title: Dorsal Striatum D4A

description: Paired End

value: Dorsal Striatum


title: C0006JT

status: Public on Sep 01 2021

type: SRA

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

country: France

institute: Assistance Publique des Hôpitaux de Paris

library_source: transcriptomic

data_processing:
Fastq files produced after RNA-seq sequencing have been processed by in-house CNRGH (Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France ) tools in order to assess quality of raw and genomic-aligned nucleotides
Quality control was performed on a random selection of 2 x 10 million reads, including the following steps: removal of adapters and poor-quality sequences to evaluate the % of usable reads (use of trimmomatic); alignment on the reference genome (Hisat2) as well as on the transcriptome and rRNAs (Bowtie2)
Use of rseqc and picardTools to evaluate the % of mapping on the genome and transcriptome, the % of duplicate sequences, the % of rRNA and the total number of usable sequences
Fastq files were aligned against the human GRCh38 genome assembly using STAR-2.6.0 according to author’s procedure (Dobin et al. 2016)
Genome_build: human GRCh38 genome assembly
Supplementary_files_format_and_content: table count

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Promega Maxwell® technology (simply RNA tissue kit, AS1340)
Libraries have been prepared using the "TruSeq Stranded Total RNA Gold” Kit from Illumina

tag: individual

value: Recipient

tag: age

tag: couple number

tag: gender

value: M

tag: cell type

value: PBMC

tag: cohort

value: National multicentric cohort

tag: outcome related


title: WT_Caffeine_10000_b1_p4_F04

city: Singapore

first: Fan

last: Lee

address: 31 Biopolis Way, The NANOS, #06-01

country: Singapore

institute: Institute of Bioengineerng and Nanotechnology

description: WT pilot combined FINAL.csv

data_processing:
Data processing was performed by BioSpyder Technologies Inc.
Illumina Casava1.7 software used for base-calling
No filtering was done since aligning to known sequence
Reads were aligned using the STAR aligner 2.5.3a allowing 2 bp mismatches and not allowing indels. The softclipping option is turned on.
The Tempo-SeqR package was used to generate read counts matrix
Genome_build: rn6
Supplementary_files_format_and_content: Read counts matrix (row = treatment; column = gene)

organism: Rattus norvegicus

source_name: liver

growth_protocol: Freshly isolated hepatocytes were maintained in collagen sandwich at 25,000 cells/well in a 96-well plate with William’s medium E containing 1 mg/mL BSA, 0.5 µg/mL insulin, 2 mM L-glutamine, 100 nM dexamethasone, 10 ng/mL EGF, 100 μg/mL streptomycin and 100 U/mL penicillin.

extract_protocol:
After 24 h of chemical treatment, the spent medium was removed and the wells were washed with 100 µL of PBS twice. Cells were lysed by adding 20 µL of 1X TempO-Seq lysis buffer (BioSpyder) in PBS. The cell lysates were shipped frozen on dry ice to to BioSpyder Technologies, Inc. (Carlsbad, CA, USA), where libraries were prepared directly from the cell lysates and RNA-seq was performed.
2 μL of sample lysate was hybridized with detector oligos from the TempO-Seq rat surrogate (ST) or whole-transcriptome (WT) assay, with 1 h hybridization period for the ST assay and overnight for the WT assay. After ligation and nuclease digestion, the ligated products were added into an amplification mix with sample-specific PCR primer pairs which include the standard Illumina adaptor and a sample-specific barcode sequence. Amplicons were pooled and purified using a PCR clean-up kit (Macherey-Nagel, Mountain View, CA, United States).

treatment_protocol: Chemical treatments were performed in culture medium containing 0.5 % DMSO for 24 h.

tag: strain

value: Wistar

value: Male

value: hepatocytes

tag: tempo-seq assay

value: rat whole transcriptome assay

tag: chemical

value: Caffeine

tag: dose (um)


title: Dorsal Striatum D3A

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

country: USA

institute: Middlebury College

description: Paired End

data_processing:
SOAPnuke v.1.5.2 was used to filter reads with adapters, reads with unknown bases more than 10%, low quality reads (the percentage of base which quality is lesser than 15 is greater than 50% in a read)
HiSat2 used for allignment using mm10 build and GRCm38 GTF file. FeatureCounts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Genome_build: mm10

molecule: polyA RNA

organism: Mus musculus

source_name: Dorsal Striatum

growth_protocol: Animals were grown at Jackson labs

extract_protocol:
The poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: No treatments were applied

tag: tissue

tag: genotype

value: Control

tag: Sex

value: male


title: WT_media_media_b1_p4_F08

description: WT pilot combined FINAL.csv

value: media


title: WT_Caffeine_400_b1_p4_F03

description: WT pilot combined FINAL.csv


title: WT_media_media_b1_p4_F09

description: WT pilot combined FINAL.csv


title: C0006KD


title: Dorsal Striatum D2A

description: Paired End


title: C0006KL

value: F


title: -G3h_1

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

country: China

institute: Shenzhen University

data_processing:
Raw reads were trimmed and clipped with SeqPrep and Sickle
De novo transcriptome assembly was performed with Trinity software
RSEM software was used to calculate gene expression levels from RNA-seq data
Supplementary_files_format_and_content: matrix table include TPM values for each Sample

organism: Nitzschia laevis

source_name: microalgae

growth_protocol: All cultures were grown in LDM medium in the 250-mL column (3-cm diameter) photoreactor with aeration of 1.5% CO2 enriched air. And continuous illumination at 40 μmol photons m-2 s-1 was applied. Cells were pre-cultivated under autotrophic conditions without glucose at 25 °C.

extract_protocol:
Total RNA was extracted using the plant RNA extraction kit (TaKaRa, Tokyo, Japan), and contaminating DNA was removed with RNase-free DNase I. The assessment of RNA concentration and quality was performed by Nano-Drop (ND1000 UV–Vis spectrophotometer; NanoDrop Technologies) and Agilent 2100 Bio analyzer (Agilent Technologies, Inc.).
Poly-A containing mRNA molecules were purified, fragmented and copied into cDNA, then subsequent ligation of the adapter was performed. The products were purified and enriched with PCR amplification. The PCR yield was quantified by QuantiFluor® dsDNA System, and samples were pooled together to form the final library. The pooled samples were subject to cluster generation and sequenced using an Illumina HiSeq.

treatment_protocol: To apply trophic transition, cells from autotrophic cultures were inoculated into LDM medium with addition of 5g/L glucose (+G). Cultures in autotrophic conditions were maintained as control (-G). RNA sequencing (RNA-seq) experiment was performed on 18 samples collected at 3 h, 6 h and 12 h after inoculation in treated medium with glucose addition (+G) and control group (-G) respectively.

value: UTEX 2047


title: +G12h_1


title: WT_Caffeine_10000_b1_p4_F02

description: WT pilot combined FINAL.csv


title: +G6h_3


title: Cortex C10A

description: Paired End

source_name: Cortex

value: Cortex

value: Mecp2 -/-


title: +G12h_2


title: Dorsal Striatum D1A

description: Paired End

value: Dorsal Striatum


title: WT_Doxorubicin_0.08_b1_p4_E11

description: WT pilot combined FINAL.csv

value: Doxorubicin


title: C0006JN

value: Recipient


title: C0006IT

value: PBMC


title: +G6h_2


title: Cortex C8A

description: Paired End


title: +G6h_1


title: Cortex C9A

description: Paired End


title: WT_Doxorubicin_2_b1_p4_E10

description: WT pilot combined FINAL.csv


title: Cortex C7A

description: Paired End


title: C0006KR

value: National multicentric cohort


title: +G3h_3


title: WT_Doxorubicin_0.08_b1_p4_E09

description: WT pilot combined FINAL.csv

value: Wistar


title: Cortex C6A

description: Paired End


title: C0006IR

value: M


title: C0006LB


title: +G3h_2


title: WT_Doxorubicin_2_b1_p4_E08

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes


title: WT_Diclofenac_16_b1_p4_E07

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

value: Diclofenac


title: C0006JV


title: +G3h_1


title: WT_Diclofenac_400_b1_p4_E06

description: WT pilot combined FINAL.csv


title: Cortex C5A

description: Paired End

value: Control

value: male


title: C0006JR


title: Cortex C4A

description: Paired End


title: WT_Diclofenac_16_b1_p4_E05

description: WT pilot combined FINAL.csv


title: B16.F10-Tumor_NanoISD-Treated_Rep4

type: RNA

city: Nashville

first: John

last: Wilson

state: TN

address: 2400 Highland Ave., 107 Olin Hall

institute: Vanderbilt University

description:
Each biologial sample was evaluated for the mRNA expression of 43 myeloid-related genes along with 5 house-keeping genes (i.e. Gapdh, Gusb, Hdac3, Rpl19, and Tbp)
100 µL, containing 1x10^6 B16.F10 tumor cells in PBS, was subcutaneously inoculated into 6-8 week old C57BL/6J mice.

hyb_protocol: RNA was incubated with target-specific fluorescent barcodes at 67 ºC for 16 hours.

scan_protocol: Samples were prepped and analyzed using the NanoString nCounter Max Analysis system.

data_processing: Data processing was performed using the NanoString nSolver data analysis software. The raw data were divided by that of the PBS-treated group, and results were then subject to Log2 normalization.

label: NanoString Probes

source_name: B16.F10 Tumor

label_protocol: 100 ng of RNA extracted from tumor tissue was hybridized to a myeloid panel of target-specific fluorescent barcodes.

extract_protocol: 6 hours after intratumoral treatment, the tumors were harvested and homogenized using TissueLyser II (Qiagen). Tumor RNA was isolated using the RNeasy® Plus Mini Kit (Qiagen).

treatment_protocol: When tumors were ~ 200 mm^3 in volume, a 100 µL intratumoral injection of 2 µg NanoISD, free D-PDB at an equivalent dose, or PBS was administered.

value: B16.F10 Murine Melanoma

tag: mouse strain

value: 6-8 weeks old

value: Female

tag: tumor volume


title: C0006LL

value: F


title: Cortex C3A

description: Paired End

value: Cortex


title: WT_Diclofenac_400_b1_p4_E04

description: WT pilot combined FINAL.csv


title: C0009L1


title: Cortex C2A

description: Paired End


title: B16.F10-Tumor_NanoISD-Treated_Rep2


title: B16.F10-Tumor_NanoISD-Treated_Rep3


title: WT_Diclofenac_16_b1_p4_E03

description: WT pilot combined FINAL.csv


title: C0006LJ


title: WT_Diclofenac_400_b1_p4_E02

description: WT pilot combined FINAL.csv


title: C0006JX


title: B16.F10-Tumor_NanoISD-Treated_Rep1


title: WT_Simvastatin_2.4_b1_p4_D11

description: WT pilot combined FINAL.csv

value: Simvastatin


title: WT_Simvastatin_60_b1_p4_D10

description: WT pilot combined FINAL.csv


title: NK donor 6 NKG2A-KO

city: Maastricht

first: Roel

last: Klein Wolterink

address: Universiteitssingel 50

department: Internal Medicine

country: Netherlands

institute: Maastricht University

data_processing:
Data was analyzed on the Galaxy Europe platform.
Sequenced reads were trimmed using Trimmomatic (HEADCROP, 12), followed by mapping to the hg38 genome using HISAT2 2.1.0 with standard paramters for paired-end reads on the Galaxy Europe platform.
Count tables were generated using FeatureCounts 2.0.1 (unstranded data, hg38 reference genome) with standard settings from the Galaxy Europe platform (featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930. https://doi.org/10.1093/bioinformatics/btt656)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files contain read counts for each sample
Supplementary_files_format_and_content: matrix table with gene counts for all samples of all genotypes

source_name: expanded NK cells

growth_protocol: NK cells were cultured in RPMI-1640 supplemented with 10% fetal calf serum and 100 U/mL penicillin-streptomycin. NK cells were expanded with K562/mIL-21/4-1BBL feeder cells.

