title: M12

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

source_name: PE01R Xenograft replicate 3

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit
Illumina

treatment_protocol: In vivo tumorgenicity experiments were performed to establish the growth rate of the two cell lines, PEO1 and PEO1R, at different cell concentrations. The experiments were conducted under the UK Home Office Project Licence number PPL P435A9CF8. LASA good practice guidelines, FELASA working group on pain and distress guidelines and ARRIVE reporting guidelines were also followed.Female immunodeficient CD-1 NuNu mice at 7-8 weeks old were purchased from Charles River UK.  The condition of the animals was monitored throughout the study by an experienced animal technician. After a week’s acclimatisation, the mice were initiated with tumours using cultured cells. Cells with viability of >90% were re-suspended, for in vivo administration, in standard matrigel at 2e5, 1e6 and 2e6/100ul for subcutaneous injection into the left flank. Three mice were implanted per cell concentration for each of the two cell lines. Tumour establishment and growth was measured by Vernier calipers (Camlab) twice weekly and animals weighed weekly. The mice were also photographed weekly to record tumour development. The scientific end point was determined to be when the first tumour reached maximum allowable size under the PPL i.e.1.2cm diameter. At this point, all mice were culled by cervical dislocation, tumours were dissected out and were photographed ex vivo. Tumours were preserved by snap freezing, fixation (NBF) 50:50 and by freezing in RNA later.

value: Mirin resistant derivative PE01R


title: RL1898_ChIPseq_DoxMut_HAflag_rep1

status: Public on Jul 04 2022

type: SRA

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

library_source: genomic

data_processing:
CASAVA v1.8.2
The WGBS sequenced reads were first trimmed using bbduk, and overlapping pairs were merged using BBMerge(Bushnell, Rood, and Singer 2017). The reads were mapped to the hg19 genome including the lambda and pUC19 sequences using BS-Seeker2 with Bowtie 2 as back-end aligner (-e 300 -X 2000)(Guo et al. 2013). The duplicated reads were removed using Sambamba markdup for paired-end reads and PALEOMIX for merged reads(Schubert et al. 2014). We then used CGmapTools to generate methylation calls(Guo et al. 2018).
Sequenced ATAC-seq reads were then trimmed with bbduk for Nextera adapters and mapped to the genome using Bowtie 2. Duplicated reads were removed and blacklisted regions filtered as with ChIP-seq, and peaks were called using MACS2 with “--nomodel -f BAM --keep-dup all” parameters. Replicates were merged using IDR, and each sample was validated visualising the insert size distribution following nucleosome periodicity
ChIP-seq reads were trimmed with bbduk(Bushnell, n.d.) and mapped to the genome using Bowtie 2(Langmead and Salzberg 2012) allowing for an insert site of 2000 bp, reads were deduplicated using Sambamba markdup function(Tarasov et al. 2015) and reads mapping to blacklisted genomic regions were filtered out using SAMtools(H. Li et al. 2009). We then used MACS2 to call peaks with the matched chromatin input sample as background for each ZF-D3A HA ChIP-seq experiment, specifying the parameters “-f BAMPE -q 0.05 --down-sample”(Feng et al. 2012). The peaks for replicate pairs were merged using IDR (https://github.com/nboley/idr)(Q. Li et al. 2011).
The RNA-seq reads were trimmed using fastp with default parameters(Chen et al. 2018), then mapped with HISAT2 (--rna-strandness RF) to an index including hg19 genome assembly and ERCC spike-in sequences(Sirén, Välimäki, and Mäkinen 2014). Then, RNA-seq read-pair counts were read into R using summarizeOverlaps function within the GenomicAlignments package and mapped to the UCSC hg19 gtf(Lawrence et al. 2013).
Genome_build: hg19 UCSC
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2/CGmaptools (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).
Supplementary_files_format_and_content: NarrowPeak files are the output of MACS2 software, ZF_Counts_table_GEO.tsv.gz was computed mapping RNA-seq with HISAT2 and extracting the counts with "featureOverlaps" in R.

