title: anti-H3K27ac, ChIP, H9, shZBTB12

value: anti-H3K27ac (Active Motif, #39133)


title: Calc1

status: Public on Dec 26 2022

type: SRA

city: Nanjing

first: liu

last: cuiying

address: no.87 Dingjiaqiao

department: Cardiology

country: China

institute: The Medical School of Southeast University

library_source: transcriptomic

data_processing:
After sequencing, raw reads were filtered using fastp software to remove low quality reads and residual Illumina adapters.
After clipping, miRdeep2 software was used to align known miRNAs, allowing for 1 base mismatch.
miRNA expression corresponding to its reads were counted and calculated using edgeR software, whose significant differentially expression were identified by fold change, p-value and fdr between the two groups.
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: aortic valve

growth_protocol: Aortic valve interstitial cells were cultured with HDMEM supplemented with 10% of fetal bovine serum (FBS), 1% penicillin / streptomycin at 37℃ and 5% CO2.

extract_protocol:
RNA was extracted with TRIzol reagent (Takara).2.0 ug of total RNA was used for the construction of sequencing libraries.
small RNA libraries for miRNA-seq were prepared using TruSeq Small RNA Sample Prep Kits（Illumina,San Diego，USA） following manufacturer's protocols.

treatment_protocol: Normal VICs were cultured in complete DMEM and calcified VICs were cultured in complete HDMEM containing 1.5 mmol/l calcium and 2.0 mm/l phosphate for 72 h.

tag: tissue

value: aortic valve

tag: cell type

value: valve interstitial cells

tag: genotype

value: WT

tag: treatment

value: osteoblast differentiation


title: Calc3


title: Normal 3


title: Normal 2


title: TKO-Replicate2

city: Notre Dame

first: Xin

last: Lu

address: 109 Galvin Life Science Center

country: USA

institute: University of Notre Dame

library_source: transcriptomic single cell

data_processing:
CellRanger 7.0.0 (http://support.10xgenomics.com/) multi was utilized to process the raw sequence data.
In general, the sequencing reads were aligned to the mouse reference genome mm10 with the RNAseq aligner STAR. The aligned reads were traced back to individual cells given corresponding cell barcodes.
After removing duplicated reads due to the PCR bias based on the information of unique molecular identifiers (UMIs), we estimated abundances of transcripts detected in each cell. Cells with unique gene counts over 8000 were abolished. The filtered gene-cell count matrices generated by the CellRanger were used for further analysis.
The expression levels of genes in one cell were normalized by total read counts in the cell and multiplied by a scaling factor 10,000 with log2 transformation.
The first 30 principal components achieved from the principal component analysis (PCA) were used to cluster the cells by shared nearest neighbor (SNN) modularity optimization based clustering algorithm. Clusters were annotated to cell types using the SingleR package and fine-tuned by well-known marker genes.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

organism: Mus musculus

source_name: mouse prostate tumor

extract_protocol:
Prostate tumor was minced and dissociated with mouse dissociation kit (Miltenyi Biote,130-096-730) at 37℃ for 1h. Dissociated tumor single cell suspension were passed through 40μm strainer followed by red blood cell lysis.  Then the dead cell was removed using EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, 17899) followed by hashtag staining and labelling. Cells from different samples were counted and combined into one samples. The cells are ready for scRNA-seq
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics, user guide CG000315). 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: mouse prostate tumor

tag: cell line

value: Tissue

value: Nkx3.1CreERT2  PtenL/L, Smad4L/L, Pygo2L/L

tag: antibodies/tags


title: TKO-Replicate1


title: Calc2


title: Normal 1


title: DKO-Replicate2

value: Nkx3.1CreERT2  PtenL/L, Smad4L/L


title: DKO-Replicate1


title: Dnmt3b WT_E12.5 placenta

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
bcl2fastq: Standard parameters were used for bcl2fastq and for library barcode splitting
Assembly: mm10
Alignment and quantitation: Mapping and quantitation of 10X single nuclei RNA-Seq data was performed with CellRanger v6.0.0 against the gex-mm10-2020-A transcriptome using the --include-introns option.

source_name: Placenta

extract_protocol:
Natural timed matings between homozygous Dnmt3b floxed females and heterozygous Dnmt3b del, Sox2-Cre +ve males were used to generate cKO and WT embryos. E12.5 placentas were collected and a tail clip was used for genotyping. Single nuclei were isolated as described in the ‘Frankenstein’ protocol, available through 10X Genomics (https://www.10xgenomics.com/resources/customer-developed-protocols) and published adaptations for mouse placenta. Following collection and genotyping, Dnmt3b KO and WT E12.5 placentas were processed in parallel immediately for single nuclei isolation and 10X Genomics RNA-seq preparation. Placentas were first chopped with a razor blade in 1mL nuclei EZ lysis buffer (Sigma) for 2 mins, followed by homogenisation in a Dounce homogenizer. Nuclei were filtered through a 30µm filter, and then pelleted by centrifugation at 500g for 5 mins at 4°C. Nuclei were resuspended in fresh nuclei EZ lysis buffer, pelleted and then resuspended in nuclei wash and resuspension buffer (1% BSA, 0.2U/µL RNase Inhibitor, PBS). Nuclei were gently resuspended, pelleted and resuspended in fresh nuclei wash and resuspension buffer. Nuclei were passed again through a 30µm filter, before visual inspection of nuclei with a haemocytometer. Nuclei were then stained with DAPI (adding 1 µL of 1mg/mL DAPI) before a total of 10,000 nuclei per sample were flow sorted using the BD FACSAria Fusion sorter with 70µm nozzle into RT reaction mix (10X Genomics). Samples were immediately processed to cDNA using the Chromium Controller (10X Genomics), followed by 3’ single-nuclei RNA-seq library preparation (10X Genomics).  Libraries were multiplexed for sequencing on an Illumina NextSeq500.
Natural timed matings between heterozygous females and males were used for the Dnmt3b KO strain to generate KO and WT embryos or between homozygous Dnmt3b floxed females and heterozygous Dnmt3b del, Sox2-Cre +ve males were used to generate cKO and WT embryos. E12.5 placentas were collected and a tail clip was used for genotyping. Single nuclei were isolated as described in the ‘Frankenstein’ protocol, available through 10X Genomics (https://www.10xgenomics.com/resources/customer-developed-protocols) and published adaptations for mouse placenta. Following collection and genotyping, Dnmt3b KO and WT E12.5 placentas were processed in parallel immediately for single nuclei isolation and 10X Genomics RNA-seq preparation. Placentas were first chopped with a razor blade in 1mL nuclei EZ lysis buffer (Sigma) for 2 mins, followed by homogenisation in a Dounce homogenizer. Nuclei were filtered through a 30µm filter, and then pelleted by centrifugation at 500g for 5 mins at 4°C. Nuclei were resuspended in fresh nuclei EZ lysis buffer, pelleted and then resuspended in nuclei wash and resuspension buffer (1% BSA, 0.2U/µL RNase Inhibitor, PBS). Nuclei were gently resuspended, pelleted and resuspended in fresh nuclei wash and resuspension buffer. Nuclei were passed again through a 30µm filter, before visual inspection of nuclei with a haemocytometer. Nuclei were then stained with DAPI (adding 1 µL of 1mg/mL DAPI) before a total of 10,000 nuclei per sample were flow sorted using the BD FACSAria Fusion sorter with 70µm nozzle into RT reaction mix (10X Genomics).
Samples were immediately processed to cDNA using the Chromium Controller (10X Genomics), followed by 3’ single-nuclei RNA-seq library preparation (10X Genomics).  Libraries were multiplexed for sequencing on an Illumina NextSeq500.
single-nuclei RNA-seq

value: Placenta

tag: strain

value: Wildtype

tag: age


title: SB_3 [RNA-seq]

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to ARS1.2 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: ARS1.2
Supplementary files format and content: Rumen_gene_count_matrix.csv: Comma-delimited text file includes gene counts for each Sample.

organism: Capra hircus

source_name: rumen epithelial tissue

extract_protocol:
Total RNA for rumen epithelial transcriptome sequencing was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: breed

value: Guanzhong

tag: disease state

value: healthy

value: rumen epithelial tissue

value: infusion of sodium butyrate

tag: time point

value: Day 13

tag: individual


title: Dnmt3b cKO_E12.5 placenta

value: Dnmt3b cKO, Sox2-Cre


title: Axil_1

city: Hefei

first: yu

middle: wuyu

last: wu

state: Anhui

address: changjiang  road

department: College of Horticulture

institute: Anhui Agricultural University

data_processing:
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.
Assembly: HTSeq v0.6.1 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   (Trapnell, Cole, et al., 2010)
Supplementary files format and content: processed data.xlsx

organism: Helianthus annuus

source_name: Axil

extract_protocol:
Total RNA was qualified and quantified as follows: (1) the RNA sample was firstly qualified using 1%   agarose gel electrophoresis for possible contamination and degradation; (2) RNA purity and   concentration were then examined using NanoPhotometer® spectrophotometer; (3) RNA integrity   and quantity were finally measured using RNA Nano 6000 Assay Kit of the Bioanalyzer 2100   system.
Total RNA was used as the input material for the library preparation.
mRNA was firstly captured   using mRNA Capture Beads with Oligo(dT), and purified with Binding Buffer and Washing Buffer.   mRNA was then randomly fragmented into 100~200nt in the Fragmentation Buffer and reverse_x0002_transcribed into cDNA subsequently. Synthesized cDNA was reclaimed using DNA Clean Beads   and subjected to the adaptor ligation step. Purified cDNA was ligated to the pre-mixed adaptors with   UMI using Ligase and Ligase Buffer in a one-step PCR reaction. The ligation products were again   purified using DNA Clean Beads and then amplified using PCR. PCR products were finally purified   using DNA Clean Beads and reclaimed with nuclease-free H2O

value: Axil


title: Axil_3


title: Flower_1

source_name: Flower

value: Flower


title: SB_1 [RNA-seq]


title: Flower_2


title: Leaf_3

source_name: Leaf

value: Leaf


title: Flower_3


title: SP_3 [RNA-seq]

value: infusion of sodium propionate


title: RNAs from seed without imbibition - WT_dry [Col_1_8]

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Transcript mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Assembly: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org. and abra_mygenomebrowser_011021_mrna.fasta downloaded from GenBank number PHFN00000000 (https://www.ncbi.nlm.nih.gov/nuccore/PHFN00000000)
Supplementary files format and content: tab-delimited text files include count values for each sample

organism: Arabidopsis thaliana

source_name: entire seed

growth_protocol: Seeds were sowed in petri dishes containing 0.8% agarose (SIGMA) and cultures were incubated in a controlled growth chamber under a 16 h photoperiod (170 µmol photons m2 s-1) at 22 °C (light period)/20 °C (dark period) and a constant 70% relative humidity (Ortega-Cuadros et al. 2022)

extract_protocol:
Seeds were collected to RNA isolation using NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany). RNA quantification was obtained with a NanoDrop ND-100 (NanoDrop Technologies, DE, USA) and the RNA Integrity was measure with a 4100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA samples were sent to Beijing Genomics Institute (BGI) for cDNA library construction and paired-end sequencing (PE100) using the DNBseq™ technology

treatment_protocol: Seeds were imbibed in water, nitrate KNO3 10Mm, potassium thiocyanate KSCN 8µM during 6 h and a part of seeds were left to dry (with any imbibition)

value: entire seed

tag: ecotype

value: WT

value: dry


title: Leaf_2


title: anti-H3K27ac, ChIP, H9, shGFP

city: Santa Barbara

first: Dasol

last: Han

state: California

address: University of California Santa Barbara

institute: University of California Santa Barbara

library_source: genomic

data_processing:
fastqc to QC fastq file
Fastq files were aligned to the human reference genome hg19 using bwa-0.7.13 and samtools
Peak calling on all ChIP-Seq data was performed using MACS2  with –broad parameter and using input genomic DNA as background control
Assembly: Hg19
Supplementary files format and content: bigwig files of samples genome coverage and txt of calling peaks

molecule: genomic DNA

source_name: H9 hESCs

growth_protocol: H9 hESCs were culutred on matrigel-coated tissue culture plates with mTeSR1 media and passaged every 4-5 days depending on confluency using ReLeSR.

