title: 999232_12

description:
EXR-DGALA1plasma999232t12-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 267416_5

status: Public on Oct 30 2022

type: SRA

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

country: USA

institute: Baylor College of Medicine

description:
EXR-DGALA1plasma267416t5-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

tag: donor

tag: diagnosis

value: Type 1 Diabetes Mellitus

tag: tissue

value: Plasma

tag: anatomical location

value: Entire cardiovascular system

tag: time

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit


title: B73, mrna-22 rep2

city: wuhan

first: qian

middle: lin

last: han

state: hubei

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

country: China

institute: Huazhong Agricultural University

description:
instrument model: BGISEQ-100
slim-transcriptome.tpm
fusion.gff3
21tis-fusion-per.txt
21tis-lnc.tpm
lncrna.gff3

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.
Assembly: Zea_mays.B73_RefGen_v4
Supplementary files format and content: Files include expression values and identified protein-protein interactions
21tis-circ.tpm (abundance measurements)
21tis-fusion-per.txt (abundance measurements)
21tis-lnc.tpm (abundance measurements)
21tis-srna.tpm (abundance measurements)
circ.gff3 (a tab-delimited text file that holds information of circular RNA)
fusion.gff3 (a tab-delimited text file that holds information of fusion RNA)
lncrna.gff3 (a tab-delimited text file that holds information of lncRNA)
PPIs-highconf.txt (high confidence protein-protein interactions)
PPIs.txt (protein-protein interactions)
slim-transcriptome.tpm (abundance measurements)
srna.gff3 (a tab-delimited text file that holds information of sRNA)
translatome.tpm (abundance measurements)
sd-slimio-lowconf.txt (Shortest distances of slim integrative omics low confidence network)
sd-slimio-highconf.txt (Shortest distances of slim integrative omics high confidence network)
sd-slimcoexpression.txt (Shortest distances of slim co-expression network)
sd-PPIs-lowconf.txt (Shortest distances of low confidence interactome network)
sd-PPIs-highconf.txt (Shortest distances of high confidence interactome network)
sd-iowithncrna-lowconf.txt (Shortest distances of integrative omics with ncRNAs low confidence network)
sd-iowithncrna-highconf.txt (Shortest distances of integrative omics with ncRNAs high confidence network)
sd-cotranslation.txt (Shortest distances of co-translation network)
sd-coexpressionwithncrna.txt (Shortest distances of co-expression with ncRNA network)
edge-slimio-lowconf.txt (Edges of slim integrative omics low confidence network)
edge-slimio-highconf.txt (Edges of slim integrative omics high confidence network)
edge-slimcoexpression.txt (Edges of slim co-expression network)
edge-iowithncrna-lowconf.txt (Edges of integrative omics with ncRNAs low confidence network)
edge-iowithncrna-highconf.txt (Edges of integrative omics with ncRNAs high confidence network)
edge-cotranslation.txt (Edges of co-translation network)
edge-coexpressionwithncrna.txt (Edges of co-expression with ncRNA network)

organism: Zea mays

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:
Two 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.
mRNA-Seq, circular RNA-Seq, small RNA-Seq, ribo-Seq and PacBio Sequel

treatment_protocol: No special treatment.

tag: cultivar

tag: Stage

tag: age

tag: fraction

value: mRNA


title: 999053_5

description:
EXR-DGALA1plasma999053t5-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999181_9

description:
EXR-DGALA1plasma999181t9-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-15 rep2


title: B73, mrna-17 rep2


title: B73, mrna-20 rep2

description:
instrument model: BGISEQ-100
slim-transcriptome.tpm


title: B73, mrna-18 rep2


title: B73, mrna-19 rep2


title: B73, mrna-16 rep2


title: B73, mrna-14 rep2


title: 267416_9

description:
EXR-DGALA1plasma267416t9-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999107_6

description:
EXR-DGALA1plasma999107t6-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-12 rep2

value: Inflorescence


title: 999023_2

description:
EXR-DGALA1plasma999023t2-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-13 rep2


title: 999243_12

description:
EXR-DGALA1plasma999243t12-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-11 rep2


title: 234171_1

description:
EXR-DGALA1plasma234171t1-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-23 rep2


title: PIK3CA-WT_1

city: Chicago

first: Mohamed

last: Abazeed

state: IL

address: 303 E Superior St Lurie

department: Radiation Oncology

institute: Northwestern University

data_processing:
Reads were aligned to a genome assembly using STAR and aligned reads were assigned.
Gene read counts were normalized within sample, averaged for replicates and log transformed.
Assembly: hg19
Supplementary files format and content: Normalized (normalized.csv) and total counts (counts.csv) for all samples are included in the respective csv files.

growth_protocol: BEAS2B cells were grown in advanced DMEM-F12 media (ThermoFisher, MA) supplemented with 1% fetal bovine serum and 100 U/mL Penicillin, 100 mg/mL of Streptomycin,  292 mg/mL L-Glutamine and 1% HEPES. All cultures were maintained at 37o C in a humidified 5% CO2 atmosphere and tested to ensure absence of Mycoplasma.  Cultures were split before >80% confluencey.

extract_protocol:
RNA was isolated using the Rneasy Plus Mini Kit.
Samples were checked using BioA and libraries were prepared using the TruSeq Stranded mRNA kit. Each library was quantified using Qubit and then pooled toether. Library pool was quantified using qPCR. Pool was then diluted to 4 nM and loaded on the HiSeq High Output Mode. Run was performed using a full flow cell (8 lanes) PE 100. 5% PhiX was spiked in to check run qaulity.

tag: cell line

tag: cell type

value: immortalized bronchial epitheial cells

tag: genotype

value: PIK3CA Wild type

tag: treatment

value: overexpression

value: Day 3


title: PIK3CA-WT_2


title: B73, mrna-21 rep2


title: 267416_8

description:
EXR-DGALA1plasma267416t8-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 999168_8

description:
EXR-DGALA1plasma999168t8-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: PIK3CA-H1047R_1

value: PIK3CA mutant


title: 999043_3

description:
EXR-DGALA1plasma999043t3-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: PIK3CA-E545K_2


title: 999171_9

description:
EXR-DGALA1plasma999171t9-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: PIK3CA-E545K_1


title: PIK3CA-H1047R_2


title: FBXW7-WT_2

value: FBXW7 Wild type


title: 234171_7

description:
EXR-DGALA1plasma234171t7-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-9 rep2


title: B73, mrna-7 rep2


title: B73, mrna-10 rep2


title: B73, mrna-5 rep2


title: B73, mrna-3 rep2


title: FBXW7-WT_1


title: B73, mrna-2 rep2


title: B73, mrna-26 rep1


title: B73, mrna-6 rep2


title: B73, mrna-25 rep1


title: B73, mrna-1 rep2


title: B73, mrna-8 rep2


title: B73, mrna-4 rep2


title: 6y_snATAC

status: Public on Oct 31 2022

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description:
genomic DNA
same donor as RL2106

library_source: genomic

data_processing:
cellranger mkfastq with Cellranger v3.1 to generate fastq files as inout for count pipeline.
cellranger count with Cellranger v3.1 to generate feature-barcode matrices of gene expression.
cellranger-atac mkfastq with Cellranger-ATAC v1.2 to generate fastq files as input for count pipeline.
cellranger-atac count with Cellranger-ATAC v1.2 to generate BED-like tabular file with contains frgaments captured by the assay and barcode information in single cell output tables.
Genome_build: hg19
Supplementary_files_format_and_content: For snRNA-seq data: feature-barcode matrices in HDF5 format containing every barcode from the fixed list of known-good barcode sequences that has at least 1 read for raw_feature files, or only containing detected cellular barcodes for filtered_feature files. For snATAC, a BED-like tabular fragment file with each line representing a unique ATAC-seq fragment captured by the assay,  an index for the fragments file as well as a singlecell file containing cell barcodes, QC information and ATAC signal.

molecule: genomic DNA

source_name: prefrontal cortex, BA46

extract_protocol:
Per sample, 50 mg of frozen brain tissue was lysed and nuclei extracted. Nuclei were then either enriched by DAPI-positive FANS for single cell gene expression library generation or cleaned with a sucrose gradient centrifugation for single cell ATAC library generation.
10X Genomics 3' Single Cell Gene Expression v2/v3 , 10X Genomics Single Cell ATAC
snRNA-seq, snATAC-seq

value: brain


title: B73, mrna-24 rep1


title: B73, mrna-22 rep1

value: Ear-leaf


title: B73, mrna-23 rep1


title: 999148_8

description:
EXR-DGALA1plasma999148t8-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: 267416_6

description:
EXR-DGALA1plasma267416t6-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: VHL-WT_2

value: VHL Wild type


title: FBXW7-V464E_1

value: FBXW7 mutant


title: 999267_13

description:
EXR-DGALA1plasma999267t13-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.

value: Type 1 Diabetes Mellitus


title: FBXW7-V464E_2


title: B73, mrna-19 rep1

description:
instrument model: BGISEQ-100
slim-transcriptome.tpm
fusion.gff3
21tis-fusion-per.txt
21tis-lnc.tpm
lncrna.gff3

source_name: 14-Base of Stage 2 leaf-L(V5)

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


title: 234171_8

description:
EXR-DGALA1plasma234171t8-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.

value: Plasma

value: Entire cardiovascular system


title: 267416_10

description:
EXR-DGALA1plasma267416t10-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.

value: total cell-free biofluid RNA

value: Homebrew Kit


title: B73, mrna-18 rep1

source_name: 13-Base of Stage 2 Leaf-N(V5)

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

value: mRNA


title: VHL-WT_1

value: immortalized bronchial epitheial cells


title: B73, mrna-21 rep1


title: B73, mrna-17 rep1


title: B73, mrna-16 rep1

source_name: 12-Tip of Stage 2 leaf-L(V5)

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


title: B73, mrna-14 rep1

source_name: 11-Tip of Stage 2 Leaf-N(V5)

