title: hamster.uninfected.CFZ.rep3

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description:
hamster_SARS2_rpkm.csv
clean-drug-3

data_processing:
Fastq files from RNA-seq were quality examined by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were processed by cutadapt to remove reads with low quality and to trim adapters.
Trimmed reads were aligned to hg38 reference genome using Tophat2
Reads assigned to each gene were counted by featureCounts  with refseq gene sets as references.
Genes without at least 1 read mapped on average in each sample were considered undetectable and were filtered out. Read counts were normalized by Trimmed Mean of M-values (TMM) method and RPKM of each gene was calculated using R package edgeR
Genome_build: hg38 for Caco-2 cells; MesAur1.0 for hamster lung tissues
Supplementary_files_format_and_content: CSV files include RPKM values for each sample

organism: Mesocricetus auratus

source_name: tissue

growth_protocol: Caco-2 cells were maintained in DMEM culture medium supplemented with 20% heat-inactivated FBS, 50 U/ml penicillin and 50 µg/ml streptomycin

extract_protocol:
Qiagen RNeasy Mini Kit
cDNA libraries were prepared by KAPA mRNA HyperPrep Kit.1 ug of total RNA was used as starting material. Manufacturer’s protocol was followed.

treatment_protocol: For the experiment on Caco-2 cells, cells were infected with/without SARS-CoV-2 virus at MOI=4 for 1 hour, followed by incubation with fresh medium with 10uM clofazimine or DMSO control. After 3 or 6 hours, cells were collected for RNA extraction. For the experiment on golden hamsters, we delivered clofazimine through oral route utilizing corn oil as vehicle. An equivalent hamster dose of 25 mg/kg/day was converted based on body surface area. Prophylactic treatment through oral administration of clofazimine was given at -3, -2 and -1 dpi (25 mg/kg/day), followed by virus challenge at 0dpi through intranasal route (10^5 PFU/hamster); therapeutic post-exposure administration of clofazimine was performed at 1, 2, and 3 dpi applying the same drug dosage and virus inoculum. Lung tissues were collected at 4dpi for prophylactic and therapeutic groups. For uninfected group, clofazimine was given for 3 consecutive days and lung tissues were collected on day 4.

value: lung tissue

tag: infection status

tag: clofazimine treatment

value: treated with clofazimine


title: 020717_Cell62-H10

status: Public on Feb 02 2021

type: SRA

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

description: New onset SJIA patient

library_source: transcriptomic

data_processing:
All single-cell libraries were pseudo-aligned to the human Ensembl version 72 transcriptome using the Kallisto through AltAnalyze version 2.1.3. as described in our previous publication [40]. To ensure quality control, libraries with less than 300,000 paired-end reads or estimated read percentage alignment <20% were excluded. Unsupervised population discovery was performed using the software ICGS version 2 (Venkatasubramanian et al. 2019, bioRxiv) and PCA-loading gene analysis and HOPACH clustering in AltAnalyze. PCA-loading genes were selected as the top-100 correlated and top-100 anti-correlated genes associated with the first 4 principal components. Initial identified predominant gene clusters from the PCA-loading analysis were excluded prior to ICGS2, by identifying genes correlated to the centroid of the gene clusters with a Pearson rho > 0.1 (21,719 genes remaining after exclusion). ICGS2 was run using the default program parameters. To expand the cell-cluster identified from the ICGS2 analysis of SJIA with donor BM macrophages, an aggerate score (sum of the TRIM8 cluster maker genes), was used to identify additional SJIA patient cells (n=12, total) enriched in TRIM8-associated genes prior to differential expression analyses. For the identification of TRIM8-cluster specific genes, we applied empirical Bayes moderated (eBayes) t-test comparing TRIM8-cluster SJIA cells to all donor macrophage cells (AltAnalyze). Only genes with a minimum average TPM >1 in the two compared populations, eBayes t-test p<0.05 (following Benjamini-Hochberg correction) and fold > 1.5 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file

molecule: total RNA

organism: Homo sapiens

source_name: sorted bone marrow macrophages

growth_protocol: Leftover bone marrow aspirates were obtained from the clinical lab, RBC lysed, and frozen until use. Cells were then thawed and bone marrow macrophages sorted as CD14+CD163+CD15-7AAD-

extract_protocol:
This suspension was then loaded onto the Fluidigm C1 Single-Cell Auto Prep System, on a 10-17um chip.  These cells were subsequently lysed, and extracted RNA converted into cDNA per manufacterers directions using v4 chemistry.
Libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA) on cDNAs with an initial concentration>180 pg/µl that were then diluted to 100 pg/µl. In each single-cell library preparation, a total of 125pg cDNA was tagmented at 55 °C for 20 minutes. Libraries were pooled and purified on AMPure® bead-based magnetic separation before a final quality control using Qubit® dsDNA HS Assay Kit (Life Technologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit. We required the majority of cDNA fragments to be between 375–425bp to qualify for sequencing.
Single cell libraries were subjected to paired-end RNA-Sequencing on a HiSeq 2500 (Illumina Inc., San Diego, CA). 96 scRNA-Seq libraries were sequenced per HiSeq 2500 gel (~300 million bp/gel).

tag: cell type

value: Macrophage (CD14+CD163+)


title: N22

city: shanghai

first: Qingshan

last: Chen

address: Changhai road 255

country: China

institute: Third Affiliated Hospital of Second Military Medical University

description: all.counts.exp.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Mus musculus

source_name: Schisandrin B treated liver

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard IonPronton protocols

treatment_protocol: Male Wistar rats (180 g ± 20 g) were randomly divided into four groups (n=8 per group) as follows: 1) normal group, 2) model group, 3) 25 mg/kg Schisandrin B (Sch B) group (CCl4+ Sch B 25 mg/kg), and 4) 50 mg/kg Sch B group (CCl4+ Sch B 50 mg/kg). Liver fibrosis model was induced by CCl4(50% CCl4/olive oil; 2 mL/kg) thrice a week for 8 weeks. In Sch B-treated group, the rats were administered CCl4 for 4 weeks and then administered Sch B at a dose of 25 or 50 mg/kg daily, respectively, together with CCl4 gavage for another 4 weeks. The rats in normal group were treated with equal volume of olive oil instead of CCl4 as sham control.

tag: tissue

value: liver

tag: strain

value: Wistar rat

tag: treatment time

value: 8 weeks

tag: treatment

value: Schisandrin B treated liver


title: RNAseq patient 37 diagnosis

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

data_processing:
BCL files were converted into FASTQ file format with bcl2fastq (v2.19) (Illumina, USA) and resulting reads were trimmed with cutadapt (v1.18).
Clean reads were aligned to the human genome reference (hg19) with STAR (Dobin et al., 2013) (v2.5.3)
Read counts per gene were calculated with quant3p (github.com/ctlab/quant3p)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix including gene-count values for each sample

source_name: Tumor plasma cells

extract_protocol:
Samples in RLT were defrosted and gDNA plus RNA were isolated with AllPrep DNA/RNA Micro Kit (Qiagen, USA) following manufacturer’s instructions. Samples in DMSO were defrosted, washed with PBS and suspended in lysis binding buffer (Ambion). Poly-A RNA was selected with Dynabeads Oligo (dT) (Ambion), and un-binded DNA was selected with SPRIselect beads, washed with EtOH and suspended in buffer EB.
We used a 3’ end RNAseq method optimized for generating libraries from low-input starting material (MARSeq), adapted for bulk RNAseq (Jaitin et al., 2014; Lavin et al., 2017) with minor modifications.
MARSeq

tag: cytogenetic alterations

value: standard-risk


title: Output 2

city: barcelona

first: benedetta

last: bolognesi

state: Barcelona

address: c comte borrell 232 5a-1a

institute: IBEC

description:
MS_BL_BB_processed_data.xlsx
from plasmid library

library_source: genomic

data_processing:
Three biological replicas were performed in this study, each of them with one INPUT (before selection) and one OUTPUT (after selection). The WT variant is the WT sequence of human Amlyoid beta (Aß) 42, and mutant variants are Aß42 sequences with one (singles) or two (doubles) mutated AA. For each variant, the WT AA and mutant AA (Mut) are indicated in the processed data file.
FastQ files from paired-end sequencing of the Aß42 library before (‘input’) and after selection (‘output’) were processed using a custom pipeline (https://github.com/lehner-lab/DiMSum). DiMSum is an R package that uses different sequencing processing tools such as FastQC (for quality assessment), Cutadapt (for constant region trimming) and USEARCH (for paired-end read alignment). Unique variants were aggregated and counted using Starcode. Variants containing indels and nonsynonymous variants with synonymous substitutions in other codons were excluded. For downstream analysis, also variants with less than 50 input reads in any of the replicates were excluded and only variants with a maximum of two aa mutations in other codons were used.
On the basis of variant counts, DiMSum was used to calculate then also calculated nucleation scores (NS) and their error estimates. For each variant in each replicate NSs were calculated as: NS=ES(i) – ES(wt), where ES(i)= log ( F i  OUTPUT) – log ( F i INPUT ) for a specific (i) variant and ES(wt)= log ( F wt OUTPUT) – log ( F wt INPUT ) for the WT Aß42. NS were merged by using the error-weighted mean of each variant across replicates (3 biological replicates). Merged NS and NS for each independent replicate, as well as their associated error estimates, are available in MS_BL_BB_processed_data.xlsx
Supplementary_files_format_and_content: Pos = aa position, WT_AA = WT aa residue, Mut = Mutated aa residue, Pos2 = aa position of mutation 2 in double mutant, Mut2 = Mutated aa residue of mutation 2 in double mutant, Pos1 = aa position of mutation 1 in double mutant, Mut1 = Mutated aa residue of mutation 1 in double mutant, WT_AA1 = WT aa residue of mutation 1 in double mutant, WT_AA2 = WT aa residue of mutation 2 in double mutant, Nmut_nt = Number of nt changes involved, Nmut_aa = Number of aa changes involved, Nmut_codons = Number of codon changes involved, STOP = Mutations causing introduction of stop codons,mean_count = Mean read counts of the input repicates, nscore[1,2,3] = Nucleation score for [1,2,3] replicates, sigma[1,2,3] = Error over nucleation score for [1,2,3] replicates, nscore = merged nucleation score, sigma = Merged error over nucleation score

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: Yeast cells were transformed with the Aβ42 plasmid library I three biological replicas. A minimum of 3.7 million yeast transformants were used for each replicate to ensure the coverage of the full library and reaching therefore a 10x coverage of each variant. Once the culture reached the exponential phase, cells were resuspended in 1L protein inducing medium (-URA, 20% glucose, 100uM Cu2SO4) at OD600=0.05. After 24h the input pellets were collected by centrifuging 220ml of cells and stored at -20C for later DNA extraction (input pellets). In parallel, 18.5 million cells of the same culture to underwent selection, with a starting coverage of at least 50 copies of each variant in the library. For selection,  cells were plated on -ADE-URA selective medium  in 145cm2 plates and let grow for 7 days at 30C. Colonies were then scraped off the plates and recovered with PBS 1x to be centrifuged and stored at -20C for later DNA extraction (output pellets).