extract_protocol:
Formaldehyde was treated to cross-link for 15 minutes. Cross-linking was quenched by Glycine. Cells were then harvested, snap-frozen and sent to ActiveMotif for ChIP-seq service.
Illumina sequencing libraries (a custom type, using standard Illumina paired read adapter oligonucleotides) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500.

treatment_protocol: H9 cells were transduced with lentiviral vectors expressing control (GFP) or ZBTB12 shRNA (shA, see manuscript). Puromycin (2μg/ml) was added to the media from 24 hr post transduction. Cells were expanded to 100mm tissue culture plate.

value: H9 (WiCell)

value: hESCs

tag: passage

value: pLKO.1 GFP shRNA (Addgene #30323)

tag: chip antibody

value: anti-H3K27ac (Active Motif, #39133)


title: SP_2 [RNA-seq]

value: Guanzhong


title: Leaf_1


title: SP_1 [RNA-seq]

value: healthy


title: SA_3 [RNA-seq]

value: rumen epithelial tissue

value: infusion of sodium acetate


title: Primed J1, shZbtb12  #3

data_processing:
Basecalling is performed by Illumina RTA software in sequencer
Sequencing reads were aligned to the mouse genome (mm10) using tophat2 and samtools
Gene expression quantification were done with cufflinks (Version 2.2.1) and differential gene expression analysis were done using DEGSeq2
Repeat region quantification were calculated using bedtools
Assembly:  mm10
Supplementary files format and content: bw files including genome coverage of samples mapped to mouse genome and txt files including FPKM of genes expression, differential expression results with DEGSeq2 and normalized repeat region

source_name: Primed J1 mEpiSCs

growth_protocol: Primed J1 mouse EpiSCs were cultured on matrigel-coated tissue culture plates with primed media(20% KOSR with bFgf and Acitvin A) and passaged every 4-5 days depending on confluency using ReLeSR.

extract_protocol:
TRIzol was treated to extract RNAs. Cells were harvested and sent to macrogen for bulk RNA sequencing.
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.  A library was independently prepared with 0.5ug of total RNA for each sample by Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., San Diego, CA, USA, #20020599). The first step in the workflow involves removing the rRNA in the total RNA. Following this step, the remaining mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers.  This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Primed J1 mouse EpiSCs were transdued with lentiviral vectors expressing control(shControl) or Zbtb shRNA (sha, see manuscript). Puromycin (2μg/ml) was added to the media from 24 hr post transduction. Cells were expanded to 100mm tissue culture plate.

value: J1 (ATCC)

value: mEpiSCs


title: Stem_3

source_name: Stem

value: Stem


title: Stem_2


title: SB_2 [RNA-seq]

value: infusion of sodium butyrate

value: Day 13


title: SA_2 [RNA-seq]


title: Primed J1, shZbtb12  #1


title: SA_1 [RNA-seq]


title: Primed J1, shControl #3


title: Root_3

source_name: Root

value: Root


title: NC_3 [RNA-seq]

value: infusion of normal saline


title: Stem_1


title: Root_2


title: NC_2 [RNA-seq]


title: Root_1


title: Wild-Type, scRNAseq

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

country: Japan

institute: keio university

description: 10x Genomics

data_processing: none provided by the submitter

source_name: kidney cortex

extract_protocol:
The digestion buffer was a mixture of Dulbecco PBS with collagenase type II (3 mg/ml, Worthington), ProNase E (1.5 mg/ml, Millipore), DNAse (62.5 U/mL, Takara), and 5 mM calcium chloride. Kidneys were harvested, minced into 1 mm3 cubes, and digested using digestion buffer with shaking at 37 °C for 20 minutes. Then, the digestion mixture was incubated in a thermomixer for 5 minutes at 37 °C with shaking at 1200 RPM. The solution was successively passed through 70- and 30-μm cell strainers. The solution was then centrifuged at 300 ×g for 5 minutes, and the resulting cell pellet was diluted with DMEM– high-glucose media (Gibco) with 10% FBS (Sigma‒Aldrich). The solution was passed through 30-μm cell strainers three times, and a single-cell suspension was obtained. The single-cell suspension was loaded onto a chip on the 10× Chromium Single Cell instrument (10× Genomics).
Bar coding and cDNA amplified were performed using Chromium Single Cell 3’ Reagent Kits v3.1 (10× Genomics) according to the manufacturer’s instructions. Sequencing is performed on an MGI tech DNBSEQ-G400 at Azenta Japan Corp. Cell Ranger v3.1 (10× Genomics) software with mouse mm10 reference sequence in prebuild Cell Ranger reference packages was used for initial data processing. After initial data processing, all processing steps were performed using Seurat v3.

value: kidney cortex

value: 12 weeks old


title: 7AKO28_S136 AKO

status: Public on Dec 25 2022

city: Lexington

first: Nirmal

last: Verma

state: Kentucky

address: 900 S Limestone

department: Pharmacology and nutritional sciences

institute: University of Kentucky

description:
males, normal diet
7AKO28_S136

data_processing:
Partek Flow 10.0.22.0228
Pre-alignment QC to filter rDNA, mtrDNA contaminants using PartekFlow RNAseq work flow default setting:Filter contaminants (Bowtie 2)-2.2.5
Filtered sequenced reads were mapped to R. norvegicus (rat)/rn7 using PartekFlow RNAseq work flow STAR 2.7.8a aligner (default parameters)
Read counts were quantified to rat rn7-Ensembl105 using PartekFlow Quantify to annotation model (Partek E/M), filterd to exclude genes with less than max 10 reads and normalized in PartekFlow
Assembly: rn7
Supplementary files format and content: tab-delimited text files include DESeq2 normalized values for each Sample

organism: Rattus norvegicus

source_name: frontal cortex

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: frontal cortex

value: AKO


title: 7AKO30_S140 AKO

description:
males, normal diet
7AKO30_S140


title: 7AKO19_S133 AKO

description:
males, normal diet
7AKO19_S133


title: 7AKO42_S144 AKO

description:
males, normal diet
7AKO42_S144


title: 6KAH98_S139 AKO

description:
males, normal diet
6KAH98_S139


title: 6KAH99_S132 AKO

description:
males, normal diet
6KAH99_S132


title: Pod-I_Ppo-1, scRNAseq

description: 10x Genomics


title: 4KAH27_S155 AKO

description:
males, normal diet
4KAH27_S155


title: 6AKO35_S149 AKO

description:
males, normal diet
6AKO35_S149


title: 4KAH35_S154 AKO

description:
males, normal diet
4KAH35_S154


title: Primed J1, shZbtb12  #2


title: 12RT23_S146 HIP

description:
males, normal diet
12RT23_S146

value: HIP


title: 10RT52_S138 HIP

description:
males, normal diet
10RT52_S138


title: NC_1 [RNA-seq]


title: 10RT54_S152 HIP

description:
males, normal diet
10RT54_S152


title: Primed J1, shControl #2


title: 10RT42_S131 HIP

description:
males, normal diet
10RT42_S131


title: Primed J1, shControl #1


title: 10RT49_S147 HIP

description:
males, normal diet
10RT49_S147


title: 10RT53_S153 HIP

description:
males, normal diet
10RT53_S153


title: skin, golden, rep3

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: East Shanshui Road 9

department: Wuxi Fisheries College

institute: Nanjing Agricultural University

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

organism: Carassius auratus

source_name: skin

value: skin

tag: group

value: gold

tag: Sex

value: female


title: 10RT46_S134 HIP

description:
males, normal diet
10RT46_S134

tag: tissue


title: 10RT57_S159 WT

description:
males, normal diet
10RT57_S159

value: WT


title: 10RT48_S143 HIP

description:
males, normal diet
10RT48_S143


title: Axil_2

value: Axil


title: skin, golden, rep1


title: 10RT51_S158 WT

description:
males, normal diet
10RT51_S158


title: 6AKO52_S156 AKO

description:
males, normal diet
6AKO52_S156


title: 10RT37_S151 HIP

description:
males, normal diet
10RT37_S151


title: skin, greenish grey, rep3

value: greenish grey


title: 10RT47_S135 WT

description:
males, normal diet
10RT47_S135


title: 10RT55_S157 WT

description:
males, normal diet
10RT55_S157


title: 10RT50_S148 WT

description:
males, normal diet
10RT50_S148


title: skin, greenish grey, rep2


title: skin, greenish grey, rep1


title: skin, golden, rep2


title: 10RT44_S142 WT

description:
males, normal diet
10RT44_S142


title: X1 cells, atm-KD-rad_rep4

city: ITHACA

first: Carolyn

last: Adler

state: NY

address: 930 Campus road

institute: Cornell University

data_processing:
Trim Galore 0.6.5 is used for adaptor trimming and base calling.
STAR 2.7.9 is used to align reads against planarian genome. dd_Smed_v6 transcriptome is used for gene annotation.
Genome_build: schMed4-2018 Assembly
Supplementary_files_format_and_content: Each text file contains raw reads of every gene.

organism: Schmidtea mediterranea

source_name: X1 cells

extract_protocol:
Total RNA of sorted X1 cells  is extracted using standard Trizol protocol.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

tag: cell type

value: X1 cells

tag: treatment 1

value: atm(RNAi)

value: atm knockdown

tag: treatment 2

value: 1 day-post-irradiation, 2000rads


title: 10RT41_S130 HIP

description:
males, normal diet
10RT41_S130

tag: genotype


title: 10RT43_S150 WT

description:
males, normal diet
10RT43_S150


title: 10RT39_S145 WT

description:
males, normal diet
10RT39_S145


title: X1 cells, atm-KD-rad_rep2


title: X1 cells, unc-KD-rad_rep3

value: unc knockdown


title: 10RT38_S141 WT

description:
males, normal diet
10RT38_S141


title: X1 cells, unc-KD-rad_rep2


title: X1 cells, unc-KD-rad_rep1


title: X1 cells, atm-KD-unirrad_rep4

value: unirradiated


title: 10RT45_S137 WT

description:
males, normal diet
10RT45_S137


title: pAct2_Total_biorep3

city: Yokohama

first: Shuta

last: Asai

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN

data_processing:
Illumina sequence was quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50, and reads containing “N” are discarded.
Quality-filtered libraries were aligned to the Arabidopsis Col-0 genome using CLC Genomic Workbench 20.
Assembly: Araport11
Supplementary files format and content: Tab-delimited text files include the transcription levels for each transcript as TPM (transcripts per million).