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


title: B73, mrna-13 rep1


title: VHL-L158V_2

value: VHL mutant

value: overexpression

value: Day 3


title: B73, mrna-15 rep1


title: VHL-R161P_1


title: B73, mrna-10 rep1

source_name: 08-First Leaf-N(V3)

value: First Leaf-N(V3)


title: 267416_12

description:
EXR-DGALA1plasma267416t12-BS
Samples were collected sequentially at 1- to 3-month-intervals depending on the study logistic. Time value indicates the sequential sample on the subject.


title: B73, mrna-12 rep1

source_name: 09-Third Leaf(V3)

value: Third Leaf(V3)


title: B73, mrna-11 rep1


title: B73, mrna-9 rep1


title: VHL-L158V_1


title: donor 45 allergic EVs [Sample 39]

city: Utrecht

first: Martijn

last: van Herwijnen

address: Yalelaan 2

country: Netherlands

institute: Universiteit Utrecht

data_processing:
For each sample, 4 lanes were combined in a single fastq file. Samples sequenced in 2 flow cells were combined (flow cell 1: HLF5JBGXX and 2: HL5CMBGXX). In total 20 fastq files from non-allergic donors and 20 from allergic donors were obtained.
FastQC (version 0.11.5) [Andrews] was used to perform quality control checks on sequencing data. Remaining TruSeq small RNA adapter sequences were checked and clipped from all reads at the 3' end using cutadapt (version 2.8, with settings of “-a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC --error-rate 0.1 --times 1 -m 15”) [Martin].
Remaining adapters were removed from the 5’ end of the reads using cutadapt (version 2.8, with settings of “-g CGACAGGTTCAGAGTTCTACAGTCCGACGATC --error-rate 0.1 --times 1 -m 15) [Martin]. Low quality bases were trimmed from all sequence reads using sickle (version 1.33, with settings of “-t sanger -l 15”) [Joshi].
All sequence reads shorter than 15 bases were discarded. The processed reads were aligned to human reference genome GRCh38 from Ensembl [Cunningham] (Homo sapiens primary assembly, soft-masked) and the number of aligned reads per annotated sRNA was calculated by Manatee algorithm (version 1.2) [Handzlik] applying bowtie to align reads (version 1.0.1, with settings of “--best --strata -m 50 -k 3 -v 3”) [Langmead], allowing for alignments to a maximum of 50 loci and reporting 3 of them, with equal alignment scores, and a maximum of 3 mismatches.
Manatee counts output was rounded and used as raw expression data.
Assembly: The processed reads were aligned to human reference genome GRCh38 from Ensembl [Cunningham] (Homo sapiens primary assembly, soft-masked) and the number of aligned reads per annotated sRNA was calculated by Manatee algorithm (version 1.2) [Handzlik] applying bowtie to align reads (version 1.0.1, with settings of “--best --strata -m 50 -k 3 -v 3”) [Langmead]
Supplementary files format and content: tab-delimited text file containing the combined flow cell data of the 40 individual human donors included in the studies. CPM values for each sample and RNA type are given

source_name: breast milk

extract_protocol:
Extracellular Vesicles (EVs) were seperated from human milk using differential centrifugation and sucrose density gradient seperation. EVs were pelleted and sotred in Qiazol until RNA isolation. Small RNA (< 200 nt) was isolated using the miRNeasy micro kit (Qiagen) according to manufacturer’s instructions. Input quantity of sRNA for library preparation was based on equal volume of purified milk EVs and ranged between 10-150 ng of sRNA per sample.
The Illumina® Truseq small RNA Sample Prep Kit was used to process the samples according to the kit-specific guidelines.

value: breast milk

tag: subject

value: donor 45

tag: source

value: allergic donor


title: donor 44 allergic EVs [Sample 38]

value: donor 44


title: donor 49 non-allergic EVs [Sample 40]

value: donor 49

value: non-allergic donor


title: B73, mrna-8 rep1

source_name: 06-Topmost Leaf-N(V3)

value: Topmost Leaf-N(V3)


title: B73, mrna-5 rep1


title: B73, mrna-7 rep1


title: MAP2K1-WT_2

value: MAP2K1 Wild type


title: B73, mrna-6 rep1

value: mRNA


title: donor 43 non-allergic EVs [Sample 37]

value: donor 43


title: B73, mrna-4 rep1

source_name: 02-Primary Root(V1)

value: Primary Root(V1)


title: donor 42 allergic EVs [Sample 36]

value: donor 42


title: MAP2K1-WT_1

value: immortalized bronchial epitheial cells


title: VHL-R161P_2

value: VHL mutant

value: overexpression


title: donor 41 allergic EVs [Sample 35]

value: donor 41


title: B73, mrna-3 rep1


title: donor 40 non-allergic EVs [Sample 34]

value: donor 40


title: MAP2K1-E203K_2

value: MAP2K1 mutant

value: Day 3


title: B73, mrna-2 rep1

description:
instrument model: BGISEQ-100
slim-transcriptome.tpm


title: B73, mrna-1 rep1


title: B73, circ-21 rep1

description:
instrument model: BGISEQ-100
circ.gff3
21tis-circ.tpm

value: circular RNA


title: B73, circ-20 rep2


title: MAP2K1-E203K_1


title: SPOP-WT_2

value: SPOP Wild type


title: donor 39 non-allergic EVs [Sample 33]

value: breast milk

value: donor 39


title: donor 37 allergic EVs [Sample 32]

value: donor 37

value: allergic donor


title: B73, circ-20 rep1


title: B73, circ-21 rep2


title: SPOP-WT_1


title: B73, mrna-20 rep1

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

value: mRNA


title: B73, circ-19 rep2


title: B73, circ-19 rep1


title: B73, circ-18 rep2


title: donor 36 non-allergic EVs [Sample 31]

value: donor 36

value: non-allergic donor


title: SPOP-F133C_2

value: immortalized bronchial epitheial cells

value: SPOP mutant


title: donor 35 allergic EVs [Sample 30]

value: donor 35


title: SPOP-F133C_1

value: overexpression


title: donor 34 non-allergic EVs [Sample 29]

value: donor 34


title: B73, circ-17 rep2

value: Inflorescence


title: EGFR-WT_2

value: EGFR Wild type

value: Day 3


title: B73, circ-17 rep1

value: circular RNA


title: melanoma RNA 9926_309_1

city: Tianjin

first: Chao

last: Zhang

address: 1 Huahuxi Road, Hexi

institute: Tianjin Medical University Cancer Hospital & Institute

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
Assembly: GCF_000001405.39_GRCh.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 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.

tag: type

value: acral melanoma

value: no-treatment


title: B73, circ-16 rep2


title: B73, circ-18 rep1


title: melanoma RNA 537822T


title: EGFR-WT_1


title: EGFR-L858R+T790M_2

value: EGFR mutant


title: donor 33 allergic EVs [Sample 28]

value: breast milk

value: donor 33

value: allergic donor


title: melanoma RNA 498825T


title: melanoma RNA 493925T


title: EGFR-L858R+T790M_1


title: donor 32 non-allergic EVs [Sample 27]

value: donor 32


title: donor 30 non-allergic EVs [Sample 25]

value: donor 30

value: non-allergic donor


title: donor 31 allergic EVs [Sample 26]

value: donor 31


title: B73, circ-16 rep1


title: EGFR-L858R_2

value: immortalized bronchial epitheial cells


title: melanoma RNA 493611T


title: B73, circ-14 rep2


title: EGFR-L858R_1

value: overexpression


title: melanoma RNA 470249T


title: donor 28 allergic EVs [Sample 23]

value: donor 28


title: B73, circ-14 rep1


title: melanoma RNA 464893T


title: BRAF-WT_1

value: BRAF Wild type


title: donor 27 allergic EVs [Sample 22]

value: donor 27


title: B73, circ-13 rep1


title: BRAF-G466V_2

value: BRAF mutant

value: Day 3


title: donor 24 allergic EVs [Sample 20]

value: donor 24


title: melanoma RNA 451015T

value: acral melanoma

value: no-treatment


title: B73, circ-12 rep2

value: circular RNA


title: B73, circ-15 rep1


title: melanoma RNA 450984T


title: B73, circ-12 rep1


title: donor 23 non-allergic EVs [Sample 19]

value: breast milk

value: donor 23


title: melanoma RNA 439345T

value: cutaneous melanoma


title: donor 22 allergic EVs [Sample 18]

value: donor 22

value: allergic donor


title: donor 29 allergic EVs [Sample 24]

value: donor 29


title: B73, circ-15 rep2


title: BRAF-R682W_2

value: immortalized bronchial epitheial cells


title: donor 21 allergic EVs [Sample 17]

value: donor 21


title: melanoma RNA 429938T


title: BRAF-WT_2

value: overexpression


title: melanoma RNA 425623T


title: donor 20 allergic EVs [Sample 16]

value: donor 20


title: B73, circ-11 rep1


title: B73, circ-10 rep2

value: Ear-leaf


title: melanoma RNA 460874T


title: donor 25 allergic EVs [Sample 21]

value: donor 25


title: NRAS-WT_1

value: NRAS Wild type

value: Day 3


title: melanoma RNA 421280T


title: BRAF-G466V_1

value: BRAF mutant


title: melanoma RNA 417036T

value: no-treatment


title: donor 18 non-allergic EVs [Sample 14]

value: donor 18

value: non-allergic donor


title: NRAS-Q61K_1

value: NRAS mutant


title: B73, circ-13 rep2

value: circular RNA


title: NRAS-Q61K_2


title: B73, circ-9 rep2

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


title: B73, circ-10 rep1


title: BRAF-R682W_1


title: B73, circ-9 rep1


title: melanoma RNA 413736T

value: cutaneous melanoma


title: NRAS-G13R_2


title: B73, circ-8 rep2

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


title: B73, circ-11 rep2


title: donor 17 non-allergic EVs [Sample 13]

value: breast milk

value: donor 17


title: melanoma RNA 410250T


title: donor 16 non-allergic EVs [Sample 12]

