1 EE-1

description:
Oslec1_7-DAP embryo_sample1
Rice_R814-02-T04


title: NIP EE-3

description:
NIP_7-DAP embryo_sample3
Rice_R814-02-T03

source_name: RNA-seq datasets of NIP 7-DAP embryos


title: RBM46_IgG_replicate_2

city: Jinan

first: Yuling

last: Cai

state: Shandong

address: Qianfoshan Street

department: CCenter of reproductive medicine

institute: Shandong University

description: out1.RBM46-IgG-L.rmDup.normalizeToRBM46-HA-L.bigwig

data_processing:
library strategy: LACE-seq
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences and the polyA tails at the 3' end were removed sequentially using Cutadapt v1.15 with the following two parameters: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n, and -f fastq -a A{15} -m 18 -n 2.
After filtering, the LACE-seq reads were first aligned to human or mouse pre-rRNA by bowtie with default parameters, and the remaining unmapped reads were then aligned to the hg19 or mm9 reference genome. For LACE-seq data mapping, two mismatches and at most 10 multiple hits were allowed (bowtie parameters: -v 2 -m 10 --best --strata).
Assembly: mm9
Supplementary files format and content: Bigwig files were generated using bedtools genomecov v2.28.0 and bedGraphToBigWig v4 software.

source_name: testis

growth_protocol: Mice housing and all experimental protocols were approved by the Regional Ethics Committee of Shandong University.

extract_protocol: After UV-C irradiation, RNA cross-linked to protein is purified and ligated with an adenylated DNA linker at the 3’end. Next, cDNA fragments, which stop exactly at the cross-link site in RNA, are generated through reverse transcription (RT), followed by polyadenylation, in vitro transcription (IVT), PCR amplification and high-throughput sequencing.

treatment_protocol: Fluorescence-activated cell sorting (FACS) purification was conducted as previously described to collect leptotene spermatocyte from PD12 HA-RBM46 mice for LACE-seq . After removed the tunica albuginea, the testes were placed in 5 ml PBS containing collagenase type I (120 U/ml) and mixed for 10 min at 35°C. The testes were digested in 5 ml of 0.25% trypsin plus 0.1 ml of deoxyribonuclease I (5 mg/ml) at 35°C for 8 min and then terminated by the addition of 0.5 ml fetal ovine serum (FBS). The suspension was passed through a 70 μm honeycomb filter. Centrifuge the cell suspension at 4℃ at 500g for 5 min and remove the supernatant. And then cells sediment was resuspended in 1 ml DMEM with 40 μg Hoechst 33342, 2 μl Zombie NIR™ dye and 5 μl DNase I. The cell suspension was stirred at 34  °C for 20 min, then centrifuged at 500g for 5 min at 4°C and resuspended in PBS at a concentration of 105 ml for sorting. Using FACS, populations of fluorescently labeled collection cells were collected according to the sorting channel into 1.5-ml LoBind microcentrifuge tubes (Eppendorf, 022431021) containing 0.5 mL PBS. The cell suspension was centrifuged and some of the supernatant was removed leaving about 10μl PBS.

value: testis

value: leptotene spermatogonia

value: immunoprecipitation with IgG antibody for RNA/protein complex as negtive control


title: RBM46_HA_replicate_2

description: out1.RBM46-HA-L.rmDup.normalizeToRBM46-HA-L.bigwig

value: immunoprecipitation with HA-tag antibody for RNA/protein complex as test group


title: RBM46_IgG_replicate_1


title: NIP EE-2

description:
NIP_7-DAP embryo_sample2
Rice_R814-02-T02


title: AAV9-N+F 2

city: Seoul

first: Yunseon

address: 222, Wangsimni-ro

country: South Korea

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling/1000000019358 v02
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat/HISAT2
Read count extraction and nomalization were performed using edgeR/quantile normalization
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Hippocampus of 3xTg mouse