extract_protocol:
The input and output pellets (3 replicates, 6 tubes in total) were thawed and resuspended in 2ml extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris pH 8, 1mM EDTA pH 8), and underwent two cycles of freezing and thawing in an ethanol-dry ice bath (10 min) and at 62C (10min).  Samples were then vortexed together with 1.5ml of phenol:chloroform:isoamyl 25:24:1 and 1.5g of glass beads (sigma). The aqueous phase was recovered by centrifugation and mixed again with 1.5ml phenol:chloroform:isoamyl 25:24:1. DNA precipitation was performed by adding 1:10V of 3M NaOAc and 2.2V of 100% cold ethanol to the aqueous phase and incubating the samples at -20C for 1h. After a centrifugation step, pellets were dried overnight at room temperature. Pellets were resuspended in 1ml resuspension buffer (10mM Tris pH 8, 1mM EDTA pH 8) and treated with 7.5ul RNase A (Thermo Scientific) for 30min at 37C. The DNA was finally purified using 75ul of silica beads (QIAEX II Gel Extraction Kit, Qiagen), washed and eluted in 375ul elution buffer.
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 300 million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Ilumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. DNA concentration was then quantified by means of a Quant-iT™ PicoGreen® dsDNA Assay Kit (Promega). All replicates were pooled together in an equimolar ratio. Finally, the pooled sequencing library was run on a 2% agarose gel, purified and sent for 125 bp paired-end Illumina sequencing.

tag: genotype/variation

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)


title: hamster.uninfected.CFZ.rep2

description:
hamster_SARS2_rpkm.csv
clean-drug-2

molecule: polyA RNA


title: Output 3


title: Input 1


title: 020717_Cell61-G10

description: New onset SJIA patient


title: Input 2


title: RNAseq patient 38 diagnosis


title: Output 1


title: Input 3


title: 020717_Cell60-F10

description: New onset SJIA patient


title: 020717_Cell6-G1

description: New onset SJIA patient


title: RNAseq patient 36 diagnosis_2

value: high-risk


title: hamster.uninfected.vehicle.rep2

description:
hamster_SARS2_rpkm.csv
clean-DMSO-3


title: hamster.uninfected.vehicle.rep1

description:
hamster_SARS2_rpkm.csv
clean-DMSO-2


title: hamster.uninfected.vehicle.rep3

description:
hamster_SARS2_rpkm.csv
clean-DMSO-4


title: RNAseq patient 36 diagnosis_1


title: 020717_Cell59-E10

description: New onset SJIA patient


title: N18

description: all.counts.exp.txt


title: Sample K3: Stem Globulus 20°C

city: Campinas

first: Paulo

last: Mazzafera

state: Sao Paulo

address: Rua Monteiro Lobato

department: Plant Physiology

country: Brazil

institute: State University of Campinas

data_processing:
Next generation sequencing enables uncover the effects of high and low temperature and carbon dioxide in two eucalyptus species
Purpose: The use of Next generation sequence (NGS) analysis aiming to understand  changes in the expression of genes related with biosynthesis and remodeling of the cell wall, as well as genes related with carbon partitioning and hormonal regulation.
Methods: Eucalyptus stem of 35-day-old plants profile were generated by deep sequencing, in triplicate, using Illumina platform HISEQ2500 . It was considered the larger splicing variant of each loci using Bowtie2 program (Langmead and Salzberg 2012).  Avadis NGS software (Thermo Fisher) was used to visualize and analyze mapped reads. P-values (p <0,05) were calculated using the DESeq statistical method, which is based on the negative binomial distribution with variance and mean linked by local regression. For gene differential expression we used Moderate t-Test and One-way ANOVA. Multiple test correction was done using Benjamini Hochberg FDR (false discovery rate)
Results: There was an upregulation of ethylene and auxin biosynthetic genes in both species, but it was stronger under high and low temperature in E.globulus. Temperature was more effective to change cell wall biosynthetic genes than CO2 and CO2 stimulated lignin biosynthetic pathway. We also analyzed lignin composition and structure. There was an increase in F5H and COMT expression and the S/G ratio also increased under high CO2 in E.globulus. Thus, the species responded differently to treatments and stem composition and development was highly affected by temperature and CO2 concentration
Conclusion: In general our analysis using different temperatures, from low to high, associated with high CO2, as suggested in some global warming scenarios, showed an intense and diverse changes in cell wall related genes. Whether these scenarios will be confirmed or not, or in which degree and proportions changes in the temperature and atmospheric CO2 will happen is a matter of discussion, but certainly woody plants will change cell wall composition and the content of its components. Our results showed that temperature induced more genes related to cell wall formation in both species studied here and eCO2 genes related to lignin biosynthesis.
Genome_build: PhytozomeV10: Egrandis_201_v1
Supplementary_files_format_and_content: Matrix table with gene fold change for every comparisons between treatments for both species

organism: Eucalyptus globulus

source_name: eucalyptus globulus stem

growth_protocol: Six-months-old seedlings of Eucalyptus grandis and E. globulus (seedlings produced from clonal seeds obtained from Sementes Caiçara – Brazil, www.sementescaicara.com) were used in this experiment. They were grown in 1 L plastic pots containing a mixture of soil and vermiculite (2:1, V/V) and maintained under greenhouse conditions (mean air temperature of 25°C and a relative humidity of 73%).

extract_protocol:
Stem total RNA were extracted using CTAB protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the seedlings reached approximately 25 cm in height they were transferred to growth chambers and left to acclimate for one week before the temperature and CO2 treatments. At this time, they had 5-6 fully expanded leaves. The chambers were adjusted for 10 h of light, which was provided by a set of blue and red light-emitting diodes (LED, 280 µmol photons m2.s-1 at the top of the plants) positioned 30 cm above the seedlings. We combined three temperatures (10-12°C -  low, 22-24°C - normal, 33-35°C - high) with two CO2 concentrations (390 ppm - normal and 700 ppm - elevated). The plants were maintained 35 days in these conditions. A cylinder with pure CO2 was used to attain 700 ppm. The gas flow was controlled with a microvalve and we used an Infra-Red Gas Analyzer for calibration of the CO2 inside the chamber (Licor 6400 model). The temperatures were set with cooling and heating systems placed inside the chamber. The air circulation inside of the chambers was provided by two small fans positioned in opposite sides of the chamber (1.5 m x 3.0 m x 2.2 m, W x L x H). We named as control treatments those plants growing at 22oC and ambient CO2, which varied between 380-390 ppm. Plants were watered every second day. They were maintained for five weeks under these conditions.

value: stem

value: controle temperature


title: RNAseq patient 1 MRD


title: Sample K2: Stem Globulus 20°C


title: RNAseq patient 35 diagnosis


title: 020717_Cell58-D10

description: New onset SJIA patient


title: hamster.uninfected.CFZ.rep1

description:
hamster_SARS2_rpkm.csv
clean-drug-1


title: Sample I3: Stem Globulus CO2 20°C

value: carbon dioxide control temperature


title: Sample K1: Stem Globulus 20°C


title: RNAseq patient 34 diagnosis_2


title: 020717_Cell56-B10

description: New onset SJIA patient


title: Sample H3: Stem Globulus CO2 30°C

value: carbon dioxide high temperature


title: RNAseq patient 32 diagnosis


title: 020717_Cell55-H9

description: New onset SJIA patient


title: Sample H2: Stem Globulus CO2 30°C


title: Sample I1: Stem Globulus CO2 20°C


title: RNAseq patient 34 diagnosis_1


title: RNAseq patient 31 diagnosis


title: Sample G3: Stem Globulus 30°C

value: high temperature


title: Sample H1: Stem Globulus CO2 30°C


title: 020717_Cell53-F9

description: New onset SJIA patient


title: Sample G2: Stem Globulus 30°C


title: RNAseq patient 30 diagnosis


title: RNAseq patient 29 diagnosis


title: Sample G1: Stem Globulus 30°C


title: 020717_Cell50-H9

description: New onset SJIA patient


title: 020717_Cell54-G9

description: New onset SJIA patient


title: Sample B3: Stem Globulus 10°C

value: low temperature


title: RNAseq patient 28 diagnosis


title: 020717_Cell5-F1

description: New onset SJIA patient


title: 020717_Cell52-D9

description: New onset SJIA patient


title: Sample I2: Stem Globulus CO2 20°C


title: Sample B2: Stem Globulus 10°C


title: 020717_Cell51-A9

description: New onset SJIA patient


title: RNAseq patient 26 diagnosis


title: RNAseq patient 27 diagnosis


title: Sample B1: Stem Globulus 10°C


title: 020717_Cell48-F8

description: New onset SJIA patient


title: 020717_Cell47-E8

description: New onset SJIA patient


title: 020717_Cell49-G8

description: New onset SJIA patient


title: RNAseq patient 33 diagnosis


title: Sample A3: Stem Globulus CO2 10°C

value: carbon dioxide low temperature


title: RNAseq patient 25 diagnosis


title: RNAseq patient 24 diagnosis


title: 020717_Cell46-A8

description: New onset SJIA patient


title: asthma8

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from bronchial asthma

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: patient with bronchial asthma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

extract_protocol: PBMCs were isolated from peripheral blood using a previously reported method (Duan et al., 2020). We collected venous blood (6 ml) from each participant using an EDTA-anticoagulated tube. PBMCs were isolated via density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare) and were stored at -80°C. Total RNA was isolated using TRIzol reagent (Life Technologies, Carlsbad, CA, USA) and purified with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

tag: gender

value: Male

value: PBMCs


title: Sample A2: Stem Globulus CO2 10°C


title: asthma9

value: Female


title: asthma7


title: asthma4


title: RNAseq patient 23 diagnosis


title: asthma2


title: asthma6


title: Sample A1: Stem Globulus CO2 10°C


title: 020717_Cell45-H7

description: New onset SJIA patient

value: Macrophage (CD14+CD163+)


title: 020717_Cell43-E7

description: New onset SJIA patient


title: RNAseq patient 22 diagnosis


title: asthma5


title: RNAseq patient 20 diagnosis


title: RNAseq patient 19 diagnosis


title: asthma3


title: asthma10


title: RNAseq patient 21 diagnosis


title: 020717_Cell40-A7

description: New onset SJIA patient


title: 020717_Cell41-B7

description: New onset SJIA patient


title: RNAseq patient 18 diagnosis


title: 020717_Cell42-C7

description: New onset SJIA patient


title: 020717_Cell4-E1

description: New onset SJIA patient


title: 020717_Cell39-H6

description: New onset SJIA patient


title: RNAseq patient 17 diagnosis


title: 020717_Cell38-G6

description: New onset SJIA patient


title: asthma1

description: Gene expression data from healthy control


title: RNAseq patient 16 diagnosis


title: RNAseq patient 15 diagnosis


title: control9

source_name: healthy control


title: 020717_Cell35-A6

description: New onset SJIA patient


title: RNAseq patient 14 diagnosis


title: control5


title: control8


title: control7


title: control3


title: 020717_Cell34-H5

description: New onset SJIA patient


title: RNAseq patient 13 diagnosis


title: RNAseq patient 12 diagnosis


title: 020717_Cell33-F5

description: New onset SJIA patient


title: RNAseq patient 11 diagnosis


title: 020717_Cell32-E5

description: New onset SJIA patient


title: control4


title: control6


title: RNAseq patient 10 diagnosis


title: 020717_Cell3-C1

description: New onset SJIA patient


title: Small intestine neuroendocrine tumor (SINET), 131

type: genomic

city: Gothenburg

first: Yvonne

last: Arvidsson

address: Box 425

department: Biomedicin

country: Sweden

institute: University of Gothenburg

hyb_protocol: SureTag DNA Labeling Kit; Agilent Technologies Inc

scan_protocol: Arrays were scanned using the Agilent G2565BA Microarray Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

source_name: Tumor

extract_protocol: Genomic DNA was isolated from the biopsies using the DNeasy® Blood and Tissue kit (Qiagen GmbH, Hilden, Germany).