value: donor 16


title: melanoma RNA 416681T

value: acral melanoma


title: NRAS-G12C_2

value: immortalized bronchial epitheial cells

value: overexpression


title: melanoma RNA 403294T


title: donor 15 non-allergic EVs [Sample 11]

value: donor 15


title: donor 19 allergic EVs [Sample 15]

value: donor 19

value: allergic donor


title: B73, circ-8 rep1


title: NRAS-WT_2

value: NRAS Wild type

value: Day 3


title: NRAS-G12C_1


title: melanoma RNA 400282T

value: no-treatment


title: donor 11 non-allergic EVs [Sample 9]

value: donor 11

value: non-allergic donor


title: donor 14 allergic EVs [Sample 10]

value: donor 14


title: HIF1A-WT_2

value: HIF1A Wild type


title: B73, circ-6 rep2

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

value: circular RNA


title: melanoma RNA 392626T


title: HIF1A-WT_1


title: B73, circ-7 rep2

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


title: NRAS-G13R_1

value: NRAS mutant


title: melanoma RNA 386901T

value: acral melanoma


title: donor 10 non-allergic EVs [Sample 8]

value: breast milk

value: donor 10


title: B73, circ-6 rep1


title: melanoma RNA 384960T


title: melanoma RNA 384610T

value: cutaneous melanoma


title: donor 6 non-allergic EVs [Sample 5]

value: donor 6


title: HIF1A-K251R_1

value: immortalized bronchial epitheial cells

value: HIF1A mutant

value: overexpression


title: B73, circ-5 rep1

value: Third Leaf(V3)


title: donor 7 non-allergic EVs [Sample 6]

value: donor 7


title: donor 4 non-allergic EVs [Sample 3]

value: donor 4

value: non-allergic donor


title: donor 5 non-allergic EVs [Sample 4]

value: donor 5


title: B73, circ-7 rep1


title: B73, circ-4 rep2

value: First Leaf-N(V3)


title: B73, circ-4 rep1

value: circular RNA


title: IDH1-WT_1

value: IDH1 Wild type

value: Day 3


title: IDH1-R132H_2

value: IDH1 mutant


title: B73, circ-3 rep2

value: Topmost Leaf-N(V3)


title: melanoma RNA 369939T

value: acral melanoma

value: no-treatment


title: donor 8 allergic EVs [Sample 7]

value: breast milk

value: donor 8

value: allergic donor


title: B73, circ-3 rep1


title: melanoma RNA 369742T


title: IDH1-R132H_1

value: immortalized bronchial epitheial cells

value: overexpression


title: melanoma RNA 370989T


title: melanoma RNA 369691T


title: donor 2 allergic EVs [Sample 2]

value: donor 2


title: KEAP1-WT_2

value: KEAP1 Wild type


title: B73, circ-2 rep2


title: melanoma RNA 365019T


title: HIF1A-K251R_2

value: HIF1A mutant


title: B73, circ-5 rep2

value: Third Leaf(V3)


title: donor 1 non-allergic EVs [Sample 1]

value: donor 1

value: non-allergic donor


title: melanoma RNA 371587T


title: IDH1-WT_2

value: IDH1 Wild type


title: KEAP1-WT_1

value: Day 3


title: B73, circ-2 rep1

value: circular RNA


title: SK-N-AS, siCFDP1, replicate 1

city: Napoli

first: Mario

last: Capasso

address: Via Gaetano Salvatore, 486

department: Dept. of  Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Napoli "Federico II" - CEINGE Biotecnologie Avanzate Scarl

data_processing:
The RNA sequencing data were first checked for quality using FastQC. Total reads, Q20, Q30 and other metrics were collected.
FASTQ data were then analyzed using the Tuxedo suite: TopHat (v2.0.14) and Cufflinks v2.1.0. TopHat was run using the default options by providing the reference genome and its related RefSeq reference transcriptome (assembly GRCh37/hg19).
Cufflinks was used to assemble the mapped reads into possible transcripts and generate a final transcriptome assembly. Gene-level expression is reported as normalized fragments per kilobase of exon per million fragments mapped (FPKM) counts.
Cuffdiff was used to detect differentially expressed genes between the two experimental conditions (siCFDP1 vs. siScrambled).
The results were analyzed using the R Bioconductor package CummeRbund (v2.16.0).
Assembly: hg19
Supplementary files format and content: Gene-level normalized counts (FPKM) were uploaded as the processed per-sample data files obtained by Cufflinks program. The files report the following columns. tracking_id: the gene symbol; class_code: empty column; nearest_ref_id: empty column; gene_id: the gene symbol; gene_short_name: the gene symbol; tss_id: Cufflinks internal ID; locus: hg19 coordinates as chrom-start-end; length: empty column; coverage: empty column; FPKM: normalized read counts; FPKM_conf_lo: confidence interval low; FPKM_conf_hi : confidence interval high; FPKM_status: reliability of the FPKM measure.
Supplementary files format and content: Gene-level normalized count (FPKM) matrix was uploaded as supplementary file. The file reports the following columns. GeneSymbol: the gene symbol; siScram_rep1: FPKM measure for siScram_rep1; siScram_rep2: FPKM measure for siScram_rep2; CFDP1_rep1: FPKM measure for CFDP1_rep1; CFDP1_rep2: FPKM measure for CFDP1_rep2.

molecule: polyA RNA

source_name: Neuroblastoma tumor cell line

extract_protocol:
RNA was isolated from SK-N-AS cells using TRIzol (ThermoFisher Scientific, Waltham, MA, USA) according to manufacturer’s instructions. RNA purity was checked using the NanoPhotometer spectrophotometer (Implen, Inc., Westlake Village, CA, USA). RNA concentration was measured using the NanoDrop ND1000 spectrophotometer (Nano-Drop, Wilmington, DE, USA). RNA with an OD260/280 between 1.8 and 2.2 and an OD260/230 ≥ 1.8 was used for the construction of cDNA libraries. RNA integrity was assessed using Agilent 2100 Bioanalyzer RNA Nano chip device (Agilent, Santa Clara, CA, USA).
In total, one μg RNA per sample was used as input material for RNA sample preparations. The mRNA content was concentrated from total RNA using RNase-free DNase I (TaKaRa) and magnetic oligo (dT) beads. The mRNA was mixed with the fragmentation buffer and broken into short fragments (~200 bp long). Then, the first strand of cDNA was synthesized with random hexamer primers. The second strand was synthesized using the SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen, Camarillo, CA) and was purified via magnetic beads. The ends were repaired and tailed with a single 3’ adenosine. Subsequently, the cDNA fragments were ligated to sequencing adapters.

value: Neuroblastoma tumor cell line

value: SK-N-AS, ATCC #CRL-2137

value: silenced CFDP1


title: KEAP1-R470S_2

value: KEAP1 mutant


title: SK-N-AS, siCFDP1, replicate 2


title: melanoma RNA 363835T

value: acral melanoma

value: no-treatment


title: KEAP1-R470S_1

value: immortalized bronchial epitheial cells


title: melanoma RNA 361834T

value: cutaneous melanoma


title: B73, circ-1 rep2

value: Primary Root(V1)


title: B73, circ-1 rep1


title: SK-N-AS, siScramble, replicate 2

value: control


title: SK-N-AS, siScramble, replicate 1


title: KEAP1-E177K_2

value: overexpression


title: KEAP1-E177K_1


title: melanoma RNA 353517T


title: B73, srna-21 rep2

description:
instrument model: BGISEQ-50
21tis-srna.tpm
srna.gff3

value: small RNA


title: B73, srna-21 rep1


title: B73, srna-20 rep2


title: NFE2L2-WT_2

value: NFE2L2 Wild type


title: NFE2L2-E79K_2

value: NFE2L2 mutant


title: melanoma RNA 341526T


title: melanoma RNA 349088T


title: B73, srna-19 rep2


title: melanoma RNA 335722T


title: NFE2L2-E79K_1


title: B73, srna-19 rep1


title: AKT-E17K_2

value: AKT mutant


title: melanoma RNA 334618T


title: melanoma RNA 323330_130702T


title: AKT-E17K_1

value: Day 3


title: B73, srna-18 rep2


title: melanoma RNA 355528T


title: melanoma scRNA Cutaneous3

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: h5. filtered gene expression counts for called cells, along with cell annotations

extract_protocol:
Fresh tumor samples were surgically removed from patients and immersed in a complete medium containing 90% Dulbecco’s modified eagle medium (DMEM; Cat# 11054001, GIBCO) and 10% fetal bovine serum (FBS; Cat# 16140071, GIBCO), and transported to the lab in a refrigerated container. Suitable small tissue blocks were cut into pieces (diameter 1-3 mm). The pieces were transferred to the gentle MACS C Tubes (Cat# 130-096-334, Miltenyi Biotec), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Cat# 130-095-929, Miltenyi Biotec). Then the tissues were made into single-cell suspension using the gentle MACS Dissociator (Cat# 130-093-235, Miltenyi Biotec) following these steps: milled; incubated at 37℃ for 30 min on a shaker; milled; incubated at 37℃ for 30 min; milled; filtered through a 70 um filter, plus 2% FBS. Finally, the single-cell suspension was centrifugated at 400 g for 7 mins, resuspended in CELLSAVING (Cat# C40050, NCM biotech), cryopreserved in Cryotubes (Cat# 430488, Corning) and then stored at -80℃
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). 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: human tumor


title: A549 NANOG- (non-CSCs)_C3

type: RNA

city: Changsha

first: Jun

last: Wang

address: No. 87, Xiangya Road

institute: Xiangya Hospital, Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: non-CSC