extract_protocol:
1E6 NK cells were lysed in TRIzol, stored and shipped at -80C. RNA isoaltion and quality check were performed by BGI on an Agilent 2100 Bioanalyzer, with RIN>7.8 for all samples.
Oligo(dT) primers were used for cDNA library generation

treatment_protocol: NK cells were electroporated with Cas9 RNP with or without KLRC1-targeting gRNA. Culture was continued for 7 days until analysis.

value: KO

tag: donorid


title: NK donor 5 NKG2A-WT (control)

value: WT


title: C0006LX

tag: individual

value: Recipient

value: PBMC

value: National multicentric cohort


title: C0006L9

tag: age


title: B16.F10-Tumor_D-PDB-Treated_Rep4


title: NK donor 5 NKG2A-KO


title: B16.F10-Tumor_D-PDB-Treated_Rep2


title: B16.F10-Tumor_D-PDB-Treated_Rep3


title: C0006M9

tag: couple number

value: M


title: WT_Simvastatin_60_b1_p4_D08

description: WT pilot combined FINAL.csv

value: Wistar

tag: gender

value: Male

value: hepatocytes


title: Cortex C1A

description: Paired End

value: Control


title: C0006KT

tag: cell type


title: WT_Valproic_400_b1_p4_D07

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

value: Valproic


title: C0009KI

tag: cohort


title: NK donor 3 NKG2A-WT (control)


title: B16.F10-Tumor_PBS-Treated_Rep3

value: B16.F10 Murine Melanoma

value: 6-8 weeks old


title: WT_Valproic_10000_b1_p4_D06

description: WT pilot combined FINAL.csv


title: B16.F10-Tumor_PBS-Treated_Rep4

value: Female


title: NK donor 6 NKG2A-WT (control)


title: WT_Simvastatin_2.4_b1_p4_D09

description: WT pilot combined FINAL.csv


title: NK donor 4 NKG2A-KO


title: NK donor 3 NKG2A-KO


title: WT_Valproic_400_b1_p4_D05

description: WT pilot combined FINAL.csv


title: C0006LT

tag: outcome related


title: B16.F10-Tumor_PBS-Treated_Rep2


title: B16.F10-Tumor_D-PDB-Treated_Rep1


title: NK donor 4 NKG2A-WT (control)


title: B16.F10-Tumor_PBS-Treated_Rep1


title: C0009LN


title: ACP4_n

city: Norwich

first: Wenbo

last: Ma

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description:
ACP_3_S41_L007
Biological replicate 4

data_processing:
The quality of the raw sequencing data was checked with FastQC v0.11.9
Read adapters were trimmed from reads using Trimmomatic v 0.36
reads were aligned with the indexed CLas-Psy62 isolate genome assembly (NC_012985.3) and parsed to it using HISAT2 v2.1.0
The number of reads mapped to each gene was counted using the feature counts function of the Rsubread package
Read counts were normalized for each sample for differential expression analysis using DESeq2 v1.30.1
Genome_build: NC_012985.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized read counts for every genes and every sample

organism: Diaphorina citri

source_name: whole insects

extract_protocol:
Freeze-dried HLB-infected midribs (from 15–25 leaves) were ground to a fine powder in liquid nitrogen. 1ml of TLE extraction buffer was added to 100 mg citrus powder or the pellet obtained after the above bacterial isolation. Then, 60 µL of 500 mM CaCl2 was added, mixed thoroughly, and placed on ice for 10 min. Centrifugation at 12,000 x g for 10 min at 4 °C was performed, followed by two rounds of separation with 500 µl of phenol:Chloroform:isoamyl alcohol (25:25:1) and centrifugation at 15,000 x g for 10 min at 4 °C. The supernatant was mixed with 2 M LiCl and incubated overnight at -20 °C. RNA was precipitated by centrifugation at 15,000 x g for 30 min, washed twice with ice-cold 75% ethanol, centrifuged at 15,000 x g for 15 min and re-suspended in 20 µl of RNAse-free water. 10–15 adult psyllids were ground in liquid nitrogen, immediately suspended in 50 μl TRIzol® (Invitrogen) and ground until complete homogenization. An additional 950 μl of TRIzol® was added to the homogenate, followed by separation with 200 µl of chloroform, precipitation with 500 µl of isopropanol, and two washes with 75% ethanol as indicated by the manufacturer. The pellet was resuspended in 20-30 µl of RNAse-free water.
RNA was converted into sequencing-ready libraries for Illumina sequencing using TruSeq Stranded Total RNA reagents. Poly(A) Polymerase (NEB) treatment (polyA) and Poly(dT)-depleted library construction was tested in parallel. cDNA libraries were subjected to RNASeq, using an Illumina HiSeq-4000 system with 150-bp strand-specific single-end reads with technical duplicates.

treatment_protocol: pre-enrichment (bacterial isolation) performed according to Nobori et al. 2018, 1-step post enrichment using MICROBEnrich, 2-step enrichment using MICROBEnrich followed byRiboMinus Eukaryote Kit. All samples underwent ribodepletion using Illumina Ribo-Zero Plus except a subset of 2-step enrichmed RNA samples that underwent poly(A) polymerase treatment (polyA)

value: whole insects

tag: treatment


title: NK donor 2 NKG2A-WT (control)


title: C0006L3

value: F


title: WT_Valproic_10000_b1_p4_D04

description: WT pilot combined FINAL.csv

tag: strain

tag: tempo-seq assay


title: WT_Valproic_400_b1_p4_D03

description: WT pilot combined FINAL.csv

tag: chemical

tag: dose (um)


title: NK donor 1 NKG2A-WT (control)


title: NK donor 2 NKG2A-KO

value: KO


title: C0006M3


title: WT_Valproic_10000_b1_p4_D02

description: WT pilot combined FINAL.csv


title: ACP2_n

description:
S2_June_S133_L003
Biological replicate 2

tag: tissue


title: ACP1_n

description:
S2_S135_L004
Biological replicate 1


title: C0009L7


title: C0009K6


title: C0009KO


title: ACP5_n

description:
ACP_4_S42_L007
Biological replicate 5


title: ACP1_e1

description:
S1_S131_L003
Biological replicate 1

value: 1-step enrichment


title: WT_Simvastatin_60_b1_p4_C10

description: WT pilot combined FINAL.csv

value: Simvastatin


title: ACP2_e1

description:
S1_June_S136_L004
Biological replicate 2


title: NK donor 1 NKG2A-KO


title: C0006LH

value: Recipient

value: PBMC


title: siRNF187_2

city: Xinxiang

first: Ting

last: Zhuang

state: Henan

address: Jinsui Road 601

institute: Xinxiang Medical University

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

source_name: human breast cancer cell line MCF-7

growth_protocol: MCF7 cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: MCF-7 cells were transfected with siControl or siRNF187.

tag: cell line

value: breast cancer

tag: sirna


title: WT_Naproxen_80_b1_p4_C09

description: WT pilot combined FINAL.csv

value: Wistar

value: Naproxen


title: WT_Naproxen_2000_b1_p4_C08

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes


title: siRNF187_3


title: ACP3_e2r

description:
ACP_NK_S119_L006
Biological replicate 3

value: 2-step enrichment ribodepletion


title: WT_Simvastatin_2.4_b1_p4_C11

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay


title: C0006LF

value: M

value: National multicentric cohort


title: C0009K8


title: C-8 transition stageEndosperm replicate-2

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
replicate-2
Rawcount.xlsx

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to the IWGSC RefSeq v2.0 assembly wheat genome using STAR.
Read counting was carried out with FeatureCounts.
Genome_build: IWGSC RefSeq v2.0 assembly wheat genome
Supplementary_files_format_and_content: Matrix table files include raw counts for each sample

organism: Triticum turgidum

source_name: transition stageEndosperm

growth_protocol: Plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity was set to 100 to 120 μmol m−2 s−1 for whole life cycle.

extract_protocol:
Embryo, endosperm and pericarp tissue isolation procedure were precisely performed as described in Xiang et al., 2019.
For RNA-seq profile analysis, Illumina mRNA-seq libraries were constructed using the TruSeq RNA kit (version 1, rev A).

treatment_protocol: Flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.

value: Endosperm

tag: Stage

value: transition stage

tag: ecotype

value: CDC commander


title: C-9 leaf late stageEndosperm replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf late stageEndosperm

value: leaf late stage


title: WT_Isoniazid_400_b1_p4_C07

description: WT pilot combined FINAL.csv

value: Isoniazid


title: ACP3_e2a

description:
CL100125429_L2_HK500CITdpmRAACRAAPEI-507
Biological replicate 3

value: whole insects

value: 2-step enrichment polyA


title: siControl_1

value: siControl


title: C0006LR

tag: individual

value: Recipient

value: PBMC


title: WT_Isoniazid_10000_b1_p4_C06

description: WT pilot combined FINAL.csv

value: Wistar


title: C0006KZ

tag: age

value: F


title: WT_Isoniazid_10000_b1_p4_C04

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes


title: siControl_2

value: breast cancer


title: C0006KW

value: Donor

tag: couple number

value: M


title: siControl_3


title: siRNF187_1


title: C-7 mature stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: mature stageEmbryo

value: Embryo

value: mature stage


title: C0009K9

tag: gender

value: National multicentric cohort


title: WT_Isoniazid_400_b1_p4_C03

description: WT pilot combined FINAL.csv

tag: cell type

value: rat whole transcriptome assay


title: C-6 leaf late stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf late stageEmbryo

value: leaf late stage

value: CDC commander


title: C-5 leaf middle stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf middle stageEmbryo

value: leaf middle stage


title: WT_Isoniazid_10000_b1_p4_C02

description: WT pilot combined FINAL.csv

value: Isoniazid


title: mRNA KS9_2

city: Kanagawa

first: Manami

last: Tanaka

address: 2-22-9 Hiratsuka, Kanagawa 259-1211, Japan

country: Japan

institute: Bradeion Institute of Medical Sciences

description:
blood sample- 30 days after taking Huaier
stage I,  metastasis to hypopharynx

data_processing:
RNA: Alignment:Hisat2 and Bowtie2
RNA: Expression of genes by RSEM
Call DEGs by PossionDis method
Predicted novel transcripts by StringTie and call SNP by GATK
hg38
Genome_build: TXT, FA

source_name: blood

growth_protocol: The samples (4ml blood) in PAXgene Blood RNA tube was handled and kept at –80 C until shipping to BGI Shenzhen by dry-ice cargo.  The RNA extraction, quality check for sequencing were performed in BGI Shenzhen according to the BGI protocols.

