title: Luteolin added high-fat diet, rep2

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

description: replicate 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-6 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

data_processing:
The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).
All probe signal value was transformed by logarithm and normalized by quantile method.
The 1-way anova test, tukey HSD test and fold change were applied. Statistical significance was adjusted by the Benjamini-Hocbherg multiple-testing correction with false discovery rate(FDR).
All data analysis was conducted using R statistical language v. 2.4.1.

source_name: Mouse Muscle

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: Twenty-four male C57BL/6J mice were obtained from the Joongang Laboratory Animal at 4 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-76 semi-purified diet for a one-week acclimation period after arrival

extract_protocol: Total RNA was extracted from the gastronemius muscle using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were fed a normal diet (ND, n=8), high-fat diet consisting of 20% fat and 1% cholesterol (HFD, n=8) or HFD with 0.01% (w/w) luteolin (LU, n=8) for 20 weeks

tag: Sex

value: male

value: 4 weeks

value: Muscle

value: Luteolin added high-fat diet


title: Luteolin added high-fat diet, rep1

status: Public on Jul 27 2022

type: RNA

description: replicate 1

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

tag: tissue

tag: treatment


title: Luteolin added high-fat diet, rep3

description: replicate 3


title: High-fat diet, rep1

description: replicate 1

value: High-fat diet


title: ZT07

type: SRA

city: Hangzhou

first: zuorui

last: xie

address: Zhejiang Gongshang University

country: China

institute: ZFM

description: C57BL/6 mice

library_source: genomic

data_processing:
Total DNA extracted from the sample
Using FLASH v1.2.7 software, the reads of each sample were spliced by overlapping, and the obtained splicing sequence was the original Tag data (Raw Tags)
Using Trimmomatic v0.33 software to filter the spliced Raw Tags to obtain high-quality Tag data (Clean Tags)
Using UCHIME v4.2 software to identify and remove chimera sequences to obtain final effective data (Effective Tags)
Use Usearch software to cluster effective data at the 100% similarity to obtain Amplicon Sequence Variant (ASV). By comparing the representative sequences of OTUs with the Silva (bacteria) taxonomy database, the species classification information corresponding to each OTU can be obtained, and then the community composition of each sample can be counted at each level (phylum, class, order, family, genus, species). The QIIME software was used to generate species abundance tables at different taxonomic levels, and then the R language tool was used to draw the community structure map of the samples at each taxonomic level.
Assembly: V3-V4 region of the 16S rRNA gene
Supplementary files format and content: Clean gene for every gene and every sample
Supplementary files format and content: OTU_stat: Seqs detail of all samoles
Supplementary files format and content: OTU_stat_detail: Tag number and OTU number of all samples
Supplementary files format and content: OTU_shared_for_alpha_diversity: OTU shared for alpha diversity of all samples

molecule: genomic DNA

organism: feces metagenome

source_name: gastric contents

growth_protocol: The experiment was performed in accordance with the ethical guidelines for animal use and with permission from Shanghai Public Health Clinical Center Animal Ethics Committee. Specific pathogen free C57BL/6 mice (6-week old, 18~20 g) were obtained from Sino-British SIPPR/BK Lab Animal Ltd. (Shanghai, China) and experiment was conducted in Laboratory Animal Department of Shanghai Public Health Clinical Center. The mice were grouped into two experimental groups: (i) Preventive group, and (ii) Therapeutic group.

extract_protocol:
Genomic DNA was extracted from thegastric contents with a QIAamp PowerFecal DNA extraction kit, according to the manufacturer’s instructions.
16S rRNA gene high-throughput sequencing of the V3-V4 region was performed by BGI Genomics Co., Ltd. (Shenzhen, China).

treatment_protocol: Mice model by administering L. paracasei ZFM54 before (pretreatment) and after (treatment) H. pylori challenge. The gastric contents were immediately collected from experimental mice.

value: mice challenged with Helicobacter pylori


title: Normal diet, rep2

description: replicate 2

value: Normal diet


title: Normal diet, rep1

description: replicate 1


title: High-fat diet, rep3

description: replicate 3


title: High-fat diet, rep2

description: replicate 2


title: Normal diet, rep3

description: replicate 3


title: 7046-100pg

type: genomic

city: Fort Worth

first: Jianye

last: Ge

state: TX

address: 3500 Camp Bowie Blvd

department: Center for Human Identification

country: USA

institute: University of North Texas Health Science Center

hyb_protocol: Following resuspension, the samples were combined back into their original wells, and 70µL was loaded onto the Omni5 beadchips (four samples per chip). Hybridization of the samples to the beadchips was carried out in a 48°C hybridization oven for about 24 hours. Beadchips were washed to prepare for the staining process and assembled into Flow-Through Chambers using LCG glass and LCG spacers.

scan_protocol: Flow-Through Chambers were placed into the Chamber Rack of a 44°C water circulator where RA1 reagent was used to wash away unhybridized DNA. Extension and staining (XStain) were performed on each beadchip:  the surface of the beadchips was conditioned for the extension reaction, primer extension was performed using labeled nucleotides, hybridized DNA was removed using 95% formamide/1mM EDTA, and the labeled extended primers underwent a multi-layer staining process. The stained beadchips were washed and coated, and then dried in a vacuum desiccator for approximately one hour before imaging on the Illumina iScan.

data_processing:
Initial data screening, including assessment of Illumina’s internal controls, was performed using GenomeStudio 2.0.5 software.
Processed data contains: Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

organism: Homo sapiens

source_name: UTAH/CEPH cell line

label_protocol: The DNA samples were denatured and neutralized before adding the Amplification Master Mix.  The amplification plate was incubated in a 37°C hybridization oven for approximately 23 hours. Samples were then split in half for subsequent processing, with both halves receiving the same treatment. Enzymatic fragmentation was carried out by adding FRG to each sample and incubating the plate at 37°C for one hour. The DNA was precipitated out using PA1 and 100% 2-propanol, which resulted in a blue pellet in the bottom of each well. Reagent RA1 was added to each sample to resuspend the precipitated DNA.

extract_protocol: DNA extraction protocol not provided.

tag: cell line

value: UTAH/CEPH

tag: cell type

value: lymphoblastoid cell lines

tag: dna amount

value: 100pg DNA sample


title: 7035-100pg


title: 7028-100pg


title: 7013-100pg


title: 13047-100pg


title: 13053-100pg


title: rSPL10 (r10)-Mock biological replicate 1

city: Athens

first: Lanxi

last: Hu

address: 120 Charlton street

institute: University of Georgia

description: Eukaryotic Strand-specific Transcriptome Resequencing

library_source: transcriptomic

data_processing:
The data was filtered using SOAPnuke software in BGI. Specifically, the entire read was deleted in either of the following scenarios, 1) more than 28% of a read matches the adapter sequence, 2) more than 40% bases having a quality value lower than 20, 3) more than 3% N in the read. As results, ~48 M clean reads with average Q30 ≥ 88.81% per sample was obtained.
Differential expression analysis was done by comparing transcript levels using DEseq2 (LFC ≥ ±0.58, padj ≤ 0.05) {Love, 2014}. Gene ontology was analyzed against the whole Arabidopsis genome at TAIR Gene Ontology terms website, http://geneontology.org/ {Ashburner 2000, The Gene Ontology Consortium 2020}, and which was confirmed using total detected 22,622 (covers 88.7% of known genes in Arabidopsis genome) genes of the RNA-seq results on agriGO website http://systemsbiology.cau.edu.cn/agriGOv2/# {Tian, 2017}.
Figures were generated in R software. R scripts are available in the supplementary data of the paper.
Assembly: The clean RNA-seq data were aligned against the TAIR10 reference genome using with HiSAT2 (v.2.1.0, {Kim, 2019}) with following parameters, hisat2 -p 4 -x TAIR10indexed -1 sample_strand1.fq.gz -2 sample_strand2.fq.gz -S aligned_sample.sam. The aligned reads were assembled into transcripts according to the TAIR10 annotation {Lamesch, 2012;Swarbreck, 2008} using Stringtie {Pertea, 2016}. ~99% overall alignment rate was reached for each sample.
Supplementary files format and content: A combined gene count matrix sorted in .csv format

organism: Arabidopsis thaliana

source_name: Bulk

growth_protocol: We used 33 days old juvenile leaves or r10 leaves and 52 days old adult leaves. Detailed plant growth condition was described in the section of materials and methods.

extract_protocol:
Total RNAs were extracted using E.Z.N.A. Total RNA kit (Omega BIO-TEK). RNA quality was assessed with a 2100 Bioanalyzer instrument (Agilent, RIN score ≥ 7, 28S/18S ≥ 1). RNA concentration was measured using a Nanodrop spectrophotometer (Thermo Scientific, RNA concentration ≥ 50 ng/μL, 260/280 ~2.0). RNA samples were sequenced at BGI, San Jose lab.
Oligo dT based mRNA enrichment was followed by random N6 primer based reverse transcription. Synthesized cDNAs were then tailed with an Adenine each and then ligated with a bubble adapter. The DNA products were further amplified through PCR, separated with heat and cyclized using splint oligo. The synthesized DNA nanoballs were then sent for non-stranded mRNA sequencing (PE100) on a DNA Nanoball Sequencing (DNBseq) platform.

treatment_protocol: Pto DC3000 (1 x 108 CFU/mL suspended in 10mM MgCl2) was infiltrated into juvenile and adult wild type (Col-0) leaves and leaves 1-2 from rSPL10 plants. 10 mM MgCl2 was used as the mock treatment. Three hours after inoculation, 20 leaf discs with comparable size from 5-10 individual plants were cored and collected as one biological repeat per genotype per treatment. Three biological repeats were prepared for each genotype/treatment.

value: Bulk

tag: genotype

value: Mock

tag: time


title: Juvenile (Juv)-Mock biological replicate 1


title: ZI07

description: C57BL/6 mice

value: mice challenged with Helicobacter pylori before antibiotic treatment


title: Juvenile (Juv)-Mock biological replicate 2


title: Attached cells with F. serratus rep 3

city: Roscoff

first: Francois

last: Thomas

address: Place George Teissier

department: UMR8227, CNRS-UPMC

country: France

institute: Station Biologique de Roscoff

description:
Att_Fser3
norm_genes_count_matrix_Free-living_vs_Attached.txt

data_processing:
Quality filtering using Trimmomatic v0.38.0 on https://galaxy.sb-roscoff.fr
Transcript quantification using Salmon v0.8.2 on https://galaxy.sb-roscoff.fr
Read count noralization and downstream processing analyses were performed using the DESeq2 v1.26.0 package in R v3.6.2.
Genome_build: NC_015844.1
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every genes and every samples from free-living cells. Used for comparison between the different carbon sources.
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every genes in samples from microcosms with L. digitata and F. serratus (free-living and algae-attached cells). Used for comparison between free-living and algae-attached cells.