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

value: Hippocampal cell

tag: gene manipulation

value: Nurr1+Foxa2 (AAV9)

value: Amyloid beta


title: AAV9-N+F 4


title: AAV9-N+F 3


title: GUAD

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Library strategy: CRISPR screen
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.14) to extract the 20bp guide sequence
sgRNAs that were enriched or depleted in response to HMA treatment relative to T0 or DMSO determined using MAGeCK (v0.5.6)
Genome_build: N/A
Supplementary_files_format_and_content: normalized count file generated by MAGeCK

organism: synthetic construct

extract_protocol:
Genomic DNA was extracted with the DNAase Blood and Tissue kit (Qiagen, Hilden, Germany)
sgRNA sequences PCR amplified in multiple reactions using staggered P5 primers and barcoded P7 primers using Ex Taq DNA Polymerase (Takara; Japan). PCR products were pooled, purified using AMPure XP beads (Beckman Coulter)

treatment_protocol: Hut78 Cas9-expressing cells were transduced with a library of sgRNAs targeting epigenetic regulators at ~2000x representation and treated with DMSO, Azacitidne (300nm) or Guadecitabine (150nM) for 24 days

tag: cell line used for assay

value: Guadecitabine 150nM 24 days

tag: molecule subtype

value: sgRNA library


title: RBM46_HA_replicate_1


title: AAV9-N+F 1


title: AAV9-Cont 3

value: Control (AAV9)


title: AZA

value: Azacitidine 300nM 24 days


title: NIP EE-1

description:
NIP_7-DAP embryo_sample1
Rice_R814-02-T01


title: DMSO

value: DMSO 24 days


title: Oslec1 LE-1

description:
Oslec1_25-DAP embryo_sample1
Rice_S233-01-T04

value: Nipponbare


title: negative control-miRNA(A3）

description:
S20L0599
B_vs_A_diff.xls

value: tumor cell

value: colorectal

value: control


title: AAV9-Cont 1


title: T0

value: time-point 0


title: Oslec1 EE-3

description:
Oslec1_7-DAP embryo_sample3
Rice_R814-02-T06

value: embryo


title: Adult 7 Drug

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Reads were mapped to the human genome (hg19) using RefSeq annotation
Transcript estimation was performed using RNA-Seq by Expectation Maximization method (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics. 2011;12(323)
Differenential expression was performed using the EBSeq method (Leng N, Dawson JA, Thomson JA, et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013;29(8):1035-1043.)
Genome_build: hg19
Supplementary_files_format_and_content: Transcript estimates

source_name: Articular chondrocytes

extract_protocol:
RNEasy kits
Illumnia TruSeq

value: Adult

tag: 3d cultured

value: Yes

value: yes


title: Smz1_GUAD_rep3

description: Smz1 cells treated with Guadecitabine 100nM

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.9.1) to remove poor quality ends.
Read data was then aligned using Hisat2 (2.0.4) to the mouse reference genome (hg19)
Read counting was performed with featureCounts from the subread package(v1.5.0-p3).
Read counts were summarized by Ensembl Gene ID using the Subread featureCounts function.
Genome_build: hg19
Supplementary_files_format_and_content: count file generated by featureCounts

extract_protocol:
RNA was extracted using the Direct-zol™ RNA miniprep kit (Zymo Research) according to manufacturer’s instructions.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

treatment_protocol: Hut78 and Smz1 cells were treated with DMSO, Azacitidne (100nm) or Guadecitabine (100nM) for 72 hrs