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF-7 cell line - ZF-D3A-mut

growth_protocol: complete media with 1000 ng/ml doxycyline for 3 days

extract_protocol:
Cells were washed two times with 10 ml of PBS and crosslinked for 5 minutes in 50 mM HEPES-KOH, pH 7.5, 100 mM NaCl, 1mM EDTA, 1% formaldehyde. The crosslinking reaction was quenched by the addition of glycine to a final concentration of 125 mM and washed twice with phosphate buffered saline (PBS). All subsequent solutions were supplemented with a protease inhibitor cocktail (Sigma Cat. # P8340). Cells were scraped off the plates with a rubber policeman in 10 ml of PBS and centrifuged at 3,000 rpm for 5 minutes in a swinging bucket rotor. The cell pellets were resuspended in 10 ml of 50 mM HEPES-KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, incubated on ice for 10 minutes and centrifuged at 3,000 rpm for 10 minutes in a swinging bucket rotor. Cell pellets were washed twice by gently adding 10 mM Tris-HCl, pH 8.1, 200 mM NaCl, 1 mM EDTA to the cell pellets, trying not to disturb the pellets, and centrifuged at 3,000 rpm for 5 min. Finally the cell pellets were resuspended in 0.1% SDS, 1 mM EDTA and transferred to a Covaris TC12x12 tube. The chromatin was sheared using a Covaris S2 sonicator with the following settings: time 12 min, duty cycle 5%, intensity 4, cycles per burst 200, temperature 4˚C, power mode frequency sweeping. Triton X-100 and NaCl were added to a final concentration of 1% and 150 mM respectively. The sheared chromatin was centrifuged at maximum speed in a microfuge for 15 minutes at 4˚C and the supernatant was transferred to a new tube.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

tag: cell line

tag: genotype


title: WT_H2O_2

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

library_source: transcriptomic single cell

data_processing:
Sequencing libraries were processed with CellRanger (v3.1.0) against the mouse genome (mm10) augmented by the APP and PS1 transgenes
background removal with CellBender
snRNA-seq data analysis was performed in R (v3.6.3) with Seurat (v3.2.1)
Cells with at least 250 but less than 6000 genes and less than 10% mitochondrial RNA content were combined from each library, and clustering and UMAP embedding was computed based on log normalized gene counts, with total RNA content regressed out during scaling and using 20 PCA components
Assembly: mm10 + APP/PS1 transgenes
Supplementary files format and content: raw cellranger count matrix (h5 format)
Supplementary files format and content: final seurat object

molecule: polyA RNA

organism: Mus musculus

source_name: Cerebrum

extract_protocol:
Mouse hemispheres were harvested from male mice at the age of 180 days and immediately snap frozen in liquid nitrogen and stored at -80°C until further processing for nuclei isolation. Nuclei were isolated from a single mouse hemisphere in 2 ml of pre-chilled EZ PREP lysis buffer (NUC-101, Sigma) using a glass Dounce tissue grinder (D8938, Sigma) (25 strokes with pastel A and 25 strokes with pastel B) followed by incubation for 5 minutes on ice with additional 6 ml of EZ PREP buffer. During incubation, 1 µM DAPI was added to the homogenate and subsequently filtered through a 35 µm strainer. Intact nuclei were sorted with a BD FACSAriaIII with a 70 µm configuration into 1.5 ml-Eppendorf tubes with 40 µl of 4 % BSA in PBS and RiboLock RNase Inhibitor (25 U/µl, EO0381, ThermoFisher). A FSC/SSC based gate was used to exclude debris followed by exclusion of damaged nuclei in a DAPI-A/DAPI-H (see Supplementary Fig. 5a). 150,000 events were sorted for each sample. The concentration of sorted nuclei was determined based on brightfield images and DAPI fluorescence using a Neubauer counting chamber and a Leica DMi8 microscope.
Single nuclei libraries were generated according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (CG000204) by 10x Genomics. Briefly, a droplet emulsion was generated in a microfluidic chip followed by barcoded cDNA generation inside these droplets. Purified and amplified cDNA was then subjected to library preparation and sequenced on a NovaSeq 6000 instrument (Illumina) to a median depth of 45-90k reads per cell.