organism: Zobellia galactanivorans

source_name: Marine flavobacteria

growth_protocol: Z. galactanivorans was grown with the respective carbon source (either 10 algal pieces or 4 g/l of purified sugars) at 20 °C under agitation in 50 ml of marine minimum medium supplement with antibiotics to which the strain is resistant. Initial OD = 0.05.

extract_protocol:
Free-living bacterial cells were lysed by adding 400 μl of lysis buffer (4 M guanidine thiocyanate, 25 mM sodium acetate pH 5.2, 5 g.l-1 N-laurylsarcosinate) and 500 μl of phenol and incubated 5 min at 65 °C. RNA was extracted using phenol-chloroform. Extracts were treated 1 h at 37 °C with 2 units of Turbo DNAse and purified on mini-columns NucleoSpin RNA Clean-up following the manufacturer's instructions. RNA was eluted in 50 μl of nuclease-free water. RNA from algae-attached bacteria was extracted as follows. Two algal pieces were immersed in killing buffer, vortexed and placed 7 min in an ultrasonic bath to detach bacteria from the algal surface. Algae were removed and cell pellets resuspended in lysis buffer. RNA extraction and DNAse treatment were performed as described above for the free-living bacteria. DNAse were inactivated using DNAse inactivation reagent following the manufacturer instructions.
Librairies were performed by the Plateforme de Séquençage I2BC (UMR9198, CNRS, Gif-sur-Yvette) on a NextSeq instrument (Illumina) using the NextSeq 500/550 High Output Kit v2 (75 cycles) which included a Ribo-Zero ribosomal RNA depletion step.

treatment_protocol: During the exponential phase, 10 ml of culture medium and algal pieces (when applicable) were retrieved on ice. 0.5 volume of killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3) was added to the liquid samples and cell pellets were frozen in liquid nitrogen. Algal pieces were washed twice in killing buffer:H2O (1:1) and frozen in liquid nitrogen. Samples were stored at -80 °C before further RNA extraction.

value: DsijT

tag: carbon source

value: Fucus serratus

value: algae-attached


title: 13050-100pg


title: ZI03

description: C57BL/6 mice


title: 7035-500pg

value: 500pg DNA sample


title: 7437-500pg


title: ZT01

description: C57BL/6 mice


title: 7013-500pg


title: Attached cells with F. serratus rep 2

description:
Att_Fser2
norm_genes_count_matrix_Free-living_vs_Attached.txt


title: 7028-500pg


title: 13053-500pg


title: Juvenile (Juv)-Mock biological replicate 3


title: ZI05

description: C57BL/6 mice


title: ZI06

description: C57BL/6 mice


title: ZI04

description: C57BL/6 mice


title: ZI01

description: C57BL/6 mice


title: Attached cells with L. digitata rep 3

description:
Att_Ldig3
norm_genes_count_matrix_Free-living_vs_Attached.txt

value: Laminaria digitata


title: 7046-500pg


title: ZH07

description: C57BL/6 mice

value: normal mice


title: 13050-500pg


title: 13047-500pg


title: 7046-50ng

value: 50ng DNA sample


title: Attached cells with L. digitata rep 1

description:
Att_Ldig1
norm_genes_count_matrix_Free-living_vs_Attached.txt


title: ZH04

description: C57BL/6 mice


title: 7035-50ng


title: 7437-50ng


title: Free-living cells with maltose rep 3

description:
FL_Maltose3
norm_gene_count_matrix_CarbonSource.txt

value: Maltose

value: free-living


title: Free-living cells with maltose rep 1

description:
FL_Maltose1
norm_gene_count_matrix_CarbonSource.txt


title: Free-living cells with maltose rep 2

description:
FL_Maltose2
norm_gene_count_matrix_CarbonSource.txt


title: 13053-50ng


title: ZH03

description: C57BL/6 mice


title: Free-living cells with FCSP rep 3

description:
FL_FCSP3
norm_gene_count_matrix_CarbonSource.txt

value: FCSP


title: 13047-50ng


title: ZH01

description: C57BL/6 mice


title: ZH05

description: C57BL/6 mice


title: 13050-50ng


title: ZG07

description: C57BL/6 mice

value: mice challenged with Helicobacter pylori before Lactobacillus paracasei ZFM54 treatment


title: ZH02

description: C57BL/6 mice


title: 7013-50ng

value: UTAH/CEPH


title: Free-living cells with FCSP rep 1

description:
FL_FCSP1
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Healthy, H7

city: Tehran

first: Fariborz

last: Bahrami

address: 69 Pasteur Ave.

department: Immunology

country: Iran

institute: Pasteur Institute of Iran

description:
2018 Samples
Sample name: H7

data_processing:
Trace data were analyzed using GeneMapper software 5 package (Applied Biosystems, Bleiswijk, The Netherlands), assigned the threshold value.
The areas of each assigned peak (in arbitrary units) were exported for further analysis in Microsoft Excel.
Data were normalized to GAPDH, and signals below the threshold value for noise cutoff in GeneMapper (Log2-transformed peak area of 7.64) were assigned the threshold value. The normalized data were Log2-transformed for statistical analysis.

label: MLPA reagents (MRC-Holland)

source_name: Whole Blood

label_protocol: A specific reverse transcription (RT) primer was designed for each target-specific sequence (see PMID 21956656; Supplementary Table 1), located immediately downstream of the left- and right-hand half-probe target sequence. RNA was reverse-transcribed and the left- and right-hand half-probes were hybridized to the cDNA at 60°C overnight. Annealed half-probes were ligated by ligase and were subsequently amplified by PCR (33 cycles of 30 s/95°C, 30 s/58°C, 60 s/72°C, followed by 1 cycle of 20 min/72°C). Primers and probes were from Sigma-Aldrich Chemie (Zwijndrecht, The Netherlands) and MLPA reagents from MRC-Holland (Amsterdam, The Netherlands). Reverse transcription primers and half-probes were designed by Leiden University Medical Center (Department of Infectious Diseases, Leiden

extract_protocol: RNA from each 2.5-ml PAXgene blood sample was extracted by PAXgene Blood RNA kit (PreAnalytiX, UK), according to the manufacturer's instruction and kept at -80oC until use.

treatment_protocol: Volunteers who appeared healthy and did not meet the exclusion criteria (pregnancy, lactating, major illnesses such as immunosuppression, HIV infection, cancer, renal failure, heart diseases, tuberculosis, jaundice, diabetes mellitus, allergies and recent major surgeries) were subjected to leishmanin skin test (LST) and 48 h later, the LST+ and the LST- groups were assigned as the asymptomatic and the healthy groups, respectively. TDR/WHO reference leishmanin (0.1 ml) was injected intradermally into the inner surface of the left forearm. The diameter of induration at the injection site was measured by a millimeter graduated ruler at 48 h later using the ball-point pen technique. Indurations more than or equal to 5 mm were considered as positive LST. Healed volunteers had one or two CL scars during the previous CL season (September-December 2017). Patients had active cutaneous lesions. L. tropica patients were diagnosed by an ITS1 PCR–RFLP assay. Samples were obtained using a non-invasive tape disc-based sampling method and genomic DNA was used for a PCR, targeting ITS1 region of  Leishmania, followed by RFLP for species- specific identification. Blood samples were taken using PAXgene tubes. After extraction of RNA from the PAXgene tubes, RNA was reverse-transcribed and the left- and right-hand half-probes were hybridized to the cDNA at 60°C overnight. Annealed half-probes were ligated by ligase and were subsequently amplified by PCR (33 cycles of 30 s/95°C, 30 s/58°C, 60 s/72°C, followed by 1 cycle of 20 min/72°C). Primers (see PMID: 21956656; Supplementary Table 1) and probes were from Sigma-Aldrich Chemie (Zwijndrecht, The Netherlands) and MLPA reagents from MRC-Holland (Amsterdam, The Netherlands). Reverse-transcription primers and half-probes were designed by Leiden University Medical Center (Department of Infectious Diseases, Leiden, The Netherlands) and comprised sequences for a housekeeping gene (GAPDH) along with 144 selected genes to profile innate, adaptive, and inflammatory immune responses. Trace data were analyzed using GeneMapper software 5 package (Applied Biosystems, Bleiswijk, The Netherlands). The areas of each assigned peak (in arbitrary units) were exported for further analysis in Microsoft Excel. Data were normalized to GAPDH, and signals below the threshold value for noise cutoff in GeneMapper (Log2-transformed peak area of 7.64) were assigned the threshold value. The normalized data were Log2-transformed for statistical analysis.

tag: disease state

value: Healthy

tag: lesion status

value: No Lesion LST-

value: Whole Blood


title: Whole Blood, Healthy, H5

description:
2018 Samples
Sample name: H5


title: Whole Blood, Healthy, H2

description:
2018 Samples
Sample name: H2


title: Free-living cells with FCSP rep 2

description:
FL_FCSP2
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Patient, O

description:
2018 Samples
Sample name: O

value: Patient (active Cutaneous leishmaniasis (CL) lesions)

value: Fresh Lesion


title: ZG05

description: C57BL/6 mice


title: Whole Blood, Patient, L

description:
2018 Samples
Sample name: L


title: Whole Blood, Healthy, H1

description:
2018 Samples
Sample name: H1


title: Free-living cells with alginate rep 2

description:
FL_Alginate2
norm_gene_count_matrix_CarbonSource.txt

value: DsijT

value: Alginate


title: Free-living cells with alginate rep 3

description:
FL_Alginate3
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Patient, Q

description:
2018 Samples
Sample name: Q


title: 7028-50ng

value: lymphoblastoid cell lines


title: Whole Blood, Patient, P

description:
2018 Samples
Sample name: P


title: ZG04

description: C57BL/6 mice


title: Whole Blood, Patient, M

description:
2018 Samples
Sample name: M


title: Whole Blood, Patient, G

description:
2018 Samples
Sample name: G


title: Whole Blood, Patient, I

description:
2018 Samples
Sample name: I


title: Free-living cells with F. serratus rep 3

description:
FL_Fser3
norm_genes_count_matrix_Free-living_vs_Attached.txt
norm_gene_count_matrix_CarbonSource.txt

value: Fucus serratus


title: Free-living cells with A. nodosum rep 3

description:
FL_Anod3
norm_gene_count_matrix_CarbonSource.txt

value: Ascophyllum nodosum


title: Whole Blood, Patient, F

description:
2018 Samples
Sample name: F


title: Whole Blood, Healed, 62

description:
2018 Samples
Sample name: 62

value: Healed

value: Cured Lesion


title: Whole Blood, Patient, K

description:
2018 Samples
Sample name: K


title: Free-living cells with alginate rep 1

description:
FL_Alginate1
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Healed, 63