source_name: whole plant

extract_protocol:
RNAs were extracted by RNeasy Plant Mini Kit (QIAGEN).
library was constructed using EXPRSS tag-seq protocol (BMC Genomics 2014, 15:341)

value: whole plant

tag: treatment


title: pPR1_Total_biorep1


title: pDMR6_Total_biorep1


title: pDMR6_Total_biorep2


title: X1 cells, unc-KD-unirrad_rep3


title: pPR1_Total_biorep2


title: X1 cells, atm-KD-unirrad_rep1


title: X1 cells, atm-KD-unirrad_rep3


title: X1 cells, unc-KD-unirrad_rep2


title: X1 cells, atm-KD-rad_rep3


title: X1 cells, unc-KD-unirrad_rep4


title: X1 cells, unc-KD-unirrad_rep1


title: pDMR6_Total_biorep3


title: pAct2_IP_biorep3


title: X1 cells, atm-KD-rad_rep1


title: X1 cells, unc-KD-rad_rep4


title: pAct2_IP_biorep2


title: pPR1_IP_biorep3


title: pAct2_Total_biorep1


title: srna-26

city: wuhan

first: qian

middle: lin

last: han

state: hubei

address: Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description:
sRNA-TPM.txt
small RNA

data_processing:
Quality control: Raw RNA-seq and circRNA-Seq data were processed by SOAPnuke1.6.548 with the parameters “-n 0.01 -l 20 -q 0.3 -A 0.25” and used SOAPnuke1.6.548 filters RNA to process the raw sRNA-Seq data with the parameters “-p 1 -z 18 -s -Q 2 --sanger”. Ribo-Seq data was removed adaptors and controled low quality by FASTX_Toolkit-0.0.14 fastx_clipper with the parameters "-l 5 -c -n -v -Q33" and fastx_trimmer with the parameters "-f 1 -Q 33".
Alignment: Clean reads were aligned to the maize AGPv4 reference genome. Total RNA-seq data from the 26 tissues or stages were mapped to the B73 AGPv4 reference genome using the default parameters of HISAT and StringTie; small RNAs which size were 18–26 nt were mapped to the maize AGPv4 reference genome using Bowtie-1.1.2 with the parameters unique location and no mismatch; the Ribo-Seq reads were aligned to the rRNA reference sequence using Bowtie-1.1.267 to filter out reads derived from rRNAs and retained reads were mapped to the maize AGPv4 reference genome.
Identification of non-coding RNA: Mapsplice-v2.1.8 was used to identify fusion RNAs from total RNA-seq data from each tissue; and improved version of LncRNA_Finder was used to identify lncRNAs from total RNAs. CIRI v2.0.5 was used to identify circRNAs by aligning them to the maize AGPv4 reference genome.
Quantification of RNA: Total RNAs including lncRNAs and mRNAs bound by ribosome were calculated expression by RSEM. CIRCexplorer2 v2.0.1 was used quantify the expression levels of the circRNAs. The expression of fusion RNA and small RNA was calculated according to the TPM standard formula.
PPIs: The libraries were sequenced on the PacBio platform, and Circular Consensus Sequencing reads were called using SMRTLink-5.1.0.26412. The following analysis was performed to obtain PPIs: Firstly, reads in FASTA format were extracted from BAM files using SAMtools-1.9. Next, because ten barcoded samples were combined to generate each sequencing library, reads from each sample were divided based on their barcode sequences using Cutadapt-1.9.1. Parameters -e and -m for running reads separation were 0.3 and 200, respectively. The reads were aligned to the coding sequence data from the maize AGPv4 genome to identified candidate PPI genes using BLAST+/2.7.1. Only PPI genes with BLAST e-value < 1.0e−4 that matched to two genes were retained. If a CCS contained sequences from two different genes, and the primer sequence and the recombination sequence were aligned consistently, the proteins encoded by the two genes were considered to be interacting proteins.
Genome_build: Zea_mays.B73_RefGen_v4
Supplementary_files_format_and_content: tab-delimited text files named "TPM" or "CPM" include expression values for each samples.
Supplementary_files_format_and_content: tab-delimited text files named "PPIs" include identified protein-protein interactions.

organism: Zea mays

source_name: Topmost Leaf-N(V3)

growth_protocol: Twenty-six tissues or stages were sampled from B73 maize plants in a greenhouse. The plants were cultivated under a 12-h light/12-h dark cycle at 25 ℃.

extract_protocol:
Three replicates were prepared per tissue. RNA was extracted from 5–10 individual plants per replicate. Equal amounts of the three replicates were used for sequencing. Total RNA was isolated from the 26 tissues using a Direct-zol RNA Microprep kit (Zymo Research) following the manufacturer’s guidelines.
RNA libraries were prepared for sequencing using corresponding standard protocols.

treatment_protocol: No special treatment.

tag: cultivar


title: srna-25

description:
sRNA-TPM.txt
small RNA

source_name: Topmost Leaf-L(V3)

tag: age


title: pAct2_IP_biorep1


title: pPR1_IP_biorep2


title: pPR1_Total_biorep3


title: pPR1_IP_biorep1


title: srna-24

description:
sRNA-TPM.txt
small RNA

source_name: Tip of Stage 2 Leaf-N(V5)


title: X1 cells, atm-KD-unirrad_rep2


title: srna-23

description:
sRNA-TPM.txt
small RNA

source_name: Tip of Stage 2 leaf-L(V5)


title: pAct2_Total_biorep2


title: srna-22

description:
sRNA-TPM.txt
small RNA

source_name: Third Leaf(V3)


title: pDMR6_IP_biorep3


title: pDMR6_IP_biorep2


title: srna-21

description:
sRNA-TPM.txt
small RNA


title: srna-20

description:
sRNA-TPM.txt
small RNA


title: srna-16

description:
sRNA-TPM.txt
small RNA

source_name: Primary Root(6DAS)


title: srna-19

description:
sRNA-TPM.txt
small RNA


title: srna-17

description:
sRNA-TPM.txt
small RNA

source_name: Primary Root(V1)


title: Ptr SDX cells

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

data_processing:
Details of data processing steps are provided in the manuscript.
Genome_build: Phytozome Populus trichocarpa genome v4.1, Phytozome Eucalyptus grandis genome v2.0, Liriodendron chinense genome (Chen et al., 2018), Trochodendron aralioides genome (Strijk et al., 2019)
Supplementary_files_format_and_content: For P. trichocarpa and L. chinense, the raw UMI counts of unfiltered (raw) and cellular (filtered) barcodes were generated using Cell Ranger (v5.0.1) including H5 files and tar archives containing sparse matrices (MTX files) and feature and barcode sequences (TSV files).
Supplementary_files_format_and_content: For E. grandis and T. aralioides, the raw UMI counts of unfiltered barcodes in TXT format were generated using the MARS-seq2.0 pipeline. The raw UMI counts of the barcodes with more than or equal to 100 UMI counts were then converted to H5 files for Cell Ranger.
Supplementary_files_format_and_content: For three SDX cell types of Populus trichocarpa, the TPM of each gene are in TXT format.

organism: Populus trichocarpa

source_name: SDX protoplasts

extract_protocol:
SDX protoplasts were isolated and loaded into a Chromium Single Cell Instrument (10x Genomics) for single-cell sequencing library construction.
Single-cell sequencing libraries were generated using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10x Genomics) according to user manual.

value: SDX cells


title: srna-18

description:
sRNA-TPM.txt
small RNA

source_name: SAM (V3)


title: R14_LS_46

city: Portland

first: Suzy

middle: CP

last: Renn

state: Oregon

address: 3203 SE Woodstock Blvd., Biology Room B124

department: Biology

institute: Reed College

description:
Lab stock female brain sampled 14 days after initial release of fry
SR46

data_processing:
Paired end RNA-seq reads were preprocessed with TrimGalore v0.6.4 for adaptor trimming and FastQC v0.11.3 for quality filtering
Remaining paired reads were aligned to the A. burtoni reference genome with STAR v.2.5.3, using the associated RefSeq GTF file to guide the alignment
Resultling GTF files were merged to create a merged GTF file that contained RefSeq annotated loci as well as novel alignments.
Reads were re-mapped to this merged GTF file so both annotated and novel alignment counts could be compared across samples.
Aligned reads were assembled and quantified using StringTie v1.3.4, which produced GTF files used to generate count tables for differential expression analysis.
Genome_build: NCBI accesion: GCF_000239415.1
Supplementary_files_format_and_content: Processed data files include GTF files produced by StringTie v1.3.4 that includes coverage metrics for annotated and novel transcripts.

organism: Haplochromis burtoni

source_name: whole brain

extract_protocol:
Brains were removed from RNAlater and placed in 200 ųl of 1-Thioglycerol/Homogenization Solution from the MAxwell 16 LEV Simply RNA Tissue Kit (Promega cat# AS1280). Samples were homogenized using a hand held pestle motor and plastic pestle in a microcentrifuge tube. Homogenized samples were transferred to the MAxwell 16 LEV Simply RNA Tissue Kit cartridge and processed in the Maxwell 16 Instrument (Promega AS1000) using the High Strength LEV Magnetic Rod and Plunger Bar Adaptor (Cat.# SP1070). Standard DNAse treatment was included and samples were eluted in 50 ųl H20 including RNAse inhibitors.
Library construction was performed by NovoGene as follows: After the QC procedures, mRNA was enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is 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 are 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 is completed through size selection and PCR enrichment.

tag: reproductive time-point

tag: stock

value: LS

value: whole brain


title: Lch SDX cells

organism: Liriodendron chinense

extract_protocol:
SDX protoplasts were isolated and loaded into a Chromium Single Cell Instrument (10x Genomics) for single-cell sequencing library construction.
Single-cell sequencing libraries were generated using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to user manual.