tag: cell line

value: T-cell lymphoma

value: Guadecitabine 100nM 72hrs


title: Smz1_GUAD_rep2


title: Adult 6 Drug


title: Smz1_GUAD_rep1


title: Adult 4 Drug


title: Smz1_DMSO_rep3

description: Smz1 cells treated with DMSO

value: DMSO 72hrs


title: Smz1_DMSO_rep1

description: Smz1 cells treated with DMSO


title: Adult 3 Drug


title: Adult 2 Drug


title: Smz1_DMSO_rep2

description: Smz1 cells treated with DMSO


title: Smz1_AZA_rep1

description: Smz1 cells treated with Azacitidine 100nM

value: Azacitidine 100nM 72hrs


title: AAV9-Cont 2

value: Hippocampal cell

value: Amyloid beta


title: Adult 4 Control

value: no


title: Adult 7 Control


title: Adult 1 Drug


title: Hut78_GUAD_rep3

description: Hut78 cells treated with Guadecitabine 100nM


title: Hut78_GUAD_rep1


title: Adult 3 Control


title: Hut78_DMSO_rep3

description: Hut78 cells treated with DMSO


title: Hut78_GUAD_rep2


title: Adult 2 Control


title: Smz1_AZA_rep3


title: Hut78_DMSO_rep2

description: Hut78 cells treated with DMSO


title: Adult 5 Drug


title: Hut78_DMSO_rep1

description: Hut78 cells treated with DMSO


title: Smz1_AZA_rep2


title: Adult 1 Control


title: Adult 2

source_name: BMPR1B+ articular chondrocytes

value: No


title: ryhBs_1 rep1

first: Mengping

last: He

address: Shuangqiao Street

institute: Yangzhou university

data_processing:
Illumina HiSeq TM2500/MiseqTM software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012)
Assembly: P125109

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Salmonella strains

extract_protocol:
S. Enteritidis wild type (WT) strain 50336 and mutants △ryhB-1, △ryhB-2, and △ryhB-1/ryhB-2 were grown overnight in 50 mL of the LB medium with 160 rpm shaking at 37°C under aerobic condition, washed thrice, and re-suspended with iron-limited and nutrient-limited medium. The above prepared bacterial cells were cultured for 2 h at 37°C in the anaerobic workstation. Each sample was analysed in triplicate. Total RNA of the above stains was extracted using TRIzol reagentwith DNase digestion according to the manufacturer’s instruction. Ribosome RNA was removed using a Ribo-Zero rRNA removal kit (Illumina) that leaves the mRNA.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

tag: genotype

value: ryhB-1/ryhB-2 KO


title: ryhBs_3 rep3


title: Adult 6 Control


title: ryhB-2_3 rep3

value: ryhB-2 KO


title: Hut78_AZA_rep3

description: Hut78 cells treated with Azacitidine 100nM


title: ryhBs_2 rep2


title: Adult 5 Control


title: ryhB-2_1 rep1


title: Fetal 4

value: Second trimester


title: Hut78_AZA_rep1


title: ryhB-1_1 rep1

value: ryhB-1 KO


title: Adult 3


title: Fetal 2


title: ryhB-1_3 rep3


title: Hut78_AZA_rep2


title: ryhB-1_2 rep2


title: Adult 1


title: Fetal 3


title: Root, SM1, low P, rep1

city: Montpellier

first: Christophe

last: Maurel

address: 2 place Pierre Viala

department: Water, signaling and hydraulic architecture

country: France

institute: Institute for Plant Sciences of Montpellier (IPSiM)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp tool  (parameter: --qualified_quality_phred 20 --unqualified_percent_limit 50 –n_base_limit 10)
Trimmed sequence reads were mapped to B73_RefGen_v4, release 44 using hisat2
Read count extraction were performed using htseq-count (parameter: --mode union)
Assembly: Zea_mays.B73_RefGen_v4, release 44
Supplementary files format and content: Tab-separated text files include read count values for each sample
Supplementary files format and content: Tab-separated text files include FPKM values for each sample

organism: Zea mays

source_name: Root

extract_protocol:
RNA was harvested using innuPREP Plant RNA Kit (Analytik Jena AG, Jena, Germany).
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: Root

value: low P


title: Root, SM1, low P, rep2


title: WT_3 rep3

value: wild type


title: Root, SM1, low P, rep3


title: ryhB-2_2 rep2


title: ME49_TgCyc5_Bz_+aux_rep2

city: Tampa

first: Elena

last: Suvorova

state: FL

address: IRB 3720 Spectrum Blvd Suite 304

institute: University of South Florida

data_processing:
fastqs were mapped to ME49 genome with hisat2 1.2 with default options
gene counts were quantified with stringtie 1.35 with default options
Assembly: Toxodb ME49 release 42
Supplementary files format and content: gene abundance matrix from stringie / prepDE.py