description:
2018 Samples
Sample name: 63


title: Whole Blood, Healed, 64

description:
2018 Samples
Sample name: 64


title: Whole Blood, Healed, 61

description:
2018 Samples
Sample name: 61


title: Free-living cells with L. digitata rep 3

description:
FL_Ldig3
norm_genes_count_matrix_Free-living_vs_Attached.txt
norm_gene_count_matrix_CarbonSource.txt

value: Laminaria digitata


title: Whole Blood, Healed, 60

description:
2018 Samples
Sample name: 60


title: YTH02

description: C57BL/6 mice

value: mice admininstrated with Lactobacillus paracasei ZFM54


title: ZG01

description: C57BL/6 mice


title: ZG02

description: C57BL/6 mice


title: YTH07

description: C57BL/6 mice


title: Whole Blood, Patient, D

description:
2018 Samples
Sample name: D


title: Free-living cells with A. nodosum rep 2

description:
FL_Anod2
norm_gene_count_matrix_CarbonSource.txt

value: free-living


title: Whole Blood, Healed, 50

description:
2018 Samples
Sample name: 50


title: YTH06

description: C57BL/6 mice


title: Whole Blood, Healed, 49

description:
2018 Samples
Sample name: 49


title: Free-living cells with A. nodosum rep 1

description:
FL_Anod1
norm_gene_count_matrix_CarbonSource.txt


title: YTH01

description: C57BL/6 mice


title: Whole Blood, Patient, C

description:
2018 Samples
Sample name: C


title: YTH03

description: C57BL/6 mice


title: Whole Blood, Healed, 52

description:
2018 Samples
Sample name: 52


title: ZG03

description: C57BL/6 mice

value: mice challenged with Helicobacter pylori before Lactobacillus paracasei ZFM54 treatment


title: Whole Blood, Healed, 44

description:
2018 Samples
Sample name: 44


title: Whole Blood, Healed, 42

description:
2018 Samples
Sample name: 42


title: Whole Blood, Healed, 65

description:
2018 Samples
Sample name: 65


title: YTH04

description: C57BL/6 mice


title: Free-living cells with L. digitata rep 2

description:
FL_Ldig2
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Asymptomatic, 36

description:
2018 Samples
Sample name: 36

value: Asymptomatic

value: No Lesion LST+


title: YH04

description: C57BL/6 mice

value: normal mice


title: Whole Blood, Asymptomatic, 35

description:
2018 Samples
Sample name: 35

value: Whole Blood


title: Free-living cells with L. digitata rep 1

description:
FL_Ldig1
norm_genes_count_matrix_Free-living_vs_Attached.txt
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Healed, 48

description:
2018 Samples
Sample name: 48


title: Free-living cells with F. serratus rep 2

description:
FL_Fser2
norm_genes_count_matrix_Free-living_vs_Attached.txt
norm_gene_count_matrix_CarbonSource.txt


title: Whole Blood, Asymptomatic, 30

description:
2018 Samples
Sample name: 30


title: YH03

description: C57BL/6 mice


title: YH05

description: C57BL/6 mice


title: YH07

description: C57BL/6 mice


title: YG07

description: C57BL/6 mice

value: mice challenged with Helicobacter pylori


title: Whole Blood, Healthy, 25

description:
2018 Samples
Sample name: 25

value: Healthy

value: No Lesion LST-


title: Whole Blood, Healthy, 24

description:
2018 Samples
Sample name: 24


title: Whole Blood, Asymptomatic, 23

description:
2018 Samples
Sample name: 23


title: Whole Blood, Asymptomatic, 22

description:
2018 Samples
Sample name: 22


title: YG06

description: C57BL/6 mice


title: Whole Blood, Healthy, 21

description:
2018 Samples
Sample name: 21


title: Whole Blood, Healthy, 20

description:
2018 Samples
Sample name: 20


title: Whole Blood, Healed, 51

description:
2018 Samples
Sample name: 51


title: YG05

description: C57BL/6 mice


title: Whole Blood, Asymptomatic, 31

description:
2018 Samples
Sample name: 31


title: Whole Blood, Healthy, 34

description:
2018 Samples
Sample name: 34


title: YH02

description: C57BL/6 mice


title: Whole Blood, Healed, 41

description:
2018 Samples
Sample name: 41


title: Whole Blood, Asymptomatic, 18

description:
2018 Samples
Sample name: 18


title: Whole Blood, Asymptomatic, 16

description:
2018 Samples
Sample name: 16


title: Whole Blood, Healthy, 33

description:
2018 Samples
Sample name: 33


title: Whole Blood, Healthy, 13

description:
2018 Samples
Sample name: 13


title: YH01

description: C57BL/6 mice


title: YG01

description: C57BL/6 mice


title: Whole Blood, Asymptomatic, 12

description:
2018 Samples
Sample name: 12


title: YG04

description: C57BL/6 mice


title: Whole Blood, Asymptomatic, 5

description:
2018 Samples
Sample name: 5


title: 42-C243

city: Santa Barbara

first: Laurel

middle: S.

last: Hiebert

state: CA

address: Molecular, Cellular, and Developmental Biology

institute: University of California Santa Barbara

data_processing:
Raw sequencing reads were cleaned and trimmed. First, the program Rcorrector was used to correct random sequencing errors and to eliminate read pairs where reads were flagged as ‘uncorrectable’ (Song and Florea, 2015). Next, Trim Galore! was used to remove low-quality reads from the dataset (with a quality Phred score cutoff of 5, a minimum read length threshold of 36 bp, a stringency parameter of 1 for adapter sequence overlap, and a maximum allowed error rate of 0.1) and to trim Illumina adapters sequences from raw sequencing reads (https://github.com/FelixKrueger/TrimGalore; Martin, 2011). Ribosomal RNA was removed by eliminating reads that mapped to the SILVA large and small subunit databases (SILVA_132_LSUParc_tax_silva.fasta and SILVA_138_SSURef_NR99_tax_silva.fasta) using Bowtie2 (Langmead and Salzberg, 2012). Finally, we used the software FastQC to identify overrepresented sequences from the read set, which we removed (Andrews, 2010).
Transcriptomes were assembled using the software Trinity with in silico read normalization (Grabherr et al., 2011). For each species, raw read data from all conditions and replicates were pooled to create a single reference assembly per species. The reference assemblies were taxon-filtered to remove contaminant transcripts. First, two BLAST searches were conducted to identify possible contaminants: a Diamond Blastx against the uniprot ref database and a blastn search against the NCBI’s nr database (both with E-value set to 1e-25). The program Blobtools was used to assign a taxon to each transcript using the blast results (using option “bestsumorder”) and then to remove transcripts that were assigned to anything other than chordate, no-hit, or undefined. Next, the program Transdecoder was used to select only the single best open reading frame per transcript, and only keep those with a minimum length of 90. The program cd-hit was used to collapse similar transcripts (parameters: -M 0 -T 20). Low-expression transcripts were removed using Kallisto to estimate abundance and the trinity script “filter_low_expr_transcripts.pl” to remove transcripts with expression level lower than 5 TPM. Assemblies were assessed by looking at basic summary matrices and by quantifying completeness using the program BUSCO (v3) by searching for a curated set of single copy orthologs present in all metazoans (metazoa odb9 database) (Seppey et al., 2019).
Orthologous genes between the two species were identified using a reciprocal best blast hit strategy and the program Blast-Besties (https://github.com/Adamtaranto/blast-besties). Genes were annotated first by diamond blastx to human refseq database (e-value 1e-25), then those without human ortholog matches, further diamond blastx searches were conducted against uniprot reference proteome database (e-value 1e-25) to identify lineage-specific transcripts.
The program Kallisto was used to quantify abundances of transcripts and align raw reads onto the assembled contigs (using 100 bootstraps) (Bray 2016). The Trinity analysis program ‘PtR’ was used to compare biological replicates across samples, by constructing a correlation matrix for each sample in an assembly, and principal components analysis plots, labeled by stage and replicate. Outliers were removed and treatments were combined as necessary at this step. Differential transcript expression was assessed using the program voom (Law et al., 2014). Data were normalized using rlog transformation. All pairwise comparisons of sample type within species were tested. Transcripts were considered differentially expressed if they showed a 2-fold average difference in expression between sample types with a false discovery rate (FDR) p-value of <0.001.
Tissue-specific expression patterns were computed using perl scripts packaged with Trinity, and we selected the “DE_pairwise_summary.txt.class_down_priority” files, which prioritize the up-regulated genes.
Genome_build: N/A
Supplementary_files_format_and_content: Kallisto matrix files with expression data for each sample

organism: Clavelina lepadiformis

source_name: activated

extract_protocol:
Tissues were flash-frozen in liquid nitrogen and RNA was extracted with NucleoSpin RNA extraction kit (Machery-Nagel)
NEB Next® Ultra RNA Library Prep Kit for Illumina
Sequencing was done on a Novaseq 6000 PE150 Illumina sequencing platform. Samples were split between two sequencing lanes with at least one of each replicate per stage in each lane to reduce lane-effects.

value: Germinating 24 degrees


title: Whole Blood, Asymptomatic, 17

description:
2018 Samples
Sample name: 17


title: Whole Blood, Healthy, 7

description:
2018 Samples
Sample name: 7


title: Whole Blood, Healthy, 14

description:
2018 Samples
Sample name: 14


title: YC07

description: C57BL/6 mice

value: mice challenged with Helicobacter pylori after Lactobacillus paracasei ZFM54 pretreatment


title: Whole Blood, Asymptomatic, 8

description:
2018 Samples
Sample name: 8


title: YC01

description: C57BL/6 mice


title: YC05

description: C57BL/6 mice


title: 39-C183

value: Germinating 18 degrees


title: YC03

description: C57BL/6 mice


title: YC02

description: C57BL/6 mice


title: Whole Blood, Asymptomatic, 15

description:
2018 Samples
Sample name: 15


title: Whole Blood, Asymptomatic, 4

description:
2018 Samples
Sample name: 4


title: YC04

description: C57BL/6 mice


title: YG02

description: C57BL/6 mice


title: Jurkat_n3

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

description: replicate 3

data_processing:
RNAseq libraries were sequenced on a NovaSeq PE150, Illumina (paired-end mode)
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Filtering with PrinSeq (0.20.4)
RNA-seq data were analyzed using FaRLine with the FasterDB database (Benoit-Pilven et al., 2018; Mallinjoud et al., 2014).  The differential gene expression (DEG) between conditions was calculated with DESeq2.
Assembly: hg19
Supplementary files format and content: raw read counts

source_name: Jurkat cell line

growth_protocol: ATL-2, MOLT-4 and Jurkat T cells were cultured in RPMI supplemented with 10% heat inactivated fetal calf serum. Jurkat-HBZ expressing cells were maintained in complete RPMI medium under puromycin selection (5μg/ml).