tag: case

tag: gender male (m), female (f)

value: F

value: liver metastasis

source_name: Human Reference DNA female (Agilent)

tag: gender reference

value: Male (M), Female (F):F


title: control1


title: control2


title: RNAseq patient 9 diagnosis


title: 020717_Cell31-D5

description: New onset SJIA patient


title: RNAseq patient 8 diagnosis

value: standard-risk


title: Small intestine neuroendocrine tumor (SINET), 130

label_protocol: SureTag DNA Labeling Kit; Agilent Technologies Inc


title: 020717_Cell28-A5

description: New onset SJIA patient


title: 020717_Cell27-H4

description: New onset SJIA patient


title: RNAseq patient 6 diagnosis


title: RNAseq patient 7 diagnosis


title: 020717_Cell25-F4

description: New onset SJIA patient


title: 020717_Cell24-E4

description: New onset SJIA patient


title: 020717_Cell22-C4

description: New onset SJIA patient


title: Small intestine neuroendocrine tumor (SINET), 127


title: RNAseq patient 5 diagnosis


title: RNAseq patient 4 diagnosis


title: RNAseq patient 3 diagnosis


title: Small intestine neuroendocrine tumor (SINET), 128

value: M

source_name: Human Reference DNA male (Agilent)

value: Male (M), Female (F):M


title: 020717_Cell21-B4

description: New onset SJIA patient


title: Small intestine neuroendocrine tumor (SINET), 125


title: Small intestine neuroendocrine tumor (SINET), 124


title: Small intestine neuroendocrine tumor (SINET), 129


title: Small intestine neuroendocrine tumor (SINET), 126


title: Small intestine neuroendocrine tumor (SINET), 123


title: Small intestine neuroendocrine tumor (SINET), 122

value: primary tumor


title: Small intestine neuroendocrine tumor (SINET), 120


title: 020717_Cell26-G4

description: New onset SJIA patient


title: RNAseq patient 2 diagnosis

value: high-risk


title: 020717_Cell2-B1

description: New onset SJIA patient


title: 020717_Cell20-H3

description: New onset SJIA patient


title: Small intestine neuroendocrine tumor (SINET), 121


title: 020717_Cell17--E3

description: New onset SJIA patient


title: 020717_Cell16-C3

description: New onset SJIA patient


title: dro3_3h

city: Verona

first: Fabio

last: Arruda-Silva

state: VR

address: strada Le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
FastQC High Throughput Sequence QC Report (Version 0.11.8) was used to assess the quality of the sequencing on the FASTQ files
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh38.p13 transcriptome using mapping-based mode of Salmon v0.13.1, with the following parameters: “-i index -l SR -r name–validateMappings–gcBias”
Salmon output was imported in RStudio environment (R Version 3.5.3; R studio version 1.1.463) using the tximport (Version 1.10.10). Differential expression analysis was performed using the Bioconductor/R package DESeq2 (Version 1.22.2). DESeq2's lfcShrink function was applied to shrink log2FoldChanges.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: excel files include DESeq2 output and TPM values for each sample

source_name: 16HBE cell line

growth_protocol: 16HBE cells were grown for 1week in EMEM medium supplemented with FBS 10%, (including 2mM ultraglutamine, 100U/mL penicillin and 100ug/mL streptomycin), starting from cryogenated samples (2x106 cell/vial). Fibronectin/collagen/BSA coated flasks were used . Culture medium was replaced every three days.

extract_protocol:
Total RNA from cultured 16HBE cells was isolated using the RNeasy mini Kit (Qiagen, Venlo, Limburg, Netherlands), according to the manufacturer instructions. An on-column DNase digestion with the RNase-free DNase set (Qiagen) was also performed during total RNA isolation to completely remove any possible contaminating DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: On day 1 cells were seeded in 24-well plates (uncoated) at a density of 0.4 x106 cell/well in EMEM medium with 2% FBS (including ultraglutamine and pen/strep antibiotics). The plates were incubated until complete adhesion of the cells (16-20h). On day 2, the culture medium was replaced by 900 ul of fresh EMEM with 2% FBS. Drosera 3x or CTRL3x solution were added (100 µl/well).

value: Bronchial epithelial cells

tag: passages


title: 020717_Cell15-B3

description: New onset SJIA patient


title: dro2_3h


title: dro4_3h


title: 020717_Cell14-H2

description: New onset SJIA patient


title: RNAseq patient 1 diagnosis


title: Small intestine neuroendocrine tumor (SINET), 118


title: 020717_Cell10-C2

description: New onset SJIA patient


title: ctrl4_3h


title: dro1_3h


title: ctrl2_3h


title: Small intestine neuroendocrine tumor (SINET), 117


title: Small intestine neuroendocrine tumor (SINET), 119


title: Small intestine neuroendocrine tumor (SINET), 116


title: ctrl1_3h


title: 020717_Cell1-A1

description: New onset SJIA patient


title: Small intestine neuroendocrine tumor (SINET), 112


title: Small intestine neuroendocrine tumor (SINET), 115


title: Small intestine neuroendocrine tumor (SINET), 111


title: Small intestine neuroendocrine tumor (SINET), 114


title: Small intestine neuroendocrine tumor (SINET), 113


title: OBF1sh1_Raji_rep3

city: Basel

first: Shuang

last: Song

state: Basel

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Sequencing reads were aligned using qAlign from the Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0) to the mouse genome (mm9) with default parameters except for splicedAlignment = TRUE. Alignments were quantified with qCount from the Bioconductor package QuasR [Gaidatzis et al 2015] (package version 1.16.0) for known UCSC genes obtained from the TxDb.Mmusculus.UCSC.mm9.knownGene package (package version 3.2.2) using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing the count table

growth_protocol: Burkitt’s lymphoma cell lines (Raji) were cultured in T75 flasks in RPMI1640 medium (10% FBS, 50 μm 2-mercaptoethanol). B Lymphoma cells were passaged every two to three days.

extract_protocol:
QIAGEN RNeasy Micro kit
The Illumina TruSeq Stranded mRNA protocol was used for library preparation for next generation sequencing.

treatment_protocol: pLKO.1 vectors (lentiviral vector) with specific shRNAs for human Pou2f1, human Pou2f2 and human Pou2af1 were purchased from Sigma. shRNA sequences used in this paper are listed in Table S3. To prepare lentivirus for infection, 1.3 × 106 293T cells were seeded on T25 flask with 5ml DMEM medium 24 hours before transfection and, the following day, 7 μg pLKO.1-shRNA vector, together with plasmids coding for Rev, Vsv-g, Tat and Gag/Pol, was transfected into 293T cells with FuGENE HD. Supernatant was collected at 24, 48 and 72 hours post transfection, and filtered through 0.4 μm EMD Millipore Steriflip Sterile Disposable Vacuum Filter units. Lentivirus particles in this 15 ml suspension were then concentrated by adding 5 ml of LentiX concentrator (Takara), and incubated for 24 hours at 4 ℃. Post incubation, lentiviral particles were precipitated and centrifuged at 1500 g for 45 min at 4 ℃. Pelleted lentiviruses were then concentrated 150 times by resuspending with 100 μl culture medium (RPMI1640, 10% FCS, 50 μm 2-mercaptoethanol). 10 μl lentivirus suspension was added to 2 × 105 cells (Raji and Ramos) in 6-well plate containing 8 μg/ml Polybrene (Millipore) in RPMI1640 medium. B Lymphoma cells with lentiviruses were infected for 5 days at 37℃ and 5% CO2. Post infection, stable integrations were selected for 7 days in the presence of 3 μg/ml Puromycin (GIBCO). Non-target shRNA (Cat# SHC002, Sigma) was used as a control in shRNA-mediated gene knockdown experiments. After selection, stably integrated B lymphoma cells were used for downstream assays.

tag: shRNA clone

value: OBF1sh1 (OBF1 specific shRNA)

tag: cell line

value: Raji

value: GC-derived Burkitt's lymphoma


title: dro3_6h


title: dro2_6h


title: OBF1sh1_Raji_rep2


title: OBF1sh1_Raji_rep1


title: 020717_Cell11-D2

description: New onset SJIA patient


title: dro1_6h


title: 020717_Cell12-E2

description: New onset SJIA patient


title: Small intestine neuroendocrine tumor (SINET), 109


title: ctrl3_3h


title: SHC002_Raji_rep3

value: SHC002 (Control)


title: Small intestine neuroendocrine tumor (SINET), 108


title: ctrl4_6h


title: dro4_6h


title: ctrl3_6h


title: SHC002_Raji_rep1


title: Small intestine neuroendocrine tumor (SINET), 106


title: ctrl2_6h


title: rice seed, F1288GIF2 Rep3

city: Shanghai

first: Ma

last: Bin

state: Shanghai

address: Fenglin 300 Road, Shanghai, China

institute: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Os125827RS1
Supplementary_files_format_and_content: tab-delimited text file includes counts and FPKM values for each Sample

organism: Oryza sativa

source_name: rice seed

growth_protocol: NILs plants were normally grown in paddy field.

extract_protocol:
Total RNA were extracted using RNeasy Plant Mini Kit (Cat 74904, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 15 DAF at filling stage

value: developing seeds tissues

tag: genotype

value: wild type

tag: near isogenic line


title: Dp4_4D_rep3[RNA-seq]

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

institute: Zhejiang University

description:
Dp4_22C_5
diff_Dp4.txt

data_processing:
mRNA-seq: Adaptors at the 3' end of the reads were trimmed using cutadapt version 1.16. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). mRNA reads were aligned to ERCC sequences using Bowtie 2 with default parameters. The remaining non-ERCC reads were aligned to maize chloroplast and mitochondrial genome using TopHat2 with default parameters so that the organellar transcripts are excluded for further study. The remaining reads were then mapped to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts, which were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses (mRNA-seq) and tables reporting RPKM normalized counts in DNA-seq.