title: srna-15

description:
sRNA-TPM.txt
small RNA


title: B02_LS_45

description:
Lab stock female brain sampled 2 days after the start of mouthbrooding
SR45


title: pDMR6_IP_biorep1


title: R14_LS_44

description:
Lab stock female brain sampled 14 days after initial release of fry
SR44


title: R02_WS_47

description:
Wild stock female brain sampled 2 days after initial release of fry
SR47

value: WS


title: srna-13

description:
sRNA-TPM.txt
small RNA

source_name: Husk leaf

value: not collected


title: R02_WS_48

description:
Wild stock female brain sampled 2 days after initial release of fry, two sequencing runs from same library
SR48


title: R02_LS_43

description:
Lab stock female brain sampled 2 days after initial release of fry
SR43


title: srna-12

description:
sRNA-TPM.txt
small RNA

source_name: First Leaf-N(V3)


title: srna-14

description:
sRNA-TPM.txt
small RNA

source_name: Inflorescence


title: srna-11

description:
sRNA-TPM.txt
small RNA

source_name: First Leaf-L(V3)


title: srna-10

description:
sRNA-TPM.txt
small RNA


title: B02_LS_42

description:
Lab stock female brain sampled 2 days after the start of mouthbrooding
SR42


title: B14_LS_41

description:
Lab stock female brain sampled 14 days after the start of mouthbrooding
SR41


title: srna-9

description:
sRNA-TPM.txt
small RNA


title: srna-8

description:
sRNA-TPM.txt
small RNA

source_name: Ear leaf


title: R14_LS_39

description:
Lab stock female brain sampled 14 days after initial release of fry
SR39


title: R02_LS_37

description:
Lab stock female brain sampled 2 days after initial release of fry
SR37


title: srna-7

description:
sRNA-TPM.txt
small RNA

source_name: Base of Stage 2 Leaf-N(V5)


title: MB bio rep 7

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

description: coronal section

data_processing:
A pre-built reference (refdata-gex-mm10-2020-A) was downloaded from 10x Genomics website and used as a reference for data processing with Space Ranger v1.3.1
Raw fastq files and H&E images were processed with the Space Range v1.3.1 command line tool to produce processed data files: expression matrices (h5 files), scaled H&E images (png files), spot coordinate tables (csv files) and scale factors (json files)
Assembly: mm10
Library strategy: Visium spatial gene expression (RNA)

source_name: brain

extract_protocol:
snap-frozen tissue specimens were embedded in OCT, cryo-sectioned at 10um thickeness and placed onto Visium gene expression array (10x Genomics)
spatial gene expression libraries were generated following 10X Genomic Visium Spatial Gene Expression protocol (User Guide, CG000239 Rev F) or The Visium Spatial Gene Expression for FFPE reagent kit (10x Genomics, User Guide CG000407 Rev C, mouse transcriptome, human transcriptome)

value: brain

value: young mice

tag: array id

tag: protocol

value: standard


title: MB bio rep 8

description: coronal section


title: srna-5

description:
sRNA-TPM.txt
small RNA

source_name: 5mm Ear


title: MB bio rep 6

description: coronal section


title: MB bio rep 5

description: coronal section


title: MB bio rep 3

description: coronal section

value: RRST


title: R02_LS_35

description:
Lab stock female brain sampled 2 days after initial release of fry
SR35

value: female


title: MB bio rep 4

description: coronal section


title: R14_LS_34

description:
Lab stock female brain sampled 14 days after initial release of fry
SR34


title: srna-4

description:
sRNA-TPM.txt
small RNA

source_name: 2mm Tassel


title: MB bio rep 2

description: coronal section


title: srna-3

description:
sRNA-TPM.txt
small RNA

source_name: 2mm Ear


title: P11 bio rep 3

description: coronal section

source_name: bone/cartilage

value: bone/cartilage

value: postnatal day 11


title: R14_WS_33

description:
Wild stock female brain sampled 14 days after initial release of fry
SR33


title: P11 bio rep 2

description: coronal section


title: R02_LS_32

description:
Lab stock female brain sampled 2 days after initial release of fry
SR32


title: R02_LS_40

description:
Lab stock female brain sampled 2 days after initial release of fry
SR40


title: srna-2

description:
sRNA-TPM.txt
small RNA

source_name: 1cm Tassel


title: P11 bio rep 1

description: coronal section


title: P4 bio rep 3

description: growth plate specimens collected before SOC formation, postnatal day 4

value: postnatal day 4


title: P4 bio rep 2


title: R02_WS_31

description:
Wild stock female brain sampled 2 days after initial release of fry
SR31


title: P4 bio rep 1


title: total-26

description: totalRNA-TPM.txt

source_name: Topmost Leaf-N(V3)


title: srna-1

description:
sRNA-TPM.txt
small RNA

source_name: 1cm Ear


title: total-25

description: totalRNA-TPM.txt

source_name: Topmost Leaf-L(V3)


title: srna-6

description:
sRNA-TPM.txt
small RNA

source_name: Base of Stage 2 leaf-L(V5)


title: R14_WS_30

description:
Wild stock female brain sampled 14 days after initial release of fry
SR30

source_name: whole brain


title: MB bio rep 1

description: coronal section


title: total-23

description: totalRNA-TPM.txt

source_name: Tip of Stage 2 leaf-L(V5)


title: total-24

description: totalRNA-TPM.txt

source_name: Tip of Stage 2 Leaf-N(V5)


title: R14_LS_36

description:
Lab stock female brain sampled 14 days after initial release of fry
SR36


title: total-22

description: totalRNA-TPM.txt

source_name: Third Leaf(V3)


title: total-20

description: totalRNA-TPM.txt


title: 231_shVASP_3

city: Wuhan

first: Kai

last: Li

address: 185 Donghu Road, Wuchang District

institute: Wuhan University

data_processing:
Row data were filtered using Trim_galore version 0.6.4.
RNA-seq reads were aligned to the  hg38 genome assembly using STAR version 2.7.1a.
The counts were calcluted using FeatureCounts v1.6.4 for each gene.
Genome_build: hg38

source_name: human breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in Eagle’s minimum essential medium (EMEM; Genom, 11700) with 10% FBS, 0.01 mg/mL human recombinant insulin (Sigma, I9278), and nonessential amino acids (Invitrogen, 11140050).

extract_protocol:
After transfected for 48 hours, MDA-MB-231 cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transient transfection of cells with siR-NC and siR-VASP was performed using Lipofectamine 2000 (Invitrogen, 11668) reagent according to the instructions.

value: human breast cancer cells

tag: cell line

tag: sirna transfection

value: VASP siRNA


title: 231_shVASP_1


title: 231_shVASP_2


title: 231_plko_3

value: negative control siRNA


title: total-18

description: totalRNA-TPM.txt

source_name: SAM (V3)


title: total-21

description: totalRNA-TPM.txt


title: B02_WS_28

description:
Wild stock female brain sampled 2 days after the start of mouthbrooding
SR28


title: total-17

description: totalRNA-TPM.txt

source_name: Primary Root(V1)


title: B02_WS_27

description:
Wild stock female brain sampled 2 days after the start of mouthbrooding
SR27


title: R14_WS_26

description:
Wild stock female brain sampled 14 days after initial release of fry
SR26


title: B14_WS_29

description:
Wild stock female brain sampled 14 days after the start of mouthbrooding
SR29


title: total-19

description: totalRNA-TPM.txt


title: total-16

description: totalRNA-TPM.txt

source_name: Primary Root(6DAS)


title: total-15

description: totalRNA-TPM.txt


title: total-14

description: totalRNA-TPM.txt

source_name: Inflorescence


title: 231_plko_2


title: R14_LS_24

description:
Lab stock female brain sampled 14 days after initial release of fry
SR24


title: total-13

description: totalRNA-TPM.txt

source_name: Husk leaf


title: total-12

description: totalRNA-TPM.txt

source_name: First Leaf-N(V3)


title: R14_WS_23

description:
Wild stock female brain sampled 14 days after initial release of fry
SR23


title: total-11

description: totalRNA-TPM.txt

source_name: First Leaf-L(V3)


title: B14_LS_22

description:
Lab stock female brain sampled 14 days after the start of mouthbrooding
SR22


title: KO, rep2 (RNA-seq)

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim galore0.6.6
The clean reads were aligned to mm10 by Hisat2 with default parameter and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05 using DEseq2
Assembly: mm10
Supplementary files format and content: FPKM.txt

source_name: B16-OVA-infiltrating OT-I cells

growth_protocol: Co-transferred WT and Stat3-/- OT-I cells were FACS-sorted from B16-OVA tumors at about day 16 post inoculation for RNA-seq.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: No

value: B16-OVA-infiltrating OT-I cells


title: KO, rep1 (RNA-seq)


title: total-10

description: totalRNA-TPM.txt


title: total-9

description: totalRNA-TPM.txt


title: total-8

description: totalRNA-TPM.txt

source_name: Ear leaf


title: WT, rep1 (RNA-seq)

value: WT


title: R14_WS_25

description:
Wild stock female brain sampled 14 days after initial release of fry
SR25


title: total-7

description: totalRNA-TPM.txt

source_name: Base of Stage 2 Leaf-N(V5)


title: H3K27ac, KO, 2 (ChIP-seq)

data_processing:
Reads were trimmed and ﬁltered for quality control using Trim Galore v0.4.4
Clean reads were mapped to the mouse genome mm10 by bowtie2(version2.2.5)
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 0.01
ChIPseeker was used for peak annotation
Assembly: mm10
Supplementary files format and content: bigwig file

source_name: in vitro activated Stat3-/- CD8+ T cells

extract_protocol:
The ChIP assay was performed using ChIP-IT Express Chromatin Immunoprecipitation Kits (Active Motif) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: FACS sorted naïve CD8+ T cells were activated with the plate-bound anti-CD3 and anti-CD28 for three days. For pSTAT3 ChIP-seq, the activated WT CD8+ T cells were cultured at 37 ℃ for 30 minutes in fresh medium with 10ng/ml IL-6, 10ng/ml IL-10 or 10ng/ml IL-21. For H3K27ac ChIP-seq, the activated WT and Stat3-/- CD8+ T cells were stimulated by 10ng/ml IL-10 for another three days.

value: CD8+ T cells

tag: strain

tag: chip antibody

value: anti-H3K27ac antibody (Active Motif, 39133)

value: stimulated by 10ng/ml IL-10 for three days


title: B14_WS_21

description:
Wild stock female brain sampled 14 days after the start of mouthbrooding
SR21

value: WS

value: whole brain

tag: Sex


title: total-6

description: totalRNA-TPM.txt

source_name: Base of Stage 2 leaf-L(V5)


title: B14_WS_20

description:
Wild stock female brain sampled 14 days after the start of mouthbrooding
SR20

source_name: whole brain

tag: tissue


title: total-4

description: totalRNA-TPM.txt

source_name: 2mm Tassel

value: not collected


title: B14_LS_19

description:
Lab stock female brain sampled 14 days after the start of mouthbrooding
SR19

value: LS


title: Input, KO, 2 (ChIP-seq)

growth_protocol: FACS sorted naïve CD8+ T cells were activated with the plate-bound anti-CD3 and anti-CD28 for three days.

tag: cell type


title: total-5

description: totalRNA-TPM.txt

source_name: 5mm Ear


title: total-2

description: totalRNA-TPM.txt

source_name: 1cm Tassel


title: total-3

description: totalRNA-TPM.txt

source_name: 2mm Ear


title: B14_LS_18

description:
Lab stock female brain sampled 14 days after the start of mouthbrooding
SR18


title: circ-26

description:
circRNA-CPM.txt
circular RNA

source_name: Topmost Leaf-N(V3)


title: H3K27ac, KO, 1 (ChIP-seq)


title: total-1

description: totalRNA-TPM.txt

source_name: 1cm Ear


title: 231_plko_1

source_name: human breast cancer cells


title: R14_WS_17

description:
Wild stock female brain sampled 14 days after initial release of fry
SR17


title: circ-24

description:
circRNA-CPM.txt
circular RNA

source_name: Tip of Stage 2 Leaf-N(V5)


title: B14_WS_16

description:
Wild stock female brain sampled 14 days after the start of mouthbrooding
SR16


title: WT, rep2 (RNA-seq)


title: circ-23

description:
circRNA-CPM.txt
circular RNA

source_name: Tip of Stage 2 leaf-L(V5)


title: B14_WS_15

description:
Wild stock female brain sampled 14 days after the start of mouthbrooding
SR15


title: H3K27ac, WT, 2 (ChIP-seq)

source_name: in vitro activated WT CD8+ T cells


title: K562 WT_rep2

city: New York

first: Seungjae

last: Lee

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

description: 50-80 nt RNA

data_processing:
After removing 3' adaptor sequences, we mapped RNA reads to human (hg38) genome assembly. Unmapped reads were iteratively trimmed one nucleotide each iteration retaining a read length of ≥15 nt, and then mapped to the genome using Bowtie with no mismatches, up to 5 iterations. After removing both 5’ and 3’ adaptor sequences, we mapped intermediate-length RNA reads to human (hg38) genome assembly using Biowtie2 with the default parameters. The uniquely mapped reads were extracted by “samtools view -bq 20” and the coverage normalized by library sizes were generated for the downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwig files

extract_protocol:
Four days after virus infection and puromycin selection, cells were collected for Ago2 IP using Ago2 antibody (Abnova) and the RNA products were purified using Trizol and PAGE-size selected for the intermediate fragments between 40 nt and 80 nt.
Isolated RNAs are ligated to 3’ adapter using T4 RNA Ligase 2 (truncated KQ) and then purified for reverse transcription by barcoded primer containing complementary sequences to the 3’ adaptor on the RNA. Following, the cDNA products are purified on PAGE and circularized using CircLigase II, annealed to the Cut Oligo and digested using BamHI. Finally, the library is amplified from the linear cDNAs using Phusion High-Fidelity PCR master mix with P5/P3 Solexa primers for 20 cycles. The PCR products are purified on Novex 8% TBE gel and send for sequencing with HiSeq 4000 in PE100 mode.