extract_protocol:
Total RNA extraction was performed with the RNeasy Mini kit (QIAGEN; 74104) following the manufacturer’s protocol, including a DNAse digestion step (RNase-Free DNase Set; QIAGEN; 79254) after the first wash with RW1 buffer. RNA concentration was assessed using the NanoDrop (Thermo Scientific) and RNA quality was verified by electrophoresis on an agarose gel.
Directional (rRNA removal) and mRNA library preparation were generated at Novogene (Hong Kong, China) using Stranded RNA Sample Pre Kit (Illumina) and sequenced NovaSeq PE150 (15 G raw data per sample)

value: lymphocyte

value: Jurkat parental


title: Whole Blood, Asymptomatic, 9

description:
2018 Samples
Sample name: 9


title: Whole Blood, Healthy, 11

description:
2018 Samples
Sample name: 11


title: 40-C241


title: 41-C242


title: Whole Blood, Healthy, 6

description:
2018 Samples
Sample name: 6


title: Whole Blood, Asymptomatic, 10

description:
2018 Samples
Sample name: 10


title: Jurkat_n2

description: replicate 2


title: 37-C181


title: Whole Blood, Asymptomatic, 3

description:
2018 Samples
Sample name: 3


title: 38-C182


title: Jurkat_n1

description: replicate 1


title: Myc_HBZ_G7_2

source_name: Jurkat cell line stably expressing HBZ

value: Jurkat cell line stably expressing HBZ


title: 33-CS3

source_name: stolons

value: Stolon


title: 29-CD2

source_name: dormant

value: Dormant


title: 27-CB3

source_name: budding chamber

value: Bud


title: 32-CS2


title: heart WT2

city: Beijing

first: li

middle: guo

last: qi

state: Chaoyang

address: Anzhen number 2 road

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: transverse aortic constriction 8 weeks

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Raw counts and Fragments Per Kilobase Million(FPKM) were calculated by stringtie v1.3.3
Genome_build: mm9
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: heart

extract_protocol:
After TAC 8 weeeks, the heart tissue was put in liquid nitrogen quickly, and preserved in low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from granulosa cells following a manufacturer’s protocol. Total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running an 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

value: wildtype

value: heart

value: transverse aortic constriction


title: MOLT4_n3

description: replicate 3

source_name: MOLT4 cell line

value: acute T lymphoblastic leukaemia


title: 28-CD1


title: heart KO1

description: transverse aortic constriction 8 weeks

value: miR-27b-3p knockout


title: Myc_HBZ_E9_2


title: 26-CB2


title: 25-CB1


title: heart KO3

description: transverse aortic constriction 8 weeks


title: MOLT4_n1

description: replicate 1


title: heart WT1

description: transverse aortic constriction 8 weeks


title: MOLT4_n2

description: replicate 2


title: 22-CZ1

source_name: zooid

value: Zooid


title: Myc_HBZ_F11_2


title: Myc_HBZ_D7_2


title: 31-CS1


title: 21-P243

organism: Polyandrocarpa zorritensis


title: 20-P242


title: heart WT3

description: transverse aortic constriction 8 weeks


title: 23-CZ2


title: heart KO2

description: transverse aortic constriction 8 weeks


title: ATL2_n3

description: replicate 3

source_name: ATL2 cell line

value: Adult T-cell Leukemia

value: ATL


title: 30-CD3


title: 24-CZ3


title: 19-P241

value: Germinating 24 degrees


title: 18-P183


title: 17-P182


title: Mock_transduced_RPTECs

city: Fukuoka

first: Satoru

last: Koyanagi

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

country: Japan

institute: Kyushu University

hyb_protocol: Labelled RNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human miRNA V21.0 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v9.5.3.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data was further analyzed using GeneSpring GX Software (14.9,1 ).

source_name: RPTECs SA7K clone, mock-transduced

label_protocol: Total RNA was labelled using a miRNA Complete Labeling and Hyb kit (Agilent Technologies).

extract_protocol: Total RNA including low molecule RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using miRNeasy (Qiagen)

value: renal proximal tubular epithelial cells (RPTECs; SA7K clone)

value: kidney


title: 16-P181

value: Germinating 18 degrees


title: mESCS-C5_HISeq-1

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
ATAC-seq: Peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” [34], [35]. Then, peak summits were extended by 250 bp on both sides  to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions [36]  (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
Next, significance peak scores “(-log10(p-value))” were converted to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million.  This normalized score per million value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield higher number of peaks and higher significance scores overall. Thus, scores per million allow the direct comparison of peaks across biological replicates.
Next, we compiled a condition - MEF, mESC- and sequencer specific - BGI, Illumina - peak set containing reproducible peaks observed in a particular cell type and sequencing platform. For that, we generated a cumulative peak set per cell type and sequencing platform and performed the same iterative approach as mentioned above. Therefore, maintaining the peak with the highest significance or score per million. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered.
Assembly: mm10
Supplementary files format and content: bigwig for ATAC-seq samples, called peaks in (.gtf) format and counts per peak in .txt format.

source_name: mouse embryonic stem cells

extract_protocol: OMNI-ATACseq libraries were generated from FACS purified cells (in case of MEFs: Thy1+ ; in case of mESCs: Thy1-/Ssea1+/Epcam+)  according to the standard protocol (see doi: 10.1038/nmeth.4396). Afterwards, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations. Library fragments ranging from 150 to 700 bp were enriched and the final elution volume was 21 ul. The finalized libraries were provided to BGI for sequencing. HiSeqX10 sequencing was performed in 150bp PE mode followed by read trimming to 100bp PE for analysis. In case of sequencing on the DNBSEQ-G400 instrument libraries were converted to nanoballs and sequenced according to established workflows in 100bp PE mode (see doi: 10.1093/nargab/lqaa034).

value: mouse embryonic stem cells

value: C57/Bl6 background


title: ATL2_n1

description: replicate 1


title: mESCS-C3_HISeq-2


title: 12-PS3

value: Stolon


title: ATL2_n2

description: replicate 2


title: 10-PS1


title: ADAR1-KD_RPTECs

source_name: RPTECs SA7K clone, ADAR1-KD


title: mESCS-C1_HISeq-3


title: 9-PD3

value: Dormant


title: MEFS-C1_HISeq-7

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: 3-PZ3


title: MEFS-C2_HISeq-6


title: MEFS-C4_HISeq-4


title: shTRPV4-8cP3

city: Washington

first: Jiaxiang

last: Tao

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

data_processing:
Sequence reads were mapped to human genome GRCh38.p13 using HISAT2 (2.2.1 version) with paired option
.sam files and corresponding index files were generated using samtools (1.1.3 version)
Read count extraction and annotation using HTSEQ (0.13.5 version) and Ensembl 104 annotation
Reads were normalized using DESeq.2 package
Assembly: GRCh38.p13
Supplementary files format and content: .txt files containing totaled exon reads

growth_protocol: See "Cell culture and reagents" section in corresponding manuscript

extract_protocol:
Total RNA was extracted and purified by Zymo Research Quick-DNA/RNA MiniPrep Plus Kit (Zymogen) as per manufacturer’s recommendations.
Strand specific mRNA libraries were generated using the NEBNext Ultra II Directional RNA library prep Kit for Illumina (New England BioLabs #E7760), and mRNA was isolated using Poly(A) mRNA magnetic isolation module (New England BioLabs #E7490). Preparation of libraries followed the manufacturer’s protocol (2.2 05/19).  Input was 1 µg and samples were fragmented for 15 min for RNA insert size of ~200 bp.  The following PCR cycling conditions were used: 98°C for 30 s / 8 cycles: 98°C for 10 s and 65°C for 75 s / and final extension of 65°C for 5 min.

treatment_protocol: Cells were treated with media of viscosities 0.77 cP or 8 cP

value: Human Epithelial Breast Cancer

value: TRPV4 knockdown

value: sh TRPV4, High viscosity

value: Day 6


title: shTRPV4-8cP2


title: 6-PB3

source_name: budding nest

value: Bud


title: 7-PD1


title: 8-PD2


title: 2-PZ2

value: Zooid


title: 5-PB2


title: WGS_129

city: Tokyo

first: Yuta

last: Hiraike

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

data_processing:
Library strategy: WGS
Fastq reads were aligned to reference mouse genome build mm9 (canonical) by using BWA-MEM 0.7.10 with default parameters
The mapped reads were assigned to read groups and sorted using Picard software (ver 2.9.4).
Presumed PCR duplicate reads were eliminated using Novosort ver.1.03.01 (Novocraft Technologies, Malaysia).
The variant calling of single nucleotide variants (SNVs) was performed using Genome Analysis Toolkit (GATK) Best Practice Workflow pipeline using HaplotypeCaller (ver 3.7-0-gcfedb67) according to the GATK Best Practices for somatic short variant discovery
Genome_build: mm9
Supplementary_files_format_and_content: vcf showing single nucleotide variants (SNVs) compared to the ncbi37/mm9 C57BL/6J genome.

source_name: liver

extract_protocol:
Genomic DNA were extracted from the liver of 129 mouse using NucleoSpin Tissue kit (U0952S, Takara-Bio).
Whole genome sequencing libraries were prepared from genomic DNA using the Nextera DNA Sample Prep kit (Illumina).

value: liver


title: 4-PB1


title: SC-8cP2

value: WT

value: scramble RNA, High viscosity


title: SC-8cP3


title: 1-PZ1


title: 11-PS2


title: L6 for sncRNA-seq

city: Guangzhou

first: Wenli

last: Xu

state: Guangdong

address: Guangzhou, Guangdong Province, 510630, China.

institute: The Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Cutadapt was used to trim adapters and filter for sequences.
The software SPORTS (v 1.1) was applied to annotate the raw sncRNA-seq data with one mismatch tolerance.
DESeq2 package was used to detect the differential expressed genes (p<0.05 and |FC|≥2)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include the differential expression between two groups(H vs N; L vs N).

source_name: plasma exosome

extract_protocol:
For small RNA-seq profiling, the plasma exosome RNA was purified from 13 subjects, respectively. The exosome RNA was isolated from plasma exosome using the RNA isolation reagent TRIzol (Invitrogen).
By using the QIAseq® miRNA Library Kit (QIAgen, Cat# 331505), small RNA-seq libraries were constructed with 2~10 ng of the prepared exosomal small RNA in line with the manufacturer’s protocols.
Small RNA-seq libraries were prepared according to Illumina’s instructions and sequenced on an Illumina 3000 analyzer by EPIBIOTEK Company (Guangzhou, China).

