title: T47D_MC_2

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Trimmed using Trim_Galore (v 0.5.0) https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/  Aligned using STAR (v 2.6.0) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

growth_protocol: We grew cells for 24 hours in 10cm polystyrene, cell culture-treated dishes in full medium (DMEM (#11995, Gibco, Thermo Fisher, Grand Island, NY, USA) with 10% FBS (HyClone, ThermoScientific, Waltham, MA, USA), 1% GlutaMAX (#35050, Gibco), and 1% Penicillin-Streptomycin (P/S, #15140, Gibco)). We seeded cells either by themselves (monoculture) or in co-culture at a ratio of 10% cancer cells with 90% MSCs. After 24 hours, we changed medium to low glucose, phenol-red free DMEM (LG/LF, #11054, Gibco) with 1% FBS, 1% GlutaMAX, 1% P/S, and 10 nM β-Estradiol (#E2758, Sigma-Aldrich, Millipore Sigma, Saint Louis, MO, USA). We waited 48 hours after changing media to harvest cells

extract_protocol:
To separate cancer cells from stromal cells in co-culture conditions, we used human CD326 (EpCAM) Microbeads (#130-061-101, Miltenyi, Auburn, California, USA) and LS columns (#130-042-401, Miltenyi) and followed the manufacturer’s recommendations for separation.  We extracted RNA using the RNeasy Mini Kit following manufacturer’s instructions (#74104, Qiagen, Hilden, Germany)
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Mono culture and coculture

value: breast cancer cells

tag: sample group


title: monocyte-derived Langerhans cells, P(I:C)+CL075+AEA treated, D4

status: Public on Jun 21 2024

type: SRA

city: Debrecen

first: Attila

middle: Gábor

last: Szöllősi

address: Egyetem tér 1.

department: Department of Immunology

country: Hungary

institute: University of Debrecen

library_source: transcriptomic

data_processing:
HISAT2 algorithm was used for alignment of raw sequencing reads to human reference genome version GRCh38.
Aligned data were normalized by using limma-voom algorithm, then differentially expressed genes were determined by moderated T-test. P value < 0.05 was considered to significant change.
Assembly: GRCH38 human reference genome
Supplementary files format and content: Tab-delimited text files for each sample containing gene IDs and read counts.

molecule: total RNA

organism: Homo sapiens

source_name: monocyte-derived Langerhans cell

growth_protocol: CD14+ monocytes were  cultured in RPMI 1640 medium containing 10% heat-inactivated FBS, 10% HEPES, 50 mM 2-mercaptoethanol, 1% penicillin. The cells were seeded in 12-well tissue-culture plates (1 000 000 per well) containing  media supplemented with GM-CSF (200 ng/mL), TGF-β1 (10 ng/mL), TNF-α (20 ng/mL), and IL-4 (20 ng/mL for the first 48 hrs) for 5 days at 37 °C to differentiate moLCs.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AEA was  applied on day 0, day 2 and day 4  to relevant samples, while p(I:C) and CL075 was applied on day 4 to  relevant samples. Control cells were treated with appropriate vehicle on the same  days.

tag: cell type

value: monocyte-derived Langerhans cell

tag: treatment

value: moLC differentiated with AEA, activated with p(I:C) and CL078


title: monocyte-derived Langerhans cells, P(I:C)+CL075+AEA treated, D3

value: moLC differentiated with AEA, activated with p(I:C) and CL077


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description:
sample 5-3-4
RCM_tonifying_A549.txt

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human non-small cell lung carcinoma, A549 (CCL-185) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). A549 cells were maintained in RPMI medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Roswell Park Memorial Institute (RPMI) 1640 medium, phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.

tag: cell line

value: Rehmanniae Radix Preparata water extract 500 μg/mL

tag: time


title: T47D_CC_HS5_3

country: USA


title: T47D_MC_1


title: monocyte-derived Langerhans cells, P(I:C)+CL075+AEA treated, D2

value: moLC differentiated with AEA, activated with p(I:C) and CL076


title: A549_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep3

description:
sample 5-3-3
RCM_tonifying_A549.txt

value: Cnidii Rhizoma water extract 20 μg/mL


title: DC3000-0222-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the P. syringae 1448A genome (NC_005773.3), DC3000 (NC_004578.1), B728a (NC_007005.1) and C48 (NZ_CP032631.1) using Bowtie2 (version 2.3.4.3).
Binding peaks (q < 0.01) were identified using MACS2 software (version 2.1.0).
The enriched loci for each TF were annotated using the R package ChIPpeakAnno (version 3.18.2).
Assembly: P. syringae 1448A genome (NC_005773.3), DC3000 (NC_004578.1), B728a (NC_007005.1) and C48 (NZ_CP032631.1)
Supplementary files format and content: bigWig. narrow.Peak (except for input sample)

molecule: genomic DNA

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: bacterial cell

growth_protocol: King' B media, with rifampicin at 50 μg/ml and spectinomycin at 50 μg/ml. Bateria were culture at 28℃ at 220 rpm.

extract_protocol:
Bacterial cultures were cross-linked with 1% formaldehyde for 10 min at 28°C and then the reaction was stopped by the addition of 125 mM glycine for 5 min. The centrifugated bacteria were washed twice with Tris Buffer (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl) and washed again with IP Buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail).
The 150-250-bp DNA fragments were selected  for library construction. The libraries were sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all ChIP-seq experiments.

treatment_protocol: Cutured to OD=0.6.

value: bacterial cell

tag: genotype

value: WT

tag: chip antibody

value: HA


title: T47D_CC_HS5_2


title: A549_BatchB_water extract of Cinnamomi Cortex (High dose)_rep1

description:
sample 6-1-1
RCM_tonifying_A549.txt

value: Cinnamomi Cortex water extract 500 μg/mL


title: monocyte-derived Langerhans cells, P(I:C)+CL075+AEA treated, D1

value: moLC differentiated with AEA, activated with p(I:C) and CL075


title: T47D_MC_3


title: DC3000-2193-2


title: DC3000-0222-1


title: A549_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep3

description:
sample 5-3-2
RCM_tonifying_A549.txt

value: Cnidii Rhizoma water extract 100 μg/mL


title: T47D_CC_HS5_1


title: CM_HS5_3


title: A549_BatchB_water extract of Cnidii Rhizoma (High dose)_rep3

description:
sample 5-3-1
RCM_tonifying_A549.txt

value: Cnidii Rhizoma water extract 500 μg/mL


title: monocyte-derived Langerhans cells, P(I:C)+CL075 treated, D4

value: Control moLC activated with p(I:C) and CL075


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep2

description:
sample 5-2-6
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata water extract 20 μg/mL


title: DC3000-4127-1


title: monocyte-derived Langerhans cells, P(I:C)+CL075 treated, D3


title: DC3000-4127-2


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep2

description:
sample 5-2-5
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata water extract 100 μg/mL


title: DC3000-OmpR-2


title: CM_HS5_2

value: breast cancer cells


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep2

description:
sample 5-2-4
RCM_tonifying_A549.txt


title: CM_HS5_1


title: monocyte-derived Langerhans cells, P(I:C)+CL075 treated, D1

value: monocyte-derived Langerhans cell


title: DC3000-2193-1


title: A549_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep2

description:
sample 5-2-3
RCM_tonifying_A549.txt


title: DC3000-OmpR-1


title: MCF7_MC_3

value: ER+ breast cancer cells


title: DC3000-EV-4

description: no processed data file


title: monocyte-derived Langerhans cells, AEA treated, D4

value: moLC differentiated with AEA


title: MCF7_MC_2


title: monocyte-derived Langerhans cells, P(I:C)+CL075 treated, D2


title: monocyte-derived Langerhans cells, AEA treated, D3


title: MCF7_MC_1


title: A549_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep2

description:
sample 5-2-2
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep1

description:
sample 5-1-6
RCM_tonifying_A549.txt


title: DC3000-EV-2

description: no processed data file


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep1

description:
sample 5-1-5
RCM_tonifying_A549.txt


title: DC3000-EV-3

description: no processed data file


title: MCF7_CC_HS5_3


title: MCF7_CC_HS5_2


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep1

description:
sample 5-1-4
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata water extract 500 μg/mL


title: A549_BatchB_water extract of Cnidii Rhizoma (High dose)_rep2

description:
sample 5-2-1
RCM_tonifying_A549.txt


title: MCF7_CC_HS5_1


title: monocyte-derived Langerhans cells, control, D4

value: Control moLC


title: monocyte-derived Langerhans cells, control, D2


title: A549_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep1

description:
sample 5-1-2
RCM_tonifying_A549.txt


title: MCF7_CC_HS27a_3


title: retina, Samd7 wt, rep1

city: St. Louis

first: Ramiz

last: Somjee

state: Missouri

address: 660 S Euclid ave

institute: Washington University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.
cutadapt 3.0 for read processing
STAR 2.7.3a for read mapping to genome
HTSeq 0.12.4 to generate counts, using samtools version 1.9 for index generation
DeSeq2 was used to analyze differential expression between Samd7 KO and wt and to test for significant differential expression with a thershold-based Wald test that abs(Log2(fold-change)) > 1
Assembly: GRCm38/mm10
Supplementary files format and content: .csv, DeSeq2 output including DESeq2 statistics and normalized counts.

molecule: polyA RNA

organism: Mus musculus

source_name: retina

extract_protocol:
After euthineasia with carbon dioxide, the retina was isolated from the eye and stored in RNAlater (invitrogen) until processing. RNA extraction from one retina per replicate using Rneasy mini with on column RNAse-free Dnase treatment (Qiagen). Lysis was performed in 450 ul of lysis buffer using a pestle gun.
cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

tag: tissue

value: retina

value: c57Bl6/j wt

tag: age

value: postnatal day 36

tag: Sex

value: Male


title: retina, Samd7 wt, rep3


title: retina, Samd7 wt, rep2


title: MCF7_CC_HS27a_2


title: monocyte-derived Langerhans cells, AEA treated, D2


title: monocyte-derived Langerhans cells, AEA treated, D1


title: DC3000-EV-1

description: no processed data file

value: bacterial cell

value: WT

value: HA


title: A549_BatchB_water extract of Cnidii Rhizoma (High dose)_rep1

description:
sample 5-1-1
RCM_tonifying_A549.txt

value: Cnidii Rhizoma water extract 500 μg/mL


title: monocyte-derived Langerhans cells, control, D3


title: 6h cip media rep3

city: Brookings

first: Nicholas C

last: Butzin

state: SD

address: 1224 Medary Ave.