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
RNA extracted by mirVana™ miRNA Isolation Kit; DNA extracted by DNeasy Plant Mini Kit (QIAGEN)
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: group (aneuploidy vs. whole-ploidy)

value: aneuploidy comparison (Dp4)


title: ctrl1_6h

tag: cell type


title: rice seed, F1288GIF2 Rep1

tag: tissue


title: pig longissimus dorsi muscle - lincRNA_rep

city: Wuhan

first: shanshan

last: Wang

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: Animal Sciences & Technology

institute: Huazhong Agricultural University

description: lincRNA-seq

data_processing:
The raw data from RIP-seq and lincRNA-seq were cleaned through the following quality control (QC) steps: 1) clip adaptor; 2) discard reads containing more than 5% N; 3) remove low-quality reads (the percentage of bases with quality score <20); and 4) remove short reads.
clean reads were aligned to pig reference genome(Sus_scrofa 10.2) by Tophat2,, which were assembled into transcripts using Cufflinks
all novel transcripts were selected for lincRNA identification using the following conditions: 1) transcript length ≥ 200bp, 2) located in the intergenic region and was at least 1 Kb from neighboring transcripts.
For all selected transcripts, the coding potentials were evaluated using the CPC software,and the cross-species conservation were evaluated by blast with the EST databases of pig, mouse and human. And the expression levels expressed as Fragments Per Kilobase per Million mapped fragment (FPKM) for all characterized transcripts were compared using Cuffdiff among different sequencing dataset.
Genome_build: Sus_scrofa 10.2
Supplementary_files_format_and_content: text files include FPKM values for each Sample

organism: Sus scrofa

source_name: large White female pigs

extract_protocol:
RNA from longissimus dorsi muscle was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: longissimus dorsi muscle

value: one-month-old


title: SHC002_Raji_rep2


title: rice seed, F1287gif2 Rep2

value: mutant


title: rice seed, F1287gif2 Rep3


title: rice seed, F1287gif2 Rep1


title: Dp4_4D_rep2[RNA-seq]

description:
Dp4_22C_1
diff_Dp4.txt


title: Dp4_4D_rep1[RNA-seq]

description:
Dp4_22C_13
diff_Dp4.txt


title: Small intestine neuroendocrine tumor (SINET), 107

value: F

value: Male (M), Female (F):F


title: Small intestine neuroendocrine tumor (SINET), 110

value: M

value: liver metastasis

value: Male (M), Female (F):M


title: Dp4_3D_rep4[RNA-seq]

description:
Dp4_21C_6
diff_Dp4.txt


title: Dp4_3D_rep3[RNA-seq]

description:
Dp4_21C_14
diff_Dp4.txt


title: mutant WT darckness rep2

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

data_processing:
Read quality was analyzed using the FastQC software
High-quality reads were then mapped to the predicted transcripts of the T. atroviride v2 genome using the Kallisto software
The expression matrix generated was used for differential expression analysis using R-Studio and the edgeR (Robinson et al., 2009) and limma (Ritchie et al., 2015) packages.
Differentially expressed genes were determined using the “Generalized Linear Probability Radius Test (GLM) method with a Log Fold-Change of ± 1 and a FDR ≤ 0.05.
Genome_build: http://genome.jgi.doe.gov/Triat2/Triat2.home.html
Supplementary_files_format_and_content: matrix containing the transcripts per million (kallisto output)

organism: Trichoderma atroviride IMI 206040

source_name: WT strain

growth_protocol: the strains grew on Petri dishes with 30 mL of PDA medium covered with cellophane.

extract_protocol:
Total RNA was extracted using the TRIzol protocol (Invitrogen).
RNA libraries were prepared with the TruSeq v2 RNA Sample Preparation Kit (Illumina). The size and quality of the library were determined using a Bioanalyzer (Agilent Technologies). Three biological replicates of all conditions were sequenced on an Illumina HiSeq 2000 platform with an average of 20 million reads per library.

treatment_protocol: Mycelium of the WT, Δblr-1 / -2, Δenv-1, Δcry-DASH and Δcry-1 strains were collected 30 min following a blue light pulse of 200 μmol.m-2  and immediately frozen in liquid nitrogen. A set of plates of all the strains was used as control; these plates were not exposed to blue light.

value: mycelium

value: 36 hr growing in PDA

tag: treatment

value: darkness


title: mutant WT  darckness rep3


title: Dp4_3D_rep2[RNA-seq]

description:
Dp4_21C_11
diff_Dp4.txt


title: rice seed, F1288GIF2 Rep2


title: Dp4_3D_rep1[RNA-seq]

description:
Dp4_21C_10
diff_Dp4.txt


title: Small intestine neuroendocrine tumor (SINET), 103

value: primary tumor


title: Small intestine neuroendocrine tumor (SINET), 104


title: mutant WT  darckness rep1


title: mutant WT  light rep3

value: blue light pulse


title: Small intestine neuroendocrine tumor (SINET), 105


title: Small intestine neuroendocrine tumor (SINET), 101


title: Small intestine neuroendocrine tumor (SINET), 102


title: mutant WT  light rep2


title: Dp4_2D_rep2[RNA-seq]

description:
Dp4_20C_3
diff_Dp4.txt


title: mutant WT light rep1


title: Dp4_2D_rep3[RNA-seq]

description:
Dp4_20C_4
diff_Dp4.txt


title: adjacent nontumor tissue rep1

city: Fuzhou City

first: Yong-Jin

last: Cao

address: Chazhong Road

department: Department of Thyroid and Breast Surgery

institute: The First Affliated Hospital of Fujian Medical University

description: circRNA expression in breast cancer and adjacent nontumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software limma package.

source_name: adjacent nontumor tissue rep1

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: RNA isolation was performed using TRIzol reagent according to the manufacturer’s protocol.The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

value: breast

value: female


title: breast cancer tissue rep4

source_name: breast cancer tumor tissue rep4


title: pig longissimus dorsi muscle - IgG_rep

extract_protocol:
Tissues were crushed in liquid nitrogen and lysed in ice-cold lysis buffer and EZH2 binding transcripts were were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: IgG


title: Dp4_2D_rep1[RNA-seq]

description:
Dp4_20C_16
diff_Dp4.txt

value: aneuploidy comparison (Dp4)


title: mutant cry1 darckness rep3

source_name: cry1 gene mutant


title: adjacent nontumor tissue rep3

source_name: adjacent nontumor tissue rep3


title: 1La_3D_rep4[RNA-seq]

description:
1La45
diff_1La.txt

value: aneuploidy comparison (TB-1La)


title: breast cancer tissue rep3

source_name: breast cancer tumor tissue rep3


title: pig longissimus dorsi muscle - EZH2_rep

value: longissimus dorsi muscle

value: one-month-old


title: mutant cry1 darckness rep2


title: 1La_3D_rep3[RNA-seq]

description:
1La42
diff_1La.txt


title: mutant cry1 darckness rep1


title: Dp4_2D_rep4[RNA-seq]

description:
Dp4_20C_7
diff_Dp4.txt


title: adjacent nontumor tissue rep4

source_name: adjacent nontumor tissue rep4


title: breast cancer tissue rep1

source_name: breast cancer tumor tissue rep1


title: mutant cry1 light rep3


title: 1La_3D_rep1[RNA-seq]

description:
1La40
diff_1La.txt


title: 1La_3D_rep2[RNA-seq]

description:
1La41
diff_1La.txt


title: mutant cry1 light rep2


title: 1La_1D_rep4[RNA-seq]

description:
1La30
diff_1La.txt


title: mutant cry1 light rep1


title: adjacent nontumor tissue rep2

source_name: adjacent nontumor tissue rep2


title: mutant cry-DASH  darckness rep3

source_name: cry-DASH gene mutant


title: mutant cry-DASH  darckness rep1


title: mutant cry-DASH darckness rep2


title: 1La_1D_rep1[RNA-seq]

description:
1La21
diff_1La.txt


title: 1La_1D_rep2[RNA-seq]

description:
1La27
diff_1La.txt


title: mutant cry-DASH  light rep3


title: 1La_2D_rep3[RNA-seq]

description:
1La17
diff_1La.txt


title: mutant cry-DASH  light rep2


title: mutant cry-DASH light rep1


title: mutant env1 darckness rep3

source_name: env1 gene mutant


title: 1La_2D_rep1[RNA-seq]

description:
1La14
diff_1La.txt


title: breast cancer tissue rep2

source_name: breast cancer tumor tissue rep2


title: 1La_2D_rep2[RNA-seq]

description:
1La16
diff_1La.txt


title: mutant env1 darckness rep2


title: 1La_1D_rep3[RNA-seq]

description:
1La29
diff_1La.txt


title: Control rep3

first: Yang

last: Cheng

address: No. 528 Zhangheng Road

department: Institute of liver diseas

institute: Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine

data_processing:
Image base calling was performed by using the software Bcl2fastq (v2.17.1.14, Illumina, USA) on the original image data of the sequencing results.
Cutadapt (version 1.9.1) was used for filtering of sequencing data. Short readings was compared using Hisat2 (v2.0.1) software. All mapped reads were aligned to various parts of the genome and to individual chromosomes.
LncRNA and mRNA expression were calculated using Rsem software (V1.2.6, R package)
Differential genetic analysis was undertaken using DESeq2 (V1.6.3) of the Bioconductor software package.
Based on the threshold of Log2FC more than 2 times and P Value less than 0.05, differential expressed lncRNAs were screened.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HepG2 cells

growth_protocol: The cells were incubated in DMEM medium supplied with 10% fetal bovine serum and 1% PS in the 5% CO2 incubator

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA kit (#634891, Clontech, Japan) was used for RNA extraction.After deproteinization and DNase treatment, complete total RNA was obtained. Agilent Bioanalyzer was used to perform capillary electrophoresis, the sample quality was evaluated with the software RIN (RNA Integrity Number) score, and the RIN value should be greater than 8.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were  grouped Atractylon group(treated by 20 μM Atractylon) and control group, each group had 3 replicates.

value: without Atractylon


title: Control rep2


title: 1La_2D_rep4[RNA-seq]

description:
1La20
diff_1La.txt


title: Small intestine neuroendocrine tumor (SINET), 39

source_name: Tumor

source_name: Human Reference DNA male (Agilent)


title: mutant env1 darckness rep1


title: Small intestine neuroendocrine tumor (SINET), 38

value: F

source_name: Human Reference DNA female (Agilent)

value: Male (M), Female (F):F


title: Atractylon rep3

value: 20 uM Atractylon


title: mutant env1 light rep3


title: Small intestine neuroendocrine tumor (SINET), 36

value: M

value: Male (M), Female (F):M


title: Control rep1


title: HRT18-BPV

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

country: South Korea

institute: Chungbuk National University

data_processing:
Raw sequences were checked the quality of the data  with FastQCv0.11.7 program before proceeding.
The adapter sequence was removed with Trimmomatic 0.38 program. Trimmed data was generated by removing base qulity less than 3 from reads ends and base unsatisfied with window size =4, mean quality =15 using the sliding window trim method.
cDNA fragment were mapped GRCh37 or Chlorocebus_sabeus_1.1_NCBI_100 genomic DNA reference with Bowtie 2 2.3.4.1 aligner.
The mapped reads were assembled with the known gene/transcript with StringTie version 2.1.3b program.
The amount of abundance of the transcript was normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value considering read count, transcript length and depth of coverage.
Statistical analysis for each comparision combination was processed with fold change, exactTest using edgeR. Significant results were selected under the condition |fc|>=2 & exactTest raw p-value<0.05.
Genome_build: GRCh37

growth_protocol: MARC145 derived African green monkey kidney origin, was cultured in DMEM(Gibco) supplemented with antibiotic-antimycotic(100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL amphotericin B, Gibco) and 10% fetal bovine serum(Gibco, USA). HEK-293, A549 and HRT18 cell line derived human kidney, lung and colon origin, was cultured in MEM, F-12k and RPMI1640 media with 10% fetal bovine serum and antibiotic-antimycotic. All cell was  maintained routinely by re-plating with 2~3×10^6 cells into cell culture flask (T75) for 3~4 days in each growth medium.