value: plasma exosome

tag: patient diagnosis

value: HBV-ACLF


title: SC-8cP1


title: L4 for sncRNA-seq


title: SC-0.77cP3

value: scramble RNA


title: L5 for sncRNA-seq


title: SC-0.77cP2


title: AML patient 45

city: Seoul

first: Chansub

last: Lee

address: 101, Daehak-ro, Jongno-gu

institute: Seoul National University Hospital

description: Human bone marrow mononuclear cells (MNCs) from patients with AML were isolated using Ficoll gradient method and cryopreserved in Cell banker 2, a serum-free medium. The MNCs of the patients were thawed at 37℃ in Iscove’s modified Dulbecco’s media containing 10% fetal bovine serum before the experiment. We checked RNA integrity using Agilent 2100 BioAnalyzer (Agilent Technologies, CA, USA) with RNA integrity number being greater than six. For each gene, probes were screened for hybridization efficiency, the potential for cross-hybridization, and GC content. Finally, the best scoring probe was selected. Hybridization reactions were performed according to the manufacturer’s protocol.

scan_protocol: NanoString nCounter manufacturer’s protocol.

label: NanoString

source_name: Acute myeloid leukemia

value: bone marrow mononuclear cells


title: shTRPV4-8cP1


title: AML patient 47

hyb_protocol: For each gene, probes were screened for hybridization efficiency, the potential for cross-hybridization, and GC content. Finally, the best scoring probe was selected. Hybridization reactions were performed according to the manufacturer’s protocol.

data_processing: NanoString nCounter manufacturer’s protocol.

growth_protocol: Human bone marrow mononuclear cells (MNCs) from patients with AML were isolated using Ficoll gradient method and cryopreserved in Cell banker 2, a serum-free medium. The MNCs of the patients were thawed at 37℃ in Iscove’s modified Dulbecco’s media containing 10% fetal bovine serum before the experiment.


title: AML patient 44

label_protocol: NanoString nCounter manufacturer’s protocol.


title: L3 for sncRNA-seq


title: AML patient 46


title: SC-0.77cP1


title: AML patient 43


title: AML patient 41


title: L2 for sncRNA-seq


title: AML patient 42


title: AML patient 36


title: AML patient 39


title: AML patient 38


title: AML patient 35


title: H2 for sncRNA-seq

value: chronic hepatitis B (CHB) with flare


title: H4 for sncRNA-seq


title: AML patient 34


title: AML patient 40


title: AML patient 37


title: H1 for sncRNA-seq


title: AML patient 33


title: AML patient 31


title: L1 for sncRNA-seq


title: N3 for sncRNA-seq

value: normal


title: AML patient 30


title: AML patient 29


title: N2 for sncRNA-seq


title: AML patient 26


title: H3 for sncRNA-seq


title: AML patient 27


title: AML patient 28


title: ZCCHC4 Flag

city: Shanghai

first: Ha

last: Zhu

address: 800 Xiangyin Road

department: Institute of Immunology

institute: Second Military Medical University

description: Cells are transfected with ZCCHC4-Flag vector to overexpress ZCCHC4.

data_processing:
Library strategy: CLIP-seq
Primary sequencing data that produced by Illumina HiSeq 3000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Reads preprocessing, mapping and CITS analysis with raw data followed CLIP Tool Kit published in the article named CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
The information of input serves as a control to find positive binding information of protein and RNA.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Z4_peaks.txt: Tab-delimited text file includes peaks.

source_name: HepG2 cells

growth_protocol: 2×10^7 HepG2 cells transfected with Flag-tagged ZCCHC4 recombinant vectors or control empty vectors, and cultured in DMEM (Gibco) with 10% FBS (Gibco).

extract_protocol:
UV-CLIP was performed using anti-Flag M2 Magnetic Beads, and the isolated RNA was further processed into UV-CLIP-seq library and then standard Illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HepG2 cells

value: wildtype

value: transfection with ZCCHC4-Flag vector to overexpress ZCCHC4

tag: clip antibody

value: anti-Flag M2 Magnetic Beads (Sigma-Aldrich)


title: AML patient 25


title: AML patient 24


title: AML patient 23


title: AML patient 32


title: input

description: Cells are transfected with mock vector.

value: transfection with mock vector


title: ZCCHC4 KO1 rep2

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the human reference genome (GRCh38/hg38).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: gene_expression_HepG2_ZCCHC4_KO.txt: Tab-delimited text file includes FPKM values.

growth_protocol: Wild type cells and ZCCHC4 KO cells are seeded into 6 well plate and cultured until 80% confluence in DMEM (Gibco) with 10% FBS (Gibco), and then subjected for RNA-seq. Each group has two repetitions.

extract_protocol:
Total RNA was extracted with Trizol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

value: ZCCHC4 knockout

value: untreated


title: AML patient 22


title: ZCCHC4 KO1 rep1


title: AML patient 21


title: AML patient 20


title: AML patient 18


title: AML patient 17


title: WT rep2


title: N1 for sncRNA-seq


title: AML patient 19


title: AML patient 15


title: WT rep1


title: AML patient 14


title: LP-236

city: NYC

first: Isha

last: Monga

state: NY

address: 1300 York Ave

department: Neurology

institute: weill cornell medicine

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.BAM files were generated as a result of this step
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. These hit counts were used to perform downstream differential gene expression, and pathway analyses. The differential gene expression analysis was performed by using the  DESeq2 package in Bioconductor. Differential gene expression analysis was performed on the batch corrected data set based on the negative binomial distribution using a significance of FDR<0.05 comparing  Normal control cohort to the each kind of PCA subtype.
Gene count files obtained as txt files and DEseq2 in csv format
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: RNA sequencing of skin-biopsy of Lichen planopilaris (LPP) patient

extract_protocol:
Skin biopsies were taken from lesional and non-lesional scalp sites as identified by the treating dermatologist; NC samples were donated by healthy volunteers from other studies as part of our normal scalp database. Specimens were fixed in PAX gene Tissue Containers and bisected. One half of the sample was processed for RNA extraction and the other was formalin-fixed and paraffin embedded (FFPE) for immunohistochemistry. RNA was extracted using Qiagen RNeasy Mini Kit (Cat. No. / ID: 74104) and used for high-throughput bulk RNAseq (GENEWIZ).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Skin biopsies

tag: disease category

value: Lichen planopilaris (LPP)


title: AML patient 13


title: AML patient 12


title: LP-235


title: AML patient 10


title: AML patient 11


title: AML patient 7


title: AML patient 8


title: LP-233

source_name: RNA sequencing of skin-biopsy of Central Centrifugal Cicatricial Alopecia (CCCA) patient


title: LP-230

source_name: RNA sequencing of skin-biopsy of Frontal fibrosing alopecia (FFA) patient

value: Frontal fibrosing alopecia (FFA)


title: AML patient 9


title: AML patient 6


title: AML patient 16


title: LP-229


title: AML patient 3


title: AML patient 1


title: LP-226


title: AML patient 5


title: LP-231


title: AML patient 4


title: AML patient 2


title: LP-222


title: LP-224


title: LP-227


title: LP-228


title: LP-220


title: LP-234


title: LP-225


title: LP-221


title: LP-219


title: LP-218


title: pos2_03

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

institute: Osaka University

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Adapter sequence was trimmed using TrimGalore with the parameter (--nextera -–paired).
Trimmed reads were aligned on the mouse reference genome and the expression levels of transcripts was quantified using RSEM with the following parameters (rsem-calculate-expression –paired-end –star –output-genome-bam).
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files are zipped RSEM output (.genes.results)

source_name: cultured macrophages

growth_protocol: RPMI containing 10% FBS, 20ng/ml M-CSF, 1%P/S and 1% glutamine, medium refreshed on day 4.

extract_protocol:
On day 7, medium was removed and RNA was harvested using RNeasy Plus Micro Kit (Cat#74034).
Libraries were prepared according to KAPA RNA HyperPrep Kit with RiboErase (HMR) (Cat# KK8560). Briefly, total RNA was depleted of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed on DNA and original DNA oligonucleotides. After fragmenting the RNA using heat and magnesium, the first strand cDNA was synthesized using random priming, followed by a combined second strand synthesis and A-tailing process. Libraries were amplified by PCR after the addition of adapters, and finally purified and size selected using magnetic beads. Libraries were sequenced on the Illumina NextSeq2000 following the manufacturer's protocols.

treatment_protocol: Monocyte subsets were FACS-sorted from bone marrow and differentiated to macrophages in M-CSF containing medium for 7 days.

tag: cell markers

value: LFA1-hi Itgam-hi

value: bone marrow monocyte derived macrophage


title: LP-217


title: neg2_02

value: LFA1-lo Itgam-lo


title: LP-216


title: neg2_01


title: pos2_01


title: LP-215


title: LP-212


title: LP-214


title: LP-211


title: neg2_03


title: LP-213


title: pos2_02


title: LP-210


title: NHEK_UVB_6h_KAS-seq.rep2

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
First, the trim-galore package was used to remove low-qualified bases and adapter-containing reads from raw KAS-seq data. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome (hg19) using bowtie2 (v2.3.3.1) under default parameters.
Sam files were subsequently converted and sorted to bam files using samtools (v1.9). Duplicated mapped reads were removed using picard MarkDuplicates (v1.141).
For single-end spKAS-seq data, deduplicated unique mapped reads were extended to 150 bp to match the average length of DNA fragments (awk command).
Bed files were converted to bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Assembly: hg19
Supplementary files format and content: bed, peaks list.
Supplementary files format and content: bigWig, reads density.
Library strategy: KAS-seq

source_name: NHEK

extract_protocol:
After labeling, cells were harvested for genomic DNA isolation by using the PureLink Genomic DNA mini kit (Thermo, K182002). Around 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin (Sigma, 760749). The mixture was gently shacked at 37 °C for 1.5 h, after which 5 µL RNase A (Thermo, 12091039) was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit (Zymo, D4013) and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. Save 5% of the sonicated DNA as input and use the rest for enrichment with 10 µL Dynabeads MyOne Streptavidin C1 (Thermo, 65001). The beads were washed by 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. The binding was performed at room temperature for 15 min. The beads were washed once in 1× B&W buffer and then washed twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal. A final wash with 1× B&W buffer was followed, and DNA was eluted in 10 µL H2O by heating the beads at 95 °C for 10 min.
Input and enriched DNA were used for library construction by using the Accel-NGS Methyl-seq DNA library kit (Swift, 30024). Libraries were sequenced on Illumina platforms with pair-end more with around 60 million reads per library.