department: Biology and Microbiology

institute: South Dakota State University

data_processing:
Fastq files were aligned to NC_000913.3 and the plasmid p24KmNB82 using Geneious v. 2022.0.2
Raw read counts were calculated using 'calculate expression tool' in Geneious v. 2022.0.2
Assembly: NC_000913.3
Supplementary files format and content: Table with raw read counts for every gene and sample; comma separated values

organism: Escherichia coli

growth_protocol: Cultures were grown in modified MMB+ media, which consists of the following: K2HPO4 (10.5 mg/ml), KH2PO4 (4.5 mg/ml), (NH4)2SO4 (2.0 mg/ml), C6H5Na3O7 (0.5 mg/ml), NaCl (1.0 mg/ml), 2 mM MgSO4 x 7H2O, 100 µM CaCl2, thiamine (10 µg/ml), 0.5% glycerol, amino acids (40 µg/ml) and kanamycin (25 µg/ml)

extract_protocol:
Samples were treated with Tween (0.2%) and chloramphenicol (5 µg/ml) then immediately filtered out of solution and resuspended in lysis buffer containing 25 mM Tris pH 8.0, 25 mM NH4Cl, 10 mM MgOAc, 0.8 % Triton X-100, 0.1 U/µL RNase-free DNase I, 1 U/μL. Then immediately frozen in liquid nitrogen and stored at -80 C.  Frozen pellets were thawed on ice and centrifuged for 20 minutes at 16,000 x g at 4 °C with 0.3% Sodium Deoxychorate to pellet particulate matter. The supernatant was then removed and RNA was column purified (Qiagen miRNeasy cat. No. 217004) before removing rRNA (Invitrogen RiboMinus cat no. K155004) Superase-In, ~60 U/µl ReadyLyse Lysozyme, 1.55 mM Chloramphenicol, and 17 μΜ 5′-guanylyl imidodiphosphate (GMPPNP).
cDNA libraries were prepared and multiplexed according to manufacturer's protocols: NEBNext Ultra II cat no. E7103S. Libraries were then pooled and sequenced by Illumina HiSeq paired-end sequencing.

treatment_protocol: Stationary phase cultures were diluted 1/100 into fresh MMB+ media and collected after 24 h . Ampicillin treated cultures also contained 0.1 mg/mL ampicillin.  Cip treatment at a concentration of 10 μg/mL for 6 h.

tag: strain

tag: plasmid

value: ciprofloxacin (6h)


title: HS5_MC_3

value: bone marrow mesenchymal stem cells


title: 6h cip media rep2


title: A549_BatchB_Vehicle(DMSO)_rep2

description:
sample B1-2-1
RCM_tonifying_A549.txt

value: 0.1% DMSO


title: HS5_MC_2


title: A549_BatchB_Vehicle(DMSO)_rep3

description:
sample B1-3-1
RCM_tonifying_A549.txt


title: retina, Samd7 KO, rep1

value: Samd7 knockout (-10A)

value: postnatal day 31


title: HS5_MC_1


title: nF-iLB-C1-30m

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

description: Non-malignant fibroblast

data_processing:
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing. Data analyses on fastq files were conducted with CLC Genomics Workbench (version 12.0.2, QIAGEN, Venlo. NL). The reads of all probes were adapter (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides max. 2).
Assembly: Mapping was done against theHomo sapiens(hg38.88) (May 25, 2017) genome sequence.
Supplementary files format and content: Statistical differential expression tests were determined using the ‘Differential Expression in Two Groups’ tool (version 1.02). The resultingp-values were corrected for multiple testing by false discovery rate- (FDR) and Bonferroni-correction. Ap-value of ≤0.05 was considered significant.

source_name: Non-malignant fibroblast

growth_protocol: CAF and nF cultures were cultivated in DMEM + 10 % FCS, + 1 % Pen/Strep, + 1 % L-Glutamine, 1 % Non-essential aminoacids, 100 µM b-Mercaptoethanol

extract_protocol:
RNA was isolated using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manual
RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific, Meerbusch, Germany) and quality was measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ (Agilent Technologies Inc., Santa Clara, USA). The library preparation was performed according to the manufacturer’s protocol (‘VAHTS Stranded mRNA-Seq Library Prep Kit’). 300ng totalRNA were used for mRNA capturing, fragmentation, synthesis of cDNA, adapter ligation, and library amplification. Bead purified libraries were normalized.
RNA sequencing performed on the HiSeq3000/4000 system (Illumina Inc., San Diego, USA) with a read setup of 1x150basepairs (bp).

treatment_protocol: Primary CAF isolated from fresh ex vivo GCT patient tissue

value: Non-malignant fibroblast


title: nF-LB-C2-36m

description: Non-malignant fibroblast


title: A549_BatchB_Vehicle(DMSO)_rep1

description:
sample B1-1-1
RCM_tonifying_A549.txt


title: 24h amp media rep3

value: ampicillin (24h)


title: HS27a_MC_3


title: retina, Samd7 KO, rep3


title: 24h amp media rep2


title: nF-LB-C18m

description: Non-malignant fibroblast


title: 24h amp media rep1


title: MCF7_CC_HS27a_1

value: ER+ breast cancer cells


title: A549_BatchA_water extract of Paeoniae Radix (Low dose)_rep3

description: sample 4-3-6

value: Paeoniae Radix water extract 20 μg/mL


title: HS27a_MC_1


title: retina, Samd7 KO, rep2

value: retina


title: THX20

city: Beijing

first: Teng

last: Song

address: Yuanmingyuan West Road

country: China

institute: China agricultural university

data_processing:
Illumina software used for base calling
Trimmomatic (version 0.39) was used to trim the fastq files as follows: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, HEADCROP:0, MINLEN:75 and bowtie2 (version: 2.4.1)  was used to align them to the B73 v4 reference genome with the following parameters: -I 75 -X 1000 --no-discordant --no-mixed.
Peaks were called using GEM v3.4 with the following parameters: --d Read_Distribution_default.txt --k_min 4 --k_max 12 --outNP --q 3 --nrf --outNP --outHOMER –outMEME. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak
Library strategy: ampDAP-seq

organism: Zea mays

source_name: leaf

growth_protocol: B73 inbried line cultivated in the greenhouse of China Agricultural University (Beijing, China)

extract_protocol:
gDNA was extracted from maize B73 14 DAG leaf. gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (TIANGEN) according to the manufacturer’s instructions.
gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (TIANGEN) according to the manufacturer’s instructions. Full length maize transcription factors’ coding sequences were cloned from maize 14 DAG leaf cDNA into the NotI and AscI sites of pUC57-Halo using MultlF Seamless Assembly Mix (ABclonal). Protein expression was using TNT SP6 High-YIELD Wheat Germ Master Protein Expression System (Promega) according to the manufacturer’s instructions. Halo-fusion protein was bound to Magne HaloTag Beads (Promega) and washed three times using TBSN buffer( 100 mM Tris buffer, pH 7.5, 50 mM NaCl, 0.005 % NP40). Then, 500 ng gDNA libraries was added and incubated at room temperature for 1.5 h. After incubation the beads was washed four times. Resuspended the beads in 30µl of EB buffer to recover DNA. The recovered DNA was were cleaned up with Silane magnetic beads, and amplified via PCR. The PCR products were cleaned up with Silane magnetic beads and sequenced using an NovaSeq platform (Illumina) by BerryGnomics (China).

value: leaf

tag: background

tag: gene id

value: 14 DAG


title: nF-LB-35m

description: Non-malignant fibroblast


title: A549_BatchA_water extract of Paeoniae Radix (High dose)_rep3

description: sample 4-3-4

value: Paeoniae Radix water extract 500 μg/mL


title: nF-MPAF

description: Non-malignant fibroblast


title: 6h cip media rep1

value: bacterial cell


title: A549_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep3

description: sample 4-3-3

value: Angelicae Gigantis Radix water extract 20 μg/mL


title: CM_HS5 2


title: A549_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep3

description: sample 4-3-2

value: Angelicae Gigantis Radix water extract 100 μg/mL


title: OBF4


title: A549_BatchA_water extract of Paeoniae Radix (Medium dose)_rep3

description: sample 4-3-5

value: Paeoniae Radix water extract 100 μg/mL


title: Mix-CAF007

description: CAF from seminoma and non-seminoma

source_name: CAF from seminoma and non-seminoma

value: CAF from seminoma and non-seminoma


title: CPP2


title: HS27a_MC_2

value: bone marrow mesenchymal stem cells


title: TE-CAF019

description: CAF from non-seminoma, teratoma

source_name: CAF from non-seminoma, teratoma

value: CAF from non-seminoma, teratoma


title: C3H23


title: A549_BatchA_water extract of Paeoniae Radix (Low dose)_rep2

description: sample 4-2-6


title: Double-3

data_processing:
Trimmomatic  (version 0.39) was used to trim the sequence reads and Hisat2 (version 2.2.1) was used to align them to the B73 v4 reference genome.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: Matrix table with raw counts for every sample (column) and gene (rows)

source_name: Endosperm

extract_protocol:
5-10 of 15 DAP endosperms of wild type and mutant were pooled for extracting total RNA with an RNAprep Pure Plant Kit (TIANGEN)
MP3RNA-seq

value: Endosperm

value: 15 DAP


title: CM_HS5 1


title: A549_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep3

description: sample 4-3-1

value: Angelicae Gigantis Radix water extract 500 μg/mL


title: CM_HS27a_3


title: TE-CAF017

description: CAF from non-seminoma, teratoma


title: Mix-CAF008

description: CAF from seminoma and non-seminoma


title: CM_HS27a_2


title: A549_BatchA_water extract of Paeoniae Radix (Medium dose)_rep2

description: sample 4-2-5


title: A549_BatchA_water extract of Paeoniae Radix (High dose)_rep2

description: sample 4-2-4


title: Double-2


title: TE-CAF012

description: CAF from non-seminoma, teratoma


title: CM_HS5 3


title: EC-CAF014

description: CAF from non-seminoma, embryonal carcinoma


title: A549_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep2

description: sample 4-2-3


title: CM_HS27a_1


title: Double-1


title: MCF7_Wt_NS_NE1_S7

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

growth_protocol: WT and GIV-KO MDA-MB231 cells grown in 0% and 10% serum concentration in p10 dishes (Corning) for 16 h prior to harvest

extract_protocol:
RNA extraction was done  using a kit (R2052, Zymo Research) as per manufacturer’s protocol
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: 0% and 10% serum concentration