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using PureLink RNA Mini Kit (ThermoFisher, 12183018A). The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: cell population

value: NANOG -


title: A549 NANOG+ (CSCs)_T3

source_name: CSC

value: NANOG +


title: melanoma RNA 352108T


title: B73, srna-18 rep1

tag: tissue


title: melanoma RNA 320719T


title: A549 NANOG- (non-CSCs)_C1


title: NFE2L2-WT_1


title: B73, srna-20 rep1


title: AKT-WT_1

value: AKT Wild type


title: B73, srna-17 rep2

value: Inflorescence


title: B73, srna-17 rep1


title: A549 NANOG- (non-CSCs)_C2


title: melanoma RNA 281495T


title: melanoma scRNA Acral6

value: acral melanoma


title: melanoma scRNA Cutaneous1Lym

value: no-treatment


title: melanoma scRNA Cutaneous1


title: B73, srna-16 rep1


title: PLX307_2

value: immortalized bronchial epitheial cells

value: vector control


title: melanoma scRNA Acral5


title: PLX307_1


title: melanoma RNA 309396T


title: AKT-WT_2


title: melanoma scRNA Cutaneous2

value: cutaneous melanoma


title: A549 NANOG+ (CSCs)_T2


title: melanoma RNA 28034A1


title: melanoma RNA 277914T


title: PLX306_2


title: melanoma RNA 277554T


title: PLX306_1


title: melanoma scRNA Acral3post

value: with anti-PD1 treatment


title: melanoma RNA 26119A1


title: B73, srna-15 rep1


title: B73, srna-15 rep2


title: A549 NANOG+ (CSCs)_T1


title: B73, srna-16 rep2


title: melanoma scRNA Acral3pre


title: KRAS-WT_1

value: KRAS Wild type

value: overexpression


title: melanoma RNA 258030T


title: melanoma scRNA Acral2


title: melanoma scRNA Acral1


title: melanoma RNA 249013T


title: B73, srna-13 rep2

value: small RNA


title: melanoma RNA 23723A1


title: melanoma scRNA Acral4


title: B73, srna-14 rep2


title: B73, srna-13 rep1


title: KRAS-Q61L_1

value: KRAS mutant


title: melanoma RNA 236978T


title: KRAS-G12C_2


title: B73, ribo-16 rep2

description: translatome.tpm

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.
Assembly: Zea_mays.B73_RefGen_v4
Supplementary files format and content: Files include expression values and identified protein-protein interactions
21tis-circ.tpm (abundance measurements)
21tis-fusion-per.txt (abundance measurements)
21tis-lnc.tpm (abundance measurements)
21tis-srna.tpm (abundance measurements)
circ.gff3 (a tab-delimited text file that holds information of circular RNA)
fusion.gff3 (a tab-delimited text file that holds information of fusion RNA)
lncrna.gff3 (a tab-delimited text file that holds information of lncRNA)
PPIs-highconf.txt (high confidence protein-protein interactions)
PPIs.txt (protein-protein interactions)
slim-transcriptome.tpm (abundance measurements)
srna.gff3 (a tab-delimited text file that holds information of sRNA)
translatome.tpm (abundance measurements)
sd-slimio-lowconf.txt (Shortest distances of slim integrative omics low confidence network)
sd-slimio-highconf.txt (Shortest distances of slim integrative omics high confidence network)
sd-slimcoexpression.txt (Shortest distances of slim co-expression network)
sd-PPIs-lowconf.txt (Shortest distances of low confidence interactome network)
sd-PPIs-highconf.txt (Shortest distances of high confidence interactome network)
sd-iowithncrna-lowconf.txt (Shortest distances of integrative omics with ncRNAs low confidence network)
sd-iowithncrna-highconf.txt (Shortest distances of integrative omics with ncRNAs high confidence network)
sd-cotranslation.txt (Shortest distances of co-translation network)
sd-coexpressionwithncrna.txt (Shortest distances of co-expression with ncRNA network)
edge-slimio-lowconf.txt (Edges of slim integrative omics low confidence network)
edge-slimio-highconf.txt (Edges of slim integrative omics high confidence network)
edge-slimcoexpression.txt (Edges of slim co-expression network)
edge-iowithncrna-lowconf.txt (Edges of integrative omics with ncRNAs low confidence network)
edge-iowithncrna-highconf.txt (Edges of integrative omics with ncRNAs high confidence network)
edge-cotranslation.txt (Edges of co-translation network)
edge-coexpressionwithncrna.txt (Edges of co-expression with ncRNA network)

value: mRNA bound by ribosome


title: B73, srna-12 rep1


title: melanoma RNA 236740T


title: B73, srna-12 rep2


title: B73, ribo-16 rep1

description: translatome.tpm


title: KRAS-WT_2

value: Day 3


title: KRAS-G12C_1


title: melanoma RNA 182806T


title: KRAS-G13D_2


title: B73, ribo-15 rep2

description: translatome.tpm


title: B73, srna-14 rep1


title: KRAS-G13D_1


title: melanoma RNA 182046T


title: KRAS-Q61L_2


title: B73, srna-11 rep2


title: KRAS-G12R_2


title: B73, ribo-14 rep2

description: translatome.tpm


title: B73, srna-10 rep2

value: Ear-leaf


title: melanoma RNA 15761A1


title: B73, ribo-15 rep1

description: translatome.tpm


title: B73, srna-11 rep1


title: B73, ribo-14 rep1

description: translatome.tpm


title: B73, ribo-13 rep2

description: translatome.tpm


title: B73, srna-10 rep1


title: KRAS-G12V_2


title: melanoma RNA 15417A1


title: KRAS-G12R_1


title: B73, srna-9 rep2

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


title: melanoma RNA 159419T


title: KRAS-G12V_1


title: B73, srna-9 rep1


title: B73, srna-8 rep2

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


title: B73, ribo-12 rep1

description: translatome.tpm


title: KRAS-D33E_1


title: B73, ribo-13 rep1

description: translatome.tpm


title: KRAS-D33E_2


title: B73, srna-8 rep1


title: BEME_355G, Endometriosis

city: Los Angeles

first: Marcos

last: Fonseca

state: CA

address: 8000 Beverly Boulevard

department: Division of Gynecologic Oncology, Department of Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

description: 10X Visium spatial gene expression

data_processing:
library strategy: spatial transcriptomics
for scRNA-seq: Raw reads were aligned to the hg38 reference genome, UMI (unique molecular identifier) counting was performed using Cell Ranger v.3.1.0 (10X Genomics) pipeline with default parameters. keratin-positive, mesenchymal and endothelial cells were extract from BAM files using cellranger 5.0.1 bamtofastq command.
for visium: Slides were processed by Cedars-Sinai Applied Genomics, Computation and Translational core. Alignment and QC was performed using Space Ranger (version 1.2.1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Endometriosis

extract_protocol:
For Visium spatial transcriptomics - H&E stained slides were made and reviewed to confirm the presence of endometriosis lesions. Tissue sections were cut by pathology intraoperative consult staff onto Visium slides according to the 10X Genomics Visium spatial tissue preparation guide
10X 3' scRNA-seq, 10X Visium spatial gene expression

value: Endometriosis

value: tissue

tag: tissue type

value: frozen


title: B73, ribo-11 rep2

description: translatome.tpm


title: B73, ribo-12 rep2

description: translatome.tpm


title: CTNNB1-WT_2

value: CTNNB1 Wild type

tag: time


title: B73, ribo-11 rep1

description: translatome.tpm


title: CTNNB1-WT_1

value: immortalized bronchial epitheial cells


title: BEME_346, Endometriosis

description: 10X Visium spatial gene expression

value: keratin-positive, mesenchymal and endothelial

tag: menstrual cycle_phase

value: Luteal


title: CTNNB1-S45F_2

value: CTNNB1 mutant


title: CQWIN1

city: Nanchong

first: Qin

address: No. 234, Fujiang Road, Shunqing District, Nanchong, Sichuan

institute: North Sichuan medical college

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
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 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.

treatment_protocol: The A549 was treated with  CDWIN-PM2.5(100 μg/mL),CDSUM-PM2.5 (100 μg/mL), CQWIN-PM2.5 (100 μg/mL),and CQSUM-PM2.5 (100 μg/mL), the same volumes of DMSO  for 24h and RNA was extracted

value: lung

value: Type II alveolar epithelial cells


title: CQWIN2


title: CTNNB1-S45F_1

value: overexpression


title: CQWIN3


title: B73, srna-7 rep1

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

value: small RNA


title: B73, ribo-10 rep2

description: translatome.tpm

value: Inflorescence

value: mRNA bound by ribosome


title: B73, srna-6 rep2

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


title: B73, ribo-10 rep1

description: translatome.tpm


title: CQSUM3


title: CQSUM2


title: CTNNB1-S33N_2

value: Day 3


title: B73, ribo-9 rep2

description: translatome.tpm


title: B73, srna-5 rep2

value: Third Leaf(V3)


title: CQSUM1


title: CTNNB1-S33N_1


title: CDWIN3


title: B73, ribo-9 rep1

description: translatome.tpm


title: CTNNB1-F777S_2


title: B73, srna-5 rep1


title: B73, ribo-8 rep2

description: translatome.tpm


title: B73, srna-7 rep2


title: CDWIN2


title: CTNNB1-F777S_1


title: B73, srna-4 rep2

value: First Leaf-N(V3)


title: B73, ribo-8 rep1

description: translatome.tpm


title: B73, srna-4 rep1


title: CDWIN1


title: B73, srna-3 rep2

value: Topmost Leaf-N(V3)


title: CTNNB1-E334K-1


title: B73, ribo-7 rep2

description: translatome.tpm


title: CTNNB1-E334K-2


title: B73, srna-6 rep1


title: B73, ribo-7 rep1

description: translatome.tpm


title: CDSUM3


title: B73, srna-3 rep1


title: CTNNB1-A622S_2


title: B73, ribo-6 rep1

description: translatome.tpm


title: B73, ribo-6 rep2

description: translatome.tpm


title: CDSUM2


title: CDSUM1


title: CTNNB1-A622S_1


title: B73, srna-2 rep2


title: B73, ribo-5 rep2

description: translatome.tpm


title: silica crystals

city: London

first: Claudio

last: Bussi

state: London

address: 1 Midland Road, Host-Pathogen Lab NE422

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Raw read count matrix for each sample in form of the Cell Ranger matrix (matrix.mtx), features (features.tsv) and barcodes (barcodes.tsv) files.