extract_protocol:
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA).

treatment_protocol: Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA), according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25μL~100μL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA)

tag: tumor origin

value: oesophageal squemous cell cancer


title: mRNA KS9_3

description:
blood sample- 90 days after taking Huaier
stage I,  metastasis to hypopharynx


title: C0006J6

value: PBMC

tag: cohort

tag: outcome related


title: mRNA KS9_1

description:
blood sample-before taking Huaier
stage I,  metastasis to hypopharynx


title: C0009LM


title: C-4 leaf early stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf early stageEmbryo

value: leaf early stage


title: WT_Naproxen_80_b1_p4_B11

description: WT pilot combined FINAL.csv

tag: strain

value: Wistar

value: Naproxen


title: WT_Isoniazid_400_b1_p4_C05

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes

tag: tempo-seq assay


title: mRNA KS8_6

description:
blood sample- 14 months after taking Huaier
stage I,pancreas metastasis suspected

value: hepatoma


title: WT_Naproxen_2000_b1_p4_B10

description: WT pilot combined FINAL.csv

tag: chemical


title: C0006LY

value: Donor

value: M


title: C-3 transition stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: transition stageEmbryo

value: Embryo

value: transition stage


title: mRNA KS8_5

description:
blood sample- 9 months after taking Huaier
stage I,pancreas metastasis suspected


title: WT_Naproxen_80_b1_p4_B09

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

tag: dose (um)


title: C-2 preembryo stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: preembryo stageEmbryo

tag: tissue

value: preembryo stage


title: C0009K3

source_name: PBMC

value: F

value: National multicentric cohort


title: C0006JI


title: mRNA KS8_3

description:
blood sample- 90 days after taking Huaier
stage I,pancreas metastasis suspected


title: C-20 leaf early stagePericarp replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf early stagePericarp

value: Pericarp

value: CDC commander


title: C0006J4

value: PBMC


title: ST_Chloramphenicol_18_b1_p5_G07

description: ST pilot combined FINAL.csv

source_name: liver

value: S1500+ rat surrogate assay

value: Chloramphenicol


title: C-1 two cell stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: two cell stageEmbryo

value: two cell stage


title: C0006M0


title: mRNA KS8_2

description:
blood sample- 30 days after taking Huaier
stage I,pancreas metastasis suspected


title: mRNA KS8_1

description:
blood sample-before taking Huaier
stage I,pancreas metastasis suspected


title: C-19 leaf late stageEndosperm replicate-1

description:
replicate-1
Rawcount.xlsx

value: Endosperm

value: leaf late stage


title: C-18 transition stageEndosperm replicate-1

description:
replicate-1
Rawcount.xlsx


title: ST_Chloramphenicol_18_b1_p5_G05

description: ST pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes


title: C0006JA

value: Donor

value: M


title: C-17 mature stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: Embryo

value: mature stage


title: ST_Chloramphenicol_450_b1_p5_G04

description: ST pilot combined FINAL.csv


title: mRNA KS8_4

description:
blood sample- 6 months after taking Huaier
stage I,pancreas metastasis suspected

value: hepatoma


title: WT_Naproxen_2000_b1_p4_B08

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

value: Naproxen


title: ST_Chloramphenicol_18_b1_p5_G03

description: ST pilot combined FINAL.csv


title: C0006JC

value: F

value: National multicentric cohort


title: C0006JE

value: PBMC


title: mRNA KS7_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis

value: colorectal cancer (adenocarcinoma)


title: mRNA KS6_2

value: stomach cancer (signet ring cell carci.)


title: mRNA KS6_1


title: C-15 leaf middle stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: leaf middle stage

value: CDC commander


title: ST_Sulfasalazine_4_b1_p5_F07

description: ST pilot combined FINAL.csv

value: Wistar

value: S1500+ rat surrogate assay

value: Sulfasalazine


title: C-14 leaf early stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: leaf early stage


title: mRNA KS5_6

description:
blood sample- 18 months after taking Huaier
stage IV, metastasis to lboth ungs

value: oesophageal squemous cell cancer


title: ST_Sulfasalazine_100_b1_p5_F06

description: ST pilot combined FINAL.csv

value: Male

value: hepatocytes


title: C0009K1

value: Donor

value: M


title: C0006J2


title: C-13 transition stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: Embryo

value: transition stage


title: mRNA KS7_2

description:
blood sample- 30 days after taking Huaier
stage IV, multiple metastasis


title: ST_Chloramphenicol_450_b1_p5_G06

description: ST pilot combined FINAL.csv

value: Chloramphenicol


title: mRNA KS5_5

description:
blood sample- 14 months after taking Huaier
stage IV, metastasis to lboth ungs


title: ST_Sulfasalazine_4_b1_p5_F05

description: ST pilot combined FINAL.csv


title: C0006LU

value: F

value: PBMC

value: National multicentric cohort


title: C-12 preembryo stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: preembryo stage


title: ST_Sulfasalazine_100_b1_p5_F04

description: ST pilot combined FINAL.csv


title: C-16 leaf late stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: leaf late stage

value: CDC commander


title: mRNA KS5_4

description:
blood sample- 11 months after taking Huaier
stage IV, metastasis to lboth ungs


title: C-11 two cell stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

value: two cell stage


title: ST_Chloramphenicol_450_b1_p5_G02

description: ST pilot combined FINAL.csv

value: Wistar

value: S1500+ rat surrogate assay


title: mRNA KS5_3

description:
blood sample- 90 days after taking Huaier
stage IV, metastasis to lboth ungs

value: oesophageal squemous cell cancer


title: mRNA KS5_2

description:
blood sample- 30 days after taking Huaier
stage IV, metastasis to lboth ungs


title: ST_Sulfasalazine_100_b1_p5_F02

description: ST pilot combined FINAL.csv

value: Male

value: Sulfasalazine


title: C0006IY

value: Donor


title: C-10 leaf early stagePericarp replicate-1

description:
replicate-1
Rawcount.xlsx

value: Pericarp

value: leaf early stage


title: C0006LC

value: M


title: C0009KJ


title: mRNA KS5_1

description:
blood sample-before taking Huaier
stage IIb, metastasis to both lungs


title: Villin-Wls cKO 5

city: Ankara

first: Bahar

last: Degirmenci

address: Faculty of Science, B Building Room 241

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

data_processing:
Basecalling was performed using Illumina HiSeq Control Software 2.0.12.0, default parameters.
The quality of the reads were checked using FastQC.
The reads were mapped against NCBI Mus musculus reference genome (GRCm38.p5) using TopHat v.2.1.1.
Cufflinks v.2.2.1 was used to assemble transcripts and quantify their expressions.
FPKM values and differentially expressed genes were calculated through CuffDiff after merging WT and KO samples with CuffMerge.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Processed_FPKM_DataMatrix.csv: Comma-separated text file includes FPKM values.

source_name: Tumor

extract_protocol:
Sample extraction: Macrodissected colon tumor sample, fresh frozen samples were homogenized manually with an RNase free pestle. Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, 740955.250) according to the manufacturer’s instructions. All samples were ethanol precipitated. RNA integrity of each sample was assessed using a Fragment Analyzer (Advanced Analytical).
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina, RS-122-2101) according to the manufacturer’s instructions.

tag: genotype

value: Villin-Wls cKO (Villin-Cre ERT2, Wls flox/flox)

value: Colon tumor


title: ST_Indomethacin_12_b1_p5_E07

description: ST pilot combined FINAL.csv

value: hepatocytes

value: Indomethacin


title: C0006K8

value: PBMC

value: National multicentric cohort


title: Villin-Wls cKO 4


title: C0006J0


title: ST_Indomethacin_300_b1_p5_E06

description: ST pilot combined FINAL.csv


title: mRNA KS4_3

description:
blood sample- 90 days after taking Huaier
stage IIb, metastasis to liver

value: cholangiocarcinoma


title: C0006IW


title: ST_Indomethacin_12_b1_p5_E05

description: ST pilot combined FINAL.csv


title: ST_Indomethacin_300_b1_p5_E04

description: ST pilot combined FINAL.csv


title: C0006IU


title: Villin-Wls cKO 3


title: C0006KU

value: F


title: mRNA KS4_2

description:
blood sample- 30 days after taking Huaier
stage IIb, metastasis to liver


title: Villin-Wls cKO 1


title: Villin-Wls cKO 2


title: C0006JK


title: mRNA KS3_3

description:
blood sample- 90 days after taking Huaier
stage IV, peritoneal metastasis

value: pancreas cancer


title: mRNA KS3_2

description:
blood sample- 30 days after taking Huaier
stage IV, peritoneal metastasis


title: ST_Indomethacin_12_b1_p5_E03

description: ST pilot combined FINAL.csv

value: Wistar

value: S1500+ rat surrogate assay


title: ST_Indomethacin_300_b1_p5_E02

description: ST pilot combined FINAL.csv

value: Male


title: C0006LO


title: Wls WT 5

value: Wls control (Wls flox/flox)


title: Wls WT 4


title: ST_Acetaminophen_400_b1_p5_D07

description: ST pilot combined FINAL.csv

value: Acetaminophen


title: C0006K2

value: Donor


title: mRNA KS3_1

description:
blood sample-before taking Huaier
stage IV, peritoneal metastasis


title: mRNA KS31_2


title: ST_Acetaminophen_10000_b1_p5_D06

description: ST pilot combined FINAL.csv


title: Wls WT 2


title: C0006JO


title: mRNA KS4_1

description:
blood sample-before taking Huaier
stage IIb, metastasis to liver


title: mRNA KS31_1


title: ST_Acetaminophen_400_b1_p5_D05

description: ST pilot combined FINAL.csv


title: Wls WT 1


title: mRNA KS30_2


title: C0006KO


title: C0006IG


title: mRNA KS30_1


title: 94E

city: Aurora

first: Amy

last: Kelly

state: Colorado

address: 12700 East 19th Avenue, Mail Stop 8613, P.O. Box 6511

institute: University of Colorado

data_processing:
Raw sequences were de-multiplexed using Illumina Casava v1.8 software.
Adpaters were trimmed and sequence reads with Phred scores ≥ Q30 were retained.
Sequence reads were aligned against the mouse reference genome (mm10) using STAR 2.5.3a.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow and annotated with RefSeq transcripts from NCBI annotation release 84.
Transcript abundances were normalized by the Trimmed mean of M-values method.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table of transcript counts before normalization for genes in 20 samples.
Supplementary_files_format_and_content: Matrix table of transcript counts after normalization for genes in 20 samples.