value: NHEK

value: Normal Human Epidermal Keratinocytes

value: WT

value: UVB radiation


title: HeLa-S3_spKAS-seq.rep1

data_processing:
First, the trim-galore package was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome (hg19) using bowtie2 (v2.3.3.1) under default parameters.
Sam files were subsequently converted and sorted to bam files using samtools (v1.9). Duplicated mapped reads were removed using picard MarkDuplicates (v1.141).
For paired-end spKAS-seq data, SAMtoBED.py was used to combine “properly paired” alignments into a single BED interval. For single-end spKAS-seq data, deduplicated unique mapped reads were extended to 150 bp to match the average length of DNA fragments (awk command).
Bed files were converted to bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Assembly: hg19
Supplementary files format and content: bigWig, spKAS-seq density on plus and minus strands.
Supplementary files format and content: bed, spKAS-seq peaks list.
Library strategy: KAS-seq

treatment_protocol: Cells were treated with 5 mM N3-kethoxal dissolved in their culture media for 10 min at 37 °C, 5% CO2.

value: Human cervix cells

value: no treatment


title: LP-208


title: HeLa-S3_spKAS-seq.rep2


title: 08_DA1-3b/p65/relA WT

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: murine p65/RelA and D361 mutan

hyb_protocol: Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: WT

label_protocol: manufacturer's instructions

growth_protocol: DMEM, 10% FCS, 1% NEAA and 1% Pen/Strep, 37°C, 5% CO2

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Murine DA1-3B Bcr-ABL+ cell line were transfected with void plasmid, p65/RelA WT, p65/RelA D361E, p65/RelA 1-361, p65/RelA 362-549 and p65/RelA 1-361 +p65/RelA 362-+549 plamsids respectively

value: mouse C3H eOuJ


title: 02_DA1-3b/p65/relA WT

description: murine p65/RelA and D361 mutan


title: 20_DA1-3b/p65/relA WT

description: murine p65/RelA and D361 mutan


title: 16_DA1-3b/p65/relA 1-361

description: murine p65/RelA and D361 mutan


title: NHEK_UVB_6h_KAS-seq.rep1


title: NHEK_UVB_3h_KAS-seq.rep2


title: 04_DA1-3b/p65/relA 1-361

description: murine p65/RelA and D361 mutan


title: 03_DA1-3b/p65/relA  D361E

description: murine p65/RelA and D361 mutan


title: LP-207


title: LP-209


title: 14_DA1-3b/p65/relA WT

description: murine p65/RelA and D361 mutan


title: LP-206


title: NHEK_UVB_3h_KAS-seq.rep1


title: 09_DA1-3b/p65/relA  D361E

description: murine p65/RelA and D361 mutan


title: 15_DA1-3b/p65/relA D361E

description: murine p65/RelA and D361 mutan


title: 11_DA1-3b/p65/relA 362-549

description: murine p65/RelA and D361 mutan


title: 17_DA1-3b/p65/relA 362-549

description: murine p65/RelA and D361 mutan


title: 18_DA1-3b/p65/relA 1-361+362-549

description: murine p65/RelA and D361 mutan


title: 05_DA1-3b/p65/relA 362-549

description: murine p65/RelA and D361 mutan


title: 10_DA1-3b/p65/relA 1-361

description: murine p65/RelA and D361 mutan


title: NHEK_UVB_30min_KAS-seq.rep2


title: NHEK_UVB_30min_KAS-seq.rep1


title: 21_DA1-3b/p65/relA D361E

description: murine p65/RelA and D361 mutan


title: 20_B16:p65:relA 1-361+362-549

description: murine p65/RelA and D361 mutan

treatment_protocol: Murine B16 Bcr-ABL+ cell line were transfected with void plasmid, p65/RelA WT, p65/RelA D361E, p65/RelA 1-361, p65/RelA 362-549 and p65/RelA 1-361 +p65/RelA 362-+549 plamsids respectively


title: 06_DA1-3b/p65/relA 1-361+362-549

description: murine p65/RelA and D361 mutan


title: 18_B16:p65:relA 1-361+362-549

description: murine p65/RelA and D361 mutan


title: NHEK_UVB_1.5h_KAS-seq.rep2


title: 19_B16:p65:relA 1-361+362-549

description: murine p65/RelA and D361 mutan


title: LP-204


title: 12_DA1-3b/p65/relA 1-361+362-549

description: murine p65/RelA and D361 mutan


title: LP-203


title: NHEK_UVB_1.5h_KAS-seq.rep1


title: LP-205


title: LP-201


title: LP-202


title: NHEK_UVB_0min_KAS-seq.rep2


title: 13_B16:p65:relA 1-361

description: murine p65/RelA and D361 mutan


title: NHEK_UVB_12h_KAS-seq.rep2


title: NHEK_UVB_12h_KAS-seq.rep1


title: LP-069


title: 17_B16:p65:relA 1-361+362-549

description: murine p65/RelA and D361 mutan


title: LP-068


title: 14_B16:p65:relA 1-361

description: murine p65/RelA and D361 mutan


title: 15_B16:p65:relA 1-361

description: murine p65/RelA and D361 mutan


title: 12_B16:p65:relA 362-549

description: murine p65/RelA and D361 mutan


title: 16_B16:p65:relA  1-361+362-549

description: murine p65/RelA and D361 mutan


title: 08_B16:p65:relA D361E

description: murine p65/RelA and D361 mutan


title: 10_B16:p65:relA 362-549

description: murine p65/RelA and D361 mutan


title: 11_B16:p65:relA 362-549

description: murine p65/RelA and D361 mutan


title: 07_B16:p65:relA D361E

description: murine p65/RelA and D361 mutan


title: 09_B16:p65:relA D361E

description: murine p65/RelA and D361 mutan


title: LP-066


title: LP-065


title: LP-064


title: LP-067


title: NHEK_UVB_0min_KAS-seq.rep1


title: HepG2_KAS-Input.rep1

value: Human hepatocellular carcinoma cells


title: HepG2_KAS-Input.rep2


title: HepG2_KAS-IP.rep2


title: 04_B16:p65:relA WT

description: murine p65/RelA and D361 mutan


title: LP-063


title: 06_B16:p65:relA WT

description: murine p65/RelA and D361 mutan


title: HepG2_KAS-IP.rep1


title: LP-062


title: HCT116_KAS-IP.rep1

value: Human colorectal carcinoma cells


title: HCT116_KAS-IP.rep2


title: LP-060


title: HCT116_KAS-Input.rep1


title: 03_B16:p65:relA Blanck

description: murine p65/RelA and D361 mutan

source_name: Blanck


title: 05_B16:p65:relA WT

description: murine p65/RelA and D361 mutan


title: 02_B16:p65:relA Blanck

description: murine p65/RelA and D361 mutan


title: 01_B16:p65:relA Blanck

description: murine p65/RelA and D361 mutan


title: 21_DA1-3B-p65/RelA-D361E

value: C3H eOuJ

value: DA1-3B Bcr-ABL+

tag: transfection


title: A375_KAS-IP.rep2

value: Human melanoma cells


title: LP-059

value: Skin biopsies

value: Lichen planopilaris (LPP)


title: 16_DA1-3B-p65/RelA-p1-361

tag: strain


title: 24_DA1-3B-p65/RelA-p1-361+p363-549


title: 23_DA1-3B-p65/RelA-p363-549


title: HCT116_KAS-Input.rep2


title: 22_DA1-3B-p65/RelA-p1-361


title: 18_DA1-3B-p65/RelA-p1-361+p363-549


title: 20_DA1-3B-p65/RelA-WT


title: 14_DA1-3B-p65/RelA-WT


title: 17_DA1-3B-p65/RelA-p363-549


title: LP-058


title: A375_KAS-IP.rep1


title: 15_DA1-3B-p65/RelA-D361E


title: LP-057

value: Frontal fibrosing alopecia (FFA)


title: A375_KAS-Input.rep2


title: A375_KAS-Input.rep1


title: 19_DA1-3B-VOID

source_name: VOID

value: VOID


title: LP-061


title: LP-054


title: LP-056


title: LP-053


title: LP-052


title: LP-055


title: Ile_spheroid_rep_3

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
Assembly: hg19
Supplementary files format and content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

source_name: human embryonic stem cell derived

growth_protocol: hESC, DE, Duo/Ile spheroids and Duo/Ile organoids were generated through a directed differentiation method detailed in Tsai et al., (2017) (PMID: 27927684).

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

tag: cell identity

value: ileal spheroid


title: Duo_organoid_rep_2

value: duodenal organoid


title: Ile_spheroid_rep_4


title: Ile_organoid_rep_1

value: ileal organoid


title: 06_DA1-3B-p65/RelA-p1-361+p363-549


title: LP-051

tag: tissue


title: 05_DA1-3B-p65/RelA-p363-549


title: 10_DA1-3B-p65/RelA-p1-361


title: 07_DA1-3B-VOID


title: 01_DA1-3B-VOID


title: 12_DA1-3B-p65/RelA-p1-361+p363-549


title: 09_DA1-3B-p65/RelA-D361E


title: 13_DA1-3B-VOID


title: 03_DA1-3B-p65/RelA-D361E


title: 04_DA1-3B-p65/RelA-p1-361


title: 11_DA1-3B-p65/RelA-p363-549


title: Ile_spheroid_rep_2


title: 08_DA1-3B-p65/RelA-WT


title: 02_DA1-3B-p65/RelA-WT


title: Ile_spheroid_rep_1


title: LP-050


title: Duo_spheroid_rep_6

value: duodenal spheroid


title: Duo_spheroid_rep_5


title: Duo_organoid_rep_1


title: LP-049


title: Duo_spheroid_rep_4


title: Duo_spheroid_rep_2


title: Duo_spheroid_rep_3


title: LP-048


title: Duo_spheroid_rep_1


title: DE_rep_2

value: definitive endoderm


title: DE_rep_1


title: LP-046


title: hESC_rep_2

value: human embryonic stem cell


title: LP-044


title: DE_rep_3


title: LP-041


title: LP-043


title: LP-045


title: hESC_rep_1


title: LP-047


title: Reh-sgROSA

city: New York

first: Soobeom

address: 550 First Avenue, Smilow 1307 New York NY

institute: NYU

data_processing:
The libraries were sequenced in paired-end by NovaSeq 6000 at 100 cycles.
RNA-seq reads were aligned to the human reference genome (GRCh37/hg19) using STAR aligner8 with default parameters.
Quantification of mapped reads to each gene was performed using FeatureCount of the Subread package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Raw counts matrix in the CSV file format

source_name: Reh

growth_protocol: All cell lines were cultured in RPMI-1640 media supplemented with 20% fetal bovine serum, 55 μM β-mercaptoethanol (Gibco # 21985023) and penicillin, streptomycin (Gibco #15140122).

extract_protocol: RNA isolation was performed using Qiagen RNEasy Mini Kit (Qiagen, #74134). RNA-seq libraries were prepared using NEXTflex Rapid Illumina Directional RNA-seq Library prep kit as per manufacturer’s guidelines.