value: control WT


title: N130-3


title: EC-CAF010

source_name: CAF from non-seminoma, embryonal carcinoma


title: A549_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep2

description: sample 4-2-2


title: EC-CAF005

value: CAF from non-seminoma, embryonal carcinoma


title: A549_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep2

description: sample 4-2-1


title: MCF7_Wt_NS_NE3_S9

value: ER+ breast cancer cells


title: SE-CAF022

description: CAF from seminoma

source_name: CAF from seminoma

value: CAF from seminoma


title: A549_BatchA_water extract of Paeoniae Radix (Low dose)_rep1

description: sample 4-1-6

value: Paeoniae Radix water extract 20 μg/mL


title: N130-1


title: N130-2


title: MCF7_Giv_NS_NE2_S2

value: stably expressed full-length GIV


title: A549_BatchA_water extract of Paeoniae Radix (Medium dose)_rep1

description: sample 4-1-5


title: N128-3


title: MCF7_Giv_NS_NE1_S1


title: SE-CAF020

description: CAF from seminoma


title: N128-2


title: A549_BatchA_water extract of Paeoniae Radix (High dose)_rep1

description: sample 4-1-4

value: Paeoniae Radix water extract 500 μg/mL


title: A549_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep1

description: sample 4-1-3


title: MCF7_Wt_NS_NE2_S8


title: SE-CAF018

description: CAF from seminoma


title: MCF7_Giv_NS_NE3_S3


title: N128-1


title: A549_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep1

description: sample 4-1-2


title: SE-CAF011

description: CAF from seminoma


title: WT3

value: Wild type


title: MDA468_KO_rep3

city: Cambridge

first: Laura

last: Woods

address: Downing Street

department: Centre for Trophoblast Research

country: United Kingdom

institute: University of Cambridge

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
STAR 2.6.1d alignment to hg38 genome
STAR quant mode reverse to obtain gene counts
DESeq2 1.32.0 for differential expression analysis
Assembly: hg38
Supplementary files format and content: raw_counts.tsv: raw counts in hg38 genes

source_name: Cell line

extract_protocol: Not provided

value: Cell line

value: Breast cancer

value: FOXC1 KO

tag: biological replicate


title: MDA468_KO_rep2


title: SE-CAF021

description: CAF from seminoma


title: WT2


title: SE-CAF009

description: CAF from seminoma


title: A549_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep1

description: sample 4-1-1


title: A549_BatchA_water extract of Panax Ginseng (Low dose)_rep3

description: sample 3-3-6

value: Panax Ginseng water extract 20 μg/mL


title: MDA468_WT_rep3


title: Pm_caps_rep3_index20

city: Evanston

first: Joshua

middle: Ryan

last: York

state: Illinois

address: 2205 Tech Dr

department: Molecular Biosciences

institute: Northwestern University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v0.23.2) using default parameters
Trimmed sequence reads were mapped to Xl9.2 (Xenopus) or GCF_010993605.1_kPetMar1 (lamprey) using STAR (v2.6.0)
Read counts were obtained using HTSeq (v1.99.2)
Assembly: Xl9.2 (Xenopus)  and kPetMar1 (lamprey)
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

organism: Petromyzon marinus

source_name: T11 blastula cells

growth_protocol: animal caps were dissected and cultured in 1X Marc's Modified Ringers (MMR)

extract_protocol:
total RNA was extracted using TRIZOL reagent and LiCl precipitation
RNA-Seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, along with the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext High-Fidelity 2 × PCR Master Mix using the manufacturer’s protocol

treatment_protocol: animal caps were either untreated or injected at the 2-cell stage with wnt8a and chordin mRNA

value: embryonic cells

value: animal pole stem cells

value: WT


title: IgG_ZmNAC130_ChIP2

data_processing:
Illumina software used for base calling
Trimmomatic (version 0.39) was used to trim the fastq files as follows: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, HEADCROP:0, MINLEN:75 and bowtie2 (version: 2.4.1)  was used to align them to the B73 v4 reference genome with the following parameters: -p 40 -I 75 -X 1000 --no-discordant --no-mixed.
Peak calling was performed separately for each biological replicate using MACS2 (v2.0.10) with specific parameters: -m 10 30 -g 2.106e9.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak

source_name: Kernel

growth_protocol: W22 inbried line and zmnac128 mutant cultivated in the field of Shangzhuang Experimental Station of China Agricultural University (Beijing, China)

extract_protocol:
About 2 g of kernel powder was resuspended in pre-cold  M1 buffer (10 mM sodium phosphate[pH 7], 0.1 M NaCl, 1 M 2-methyl 2,4-pentanediol, 10 mM β-mercaptoethanol and complete protease inhibitor cocktail). Cell nuclei were extracted using pre-cold M2 buffer (like M1 buffer with 10 mM MgCl2 and 0.5% Triton X-100),  and M3 buffer (like M1 buffer without 2-methyl 2,4-pentanediol), then washed 5 times separately.
Cell nuclei were incubated with ZmNAC128, ZmNAC130 and IgG antibodies (final concentration, 20 μg/mL) for 12 h at 4℃. Then supernatant were incubated with dynabeads Protein A (Invitrogen) for 2 h at 4℃. After washing the samples four times, they were incubated with Tn5 transposome and tagmentation buffer (10 mM TAPS-NaOH (pH 8.5), 10 mM MgCl2, 10% (v/v) DMF, 0.5 mM spermidine, 0.05% (v/v) digitonin, and 1% (v/v) plant cocktail) at 37℃ for 5 min.  The reactions were stopped and then the protein-DNA complexes were eluted from the beads. Finally, after proteinase k (Invitrogen) treatment, ChIP-DNA libraries were constructed and sequenced using an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) by BerryGenomics (China).

value: Kernel

value: 15 DAP


title: WT1

value: Endosperm


title: Pm_caps_rep2_index18


title: MDA468_KO_rep1


title: monocyte-derived Langerhans cells, control, D1

value: monocyte-derived Langerhans cell

value: Control moLC


title: MDA468_WT_rep2


title: A549_BatchA_water extract of Panax Ginseng (Medium dose)_rep3

description: sample 3-3-5

value: Panax Ginseng water extract 100 μg/mL


title: Anti130_ZmNAC130_ChIP2


title: MDA468_WT_rep1


title: A549_BatchA_water extract of Panax Ginseng (High dose)_rep3

description: sample 3-3-4

value: Panax Ginseng water extract 500 μg/mL


title: IgG_ZmNAC130_ChIP1


title: MDA231_KO_rep3


title: A549_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep3

description: sample 3-3-3

value: Glycyrrhizae Radix water extract 20 μg/mL


title: Anti130_ZmNAC130_ChIP1


title: HT25 cells, Lv-Ntoco

city: Chengdu

first: Linbo

last: Gao

state: Sichuan

address: No. 17, Section 3, Renmin South Road, Wuhou District

institute: Sichuan University

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq(2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw FPKM for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.


title: HT23 cells, sh-Ntoco


title: MDA231_KO_rep1


title: MDA231_KO_rep2


title: HT24 cells, Vector


title: Mu_ZmNAC128_ChIP2


title: W22_ZmNAC128_ChIP2


title: A549_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep3

description: sample 3-3-1

value: Glycyrrhizae Radix water extract 500 μg/mL


title: Pm_caps_rep1_index16


title: MDA231_WT_rep3


title: HT22 cells, sh-Ctrl


title: Mu_ZmNAC128_ChIP1


title: A549_BatchA_water extract of Panax Ginseng (Low dose)_rep2

description: sample 3-2-6


title: MDA231_WT_rep2


title: A549_BatchA_water extract of Panax Ginseng (Medium dose)_rep2

description: sample 3-2-5


title: A549_BatchA_water extract of Panax Ginseng (High dose)_rep2

description: sample 3-2-4


title: WC_St17_Rep3

organism: Xenopus laevis

source_name: st17 induced neural crest

value: neural crest cells

value: Wnt/Chordin induced


title: W22_ZmNAC128_ChIP1


title: MDA231_WT_rep1

value: Cell line

value: Breast cancer


title: WC_St17_Rep2


title: Hs578_KO_rep3

value: FOXC1 KO


title: A549_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep2

description: sample 3-2-2

value: Glycyrrhizae Radix water extract 100 μg/mL


title: A549_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep2

description: sample 3-2-3


title: A549_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep3

description: sample 3-3-2


title: WC_St17_Rep1

value: embryonic cells


title: Hs578_KO_rep1


title: Hs578_WT_rep3

value: FOXC1 WT


title: CTRL_St17_Rep3

source_name: st17 epidermis

value: epidermal cells

value: WT


title: Hs578_KO_rep2


title: Hs578_WT_rep2


title: A549_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep2

description: sample 3-2-1


title: CTRL_St17_Rep2


title: CTRL_St17_Rep1


title: Hs578_WT_rep1


title: A549_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep1

description:
sample 5-1-3
RCM_tonifying_A549.txt

value: Cnidii Rhizoma water extract 20 μg/mL


title: A549_BatchA_water extract of Panax Ginseng (Medium dose)_rep1

description: sample 3-1-5


title: WC_St13_Rep3

source_name: st13 induced neural crest


title: A549_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep1

description: sample 3-1-3


title: A549_BatchA_water extract of Panax Ginseng (Low dose)_rep1

description: sample 3-1-6

value: Panax Ginseng water extract 20 μg/mL


title: Batch 2,  1.0 mg/ml,  biological rep2

type: RNA

city: Laurel

first: Xiugong

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 1.0 mg/ml in batch 2

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: Data were processed using the Affymetrix Transcriptome Analysis Console (TAC) software (v.4.0).

label: biotin

label_protocol: The total RNA samples (100 ng each) were labeled using the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Commercial iPSC-derived hepatocytes (iCell Hepatocytes 2.0) from FUJIFILM Cellular Dynamics (Madison, WI) were cultured following the manufacturer’s protocols.

extract_protocol: Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: Cells cultured at day 8 after seeding were exposed to BioPure grade 20 nm AgNPs from nanoComposix (San Diego, CA) at varying concentrations (0.01 - 25 µg/ml) in triplicate for 24 h.

value: hepatocyte

value: AgNPa at 1.0 mg/ml

tag: batch

value: batch 2


title: Batch 2,  5.0 mg/ml,  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 5.0 mg/ml in batch 2

value: AgNPa at 5.0 mg/ml


title: Batch 2,  1.0 mg/ml,  biological rep1

source_name: iPSC-derived hepatocytes exposed to AgNPa at 1.0 mg/ml in batch 2


title: Batch 2,  5.0 mg/ml,  biological rep1

source_name: iPSC-derived hepatocytes exposed to AgNPa at 5.0 mg/ml in batch 2


title: WC_St13_Rep2


title: Batch 2,  5.0 mg/ml,  biological rep2


title: BT549_KO_rep3


title: Batch 2,  1.0 mg/ml,  biological rep3


title: BT549_KO_rep2


title: A549_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep1

description: sample 3-1-2


title: Batch 2,  0.5 mg/ml,  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 0.5 mg/ml in batch 2

value: AgNPa at 0.5 mg/ml


title: WC_St13_Rep1

value: neural crest cells


title: Batch 2,  0.5 mg/ml,  biological rep2

source_name: iPSC-derived hepatocytes exposed to AgNPa at 0.5 mg/ml in batch 2


title: Batch 2,  0.5 mg/ml,  biological rep1


title: A549_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep1

description: sample 3-1-1

value: Glycyrrhizae Radix water extract 500 μg/mL


title: A549_BatchA_water extract of Panax Ginseng (High dose)_rep1

description: sample 3-1-4

value: Panax Ginseng water extract 500 μg/mL


title: CTRL_St13_Rep3

source_name: st13 epidermis


title: BT549_WT_rep3

value: Cell line

value: Breast cancer


title: A549_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep3

description: sample 2-3-6

value: Atractylodis Rhizoma water extract 20 μg/mL


title: CTRL_St13_Rep2

value: embryonic cells


title: BT549_KO_rep1

value: FOXC1 KO


title: BT549_WT_rep2

value: FOXC1 WT


title: A549_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep3

description: sample 2-3-5

value: Atractylodis Rhizoma water extract 100 μg/mL


title: CTRL_St13_Rep1

value: epidermal cells

value: WT


title: Batch 2,  0.1 mg/ml,  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 0.1 mg/ml in batch 2

value: hepatocyte

value: AgNPa at 0.1 mg/ml


title: Batch 2,  0.1 mg/ml,  biological rep1

source_name: iPSC-derived hepatocytes exposed to AgNPa at 0.1 mg/ml in batch 2

value: batch 2


title: A549_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep3

description: sample 2-3-4

value: Atractylodis Rhizoma water extract 500 μg/mL


title: Batch 2,  0.05 mg/ml,  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 0.05 mg/ml in batch 2

value: AgNPa at 0.05 mg/ml


title: recombinant CDV-infected VerodogSLAMtag cells (passage 0)