treatment_protocol: APPPS1+/− mice and littermate wild type control (WT) mice were treated with 3 mM spermidine dissolved in their drinking water (changed twice a week) from an age of 30 days until an age of 180 days. Control mice received only water (H2O). Prior to each exchange of the drinking bottles, the weight of the bottles was determined and used to calculate the average volume consumed per animal per day. Animals were kept in individually ventilated cages with a 12 h light cycle with food and water ad libitum.

tag: tissue

value: Cerebrum

tag: age

value: 180 days

tag: Sex

value: male

value: WT

tag: treatment


title: THLE-2 EZH2 2nd [CLIP-seq]

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

description:
Pulldown RNA by immunoprecipitation.
processed data file: THLE2_EZH2_IP_2_peak_info.txt

library_source: transcriptomic

data_processing:
Library strategy: CLIP-seq
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACT) trimmed with fastx_clipper.
Reads were mapped using tophat2 -N 4. Unique mapped reads were remained. While several mapped reads have the same start position and end position, only one is considered.
Reads with overlap region on the locus of genome were clustered. The read number (N), read length and observed max depth were then counted for each cluster. For each gene, a same number of reads with coincident lengths were generated using computational simulation. The outputting reads were further randomly placed to same genes to generate max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p value ＜ 0.01) were selected, while the EZH2 and JARID2 peaks that have an overlap with control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_peak_info.txt: Tab-delimited text files include peak information for each group.

molecule: total RNA

source_name: cell line

extract_protocol:
For immunoprecipitation, the supernatant was incubated overnight at 4 °C with 15ug antibody or control IgG antibody.
Carry the recovered RNA through a standard cDNA library preparation protocol originally described for cloning of small regulatory RNAs. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NextSeq 500 system for 100 nt pair-end sequencing by ABlife, Inc (Wuhan, China).

treatment_protocol: Cells were cross-linked on ice with UV irradiation type C (254 nm) at 400 mJ/cm2 in the presence of cold PBS (4 ml per 15-cm dish).

tag: cell type

value: Normal liver epithelial cells

tag: antibody


title: AD_SPM_3

value: SPM


title: AD_SPM_1


title: EC, brDura, naive, 1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: CD31+ endothelial cells sorted from naïve brain dura

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20
STAR version 2.5 was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in rn6 version 87
Assembly: rn6 version 87
Supplementary files format and content: Tab-delimited gene counts

organism: Rattus norvegicus

source_name: Brain dura

extract_protocol:
CD31+ endothelial cells were isolated from tissues by digestion with 0.4 U ml-1 Liberase TM and 60 U ml-1 of DNase1 subsequently FACS sorted. Total RNA was purified from sorted cells using the TRIzol protocol (Invitrogen)
Library preparation was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS–122–2002) starting from 100-500ng of total RNA

value: Brain dura

tag: strain

value: Lewis

value: wt

value: CD31+ CD45- CD11b- endothelial cells (sorted)

tag: time point

value: naïve animals


title: M11

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

source_name: PE01R Xenograft replicate 2

growth_protocol: Cells were maintained in vitro in RPMI culture medium (Sigma, UK) containing 10% (v/v) heat inactivated foetal bovine serum (Sigma, Poole, UK) & 2 mM L-glutamine (Sigma, UK) at 370C in 5% CO2 and humidified conditions. Cells from sub-confluent monolayers were harvested with 0.025% EDTA, washed in culture medium and counted.