treatment_protocol: Lentiviral particles for control shRNA was produced in HEK293T cells and 5 ml cell culture supernatants containing lentivirus were added to K562 cells grown in 60 mm dishes.

value: lymphoblast cells isolated from the bone marrow

value: wild-type

value: Control shRNA


title: K562 WT_rep1

description: 50-80 nt RNA


title: Input, WT, 2 (ChIP-seq)


title: circ-22

description:
circRNA-CPM.txt
circular RNA

source_name: Third Leaf(V3)


title: circ-21

description:
circRNA-CPM.txt
circular RNA


title: H3K27ac, WT, 1 (ChIP-seq)


title: TUT247_rep2

data_processing:
Each of the TUTase small RNA sequencing libraries were processed by merging two overlapping paired reads into a single read using BBMerge, and the adaptor sequences were subsequently removed. The reads were then collapsed to remove PCR artifacts using fastx_collapser, and the 5' and 3’ end linker sequences were clipped. We then mapped small RNA-seq reads from these datasets to the hg38 genome assembly. Unmapped reads were iteratively trimmed one nucleotide each iteration retaining a read length of 15 nt, and then mapped to the genome using Bowtie with no mismatches, up to 30 iterations. The reads were required to match the microRNA mature sequences of both canonical miRNAs and mirtrons (Wen et al., 2015) with at least 15 nt overlap and within 2 nt of the 5’ end. The reads mapped to the spike-in sequences were counted.
Assembly: hg38

extract_protocol:
We extracted RNA from HEK293T cells using Trizol (Invitrogen) according to the manufacturer’s instructions.
1 ug of total RNA were used to generate small RNA libraries for each sample. 3’ linker was ligated to total RNA in the reaction containing 100μM 3’ linker, T4 RNA Ligase 2, truncated KQ (NEB), 10% PEG8000, 1X RNA ligation buffer, and 20 U RNase OUT overnight at 17°C. Using radio-labeled oligonucleotides as size-markers, 48-57 nucleotide sized 3’ linker-ligated small RNAs were purified by 12% Urea-PAGE gel. The small RNA-linker hybrid was then subjected to 5’ ligation reaction overnight at 17°C containing 100 μM 5’ adaptor, 20% PEG8000, 1X RNA ligase buffer, 1 mM ATP, 20 U RNaseOUT and 5 U T4 RNA ligase 1. The linker ligated RNAs were reverse transcribed, and PCR amplified using 12 cycles of PCR with forward and Illumina index reverse primers and the amplified libraries were purified by 8% non-denaturing acrylamide gel.

value: immortalized human embryonic kidney cells

value: TENT2/TUT4/TUT7 KO


title: circ-20

description:
circRNA-CPM.txt
circular RNA


title: Input, WT, 1 (ChIP-seq)


title: pSTAT3(Y705), IL-21 (ChIP-seq)

source_name: in vitro activated CD8+ T cells

value: anti-pSTAT3(Y705) antibody (CST, 9131S)

value: stimulated by 10ng/ml IL-21 at 37 ℃ for 30 minutes


title: circ-19

description:
circRNA-CPM.txt
circular RNA


title: B02_LS_14

description:
Lab stock female brain sampled 2 days after the start of mouthbrooding
SR14

value: female


title: circ-25

description:
circRNA-CPM.txt
circular RNA

source_name: Topmost Leaf-L(V3)


title: B14_LS_12

description:
Lab stock female brain sampled 14 days after the start of mouthbrooding; two sequencing runs from same library
SR12


title: TUT47_rep1

value: TUT4/TUT7 KO


title: B02_WS_11

description:
Wild stock female brain sampled 2 days after the start of mouthbrooding
SR11


title: Input, KO, 1 (ChIP-seq)


title: TUT47_rep2


title: circ-18

description:
circRNA-CPM.txt
circular RNA

source_name: SAM (V3)


title: B02_WS_09

description:
Wild stock female brain sampled 2 days after the start of mouthbrooding
SR09


title: TUT247_rep1


title: B02_LS_13

description:
Lab stock female brain sampled 2 days after the start of mouthbrooding
SR13


title: pSTAT3(Y705), IL-6 (ChIP-seq)

value: WT

value: stimulated by 10ng/ml IL-6 at 37 ℃ for 30 minutes


title: circ-17

description:
circRNA-CPM.txt
circular RNA

source_name: Primary Root(V1)


title: R02_WS_08

description:
Wild stock female brain sampled 2 days after initial release of fry
SR08


title: WT_rep2


title: pSTAT3(Y705), IL-10 (ChIP-seq)

value: CD8+ T cells

value: stimulated by 10ng/ml IL-10 at 37 ℃ for 30 minutes


title: WT_rep1


title: B14_LS_07

description:
Lab stock female brain sampled 14 days after the start of mouthbrooding
SR07


title: circ-16

description:
circRNA-CPM.txt
circular RNA

source_name: Primary Root(6DAS)


title: circ-15

description:
circRNA-CPM.txt
circular RNA


title: Group 4 rep2

description:
PPIs.txt
cDNA


title: B14_WS_06

description:
Wild stock female brain sampled 14 days after the start of mouthbrooding
SR06

source_name: whole brain

value: WS


title: WT, rep2 (ATAC-seq)

data_processing:
Raw ATAC-seq reads were trimmed and ﬁltered for quality control using Trim Galore v0.4.4 with parameters ‘-q 10 –length 30 –strin- gency 5 0 .
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2 v2.2.9 with –x2000.
Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were ﬁltered by Samtools.
PCR duplicates were removed with picard MarkDuplicates. Only concordantly mapped reads were used for further analyzing.
Peaks were determined by MACS2 with parameters ‘–nomodel–keep-dup all -q 0.01-shift 100-extsize 200 -call-summits -g mm’.
Peaks with differential accessibility were determined using DiffBind with at least 2 folds of change and FDR adjusted p value of 0.01.
ATAC-seq peak were annotated to the nearest gene using R package ChIPseeker. BedTools was used to ﬁnd common intersection between identiﬁed peaks (1 bp minimum overlap) and merged together. HOMER was used to ﬁnd TF motifs.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: B16-OVA-infiltrating OT-I cells

growth_protocol: Co-transferred WT and Stat3-/- OT-I cells were FACS-sorted from B16-OVA tumors at about day 16 post inoculation for ATAC-seq.

extract_protocol:
ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 and TruePrep Index Kit V2 for Illumina.
Sequencing was performed using Hiseq-PE150 (Illumina) made by Novogene.

value: B16-OVA-infiltrating OT-I cells


title: B02_LS_05

description:
Lab stock female brain sampled 2 days after the start of mouthbrooding
SR05

value: whole brain


title: KO, rep1 (ATAC-seq)


title: Group 2

description:
PPIs.txt
cDNA

source_name: First Leaf - L(V3); Topmost Leaf  - L(V3); Tip of 2 Stage leaf  - L(V5); Base of 2 Stage leaf - L (V5); Husk leaf; Ear leaf


title: circ-14

description:
circRNA-CPM.txt
circular RNA

source_name: Inflorescence

value: not collected


title: circ-13

description:
circRNA-CPM.txt
circular RNA

source_name: Husk leaf


title: R02_WS_02

description:
Wild stock female brain sampled 2 days after initial release of fry
SR02


title: R02_WS_03

description:
Wild stock female brain sampled 2 days after initial release of fry
SR03


title: WT, rep1 (ATAC-seq)


title: circ-11

description:
circRNA-CPM.txt
circular RNA

source_name: First Leaf-L(V3)


title: Group 4 rep1

description:
PPIs.txt
cDNA


title: PBMC, mRNA-derived cDNA 3309-2_S6_L002

city: Stanford

first: Prasanna

last: Jagannathan

state: CA

address: 240 Pasteur Drive Room 3456

department: Department of Medicine

institute: Stanford Universit

description:
PBMC, mRNA-derived cDNA
polyA RNA
3' mRNA library: I1, I2, R1 and R2 are index 1, 2 and read 1,2 respectively
Antibody-derived oligonucleotide (ADT)

data_processing:
To estimate the background signal for  each protein, a two-component Gaussian mixture model, implemented in the R package  function ‘mclust’ (v5.4.7), was fit across the droplets with a total UMI count of >10 and <100  from each experimental sample separately. The mean of the first Gaussian mixture model  component for each protein was then subtracted from the log counts per million from the QCpassed droplets in the respective experimental sample.
Raw data was filtered to remove cells  that expressed fewer than 200 genes and >10% mitochondrial reads.
We used the variable stabilization transformation (VST) from the Seurat R package to integrate and transform the  count data into normalized and scaled data that can be used for downstream analysis

source_name: peripheral blood -lane2

extract_protocol:
Approximately 1,000,000 cells from 10 patient samples were stained with Human TruStain FcX  Fc Blocking Reagent (BioLegend, 422302) for 10 min at room temperature. The cells were  stained for 30 min at 4 °C. Cells were then washed twice with PBS supplemented with 2% FCS  and 2 mM EDTA (Sigma) before resuspending in PBS and counting. Approximately 10,000 cells  per sample were loaded onto the 10x Chromium controller
Gene expression libraries were prepared for each sample according to the manufacturer’s protocol (10x Genomics). Cell-surface protein libraries were subjected to double the manufacturer’s recommended primer concentration and seven to eight amplification cycles during the sample index PCR to reduce the likelihood of daisy chains forming. All libraries were sequenced using a NovaSeq 6000 (Illumina) to achieve a minimum of 50,000 paired-end reads per cell for gene expression and 20,000 paired-end reads per cell for cell-surface protein  libraries.
CITE-seq

value: peripheral blood -lane2

tag: timepoint

tag: gender

value: Female

value: peripheral blood mononuclear cells (PBMC)

tag: library type

value: mRNA

tag: antibodies/tags


title: E12_3

first: Sini

last: Cai

address: Badachu #33 road

institute: Palate of plastic surgery hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: lambdoidal junction tissues