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

data_processing:
Assembly: GCA_000409795.2
Adapter sequences were removed from raw fastq files using SeqPurge v0.1-1000-gb4d1b1c. Quality trimming was disabled (-qcut 0 -ncut 0) and adapter recognition sequences (read 1: GATCG GAAGA GCACA CGTCT GAACT CCAGT CACNN NNNNA TCTCG TATGC CGTCT TCTGC TTG; read2: AGATC GGAAG AGCGT CGTGT AGGGA AAGAG TGTAG ATCTC GGTGG TCGCC GTATC ATT) were provided.
Quality trimming and filtering was performed using Atropos version 1.1.17 with minimum base quality cutoffs of 30 at both sides of the read (-q 30,30) and discarding reads with Ns and a length below 30 bp after trimming (-max-n 0 -m 30).
Mapping was performed with BWA mem v 0.7.12-r1039 using default parameters unless stated otherwise. Host sequences in ferret- and cell culture-derived samples were removed by mapping quality-controlled reads against either the ferret (Mustela putorius furo) or the African green monkey genome (Chlorocebus sabeus), respectively, specifying the minimum seed length (-k 31). Unmapped reads were extracted using samtools v1.7, and bamToFastq v2.17.0, and subsequently mapped to the CDV reference genome.
Host-free alignments were deduplicated using picard-tools MarkDuplicates (http://broadinstitute.github.io/picard) and left aligned using GATK LeftAlignIndels v4.0.
Assembly: CDV5804_NGS_ref.fasta
Supplementary files format and content: base count tables (wig format) of bam alignments to CDV5804_NGS_ref.fasta reference sequence

organism:
Chlorocebus sabaeus
canine distemper virus

source_name: VerodogSLAMtag

growth_protocol: cells were infected with recombinant CDV at low MOI and harvested at maximun CPE (=P0).

extract_protocol:
RNA was isolated from cell-associated infectious virus released from infected cells by freeze-thawing. 100 µl virus stock aliquots were processed with Trizol reagent using the Zymo Direct-zol RNA kit (Zymo Research Europe GmbH, Freiburg, Germany). To extract RNA from tissues, 100 mg pieces were homogenized in 350 µl RLT buffer and processed according to the instructions of the RNeasy Mini kit manual (Qiagen, Hilden, Germany).
500 µg of purified RNA were processed with the Illumina TrueSeq StrandedTotal RNA kit (Illumina, San Diego, USA), including depletion of ribosomal RNA via Ribo-Zero Gold rRNA Removal kit (Illumina, San Diego, USA) following the manufacturer’s protocols. Libraries generated with single indexed adapters were then validated and sequenced as 2x150 base pairs paired-end reads.

value: VerodogSLAMtag

value: kidney epithelial cell

value: recombinant CDV r5804

value: passage 0


title: WC_St9_Rep2

source_name: st9 induced neural crest

value: animal pole stem cells

value: Wnt/Chordin induced


title: A549_BatchA_water extract of Poria Cocos (Low dose)_rep3

description: sample 2-3-3

value: Poria Cocos water extract 20 μg/mL


title: BT549_WT_rep1

value: Cell line

value: Breast cancer


title: WC_St9_Rep3

value: embryonic cells


title: A549_BatchA_water extract of Poria Cocos (Medium dose)_rep3

description: sample 2-3-2

value: Poria Cocos water extract 100 μg/mL


title: CDV-infected VerodogSLAMtag cells (passage 0)

growth_protocol: cells were infected with CDV at low MOI and harvested at maximun CPE (=P0).

value: tissue culture-adapted CDV isolate 5804


title: CTRL_St9_Rep3

source_name: st9 blastula cells

value: WT


title: Batch 2,  0.1 mg/ml,  biological rep2

value: hepatocyte

value: AgNPa at 0.1 mg/ml


title: Batch 2,  0.05 mg/ml,  biological rep2

source_name: iPSC-derived hepatocytes exposed to AgNPa at 0.05 mg/ml in batch 2

value: batch 2


title: A549_BatchA_water extract of Poria Cocos (High dose)_rep3

description: sample 2-3-1

value: Poria Cocos water extract 500 μg/mL


title: A549_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep2

description: sample 2-2-6

value: Atractylodis Rhizoma water extract 20 μg/mL


title: CTRL_St9_Rep2


title: A549_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep2

description: sample 2-2-5

value: Atractylodis Rhizoma water extract 100 μg/mL


title: CTRL_St9_Rep1


title: A549_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep2

description: sample 2-2-4

value: Atractylodis Rhizoma water extract 500 μg/mL


title: WC_St9_Rep1


title: tumor with cell pool B, PD1 treated, replicate 3

city: Houston

first: Jielin

last: Liu

state: TX

address: 7455 Fannin St

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

description:
mDB_PD1_3
PD1_counts.csv

library_source: other

data_processing:
Fastq files were aligned to custom index to generate count files using the makeCounts function in the casTLE software.
Counts from the plasmid library were bind column-wise.
Counts from tumor samples were first normalized to sequencing depth, mean counts for each condition were then calculated and reported.
Assembly: A custom bowtie index was generated for each sub library using the makeIndices function in the casTLE software.
Supplementary files format and content: raw counts
Supplementary files format and content: mean counts
Library strategy: Amplicon-seq

molecule: other

source_name: tumor

extract_protocol:
plasmid DNA was extracted using Midiprep kit (QIAGEN); DNA from cell pools and tumors were extracted using Quick-DNA Midiprep Plus kit (ZYMO Research).
Library was generated by two rounds of PCR to amplify DNA fragments containing sgRNA sequences.

value: tumor


title: A549_BatchA_water extract of Poria Cocos (Medium dose)_rep2

description: sample 2-2-2


title: A549_BatchA_water extract of Poria Cocos (Low dose)_rep2

description: sample 2-2-3


title: tumor with cell pool B, PD1 treated, replicate 1

description:
mDB_PD1_1
PD1_counts.csv


title: tumor with cell pool B, PD1 treated, replicate 2

description:
mDB_PD1_2
PD1_counts.csv


title: tumor with cell pool B, PBS treated, replicate 4

description:
mDB_PBS_4
PBS_counts.csv

value: PBS


title: Batch 2,  0.01 mg/ml,  biological rep2

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 0.01 mg/ml in batch 2

value: AgNPa at 0.01 mg/ml


title: tumor with cell pool B, PD1 treated, replicate 4

description:
mDB_PD1_4
PD1_counts.csv


title: Batch 2,  0.01 mg/ml,  biological rep1

source_name: iPSC-derived hepatocytes exposed to AgNPa at 0.01 mg/ml in batch 2


title: A549_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep1

description: sample 2-1-5


title: A549_BatchA_water extract of Poria Cocos (High dose)_rep2

description: sample 2-2-1


title: Batch 2,  0.0 mg/ml (control),  biological rep2

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 0.0 mg/ml (control) in batch 2

value: AgNPa at 0.0 mg/ml (control)


title: Batch 2,  0.01 mg/ml,  biological rep3


title: A549_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep1

description: sample 2-1-6


title: Batch 2,  0.05 mg/ml,  biological rep1

value: AgNPa at 0.05 mg/ml


title: Batch 2,  0.0 mg/ml (control),  biological rep3

source_name: iPSC-derived hepatocytes exposed to AgNPa at 0.0 mg/ml (control) in batch 2


title: Batch 2,  0.0 mg/ml (control),  biological rep1


title: A549_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep1

description: sample 2-1-4


title: Batch 1,  25 mg/ml,  biological rep2

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 25 mg/ml in batch 1

value: AgNPa at 25 mg/ml

value: batch 1


title: tumor with cell pool B, PBS treated, replicate 2

description:
mDB_PBS_2
PBS_counts.csv


title: A549_BatchA_water extract of Poria Cocos (Low dose)_rep1

description: sample 2-1-3

value: Poria Cocos water extract 20 μg/mL


title: Batch 1,  25 mg/ml,  biological rep3

source_name: iPSC-derived hepatocytes exposed to AgNPa at 25 mg/ml in batch 1


title: A549_BatchA_water extract of Poria Cocos (Medium dose)_rep1

description: sample 2-1-2

value: Poria Cocos water extract 100 μg/mL


title: Batch 1,  25 mg/ml,  biological rep1


title: tumor with cell pool B, PBS treated, replicate 1

description:
mDB_PBS_1
PBS_counts.csv


title: tumor with cell pool A, PD1 treated, replicate 1

description:
mDA_PD1_1
PD1_counts.csv


title: tumor with cell pool B, PBS treated, replicate 3

description:
mDB_PBS_3
PBS_counts.csv


title: A549_BatchA_water extract of Poria Cocos (High dose)_rep1

description: sample 2-1-1


title: tumor with cell pool A, PD1 treated, replicate 2

description:
mDA_PD1_2
PD1_counts.csv


title: tumor with cell pool A, PBS treated, replicate 2

description:
mDA_PBS_2
PBS_counts.csv


title: A549_BatchA_Wortmannin_rep2

description: sample 1-2-4

value: wortmannin 10 uM


title: tumor with cell pool A, PBS treated, replicate 1

description:
mDA_PBS_1
PBS_counts.csv


title: Batch 1,  10 mg/ml,  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPs at 10 mg/ml in batch 1

value: hepatocyte

value: AgNPs at 10 mg/ml


title: Batch 1,  20 mg/ml,  biological rep2

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPa at 20 mg/ml in batch 1

value: AgNPa at 20 mg/ml


title: Batch 1,  5.0 mg/ml,  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPs at 5.0 mg/ml in batch 1

value: AgNPs at 5.0 mg/ml


title: A549_BatchA_Wortmannin_rep1

description: sample 1-1-4


title: Batch 1,  20 mg/ml,  biological rep3

source_name: iPSC-derived hepatocytes exposed to AgNPa at 20 mg/ml in batch 1


title: Batch 1,  10 mg/ml,  biological rep1

source_name: iPSC-derived hepatocytes exposed to AgNPs at 10 mg/ml in batch 1


title: Batch 1,  10 mg/ml,  biological rep2


title: cell pool B, replicate 2

description:
cDB2
plasmid_and_cell_pool_counts.csv

value: mouse bladder cancer cell line


title: Batch 1,  20 mg/ml,  biological rep1


title: A549_BatchA_Vehicle(DMSO)_rep3

description: sample A1-3-1

value: 0.1% DMSO


title: Batch 1,  5.0 mg/ml,  biological rep2

source_name: iPSC-derived hepatocytes exposed to AgNPs at 5.0 mg/ml in batch 1


title: nF-LB-35m

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Bead array (850k) using standard Illumina protocol