organism: Mus musculus

source_name: Bronchoalveolar lavage

extract_protocol:
https://doi.org/10.1038/nprot.2009.95 - http://dx.doi.org/10.1038/ni.1631 - https://doi.org/10.1172/jci.insight.126556
The cells were partitioned into nanolitre scale Gel Beads in emulsions (GEMs) and lysed using the 10x Genomics Single Cell 3′ Chip V3.1 GEM, Library and Gel Bead Kit (cat: PN-1000121). cDNA synthesis and library construction were performed as per the manufacturer’s instructions. The RNA was reversed transcribed and amplified using 14 cycles of PCR. Libraries were prepared from 10μl of the cDNA and 12 cycles of amplification. Each library was prepared using Single Index Kit T Set A (cat: PN-1000213).
Libraries were pooled according to estimated cell load, the pool was sequenced at 200pM on the HiSeq4000 system (Illumina) using the configuration 28-8-98 on a single-index paired-end run.

treatment_protocol: Eight- to ten-week-old, C57BL/6NJ mice were exposed by intratracheal intubation of 40-μl aqueous suspensions of 200 μg silica crystals (MIN-U-SIL-15) or 200 μg red-fluorescent silica.

tag: strain

value: Wild type

value: 8-10 weeks

value: Bronchoalveolar lavage cells

value: Silica crystals


title: B73, srna-1 rep2

tag: cultivar

value: Primary Root(V1)


title: CK2

value: lung

value: DMSO


title: CK3

value: Type II alveolar epithelial cells


title: B73, srna-2 rep1

tag: Stage


title: B73, ribo-5 rep1

description: translatome.tpm

tag: age


title: B73, ribo-4 rep2

description: translatome.tpm

source_name: 07-Topmost Leaf-L(V3)

value: Topmost Leaf-L(V3)

tag: fraction


title: B73, srna-1 rep1

value: small RNA


title: silica beads

value: Silica beads


title: B73, ribo-4 rep1

description: translatome.tpm

value: mRNA bound by ribosome


title: CK1

tag: cell line


title: B73, ribo-3 rep2

description: translatome.tpm


title: B73, ribo-3 rep1

description: translatome.tpm


title: B73, ribo-2 rep2

description: translatome.tpm


title: B73, ribo-2 rep1

description: translatome.tpm


title: AML12 cells,H6R2_3

city: Zhengzhou

first: Jiye

last: Li

address: No. 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: the First Affiliated Hospital of Zhengzhou University

data_processing:
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced (PE150) with Illumina NovaSeq 6000.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the mouse reference genome GRCm38 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include readcount values and RPKM values for each Sample

source_name: AMl12 cells

growth_protocol: Cells were cultured in DMEM/F12 medium (Gibco, 11330-032) supplemented with 10% fetal bovine serum (Gibco), ITS Liquid Media Supplement (Sigma, I3146) and 40 ng/ mL Dexamethasone (Sigma, D4902-100mg).

extract_protocol:
Total RNAs were extracted using Trizol Reagent for RNA-seq analysis. 2ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing library preparation was constructed using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: To induce anoxia, the media was replaced with serum-free and glucose-free media, and then cells were placed in an anoxic chamber with 1% oxygen, 5% CO2, and balanced N2 at 37°C for 6 hours, followed by reoxygenation for 2 hours. Cells were routinely cultured in 21% O2 and 5% CO2 (normoxic conditions) as controls.

value: AMl12 cells

tag: cell type

value: hepatocyte

value: WT

value: 6 hours of hypoxia followed by 2 hours of reoxygenation


title: AML12 cells,H6R2_2

tag: genotype


title: U2OS_M11_1

first: Zhenyi

last: Ma

address: No.22，Qixiangtai Road

institute: Tianjin Medical University

description: U2OS(M11) rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
HTseq was used to quantify gene count.
Assembly: grch38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: U2OS(con) and U2OS (M11) cells  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.

treatment_protocol: U2OS(con) treated with sdAb con,U2OS(M11)treated with anti-MN1 sdAb

value: Osteosarcoma

value: add anti-MN1 sdAb

tag: treatment

value: drug treatment


title: B73, ribo-1 rep2

description: translatome.tpm


title: KO_L3

city: Rochester

first: Tatsuaki

last: Kurosaki

state: NY

address: 601 Elmwood Avenue, Box 712

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using FastP version 0.20.0 with parameters "–length_required 35 –cut_front_window_size 1 –cut_front_mean_quality 13 –cut_front –cut_tail_window_size 1 –cut_tail_mean_quality 13 –cut_tail -w 8 -y –r -j".
Cleaned reads were then mapped to the Homo Sapiens reference genome (GRCh38.p13 + Genocode-31 Annotation) using STAR_2.7.0f and parameters "–twopassMode Basic –runMode alignReads –outSAMtype BAM Unsorted –outSAMstrandField intronMotif –outFilterIntronMotifs RemoveNoncanonical".
Gene-level read quantitation was derived using the subread-1.6.4 package (featureCounts) with a GTF annotation file (Gencode-31) and parameters "-s 2 -t exon -g gene_name".
Differential expression analysis was performed using DESeq2-1.22.1 with an adjusted P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).
Genome_build: (GRCh38.p13 + Genocode-31 Annotation)
Supplementary_files_format_and_content: text file with raw gene counts for all reference genes

source_name: FMR-KO SH-SY5Y cells culturing in SILAC light medium

growth_protocol: Wild-type (WT) SH-SY5Y cells or each of three independently generated FMR1-KO SH-SY5Y cell lines were cultured (~8×106 cells/150-mm dish) for two weeks in DMEM:F-12 SILAC medium (Thermo Fisher Scientific) supplemented with 1× GlutaMAX (Thermo Fisher Scientific), 2.44 mg/ml sodium bicarbonate (Thermo Fisher Scientific), 10% dialyzed fetal bovine serum (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted and purified using TRIzol reagent following manufacturer’s instructions (Thermo Fisher Scientific).
Total-cell RNA concentrations were determined using a NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE). RNA quality was assessed using the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for library construction following the manufacturer’s protocols.

treatment_protocol: Cells were cultured either L-lysine-2HCl and L-arginine-HCl for light medium or 13C6 15N2 L-lysine-2HCl and 13C6 15N4 L-arginine-HCl for heavy medium.

value: SH-SY5Y (ATCC, CRL-2266)

value: FMR-KO (FMR1-KO#3, Kurosaki et al., Nat Cell Biol 2021)

value: Culturing in SILAC light medium (containing 12C6,14N4 L-arginine and 12C6 L-lysine)


title: U2OS_M11_2

description: U2OS(M11) rep2


title: AML12 cells,H6R2_1


title: U2OS_con1

description: U2OS(con) rep1

value: add sdAb con


title: U2OS_con2

description: U2OS(con) rep2


title: AML12 cells,Control_3

value: normoxia


title: B73, Group 4 rep2

description:
PPIs-highconf.txt
PPIs.txt

source_name: SAM (V3)

value: SAM (V3)

value: cDNA


title: B73, ribo-1 rep1

description: translatome.tpm


title: KO_L2

value: FMR-KO (FMR1-KO#2, Kurosaki et al., Nat Cell Biol 2021)


title: AML12 cells,Control_2


title: B73, Group 7 rep2

description:
PPIs-highconf.txt
PPIs.txt

source_name: Anther; Tassel (2 cm)

value: Anther; Tassel (2 cm)


title: AML12 cells,Control_1


title: KO_L1

value: FMR-KO (FMR1-KO#1, Kurosaki et al., Nat Cell Biol 2021)


title: B73, Group 2

description:
PPIs-highconf.txt
PPIs.txt

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: KO_H3

source_name: FMR-KO SH-SY5Y cells culturing in SILAC heavy medium

value: Culturing in SILAC heavy medium (containing 13C6,15N4 L-arginine and 13C6,15N2 L-lysine)


title: B73, Group 4 rep1

description:
PPIs-highconf.txt
PPIs.txt


title: TCDD_3

city: Jinan

first: Ping

last: Mi

address: Wenhuaxi 44

institute: Shandong University

data_processing:
Raw data of fastq format were firstly fliterd to the low quality reads, reads with adapter sequences and reads with high levels of N base. In this step clean data were obtained.
Index of the reference genome was built using Bowtie2 and paired-edn reads werealigned to the reference genome.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: heart

growth_protocol: zebrafish embryos were collected and exposure in different treatment from 2 hours postfertilization.

extract_protocol:
Total RNA was extracted by using Trizol (Invitrogen, USA) according to manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: zebrafish embryos were exposured in DMSO or TCDD from 2 hours postfertilization to 5 days postfertilization

value: heart

value: TCDD exposure


title: TCDD_4


title: KO_H2


title: TCDD_2


title: LPS-Ac-H3K27

city: Nanjing

first: yang

last: wang

address: 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing medical university

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm10 genome assembly using Agilent 2100 Bioanalyzer
peaks were called using PeaksFind
Genome_build: mm10

source_name: Female germ cells of mice

growth_protocol: oocytes were obtained from the ovaris of 3- to 4-week old ICR female mice,and cultured in MEM+ medium

extract_protocol:
We used Vazyme Hyperactive In-Situ ChIP Library Prep Kit for Illumina（pG-Tn5）
We used Vazyme Hyperactive In-Situ ChIP Library Prep Kit for Illumina（pG-Tn5）

treatment_protocol: 10ug/ml CSF1 treated 20h; 10EU/ml LPS treated 20h.