extract_protocol:
lambdoidal junction tissues were acquired, flash frozen on dry ice, 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

value: lambdoidal junction tissues

tag: developmental stage

value: embryonic day 12.5


title: PBMC, mRNA-derived cDNA 3309-2_S6_L001

source_name: peripheral blood -lane1

value: peripheral blood -lane1

tag: age


title: Group 5&6 rep2

description:
PPIs.txt
cDNA

source_name: Ear (2 mm); Tassel (2 mm); Ear (5 mm); Silk; Ear (3 cm)

tag: cultivar


title: circ-10

description:
circRNA-CPM.txt
circular RNA


title: E12_2


title: E12_1


title: Group 3

description:
PPIs.txt
cDNA

source_name: Endosperm (15 DAP); Endosperm (25 DAP)


title: Input (ChIP-seq)

tag: genotype

tag: treatment


title: PBMC, ADT-derived cDNA 3309-2-FB_S16_L002

description:
PBMC, ADT-derived cDNA
protein
Antibody-derived oligonucleotide library: I1, I2, R1 and R2 are index 1, 2 and read 1,2 respectively
poly A RNA

value: ADT


title: KO, rep2 (ATAC-seq)


title: circ-9

description:
circRNA-CPM.txt
circular RNA


title: Group 1

description:
PPIs.txt
cDNA

source_name: Primary Root (6 DAS); Primary Root (V1)

value: 6 DAS, V1


title: Group 7 rep2

description:
PPIs.txt
cDNA

source_name: Anther; Tassel (2 cm)


title: E11_3

value: embryonic day 11.5


title: PBMC, ADT-derived cDNA 3309-2-FB_S16_L001


title: circ-8

description:
circRNA-CPM.txt
circular RNA

source_name: Ear leaf


title: circ-12

description:
circRNA-CPM.txt
circular RNA

source_name: First Leaf-N(V3)


title: PBMC, mRNA-derived cDNA 3309-1_S5_L002


title: circ-7

description:
circRNA-CPM.txt
circular RNA

source_name: Base of Stage 2 Leaf-N(V5)


title: Group 7 rep1

description:
PPIs.txt
cDNA


title: E11_1


title: Group 8

description:
PPIs.txt
cDNA

source_name: Embryo (15 DAP); Embryo (25 DAP)


title: Group 5&6 rep1

description:
PPIs.txt
cDNA


title: E10_3

value: embryonic day 10.5


title: circ-6

description:
circRNA-CPM.txt
circular RNA

source_name: Base of Stage 2 leaf-L(V5)


title: circ-5

description:
circRNA-CPM.txt
circular RNA

source_name: 5mm Ear


title: Group 5

description:
PPIs.txt
cDNA

source_name: Ear (2 mm); Tassel (2 mm); Ear (5 mm)


title: Tar SDX cells_batch2

data_processing:
Details of data processing steps are provided in the manuscript.
Assembly: Phytozome Populus trichocarpa genome v4.1, Phytozome Eucalyptus grandis genome v2.0, Trochodendron aralioides genome (Strijk et al., 2019)
Supplementary files format and content: For P. trichocarpa, the raw UMI counts of unfiltered (raw) and cellular (filtered) barcodes were generated using Cell Ranger (v5.0.1) including H5 files and tar archives containing sparse matrices (MTX files) and feature and barcode sequences (TSV files).
Supplementary files format and content: For P. trichocarpa, E. grandis and T. aralioides, the raw UMI counts of unfiltered barcodes in TXT format were generated using the MARS-seq2.0 pipeline. The raw UMI counts of the barcodes with more than or equal to 100 UMI counts were then converted to H5 files for Cell Ranger.

organism: Trochodendron aralioides

source_name: SDX protoplasts

extract_protocol:
SDX protoplasts were isolated into individual wells of the prepared 384-well plates using cell sorter.
Single-cell sequencing libraries were generated following the MARS-seq2.0 protocol.

value: SDX cells


title: PBMC, mRNA-derived cDNA 3309-1_S5_L001


title: PBMC, ADT-derived cDNA 3309-1-FB_S15_L002


title: PBMC, ADT-derived cDNA 3309-1-FB_S15_L001


title: E10_2


title: circ-4

description:
circRNA-CPM.txt
circular RNA

source_name: 2mm Tassel


title: E10_1


title: Tar SDX cells


title: circ-3

description:
circRNA-CPM.txt
circular RNA

source_name: 2mm Ear


title: circ-2

description:
circRNA-CPM.txt
circular RNA

source_name: 1cm Tassel


title: PBMC, mRNA-derived cDNA 3238_S9_L001_I2

source_name: peripheral blood -lane2


title: Section5_bio6

data_processing:
Details of data processing steps are provided in the manuscript.
Assembly: Phytozome Populus trichocarpa genome v4.1
Supplementary files format and content: For SDX from different internodes in Populus trichocarpa, the results of differential expression analysis of each gene are in CSV format.

source_name: SDX

extract_protocol:
Total RNA from SDX tissue was extracted using RNeasy Plant Mini Kit (QIAGEN, USA)
RNA sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, USA)

value: SDX


title: PBMC, mRNA-derived cDNA 3238_S9_L001_I1

source_name: peripheral blood -lane1


title: Egr SDX cells_batch2

organism: Eucalyptus grandis


title: Section5_bio5


title: E11_2

source_name: lambdoidal junction tissues


title: circ-1

description:
circRNA-CPM.txt
circular RNA

source_name: 1cm Ear


title: PBMC, ADT-derived cDNA 3238-FB_S19_L002


title: Section5_bio4


title: ribo-20

description:
ribo-TPM.txt
mRNA bound by ribosome

data_processing:
Library strategy: Ribo-Seq
Quality control: Raw RNA-seq and circRNA-Seq data were processed by SOAPnuke1.6.548 with the parameters “-n 0.01 -l 20 -q 0.3 -A 0.25” and used SOAPnuke1.6.548 filters RNA to process the raw sRNA-Seq data with the parameters “-p 1 -z 18 -s -Q 2 --sanger”. Ribo-Seq data was removed adaptors and controled low quality by FASTX_Toolkit-0.0.14 fastx_clipper with the parameters "-l 5 -c -n -v -Q33" and fastx_trimmer with the parameters "-f 1 -Q 33".
Alignment: Clean reads were aligned to the maize AGPv4 reference genome. Total RNA-seq data from the 26 tissues or stages were mapped to the B73 AGPv4 reference genome using the default parameters of HISAT and StringTie; small RNAs which size were 18–26 nt were mapped to the maize AGPv4 reference genome using Bowtie-1.1.2 with the parameters unique location and no mismatch; the Ribo-Seq reads were aligned to the rRNA reference sequence using Bowtie-1.1.267 to filter out reads derived from rRNAs and retained reads were mapped to the maize AGPv4 reference genome.
Identification of non-coding RNA: Mapsplice-v2.1.8 was used to identify fusion RNAs from total RNA-seq data from each tissue; and improved version of LncRNA_Finder was used to identify lncRNAs from total RNAs. CIRI v2.0.5 was used to identify circRNAs by aligning them to the maize AGPv4 reference genome.
Quantification of RNA: Total RNAs including lncRNAs and mRNAs bound by ribosome were calculated expression by RSEM. CIRCexplorer2 v2.0.1 was used quantify the expression levels of the circRNAs. The expression of fusion RNA and small RNA was calculated according to the TPM standard formula.
PPIs: The libraries were sequenced on the PacBio platform, and Circular Consensus Sequencing reads were called using SMRTLink-5.1.0.26412. The following analysis was performed to obtain PPIs: Firstly, reads in FASTA format were extracted from BAM files using SAMtools-1.9. Next, because ten barcoded samples were combined to generate each sequencing library, reads from each sample were divided based on their barcode sequences using Cutadapt-1.9.1. Parameters -e and -m for running reads separation were 0.3 and 200, respectively. The reads were aligned to the coding sequence data from the maize AGPv4 genome to identified candidate PPI genes using BLAST+/2.7.1. Only PPI genes with BLAST e-value < 1.0e−4 that matched to two genes were retained. If a CCS contained sequences from two different genes, and the primer sequence and the recombination sequence were aligned consistently, the proteins encoded by the two genes were considered to be interacting proteins.
Genome_build: Zea_mays.B73_RefGen_v4
Supplementary_files_format_and_content: tab-delimited text files named "TPM" or "CPM" include expression values for each samples.
Supplementary_files_format_and_content: tab-delimited text files named "PPIs" include identified protein-protein interactions.

source_name: Topmost Leaf-L(V3)


title: Ptr SDX cells_MARS-seq_batch2


title: PBMC, ADT-derived cDNA 3238-FB_S19_L001


title: Ptr SDX cells_MARS-seq_batch1


title: Section5_bio3


title: ribo-19

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Tip of Stage 2 leaf-L(V5)


title: PBMC, mRNA-derived cDNA 3147_S7_L002

value: Male


title: ribo-18

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Third Leaf(V3)


title: PBMC, mRNA-derived cDNA 3147_S7_L001


title: Section5_bio2


title: Section5_bio1


title: Ray-rep1

extract_protocol:
Total RNA from dissected cells was extracted using RNeasy Plant Mini Kit (QIAGEN, USA) and the mRNA was amplified using Arcturus® RiboAmp® HS PLUS RNA Amplification Kit (Applied Biosystems, USA)
RNA sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, USA)

value: Ray parenchyma cells


title: Section4_bio6


title: ribo-16

description:
ribo-TPM.txt
mRNA bound by ribosome


title: PBMC, ADT-derived cDNA 3147-FB_S17_L002


title: PBMC, ADT-derived cDNA 3147-FB_S17_L001


title: Ray-rep2


title: ribo-17

description:
ribo-TPM.txt
mRNA bound by ribosome


title: Section4_bio4


title: PBMC, mRNA-derived cDNA 3280-2_S4_L002


title: Section4_bio5


title: ribo-15

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: SAM (V3)


title: Vessel-rep3

value: Vessel elements


title: Egr SDX cells


title: Vessel-rep2


title: Section4_bio3


title: PBMC, mRNA-derived cDNA 3280-2_S4_L001


title: ribo-14

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Primary Root(V1)


title: Vessel-rep1


title: ribo-13

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Primary Root(6DAS)


title: Section4_bio2


title: Ray-rep3


title: ribo-12

description:
ribo-TPM.txt
mRNA bound by ribosome


title: PBMC, ADT-derived cDNA 3280-2-FB_S14_L001


title: Section4_bio1


title: Fiber-rep3

value: Libriform fibers


title: Fiber-rep2


title: PBMC, mRNA-derived cDNA 3280-1_S3_L002

value: peripheral blood -lane2


title: Section3_bio6


title: ribo-10

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Husk leaf

value: not collected


title: PBMC, mRNA-derived cDNA 3280-1_S3_L001

value: peripheral blood mononuclear cells (PBMC)


title: Section3_bio5


title: Fiber-rep1


title: ribo-9

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: First Leaf-N(V3)


title: ribo-8

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: First Leaf-L(V3)


title: Section3_bio4


title: Section3_bio3


title: PBMC, ADT-derived cDNA 3280-1-FB_S13_L002


title: ribo-7

description:
ribo-TPM.txt
mRNA bound by ribosome


title: A49 Input ChIP-seq rep2

city: Tianjin

first: Xinyi

last: Lu

address: 94 Weijin Road

institute: Nankai University

data_processing:
Raw Chip-Seq reads were aligned to mouse genome (mm10) by BOWTIE2 with parameter “--local -k 1”. This setting would ensure if one more equivalent best alignment is found, only one of those hits will be reported randomly. Therefore, instead of excluding reads from repetitive elements, multiple hits reads will be evenly distributed over highly similar repeat elements across genome. The peaks of H3K9me3 were called using DFilter (v1.5) with setting “ks=20 -lpval=3 –nonzero”.
genome build: mm10
processed data files format and content: bedgraph file generated using Bedtools

source_name: ES Cell

growth_protocol: The embryonic stem cells were cultured on feeder in medium consisted of knock-out DMEM (Invitrogen) containing 20% FBS (HyClone), 1,000 U/ml mouse leukemia inhibitory factor (LIF; ESG1107, Millipore), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 μg/ml). For the culture of ESCs, the medium was changed daily, and cells were routinely passaged every two days.