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

data_processing:
Data and bioinformatic analyses were carried out using ‘GenomeStudio’ software (version 2011.1, Methylation Module v1.9) (Illumina) and. A detailed report on quality controls and internal control measurements provided by the Department of Neuropathology of the University Hospital Hamburg-Eppendrof (Hamburg-Eppendorf, Germany)  is available upon request.
Data processing and QC according to the in-house analysis pipeline of the Department of Neuropathology of the University Hospital Hamburg-Eppendrof (Hamburg-Eppendorf, Germany) and calculation of beta-values.

label: cy3, cy5

source_name: Non-malignant fibroblast

label_protocol: The Infinium MethylationEPIC array BeadChip (Illumina, San Diego, CA, USA) was carried out by the Department of Neuropathology of the University Hospital Hamburg-Eppendorf (Hamburg-Eppendorf, Germany) following an established in-house analysis pipeline. For each sample, 500 ng of DNA were used for sodium-bisulfite conversion using the EZ-96 DNA Methylation Kit (Zymo Research, Freiburg im Breisgau, Germany). Bisulfite conversion was controlled by qPCR. One assay targeting a methylated region of DNAJC15 and two assays targeting the GNAS locus (one assay for the unmethylated allele and one assay for the methylated allele) was used for quality control. Deaminated DNA derived from blood was amplified in parallel and served as positive control. A sample passed the quality control when the received Ct-value either for the two GNAS loci or the DNAJC15 locus reaches the threshold not later than five cycles compared to the positive control.

extract_protocol: Genomic DNA used for the Infinium MethylationEPIC BeadChip array (850k) was isolated and purified by PCI precipitation including a RNaseA treatment. DNA concentrations were measured by the ‘Qubit 4 Fluorometer’ (Thermo Fisher Scientific).

value: Non-malignant fibroblast


title: A549_BatchA_Wortmannin_rep3

description: sample 1-3-4


title: A549_BatchA_Vehicle(DMSO)_rep1

description: sample A1-1-1


title: nF-iLB-C1-30m


title: A549_BatchA_Vehicle(DMSO)_rep2

description: sample A1-2-1


title: Batch 1,  0.0 mg/ml (control),  biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to AgNPs at 0.0 mg/ml (control) in batch 1

value: AgNPs at 0.0 mg/ml (control)


title: cell pool B, replicate 1

description:
cDB1
plasmid_and_cell_pool_counts.csv


title: Batch 1,  0.0 mg/ml (control),  biological rep2

source_name: iPSC-derived hepatocytes exposed to AgNPs at 0.0 mg/ml (control) in batch 1


title: nF-LB-C18m


title: Batch 1,  5.0 mg/ml,  biological rep1


title: Late Log yeast, replicate 2, NETseq

status: Public on Jun 20 2024

city: Birmingham

first: Catarina

middle: Alexandra

last: Mendes Felgueira

state: AL

address: 1720 University Blvd

institute: University of Alabama at Birmingham

description:
Mid_vs_Late_sumnorm.csv
Early_vs_Late_sumnorm.csv

data_processing:
Base-calling was performed using bclconvert software.
Reads were deduplicated using Fqtrim (version 0.9.7) with the "-C" option selected.
Cutadapt (version 3.4-GCCcore-10.3.0) was used to trim 5' sequence with (5'-AGNNNNNNNNTG-3') using "-g -no-indels" option. Cutadapt also was used to trim 3' sequence (5'-CTGTAGGCACCAT-3') using "-a -no-indels" option. Only reads that contained both of these sequences were retained.
Reads were aligned to the S. cerevisiae genome using STAR (version 2.7.3a-GCC-6.4.0-2.28) with "-alignIntronMax" parameter set to 1.
SAMtools (version 1.12-GCC-10.2.0) was used to sort and index aligned BAM files.
BAM files were converted to BED files using BEDTools (version 2.28.0-foss-2018b).
BEDTools was used to generate genome coverage files with the genomecov function and parameters "-d -5 -stand +" and "-d -5 -stand -" for plus and minus strands, respectively.
Count files were further processed and visualized using R (version 4.3.1) and Rstudio (version 2024.04.0+735).
Assembly: S. cerevisiae R64-1-1  (GenBank assembly: GCA_000146045.2)
Supplementary files format and content: Processed data are in three separate .csv files. One file for each two-way comparison between the three sample groups (e.g. Early_vs_Mid_sumnorm.csv).
Supplementary files format and content: The column names specificy which sample and replicate the values belong to. In each .csv file, column header "wt" refers to the first sample in the file name and "mut" refers to the second sample in the filename. That is: In the file Early_vs_Mid_sumnorm.csv, columns named "wt" refer to Early log samples and columns named "mut" refer to Mid log samples. In the file Early_vs_Late_sumnorm.csv, columns named "wt" refer to Early log samples and columns named "mut" refer to Late log samples. In the file Mid_vs_Late_sumnorm.csv, columns named "wt" refer to Mid log samples and columns named "mut" refer to Late log samples.
Library strategy: NET-seq

organism: Saccharomyces cerevisiae

source_name: WT yeast

growth_protocol: Yeast was grown on YPD at 30ºC with nutation until indicated OD600

extract_protocol:
Yeast cells were cyogenically harveste and lysed. RNA Polymerase I immunoprecipitaion was perfomed followed by total RNA extraction using acidic phenol/chloroform.
Following RNA extraction, a DNA linker with a UMI barcode was ligated onto the 3' end of the RNA reads. RNA was fragmented and reverse trasnscribed. cDNA was circularized and amplified using Illumina N(i5) and (i7) indices. Libraries were then cleaned with PCRClean DX beads and sequenced.

value: WT yeast


title: Mid Log yeast, replicate 3, NETseq

description:
Early_vs_Mid_sumnorm.csv
Mid_vs_Late_sumnorm.csv


title: Mid Log yeast, replicate 2, NETseq


title: cell pool A, replicate 1

description:
cDA1
plasmid_and_cell_pool_counts.csv


title: Early Log yeast, replicate 2, NETseq

description:
Early_vs_Mid_sumnorm.csv
Early_vs_Late_sumnorm.csv


title: nF-LB-C2-36m


title: Early Log yeast, replicate 1, NETseq


title: Mix-CAF008

source_name: CAF from seminoma and non-seminoma

value: CAF from seminoma and non-seminoma


title: FAMApro::FAMA-MYC/fama-1, FAMA ChIP

city: Stanford

first: Dominique

middle: C.

last: Bergmann

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

data_processing:
cutadapt to trim the raw reads
picard to remove PCR duplicates
bowtie2 to align the reads to TAIR10 gemone assembly
MACS2 (ChIP-seq) or DANPOS (MNase-seq) to define bound regions
Assembly: TAIR10
Supplementary files format and content: bw files to visualize the enrichment of corresponding reads

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
DNA were extracted based on ChIP protocol or MNase-seq protocol (see methods part in the publication)
per manufacturer's instructions

value: seedling

value: 71D10;Cell Signaling Technology


title: nanopore_siFBL_rep1

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
mRNA half-life of the HEK293T cells and C4-2 cells was computed as described before. In short, the mRNA levels were first normalized to RPKM (Reads Per Kilobase Million). To reduce the noise due to genes that showed a higher expression levels after inhibition of transcription, we then scaled the FPKM values based on the expression levels of top 10 genes which were most stable between time points, so that these genes will have no change of expression between time points. The RNA degradation rate kdecay was defined as the mean values of ratio from RPKM at time 0 over the RPKM value at each other time point (0hour, 6hour, 12hour, 24hour). After that the pseudo-mRNA half-life t1/2 was calculated as ln2/kdecay.
After base-calling using guppy_basecaller (version 3.6.1), the direct RNA-seq of Nanopore reads with quality value more than 7 were aligned to the human genome (Hg38, GRCh38.p13 from GENCODE database) using Minimap with --secondary=no -ax splice -uf -k14 option. Tombo resquiggle was used to assigned to transcript sequence as reference from the website: https://www.gencodegenes.org/human . We extracted the median, standard deviation, mean, and dwell time from Nanopore raw signal data in each direct RNA sequencing read to calculate the probability of Nm modification using the training models from rRNA. The modified base supported by at least 5 modified transcripts were identified as modified Nm sites.
Assembly: hg19 for NGS RNA-seq. hg38 for Nanopore RNA-seq.
Supplementary files format and content: *.count.txt: Tab-delimited text files include abundance measurements.
Supplementary files format and content: *.bw: bigWig files.

source_name: C4-2 Cell line

extract_protocol: RNA was extracted from the HEK293T and C4-2 cells.

tag: sirna

value: siFBL


title: nanopore_siCTRL_rep2

value: siCTRL


title: Batch 1,  0.0 mg/ml (control),  biological rep1

value: batch 1


title: Late Log yeast, replicate 1, NETseq


title: cell pool A, replicate 2

description:
cDA2
plasmid_and_cell_pool_counts.csv


title: Mix-CAF007


title: IP_SPL10_2

city: Shanghai

first: Xu

last: Pengfei

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

description: DAP-seq

data_processing:
DAP-Seq reads (150-nucleotide paired-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Assembly: TAIR 10
Supplementary files format and content: narrowPeak, log
Library strategy: DAP-seq

molecule: protein

source_name: leaf

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
DAP-seq

value: leaf

tag: ecotype


title: Col, FAMA  ChIP


title: nF-MPAF

tag: cell type


title: Early Log yeast, replicate 3, NETseq


title: nanopore_siCTRL_rep1


title: IP_SPL10_1

description: DAP-seq

tag: treatment


title: TE-CAF017

source_name: CAF from non-seminoma, teratoma

value: CAF from non-seminoma, teratoma


title: Rep4 stele 3

city: Uppsala

first: Van

last: Nguyen

address: Almas Allé 5

country: Sweden

institute: Uppsala University

description:
3D-stele_S44_L007
processed data: Counts_Sample123_LCM

data_processing:
Sequencing was done by Scilife Lab (Uppsala, Sweden) and we received the raw data
Filtering was done using SortmeRNA and Trimmomatic
Mapping was done against the Picea abies genome v1.0 using STAR
Read counting was done using HTSeq-Count
Supplementary_files_format_and_content: Matrix table containing all raw counts of all samples

organism: Picea abies

source_name: Root_stele 3

growth_protocol: The seedlings were grown on plate until approximately 2 days after germination.