value: oocyte

value: ICR

tag: chip antibody

value: Acetyl-H3K27(Cell signaling technology,8173S,lot 8)


title: CSF1-Ac-H3K27


title: B73, Group 7 rep1

description:
PPIs-highconf.txt
PPIs.txt

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.
Assembly: Zea_mays.B73_RefGen_v4
Supplementary files format and content: Files include expression values and identified protein-protein interactions
21tis-circ.tpm (abundance measurements)
21tis-fusion-per.txt (abundance measurements)
21tis-lnc.tpm (abundance measurements)
21tis-srna.tpm (abundance measurements)
circ.gff3 (a tab-delimited text file that holds information of circular RNA)
fusion.gff3 (a tab-delimited text file that holds information of fusion RNA)
lncrna.gff3 (a tab-delimited text file that holds information of lncRNA)
PPIs-highconf.txt (high confidence protein-protein interactions)
PPIs.txt (protein-protein interactions)
slim-transcriptome.tpm (abundance measurements)
srna.gff3 (a tab-delimited text file that holds information of sRNA)
translatome.tpm (abundance measurements)
sd-slimio-lowconf.txt (Shortest distances of slim integrative omics low confidence network)
sd-slimio-highconf.txt (Shortest distances of slim integrative omics high confidence network)
sd-slimcoexpression.txt (Shortest distances of slim co-expression network)
sd-PPIs-lowconf.txt (Shortest distances of low confidence interactome network)
sd-PPIs-highconf.txt (Shortest distances of high confidence interactome network)
sd-iowithncrna-lowconf.txt (Shortest distances of integrative omics with ncRNAs low confidence network)
sd-iowithncrna-highconf.txt (Shortest distances of integrative omics with ncRNAs high confidence network)
sd-cotranslation.txt (Shortest distances of co-translation network)
sd-coexpressionwithncrna.txt (Shortest distances of co-expression with ncRNA network)
edge-slimio-lowconf.txt (Edges of slim integrative omics low confidence network)
edge-slimio-highconf.txt (Edges of slim integrative omics high confidence network)
edge-slimcoexpression.txt (Edges of slim co-expression network)
edge-iowithncrna-lowconf.txt (Edges of integrative omics with ncRNAs low confidence network)
edge-iowithncrna-highconf.txt (Edges of integrative omics with ncRNAs high confidence network)
edge-cotranslation.txt (Edges of co-translation network)
edge-coexpressionwithncrna.txt (Edges of co-expression with ncRNA network)


title: KO_H1


title: CTR-Ac-H3K27


title: B73, Group 1

description:
PPIs-highconf.txt
PPIs.txt

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

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


title: WT_L2

source_name: Wild-type SH-SY5Y cells culturing in SILAC light medium

value: SH-SY5Y (ATCC, CRL-2266)

value: Wild-type


title: B73, Group 3

description:
PPIs-highconf.txt
PPIs.txt

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

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


title: WT_L3

value: Culturing in SILAC light medium (containing 12C6,14N4 L-arginine and 12C6 L-lysine)


title: WT_L1


title: LPS-H3K4me3

value: H3K4me3（bioworld,BS7232,Lot CC02181）


title: Ctrl_3

value: DMSO


title: B73, Group 8

description:
PPIs-highconf.txt
PPIs.txt

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

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

value: cDNA


title: IgG-Ac-H3K27

value: Rabbit ctr IgG


title: WT_H3

source_name: Wild-type SH-SY5Y cells culturing in SILAC heavy medium


title: CSF1-H3K4me3


title: Ctrl_1


title: WT_H2


title: B73, Group 5

description:
PPIs-highconf.txt
PPIs.txt

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

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


title: Gingiva_intact

city: chengdu

first: Yixuan

last: Huang

state: sichuan

address: West China Hospital of Stomatology

institute: Sichuan University

data_processing:
the Fastq files were demultiplexed and aligned to mouse genome using Cellranger kit (10X Genomics)
The data were then input into Seurat package for subsequent analyses
Cells with less than 500 genes detected or with more than 15% mitochondrial genes were excluded from our analyses
Dimensionality reduction was carried out using principal component analysis
The clustering was visualized using uniform manifold approximation and projection
Genome_build: mm9
Supplementary_files_format_and_content: TSV, tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: MTX, Matrix table with raw gene counts for every gene and every cell

source_name: gingiva tissue

extract_protocol:
Under dissection microscope, the gingival tissue attached to the alveolar supporting all the three maxillary molars was incised  and peeled off. The excised gingival tissue was transferred to a culture dish containing 1ml PBS with 10%FBS, 2mg/ml Collagenase Type II, 1mg/ml DNAse Type I and 5mM EDTA , miced thoroughly with a No.15 blade and incubated in a shaker incubator for 20 minutes at 37℃ and 200rpm. After digestion, the cells were centrifuged at 400X for 10 minutes, resuspend in 1ml PBS+10%FBS and filtered through a 70um strainer. Each cell sample was collected from three male and three female animals. The strained single cells were stained for Ter119-FITC , CD45-FITC and CD31-FITC for 30 minutes on ice. Dead cells were labelled with 7-AAD. Ter119-CD45-CD31- live cells were collected using the FACSAria II sorter.
Sorted gingival cells were adjusted to 800-1200/ul for scRNA-seq library preparation. Libraries were constructed using Chromium Single Cell 3’ v2 Reagent Kit as instructed by the manufacturer’s manual

treatment_protocol: 5-0 silk suture was passed through the interdentium adjacent to the second maxillary molar and tied firmly at the palatal side. All ligatures were placed at the age of three months. The animals were sacrificed at three days after ligature placement.

value: gingiva tissue

value: wild type

value: Intact


title: Gingiva_inflammed

value: ligature induced inflammation


title: IgG-H3K4me3

value: oocyte

value: ICR


title: WT_H1

value: Culturing in SILAC heavy medium (containing 13C6,15N4 L-arginine and 13C6,15N2 L-lysine)


title: liver sinusoidal endothelial cells aging5

status: Public on Oct 29 2022

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

data_processing:
fastp v 0.18.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v 0.18.0
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release100
Supplementary files format and content: excel file includes count and FPKM values for each Sample

source_name: liver sinusoidal endothelial cells

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: liver sinusoidal endothelial cells

value: Wildtype

value: 8 weeks

tag: group

value: aging


title: liver sinusoidal endothelial cells aging3


title: liver sinusoidal endothelial cells aging2


title: TCDD_1

value: heart

value: TCDD exposure


title: B73, Group 5&6 rep2

first: qian

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

institute: Huazhong Agricultural University

description:
PPIs-highconf.txt
PPIs.txt

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

extract_protocol:
Two 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.
mRNA-Seq, circular RNA-Seq, small RNA-Seq, ribo-Seq and PacBio Sequel


title: liver sinusoidal endothelial cells ct3

value: 24 months

value: control


title: Ctrl_2

value: DMSO


title: liver sinusoidal endothelial cells ct1


title: liver sinusoidal endothelial cells ct2


title: CTR-H3K4me3

value: H3K4me3（bioworld,BS7232,Lot CC02181）


title: TDNV_4W_H_i

city: Oxford

first: Allison

middle: M

last: Barry

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

data_processing:
Reads were mapped to the GRCm38 (mm10) Mouse Genome using STAR alignment (Dobin et al 2013). Samtools was used to sort, index, and merge BAM files (Li et al 2009). Quality control (QC) was performed with both FastQC and Samtools prior to gene counting with HTSeq (Andrews 2010, Li et al 2009, Anders et al 2015).
Counts were corrected for effective library size in R using DESeq2 (Love et al 2014). Normalized gene counts were fitted to a negative binomial distribution. A batch effect was introduced during sample collection, and a model that included this batch effect was fitted to every gene. The significance of the model's coefficients was assessed using the Wald test.
Assembly: GRCm38 (mm10)
Supplementary files format and content: csv files contained count data (toc) from samples that pass quality control along with column data (colData), for use with DESeq2

source_name: DRG

extract_protocol:
Cold saline perfusion, lumbar DRG dissection and dissociation, FACS into lysis buffer (NEBnext)
NEB/SMARTER

treatment_protocol: spared nerve injury (SNI) at 3 days (3D) or 4 weeks (4W). Ipsilateral lumbar DRG (L3-L5) were compared to their contralateral counterparts in paired samples.