treatment_protocol: All lentiviral transfections were performed in HEK293T cells using Polyethylenimine (PEI) reagent at 4:2:3 ratios of sgRNA or Cas9 construct: pVSVG: pPax2 in OPTI-MEM solution. All retroviral transfections were performed in Platinum-E cells using Polyethylenimine (PEI) reagent with 10 μg transfer plasmid in OPTI-MEM solution. All amphitropic retroviral transfections were performed Polyethylenimine (PEI) reagent at 5:2:5 ratios of MSCV-based construct: pVSVG: pCL-Ampho retrovirus packaging construct (Novus Biologicals, NBP2-29541) in OPTI-MEM solution Viral supernatant was collected 48-hrs post-transfection. Spin infections were performed at room temperature at 1,500g for 90 mins with polybrene reagent (Fisher Scientific). Reh, 697, NALM6, K562, HG3, TMD8 Cas9-expressing cell lines were generated by lentiviral transduction with retroviral Cas9-2A-blast (Addgene, plasmid #73310). Human GM12878 Cas9 lines were generated by lentiviral transduction with Cas9-2A-EGFP (Addgene plasmid #63592). 697 Cas13d-expressing cell line was generated by transduction with lentiviral tet-inducble RfxCas13d (Addgene, plasmid # 138149). Doxycycline (Sigma) treatment was performed at 0.5 μg/mL supplemented every two days in culture.

tag: guide rna

value: sgROSA

tag: batch


title: hypg15_1 GBF2020

city: Zurich

first: Cora

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
Quality and Adapter trimming with TrimGalore! 0.6.5 in standard setttings
Counting with FeatureCounts 2.02.
Read aligning with STAR aligner 2.7.8a
Differential Expression with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene counts from FeatureCounts

molecule: polyA RNA

source_name: ATCC Jurkat cells

growth_protocol: Grown in RPMI + 10% FCS + Penicillin/Streptomycin, split every second day

extract_protocol:
Lysed cells in Trizol with shearing. RNA was extracted with Quiagen Rneasy mini kit.
Standard polyA library

tag: cell type

value: Jurkat T cells

tag: sample type

tag: treatment


title: hESC_rep_3


title: hypg15_3 GBF2020


title: LP-038


title: hypg15_2 GBF2020


title: NALM6-sgROSA


title: LP-039


title: hypg3_3 GBF2020


title: 697-sgROSA


title: LP-037


title: hypg15_4 GBF2020


title: hypg3_4 GBF2020


title: TMD8-ROSA_Rep2


title: TMD8-ROSA_Rep1


title: LP-042


title: Ctrl_4 GBF2020

value: Ctrl


title: hypg3_1 GBF2020


title: AE055

source_name: RNA sequencing of skin-biopsy of Normal Control (NC) patient

value: Normal Control (NC)


title: AE056


title: hypg3_2 GBF2020


title: TMD8-NUDT21_Rep2


title: TMD8-NUDT21_Rep1


title: Ctrl_3 GBF2020


title: Reh-ROSA_Rep1


title: L1-FGGY+57

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Raw sequencing data was aligned to hg38 reference using STAR 2.5.3a (Dobin et al., 2013) and HTseq 0.11.2 (Anders et al., 2015) was used to quantify the gene-sample expression profile.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited xls file of raw counts of  gene expression profile

source_name: lung squamous cell carcinoma tissue

extract_protocol:
Lung squamous cell carcinoma tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype


title: AE052


title: L1-FGGY+49


title: L1-FGGY+51


title: L1-FGGY+52


title: Reh-NUDT21_Rep1


title: L1-FGGY+53


title: AE053


title: L1-FGGY+54


title: Reh-ROSA_Rep2


title: AE054


title: Ctrl_1 GBF2020


title: L1-FGGY+50


title: Ctrl_2 GBF2020


title: AE051


title: NALM6-ROSA_Rep2


title: AE046


title: AE048


title: L1-FGGY+56


title: L1-FGGY+44


title: L1-FGGY+55


title: L1-FGGY+48


title: Reh-NUDT21_Rep2


title: L1-FGGY+45


title: NALM6-ROSA_Rep1


title: L1-FGGY+46


title: L1-FGGY+47


title: AE045


title: L1-FGGY+43


title: AE047


title: AE042


title: L1-FGGY+41


title: NALM6-NUDT21_Rep2


title: NALM6-NUDT21_Rep1


title: AE041


title: L1-FGGY+35


title: L1-FGGY+34


title: AE007


title: L1-FGGY+39


title: K562-ROSA_Rep2


title: L1-FGGY+38


title: AE006


title: L1-FGGY+32


title: K562-ROSA_Rep1


title: L1-FGGY+37


title: L1-FGGY+29


title: L1-FGGY+42


title: HG3-ROSA_Rep1


title: L1-FGGY+31


title: K562-NUDT21_Rep1


title: L1-FGGY+33


title: HG3-ROSA_Rep2


title: HG3-NUDT21_Rep2


title: L1-FGGY+36


title: AE008


title: AE004


title: AE009


title: L1-FGGY+27


title: L1-FGGY+30


title: L1-FGGY+40


title: L1-FGGY+28


title: AE005


title: K562-NUDT21_Rep2


title: AE003


title: L1-FGGY+26


title: L1-FGGY+25


title: HG3-NUDT21_Rep1


title: L1-FGGY+24


title: L1-FGGY+23


title: AE002


title: 697-ROSA_Rep2


title: AE001


title: L1-FGGY+22


title: 697-ROSA_Rep1


title: L1-FGGY+19


title: L1-FGGY+20


title: L1-FGGY+18


title: 697-NUDT21_Rep2


title: 697-NUDT21_Rep1


title: L1-FGGY+17


title: L1-FGGY+14


title: L1-FGGY+13


title: L1-FGGY+12


title: L1-FGGY+16


title: L1-FGGY+11


title: L1-FGGY+10


title: Ovary, revertant, 1

first: Claude

last: Desplan

address: 24 Waverly Place, Waverly Bldg 6th Floor

department: Biology

institute: New York University

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_9_S35_L005_R1_001_RG

data_processing:
Reads were aligned to Hsal v8.5 (GCF_003227715.1) with STAR (version 2.5.3a).
Reads were trimmed for quality and adapter sequence using Trimmomatic (leading: 3; trailing: 3; slidingwindow: 4:15; minlen: 36).
Reads were counted by Subreads.
Differential expression was performed using EdgeR.
Assembly: Hsal_v8.5
Supplementary files format and content: Read counts from three different tissues (brain, fat body and ovary) of three different castes (worker, gamergate and revertant) were reported in the tables with geneIDs.

organism: Harpegnathos saltator

source_name: ovary (Ov)

growth_protocol: Ants were housed in a clear plaster box floored with a humid dental plaster and a glass covered nest in a temperature-controlled room (~25°C) with 12-hour day light/dark cycle. Ants were and fed three times per week with pre-stung crickets.

extract_protocol:
Brains without optic lobes, fat body in a gaster and a pair of ovary were dissected. Total RNA was extracted with TRIzol and treated with Turbo DNAse. Each tissue from one individual was used to construct a library.
RNA libraries for RNA-seq were prepared as described in Bonasio et al science 2010 (PMID: 20798317).

treatment_protocol: Similar age-matched workers were housed together in a new empty nest without a reproductive female. Each individual was uniquely marked and monitored the behavior to determine the reproductive gamergate status after 3 months. Some of the mature gamergates were individual isolated and transferred to another established colony with the mature reproductive females where the nely transfered gamergates were policed and lost the reproductive potential or now called revertants.

value: ovary (Ov)

tag: caste

value: revertant (R)


title: Ovary, revertant, 3

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_11_S37_L005_R1_001_RG


title: Ovary, revertant, 4

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_12_S38_L005_R1_001_RG


title: Ovary, gamergate, 4

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_8_S34_L005_R1_001_G

value: gamergate (G)


title: Ovary, revertant, 2

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_10_S36_L005_R1_001_RG


title: Ovary, gamergate, 3

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_7_S33_L005_R1_001_G


title: L1-FGGY+9


title: L1-FGGY+8


title: L1-FGGY+21


title: Ovary, gamergate, 2

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_6_S32_L005_R1_001_G


title: L1-FGGY+7


title: L1-FGGY+4


title: Ovary, gamergate, 1

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_5_S31_L005_R1_001_G


title: L1-FGGY+6


title: L1-FGGY+5


title: Ovary, worker, 4

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_4_S30_L005_R1_001_W

value: worker (W)


title: L1-FGGY+3


title: L1-FGGY+15


title: Ovary, worker, 3

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_3_S29_L005_R1_001_W


title: L1-FGGY-52


title: L1-FGGY+2


title: L1-FGGY+1


title: Ovary, worker, 2

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_2_S28_L005_R1_001_W


title: NUDT21_Input_697

data_processing:
Adapters and adapter-dimers sequences were eliminated using Cutadapt
Trimmed reads were aligned to the human reference genome (GRCh37/hg19) using STAR aligner version 2.7.7 with the following parameters: --outFilterScoreMin 10, --outSAMunmapped Within, --outFilterMultimapNmax 1, outFilterMultimapScoreRange 1.
After PCR-duplicates were removed using UMI-tools, we called eCLIP peaks using PureCLIP with default parameters.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: BED files as outputs of the PureCLIP method

extract_protocol:
Cells were lysed using 1mL of eCLIP lysis mix and were subjected to two rounds of sonication for 4 minutes with 30 second ON/OFF at 75% amplitude. 5μg of pre-validated NUDT21 (Santa Cruz Biotechnology, sc-81109) antibody was then pre-coupled to 50ul of Anti-Rabbit IgG Dynabeads (ThermoFisher), added to lysate equivalent to 100μg of RNA, and then incubated overnight at 4°C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers. IP and input samples were cut from the membrane at the relative band size to 75kDa above.
RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed according to the published single-end seCLIP protocol (Van Nostrand, E. L. et al. 2017)

treatment_protocol: eCLIP studies were performed by Eclipse Bioinnovations Inc (San Diego) according to the published single-end seCLIP protocol (Van Nostrand, E. L. et al. 2017) with the following modifications. Cas9-expressing Reh, 697, NALM6 and TMD-8 cells were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation.