extract_protocol:
For zone samples, the total RNA samples were isolated using protocol adapted from Azevedo et al¸ 2003. After extraction with chloroform + isoamyl alcohol, the RNA was washed and eluted on-column using RNeasy kit (Qiagen). For LCM samples, the total RNA was extracted using RNAqueous - Micro Kit (Ambion).
Libraries were prepared according to standard Illumina protocol

value: Root

tag: segment/zone

value: stele 3


title: Rep3 stele 3

description:
3C-stele_S43_L007
processed data: Counts_Sample123_LCM


title: In_SPL10_input

description: DAP-seq

value: InPut


title: TE-CAF012


title: Rpb4 CDS deletion, 3' READS second biological replicate

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

data_processing:
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls), python
Mapping to yeast genome build Sac cer3 (first 17 non-A bases; accepting perfect matches and unique reads only), bowtie
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome, python
Tally reads by UTR position if they map to the first 400nt after an ORF end, python
Assembly: Sac cer 3
Supplementary files format and content: Tab-delimited text files with relative read counts for each position in the first 400 nt downstream of the stop codon

growth_protocol: Yeast were cultured at 30°C in YPD medium to mid-log phase

extract_protocol:
Total RNA was extracted by the hot acidic phenol method and further purified using Qiagen Rneasy columns with DNase treatment
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

treatment_protocol: Cells were collected by centrifugation and frozen at -80°C

value: log phase YPD culture

tag: cell line

value: 3' READS


title: FAMApro::FAMA-MYC/fama-1, input

tag: genotype

value: input


title: EC-CAF010

source_name: CAF from non-seminoma, embryonal carcinoma


title: Mid Log yeast, replicate 1, NETseq


title: Rep1 stele 3

description:
3A-stele_S48_L008
processed data: Counts_Sample123_LCM


title: EC-CAF014

value: CAF from non-seminoma, embryonal carcinoma


title: nanopore_siFBL_rep2


title: Sample_1_Control AnaII-III

city: New York

first: Jesse

middle: Stephen Swyer

last: Novak

state: New York

address: 1230 York Ave.

institute: Weill Cornell Institutional MD-PhD Program/The Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9). The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Assembly: mm10
Supplementary files format and content: TPM file

source_name: Skin

extract_protocol:
Unwounded epidermal samples were prepared as above, and single cells were gated on DAPI for dead cell exclusion, negative for non-epidermal markers (CD140a, CD117, CD31, and CD45; hereafter referred to as “Dump gate”) and SCA1 (LY6A/LY6E), and positively selected on high expression of integrin-a6 and CD34.
Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 machines.

value: Skin

value: Hair follicle stem cells

value: female

value: K15-CrePGR; Shh+/-

value: RU486 for 8 days

tag: Stage

value: anagen


title: Rep4 stele 2

description:
2D-stele_S41_L007
processed data: Counts_Sample123_LCM

source_name: Root_stele 2

tag: tissue

value: stele 2


title: Rep2 stele 3

description:
3B-stele_S42_L007
processed data: Counts_Sample123_LCM


title: SE-CAF021

source_name: CAF from seminoma

value: CAF from seminoma


title: Sample_Control Telo

value: telogen


title: Rep3 stele 2

description:
2C-stele_S40_L007
processed data: Counts_Sample123_LCM


title: Rep2 stele 2

description:
2B-stele_S39_L007
processed data: Counts_Sample123_LCM


title: Late Log yeast, replicate 3, NETseq

value: WT yeast


title: Rep1 stele 2

description:
2A-stele_S38_L007
processed data: Counts_Sample123_LCM

value: Root


title: TE-CAF019

value: CAF from non-seminoma, teratoma


title: GFP_neg1+neg2

first: Dominik

last: Saul

state: Minnesota

address: 200 First Street SW Rochester

library_source: transcriptomic single cell

data_processing:
After FACS, the single cell suspension was loaded onto the 10x chromium device using Version 2 chemistry. The samples were sequenced at GeneWiz where we targeted 50,000 reads per cell on an Illumina HiSeq 4000 device. We performed two lanes of sequencing using these  parameters for each sample. scRNA-seq data were aligned and quantified using the 10X  Genomics Cell Ranger Software Suite (v6.1.1) against the murine reference genome (mm10).
Assembly: scRNA-seq data were aligned and quantified using the 10X  Genomics Cell Ranger Software Suite (v6.1.1) against the murine reference genome (mm10).
Supplementary files format and content: Standard 10x output includes matrix, features, barcodes.

source_name: bone callus

extract_protocol: For the scRNA-seq study, we used a total of four mice for single cell sequencing (2 male, 2 female)  and performed a closed diaphyseal tibia fracture. After 14 days, mice were sacrificed and the left tibia was isolated. Subsequently, the visually verified  callus area was removed after cleaning the bone from surrounding tissue. The callus area was  minced with a scalpel in FACS buffer. Pieces were then digested three times for 30 minutes each  in 0.7mg/ml Collagenase solution (Sigma-Aldrich, Saint Louis, MO]) at 37°C with agitation. In between steps, the solution was filtered over a wet 70µm cell filter, washed three times with PBS  and the collected reaction stopped with FBS, while the remaining pieces were further digested.  The samples were pooled together, resuspended in RBC lysis buffer for 5 minutes and diluted in FACS buffer. The remaining solution was resuspended and kept on ice. or preparation of the samples for CyTOF. The three samples per bone were  pooled together and resuspended in RBC lysis buffer for 5 minutes and diluted in FACS buffer. The remaining solution was resuspended and kept on ice, and sorted by FACS.

value: bone callus


title: Rep4 stele 1

description:
1D-stele_S47_L008
processed data: Counts_Sample123_LCM

source_name: Root_stele 1

value: stele 1


title: P0 mouse, scRNA-seq, rep M10

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description: 10X Chromium Single Cell 3' v3

data_processing:
Sequencing reads were aligned to the mouse genome (mm10-3.0.0) with the Cell Ranger software (version 3.0.2) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger aggr. The files from "filtered_feature_bc_matrix" folders are provided (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) compressed into tar.gz files.
Assembly: mm10-3.0.0
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

source_name: Kidney tissue

extract_protocol:
Harvested P0 mouse kidneys were dissected into smaller pieces in cold Dulbecco’s phosphate-buffered saline (DPBS Ca2+-/Mg2+-, Gibco 14190-250). For cell isolations, the Bacillus licheniformis cold active protease (CAP) protocol was used to dissociate kidney tissue into cells as previously described in (Ransick et al., 2019). Briefly, tissue was lysed in the DPBS lysis buffer, with the final concentration of a 2.5 mg/ml type 2 collagenase (Worthington, #LS00417), 7.5 mg/ml B. licheniformis protease (Creative Enzymes, NATE-0633), and 125 U/ml DNase I (Worthington, #LS002058) at 12°C. After 30 mins of digestion, the reaction was terminated with 20% fetal bovine serum (FBS) in DPBS. Cells were then strained through coarse 40 um cell strainers (Falcon, #352340) and pelleted at 364g in a swinging bucket centrifuge at 6oC. Cells were resuspended in cold AutoMACs Running Buffer (AMB, Miltenyi Biotec) and strained again with fine mesh 40um strainer (VWR, #76327-098). Live cells with DNA staining (DAPI-/DRAQ5+) were sorted by ARIA II FACS (BD Biosciences) and pelleted at 350g for 10mins then resuspended in ice cold AMB.
Chromium_SingleCell_3'_ReagentKits_v2/v3_UserGuide (CG00052, CG000183)

value: Kidney tissue

value: Kidney cells

tag: age

value: at day of birth (postnatal day 0)


title: Rep4 QC area

description:
1D-Qcmer_S52_L008
processed data: Counts_Sample123_LCM

source_name: Root_QC area

value: QC area


title: P0 mouse, scRNA-seq, rep M9

description: 10X Chromium Single Cell 3' v3


title: SE-CAF020

first: Daniel

address: Moorenstr. 5


title: SE-CAF022


title: GFP_pos1+pos2


title: P0 mouse, scRNA-seq, rep M8

description: 10X Chromium Single Cell 3' v3


title: P0 mouse, scRNA-seq, rep F6

description: 10X Chromium Single Cell 3' v3


title: Rep3 stele 1

description:
1C-stele_S46_L008
processed data: Counts_Sample123_LCM


title: P0 mouse, scRNA-seq, rep F5

description: 10X Chromium Single Cell 3' v3


title: Rep4 Ground tisue

description:
1D-endo_S55_L008
processed data: Counts_Sample123_LCM

source_name: Root_Ground tisue

value: Ground tisue


title: Rep3 Ground tisue

description:
1C-endo_S54_L008
processed data: Counts_Sample123_LCM


title: P0 mouse, scRNA-seq, rep F4

description: 10X Chromium Single Cell 3' v3


title: Rep3 QC area

description:
1C-Qcmer_S51_L008
processed data: Counts_Sample123_LCM


title: P0 mouse, scRNA-seq, rep M7

description: 10X Chromium Single Cell 3' v2


title: EC-CAF005

value: CAF from non-seminoma, embryonal carcinoma


title: Rep2 stele 1

description:
1B-stele_S37_L007
processed data: Counts_Sample123_LCM


title: P0 mouse, scRNA-seq, rep M5

description: 10X Chromium Single Cell 3' v2


title: P0 mouse, scRNA-seq, rep M6

description: 10X Chromium Single Cell 3' v2


title: P0 mouse, scRNA-seq, rep M4

description: 10X Chromium Single Cell 3' v2


title: Rep1 QC area

description:
1A-Qcmer_S49_L008
processed data: Counts_Sample123_LCM


title: Rep1 stele 1

description:
1A-stele_S36_L007
processed data: Counts_Sample123_LCM


title: SE-CAF009


title: Rep2 QC area

description:
1B-Qcmer_S50_L008
processed data: Counts_Sample123_LCM


title: SE-CAF011


title: SE-CAF018


title: Rep2 Ground tisue

description:
1B-endo_S45_L007
processed data: Counts_Sample123_LCM


title: P0 mouse, scRNA-seq, rep F3

description: 10X Chromium Single Cell 3' v2


title: Rep1 Ground tisue

description:
1A-endo_S53_L008
processed data: Counts_Sample123_LCM


title: EGCs, tumor conditioned medium, 24h, rep4

city: Leuven

first: Gianluca

last: Matteoli

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7
Adapters were filtered with ea-utils fastq-mcf v1.05
Splice-aware alignment was performed with HISAT2 (PMID: 31375807) against the reference genome mm10 using the default parameters.
Assembly: mm10
Supplementary files format and content: Reads mapping to multiple loci in the reference genome were discarded. Resulting BAM alignment files were handled with Samtools v1.5