value: DRG

value: primary

value: Nociceptors

value: 4 week

tag: Sex

value: M

value: Ipsilateral

tag: batch


title: TDNV_4W_G_c

tag: tissue

value: Contralateral


title: TDNV_4W_F_i


title: TDNV_4W_C_c

value: F


title: TDNV_4W_E_c


title: TDNV_4W_D_i


title: TDNV_4W_F_c


title: TDNV_4W_G_i


title: TDNV_4W_E_i


title: B73, Group 5&6 rep1

city: wuhan

last: han

description:
PPIs-highconf.txt
PPIs.txt

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

value: cDNA


title: TDNV_4W_D_c


title: TDNV_4W_B_i


title: TDNV_4W_A_c


title: TDNV_3D_H_i

value: 3 day


title: TDNV_3D_H_c


title: TDNV_4W_B_c


title: TDNV_4W_A_i


title: TDNV_3D_G_i


title: TDNV_3D_G_c


title: TDNV_3D_E_i


title: TDNV_4W_H_c


title: TDNV_3D_F_i


title: TDNV_4W_C_i


title: TDNV_3D_C_i


title: TDNV_3D_D_c


title: TDNV_3D_E_c


title: TDNV_3D_F_c


title: TDNV_3D_C_c


title: TDNV_3D_B_i


title: TDNV_3D_B_c


title: TBAC_4W_H_i

value: AB-RA + Ad-LTMR


title: TDNV_3D_A_c


title: TDNV_3D_A_i


title: TBAC_4W_H_c


title: TBAC_4W_G_c


title: TBAC_4W_E_c


title: TBAC_4W_F_i


title: TBAC_4W_F_c


title: TBAC_4W_G_i


title: TBAC_4W_E_i


title: TBAC_4W_D_i


title: TBAC_4W_C_c


title: TBAC_4W_C_i


title: TBAC_4W_B_i


title: TBAC_4W_A_c


title: TBAC_4W_D_c


title: TBAC_3D_H_c


title: TBAC_4W_B_c


title: TDNV_3D_D_i


title: TBAC_3D_G_i


title: TBAC_3D_F_c


title: TBAC_3D_E_i


title: TBAC_3D_H_i


title: TBAC_3D_E_c


title: TBAC_3D_D_c


title: TBAC_3D_G_c


title: TBAC_3D_C_i


title: TBAC_3D_F_i


title: TBAC_4W_A_i


title: TBAC_3D_B_i


title: TBAC_3D_A_c


title: MRTD_4W_G_c

value: NP


title: MRTD_4W_H_c


title: TBAC_3D_A_i


title: MRTD_4W_E_i


title: MRTD_4W_F_c


title: MRTD_4W_F_i


title: MRTD_4W_G_i


title: MRTD_4W_E_c


title: MRTD_4W_D_c


title: MRTD_4W_D_i


title: MRTD_4W_C_i


title: TBAC_3D_D_i


title: MRTD_4W_B_i


title: MRTD_4W_A_i


title: MRTD_3D_H_c


title: MRTD_3D_H_i


title: MRTD_4W_B_c


title: MRTD_3D_F_c


title: MRTD_3D_E_i


title: MRTD_4W_A_c


title: MRTD_3D_D_c


title: MRTD_3D_E_c


title: MRTD_3D_C_i


title: TBAC_3D_C_c


title: MRTD_3D_G_c


title: MRTD_3D_G_i


title: MRTD_3D_F_i


title: MRTD_3D_A_i


title: MRTD_3D_D_i


title: TBAC_3D_B_c


title: CRTH_4W_H_i

value: C-LTMR


title: MRTD_3D_A_c


title: MRTD_4W_H_i


title: CRTH_4W_G_i


title: MRTD_3D_C_c


title: CRTH_4W_H_c


title: MRTD_3D_B_i


title: CRTH_4W_E_i


title: CRTH_4W_F_c


title: CRTH_4W_F_i


title: MRTD_3D_B_c


title: CRTH_4W_D_i


title: CRTH_4W_D_c


title: CRTH_4W_C_i


title: CRTH_4W_B_c


title: CRTH_4W_A_i


title: CL19_sgHIRA_TREAT_PILEUP, input

city: Cologne

first: Lorea

last: Valcarcel

address: FREZZA Lab, CECAD Research Center Faculty of Medicine University Hospital Cologne Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD

data_processing:
Kapa Hyperprep from Roche to pull down the DNA following manufacturer instructions.
The sequencing was done on a 75-cycle high output NextSeq 500 kit
Assembly: GRCm39
Supplementary files format and content: bigWig (except for Input sample)

source_name: Mouse Epithelial immortalized cells

extract_protocol:
2 × 107 cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature, and quenched with 0.125M glycine for at least 5 minutes. Cells were washed twice with 1 x PBS, and scraped into ice-cold 1 x PBS supplemented with protease inhibitor cocktail. Cells were snap frozen at this point and stored at - 80°C until further use.
DNA libraries were prepared using TruSeq ChIP sample prep kit (Illumina) and sequenced on a NextSeq 550 (Illumina) platform.

treatment_protocol: Control FH wild type

value: Mouse Epithelial immortalized cells

tag: antibody

value: Input


title: CRTH_4W_C_c

tag: time


title: CRTH_4W_A_c


title: CRTH_4W_G_c


title: CL19_TREAT_PILEUP, input

value: Fh1 -/- Hira wt


title: FLFL_TREAT_PILEUP, input

value: Fh fl/fl Hira wt


title: CRTH_3D_G_i

value: DRG

value: primary


title: CRTH_3D_H_i


title: CRTH_4W_E_c

value: 4 week


title: CRTH_3D_G_c

value: M


title: CL19_TREAT_PILEUP


title: CL19_sgHIRA_TREAT_PILEUP


title: FLFL_TREAT_PILEUP


title: CRTH_3D_F_c


title: CRTH_4W_B_i

value: Ipsilateral


title: FLFL_sgHIRA_PILEUP, input

value: Fh fl/fl Hira-/-


title: cKO-4, RNA-seq

city: Xi'an Shaanxi

first: Xiang

address: Changle West Road 169

institute: The Fourth Military Medical University

description:
401 407 RNA seq.xlsx
407_sequence

data_processing:
For meRIP-seq, briefly, paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
For RNA-seq, paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: For MeRIP-seq, xlsx files contain each peak of associated genes; for RNA-seq ,xlsx files include FPKM values for each Sample.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. For hepatocytes samples,primary hepatocytes were isolated as before(PMID:21633967), and RNA was harvested using Trizol reagent.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure (Meyer et al., 2012) with slight modifications. Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.  For RNA-seq, the library was constructed as follows,   1, RNA isolation.Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.2, Library Construction.RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).3, Sequencing.10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: Liver

value: 8 weeks

value: Mettl3 cKO

value: female

tag: rip antibody


title: cKO-3, input

description:
292 294 426 430 input.xlsx
430.Input

tag: strain

value: male

value: none (input)


title: CRTH_3D_H_c

value: C-LTMR

value: 3 day

value: Contralateral


title: WT-4, RNA-seq

description:
401 407 RNA seq.xlsx
401_sequence


title: CRTH_3D_D_i

value: F


title: cKO-3, IP

description:
292 294 426 430 IP.xlsx
430.IP

value: anti-m6A polyclonal antibody


title: CRTH_3D_F_i

value: DRG


title: cKO-2, input

description:
292 294 426 430 input.xlsx
292.Input


title: cKO-1, input

description:
Case & Control input.xlsx
case-1.Input

source_name: Hepatocytes

value: Hepatocytes


title: CRTH_3D_C_i

value: primary


title: CRTH_3D_D_c


title: CRTH_3D_E_c

value: M


title: CRTH_3D_B_i

value: Ipsilateral


title: cKO-2, IP

description:
292 294 426 430 IP.xlsx
292.IP


title: FLFL_sgHIRA_PILEUP

value: Mouse Epithelial immortalized cells

value: Fh fl/fl Hira-/-


title: cKO-1, IP

description:
Case & Control IP.xlsx
case-1.IP

value: 8 weeks


title: CRTH_3D_B_c


title: CRTH_3D_A_i


title: WT-3, IP

description:
292 294 426 430 IP.xlsx
426.IP

value: Liver

value: wild type


title: WT-3, input

description:
292 294 426 430 input.xlsx
426.Input

value: male


title: CRTH_3D_A_c


title: WT-2, input

description:
292 294 426 430 input.xlsx
294.Input

value: none (input)


title: CGRT_4W_H_i

value: PEP

value: 4 week


title: CGRT_4W_G_i


title: WT-1, input

description:
Case & Control input.xlsx
control-1.Input


title: CRTH_3D_C_c

value: C-LTMR

value: 3 day

value: Contralateral


title: CGRT_4W_G_c

value: DRG


title: WT-1, IP

description:
Case & Control IP.xlsx
control-1.IP

value: Hepatocytes

value: anti-m6A polyclonal antibody


title: CGRT_4W_F_i

value: primary

value: M


title: CGRT_4W_F_c


title: CGRT_4W_E_i

value: Ipsilateral


title: CGRT_4W_D_i

value: F


title: CGRT_4W_E_c


title: CGRT_4W_H_c


title: CGRT_4W_C_i


title: Cre negative rep3

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Sequencing was performed using a DNBSEQ-G400 platform at 20M, 100bp pair-end reads per sample.
Reads were filtered using SOAPnuke (v1.5.2) removing reads with adaptors and unknown bases > 0.1%.
Bowtie2 (v2.2.5) was used to map reads to the GRCm38.p6
Expression data was generated using RSEM (v1.2.12)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Spread sheets include FPKM values for each Sample and expression data for each experimental group

source_name: Left Ventricle

extract_protocol:
Left ventricles of mice taken 4 days after surgery were homogenized in TRIzol. RNA was subsequently collected and purified by phenol/chloroform extraction. RNA quality was determined using an Agilent BioAnalyzer.
RNA libraries were prepared by BGI Americas

treatment_protocol: Permenant ligation of the left anterior descending artery was conducted to produce a surgical myocardial infarction. Mice were administered tamoxifen citrate diet ad libitum immediately after surgery to promote excession of myofibroblast Yap and Wwtr1. Left ventricles were collected 4 days post injury.

tag: time point

value: 4 days post injury

value: 6 to 10 weeks

tag: cre

value: Negative

tag: injury type

value: Left anterior artery ligation

tag: parental lines

value: Jackson Laboratory stocks 027929, 029645, and 030532


title: WT-2, IP

description:
292 294 426 430 IP.xlsx
294.IP

value: Liver

tag: age

value: 8 weeks

value: wild type

value: male


title: Cre negative rep2


title: Cre positive rep3

value: Positive


title: Cre negative rep1


title: p53+iASPP siRNA+nutlin replicate 1

city: Shanghai

first: Jiale

last: Wu

address: Room 707, Science and Education Plaza  197 Rui Jin Er Road

institute: State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiaotong University

description: processed data file: FPKM of HCT116 cells by RNA-seq.xlsx

data_processing:
For the RNA-seq analysis, the expression of the transcript (hg38) was quantified by the salmon algorithm (0.14.1). The read counts of each gene were obtained by the tximport package. The differentially expressed genes were analyzed by edgeR.
Genome_build: Homo sapiens (hg38, GRCh38)
Supplementary_files_format_and_content: FPKM_of_HCT116_cells_by_RNA-seq.xlsx: Excel file includes GeneSymbols and FKPMs.

source_name: colon cancer cell line

growth_protocol: HCT116 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 37℃ under 5% CO2.

extract_protocol:
RNA was isolated using the DNA/RNA mini kit (Qiagen, #80204). mRNA was purified using the Dynabeads mRNA purification kit (Invitrogen, #61011) and converted to cDNA using SuperScript II Reverse Transcriptase (Invitrogen, #18064-014).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 cells were treated with iASPP and/or p53 RNA interference for 3 days, with or without another 0.5 days Nutlin-3 treatment.