extract_protocol:
Total RNA was extracted from shaanvirus infected host cells with Trizol LS reagent
The infected cells were harvested at 24 hours post infection, and a total RNA was extracted from the harvested cells with Trizol LS reagent. Total cDNA libraries were prepared from extracted RNA using Illumina TruSeq Stranded Total RNA LT kit according to the manufacturer’s instruction. TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E. Samples were sequenced on NovaSeq 6,000 platform.

treatment_protocol: One replicate was shaan virus infected for 24hours

value: Colon

value: Epithelial cells

value: infected with shaan virus for 24hours


title: mutant env1 light rep2

value: mycelium

value: 36 hr growing in PDA

value: blue light pulse


title: mc38 tumors GAD1-SHB3

city: Durham

first: De

last: Huang

state: NC

address: 308 Research Drive

institute: Duke university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Raw reads were processed by BBDuk (38.34) to removed adapters and trim low-quality reads. Reads ( >35bp) were aligned to the mouse genome (mm9).
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Mouse colon adenocarcinoma MC38 tumor

growth_protocol: Before tumor cell injection into C57BL/6 mouse, MC38 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum and 100 U/mL penicillin-streptomycin (typically 2~5 × 106 cells in a 10cm dish). Cells were maintained in a water-jacketed incubator with 5% CO2 at 37°C.

extract_protocol:
All the tumors were extracted 20 days after tumor implanted. Total RNA was extracted from GAD1-shA GAD1-shB and NTC MC38 tumor samples (3 replicates per group) using an RNeasy kit (Qiagen, Cat# 74104) and dissolved in RNase-free water. RNA samples were sequenced on Illumina novaseq.
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations andindex codes were added to attribute sequences to each sample.

treatment_protocol: GAD1 shRNAs (ShA and ShB) or NTC vectors together with lentiviral packaging vectors PAX2 and VSV-G were transfected into HEK293T cells using Lipofectamine 2000 (Thermo Fisher Scientific) following standard procedures. Viral particles were collected and filtered (0.45 μM) after transfection for 48 hours. For infection, lentiviral supernatant was added to cultured MC38 cells with 8 μg/mL polybrene. After incubation for 24 hours, infected cells were selected for 3 to 5 days with puromycin.

tag: strain

value: colon adenocarcinoma MC38

tag: shRNA


title: Small intestine neuroendocrine tumor (SINET), 34

tag: case

value: primary tumor


title: Small intestine neuroendocrine tumor (SINET), 32

tag: gender male (m), female (f)


title: Small intestine neuroendocrine tumor (SINET), 35

tag: gender reference


title: Atractylon rep2


title: A549-BPV

value: Lung


title: Small intestine neuroendocrine tumor (SINET), 29


title: HRT18-mock

value: untreated


title: Small intestine neuroendocrine tumor (SINET), 37


title: Small intestine neuroendocrine tumor (SINET), 31


title: mutant env1 light rep1


title: mc38 tumors GAD1-SHB2


title: Small intestine neuroendocrine tumor (SINET), 30


title: mutant blr2 darkness rep2

source_name: blr2 gene mutant

value: darkness


title: mc38 tumors GAD1-SHB1


title: Small intestine neuroendocrine tumor (SINET), 33


title: A549-mock


title: Atractylon rep1


title: mc38 tumors GAD1-SHA3


title: mutant blr2 light rep3


title: mutant blr2 darkness rep1


title: Small intestine neuroendocrine tumor (SINET), 26


title: mc38 tumors GAD1-SHA2


title: HEK293-mock

value: Embryonic kidney


title: Small intestine neuroendocrine tumor (SINET), 27


title: mc38 tumors NTC3

value: shRNA control


title: Small intestine neuroendocrine tumor (SINET), 25


title: mc38 tumors GAD1-SHA1


title: TB and HIV infected subject TB_HIV_23

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

institute: Instituto Gonçalo Moniz

description: TB and HIV infected subject

data_processing:
bcl2fastq was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to Homo sapiens GRCh38  transcriptome using salmon v1.2.1
Genome_build: Homo sapiens GRCh38

source_name: Whole Blood

extract_protocol:
Whole blood was collected in two PAXgene Blood RNA tubes (Qiagen, catalog # 762165) and was directly frozen at -800C at time of enrollment. RNA was extracted from 30 whole blood samples using the PAXgene Blood RNA kit (Qiagen, catalog # 762174) and followed by quantification using Qubit RNA assay HS (Invitrogen, Cat # Q32852). RNA purity was checked using QIAxpert and RNA integrity was assessed on TapeStation using RNA HS ScreenTapes (Agilent, Cat# 5067-5579).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: Male


title: TB and HIV infected subject TB_HIV_22

description: TB and HIV infected subject

value: Female


title: LGL98-PN-NK

city: Rennes

first: Cedric

last: PASTORET

address: 2 rue Henri Le Guilloux

country: France

institute: University Hospital Rennes

data_processing:
Base-calling with Illumina Real Time Analysis (3.4.4) with default parameters
STAR used to obtain the number of reads associated to each gene in the Genecode v31 annotation
DESeq2 package for matrix count and calculation of FPKM level
Supplementary_files_format_and_content: tab-delimited text files include reads per gene values for each Sample
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: blood sample (FACS sorted NK cells)

extract_protocol:
AllPrep DNA/RNA Micro Kit (Qiagen, Hilden, Germany)
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: FASC sorted NK cells from peripheral blood

tag: patient diagnosis

value: CLPD-NK

value: NK

value: STAT3 mutated

tag: socs3 methylation

value: SOCS3 unmethylated

tag: phenotype


title: mutant blr2 light rep2


title: TB and HIV infected subject TB_HIV_20

description: TB and HIV infected subject


title: TB and HIV infected subject TB_HIV_21

description: TB and HIV infected subject


title: HIV only infected subject HIV_19

description: HIV only infected subject


title: LGL82-FM-NK

tag: genotype

value: Wild type


title: Small intestine neuroendocrine tumor (SINET), 28

value: F

value: Male (M), Female (F):F


title: mutant blr1 darkness rep3

source_name: blr1 gene mutant

value: mycelium

value: 36 hr growing in PDA


title: mc38 tumors NTC2

value: colon adenocarcinoma MC38


title: LGL84-GR-NK


title: HIV only infected subject HIV_18

description: HIV only infected subject


title: mutant blr1 darkness rep1


title: RNF20-KO_IgG_1

first: Wei

last: Li

address: 1st Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Data from ChIP -Seq experiments were mapped to mm10 genome with Bowtie 2 using default settings, with all duplicates removed by Picard tools (http://broadinstitute.github.io/picard).
MACS2 was used to identify peaks with default parameters. Diffbind was used to analyze differences between WT and Rnf20-knockout reprogrammable cells.
For visualization, the aligned reads files (Binary Alignment Map [BAM]) were converted to normalized coverage files (bigWig) using bamCoverage from deepTools.
Normalization was performed using  bamCoverage from deepTools, with read coverage normalized to 1× sequencing depth with a renormalization by shuffled peaks to eliminate the disturbances from abnormally high-value regions.
Genome_build: mm10
Supplementary_files_format_and_content: Snapshots of the data were constructed using the Integrative Genomics Viewer (IGV). Heatmaps were generated with computeMatrix from deepTools. Metaplots were generated with deepTools.

growth_protocol: Reprogrammable cells were cultured at 37˚C in a shumidified atmosphere with 5% CO2.

extract_protocol:
Approximately 1×106 cells were crosslinked with 1% formaldehyde for 10 min at room  temperature. Fixation was stopped by adding Glycine at a final concentration of 125 mM and  incubated for 15 min at room temperature. After washing twice with PBS, cells were resuspended  in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% NP-40 and 1 × protease inhibitor  cocktail) and incubate for 10 min on ice. The cell nuclei were pelleted at 1000 rpm for 10 min at  4°C, and the nuclear pellet was resuspended in nuclei lysis buffer (50 mM Tris-HCl, pH 8.0, 10  mM EDTA, 1% SDS and 1 × protease inhibitor cocktail) and incubate for 10 min on ice.  Chromatin DNA was sheared to 250-600 bp by sonication. 5% chromatin fragments were saved  as input and the remaining were incubated with magnetic beads conjugated with antibody  overnight at 4°C. Beads were sequentially washed four times with high-salt wash buffer (50 mM  HEPES, pH 7.9, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate  and 1 × protease inhibitor cocktail), and two times with TE buffer (10 mM Tris-HCl, pH 8.0 and  1 mM EDTA). The protein-chromatin complex was eluted with elution buffer (50 mM Tris-HCl,  pH 8.0, 10 mM EDTA, 1% SDS with 1 μl of proteinase K (20 μg/μl)) for 2 h at 55°C and decrosslinked by incubation overnight at 65°C. The precipitated hybrid fragment was cleaned by  phenol:chloroform:isoamyl alcohol once, followed by ethanol precipitation.
Sequencing libraries were generated with NEBNext® UltraTM II DNA Library Prep Kit for Illumina (E7645S), according to the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA were used for library preparation. NEBNext Multiplex Oligos for Illumina (Set 1, NEB #E7600) were used for PCR amplification of adaptor-ligated DNA. Libraries were purified with SPRIselect® Reagent Kit (Beckman Coulter, Inc. #B23317). Sequencing was performed on Illumina NovaSeq 6000 System.

treatment_protocol: untreated

tag: cell line

value: reprogrammable cells

tag: time point

value: day 3 of OSKM reprogramming

tag: chip antibody

value: moue IgG (Santa Claus, sc-2050)


title: mc38 tumors NTC1

tag: cell type


title: LGL48-TM-NK

value: TET2 mutated


title: RNF20-WT_IgG_2

value: wild type

value: untreated


title: mutant blr1 darkness rep2

tag: tissue

tag: age

value: darkness


title: mutant blr2 light rep1

tag: treatment

value: blue light pulse


title: 6h.CFZ-rep3

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

institute: The University of Hong Kong

description:
CFZ_SARS2_rpkm.csv
6h-drug-3

data_processing:
Fastq files from RNA-seq were quality examined by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were processed by cutadapt to remove reads with low quality and to trim adapters.
Trimmed reads were aligned to hg38 reference genome using Tophat2
Reads assigned to each gene were counted by featureCounts  with refseq gene sets as references.
Genes without at least 1 read mapped on average in each sample were considered undetectable and were filtered out. Read counts were normalized by Trimmed Mean of M-values (TMM) method and RPKM of each gene was calculated using R package edgeR
Genome_build: hg38 for Caco-2 cells; MesAur1.0 for hamster lung tissues
Supplementary_files_format_and_content: CSV files include RPKM values for each sample

extract_protocol:
Qiagen RNeasy Mini Kit
cDNA libraries were prepared by KAPA mRNA HyperPrep Kit.1 ug of total RNA was used as starting material. Manufacturer’s protocol was followed.