tag: molecule subtype

value: input RNA

tag: cell line

tag: rip target

value: none (input)


title: L1-FGGY-51


title: L1-FGGY-50


title: NUDT21_IP_697

value: Immunoprecipitated RNA


title: NUDT21_Input_TMD8


title: FatBody, revertant, 4

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
RG_rep4_fatbody

source_name: Abdominal fat body (Fb)

value: Abdominal fat body (Fb)


title: L1-FGGY-46


title: L1-FGGY-49


title: L1-FGGY-48


title: NUDT21_IP_TMD8


title: L1-FGGY-45


title: FatBody, revertant, 2

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
RG_rep2_fatbody


title: L1-FGGY-44


title: L1-FGGY-47


title: FatBody, revertant, 3

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
RG_rep3_fatbody


title: L1-FGGY-41


title: NUDT21_Input_NALM6


title: L1-FGGY-43


title: NUDT21_IP_NALM6


title: Ovary, worker, 1

description:
raw counts of sequencing reads of the ovary tissue in worker, gamergate and revertant
Ov_W_G_R_reads
COv_1_S27_L005_R1_001_W


title: IgG_Input_NALM6


title: FatBody, gamergate, 4

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
G_rep4_fatbody


title: IgG_Input_Reh

value: Reh


title: L1-FGGY-38


title: L1-FGGY-39


title: L1-FGGY-40


title: FatBody, gamergate, 3

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
G_rep3_fatbody


title: L1-FGGY-36


title: L1-FGGY-37


title: L1-FGGY-35


title: L1-FGGY-34


title: FatBody, gamergate, 1

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
G_rep1_fatbody


title: NUDT21_Input_Reh


title: IgG_IP_NALM6

value: IgG


title: IgG_IP_Reh


title: FatBody, gamergate, 2

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
G_rep2_fatbody


title: L1-FGGY-42


title: NUDT21_IP_Reh


title: L1-FGGY-31


title: FatBody, revertant, 1

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
RG_rep1_fatbody


title: FatBody, worker, 4

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
W_rep4_fatbody


title: L1-FGGY-32


title: FatBody, worker, 3

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
W_rep3_fatbody


title: L1-FGGY-29


title: L1-FGGY-30


title: 786-O_ZHX2_shCtrl_Rep2

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were then filtered for adapter contamination using cutadapt (v1.12) and filtered using FASTX-Toolkit (v0.0.14) such that at least 90% of bases of each read had a Phred score > 20.
Reads were aligned to the reference genome (hg19) using STAR (v2.5.2b) retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using salmon (v0.11.3), and differential expression was detected using DESeq2 (v1.14.1).
Genome_build: hg19
Supplementary_files_format_and_content: sf files contain the per-gene transcript-per-million (TPM) data. The Excel table contains the full list of differential genes.

source_name: cell line

growth_protocol: The 786-0, UMRC-2, UMRC-6, OS-RC-2, RCC-4, Caki-1, 293T and HKC cells were bought from the American Type Culture Collection (ATCC) or Sigma-Aldrich. The above cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco 11965118) with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin (PS). All cells were cultured in incubator at 37℃ with 5% CO2. All cells were verified by short tandem repeat testing. Mycoplasma detection was used to ensure cells were Mycoplasma free.

extract_protocol:
Total RNA from 786-O cells (triplicates) was extracted by using RNeasy kit with on column DNase digestion (Qiagen).
Libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq2500 with paired-end 150 bp reads.

treatment_protocol: USP13 shRNA (43 and 45) were purchased from Sigma Aldrich. USP13 siRNA were purchased from Dharmacon (D006064). SgRNA targeting USP13 were inserted into CRISPR-V2 lentivirus vector. ShRNA targeting USP13 were cloned into tet-on puro vector to generate doxycycline-inducible shUSP13 plasmids. ShRNA and sgRNA sequences: Sg1: AGCGCCGGGGCGCCCTGTT. Sg2: AATAGCACTACCAAATATTG. Sg3: TGTATGCATGAATACATTTT. Sg4: TGCCCACGATCCGCGTGCCC. Sh50: CGCCTGATGAACCAATTGATA. Sh52: CCGGTGAAATCTGAACTCATT.

tag: condition

value: shCtrl

tag: shRNA


title: L1-FGGY-28


title: 786-O_ZHX2_shCtrl_Rep3


title: L1-FGGY-27


title: 786-O_ZHX2_shCtrl_Rep1


title: FatBody, worker, 2

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
W_rep2_fatbody


title: L1-FGGY-26


title: L1-FGGY-23


title: FatBody, worker, 1

description:
raw counts of sequencing reads of the fat body tissue in worker, gamergate and revertant
Fb_W_G_R_reads
W_rep1_fatbody


title: L1-FGGY-25


title: 786-O_ZHX2_sh45_Rep2


title: 786-O_ZHX2_sh45_Rep3


title: L1-FGGY-33


title: Brain, Revertant, 3

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_11_S49_L006_R1_001_rg3

source_name: non-visual brain (central brain, Br)

value: non-visual brain (central brain, Br)


title: L1-FGGY-24


title: Brain, Revertant, 4

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_12_S50_L006_R1_001_rg4


title: 786-O_ZHX2_sh43_Rep3


title: Brain, Revertant, 2

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_10_S48_L006_R1_001_rg2


title: L1-FGGY-22


title: 786-O_ZHX2_sh45_Rep1


title: L1-FGGY-19


title: Brain, Gamergate, 4

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_8_S46_L006_R1_001_G4


title: L1-FGGY-20


title: L1-FGGY-16


title: L1-FGGY-15


title: Brain, Revertant, 1

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_9_S47_L006_R1_001_rg1


title: 786-O_ZHX2_sh43_Rep1


title: L1-FGGY-12


title: L1-FGGY-14


title: L1-FGGY-13


title: 786-O_USP13_shCtrl_Rep3


title: Brain, Gamergate, 1

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_5_S43_L006_R1_001_G1


title: L1-FGGY-21


title: Brain, Gamergate, 2

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_6_S44_L006_R1_001_G2


title: L1-FGGY-18


title: L1-FGGY-10


title: 786-O_USP13_shCtrl_Rep1


title: L1-FGGY-17


title: Brain, worker, 4

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_4_S42_L006_R1_001_W4


title: L1-FGGY-8


title: L1-FGGY-6


title: L1-FGGY-7


title: L1-FGGY-9


title: Brain, Gamergate, 3

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_7_S45_L006_R1_001_G3


title: L1-FGGY-4


title: L1-FGGY-5


title: 786-O_USP13_sh52_Rep1


title: 786-O_USP13_sh52_Rep2


title: L1-FGGY-2


title: 786-O_ZHX2_sh43_Rep2


title: Brain, worker, 2

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_2_S40_L006_R1_001_W2


title: 786-O_USP13_sh52_Rep3


title: L1-FGGY-11


title: 786-O_USP13_shCtrl_Rep2


title: L1-FGGY-1


title: 786-O_USP13_sh50_Rep3


title: Brain, worker, 3

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_3_S41_L006_R1_001_W3


title: 786-O_USP13_sh50_Rep2


title: 786-O_USP13_sh50_Rep1


title: 33LungILC2_2

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
The libraries were sequenced for 60 cycles (single-end reads) on an Illumina HiSeq 1500 instrument.
Reads were mapped to mouse genome assembly version of December 2011 (mm10) by using the Bowtie2 mapping tool with a default setting.
Peaks were called using the MACS2 software with the broad option and those identified in both replicates were used for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph.gz

growth_protocol: Mice received daily i.p. injections of PBS or rIL-33 (0.5 µg) for 5 days. Then, liver and lung ILC2s (5000-50000 cells) were sorted using flow cytometry ARIA III [gating: Lin− (CD3e−Ly6G−Ly6c−CD11b−CD45R−TER119−TCRb−) CD127+Thy1+ST2+]

extract_protocol:
The nuclei were resuspended in Tagment DNA enzyme buffer supplemented with Tn5 transposase (Illumina, 15027865) to tag and fragment the accessible chromatin. The DNA fragments were purified with a MinElute kit (Qiagen, 28004)
DNA fragments were amplified by 11 - 13 PCR cycles.

treatment_protocol: described in growth protocol

value: BALB/c

value: wild type

tag: celltype

value: lung ILC2s from IL-33-treated mice


title: 33LiverILC2_2

value: liver ILC2s from IL-33-treated mice


title: 33LungILC2_1


title: L1-FGGY-3


title: Brain, worker, 1

description:
raw counts of sequencing reads of the brain tissue in worker, gamergate and revertant
Br_W_G_R_reads
COb_1_S39_L006_R1_001_W1


title: 33LiverILC2_1


title: neuroblastoma SK-N-BE(2)C xenograft, brequinar treated 72h, rep3

city: Stockholm

first: Ninib

last: Baryawno

address: Tomtebodavägen 18a

department: Department of Women's and Children's health

country: Sweden

institute: Karolinska institutet

description: xenograft sample 18

data_processing:
For xenografts, reads were aligned to a combined mm10+hg38 reference using STAR v2.7.9a (2-pass approach).
Raw reads per gene were quantified using htseq-count v0.12.4.
Assembly: Xenograft data: combined hg38+mm10 reference. Transgenic TH-MYCN data: combined hg19+mm10 reference (any reads mapping to human genes other than MYCN were filtered out priior to downstream analyses).
Supplementary files format and content: rawcounts_xenografts.csv: a matrix of read counts per gene per sample (all hg38 + mm10 genes)
Supplementary files format and content: rawcounts_thmycn.csv: a matrix of read counts per gene per sample (all mm10 genes + human MYCN)

source_name: neuroblastoma xenograft

growth_protocol: SK-N-AS and SK-N-BE(2)C cell lines were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 ug/ml streptomycin, and 100 IU/ml penicillin G (all from Life Technologies/Thermo Fisher Scientific). Female NMRI nu/nu mice (purchased from Scanbur) of four to six weeks of age were injected with 5 million SK-N-AS or SK-N-BE(2)C cells subcutaneously in the flank and monitored daily for tumor growth.

extract_protocol:
Mouse tumor tissue used for RNA sequencing was stored in RNAlater solution (Thermo Fisher, Waltham, MA, USA) at -80 °C. Total RNA from xenograft/tumor tissue was isolated using the RNeasy Mini Kit (Qiagen).
All libraries were generated using the TruSeq Stranded protocol (Illumina). All libraries were sequenced on the NextSeq500 platform. Xenograft samples were sequenced with a 75 bp single-end strategy. TH-MYCN samples were sequenced with a 2x42 bp paired-end strategy.

treatment_protocol: NMRI mice and transgenic TH-MYCN mice were treated with brequinar 50 mg/kg i.p with either one dose (24h and 72h samples) or every third day for a total of 120 days (TH-MYCN relapse samples).

value: neuroblastoma xenograft

value: neuroblastoma

value: brequinar 72h


title: neuroblastoma SK-N-BE(2)C xenograft, brequinar treated 24h, rep3

description: xenograft sample 15

value: brequinar 24h


title: neuroblastoma SK-N-BE(2)C xenograft, brequinar treated 72h, rep1

description: xenograft sample 16


title: neuroblastoma SK-N-BE(2)C xenograft, brequinar treated 72h, rep2

description: xenograft sample 17


title: neuroblastoma SK-N-BE(2)C xenograft, brequinar treated 24h, rep2

description: xenograft sample 14