organism: Toxoplasma gondii

source_name: parasite

growth_protocol: Toxoplasma gondii ME49 tachyzoites were grown in monolayers of human foreskin fibroblasts for 24 at pH 7.4, 5% CO2, 37oC then were either supplemented with 500mM IAA (auxin) or not for another 24h. Toxoplasma gondii ME49 bradyzoites were grown in monolayers of human foreskin fibroblasts for 48 at pH 8.2, ambient air, 37oC then were either supplemented with 500mM IAA (auxin) or not for another 24h.

extract_protocol:
Total RNA was extracted with TRIzol according to the manufacturer’s instructions (Invitrogen). The RNA integrity was verifed using Agilent High Sensitivity D1000 ScreenTape in an Agilent 2200 TapeStation System (Agilent Technologies).
One µg of total RNA was treated with 1 U of DNase I (Amplication Grade, Invitrogen) to remove the residual genomic DNA, and the DNase-treated RNA was used as an input for the construction of RNA-seq library using IlluminaTruSeq® Stranded mRNA Library Preparation Kit (Illumina). The mRNA was purified from total RNA using oligo (dT)-conjugated magnetic beads. Purified mRNAs were fragmented at 94°C for 8 min and first strand cDNA was synthesized using random hexamer primers and SuperScriptII Reverse Transcriptase (Invitrogen) in First Strand Synthesis Act D Mix (Illumina). Second strand cDNA synthesis was subsequently performed in Second Strand Marking Master Mix (Illumina). After adenylation of the 3' ends, RNA Adapter Index codes were ligated to their respective cDNA samples. In order to select ~280bp cDNA fragments, the libraries were purified with AMPure XP system (Beckman Coulter). To enrich adaptor-ligated cDNA fragments, the libraries were PCR-amplified (PCR Master Mix and PCR Primer Cocktail, Illumina) and purified with AMPure XP system. The quality of the libraries was confirmed using Agilent High Sensitivity D1000 ScreenTape in an Agilent 2200 TapeStation System (Agilent Technologies). The cDNA concentration was measured by qPCR and with Qubit® DNA Assay Kit in a Qubit® 2.0 Fluorometer (Thermo Scientific).
cDNA libraries were applied to NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) and sequencing on Illumina NextSeq System to obtain 5 million of 75 bp paired-end sequencing reads per sample.

treatment_protocol: To downregulate TgCycP1 or TgCyc5, parasites were grown in presence of 500mM auxin for 24h prior collection.

value: parasite

value: bradyzoite

value: DKu80Dhxgprt AtTIR1


title: ME49_Tz_-aux_rep1

value: tachyzoite

value: 48h, pH 7.4, 5% CO2, no auxin


title: Root, SF1, low P, rep3


title: WT_1 rep1


title: ME49_Bz_+aux_rep2

value: 72h, pH 8.2, ambient air, 24h with auxin


title: ME49_Tz_+aux_rep1

value: 48h, pH 7.4, 5% CO2, 24h with auxin


title: WT_2 rep2


title: OsLEC1-input DNA

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Oryza sativa IRGSP-1.0.45 genome assembly using bowtie2 v2.3.4.1 , and only uniquely mapped sequencing reads are retained.
MACS2 v2.1.2 was used to call peaks compared to input using q_value_thresholds=0.01. The aligned reads with biological replicates were processed using the irreproducibility discovery rate (IDR) v2.0.3.
Peaks were then annotated using ChIPseeker.
Genome_build: Oryza_sativa. IRGSP-1.0.45
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: wig files were generated using MACS2 v2.1.2.

source_name: OsLEC1-input DNA

growth_protocol: The NIP and 35S:3*FLAG-OsLEC1 plants were grown in greenhouse at 16 h light, 28 ℃/8 h dark, 24 ℃ cycle. The seed were harvested on their maturation.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3-'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Sterile seeds of NIP and 35S:3*FLAG-OsLEC1 were placed on CIM (N6 basal medium, supplemented with 10 μM 2,4-D, pH 5.8) and incubated 30 days in the growth chamber for callus induction with a 16-h light, 28 C/8-h dark, 24  C cycle.