source_name: enteric glial cells

extract_protocol:
RNA was isolated using  RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions.
QuantSeq 3 mRNA libraryprep (015, Lexogen) was used to generate cDNA libraries according to the manufacturer's instructions

tag: cell origin

value: embryonic neurosphere-derived

tag: time

value: enteric glial cells

value: WT

value: tumor conditioned medium


title: EGCs, healthy conditioned medium, 24h, rep4

value: healthy conditioned medium


title: EGCs, unstimulated, 24h, rep4

value: unstimulated


title: P0 mouse, scRNA-seq, rep F1

description: 10X Chromium Single Cell 3' v2

tag: strain


title: Rep5 Zone 4

description:
Sector4-E_S42_L003
processed data: Counts_Sample1234_Zones

source_name: Root_Zone 4

value: Zone 4


title: EGCs, tumor conditioned medium, 24h, rep3


title: Rep3 Zone 4

description:
Sector4-C_S40_L003
processed data: Counts_Sample1234_Zones

value: Root


title: Rep2 Zone 4

description:
Sector4-B_S39_L003
processed data: Counts_Sample1234_Zones


title: P0 mouse, scRNA-seq, rep F2

description: 10X Chromium Single Cell 3' v2


title: Rep4 Zone 4

description:
Sector4-D_S41_L003
processed data: Counts_Sample1234_Zones


title: Rep1 Zone 4

description:
Sector4-A_S38_L003
processed data: Counts_Sample1234_Zones


title: EGCs, healthy conditioned medium, 24h, rep3


title: EGCs, unstimulated, 24h, rep3


title: Rep5 Zone 3

description:
Sector3-E_S32_L003
processed data: Counts_Sample1234_Zones

source_name: Root_Zone 3

value: Zone 3


title: EGCs, tumor conditioned medium, 24h, rep2


title: Rep3 Zone 3

description:
Sector3-C_S30_L003
processed data: Counts_Sample1234_Zones


title: EGCs, healthy conditioned medium, 24h, rep2


title: EGCs, unstimulated, 24h, rep2


title: Rep2 Zone 3

description:
Sector3-B_S29_L003
processed data: Counts_Sample1234_Zones


title: Rep4 Zone 3

description:
Sector3-D_S31_L003
processed data: Counts_Sample1234_Zones


title: Rep1 Zone 3

description:
Sector3-A_S28_L003
processed data: Counts_Sample1234_Zones


title: Rep5 Zone 2

description:
Sector2-E_S27_L003
processed data: Counts_Sample1234_Zones

source_name: Root_Zone 2

value: Zone 2


title: EGCs, tumor conditioned medium, 24h, rep1


title: Rep4 Zone 2

description:
Sector2-D_S26_L003
processed data: Counts_Sample1234_Zones


title: EGCs, healthy conditioned medium, 24h, rep1


title: Rep2 Zone 2

description:
Sector2-B_S24_L003
processed data: Counts_Sample1234_Zones


title: EGCs, healthy conditioned medium, 12h, rep4


title: Rep1 Zone 2

description:
Sector2-A_S23_L003
processed data: Counts_Sample1234_Zones


title: Rep3 Zone 2

description:
Sector2-C_S25_L003
processed data: Counts_Sample1234_Zones


title: EGCs, tumor conditioned medium, 12h, rep4


title: EGCs, unstimulated, 24h, rep1


title: EGCs, tumor conditioned medium, 12h, rep3


title: EGCs, unstimulated, 12h, rep4


title: Rep4 Zone 1

description:
Sector1-D_S21_L003
processed data: Counts_Sample1234_Zones

source_name: Root_Zone 1

value: Zone 1


title: EGCs, healthy conditioned medium, 12h, rep3


title: Rpb4 CDS deletion, 3' READS first biological replicate

value: log phase YPD culture

value: 3' READS


title: Rep3 Zone 1

description:
Sector1-C_S20_L003
processed data: Counts_Sample1234_Zones


title: EGCs, unstimulated, 12h, rep3


title: Rep1 Zone 1

description:
Sector1-A_S18_L003
processed data: Counts_Sample1234_Zones


title: EGCs, tumor conditioned medium, 12h, rep2


title: EGCs, healthy conditioned medium, 12h, rep2


title: EGCs, unstimulated, 12h, rep2


title: EGCs, healthy conditioned medium, 12h, rep1


title: PAX3-KO Human RA gastruloid 120h rep2

city: Seattle

first: Nobuhiko

last: Hamazaki

state: Washington

address: Foege Building S-210 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
10X single-cell 3' RNA-seq
KO_merged.RDS

data_processing:
Base calls were converted to fastq format using cellranger v6.0.0 mkfastq function. The sequencing reads are then demultiplexed based on i5 and i7 barcodes, mapped to hg38 reference genome and assigned to GRCh38 (GENCODE v32/Ensembl 98) genes by cellranger v6.0.0 count function with default setting.
Assembly: hg38
Supplementary files format and content: Processed data files include RDS files after preprocesses.

source_name: Human RA gastruloid

growth_protocol: 4x10^4 hESCs were seeded on 0.5 μg/cm2 Vitronectin-coated 12-well plate (Gibco, A14700) in Nutristem hPSC XF medium (Biological Industries, 05-100-1A) with 10 µM Y-27632. On day 1, the medium was replaced with Nutristem containing 5 µM Y-27632. On day 2, the medium was replaced with Nutristem. On day 3, the medium was replaced with Nutristem containing 3.25 µM CHIR (Millipore, SML1046). 24 hrs later, cells were detached by StemPro Accutase and dissociated into single cells. 4,000-5,000 cells were seeded to 96 wells with 50 µl Essential 6 medium (Thermo, A1516401) containing 0.5 µM CHIR, 0.5 or 1 µM RA (Millipore Sigma, R2625), and 5 µM Y-27632. At 24 hrs, 150 µl of Essential 6 medium was added to each well. At 48 hrs, 150 µl of the medium was removed with a multi-channel pipette, and 150 µl of Essential 6 medium containing 5% Matrigel and 1 µM RA was added and maintained in 37C 5% CO2 incubator until 120 hrs. To further test the effect of the signal perturbation on gastruloid formation, we added 1 uM LDN-193189 (STEMCELL Technologies, 72147), 100 ng/ml BMP4 (R&D, 314-BP-010), or 3 uM CHIR to the medium at 48 hrs along with 5% Matrigel and 0.5 µM RA.

extract_protocol:
Gastruloids were collected from 96 wells using a micropipette and transferred to PBS (-) to wash out the medium and incubated with 0.05% Trypsin-EDTA for 8 min at 37C. After quenching the reaction by the addition of 1/10 volume of FBS, gastruloids were dissociated into single cells by repeated pipetting.
Dissociated single-cell suspensions were loaded in Chromium Next GEM Chip G Single Cell Kit (Chromium, PN-1000120) on a 10X Chromium controller according to the manufacturer's instruction. Single-cell RNA-seq libraries were generated with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (Chromium, PN-1000121) and Dual Index Kit TT Set A, 96 rxns (Chromium, PN-1000215). Library concentrations were determined by Qubit (Invitrogen) and the libraries were visualized by Tapestation (Agilent).
All libraries were sequenced on NextSeq 2000 (Illumina) (Read 1: 28 cycles, Read 2: 85 cycles, Index 1: 10 cycles, Index 2: 10 cycles).

treatment_protocol: To further test the effect of the signal perturbation on gastruloid formation, we added 1 uM LDN-193189 (STEMCELL Technologies, 72147) to the medium at 48 hrs along with 5% Matrigel and 0.5 µM RA. for genetic perturbation, RNP complexes were prepared according to the manufacturer’s procedures. Briefly, equal molars of crRNA and tracrRNA (IDT, 1072532) were mixed and heated at 95C for 5 minutes in a thermal cycler and kept at room temperature for 10-20 min for hybridization. AltR-Cas9 protein (IDT, 1081058) was added to the crRNA and tracrRNA mixture to assemble Cas9-RNPs. RUES2-GLR hESCs were trypsinized with StemPro Accutase and the reaction was quenched with StemFlex media supplemented with 10 mM Y-276322. 2x10^5 cells were transferred to a new tube and centrifuged at 250g for 5 min. Cells were resuspended in 20 µl nucleofection buffer (16.4 µl Nucleofector® Solution + 3.6 µl Supplement) provided in P3 Primary Cell 4D-Nucleofector™ X Kit S (Lonza, V4XP-3032). After the addition of 3 µl RNP and 0.5 µl of Alt-R Cas9 Electroporation Enhancer (IDT, 1075915), cells were transferred to 16-well Nucleocuvette™ Strips and nucleofected with the CA-137 program. The nucleofected cells were transferred to the 12-well plate which contains Nutristem with 10 mM Y-27632 and after 24 hrs, the medium was replaced with Nutristem without Y-27632. Cells were maintained until they reach 50-70% confluent. Then, RNP-introduced cells were transferred onto 0.5 μg/cm2 Vitronectin-coated 12-well plate and proceeded to RA-gastruloid induction steps described above and collected at 120 hrs of induction for sc-RNA-seq analysis.

tag: developmental stage

value: PAX3-KO Human RA gastruloid 120h after induction.

value: PAX3-gRNAs nucleofection


title: PAX3-KO Human RA gastruloid 120h rep1


title: EGCs, unstimulated, 12h, rep1


title: EGCs, tumor conditioned medium, 6h, rep4


title: TBX6-KO Human RA gastruloid 120h rep2

value: TBX6-KO Human RA gastruloid 120h after induction.

value: TBX6-gRNAs nucleofection


title: TBX6-KO Human RA gastruloid 120h rep1


title: EGCs, healthy conditioned medium, 6h, rep4

value: embryonic neurosphere-derived


title: B#3, hMuSC-40/PI

city: Créteil

first: Teoman

last: Ozturk

address: 8 rue du Général Sarrail

country: France

institute: INSERM IMRB U955

data_processing:
FASTQ files were aligned to the human reference genome (Ensembl Homo Sapiens GRC38.110 assembly) using the Hisat2 aligner software (Hisat2.2.1) with default parameters, and exported into BAM format. 20 to 30 million reads per sample were obtained, with more than 85% mapping efficiency. FeatureCounts was used to obtain the number of aligned reads per gene.
Assembly: hg38
Supplementary files format and content: text file include raw counts for each sample

source_name: Muscle

extract_protocol:
hMuSC were directly sorted in lysis buffer from RNA extraction Kit (#74034, Qiagen) and RNA were purified according to manufacturer recommendations
cDNA libraries were generated with 1 ng of total RNA using the Illumina Stranded total RNA prep Ligation Kit

value: Muscle

value: Muscle Stem Cells


title: B#4, hMuSC-40/PI


title: NTC Human RA gastruloid 120h rep2

value: NTC Human RA gastruloid 120h after induction.