value: cell line

tag: infection status

tag: clofazimine treatment

value: 6 hours clofazimine


title: mutant blr1 light rep1


title: mutant blr1 light rep3


title: LGL105-SF-NK

value: CLPD-NK

value: NK

value: SOCS3 unmethylated


title: mutant blr1 light rep2


title: RNF20-KO_SOX2_2

tag: strain

value: anti-SOX2 (Santa Claus, sc365823X)


title: RNF20-KO_IgG_2


title: HIV only infected subject HIV_16

description: HIV only infected subject

value: Female


title: HIV only infected subject HIV_17

description: HIV only infected subject

value: Male


title: 6h.CFZ-rep2

description:
CFZ_SARS2_rpkm.csv
6h-drug-2


title: MARC145-mock

data_processing:
Raw sequences were checked the quality of the data  with FastQCv0.11.7 program before proceeding.
The adapter sequence was removed with Trimmomatic 0.38 program. Trimmed data was generated by removing base qulity less than 3 from reads ends and base unsatisfied with window size =4, mean quality =15 using the sliding window trim method.
cDNA fragment were mapped GRCh37 or Chlorocebus_sabeus_1.1_NCBI_100 genomic DNA reference with Bowtie 2 2.3.4.1 aligner.
The mapped reads were assembled with the known gene/transcript with StringTie version 2.1.3b program.
The amount of abundance of the transcript was normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value considering read count, transcript length and depth of coverage.
Statistical analysis for each comparision combination was processed with fold change, exactTest using edgeR. Significant results were selected under the condition |fc|>=2 & exactTest raw p-value<0.05.
Genome_build: Chlorocebus_sabeus_1.1_NCBI_100

organism: Chlorocebus aethiops

value: Fetal kidney

value: Epithelial cells


title: MARC145-BPV

value: infected with shaan virus for 24hours


title: LGL35-BH-NK

value: Wild type


title: TB and HIV infected subject TB_HIV_13

description: TB and HIV infected subject


title: RNF20-KO_SOX2_1

value: reprogrammable cells

value: day 3 of OSKM reprogramming


title: 6h.CFZ-rep1

description:
CFZ_SARS2_rpkm.csv
6h-drug-1


title: RNF20-WT_SOX2_2

value: wild type

value: untreated


title: HIV only infected subject HIV_12

description: HIV only infected subject


title: TB and HIV infected subject TB_HIV_15

description: TB and HIV infected subject


title: HIV only infected subject HIV_14

description: HIV only infected subject


title: 3h.CFZ-rep3

description:
CFZ_SARS2_rpkm.csv
3h-drug-3

value: 3 hours clofazimine


title: RNF20-WT_IgG_1

value: moue IgG (Santa Claus, sc-2050)


title: RNF20-WT_SOX2_1


title: MRP6_RH_74:Rat, perforant pathway stimulation (PPS), DOFS

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
Sequencing data were quality controlled and adapter trimmed using Trim Galore
Filtered data were mapped to the rat genome Rn6 using TopHat2
Cufflinks was used to assemble transcripts from the mapped reads guided by gene annotation from Ensembl Release 87
Cuffmerge, cuffquant and cuffdiff (part of the cufflinks software package) were used to quantify transcript abundance in each sample and to perform differential expression analysis of genes and gene isoforms
Genome_build: rn6
Supplementary_files_format_and_content: Output from cuffdiff "gene_exp.diff". This shows gene names, expression and significance metrics

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
RNA is purified from frozen hippocampal tissue using Trizol
rRNA depleted using the Ribo-Zero Magnetic Kit. Libraries generated using ScriptSeq v2 kit (Illumina)

value: Sprague-Dawley

value: Hippocampus

tag: model

value: perforant pathway stimulation (PPS)

tag: period

value: DOFS


title: HIV only infected subject HIV_11

description: HIV only infected subject

tag: Sex


title: 3h.CFZ-rep2

description:
CFZ_SARS2_rpkm.csv
3h-drug-2

value: cell line


title: MRP6_RH_69:Rat, perforant pathway stimulation (PPS), DOFS


title: 3h.CFZ-rep1

description:
CFZ_SARS2_rpkm.csv
3h-drug-1


title: MRP6_RH_64:Rat, perforant pathway stimulation (PPS), DOFS


title: 403492 4-F3 (ATRX WT) ISD 3ug/ml 24 hours

first: Warren

last: Floyd

state: North Carolina

address: 450 Research Drive, LSRC Bldg, Room B324

department: Pharmacology and Molecular Cancer Biology

institute: Duke University

data_processing:
clustering of index coded samples was performed on an Illumina Novaseq sequencer according to the manufacter's instructions. After cluster generation, the libraries were sequenced on the same machine and paired end reads were available.
Downstream analysis was performed using a combination of programs including STAR, Htseq, Cufflink, and Novogene wrapped scripts
Alignments were parsed using the STAR program
Differential expressions were determine through DESeq2/edgeR.
GO and KEGG enrichment were implemented by the ClusterProfiler
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: Excel file for differential expression (column's named by sample name) are provided

growth_protocol: 10% FBS, 1% PenStep, 1% L-Glut DMEM , split 1:10

extract_protocol:
Cell Lines were washed with PBS, then harvested in Trizol and purified using Direct-Zol RNA Minprep Plus Kit (Zymo)
NEBNext UltraTM RNALibrary Prep Kit for Illumina, RNA libraries performed using standard protocol for this kit and illumina libraries

value: soft tissue sarcoma

value: ISD 3 ug/ml 24 hours


title: 403492 2-F11 (ATRX KO) ISD 3ug/ml 24 hours

value: ATRX knockout


title: TB and HIV infected subject TB_HIV_9

description: TB and HIV infected subject

value: Male


title: mock-rep3

description:
CFZ_SARS2_rpkm.csv
mock-3

value: mock


title: MRP4_RH_9:Rat, perforant pathway stimulation (PPS), 10 days

value: 10 days


title: HIV only infected subject HIV_8

description: HIV only infected subject


title: 403492 2-F11 (ATRX KO) 4 Gy 36 hours

value: 4 Gy 36 hours


title: mock-rep2

description:
CFZ_SARS2_rpkm.csv
mock-2


title: 403492 4-F3 (ATRX WT) 4 Gy 36 hours


title: MRP4_RH_4:Rat, perforant pathway stimulation (PPS), 10 days


title: HIV only infected subject HIV_7

description: HIV only infected subject


title: 403492 2-F11 (ATRX KO) untreated

value: untreated control


title: MRP4_RH_5:Rat, perforant pathway stimulation (PPS), 10 days


title: UTH-3

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

institute: University of Macau

data_processing:
Hisat2
FeatureCounts
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2_vsd_exp.txt

source_name: iPSC-EC cell line

growth_protocol: iPSCs were differentiated into endothelial cells using a monolayer chemically-defined methods.

extract_protocol:
RNA was extrated using the miRNeasy Mini Kit with DNA digestion, and collected total RNA was used for RNA-seq.
RNA-seq construction protocol of Illumina.

treatment_protocol: iPSC-ECs were seeded into 6 well plates and once they reached 60-70% confluency, cells were treated with and without UT-H for 24 hours.

value: iPSC-EC cell line

value: UT-H (uremic toxin mixture)


title: mock-rep1

description:
CFZ_SARS2_rpkm.csv
mock-1


title: MRP3_RH_3:Rat, perforant pathway stimulation (PPS), 3 days

value: 3 days


title: TB and HIV infected subject TB_HIV_6

description: TB and HIV infected subject


title: TB and HIV infected subject TB_HIV_5

description: TB and HIV infected subject


title: CTL-3

value: Vehicle


title: 403492 4-F3 (ATRX WT) untreated

value: wild type


title: HIV only infected subject HIV_10

description: HIV only infected subject


title: TB and HIV infected subject TB_HIV_25

description: TB and HIV infected subject

value: Female


title: UTH-2


title: E13.5 Sox9+Scx+ attachment progenitors

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description: Proximal forelimb Sox9+/Scx+ attachment progenitors

data_processing:
The sequencing libraries were sequenced using NovaSeq 6000 platform.
Demultiplexing and alignment were performed using cellranger (10x Genomics version 3.0.2) bioinformatics pipeline using mm10 genome, followed by detecting swapped barcodes between libraries, since the NovaSeq run contained a mix of three libraries. For this, We used R (3.6.3) and the package DropletUtiles (Lun et al., 2019) (1.6.1) with the function swappedDrops (parameter min.frac=0.9) and the molecule_info.h5 input. 1.5% of the molecules were detected as swapped. Detecting empty droplets was done with the function emptyDrops (parameter lower= 300), the number of cells detected was 2,213.
The outputs from CellRanger were further analyzed using the Seurat 3.1.5 (Butler, Hoffman, Smibert, Papalexi, & Satija, 2018) and R 3.6.3.
Using Seurat we performed  gene filtering  (gene must appear in at least 3 cells of a sample) and cell filtering, cells with over 20% expression of mitochondria genes and high and low 3% percentiles of total number of genes and UMIs; this resulted in 1218 cells. In addition, one of the clusters had significantly lower RNA counts as compare to other collected cells, which might have indicated that it contained mainly low quality cells. Indeed, examination of the 10 most highly expressed genes using heatmap demonstrated this, therefore, this cluster was removed from further analysis, with final number of 1076 cells.
Clusters were created with 2000 variable genes and 15 principal components (PCs) (resolution=0.4). UMAP plot was made with the Seurat functions RunUMAP and DimPlot and violin plots were made with the VpnPlot function.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing the gene average ln normalized expression per cluster (correspond to the cluster names in the article).  CellRanger filtered cell barcodes, features, matrix.

source_name: FACS-sorted attachment progenitors from 4 dissected proximal side of the forelimb from E13.5 Sox9-CreER, tdTomato and Scx-GFP mice

extract_protocol:
For collection of cells by FACS, 4 forelimbs from 2 E13.5 embryos were dissected and suspended in cold PBS. Single cell suspension were achieved by trypsin and collagenase type V (dissolved in DMEM, Sigma) digestion. Single-cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v3/v3.1 Chemistry).
The libraries were sequenced using NovaSeq 6000 instrument using an SP 100 cycles reagent kit   (Illumina) (R1 28 bases, R2 82 bases and I1 8 bases).
Single-cell RNA sequencing (scRNA-Seq)

value: Proximal Forelimb

value: Embryonic Day 13.5


title: HIV only infected subject HIV_4

description: HIV only infected subject


title: MRP3_RH_2:Rat, perforant pathway stimulation (PPS), 3 days

value: Sprague-Dawley

value: Hippocampus

value: perforant pathway stimulation (PPS)


title: TB and HIV infected subject TB_HIV_3

description: TB and HIV infected subject


title: mutant blr2 darkness rep3

value: mycelium

value: 36 hr growing in PDA

value: darkness


title: MRP3_RH_1:Rat, perforant pathway stimulation (PPS), 3 days


title: MRP2_RH_16:Rat, perforant pathway stimulation (PPS), 1 day

value: 1 day


title: HEK293-BPV

value: Embryonic kidney

value: Epithelial cells

value: infected with shaan virus for 24hours


title: UTH-1

value: iPSC-EC cell line

value: UT-H (uremic toxin mixture)


title: TB and HIV infected subject TB_HIV_2

description: TB and HIV infected subject

value: Male


title: CTL-1

value: Vehicle


title: MRP2_RH_11:Rat, perforant pathway stimulation (PPS), 1 day


title: TB and HIV infected subject  TB_HIV_1

description: TB and HIV infected subject


title: Lung, 240

status: Public on Feb 01 2021

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

data_processing:
Alignment to the MMUL_10 done with Kallisto
Gene summarization done with tximport
Differential expression analysis was performed with DESeq2
Genome_build: MMUL_10

organism: Macaca mulatta

source_name: Lung

extract_protocol:
total RNA was extracted with Trizol per manufacturer's guidelines.
Afer polyA selection, paired-end RNA-sequencing with 75bp was done with a depth of 30M reads.