value: Nipponbare

value: callus cells

tag: chip antibody

value: anti-DDDDK mAb (MBL, Beijing, China)


title: ME49_Bz_+aux_rep1


title: OsLEC1-ChIP


title: ME49_TgCyc5_Bz_-aux_rep1


title: ME49_TgCycP2_Bz_-aux_rep2


title: M6-5_DAL2921

city: Egham

first: Gerhard

last: Leubner-Metzger

state: Surrey

address: Bourne Building 3-30

department: Biological Sciences

institute: Royal Holloway University of London

data_processing:
Unitigs were assembled in ABySS
collapsed into a single sequence set using CD-HIT-EST at 98% identity
Collapsed unitigs were assemble using MIRA and all contigs combined using ABySS
Only those transcripts with a minimum length of 200 bp were retained
Reads were mapped to the final assembly using BWA, counts generated with Htseq
Supplementary files format and content: tab delimited data matrix of counts for each sample

organism: Lepidium sativum

source_name: seed

growth_protocol: Seeds were imbibed in treatments indicated

extract_protocol:
Messenger RNA was enriched by polyA isolation using an NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), Ipswich, MA  , USA)
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB)

value: seed

value: L. FR14; Keimsprossen; Juliwa

value: MyA imbibition 6h


title: ME49_TgCycP2_Bz_-aux_rep1


title: Fetal 1

value: Second trimester

value: No

value: no


title: Root, F142, low P, rep2

value: Root

value: low P


title: ME49_TgCycP2_Bz_+aux_rep2

value: parasite


title: M6-3_DAL2921

treatment_protocol: Seeds were imbibed in treatments indicated


title: ME49_TgCycP2_Tz_-aux_rep2

value: DKu80Dhxgprt AtTIR1


title: Root, F142, low P, rep3


title: NIP-input DNA

source_name: NIP-input DNA


title: M6-2_DAL2921


title: ME49_TgCyc5_Bz_-aux_rep2

value: bradyzoite


title: Root, SF1, low P, rep2


title: NIP-ChIP

source_name: NIP-ChIP


title: ME49_TgCycP2_Tz_+aux_rep2


title: T47D cells, palbociclib, Day5

city: Taipei City

first: Chih Yi

last: Lin

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Trimmomatic (v 0.38)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (parameter- LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36)
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using HISAT2 software (v 2.1.0) (parameters- default)
Read count extraction  were performed using FeatureCounts (v 2.0.0 )
Normalization were performed using DEGseq (v 1.40.0)
Assembly: GRCh38

growth_protocol: MCF7 epithelial cell were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. T47D epithelial cell were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Total RNA Isolate Kit (NovelGene). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer's protocols.

treatment_protocol:
Cells were fed with DMEM or RPMI-1640 medium supplemented with 10% FBS and 1% Penicillin Streptomycin.
1uM palbociclib (Selleckchem) in the presence of 10% FBS until day 5.

value: epithelial cell

value: WT

value: palbociclib

value: Day 5


title: ME49_TgCyc5_Bz_+aux_rep1


title: M6-1_DAL2921


title: Root, F160, low P, rep2


title: T47D cells, control, Day0

value: Day 0


title: ME49_TgCycP2_Tz_+aux_rep1


title: Root, F160, low P, rep3


title: ME49_TgCycP2_Bz_+aux_rep1

value: tachyzoite


title: M18-5_DAL2921

value: seed

value: MyA imbibition 18h


title: MCF7 cells, palbociclib, Day5


title: Root, F160, low P, rep1


title: M6-4_DAL2921

value: L. FR14; Keimsprossen; Juliwa

value: MyA imbibition 6h


title: HCT116, KO2, REP2

city: shanghai

first: wei

last: su

state: shanghai

address: 2800 Gongwei Road

institute: fudan university

data_processing:
Clustering and sequencing  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq6000 platform and 150 bp paired-end reads were generated.
Data Analysis   Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome  STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. [Dobin A1, Davis CA, Schlesinger F, Drenkow J, et.al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013 Jan;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.]
Quantification of gene expression level  HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: colorectal cancer