source_name: fetal heart

growth_protocol: Twelve-week-old C57BL/6J female mice were fed either a control diet (D12489, 10% calories from fat) or an obesogenic diet (Western Diet D12089B; Research Diets, 40% of calories from fat). Female mice fed the obesogenic diet had ad libitum access to 20% sucrose solution supplemented with micronutrients. Females were mated following a 25% gain in weight over the initial body weight in the obesogenic diet. All males were fed control diet.

extract_protocol:
Tissues was flash frozen in liquid nitrogen immediately after collection and stored at -80oC. Total RNA was extracted from tissue samples using the Zymo Direct-zol RNA MiniPrep kit.
RNA-Seq libraries were prepared using 100 ng of total RNA according to the KAPA Stranded mRNA-Seq protocol.

treatment_protocol: Maternal obesity by high fat high sugar diet

value: fetal heart

tag: Sex

tag: treatment

value: Obese


title: ST_Acetaminophen_10000_b1_p5_D04

description: ST pilot combined FINAL.csv


title: C0009LT

value: M


title: mRNA KS29_3

value: oesophageal squemous cell cancer


title: 94B


title: ST_Acetaminophen_400_b1_p5_D03

description: ST pilot combined FINAL.csv

value: hepatocytes


title: 52C


title: C0006LM


title: ST_WY14643_8_b1_p5_C07

description: ST pilot combined FINAL.csv


title: mRNA KS29_2


title: Wls WT 3

value: Colon tumor


title: C0006JS

value: PBMC


title: ST_Sulfasalazine_4_b1_p5_F03

description: ST pilot combined FINAL.csv

value: Sulfasalazine


title: mRNA KS28_3

description:
blood sample- 90 days after taking Huaier
stage II, multiple cancer suspected


title: C0006MA

value: National multicentric cohort


title: ST_WY14643_200_b1_p5_C06

description: ST pilot combined FINAL.csv


title: mRNA KS29_1

description:
blood sample-before taking Huaier
stage IV, metastasis to both lungs


title: ST_WY14643_8_b1_p5_C05

description: ST pilot combined FINAL.csv


title: C0006KC

value: F


title: 48H


title: mRNA KS28_2

description:
blood sample- 30 days after taking Huaier
stage II, multiple cancer suspected


title: 38B


title: mRNA KS28_1

description:
blood sample-before taking Huaier
stage II, multiple cancer suspected


title: ST_WY14643_200_b1_p5_C04

description: ST pilot combined FINAL.csv


title: 38A


title: ST_WY14643_8_b1_p5_C03

description: ST pilot combined FINAL.csv


title: mRNA KS27_3

description:
blood sample- 90 days after taking Huaier
stage I, dessected before taking Huaier

value: prostate cancer


title: ST_Acetaminophen_10000_b1_p5_D02

description: ST pilot combined FINAL.csv

value: Wistar


title: C0009LQ


title: C0006JQ


title: ST_WY14643_200_b1_p5_C02

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay


title: C0006IS


title: ST_Ketoconazole_0.6_b1_p5_B07

description: ST pilot combined FINAL.csv

value: Male

value: Ketoconazole


title: 384F


title: mRNA KS27_2

description:
blood sample- 30 days after taking Huaier
stage I, dessected before taking Huaier


title: 48F


title: mRNA KS27_1

description:
blood sample-before taking Huaier
stage I, dessected before taking Huaier


title: 57C

value: Control


title: ST_Ketoconazole_0.6_b1_p5_B05

description: ST pilot combined FINAL.csv


title: C0006KQ

value: Donor


title: C0006LA


title: ST_Ketoconazole_15_b1_p5_B04

description: ST pilot combined FINAL.csv


title: C0006IQ


title: 384A

value: fetal heart


title: mRNA KS26_3

description:
blood sample- 90 days after taking Huaier
prostate hyperplasia

value: healthy control (Japanese male)


title: 57A

value: M


title: C0006JU


title: mRNA KS26_1

description:
blood sample-before taking Huaier
prostate hyperplasia


title: mRNA KS26_2

description:
blood sample- 30 days after taking Huaier
prostate hyperplasia


title: ST_Ketoconazole_0.6_b1_p5_B03

description: ST pilot combined FINAL.csv


title: 51B


title: mRNA KS25_3

description:
blood sample- 90 days after taking Huaier
healrthy control with Huaier uptake


title: 51C


title: ST_Ketoconazole_15_b1_p5_B02

description: ST pilot combined FINAL.csv


title: 52A

value: Obese


title: C0009KF


title: C0006LI


title: ST_vehicle_vehicle_b1_p4_G11

description: ST pilot combined FINAL.csv

value: hepatocytes

value: vehicle


title: 41J


title: mRNA KS25_2

description:
blood sample- 30 days after taking Huaier
healrthy control with Huaier uptake


title: ST_Ketoconazole_15_b1_p5_B06

description: ST pilot combined FINAL.csv


title: mRNA KS25_1

description:
blood sample-before taking Huaier
healrthy control with Huaier uptake


title: mRNA KS24_2

description:
blood sample- 30 days after taking Huaier
stage IV, multiple metastasis

value: cholangiocarcinoma


title: 41E


title: ST_vehicle_vehicle_b1_p4_G10

description: ST pilot combined FINAL.csv


title: ST_Doxorubicin_0.08_b1_p4_G09

description: ST pilot combined FINAL.csv

value: Doxorubicin


title: C0006LK

value: PBMC

value: National multicentric cohort


title: mRNA KS24_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis


title: ST_Doxorubicin_2_b1_p4_G08

description: ST pilot combined FINAL.csv


title: ST_Ranitidine_160_b1_p4_G07

description: ST pilot combined FINAL.csv

value: Ranitidine


title: C0009KH

value: F


title: 27F


title: 41A


title: C0006L8


title: C0006LW


title: 45D


title: mRNA KS22_3

description:
blood sample- 90 days after taking Huaier
stage IV, multiple metastasis

value: breast cancer


title: Het-tam-C

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Basecalls performed using CASAVA version 1.4
The quality of paired reads were checked using FASTQC (v0.11.7)
PE reads were aligned with hisat2 (v2.0.5) against mm10
Subread/featureCounts (v1.5.2)  was used to count gene-level expression
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw gene counts

source_name: immortalized hematopoietic cell line

growth_protocol: Murine LSPC were derived from Ddx41-floxed mice by transduction of lineage-negative bone marrow cells with a retrovirus expressing MLL-AF9.  They are grown in IMDM media containing 10% FCS, pen/strep, and 10ng/ml of recombinant mouse IL-3, mouse SCF, and human IL-6.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells are treated with 1µM 4-hydroxy-tamoxifen or Ethanol (1:1000) for 48h to induce the activity of the Rosa-CreERT protein that is expressed in the LSPC

value: immortalized hematopoietic cell line

value: 4-OH-tamoxifen (1µM)

tag: disease state

value: MLL-AF9 immortalized


title: C0009LV

tag: individual

value: Donor


title: C0006JW

tag: age


title: ST_Ranitidine_160_b1_p4_G05

description: ST pilot combined FINAL.csv

value: Wistar

value: Male

value: S1500+ rat surrogate assay


title: mRNA KS22_1


title: C0006M8

tag: couple number


title: mRNA KS2_1

value: pancreas cancer


title: ST_Ranitidine_4000_b1_p4_G04

description: ST pilot combined FINAL.csv

tag: gender

value: hepatocytes


title: Het-tam-A

tag: cell type


title: C0006JY


title: mRNA KS21_3

tag: tumor origin

value: healthy control (Japanese male)


title: C0006LS

value: M

tag: cohort


title: mRNA KS22_2


title: 27B

value: fetal heart

value: Control


title: mRNA KS21_2


title: ST_Ranitidine_160_b1_p4_G03

description: ST pilot combined FINAL.csv


title: Het-C

value: Ethanol

value: +/flox


title: ST_Ranitidine_4000_b1_p4_G02

description: ST pilot combined FINAL.csv

value: Ranitidine


title: ST_vehicle_vehicle_b1_p4_F11

description: ST pilot combined FINAL.csv

value: vehicle


title: ST_Ranitidine_4000_b1_p4_G06

description: ST pilot combined FINAL.csv


title: Het-B

value: immortalized hematopoietic cell line


title: C0006M2

value: PBMC

value: National multicentric cohort

tag: outcome related


title: C0009KP

value: Donor

value: F


title: Het-tam-B

value: 4-OH-tamoxifen (1µM)

value: MLL-AF9 immortalized


title: mRNA KS21_1


title: Het-A


title: C0006L2


title: mRNA KS20_3

description:
blood sample- Huaier-free control
Huaier-free control

value: colorectal adenoma (benign)


title: ST_media_media_b1_p4_F10

description: ST pilot combined FINAL.csv

tag: strain

value: Wistar

value: Male

value: hepatocytes

value: S1500+ rat surrogate assay

value: media


title: mRNA KS20_2


title: ST_media_media_b1_p4_F09

description: ST pilot combined FINAL.csv

tag: tempo-seq assay


title: FF-tam-B


title: mRNA KS20_1


title: C0009K5


title: ST_media_media_b1_p4_F08

description: ST pilot combined FINAL.csv

tag: chemical


title: C0006IM


title: FF-tam-A


title: mRNA KS19_3

description:
blood sample- 90 days after taking Huaier
stage IIb, metastasis to lympy nodes

value: colorectal cancer (adenocarcinoma)


title: ST_Caffeine_400_b1_p4_F07

description: ST pilot combined FINAL.csv

value: Caffeine

tag: dose (um)


title: C0006LE

value: M


title: FF-C

value: Ethanol

value: flox/flox


title: ST_Caffeine_10000_b1_p4_F06

description: ST pilot combined FINAL.csv


title: C0006LG

value: PBMC


title: FF-B

value: immortalized hematopoietic cell line


title: mRNA KS19_2

description:
blood sample- 30 days after taking Huaier
stage IIb, metastasis to lympy nodes


title: mRNA KS19_1

description:
blood sample-before taking Huaier
stage IIb, metastasis to lympy nodes


title: FF-A


title: FF-tam-C


title: ST_Caffeine_400_b1_p4_F05

description: ST pilot combined FINAL.csv


title: ST_Caffeine_10000_b1_p4_F04

description: ST pilot combined FINAL.csv


title: C0006LQ

value: Donor

value: National multicentric cohort


title: C0009K7

value: F


title: C0006KY


title: mRNA KS18_3

description:
blood sample- 90 days after taking Huaier
stage 0,with prostate hyperploasia

value: lung cancer suspected by CT


title: mRNA KS18_2

description:
blood sample- 30 days after taking Huaier
stage 0,with prostate hyperploasia


title: WT-tam-C

value: 4-OH-tamoxifen (1µM)