extract_protocol:
For ChIP-seq, ES cells were first fixed with 1% paraformaldehyde, and then lysed and sonicated to achieve the majority of DNA fragments at 100-1000 bp. DNA fragments were then enriched by immunoprecipitation with the H3K9me3 antibody (Abcam, ab8898). The immunoprecipitated material was eluted from the beads by heating for 30 min at 68 °C. Then, samples were incubated with Proteinase K at 42 °C for 2 h followed by 67 °C for 6 h to reverse the crosslinks. The samples were extracted with phenol:chloroform:isoamyl alcohol followed by chloroform, ethanol precipitation, and resuspension in TE buffer.
For ChIP-seq, libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.

value: ESC

value: Terc knockout


title: PBMC, ADT-derived cDNA 3280-2-FB_S14_L002


title: A49 Input ChIP-seq rep1


title: ribo-6

description:
ribo-TPM.txt
mRNA bound by ribosome

extract_protocol:
Three replicates were prepared per tissue. RNA was extracted from 5–10 individual plants per replicate. Equal amounts of the three replicates were used for sequencing. Total RNA was isolated from the 26 tissues using a Direct-zol RNA Microprep kit (Zymo Research) following the manufacturer’s guidelines.
RNA libraries were prepared for sequencing using corresponding standard protocols.


title: TR10 Input ChIP-seq rep2

value: Terc rescued


title: PBMC, mRNA-derived cDNA 3515_S10_L001

value: peripheral blood -lane1

value: Female

value: mRNA


title: Section3_bio1


title: N33 Input ChIP-seq rep2

value: wildtype


title: ribo-11

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Inflorescence


title: ribo-5

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Ear leaf


title: PBMC, ADT-derived cDNA 3515-FB_S20_L002

source_name: peripheral blood -lane2

value: ADT


title: Section2_bio6

source_name: SDX


title: PBMC, mRNA-derived cDNA 3515_S10_L002


title: ribo-4

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: Base of Stage 2 leaf-L(V5)


title: PBMC, ADT-derived cDNA 3515-FB_S20_L001

source_name: peripheral blood -lane1


title: Section2_bio5


title: ribo-3

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: 5mm Ear


title: TR10 Input ChIP-seq rep1


title: PBMC, mRNA-derived cDNA 3579_S8_L002


title: PBMC, ADT-derived cDNA 3280-1-FB_S13_L001


title: Section2_bio4


title: TR10 H3K9me3 ChIP-seq rep1

value: H3K9me3 (ab8898, Abcam)


title: PBMC, mRNA-derived cDNA 3579_S8_L001


title: ribo-2

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: 1cm Tassel


title: Section2_bio3

value: SDX


title: Section3_bio2


title: ribo-1

description:
ribo-TPM.txt
mRNA bound by ribosome

source_name: 1cm Ear


title: Section2_bio2


title: PBMC, ADT-derived cDNA 3579-FB_S18_L002

value: Male


title: PBMC, ADT-derived cDNA 3579-FB_S18_L001


title: A49 H3K9me3 ChIP-seq rep1


title: N33 H3K9me3 ChIP-seq rep2


title: Si3

data_processing:
Basecalls performed using bcl2fastq version 2.18
All reads were mapped to the hg18 using hisat2 (v2.0.4)
Fragments per kilobase per million mapped reads (FPKM) were calculated using cufflinks (v2.2.1) to estimate gene expression levels.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: human breast cancer cells

growth_protocol: MCF-7 cells were cultured in Eagle’s minimum essential medium (EMEM; Genom, 11700) with 10% FBS, 0.01 mg/mL human recombinant insulin (Sigma, I9278), and nonessential amino acids (Invitrogen, 11140050).

extract_protocol:
After transfected for 48 hours, MCF-7 cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MCF-7 cells

value: breast cancer

value: VASP siRNA


title: N33 Input ChIP-seq rep1


title: Section1_bio6


title: PBMC, mRNA-derived cDNA 3089-2_S2_L002

value: peripheral blood -lane2


title: Si1


title: PBMC, mRNA-derived cDNA 3089-2_S2_L001


title: Si2


title: TR10 RNA-seq rep2

data_processing:
Raw RNA-seq reads were firstly aligned to the mouse genome (version: UCSC mm10) using STAR (version 2.5.1). To study the expression of repeat elements, for read with multiple hits, only one hit was randomly picked as final alignment by setting STAR parameter as “—outSAMprimaryFlag AllBestScore –outSAMmultNmax 1”. The CUFFDIFF (v2.2.1) was used to identify differential gene expression.
genome build: mm10
processed data files format and content: bedgraph file generated using Bedtools

extract_protocol:
For RNA-seq, total RNA was purified using an RNA mini kit (Qiagen) and treated with DNase I (Qiagen).
For RNA-seq, total RNA were poly(A) enriched with oligo(T) beads and RNA libraries were prepared for sequencing using standard Illumina protocols.


title: TR10 H3K9me3 ChIP-seq rep2


title: Section1_bio5


title: PBMC, ADT-derived cDNA 3089-2-FB_S12_L002


title: TR10 RNA-seq rep1


title: Section1_bio4


title: NC2

value: negative control siRNA


title: NC3


title: NC1


title: PBMC, mRNA-derived cDNA 3089-1_S1_L002

value: peripheral blood mononuclear cells (PBMC)


title: A49 RNA-seq rep2

value: ESC


title: A49 H3K9me3 ChIP-seq rep2

value: Terc knockout


title: Section1_bio2


title: PBMC, mRNA-derived cDNA 3089-1_S1_L001


title: A49 RNA-seq rep1


title: Section2_bio1


title: HEK293FRT, ARID1B, Rep2

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
ChIP-seq reads were aligned to the UCSC hg38 genome using bowtie2 version 2.3.4.1 with default parameters.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: To create bigWig files, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments and normalized to reads per million.
Supplementary files format and content: BED files with peaks are included. Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Branson sonicator
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. Approx 5 ng of DNA was used as starting material for ip samples. Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 275-700bp in length using 1.5% Pippin cassesstte. Libraries were validated using the HS qubit assay as well as HS BA assays.

value: Human embryonic kidney


title: N33 H3K9me3 ChIP-seq rep1


title: N33 RNA-seq rep2


title: HEK293FRT, ARID1B, Rep1


title: PBMC, ADT-derived cDNA 3089-1-FB_S11_L002


title: HEK293FRT, Input


title: Ptr SDX cells_batch2

source_name: SDX protoplasts

extract_protocol:
SDX protoplasts were isolated and loaded into a Chromium Single Cell Instrument (10x Genomics) for single-cell sequencing library construction.
Single-cell sequencing libraries were generated using Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10x Genomics) according to user manual.

value: SDX cells


title: N33 RNA-seq rep1


title: PBMC, ADT-derived cDNA  3089-1-FB_S11_L001

value: peripheral blood -lane1


title: PBMC, ADT-derived cDNA 3089-2-FB_S12_L001


title: WT_rpc1_TAP_1

status: Public on Dec 24 2022

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

data_processing:
Raw reads were trimmed using trimmomatic against the appropriate adapter sequences with options SE ILLUMINACLIP:$adapters:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were then mapped on S. pombe genome (version ASM294v2.26) using HISAT2 with option --no-splice-alignment.
Mapped reads were summarized at the gene level using featurecounts.
For the RNA-seq experiments, differential gene expression analysis was performed using the R package DESeq2 .
For the ChIP-seq experiments, normalisation factors were computed based on the number of spike-in reads mapped to the S. cerevisiae genome. Based on these normalisation factors, we used deepTools to normalized coverage files (.bigwig) with options bamCoverage --samFlagExclude 256 --maxFragmentLength --scaleFactor $size_factor -bs 1 -of bigwig.
Genome_build: ASM294v2.26
Supplementary_files_format_and_content: S2A_vs_WT_DESeq2.txt is the DESeq2 results() output including the fold change of expression upon the S2A mutation, and its associated pvalue. For the ChIP-seq experiments, genome coverage files in bigWig format are provided instead.

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: Cells were grown in YES medium at 32°C until mid-exponential phase (OD600 ~0.6).

extract_protocol:
The pellet was thawed on ice and washed with FA/SDS/PI (Hepes-KOH pH7.5 50 mM, NaCl 150 mM, EDTA 1 mM, Na deoxycholate 0.1%, Triton X-100 1%, SDS 0.1%, PMSF 1 mM), resuspended in 1.6 ml of FA/SDS/PI and incubated 15 minutes on ice. The sample was sonicated with a BioRuptor (Diagenode) (cycles of 30 seconds ON, 60 seconds OFF, 21 minutes). After transfer to 1.5 ml microcentrifuge tube and centrifugation for 30 minutes,14000 rpm, 4°C, the supernatant was transferred to a new tube. Per IP, 50μl of appropriate magnetic beads (Dynalbeads Pan Mouse IgG) were washed 4 times with PBS BSA (1mg/ml) and resuspended in PBS BSA (10 mg/ml) and then added to each 500 uL chromatin extract IP and incubated 2h at 21°C. The beads were washed 3 times with 1ml of FA/SDS+NaCl 500mM, 1 time with 500 μl of IP Buffer and 1 time with 500 μl of TE and resuspended in 125 μl of Pronase Buffer 1X and incubated 20 minutes at 65°C. RNAse A was added 1h at 37°C and the DNA sample were purified on Rapace columns.
Illumina TruSeq ChIP-seq library preparation protocol according to the manufacturer instructions.

treatment_protocol: 80 mL of cultures were incubated for 10 min at room temperature with 1% formaldehyde. After quenching the reaction with glycine, cells were washed cold Tris-buffered saline (20 mM Tris–HCl pH 7.5, 150 mM NaCl) and snap-freezed.

value: WT

tag: ip

value: TAP

value: h- Rpc1-TAP-NatR

tag: spike-in

value: 10 % S. cerevisiae Rpb3-TAP strain mixed before the crosslink


title: RNA_S2A_1

extract_protocol:
The cell pellets were resuspended in 750μL of TES buffer (10mM Tris pH 7.5, 10mM EDTA pH 8, 0.5% SDS) and the total RNA was isolated by hot phenol extraction.
1μg of total RNA was ribodepleted and analyzed by Bioanalyzer microchip electrophoresis to ensure its good quality (RIN > 8.5). 125ng of ribodepleted samples were prepared for strand-specific NGS with the TruSeq Stranded Total RNA Sample Preparation Protocol (Illumina).