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% FBS (Invitrogen, Carlsbad, CA, USA) at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cells by TRIzol reagent (Invitrogen).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The sgRNAs (KO1: GAAGGCAAACTTGGACGTCG; KO2: TTCTCCACACTCCAGAGACC) of human MUC3A were synthesized by Genomeditech, Inc. (Shanghai, China) and cloned into the lentiCRISPR v2 lentiviral vector to construct the lentiCRISPR-MUC3A knockout plasmids. Based on the instructions of the product manual, Lipofectamine 3000 (Invitrogen, Inc.) was used to cotransfect the target plasmid or the scrambled vector, psPAX2, and PMG.2G into HEK293T tool cells to obtain MUC3A knockout lentivirus or scrambled control lentivirus. Then, the lentivirus (multiplicity of infection, MOI = 10) was used to infect HCT116 cells. The MUC3A knockout cell lines HCT116-KO1, KO2 and the negative control cell lines HCT116-NC were screened by puromycin (2 μg/mL, 72 h).

value: colorectal cancer

value: colorectal cancer cell

value: MUC3A knockout

value: gene knockout


title: MCF7 cells, control, Day0


title: Root, F142, low P, rep1

value: Root

value: low P


title: ME49_TgCycP2_Tz_-aux_rep1

value: parasite

value: DKu80Dhxgprt AtTIR1


title: HCT116, KO1, REP1


title: Root, F2, low P, rep2


title: Root, SF1, low P, rep1


title: HL60/MX2(m7G MeRIP Transcriptome Seq)

city: jinan

first: bing

last: zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results.
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
Supplementary files format and content: xlsx files include methylation sites values，methylated RNA and enrichment information for each sample
Library strategy: MeRIP-seq

growth_protocol: The cells were grown in RPMI-1640 (Gibco USA)) supplemented with 10% heat-inactivated fetal calf serum (Gibco USA)), 1% (v/v) antibiotics (penicillin streptomycin) (Gibco, USA) in a humidified 5% CO2 atmosphere at 37°C

extract_protocol:
Cells in logarithmic growth phase were collected, and we extracted total RNA using TRIzol reagent,The mRNA was isolated from total RNA with oligo(dT) magnetic beads (ThermoFisher), and then subjected to immunoprecipitation with the GenSeqTM m7G-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions.
RNA was decapping with Tobacco Decapping Enzyme, and then randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m7G antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

value: Acute myeloid leukemia cells

value: drug-resistant cells

value: input


title: HL-60(m7G MeRIP Transcriptome Seq), IP

value: WT

value: IP


title: M18-2_DAL2921

value: seed


title: M12-5_DAL2921

value: MyA imbibition 12h


title: HL-60(m7G MeRIP Transcriptome Seq)


title: Root, F2, low P, rep3


title: HCT116, WT, REP1

value: wild type

value: negative control


title: M18-3_DAL2921

value: L. FR14; Keimsprossen; Juliwa

value: MyA imbibition 18h


title: M18-1_DAL2921


title: HCT116, WT, REP2

value: colorectal cancer

value: colorectal cancer cell


title: HCT116, KO2, REP1

value: MUC3A knockout

value: gene knockout


title: Root, EP1, low P, rep3

value: Root

value: low P


title: Root, F2, low P, rep1


title: Root, EP1, low P, rep2


title: HL-60/MX2(Human Transcriptome Seq)

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM.
Supplementary files format and content: xlsx files include RPKM values for each sample

extract_protocol:
Cells in logarithmic growth phase were collected, and we extracted total RNA using TRIzol reagent,The mRNA was isolated from total RNA with oligo(dT) magnetic beads (ThermoFisher), and then subjected to immunoprecipitation with the GenSeqTM m7G-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions.
Briefly, total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.