value: MLL-AF9 immortalized


title: WT-tam-B


title: mRNA KS18_1

description:
blood sample-before taking Huaier
stage 0,with prostate hyperploasia


title: C0006HI

value: Recipient

value: Local monocentric cohort


title: mRNA KS17_3

description:
blood sample- 90 days after taking Huaier
stage IV,with strong anemia

value: stomach cancer (adenocarcinoma)


title: WT-tam-A


title: ST_Doxorubicin_0.08_b1_p4_E11

description: ST pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes

value: S1500+ rat surrogate assay

value: Doxorubicin


title: ST_Caffeine_10000_b1_p4_F02

description: ST pilot combined FINAL.csv

value: Caffeine


title: WT-C

value: Ethanol


title: mRNA KS17_2

description:
blood sample- 30 days after taking Huaier
stage IV,with strong anemia


title: C0006H0

value: M

value: PBMC


title: ST_Doxorubicin_2_b1_p4_E10

description: ST pilot combined FINAL.csv


title: WT-B

value: immortalized hematopoietic cell line


title: mRNA KS17_1

description:
blood sample-before taking Huaier
stage IV,with strong anemia


title: C0006GP

value: F


title: ST_Doxorubicin_2_b1_p4_E08

description: ST pilot combined FINAL.csv


title: mRNA KS16_2

description:
blood sample- 30 days after taking Huaier
with liveer dysfunction

value: prostate cancer in situ(biopsy)


title: 423_Treated

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

library_source: genomic

data_processing:
100bp paired-end reads were sequenced on a Illumina HiSeq2500 Desktop Sequencer
QC-passed DNA reads of tumor and matched normal were aligned to mouse genome mm9 by bwa
Duplicates were removed and bam files were sorted and indexed by Picard
Somatic mutations of tumor samples were identified by Strelka and annotated using snpEff
Supplementary_files_format_and_content: vcf file contains variant calls for each sample
Genome_build: mm9

molecule: genomic DNA

source_name: bladder tumor

extract_protocol:
DNA was extracted by using DNeasy blood and tissue kit (Qiagen)
library preparation was performed using Agilent SureSelect XT Mouse all Exon kit

tag: tissue

value: bladder tumor

value: Entinostat


title: mRNA KS16_3

description:
blood sample- 90 days after taking Huaier
with liveer dysfunction


title: C0006G9

value: Recipient


title: C0006GT

value: Local monocentric cohort


title: C0006GU


title: ST_Caffeine_400_b1_p4_F03

description: ST pilot combined FINAL.csv


title: 421_Treated


title: ST_Diclofenac_400_b1_p4_E06

description: ST pilot combined FINAL.csv

value: Diclofenac


title: mRNA KS16_1

description:
blood sample-before taking Huaier
with liveer dysfunction


title: ST_Diclofenac_16_b1_p4_E05

description: ST pilot combined FINAL.csv

value: Wistar


title: mRNA KS15_3


title: 408_NonTreated

value: Vehicle


title: 413_Treated


title: 410_NonTreated


title: C0006GH


title: C0006HG


title: mRNA KS15_2


title: ST_Diclofenac_400_b1_p4_E04

description: ST pilot combined FINAL.csv

value: Male

value: hepatocytes


title: C0006GL


title: WT-A

tag: genotype

value: MLL-AF9 immortalized


title: 402_NonTreated


title: mRNA KS14_3

description:
blood sample- 90 days after taking Huaier
endoscopic polyp dissection after 90days of Huaier treatment

value: colorectal adenoma (benign)


title: C0006I3


title: C0006HF


title: mRNA KS14_2

description:
blood sample- 30 days after taking Huaier
endoscopic polyp dissection after 90days of Huaier treatment


title: ST_Doxorubicin_0.08_b1_p4_E09

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay

value: Doxorubicin


title: ST_Diclofenac_16_b1_p4_E07

description: ST pilot combined FINAL.csv


title: ST_Diclofenac_400_b1_p4_E02

description: ST pilot combined FINAL.csv


title: Diencephalon scRNA-seq

city: Neuherberg

first: Pawel

last: Smialowski

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
Raw reads were demultiplex using Je (version 2.0.2).
Raw reads were aligned to Ensembl GRCm38 mouse refernce genome using generanger
Supplementary_files_format_and_content: read counts

source_name: Diencephalon

extract_protocol: Single cell kit from 10X genomics

tag: mouse line

value: 3 months

value: Diencephalon

value: astrocyte

tag: isolation

value: MACS-sorted

tag: ephys property

value: firing


title: C0006FY

tag: individual

value: M

value: PBMC


title: ST_Simvastatin_2.4_b1_p4_D11

description: ST pilot combined FINAL.csv

value: Simvastatin


title: mRNA KS15_1

value: prostate cancer in situ(biopsy)


title: 12_w_DNA_RS3-oxBS: Articular cartilage right leg rep3 week 12

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

description: Oxidized and bisulfite converted

data_processing:
Library strategy: RRoxBS
Illumina’s CASAVA 2.17 software pipeline was used to perform image processing, base calling and demultiplexing of raw reads to produce FASTQ files.
FASTQ files passing Illumina's purity filter were adapter trimmed (using Flexbar) and trimmed reads were aligned to the mm10 build of the mouse genome.
RRoxBS quality filtered and trimmed reads were post-processed to produce methylation calls at base pair resolution using an in-house pipeline that features the Bismark aligner and methylation caller. CpG methylation calls for CpGs covered at least 10x were used for downstream analysis.
processed data files format and content: CpG methylation and coverage (text file)
Genome_build: mm10

source_name: Knee cartilage ( DMM, operated right leg )

extract_protocol:
DNA was isolated using the Gentra Puregene DNA isolation kit (Qiagen)
Briefly, 200 ng of genomic DNA were digested with MspI (New England Biolabs, Ipswich, MA), and cleaned up using QIAquick PCR purification columns (Hilden, Germany). Six uniquely indexed libraries were generated using the Ovation Ultralow Methyl-Seq DR Multiplex with TrueMethyl oxBS kit and workflow (Tecan, Redwood, CA). All six libraries were pooled together and divided into two parts, one part was subjected to oxidation and bisulfite conversion (oxBS), the other part was mock oxidized, and subjected to bisulfite conversion (BS). The library pool for BS was amplified for 7 cycles and oxBS for 9 cycles. After amplification library pools were subjected to sequencing.

value: cartilage: tibial and femoral plateaus

tag: harvest time point

value: 12 weeks, post DMM surgery


title: C0006GS

value: Recipient

tag: age

tag: couple number

value: F

value: Local monocentric cohort


title: mRNA KS1_3

value: lung cancer (small cell carciinoma)


title: mRNA KS14_1

description:
blood sample-before taking Huaier
endoscopic polyp dissection after 90days of Huaier treatment

value: colorectal adenoma (benign)


title: ST_Diclofenac_16_b1_p4_E03

description: ST pilot combined FINAL.csv

value: Wistar

tag: gender

value: Male

tag: cell type

value: hepatocytes

value: S1500+ rat surrogate assay

value: Diclofenac


title: ST_Simvastatin_2.4_b1_p4_D09

description: ST pilot combined FINAL.csv


title: mRNA KS13_2

tag: tumor origin


title: C0006E3

tag: cohort

tag: outcome related


title: 12_w_DNA_RS2-BS: Articular cartilage right leg rep2 week 12

description: Bisulfite converted

tag: strain


title: mRNA KS13_3


title: 12_w_DNA_RS2-oxBS: Articular cartilage right leg rep2 week 12

description: Oxidized and bisulfite converted


title: C0006GG


title: 12_w_DNA_RS3-BS: Articular cartilage right leg rep3 week 12

description: Bisulfite converted


title: ST_Valproic_400_b1_p4_D07

description: ST pilot combined FINAL.csv

tag: tempo-seq assay

tag: chemical

value: Valproic


title: C0006H3


title: ST_Simvastatin_60_b1_p4_D08

description: ST pilot combined FINAL.csv

tag: dose (um)


title: R1-BS: Articular cartilage right leg rep1 week 12

description: Bisulfite converted

tag: tissue


title: mRNA KS13_1


title: R1-oxBS: Articular cartilage right leg rep1 week 12

description: Oxidized and bisulfite converted


title: C0006ET


title: ST_Simvastatin_60_b1_p4_D10

description: ST pilot combined FINAL.csv


title: ST_Valproic_10000_b1_p4_D06

description: ST pilot combined FINAL.csv


title: mRNA KS1_2

description:
blood sample- 30 days after taking Huaier
stage IV, multiple metastasis


title: 12wDNA_LC3-oxBS: Articular cartilage left leg rep3 week 12

description: Oxidized and bisulfite converted

source_name: Knee cartilage ( control non operated left leg )


title: C0006EP

value: M


title: ST_Valproic_400_b1_p4_D05

description: ST pilot combined FINAL.csv


title: mRNA KS12_3

description:
blood sample- 90 days after taking Huaier
stage IV, multiple metastasis

value: lung cancer (adenocarciinoma)


title: C0006HM

value: PBMC


title: 12wDNA_LC3-BS: Articular cartilage left leg rep3 week 12

description: Bisulfite converted


title: ST_Valproic_10000_b1_p4_D04

description: ST pilot combined FINAL.csv


title: C0006FO


title: mRNA KS12_2


title: mRNA KS12_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis


title: ST_Valproic_400_b1_p4_D03

description: ST pilot combined FINAL.csv


title: C0006GK


title: ST_Valproic_10000_b1_p4_D02

description: ST pilot combined FINAL.csv


title: mRNA KS1_1


title: mRNA KS11_3

description:
blood sample- 90 days after taking Huaier
surgical dissection before taking Huaier

value: oesophageal adenocarcinoma


title: L2-BS: Articular cartilage left leg rep2 week 12

description: Bisulfite converted

value: cartilage: tibial and femoral plateaus


title: 12wDNA_LC1-oxBS: Articular cartilage left leg rep1 week 12

description: Oxidized and bisulfite converted

value: 12 weeks, post DMM surgery


title: ST_Simvastatin_2.4_b1_p4_C11

description: ST pilot combined FINAL.csv

value: Simvastatin


title: C0006GJ

value: Recipient

value: F


title: ST_Simvastatin_60_b1_p4_C10

description: ST pilot combined FINAL.csv


title: 12wDNA_LC1-BS: Articular cartilage left leg rep1 week 12

description: Bisulfite converted


title: C0006GB

value: Local monocentric cohort


title: mRNA KS11_2

description:
blood sample- 30 days after taking Huaier
surgical dissection before taking Huaier


title: DNA_4RS3-OX: Articular cartilage right leg rep3 week 4

description: Oxidized and bisulfite converted

value: 4 weeks, post DMM surgery


title: ST_Naproxen_2000_b1_p4_C08

description: ST pilot combined FINAL.csv

value: Wistar

value: Naproxen


title: mRNA KS11_1

description:
blood sample-before taking Huaier
surgical dissection before taking Huaier