tag: gestational age at treatment

value: 128 days

tag: tx 1

value: LPS

tag: tx 1 route

value: Intra-amniotic injection

tag: tx 1 dose

tag: tx 2

tag: tx2 route

tag: dose

tag: tx to delivery interval

value: 5 days

tag: gestational age at delivery

value: 133 days

value: Lung


title: Lung, 239

value: 129 days

value: 134 days

tag: tissue


title: Lung, 255

value: 126 days

value: Betamethasone-acetate

value: Intramuscular injection

value: 131 days


title: Lung, 242


title: Lung, 249

value: 127 days

value: 132 days


title: Lung, 209

value: No intervention

value: 135 days


title: Lung, 201

value: 157 days


title: Lung, 248


title: bone marrow B cells, IL6-/-

city: Stony Brook

first: Jinyu

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

hyb_protocol: The procedure was performed according to the manufacturer's instructions

scan_protocol: Arrays were stained following manufacturer's protocol in a GeneChip Fluidics 450 station. Arrays were scanned in a GeneChip Scanner 3000 G7 controlled by Affymetrix GeneChip Command Console v 4.3.3.1616

data_processing:
Affymetrix Expression Console (version 1.4.1.46) was used to perform the analysis.
Full hybridization table not available.

source_name: bone marrow B cells

label_protocol: Preparation of cDNAs for microarray analysis and sample hybridization to Affymetrix miRNA Gene Chip 4.0 Array were performed using Affymetrix protocols of the Stony Brook University DNA Microarray Core Facility.

growth_protocol: fresh bone marrow samples were prepared

extract_protocol: RNA was isolated by miRNeasy from Qiagen

treatment_protocol: B cells were isolated with a BD FACSAria cell sorter and anti-CD45R and anti-CD19 antibodies with the support of the Stony Brook University core flow cytometry facility.

value: bone marrow

tag: cell type

value: B cells

tag: genotype


title: bone marrow B cells, IL6+/+: EuMyc


title: Lung, 200

value: 156 days


title: bone marrow B cells, IL6-/-: EuMyc


title: CTL-2

value: iPSC-EC cell line

tag: treatment

value: Vehicle


title: Lung, 113

value: Lung


title: Lung, 101


title: bone marrow B cells, IL6+/+

tag: strain


title: Lung, 035

value: 130 days

value: LPS

value: Intra-amniotic injection

value: 16 hours


title: Lung, 029

value: 129 days


title: MRP2_RH_15:Rat, perforant pathway stimulation (PPS), 1 day

value: Sprague-Dawley

value: Hippocampus

tag: model

value: perforant pathway stimulation (PPS)

value: 1 day


title: Ink4a-ast_NICD1_rep3

city: Seoul

first: Eun-Jung

last: Kim

address: Anamro 5ga

institute: Korea University

data_processing:
Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Text format which includes contents; 1) NCBI gene accession ID, 2) Log2 ratio of gene expression, 3) Probability value (PA), 4) Gene symbol, 5) Gene description, 6) KEGG orthology, 7) GO component, 8) GO function, 9) GO process, 10) Blast nr

source_name: Ink4a-/- murine astrocyte

growth_protocol: Ink4a-/- astrocytes were cultured in DMEM with high glucose supplemented with 10% fetal bovine serum, 1% penicilin/streptomycin, 2mM L-glutamine and 50ug/mL gentamicin.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (3 prime) according to the manufacturer's instructions.
DNA enrichment was performed using EpiMark® Methylated DNA Enrichment Kit (New England Biolabs, UK).
Libraries were prepared for RNA-seq by using CG RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) coporation.

value: Astrocyte

value: Brain

tag: transfected with

value: pcDNA NICD puro


title: Ink4a-ast_NICD1_rep2


title: Ink4a-ast_NICD1_rep1


title: Ink4a-ast_JICD1_rep3

value: pcDNA HA-JICD1 puro


title: Ink4a-ast_JICD1_rep2


title: Ink4a-ast_Con_rep2

value: pcDNA puro (control)


title: TB and HIV infected subject TB_HIV_24

description: TB and HIV infected subject

tag: age

tag: Sex

value: Male


title: Ink4a-ast_JICD1_rep1


title: Ink4a-ast_Con_rep3


title: Ink4a-ast_Con_rep1


title: Flag-MBD2a+GFP-EV

city: Hefei

first: liu

last: zhaoji

state: Anhui

address: huangshan road

department: life science

institute: USTC

description: Breast cancer MDA-MB-231 cells infected with viruses expressing Flag-MBD2a+GFP-EV using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.

data_processing:
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads were alligned to the human genome hg19 with BOWTIE v2.2.3 and clean reads were aligned to the reference genome using TopHat v2.0.12.
Cuffdiff v2.2.1 was used to count the reads numbers mapped to each gene.
As to ChIP-seq data, raw data (raw reads) of fastq format were firstly processed through BGI programs.
Data filtering parameters：Clean Parameter: SOAPnuke1.5.0 filter -l 5 -q 0.5 -n 0.1 -i -c 25 -Q 2 --seqType 1
Sequenced reads were mapped to the UCSC human genome hg19 using software Bowtie2 (version 2.2.6). Aligned reads were used for subsequent generation of bindingprofiles, peak callings, motif analyses and traveling ratio analyses. MACS (version 1.4.2) was used for peak callings from the aligned reads
Genome_build: hg19
Supplementary_files_format_and_content: read counts for RNA-seq data and bed for ChIP-seq data

source_name: Breast cancer MDA-MB-231 cells

growth_protocol: Breast cancer MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% FBS. Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
The ChIP was performed with an EZ-ChIP kit (Millipuro) following the manufacture’s instruction as described above. In this experiment, the DNA fragments were sonicated between 100 bp to 500 bp. For Flag-MBD2a or Flag-MBD2c ChIP, 4.5×107 cells and Flag antibody (Sigma-Aldrich) were used.
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
ChIP-sequencing libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: shRNAs targeting MBD2a were commercially purchased (Sigma-Aldrich). MBD2a and MBD2c were cloned into pSin-3xFlag or pSin-GFP empty vectors.

tag: cell line

value: Breast cancer MDA-MB-231 cells

tag: chip antibody

value: Flag antibody (Sigma-Aldrich, Cat#F1804, lot:SLBK1346V)

value: stably transfected with pSin-3xFlag-MBD2a and pSin-GFP empty vectors


title: Flag-MBD2a+GFP-MBD2c

description: Breast cancer MDA-MB-231 cells infected with viruses expressing  Flag-MBD2a+GFP-MBD2c using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.

value: stably transfected with pSin-3xFlag-MBD2a and pSin-GFP-MBD2c


title: Flag-MBD2c+GFP-EV

description: Breast cancer MDA-MB-231 cells infected with viruses expressing  Flag-MBD2c+GFP-EV using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.

value: stably transfected with pSin-3xFlag-MBD2c and pSin-GFP empty vectors


title: Flag-EV+GFP-EV

description: Breast cancer MDA-MB-231 cells infected with viruses expressing  Flag-EV+GFP-EV using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.

value: stably transfected with pSin-3xFlag empty vectors and pSin-GFP empty vectors


title: sh2a

description: NTC vs sh2a.xlsx

value: stably transfected with MBD2a-targeting shRNA


title: NTC

description: NTC vs sh2a.xlsx

value: stably transfected with non-targeting control shRNA (NTC)


title: Lung, 092

tag: gestational age at treatment

tag: tx 1

value: No intervention

tag: tx 1 route

tag: tx 1 dose

value: 133 days

value: Lung


title: input

value: untreated


title: EV

description: EV vs 2c .xlsx

value: stably transfected with pSin-3xFlag empty vectors(EV)


title: Lung, 038

value: 130 days

value: LPS

value: Intra-amniotic injection

tag: tx 2

tag: tx2 route

tag: dose

tag: tx to delivery interval

value: 16 hours

value: 131 days


title: Lung, 026

tag: gestational age at delivery

tag: tissue


title: H2A_CUT&RUN_Parental

city: Hong Kong

first: Ming

middle: Kui

last: Chan

address: Tat Chee Avenue

department: Department of Biomedical Sciences

institute: City University of Hong Kong

data_processing:
library strategy: CUT&RUN
For CUT&RUN data, FastQC 0.11.7 is used to conduct quality check for the raw sequencing files. After cutting adapters by cutadapt 1.18, reads are then aligned to human genome hg19 and yeast genome sacCer3 from UCSC by bowtie2 separately. Reads from human for each sample are normalized by spike-in yeast reads. MACS2 is used to call peaks under q value < 0.05 with paired-end mode. Peak annotation is performed by using R package ChIPseeker. Chi-Squared test is performed to investigate the peak distribution difference
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using 'deepTools' normalized by spike-in reads

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cut & Run was performed according to the protocol described in Skene, P. J. & Henikoff, S. (2017) with slight modifications. All reactions were performed at 4ºC unless stated otherwise. Each centrifugation step was performed at 600 g for 3 min. 4 x 106 cells was used for each reaction. Cells were washed twice with PBS and resuspended in Buffer NE1 (20 mM HEPES-KOH pH7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol, Proteinase Inhibitor). After 10 min, cells were collected and incubated in Buffer 1 (20 mM HEPES-KOH pH7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM Spermidine, 0.1% BSA, Proteinase Inhibitor) for 5 min. Cells were collected, washed once with Buffer 2 (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, Proteinase Inhibitor) and resuspended in CUT&RUN Buffer 2. Samples were incubated with antibodies for 2 hours or overnight. Samples containing primary mouse antibodies were washed twice with Buffer 2 before incubation with anti-mouse rb IgG (Jackson ImmunoResearch, 315-005-003) for one hour. Nuclei was then collected, washed twice with Buffer 2 and incubated with pA-MNase fusion protein (150 ng) for one hour. Nuclei was washed once with Buffer 2 and once with low salt buffer (3.5 mM HEPES, Proteinase Inhibitor). Upon resuspension in low salt buffer, 10 mM CaCl2 was added to each reaction. MNase digestion was stopped after 30 min with the addition of Buffer 2 (supplemented with 10 mM EDTA, 20 mM EGTA and 28.8 pg yeast spike in). Samples were incubated for 15 min at 37 ºC. DNA was purified using NucleoSpin Gel and PCR Clean-up kit (MACHEREY-NAGEL).
CUT&RUN libraries were prepared using Ovation Ultralow System V2 (NuGEN, 0344NB).
CUT&RUN libraries were sequenced on a HiSeq X platform (Illumina) using paired end sequencing.

tag: cell type

value: Breast cancer cell line; adenocarcinoma derived

tag: genotype/variation

value: Parental


title: H2A_CUT&RUN_WT6

value: WT


title: H2A_CUT&RUN_WT11


title: H2A_CUT&RUN_E76K1

source_name: MDA-MB-231_H2BE76K mutant

value: H2BE76K mutant


title: FLAG_CUT&RUN2_WT11


title: H2A_CUT&RUN_E76K6


title: FLAG_CUT&RUN2_Parental


title: FLAG_CUT&RUN2_E76K6


title: Flag-MBD2c+GFP-MBD2a

description: Breast cancer MDA-MB-231 cells infected with viruses expressing  Flag-MBD2c+GFP-MBD2a using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.