value: h- Rpb1 CTD-S2A-kanR


title: Section1_bio3

value: SDX


title: RNA_S2A_2


title: S2A_rpc1_TAP_1

value: h- Rpb1 CTD-S2A-kanR Rpc1-TAP-NatR


title: RNA_WT_2

value: h-


title: HEK293T-E92K-3

city: Jupiter

first: Ciaran

last: Seath

state: Florida

address: 120 Scripps Way

institute: UF-Scripps

data_processing:
Data Processed by Genewiz
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Assembly: not provided

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA harveted by Genewiz
Library construction by Genewiz

tag: cell line

value: embryonic kidney cells


title: S2A_input_1

extract_protocol:
The pellet was thawed on ice and washed with FA/SDS/PI (Hepes-KOH pH7.5 50 mM, NaCl 150 mM, EDTA 1 mM, Na deoxycholate 0.1%, Triton X-100 1%, SDS 0.1%, PMSF 1 mM), resuspended in 1.6 ml of FA/SDS/PI and incubated 15 minutes on ice. The sample was sonicated with a BioRuptor (Diagenode) (cycles of 30 seconds ON, 60 seconds OFF, 21 minutes). After transfer to 1.5 ml microcentrifuge tube and centrifugation for 30 minutes,14000 rpm, 4°C, the supernatant was transferred to a new tube. 100 μl of the total extract was kept as the input fraction and was treated by adding 25 μl of Pronase Buffer 5x, 6.25 μl of Pronase and incubated 1h at 37°C, then overnight at 65°C. RNAse A was added 1h at 37°C and the DNA sample were purified on Rapace columns.
Illumina TruSeq ChIP-seq library preparation protocol according to the manufacturer instructions.

tag: strain

value: input


title: WT_input_2


title: Section1_bio1


title: WT_input_1


title: HEK293T-E92K-2


title: WT_rpc1_TAP_2


title: RNA_WT_1


title: HEK293T-E92K-1


title: HEK293T-H2A-3


title: S2A_input_2


title: HEK293T-H2A-4


title: HEK293T-E92K-4


title: S2A_rpc1_TAP_2


title: HEK293T-H2A-Pinometostat-4

data_processing:
Data Processed by Genewiz
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

treatment_protocol: 1 µM JQ1 (Sigma), and 2.5mM Pinometostat (Sigma) in the presence of 10% FBS until day from day 2.

value: Pinometostat (2.5µM)

tag: time


title: HEK293T-H2A-1


title: HEK293T-H2A-Pinometostat-3


title: HEK293T-H2A-Pinometostat-2


title: HEK293T-H2A-2


title: HEK293T-H2A-JQ1-4


title: HEK293T-H2A-JQ1-3


title: HEK293T-H2A-Pinometostat-1


title: HEK293T-H2A-JQ1-1


title: HEK293T-E92K-DMSO-3


title: HEK293T-H2A-JQ1-2


title: HEK293T-E92K-DMSO-1


title: HEK293T-E92K-DMSO-4


title: HEK293T-H2A-DMSO-4


title: HEK293T-H2A-DMSO-2


title: HEK293T-E92K-DMSO-2


title: HEK293T-H2A-DMSO-1


title: HEK293T-H2A-DMSO-3


title: 2014-B-24302

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Hybridisation was performed by means of the Agilent Gene Expression Hybridization Kit on whole genome SurePrint G3 Human GE 8x60K V3 microarrays containing probes for 26,803 coding RNAs and 30,606 lncRNAs; slides were washed using the Gene Expression Wash Buffer Kit.

scan_protocol: Slides were then scanned with the Agilent scanner version C. All protocols and kits were purchased from Agilent Technologies.

data_processing: After scanning, array image analysis was carried out using the Agilent Feature Extraction Software v12.1, and then raw expression data was processed by background subtraction (normexp offset = 50) followed by within and between array normalisation, using the LIMMA (LInear Models for Microarray Analysis) package in R software. This dataset contains log normalised intensities.

source_name: TNBC sample

label_protocol: cDNA was amplified and labelled with the Agilent SureTag DNA Labeling Kit.

extract_protocol: After tumour area selection, total RNA was isolated from macrodissected sections using the Agilent Absolutely RNA FFPE Kit; reverse-transcribed to corresponding cDNA and in vitro transcribed with the Sigma TransPlex Whole Transcriptome Amplification Kit.

value: female


title: 2015-B-21984


title: 2015-B-05514


title: 2016-B-24836


title: 2015-B-18128


title: 2015-B-21897


title: 2015-B-21498


title: 2015-B-14264


title: 2016-B-24757


title: 2015-B-12381


title: 2015-B-27524


title: 2016-B-10031


title: 2016-B-21303


title: 2015-B-24075


title: 2013-B-27646


title: 2015-B-17368


title: 2015-B-15891


title: 2015-B-20875


title: 2014-B-23683


title: TN_25


title: 2013-B-28127


title: 2016-B-00081


title: 2016-B-00119


title: TN_29


title: TN_8


title: 2014-B-16242


title: TN_2


title: TN_12


title: TN_27


title: 2015-B-15424


title: fruit skin (FS)  of WT ‘Royal Gala’, biological Sample 3

city: Zhengzhou

first: Tiyu

last: Ding

state: Henan

address: Hanghai East Road

institute: Chinese Academy of Agricultural Sciences

description:
WT_FS_3
WT_FS.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
FeatureCounts v1.5.0-p3 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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: https://www.rosaceae.org/jbrowse/index.html?data=data%2Fmalus%2Fmdomestica_gddh13_v1.1&loc=Chr00%3A21091343..31637013&tracks=DNA%2Cgenes%2CmRNA&highlight=
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Malus domestica

source_name: fruit skin (FS)

extract_protocol:
From these tissue samples, RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. 5 µg total RNA was used to construct strand-specific poly-A RNA libraries as described by (Haile et al., 2017).
Libraries were sequenced using Novaseq 6000 sequencing system (Illumina) to produce paired-end reads per library ranging from 20 – 27 million. Reads were aligned to the GDDH13 reference genome (Daccord et al., 2017) using Bowtie2 (Langmead and Salzberg, 2012).

value: tissue

value: fruit skin


title: fruit skin (FS)  of miR172 transgenic ‘Royal Gala’, biological Sample 1

description:
miR172_FS_1
miR172_FS.txt


title: fruit skin (FS)  of miR172 transgenic ‘Royal Gala’, biological Sample 3

description:
miR172_FS_3
miR172_FS.txt


title: fruit skin (FS)  of miR172 transgenic ‘Royal Gala’, biological Sample 2

description:
miR172_FS_2
miR172_FS.txt


title: fruit skin (FS)  of WT ‘Royal Gala’, biological Sample 2

description:
WT_FS_2
WT_FS.txt


title: fruit skin (FS) of WT ‘Royal Gala’, biological Sample 1

description:
WT_FS_1
WT_FS.txt


title: B cells; NC3

city: Changchun

first: Tete

state: Jilin

address: Dongminzhu Street No.519

institute: Jilin University

data_processing:
Basecalls performed using Zebracall
After reads filtering, sequenced reads were mapped to mm10 whole genome using HISAT and Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Transcripts of each sample were reconstructed using StringTie, and the reconstructed information of all samples were combined using Cuffmerge. The integrated transcripts were compared with reference annotation information using Cuffcompare. Then new transcripts were selected, defined, and predicted using CPC.
SNP and INDEL variant of each sample were detected using GATK.
Fragments per kilobase of transcript per million mapped read (FPKM)  were calculated using RSEM v1.2.8
Genome_build: mm10
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: Spleen

growth_protocol: B cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1 μM of three classes of CpG ODNs for 24 h.

extract_protocol:
B cells were collected, and RNA was extracted using the EasyPure® RNA Kit (ER101-01, TransGen Biotech)
RNA libraries were prepared for sequencing using DNBSEQ protocols

value: B cells

value: control

value: BALB/c

value: Spleen

value: post natal day 42-49


title: TN_17


title: B cells; NC2


title: TN_9


title: B cells; NC1


title: TN_47


title: TN_4


title: B cells; CpGC3

value: CpG-C


title: TN_16


title: TN_14


title: TN_20


title: B cells; CpGC2


title: TN_18


title: TN_22


title: B cells; CpGC1


title: TN_46


title: 1943_2016


title: TN_11


title: TN_19


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(Butters), 150 mins, bio rep1

city: Bethlehem

first: Vassie

last: Ware

state: PA

address: 111 research drive

department: Biological Sciences

institute: Lehigh University

description:
raw_counts
TPM_values

data_processing:
Azenta Life Sciences  Bioinformatics analysis workflow. (Differential Gene Expression and Gene Ontology Analysis)
Assembly: Mycolicibacterium smegmatis mc2155, Mycobacterium phage Island3, Mycobacterium phage Butters
Supplementary files format and content: Text document, raw_counts
Supplementary files format and content: Text document, normalized_counts
Supplementary files format and content: Excel comma separated value, DEGs

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Island3
Mycobacterium phage Butters

source_name: Lehigh University

growth_protocol: Bacteria cells were grown to saturated phase and infected with Island3 at MOI of 1:1

extract_protocol:
Azenta Life Sciences
Azenta Life Sciences RNA-seq Library Preparation Workflow

treatment_protocol: Samples were taken at early (30 mins) and late (150 mins) of infection

tag: stage of_infection

value: late infection

value: 150 mins

value: Lehigh University


title: TN_15

organism: Homo sapiens


title: TN_3


title: TN_21


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(Butters), 150 mins, bio rep3

description:
raw_counts
TPM_values


title: TN_28


title: B cells; CpGB3

organism: Mus musculus

value: CpG-B

tag: tissue


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(Butters), 150 mins, bio rep2

description:
raw_counts
TPM_values


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(Butters), 30 mins, bio rep3

description:
raw_counts
TPM_values

value: early infection

value: 30 mins


title: B cells; CpGB2

tag: cell type


title: TN_23


title: TN_26


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(Butters), 30 mins, bio rep2

description:
raw_counts
TPM_values


title: B cells; CpGB1


title: B cells; CpGA3

value: CpG-A


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(Butters), 30 mins, bio rep1

description:
raw_counts
TPM_values


title: B cells; CpGA1


title: NC3

source_name: Bone marrow

growth_protocol: pDCs were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% β-mercaptoethanol, and 0.5 μM of three classes of CpG ODNs for 24 h.

extract_protocol:
pDCs were sorted,  and RNA was extracted using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pDCs

value: Bone marrow

value: post natal day 56-63


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(pMH94[Buttersgp57r]), 150 mins, bio rep3

description:
raw_counts
TPM_values

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Island3


title: NC2


title: TN_13

value: female


title: NC1


title: TN_10


title: CpGC3


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(pMH94[Buttersgp57r]), 150 mins, bio rep2

description:
raw_counts
TPM_values


title: CpGC2


title: CpGC1


title: CpGB2


title: Mycobacterium phage Island3, infection of Mycolicibacterium smegmatis mc155(pMH94[Buttersgp57r]), 150 mins, bio rep1

description:
raw_counts
TPM_values