value: NTC-gRNAs nucleofection


title: Rep5 Zone 1

description:
Sector1-E_S22_L003
processed data: Counts_Sample1234_Zones


title: NTC Human RA gastruloid 120h rep1


title: LDN-treated Human RA gastruloid 120h

description: 10X single-cell 3' RNA-seq

value: LDN-treated Human RA gastruloid 120h after induction.


title: EGCs, unstimulated, 6h, rep3

value: enteric glial cells

value: WT

value: unstimulated


title: Human gastruloid 96h

description: 10X single-cell 3' RNA-seq

source_name: Human gastruloid

value: Human gastruloid 96h after induction.


title: EGCs, tumor conditioned medium, 6h, rep2

value: tumor conditioned medium


title: Rep2 Zone 1

description:
Sector1-B_S19_L003
processed data: Counts_Sample1234_Zones

value: Root

value: Zone 1


title: EGCs, healthy conditioned medium, 6h, rep2

value: healthy conditioned medium


title: Human RA gastruloid 120h

description: 10X single-cell 3' RNA-seq

value: Human RA gastruloid 120h after induction.


title: Human RA gastruloid 96h

description: 10X single-cell 3' RNA-seq

value: Human RA gastruloid 96h after induction.


title: EGCs, unstimulated, 6h, rep2


title: Human gastruloid 48h

description: 10X single-cell 3' RNA-seq

value: Human gastruloid 48h after induction.


title: EGCs, tumor conditioned medium, 6h, rep1

value: embryonic neurosphere-derived


title: Human gastruloid 24h

description: 10X single-cell 3' RNA-seq

value: Human gastruloid 24h after induction.


title: EGCs, tumor conditioned medium, 12h, rep1


title: EGCs, unstimulated, 6h, rep1


title: Human gastruloid 0h

description: 10X single-cell 3' RNA-seq

value: Human gastruloid 0h after induction.


title: EGCs, unstimulated, 6h, rep4


title: Sham-rep 2

city: Suzhou

first: Jiangbo

last: Guo

state: Jiangsu

address: 899 Pinghai St.

department: Department of Orthopaedics

institute: The First Affiliated Hospital of Soochow University

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged Rat pre-miRNA databases (known pre-miRNA from miRBase (v22) plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: Rnor 6.0
Supplementary files format and content: Excel file includes raw and normalized tag counts for each Sample

organism: Rattus norvegicus

source_name: nucleus pulposus

extract_protocol:
Total RNA was extracted from the nucleus pulposus tissue of each sample.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina Novaseq 6000 sequencer following the manufacturer's instructions.

value: nucleus pulposus

value: K-wires for 4 weeks


title: Sham-rep 3


title: EGCs, tumor conditioned medium, 6h, rep3


title: fus loxo_1

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

institute: University Hospital Würzburg

description: stable expression (after lentiviral infection) of doxycycline inducible SQSTM1-NTRK2 fusion, LOXO-101 inhibition of Trk kinase

data_processing:
Base calling with Illumina NextSeq RTA v3.7.17
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to human genome (GRCh38.p13 primary assembly and mitochondrion) using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version 109.20210226
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 109.20210226 for GRCh38.p13) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O –fraction).
Genome_build: GRCh38.p13 (primary assembly and mitochondrion)
Supplementary_files_format_and_content: Character (TAB) separated value file containing mRNA abundance measurements

source_name: U87MG (ATCC #HTB-14) cell line

growth_protocol: U87MG stably expressing the lentiviral TrkB constructs (either wt-TrkB, YFF or SQSTM1-NTRK2) were seeded at a density of 200.000 cells in 35 mm cell culture dishes (Falcon). All cells were grown in media containing 1µg/ml Puromycin. The cells were further treated with 1 µg/ml doxycycline to induce expression of the corresponding TrkB-related constructs (Dox on). For control, the solvent DMSO was added. 24 h after Dox-induction, some of the cell culture dishes were treated with 1 µg/ml LOXO-101 (Larotrectinib). After another 24h, cells were lysed and RNA was extracted (Qiagen RNeasy mini kit #74104). As a control, RNA was also extracted from untransformed and uninfected U87MG cells.

extract_protocol:
Total RNA was extracted from cell cultures using the Qiagen RNeasy Mini Kit.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥9.0. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~300 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 48 hours to induce expression of the corresponding TrkB-related constructs (Dox on). To acutely block kinase activity, cells were treted with the Trk kinase inhibitor 1 µg/ml LOXO-101 (Larotrectinib).

value: doxycycline, 48h; Loxo, 24h

tag: genetic background


title: fus loxo_2


title: fus loxo_3


title: fus dox_3

description: stable expression (after lentiviral infection) of doxycycline inducible SQSTM1-NTRK2 fusion

value: doxycycline, 48h


title: fus loxo_4


title: IDD-rep 1

value: Compression for 4 weeks


title: fus dox_2


title: IDD-rep 2


title: EGCs, healthy conditioned medium, 6h, rep3

value: enteric glial cells

value: WT


title: fus dox_4


title: NTS_349

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Low quality reads or reads with adapters were first filtered and removed prior to mapping. Reads containing N > 10% and those with a poor Qscore (50% bases of the read had Qscore of < or equal to 5).
Mapping of clean reads to the reference transcriptome ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4 was conducted with HISAT2. Reads were mapped to the transcriptome directly. HISAT2 software was used to alignment RNA-seq sequencing data to ensure junction reads were positioned precisely.
Expression levels were determined by the relative abundance of transcripts (count of sequencing) that mapped to a gene or exon. FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) was calculated and used to estimate expression levels.
Read counts were normalized, and a model dependent p-value estimation was conducted with an FDR correction for multiple hypothesis testing.
Genome_build: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary_files_format_and_content: excel sheet with normalized counts, fold change (log2), and FDR corrected p-values

source_name: nodose ganglion

extract_protocol: Illumina library construction for pair-end reads

value: nucleus tractus solitarius

tag: Sex

value: male


title: fus dox_1


title: NTS_347


title: Sham-rep 1


title: fus ctr_4

value: untreated


title: NTS_346


title: fus ctr_3


title: fus ctr_2


title: EGCs, healthy conditioned medium, 6h, rep1

value: healthy conditioned medium


title: NTS_344


title: Human gastruloid 72h

description: 10X single-cell 3' RNA-seq

value: Human gastruloid 72h after induction.


title: NTS_345


title: fus ctr_1


title: NTS_343


title: wt loxo_4

description: stable expression (after lentiviral infection) of doxycycline inducible TrkB-wt, LOXO-101 inhibition of Trk kinase


title: IDD-rep 3


title: NTS_342


title: wt loxo_3


title: NTS_341


title: wt loxo_2


title: S9-FF5_P3

city: Scottsdale

first: Xianfeng

last: Chen

state: AZ

address: 13400 E Shea Blvd

data_processing:
processed with our customoized pipeline which are modified from missionbio tapestri V2 pipeline
Assembly: hg19
Supplementary files format and content: ucsf_chapman.bed
Supplementary files format and content: amplicon design file

source_name: Surgical resection high grade serous ovarian carcinoma grade 3 stage 3C

extract_protocol:
flow sorting
tapestri single cell sequencing platform
scDNA-seq


title: wt loxo_1


title: S8-FFPE4_P3

value: Surgical resection high grade serous ovarian carcinoma grade 3 stage 3C


title: wt dox_4

description: stable expression (after lentiviral infection) of doxycycline inducible TrkB-wt


title: S7-FFPE3_P3

source_name: Surgical resection high grade serous ovarian carcinoma grade 1 stage 3C


title: wt dox_2


title: S6-FFPE2_P2+P3


title: YFF dox_2

description: stable expression (after lentiviral infection) of doxycycline inducible TrkB-YFF mutant


title: wt ctr_1


title: wt ctr_4


title: S14-FFPE6_P3+P4

source_name: Surgical resection ovarian endometrriod carcinoma grade 2 stage 3B


title: YFF dox_1


title: S1-FF1_P2


title: wt ctr_3


title: wt ctr_2


title: S2-FF2_P3


title: S5-FFPE1_P2


title: S4-FF4_P3


title: 11.6 Wk human fetal, snRNA-seq, rep M3

description: 10X Chromium Single Cell 3' v3

data_processing:
Sequencing reads were aligned to the human genome (GRCh38-2020-A) with the Cell Ranger software (version 5.0.1) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger aggr. The processed files (filtered_feature_bc_matrix.h5) are provided. Controlled access to raw fastq files is available through dbGaP.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: Kidney tissue

extract_protocol:
Cryopreserved human fetal kidneys were processed with optimized single-nuclei dissociation protocol to minimize potential tissue damage artifacts from frozen samples and loss of intact RNA molecules during the dissociation process. Briefly, the tissues were transported in DMEM (5% FBS, 25mM HEPES), removed from capsules, dissected into <2mm pieces and flash frozen in liquid nitrogen for later isolation. Nuclei isolation from flash frozen tissue was performed by the same protocol used with mouse tissue described above. For sex identification, a small amount of the donor tissue was lysed, and DNA was isolated by incubating in DirectPCR Lysis Reagent (Qiagen, #102-T) with 1% Proteinase K (Roche, 3115879001). Donor tissue was then sexed using primers for Y-specific human SRY (SRY-FOR: CCC ATG AAC GCA TTC ATT GTG TGG/ SRY-REV: ATT TTA GCC TTC CGA CGA GGT CGA TA), and ZFX/ZFY (ZFX/ZFY FOR: GCA CTT CTT TGG TAT CTG AGA AAG T/ ZFX/ZFY REV: ATA ATC ACA TGG AGA GCC ACA AGC T) to confirm DNA isolation quality.
Chromium_SingleCell_3'_ReagentKits_v3_UserGuide (CG000183)

value: Kidney tissue

value: Kidney cells

value: 11.6 Wk human fetal


title: YFF ctr_4


title: S12-FF8_P3


title: S3-FF3_P3

value: Surgical resection high grade serous ovarian carcinoma grade 1 stage 3C


title: S16-FFPE8_P3+P4


title: YFF ctr_3


title: wt dox_1


title: YFF dox_4


title: 10.6 Wk human fetal, snRNA-seq, rep M1

description: 10X Chromium Single Cell 3' v3

value: 10.6 Wk human fetal


title: S11-FF7_P3

source_name: Surgical resection high grade serous ovarian carcinoma grade 3 stage 3B


title: S15-FFPE7_P3+P4

value: Surgical resection high grade serous ovarian carcinoma grade 3 stage 3B


title: 11.3 Wk human fetal, snRNA-seq, rep F1

description: 10X Chromium Single Cell 3' v3

value: 11.3 Wk human fetal