title: DNA_4RS3-BS: Articular cartilage right leg rep3 week 4

description: Bisulfite converted


title: ST_Naproxen_80_b1_p4_C09

description: ST pilot combined FINAL.csv

value: Male

value: hepatocytes


title: DNA_4RS2-OX: Articular cartilage right leg rep2 week 4

description: Oxidized and bisulfite converted


title: mRNA KS10_6

description:
blood sample- 18 months after taking Huaier
surgical dissection at 6 weeks after taking Huaier

value: meningioma (benign)


title: ST_Isoniazid_400_b1_p4_C07

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay

value: Isoniazid


title: mRNA KS10_5

description:
blood sample- 14 months after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: C0006FZ

value: M


title: C0006GQ

value: PBMC


title: C0006HL


title: DNA_4RS2-BS: Articular cartilage right leg rep2 week 4

description: Bisulfite converted


title: C0006HK

value: Donor


title: mRNA KS10_3

description:
blood sample- 90 days after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: ST_Isoniazid_400_b1_p4_C05

description: ST pilot combined FINAL.csv


title: L2-oxBS: Articular cartilage left leg rep2 week 12

description: Oxidized and bisulfite converted

value: cartilage: tibial and femoral plateaus


title: mRNA KS10_4

description:
blood sample- 9 months after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: ST_Isoniazid_10000_b1_p4_C04

description: ST pilot combined FINAL.csv


title: ST_Isoniazid_10000_b1_p4_C06

description: ST pilot combined FINAL.csv


title: ST_Isoniazid_400_b1_p4_C03

description: ST pilot combined FINAL.csv


title: mRNA KS10_1

description:
blood sample-before taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: DNA_4LC3-OX: Articular cartilage left leg rep3 week 4

description: Oxidized and bisulfite converted


title: DNA_4LC3-BS: Articular cartilage left leg rep3 week 4

description: Bisulfite converted


title: small RNA KS9_3

description:
blood sample- 90 days after taking Huaier
stage I,  metastasis to hypopharynx

value: oesophageal squemous cell cancer


title: ST_Naproxen_80_b1_p4_B11

description: ST pilot combined FINAL.csv


title: C0006HS


title: C0006G5


title: DNA_4RS1-OX: Articular cartilage right leg rep1 week 4

description: Oxidized and bisulfite converted


title: DNA_4LC2-BS: Articular cartilage left leg rep2 week 4

description: Bisulfite converted


title: C0009LG


title: DNA_4LC2-OX: Articular cartilage left leg rep2 week 4

description: Oxidized and bisulfite converted


title: C0006GW


title: small RNA KS9_1

description:
blood sample-before taking Huaier
stage I,  metastasis to hypopharynx


title: ST_Naproxen_80_b1_p4_B09

description: ST pilot combined FINAL.csv


title: mRNA KS10_2

description:
blood sample- 30 days after taking Huaier
surgical dissection at 6 weeks after taking Huaier


title: DNA_4RS1-BS: Articular cartilage right leg rep1 week 4

description: Bisulfite converted


title: C0006HR


title: small RNA KS8_6

description:
blood sample- 14 months after taking Huaier
stage I,pancreas metastasis suspected

value: hepatoma


title: ST_Isoniazid_10000_b1_p4_C02

description: ST pilot combined FINAL.csv


title: small RNA KS8_5

description:
blood sample- 9 months after taking Huaier
stage I,pancreas metastasis suspected


title: C0006HN


title: DNA_4LC1-BS: Articular cartilage left leg rep1 week 4

description: Bisulfite converted


title: T3

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to the Solanum lycopersicum transcriptome with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0
Supplementary_files_format_and_content: Abiotic_ITAG4.0.counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Solanum lycopersicum

source_name: Leaf tissue

extract_protocol:
Total RNA was extracted from 1g of tomato frozen leaves using TRI-Reagent (Sigma-Aldrich) and following manufacturer's instruction.
For each RNA sample, mRNA was enriched using Dynabeads mRNA purification kit (Invitrogen) and then samples were sent to BGI-Shenzhen for RNA sequencing. Sequencing was carried out on HiSeq2000 according to the Illumina protocols for 90 × 2 pair-end sequencing covering a read length of 100 bp.

tag: treatment

value: Heat

value: Leaf tissue


title: C0006GX

city: Paris

first: David

last: Michonneau

institute: Assistance Publique des Hôpitaux de Paris

data_processing:
Fastq files produced after RNA-seq sequencing have been processed by in-house CNRGH (Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France ) tools in order to assess quality of raw and genomic-aligned nucleotides
Quality control was performed on a random selection of 2 x 10 million reads, including the following steps: removal of adapters and poor-quality sequences to evaluate the % of usable reads (use of trimmomatic); alignment on the reference genome (Hisat2) as well as on the transcriptome and rRNAs (Bowtie2)
Use of rseqc and picardTools to evaluate the % of mapping on the genome and transcriptome, the % of duplicate sequences, the % of rRNA and the total number of usable sequences
Fastq files were aligned against the human GRCh38 genome assembly using STAR-2.6.0 according to author’s procedure (Dobin et al. 2016)
Genome_build: human GRCh38 genome assembly
Supplementary_files_format_and_content: table count

extract_protocol:
Promega Maxwell® technology (simply RNA tissue kit, AS1340)
Libraries have been prepared using the "TruSeq Stranded Total RNA Gold” Kit from Illumina

value: F

value: Local monocentric cohort


title: small RNA KS8_4

description:
blood sample- 6 months after taking Huaier
stage I,pancreas metastasis suspected


title: T2


title: C0006HJ


title: small RNA KS8_3

description:
blood sample- 90 days after taking Huaier
stage I,pancreas metastasis suspected


title: R2: Articular cartilage right leg rep2 week 12

description: counts

data_processing:
Illumina’s CASAVA 2.17 software pipeline was used to perform image processing, base calling and demultiplexing of raw reads to produce FASTQ files.
FASTQ files passing Illumina's purity filter were adapter trimmed (using Flexbar) and trimmed reads were aligned to the mm10 build of the mouse genome.
RNA-Seq quality filtered and trimmed reads were aligned using STAR aligner with default parameters. Read counts for RefSeq (NCBI) transcripts were then quantified from the alignments using the featureCounts software package.
processed data files format and content: raw gene counts (text file)
Genome_build: mm10

extract_protocol:
Total RNA was isolated using TRIzol followed by RNeasy mini RNA isolation kit (Qiagen) and DNase (Qiagen) treatment.
RNA-Seq library preparations were done using established Illumina methods for mRNA-Seq (Part #RS-122-2001). Briefly, poly A+ RNA was purified from 100 ng of total RNA with oligo-dT beads and fragmented with divalent cations at elevated temperature. First strand cDNA synthesis was performed with random hexamer priming and SuperScript II Reverse transcriptase (Invitrogen, part # 18064-014). Second strand cDNA synthesis was performed using RNAseH and DNA PolI. Following dscDNA synthesis, the double stranded products are end repaired, followed by addition of a single ‘A’ base and then ligation of the Illumina TruSeq adaptors. The resulting product was amplified with 15 cycles of PCR. Each library was made with a unique Index sequence and libraries are pooled for sequencing.

value: 12 weeks, post DMM surgery


title: C0006GF


title: DNA_4LC1-OX: Articular cartilage left leg rep1 week 4

description: Oxidized and bisulfite converted

value: 4 weeks, post DMM surgery


title: R1: Articular cartilage right leg rep1 week 12

description: counts


title: C0006GR

value: Recipient


title: ST3

value: Salinity + heat


title: C0006I2


title: small RNA KS8_2

description:
blood sample- 30 days after taking Huaier
stage I,pancreas metastasis suspected


title: ST_Naproxen_2000_b1_p4_B10

city: Singapore

first: Fan

last: Lee

institute: Institute of Bioengineerng and Nanotechnology

description: ST pilot combined FINAL.csv

data_processing:
Data processing was performed by BioSpyder Technologies Inc.
Illumina Casava1.7 software used for base-calling
No filtering was done since aligning to known sequence
Reads were aligned using the STAR aligner 2.5.3a allowing 2 bp mismatches and not allowing indels. The softclipping option is turned on.
The Tempo-SeqR package was used to generate read counts matrix
Genome_build: rn6
Supplementary_files_format_and_content: Read counts matrix (row = treatment; column = gene)

extract_protocol:
After 24 h of chemical treatment, the spent medium was removed and the wells were washed with 100 µL of PBS twice. Cells were lysed by adding 20 µL of 1X TempO-Seq lysis buffer (BioSpyder) in PBS. The cell lysates were shipped frozen on dry ice to to BioSpyder Technologies, Inc. (Carlsbad, CA, USA), where libraries were prepared directly from the cell lysates and RNA-seq was performed.
2 μL of sample lysate was hybridized with detector oligos from the TempO-Seq rat surrogate (ST) or whole-transcriptome (WT) assay, with 1 h hybridization period for the ST assay and overnight for the WT assay. After ligation and nuclease digestion, the ligated products were added into an amplification mix with sample-specific PCR primer pairs which include the standard Illumina adaptor and a sample-specific barcode sequence. Amplicons were pooled and purified using a PCR clean-up kit (Macherey-Nagel, Mountain View, CA, United States).

value: Wistar

value: Male

value: hepatocytes

value: Naproxen


title: L3: Articular cartilage left leg rep3 week 12

description: counts


title: C0006I5

value: PBMC


title: T1


title: small RNA KS8_1

description:
blood sample-before taking Huaier
stage I,pancreas metastasis suspected


title: ST2


title: R3: Articular cartilage right leg rep3 week 12

description: counts


title: L2: Articular cartilage left leg rep2 week 12

description: counts


title: small RNA KS7_2

description:
blood sample- 30 days after taking Huaier
stage IV, multiple metastasis

value: colorectal cancer (adenocarcinoma)


title: C0006I4

value: Donor


title: S3

value: Salinity


title: small RNA KS7_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis


title: C0006G6

value: M


title: L1: Articular cartilage left leg rep1 week 12

description: counts

value: cartilage: tibial and femoral plateaus


title: 4RS3: Articular cartilage right leg rep3 week 4

description: counts


title: small RNA KS6_2

value: stomach cancer (signet ring cell carci.)