value: Breast cancer MDA-MB-231 cells

tag: treatment

value: Flag antibody (Sigma-Aldrich, Cat#F1804, lot:SLBK1346V)

value: stably transfected with pSin-3xFlag-MBD2c and pSin-GFP-MBD2a


title: FLAG_CUT&RUN2_E76K1


title: MBD2c

description: EV vs 2c .xlsx

value: stably transfected with pSin-3xFlag-MBD2c


title: FLAG_CUT&RUN_WT11

data_processing:
For RNAseq data, FastQC 0.11.7 is used to conduct quality check for the raw sequencing files. Reads are then aligned to the human genome hg19 with gene annotations from UCSC and further counted by STAR 2.6.1a with default parameters. R package DESeq2 is used to perform differential expression analysis with cutoff adjusted P value < 0.05 and absolute log2 fold change > 0.25. Pathway analysis based on differentially expressed genes are performed by R package HTSanalyzeR2 with FDR < 0.1.
For CUT&RUN data, FastQC 0.11.7 is used to conduct quality check for the raw sequencing files. After cutting adapters by cutadapt 1.18, reads are then aligned to human genome hg19 and yeast genome sacCer3 from UCSC by bowtie2 separately. Reads from human for each sample are normalized by spike-in yeast reads. MACS2 is used to call peaks under q value < 0.05 with paired-end mode. Peak annotation is performed by using R package ChIPseeker. Chi-Squared test is performed to investigate the peak distribution difference
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample; bigwig files were generated using deepTools; NARROWPEAK files contain peaks using either parental or IgG as control called by MACS2.

source_name: Breast cancer cell line; adenocarcinoma derived

treatment_protocol: NT and sh94 samples: WT6 cells were either treated with NT (non-targeting) or sh94 shRNAs to knockdown NAP1L1. Cells were collected 72 hours after shRNA treatment for NAP1L1 CUT&RUN experiment.

tag: strain

tag: technology

value: CUT&RUN


title: FLAG_CUT&RUN_WT6


title: FLAG_CUT&RUN_E76K6


title: FLAG_CUT&RUN_Parental


title: RNAseq2_WT11

extract_protocol:
Total RNA was extracted from KI cell lines (WT6, WT11, E76K1, E76K6) using the MiniBEST Universal RNA extraction kit (Takara). Ribosomal RNA was depleted removed using the NEBNext® rRNA Depletion Kit (NEB).
RNA-seq libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s protocol, followed by quality control using Bioanalyzer 2100.
RNA-seq libraries were sequenced on a HiSeq X platform (Illumina) using 150 bp paired-end sequencing.

value: RNAseq


title: FLAG_CUT&RUN_E76K1


title: RNAseq1_E76K6


title: RNAseq1_WT11


title: RNAseq2_E76K6


title: RNAseq2_E76K1


title: ATACseq_WT11

description: FLAG-tagged WT H2B

data_processing:
For ATACseq data, FastQC 0.11.7 is used to conduct quality check for the raw sequencing files. Trim Galore 0.6.2 is used to cut adapters with pair-end mode. Reads are then aligned to the human genome hg19 by BWA using default parameters. Reads from mitochondrial are removed and de-duplicated. Only properly aligned paired reads with quality higher than 10 are used for further analysis. Genome-wide read coverage is calculated by bamCoverage in deepTools 3.2.1 using the normalization method: Reads Per Kilobase per Million mapped reads (RPKM).
For ChIPseq data, FastQC 0.11.7 is used to conduct quality check for the raw sequencing files. After cutting adapters by cutadapt 1.18, reads are then aligned to human genome hg19 by BWA using default parameters. Reads are then de-duplicated and only properly aligned paired reads with quality higher than 10 are used for further analysis. Genome-wide read coverage is calculated by bamCoverage in deepTools 3.2.1 using the normalization method: Reads Per Kilobase per Million mapped reads (RPKM).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files were generated using deepTools.

extract_protocol:
ATAC-seq was performed according to the protocol in Buenrostro et al. (2015). 50,000 cells were suspended in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40). Crude nuclei were isolated by centrifugation at 500 g for 10 min and resuspended in 25 ml of TD Buffer (2x reaction buffer, Illumina). Nuclei pellet was collected (500 g, 5 min) and suspended in transposition reaction mix (25 ml, 2.5 ml TDE1, 22.5 ml l H2O). The reactions were incubated at 37ºC for 30 min with gentle mixing. DNA was immediately purified using Qiagen MinElute PCR Purification kit.
Libraries were PCR amplified according to protocol and purified using Qiagen MinElute PCR Purification kit. Double sided bead purification (0.5x beads volume, followed by 1.3x beads volume) was performed using AMPure XP beads to enrich for fragments between 150 bp to 1000 bp. Library quality and fragment sizes were accessed using Bioanalyzer (Agilent).
ATAC-seq libraries were sequenced with 150 bp paired end sequencing on HiSeq X (Illumina).

tag: cell line

value: Breast cancer cell line

value: ATAC-seq


title: RNAseq2_WT6


title: LGL70-BA-NK

tag: patient diagnosis

value: CLPD-NK

value: NK

tag: genotype

value: TET2 mutated

tag: socs3 methylation

value: SOCS3 methylated

tag: phenotype


title: ATACseq_E76K1

description: FLAG-tagged H2BE76K mutant


title: RNAseq1_E76K1


title: ATACseq_WT6

description: FLAG-tagged WT H2B


title: ATACseq_E76K6

description: FLAG-tagged H2BE76K mutant


title: U2OS whole genome sequencing

city: Beijing

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: for more detials see  DataFiles.README

data_processing:
Library strategy: WGS
DNA sequencing data processing. We prepared HeLa cells and U2OS cells, and then obtained the HeLa cells whole genome sequencing (WGS) data, HeLa nucleolus sequencing data, HeLa nucleolus sequencing data before and after ActD treatment and U2OS WGS data with 150 bp paired-end sequencing on Illumina XTen platform. We processed these DNA sequencing data using the normal pipeline: bowtie2 mapping, samtools sorting, and then removing the duplicates with Picard. To ensure the mapping quality, especially in nucleolus data set, we kept the mapped reads only with a MAPQ value higher than 20.
In situ Hi-C and nHi-C data processing. For all Hi-C data sets, we used the following analysis pipeline. We first trimmed each FASTQ reads to 36 bp, and then mapped reads with bowtie2. We also added the rDNA 43kb repeat unit sequence as an artificial chromosome in genome reference. After reads mapping, we only kept the reads with MAPQ higher than 20, and we filtered the illegal interactions, which contains no restriction enzyme site within a downstream 500 bp region. We then filtered out the interactions where two paired reads map to the same restriction enzyme fragment. The in situ Hi-C and nHi-C data set are processed with the same pipeline. We used the ICE normalization method35 to clean the matrix for all in situ Hi-C matrixes.
Genome_build: hg19
Supplementary_files_format_and_content: matrix file are proformed with Hi-C data processing pipeline use Python script. And each matrix can be loaded with "," as separater

source_name: U2OS whole genome sequencing

growth_protocol: HeLa and U2OS cells were cultured in DMEM medium (ATCC-30-2001) with 10% fetal bovine serum and 5% CO2 at 37°C.

extract_protocol:
Nucleoli isolation. Resuspend 2 – 5 x 106 cells with 1.5 ml 0.5% sodium dodecyl sulfate (SDS) and incubate at 62℃ for 5-10 min in order to dissolve the cell membrane. Then add 1.5 ml buffer S1 (0.25 M sucrose and 10 mM MgC12), mix well, and break the cells with ultra-sonication. Monitor the cells under a microscope and stop when over 80% of the cells are burst, leaving intact nucleolus with cytoplasmic materials. Transfer the liquid to a 15 ml tube, carefully add 3 ml buffer S2 (0.35M sucrose, 0.5mM MgC12) to the bottom of the tube and keep the two layers cleanly separated. Centrifuge at 3000 rpm for 5 min at 4℃ and discard the supernatant. Resuspend the pellet with 3 ml buffer S2, filtered with 5 um filter (Millipore) and transferred to a new 15 ml tube. Carefully add 3 ml buffer S3(0.88M Sucrose, 0.5mM MgC12) to the bottom of the tube and keep the two layers cleanly separated. Centrifuge at 4000 rpm for 10 min at 4℃ and discard the supernatant. Resuspend with 100 ul buffer S3, check pure isolated nucleoli under a microscope and store at -80℃.
All libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with ActD (10 ug /ml) for 8 hours and then harvested to perform Hi-C and RNA-seq experiments.

value: osteosarcoma


title: HeLa Nucleolus Sequencing rep2

description: for more detials see  DataFiles.README

source_name: HeLa Nucleolus Sequencing biological repeat 2

value: HeLa

value: cervical cancer


title: HeLa Nucleolus Sequencing + ActD rep2

description: for more detials see  DataFiles.README

source_name: HeLa Nucleolus Sequencing with ActD treatment biological repeat 2


title: HeLa Nucleolus Sequencing rep1

description: for more detials see  DataFiles.README

source_name: HeLa Nucleolus Sequencing biological repeat 1


title: HeLa whole genome sequencing

description: for more detials see  DataFiles.README

source_name: HeLa whole genome sequencing


title: FLAG_CUT&RUN2_WT6

value: Breast cancer cell line; adenocarcinoma derived

value: WT


title: HeLa Nucleolus Hi-C rep3 additional

description: for more detials see  DataFiles.README

data_processing:
DNA sequencing data processing. We prepared HeLa cells and U2OS cells, and then obtained the HeLa cells whole genome sequencing (WGS) data, HeLa nucleolus sequencing data, HeLa nucleolus sequencing data before and after ActD treatment and U2OS WGS data with 150 bp paired-end sequencing on Illumina XTen platform. We processed these DNA sequencing data using the normal pipeline: bowtie2 mapping, samtools sorting, and then removing the duplicates with Picard. To ensure the mapping quality, especially in nucleolus data set, we kept the mapped reads only with a MAPQ value higher than 20.
In situ Hi-C and nHi-C data processing. For all Hi-C data sets, we used the following analysis pipeline. We first trimmed each FASTQ reads to 36 bp, and then mapped reads with bowtie2. We also added the rDNA 43kb repeat unit sequence as an artificial chromosome in genome reference. After reads mapping, we only kept the reads with MAPQ higher than 20, and we filtered the illegal interactions, which contains no restriction enzyme site within a downstream 500 bp region. We then filtered out the interactions where two paired reads map to the same restriction enzyme fragment. The in situ Hi-C and nHi-C data set are processed with the same pipeline. We used the ICE normalization method35 to clean the matrix for all in situ Hi-C matrixes.
Genome_build: hg19
Supplementary_files_format_and_content: matrix file are proformed with Hi-C data processing pipeline use Python script. And each matrix can be loaded with "," as separater

source_name: HeLa Nucleolus Hi-C biological repeat 3 additional sequence


title: HeLa Nucleolus Hi-C + ActD rep1

description: for more detials see  DataFiles.README

source_name: HeLa Nucleolus Hi-C with ActD treatment biological repeat 1


title: HeLa Nucleolus Hi-C rep3

description: for more detials see  DataFiles.README

source_name: HeLa Nucleolus Hi-C biological repeat 3