tag: cell line

tag: cell type

value: Colon cancer cell line

tag: p53 status

value: Wild-type p53

tag: sirna

value: p53+iASPP siRNA

value: Nutlin


title: Cre positive rep2


title: p53+iASPP siRNA+nutlin replicate 2

tag: treatment


title: CGRT_4W_C_c

value: DRG

value: primary

value: PEP

value: 4 week

tag: Sex

value: Contralateral


title: Cre positive rep1

value: 4 days post injury

value: 6 to 10 weeks


title: iASPP siRNA+nutlin replicate 2

value: iASPP siRNA


title: iASPP siRNA+nutlin replicate 1


title: rmTBI mouse 2

city: Toronto

first: Gary

last: Bader

state: Ontario

address: 160 College St

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: CellRanger h5 file

source_name: brain

extract_protocol:
PMGC nuclear extraction and FACS protocol
10x  Genomics single cell 3' V3.1

value: brain

tag: genotype

value: wildtype

value: rmTBI


title: rmTBI mouse 1

tag: tissue


title: sham mouse 1

value: sham


title: MRTD_4W_C_c

value: NP

value: F

tag: batch


title: Cre negative, Sham surgery rep3

data_processing:
Sequencing was performed using a DNBSEQ-G400 platform at 20M single-end reads per sample.
Reads were filtered using SOAPnuke (v1.5.2) removing reads with adaptors and unknown bases > 0.1%.
Bowtie2 (v2.2.5) was used to map reads to the mm10
Expression data was generated using RSEM (v1.2.12)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and expression data for each experimental group (as indicated in the file name)

source_name: Cre negative_Sham surgery

treatment_protocol: Permenant ligation of the left anterior descending artery or sham surgeries were conducted. Mice were administered tamoxifen citrate diet ad libitum immediately after surgery to promote excession of myofibroblast yap and left ventricles were collected 4 days post injury.

value: Jackson Laboratory stocks 027929 and 029645

tag: genotype/variation

value: Cre Negative

value: sham surgery

value: Left Ventricle


title: CGRT_4W_B_i

value: DRG

value: primary

tag: time

value: Ipsilateral


title: Cre negative, Sham surgery rep2


title: sham mouse 2


title: p53 siRNA+nutlin replicate 2

value: Colon cancer cell line

value: Wild-type p53

value: p53 siRNA

value: Nutlin


title: CGRT_4W_D_c

value: PEP

value: 4 week

value: Contralateral


title: Cre negative, Sham surgery rep1

value: 6 to 10 weeks

value: 4 days post injury


title: CRTH_3D_E_i

value: C-LTMR

value: 3 day

value: M


title: p53 siRNA+nutlin replicate 1


title: Cre positive, Sham surgery rep3

source_name: Cre positive_Sham surgery

value: Jackson Laboratory stocks 027929 and 029645

value: Cre Positive

value: sham surgery


title: Cre positive, Sham surgery rep2

value: Left Ventricle


title: Cre negative, MI surgery rep3

source_name: Cre negative_MI surgery

value: Cre Negative

value: Left anterior artery ligation


title: CGRT_4W_A_i

value: DRG

value: primary

value: F

value: Ipsilateral


title: CGRT_4W_A_c

value: PEP

value: 4 week


title: Cre positive, Sham surgery rep1

value: 6 to 10 weeks


title: CTR siRNA+nutlin replicate 2

value: Colon cancer cell line

value: Wild-type p53

value: CTR siRNA

value: Nutlin


title: Cre negative, MI surgery rep2

value: Jackson Laboratory stocks 027929 and 029645

value: 4 days post injury


title: CTR siRNA+nutlin replicate 1


title: Cre positive, MI surgery rep3

source_name: Cre positive_MI surgery

value: Cre Positive


title: p53+iASPP siRNA replicate 2

value: p53+iASPP siRNA


title: CGRT_3D_H_c

value: 3 day

value: M

value: Contralateral


title: Cre positive, MI surgery rep2

value: Left anterior artery ligation

value: Left Ventricle


title: CGRT_3D_H_i

value: DRG

value: primary

value: Ipsilateral


title: Cre positive, MI surgery rep1

value: 6 to 10 weeks


title: CGRT_3D_G_i

value: PEP


title: p53+iASPP siRNA replicate 1

value: Colon cancer cell line

value: Wild-type p53


title: Cre negative, MI surgery rep1

value: Cre Negative


title: iASPP siRNA replicate 2

value: iASPP siRNA


title: CGRT_4W_B_c

value: 4 week

value: F


title: CGRT_3D_G_c


title: iASPP siRNA replicate 1


title: CGRT_3D_F_i


title: p53 siRNA replicate 2

value: p53 siRNA


title: a3-4d

first: Boya

last: Liang

address: No.336, West Nanxinzhuang Road, Qixian Street

institute: University of Jinan

data_processing:
In order to ensure the quality of information analysis, the software FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_tool kit/) is used to filter the original data and get clean reads.
Use fastx_clipper to remove connector sequences from reads
Use fastq_quality_filter to remove N from the read 3'to 5 'direction (N indicates that the base information cannot be determined) to the first base that is not N.
Use fastq_quality_filter to remove continuously occurring low-quality bases from the read 3'to 5 'direction, and delete the read itself and its paired sequences when the low-quality clean reads length is lower than 36bp.
Use local scripts to pair pair end reads (used for PE sequencing).
samtools was used to calculate read counts and RPKM
Assembly: draft genomes of strains Brevundimonas diminuta R79 and Pseudomonas balearica R90 not yet published.  FASTA files of transcript sequences are available on the series record.
Supplementary files format and content: RPKM

organism:
Brevundimonas diminuta
Stutzerimonas balearica

growth_protocol: Strains R79 and R90 were inoculated separately and mixed at 1:1 in the domestication medium, and the samples were collected at 30 ℃ for 0h, 4d and 7d, respectively, and the total RNA was extracted for transcriptome analysis.

extract_protocol:
RNA was extracted from the samples by column fecal RNAout Kit (TIANDZ). After the feces (0.5g) were ground to powder in liquid nitrogen, buffer A preheated by 1ml at 65 °C was added and mixed with 300ul buffer B and 200ul chloroform for 20 seconds. After swirling for 30 seconds, the supernatant was centrifuged, and then the buffer C of the same volume was mixed upside down and transferred to the adsorption column. After centrifugation, the penetrating solution was discarded and the 700ul universal column solution was washed once and then washed with 300ul universal column solution, and RNA was eluted with 100ulRNA elution solution. RNA is quantified using Qubit (Invitrogen, USA).
RNA digested by DNase was removed rRNA by Ribo-Zero digestion Magnetic Kit (Gram-Negative Bacteria or Gram-positive Bacteria) (Epicentre, USA): adding Ribo-Zero Reaction Buffer and Ribo-Zero rRNA Removal Solution (Gram-Negative Bacteria or Gram-positive Bacteria), adding Ribo-Zero Reaction Buffer and Ribo-Zero rRNA Removal Solution (Gram-Negative Bacteria or Gram-positive Bacteria) to 40 μ l, reacting 10min at 68 ℃, then placing 5min at room temperature, adding the treated RNA to the pre-washed magnetic beads, mixing thoroughly immediately, placing 5min at room temperature, then reacting 5min at 50 ℃, immediately placing above 1min on the magnetic rack. Absorb the supernatant, add water to 180 μ l, add 3 M Sodium Acetate and Glycogen (10 mg/ml), add 600ul anhydrous ethyl alcohol, place at-20 ℃ for more than 1 h, centrifuge to get precipitation, add water to dissolve rRNA-depleted RNA.
Take 10ng rRNA-depleted RNA from RNA library, construct library with KAPA Stranded mRNA-Seq Kit (KAPA Biosystems, USA): add KAPA Fragment,Prime and Elute Buffer (2X) to interrupt mRNA, react 6min at 94 °C, quickly put on ice; add 1stStrand synthesis Buffer and KAPA Script to synthesize the first chain of cDNA, reaction procedure: 25 °C 10 minutes, 42 °C 15 minutes, 70 °C 15 minutes; and then add 2ndStrand Marking Buffer (2x) and 2ndStrand Synthesis EnzymeMix for cDNA second chain synthesis, 16 °C reaction for 1 h. After purification with AMPure XP Beads (Agencourt, USA), add KAPA A-Tailing Buffer (10x) and A-Tailing Enzyme for terminal repair and add A, reaction procedure: 30 °C 30min, 65 °C 30 min; add Adaptor, KAPA Ligation Buffer (5x) and KAPA T4 DNA Ligase joint, 20 °C DNA Ligase reaction for 15 min; 200~300bp range of ligated cDNA was obtained by two-step AMPure XP Beads purification. PCR amplification was carried out by adding KAPA HiFi HotStart Ready Mix (2x) and KAPA Library Amplification Primer Mix (10x). The PCR reaction conditions were as follows: pre-denaturation at 98 °C for 45 Sec, denaturation at 98 °C for 15 Sec, annealing at 60 °C for 30 Sec, extension at 72 °C for 30 Sec;, and then purified with 1-fold volume of AMPure XP Beads to obtain a library for sequencing.

tag: strain

tag: medium

value: CH3COONa 5 g/L;(NH4)2SO4 0.16 g/L;K2HPO4•3H2O 0.121 g/L;KH2PO4 0.045 g/L;NaCl 16 g/L;trace element solution 1 mL/L

tag: culture time


title: p53 siRNA replicate 1


title: CTR siRNA replicate 2

value: CTR siRNA


title: CGRT_3D_F_c

value: 3 day

value: M

value: Contralateral


title: a3-0d


title: a3-7d


title: CGRT_3D_E_c

value: DRG


title: CGRT_3D_D_i

value: primary


title: CGRT_3D_D_c


title: CTR siRNA replicate 1


title: a2-0d