title: small RNA KS9_2

description:
blood sample- 30 days after taking Huaier
stage I,  metastasis to hypopharynx

value: oesophageal squemous cell cancer


title: S2

value: Leaf tissue


title: 4RS2: Articular cartilage right leg rep2 week 4

description: counts


title: C0006HQ

value: F

value: Local monocentric cohort


title: small RNA KS6_1


title: C0006EQ


title: S1


title: C0006I8


title: ST1


title: small RNA KS5_6

description:
blood sample- 18 months after taking Huaier
stage IV, metastasis to lboth ungs


title: C0006HX


title: 4LC3: Articular cartilage left leg rep3 week 4

description: counts

value: 4 weeks, post DMM surgery


title: 4RS1: Articular cartilage right leg rep1 week 4

description: counts


title: C3

value: Control


title: small RNA KS5_4

description:
blood sample- 11 months after taking Huaier
stage IV, metastasis to lboth ungs


title: small RNA KS5_5

description:
blood sample- 14 months after taking Huaier
stage IV, metastasis to lboth ungs


title: 4LC2: Articular cartilage left leg rep2 week 4

description: counts


title: C2


title: C0006GO


title: C0006GN


title: small RNA KS5_2

description:
blood sample- 30 days after taking Huaier
stage IV, metastasis to lboth ungs


title: small RNA KS5_3

description:
blood sample- 90 days after taking Huaier
stage IV, metastasis to lboth ungs


title: 4LC1: Articular cartilage left leg rep1 week 4

description: counts


title: C0006HW


title: small RNA KS5_1

description:
blood sample-before taking Huaier
stage IIb, metastasis to both lungs


title: C0006I6


title: sample15

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

data_processing:
Raw sequence reads were aligned to the human reference hg19 using Tophat2 (version 2.0.10).
We prepared a GTF file containing coding genes from RefSeq as well as lncRNAs from LNCipedia database (version 3.1 high confidence set).
The mapped reads were counted against the GTF file using HTSeq (version 0.6.1p1).
The differential analysis was performed using the R library DESeq2 to assess the significance of gene expression changes.
Genome_build: hg19

source_name: DLBCL tissue

extract_protocol:
We removed rRNA from extracted total RNA using a Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA).
We performed library preparation using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s instructions.

tag: prognosis

value: GOOD

tag: cell-of-origin (hans)

value: GC

value: Diffuse large B-cell lymphoma (DLBCL)


title: Adrenal gland, P12 weeks male

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

institute: IPMC

data_processing:
HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA-1.8.2
fastq groomer, Galaxy version 1.1.5; Bowtie2, Galaxy version 2.3.4.3
MACS2, Galaxy version 2.1.1, broad region on and minimum FDR (q-value) cutoff for peak detection = 0.05
Genome_build: mm10
Supplementary_files_format_and_content: peak .bed files were generated using MACS2
Supplementary_files_format_and_content: bigWig files were generated from Bowtie2 .bam alignment files using bamCoverage 3.2.2.0 in Galaxy deepTools

source_name: Adrenal gland

extract_protocol:
Tissues were fixed with 1% formaldehyde, lysed and sonicated. After crosslink reversal, histone-DNA complexes were immunoprecipitated with H3K27ac antibody (Abcam #4729)
Libraries were prepared from immunoprecipitated DNA using the Illumina TruSeq ChIP kit

tag: developmental stage

value: postnatal P12 weeks

tag: Sex

value: male

value: Adrenal gland

tag: chip antibody

value: H3K27ac antibody (Abcam #4729)


title: sample11

value: non-GC


title: sample14


title: small RNA KS4_3

description:
blood sample- 90 days after taking Huaier
stage IIb, metastasis to liver

source_name: blood

value: cholangiocarcinoma


title: Adrenal gland, P2 weeks male

value: postnatal P2 weeks


title: C0006HU

address: 1 avenue Claude Vellefaux

tag: individual

value: Donor

tag: age

tag: couple number

value: M

value: PBMC


title: Adrenal gland, P12 weeks female

value: female


title: sample9

value: BAD


title: C1

value: Leaf tissue


title: C0006I9

tag: gender

tag: cell type

value: Local monocentric cohort


title: C0006GV

tag: cohort

tag: outcome related


title: small RNA KS4_1

description:
blood sample-before taking Huaier
stage IIb, metastasis to liver

tag: tumor origin


title: small RNA KS4_2

description:
blood sample- 30 days after taking Huaier
stage IIb, metastasis to liver


title: C0009L3

value: F


title: ST_Naproxen_2000_b1_p4_B08

address: 31 Biopolis Way, The NANOS, #06-01

description: ST pilot combined FINAL.csv

tag: strain

value: Wistar

value: Male

value: hepatocytes

tag: tempo-seq assay

value: S1500+ rat surrogate assay

tag: chemical

value: Naproxen


title: sample8

tag: tissue

value: Diffuse large B-cell lymphoma (DLBCL)


title: sample10

tag: prognosis

value: non-GC


title: Adrenal gland, P1 male

value: postnatal P1

value: male

value: Adrenal gland

value: H3K27ac antibody (Abcam #4729)


title: C0006HT

value: Donor

value: M

value: PBMC


title: Adrenal gland, P1 female

value: female


title: C0006G3

value: Local monocentric cohort


title: Adrenal gland, input DNA

value: postnatal P12 weeks


title: sample7

value: BAD

tag: cell-of-origin (hans)

value: GC


title: P12 weeks male

data_processing:
HiSeq Control Software 2.2.58; RTA 1.18.64.0; CASAVA-1.8.2
fastq groomer, Galaxy version 1.1.5; HISAT2, Galaxy version 2.1.0, paired-end --fr
ht-seq count, Galaxy version 0.9.1 on mm10.NCBI RefSeq; DESeq2, Galaxy version 2.11.40.6
Genome_build: mm10
Supplementary_files_format_and_content: .csv file, normalized count file from DESeq2

extract_protocol:
guanidinium thiocyanate method for RNA extraction (Chomczynski & Sacchi, 1987)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage


title: small RNA KS3_3

description:
blood sample- 90 days after taking Huaier
stage IV, peritoneal metastasis

value: pancreas cancer


title: Adrenal gland, E18.5

value: embryo (E18.5)

tag: Sex

value: not determined


title: Adrenal gland, P2 weeks female

value: postnatal P2 weeks

tag: chip antibody


title: small RNA KS3_2

description:
blood sample- 30 days after taking Huaier
stage IV, peritoneal metastasis


title: sample3

value: GOOD

value: Diffuse large B-cell lymphoma (DLBCL)


title: C0009LK

tag: individual


title: sample6

value: non-GC


title: C0009LL

value: Recipient

tag: age


title: C0006G4

tag: couple number


title: small RNA KS3_1

description:
blood sample-before taking Huaier
stage IV, peritoneal metastasis


title: small RNA KS30_1


title: sample5


title: P12 weeks female

value: Adrenal gland


title: small RNA KS31_2


title: P1 female

value: postnatal P1


title: MS24


title: small RNA KS29_3

value: oesophageal squemous cell cancer


title: sample2


title: small RNA KS31_1


title: P2 weeks female


title: small RNA KS30_2


title: C0009LI

value: Donor

tag: gender

value: F

value: PBMC


title: C0009LJ

value: M

tag: cell type

value: Local monocentric cohort


title: sample1


title: P2 weeks male

value: male


title: C0006H4

tag: cohort


title: C0006FD

tag: outcome related


title: small RNA KS28_2

description:
blood sample- 30 days after taking Huaier
stage II, multiple cancer suspected

tag: tumor origin


title: MS23


title: P1 male

tag: strain


title: MS18

value: BAD

value: GC


title: small RNA KS29_2


title: C0006H6


title: MS21


title: C0009LH


title: E18.5

value: embryo (E18.5)

value: not determined


title: small RNA KS29_1

description:
blood sample-before taking Huaier
stage IV, metastasis to both lungs


title: control_6

city: Columbus

first: Pearlly

last: Yan

department: Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts
Genome_build: mm10
Supplementary_files_format_and_content: A single TSV file of measured gene expression counts from featureCounts, normalized by DESeq2.

source_name: Control scramble sample

growth_protocol: Live leukemic splenocytes (10 million CD19+CD5+hROR1+ cells) from diseased hROR1xTCL1 mice were collected and serially engrafted into 6-8-week-old C57BL/6 wild type (wt) recipient mice via tail vein.

extract_protocol:
Total RNA was extracted by using Trizol (Thermofisher Scientific, Waltham, MA) and the quality was confirmed by measuring OD260/280 with nanodrop 2000 (Thermofisher Scientific).
RNA-seq libraries were generated using TruSeq stranded mRNA kit (Illumina, San Diego, CA) according to the manufacturer's instructions. Sequencing was performed with the Illumina HiSeq 2500 system using HiSeq version 3 sequencing reagents. Each sample was sequenced to at least a depth of 40 million passed filter paired-end 50 bp, strand-specific reads.

treatment_protocol: Upon achieving the peripheral CD19+CD5+hROR1+ leukemic population to 5% of total white blood cells (WBC), mice were treated with 2A2-miR-29b-ILP, or 2A2-scramble-ILP (1.5 mg/kg/d three times/week).

value: Engraphed murine leukemia

value: splenic CD19+ B lymphocytes


title: control_8


title: small RNA KS27_3

description:
blood sample- 90 days after taking Huaier
stage I, dessected before taking Huaier

value: prostate cancer


title: MS20

value: non-GC

value: Diffuse large B-cell lymphoma (DLBCL)


title: MS19


title: XCS-7 leaf late stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

organism: Triticum aestivum

source_name: leaf late stageEmbryo

value: Embryo

tag: Stage

value: leaf late stage

tag: ecotype

value: Chinese Spring


title: small RNA KS28_1

description:
blood sample-before taking Huaier
stage II, multiple cancer suspected

value: oesophageal squemous cell cancer


title: A2_29b_3

source_name: mir29b ILP sample

tag: tissue


title: MS1

tag: prognosis

value: GOOD


title: XCS-8 leaf late stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx


title: RNA_U2392_wt_rep6

city: Cambridge

first: Daniel

middle: J

last: Hodson

address: The Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus

department: Department of Haematology

institute: Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge

description: counts.txt

data_processing:
Trimming: cutadapt 1.10, parameters: --quality-base=33 -e 0.1 -m 10 -q 20,20 -u 1 A47
Alignment: STAR 2.6.0c, parametres: --twopassMode Basic
Counting: Rsubread 1.28.1 (featureCounts function), Parameters: annot.ext = gencode.v29.annotation.gtf, countMultimapping=F, strandSpecific = 0, allowMultiOverlap = T, minOverlap = 25, GTF.featureType = "exon", GTF.attrType = "gene_id
Genome_build: GRCh 38
Supplementary_files_format_and_content: counts.txt contains read counts per gene obtained using featureCounts function from Rsubread package

source_name: U2392 cell line

growth_protocol: Lymphoma cell lines were cultured in RPMI medium (Gibco) supplemented with 10% testified tetracycline-free FBS (Gibco). All cell lines used in this study were confirmed to be free from mycoplasma contamination and identity was verified using a 16-amplicon multiplexed copy number variant fingerprinting assay(Phelan et al., 2018). All cells were cultured at 370C and 5% CO2.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA extraction kit (Machery-Nagel, Cat No. 740955.250) according to manufacturer’s protocol.
500ng of total RNA was used for preparing RNA-seq libraries using NEBNext Poly(A) mRNA magnetic isolation module (Cat No. NEB E7490) following manufacturer’s instruction. Final libraries were amplified by PCR for 12 cycles, purified with AMPure XP beads and analysed by Bioanalyser before sending out for high throughput sequencing on Illumina Hi-seq4000.