value: Acute myeloid leukemia cells


title: HL-60(Human Transcriptome Seq)


title: M12-2_DAL2921


title: Root, EP1, low P, rep1


title: HL60/MX2(m7G MeRIP Transcriptome Seq), IP

value: drug-resistant cells


title: M12-4_DAL2921


title: M18-4_DAL2921


title: P4-TI-scRNAseq

city: Dalian

first: Hai-long

last: Piao

state: Liaoning

address: No.457 Zhongshan Road

institute: Dalian Institute of chemical physics

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.17) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes

source_name: Lung

extract_protocol:
The resected tumor samples were washed by phosphate buffered saline (PBS) and completely immersed in MASC tissue storage solution (Miltenyi, Germany) at 4 ℃.Tumor dissociation for 10X Single Cell RNA Sequencing according to protocol (CG000147, https://assets.ctfassets.net/an68im79xiti/2s0LZ3yI8OMEheRtFo9Szc/1fbfbd97ec3e574b6ab8b8fa12eef0cd/CG000147_Demonstrated_Protocol_Tumor_Dissociation_RevB.pdf). Using a wide-bore pipette tip, gently and thoroughly mix the cell suspensions. Determine the cell concentration using a Countess® II Automated Cell Counter. Centrifuge cells at 300 rcf for 5 min. Remove supernatant without disrupting the cell pellet. Using a wide-bore pipette tip, add 1 ml 1X PBS with 0.04% BSA to the tube. Gently pipette mix 5 times and invert tubes to resuspend the cell pellet. 10x Genomics (US) Single Cell Protocols (CG000053). Cell Counting & Quality Control. Thoroughly vortex 0.4% trypan blue stain and centrifuge briefly. Using a wide-bore pipette tip, gently and thoroughly mix the cells. Immediately, aliquot 10 µl cells and mix with 10 µl 0.4% trypan blue stain. Gently pipette mix. Transfer 10 µl trypan blue stained cells to a chamber on Countess® II Cell Counting Slide and determine the cell concentration and cell viability.
The single cell suspension was loaded into Chromium microfluidic chips with 3’ v2 chemistry and barcoded with a 10× Chromium Controller (10X Genomics, US). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics, US) according to the manufacturer’s instructions (CG000108). The Chromium™ Single Cell 3’ v2 Protocol (CG00052) produces Single Cell 3’ libraries, ready for Illumina Novaseq PE150 platform. Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung

value: Human lung

tag: genome build


title: P4-NS-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.16) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: Root, SM1, high P, rep2

value: high P


title: P4-TS1-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.14) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: P3-NM-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.13) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: Root, SM1, high P, rep3


title: M12-3_DAL2921

value: seed


title: P4-NI-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.18) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: Root, SM1, high P, rep1


title: DS-5_DAL2921

value: dry seed


title: P4-TS2-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.15) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: Root, SF1, high P, rep3


title: DS-3_DAL2921


title: M12-1_DAL2921

value: MyA imbibition 12h


title: P3-TM2-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.12) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: Root, SF1, high P, rep2


title: P3-TM1-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.11) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: P3-TI2-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.9) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: P2-NI-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.5) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: P2-TI-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.4) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: P3-TI1-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.8) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: DS-4_DAL2921

data_processing:
Unitigs were assembled in ABySS
collapsed into a single sequence set using CD-HIT-EST at 98% identity
Collapsed unitigs were assemble using MIRA and all contigs combined using ABySS
Only those transcripts with a minimum length of 200 bp were retained
Reads were mapped to the final assembly using BWA, counts generated with Htseq
Supplementary files format and content: tab delimited data matrix of counts for each sample


title: DS-2_DAL2921


title: P1-NI-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.1) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes


title: P1-NM-scRNAseq

description: 10x Genomics

data_processing:
Raw fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 4.0.3) with default parameters. The filtered feature-barcode matrix was utilized.
Supplementary files format and content: Tab-separated  matrix files, row names represent features and column names represent barcodes