treatment_protocol: sgRNAs were cloned into pSpCas9(BB)-2A-GFP (PX458, Addgene, RRID: Addgene_48138) and the plasmid was electroporated into the cells together with annealed double strand template using Amaxa nucleofector. In addition to the mutation (R475C) to be introduced (wildtype sequence was used as control), the templates also carry silent mutation to PAM site as well as silent mutation for introducing SpeI restriction enzyme digestion site for screening positive cells. Two days after electroporation, GFP positive cells were sorted out by flow cytometer and genomic DNA was extracted and the modified segment of DDX3X was amplified followed by SpeI digestion to detect the incorporation of the templates. The cells were then single cell cloned into 96 well plates and expanded. Colonies were screened using SpeI digestion and the colonies that can be completely digested by the enzyme were sent for Sanger sequencing for confirmation. The entire DDX3X transcript in the positive clones were also amplified and sequenced to confirm that it only has the nucleotide modification at the designated positions.

tag: cell line

tag: condition

value: DDX3X wild-type


title: small RNA KS27_1

description:
blood sample-before taking Huaier
stage I, dessected before taking Huaier


title: small RNA KS28_3

description:
blood sample- 90 days after taking Huaier
stage II, multiple cancer suspected


title: RNA_U2392_R475C_rep3

description: counts.txt

value: DDX3X R475C


title: RNA_U2392_R475C_rep2

description: counts.txt


title: small RNA KS27_2

description:
blood sample- 30 days after taking Huaier
stage I, dessected before taking Huaier


title: XCS-5 leaf middle stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to the IWGSC RefSeq v2.0 assembly wheat genome using STAR.
Read counting was carried out with FeatureCounts.
Genome_build: IWGSC RefSeq v2.0 assembly wheat genome
Supplementary_files_format_and_content: Matrix table files include raw counts for each sample

source_name: leaf middle stageEmbryo

extract_protocol:
Embryo, endosperm and pericarp tissue isolation procedure were precisely performed as described in Xiang et al., 2019.
For RNA-seq profile analysis, Illumina mRNA-seq libraries were constructed using the TruSeq RNA kit (version 1, rev A).

value: leaf middle stage


title: control_5


title: control_2


title: small RNA KS26_1

description:
blood sample-before taking Huaier
prostate hyperplasia

data_processing:
RNA: Alignment:Hisat2 and Bowtie2
RNA: Expression of genes by RSEM
Call DEGs by PossionDis method
Predicted novel transcripts by StringTie and call SNP by GATK
hg38
Genome_build: TXT, FA

extract_protocol:
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA).

value: healthy control (Japanese male)


title: XCS-3 leaf early stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

source_name: leaf early stageEmbryo

value: leaf early stage


title: RNA_U2392_R475C_rep4

description: counts.txt


title: control_4


title: control_7


title: RNA_U2392_R475C_rep1

description: counts.txt


title: XCS-6 leaf middle stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx


title: RNA_U2392_wt_rep5

description: counts.txt


title: A2_29b_2


title: control_1


title: small RNA KS26_3

description:
blood sample- 90 days after taking Huaier
prostate hyperplasia


title: small RNA KS26_2

description:
blood sample- 30 days after taking Huaier
prostate hyperplasia


title: XCS-1 transition stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx

source_name: transition stageEmbryo

value: transition stage


title: MSC-Exo-2

city: Nanjing

first: Biao

last: Xu

state: Jiangsu

address: No. 321 Zhongshan Road

department: Department of Cardiology

institute: Drum Tower Hospital, Medical School of Nanjing University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from  Mus_musculus.GRCm38.89. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
Genome_build: Mus_musculus.GRCm38.89

source_name: mesenchymal stromal cell-derived exosomes

growth_protocol: Mouse bone marrow-derived MSCs are generally isolated from the tibia and femoral marrow compartments and identified by flow cytometry. MSC were cultured (typically 2–3 × 106 cells into a T75 flask) in MSC culture medium (science cell, 7501) supplemented with 5% of fetal bovine serum, 1% mesenchymal stem cell growth supplement ( science cell, 7552) and 1% Penicillin/Streptomycin. The cultures were maintained at 37 °C in 5 % CO2 and 95 % humidity. MSCs between passages 3 and 6 were used for exsomes isolation.

extract_protocol:
When MSCs reached 70% to 80% confluency, culture medium was replaced with that containing 5% of exosome-depleted FBS (System Biosciences Inc.) and incubated for 48h. Supernatants from cultured MSCs were centrifuged at 3,000g for 25 min and then 10,000g for 1h at 4°C to remove cellular debris and shedding vesicles, Subsequently, supernatants were filtered through 0.22μm membrane filters (Millipore) and then centrifuged at 100,000g for 3 h at 4 °C. The exosomes were then resuspended in PBS and then stored at -80°C.  RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（ #E7530L， NEB） was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina

value: bone-marrow derived mesenchymal stromal cells

tag: passages


title: control_3

value: Engraphed murine leukemia


title: small RNA KS25_1

description:
blood sample-before taking Huaier
healrthy control with Huaier uptake


title: A2_29b_1

value: splenic CD19+ B lymphocytes


title: RNA_U2392_wt_rep4

description: counts.txt


title: MSC-Exo-1

value: mesenchymal stromal cell-derived exosomes


title: XCS-4 leaf early stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx


title: RNA_U2392_wt_rep3

description: counts.txt


title: XCS-14 leaf early stagePericarp replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf early stagePericarp

value: Pericarp


title: small RNA KS24_2

description:
blood sample- 30 days after taking Huaier
stage IV, multiple metastasis

value: cholangiocarcinoma


title: small RNA KS25_3

description:
blood sample- 90 days after taking Huaier
healrthy control with Huaier uptake


title: L2_reference_3

city: Nashville

first: Sierra

middle: D

last: Palumbos

address: 2201 West End Ave, Nashville

department: Cell and Developmental Biology

institute: Vanderbilt University

description: 2983-DMM-27_1_sequence (paired) (GE).clc

data_processing:
Reads were mapped and analyzed using CLC Genomics Workbench Version 21. Mapping done with CLC Genomics Workbench reference genome for C. elegans
The Differential Gene Expression tool was used to analyze differential expression between WT VA and L2 reference groups and WT vs. unc-4 VA groups.
Each gene is modeled by a separate Generalized Linear Model (see CLC Genomics Workbench Vesion 21 description).
A Principle Component Analysis was performed on all datasets to verify quality of RNA seq data and to determine variability between groups.
Genome_build: C. elegans WBcel235 reference genome
Supplementary_files_format_and_content: excel file includes TPM for VA enriched genes and unc-4 regulated genes

organism: Caenorhabditis elegans

source_name: Whole L2 worm reference

growth_protocol: L2 larva were synchronized by hypochlorite treatment of adult hermaphrodites were allowed to hatch overnight in M9

extract_protocol:
Dissociated larval cells were generated as described (Spencer et al., PLoS ONE, 2014) cDNA synthesis was prepared using Clonetech Smart-Seq V3 Ultra Low Input RNA Kit
RNA libraries were prepared for sequencing using standard Illumina HiSeq 2500

treatment_protocol: A transectional labeling strategy was used to isolate VAs. VA and AVF neurons were captured by red only expression (pUnc-4::mCherry, pUnc-4C::GFP). VA neurons were isolated by FACS and collected in Trizol

value: L2 synchronized animals

tag: cell isolation strategy

value: All cells, frozen over LN2


title: XCS-2 transition stageEmbryo replicate-2

city: Saskatoon

first: Peng

last: Gao

institute: Agriculture and Agri-Food Canada

description:
replicate-2
Rawcount.xlsx

value: Embryo

value: Chinese Spring


title: RNA_U2392_wt_rep2

description: counts.txt


title: small RNA KS25_2

city: Kanagawa

first: Manami

last: Tanaka

institute: Bradeion Institute of Medical Sciences

description:
blood sample- 30 days after taking Huaier
healrthy control with Huaier uptake


title: VA_unc4_L2_3

description: 2983-DMM-66_1_sequence (paired) (GE).clc

source_name: Isolated L2 unc-4 VA neurons

value: pUnc-4::mCherry; pUnc-4C::GFP

value: FACS sorting to isolate VA


title: RNA_U2392_wt_rep1

description: counts.txt

value: DDX3X wild-type


title: L2_reference_4

description: 2983-DMM-28_1_sequence (paired) (GE).clc


title: XCS-13 leaf early stagePericarp replicate-1

description:
replicate-1
Rawcount.xlsx


title: small RNA KS24_1

description:
blood sample-before taking Huaier
stage IV, multiple metastasis


title: VA_unc4_L2_1

description: 2983-DMM-64_1_sequence (paired) (GE).clc


title: L2_reference_2

description: 2983-DMM-26_1_sequence (paired) (GE).clc


title: XCS-12 leaf late stageEndosperm replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: leaf late stageEndosperm

value: Endosperm

value: leaf late stage


title: VA_WT_L2_2

description: 2983-DMM-34_1_sequence (paired) (GE).clc

source_name: Isolated L2 wild type VA neurons


title: small RNA KS22_3

description:
blood sample- 90 days after taking Huaier
stage IV, multiple metastasis

value: breast cancer


title: XCS-11 leaf late stageEndosperm replicate-1

description:
replicate-1
Rawcount.xlsx


title: small RNA KS22_1


title: VA_unc4_L2_2

description: 2983-DMM-65_1_sequence (paired) (GE).clc


title: small RNA KS22_2


title: CSW7 mature stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: mature stageEmbryo

value: mature stage


title: VA_WT_L2_3

description: 2983-DMM-67_1_sequence (paired) (GE).clc


title: small RNA KS21_3

value: healthy control (Japanese male)


title: CSW8 transition stageEndosperm replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: transition stageEndosperm

value: transition stage


title: CSW2 preembryo stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: preembryo stageEmbryo

value: preembryo stage


title: Nepodin_DAY185

city: Gyeongsan-Si

first: Jintae

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Candida_albicans_SC5314 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: Candida_albicans_SC5314 (NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Candida albicans

source_name: Whole cell_with_nepodin

growth_protocol: 25 ml of C. albicans DAY185 at an initial turbidity of 0.1 at OD600 was inoculated into PDB broth in 250 ml Erlenmeyer flasks and incubated for 4 h at 37ºC with agitation (250 rpm)

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

treatment_protocol: Cells were incubated for 4 h at 37ºC with agitation (250 rpm) in the presence or absence of Nepodin (10 µg/ml)


title: CSW12 preembryo stageEmbryo replicate-1

description:
replicate-1
Rawcount.xlsx


title: small RNA KS21_1

source_name: blood


title: CSW1 two cell stageEmbryo replicate-2

description:
replicate-2
Rawcount.xlsx

source_name: two cell stageEmbryo

value: two cell stage