title: EC, brDura, naive, 3


title: HepG2 JARID2 1st [CLIP-seq]

description:
Pulldown RNA by immunoprecipitation.
processed data file: HepG2_Jarid2_IP_1_peak_info.txt

value: Liver carcinoma cells


title: EC, brDura, naive, 4


title: EC, brLepto, naive, 4

description: CD31+ endothelial cells sorted from naïve brain leptomeninges

source_name: Brain leptomeninges

value: Brain leptomeninges


title: HepG2 IgG for EZH2 2nd [CLIP-seq]

description:
Pulldown RNA by immunoprecipitation.
processed data file: HepG2_EZH2_IP_2_peak_info.txt

value: IgG


title: HepG2 EZH2 2nd [CLIP-seq]


title: M10

source_name: PE01R Xenograft replicate 1


title: EC, brLepto, naive, 3


title: M8

source_name: PE01 xenograft replicate 2

value: Mirin sensitive parental PE01


title: M7

source_name: PE01 xenograft replicate 1


title: M9

source_name: PE01 xenograft replicate 3


title: AD_H2O_3


title: HepG2 IgG for EZH2 1st [CLIP-seq]

description:
Pulldown RNA by immunoprecipitation.
processed data file: HepG2_EZH2_IP_1_peak_info.txt


title: HepG2 IgG for JARID2 1st [CLIP-seq]


title: EC, brLepto, naive, 2


title: EC, brLepto, naive, 1


title: AD_H2O_1


title: HepG2 EZH2 1st [CLIP-seq]


title: AD_H2O_2


title: AD_SPM_2


title: B37 (bs-seq)

status: Public on Jul 03 2022

city: Bergen

first: Oleksii

last: Nikolaienko

state: Vestland

address: Jonas Lies veg 87

department: Department of Clinical Science

country: Norway

institute: University of Bergen

description: White blood cell DNA

data_processing:
Performed as outlined in the methods section
Reads were mapped/aligned to the GRCh38 human reference genome and the methylation was called using Illumina DRAGEN Bio-IT Platform (v3.9.5) with the following parameters: --methylation-mapping-implementation single-pass, --enable-methylation-calling true, --methylation-generate-cytosine-report false, --methylation-protocol non-directional, --enable-sort false
Variant epiallele frequency calling was performed using epialleleR::generateCytosineReport with the following parameters: min.mapq=30, min.baseq=20, nthreads=4, threshold.reads=TRUE, report.context="CG"
Supplementary_files_format_and_content: Genome-wide cytosine report prepared using Illumina DRAGEN Bio-IT Platform
Supplementary_files_format_and_content: epialleleR VEF report for cytosines in CpG context
Genome_build: hg38

source_name: White blood cells

extract_protocol:
Genomic DNA was extracted from EDTA-whole blood using QIAamp DNA Mini kit (Qiagen, cat.no. 51304) according to the manufacturer’s instructions.
Libraries were prepared as outlined in the methods section. Briefly, DNA was bisulfite converted, and five DNA fragments, representing promoter regions of five established tumour suppressor genes, were amplified using custom set of primers (MLH1, chr3:36993123-36993500; CDKN2A, chr9:21974554-21974921; MGMT, chr10:129467118-129467477; CDH1, chr16:68737102-68737469; BRCA1, chr17:43125171-43125550), indexed, and sequenced on the Illumina MiSeq following the manufacturer's protocols.

value: White blood cell DNA

tag: individual

value: Taken from a healthy male (age range 18-36 years)


title: B32 (bs-seq)

description: White blood cell DNA


title: B14 (bs-seq)

description: White blood cell DNA


title: B04 (bs-seq)

description: White blood cell DNA


title: B13 (bs-seq)

description: White blood cell DNA


title: A29 (bs-seq)

description: White blood cell DNA


title: A45 (bs-seq)

description: White blood cell DNA


title: A20 (bs-seq)

description: White blood cell DNA


title: A10 (bs-seq)

description: White blood cell DNA


title: A42 (bs-seq)

description: White blood cell DNA


title: A02 (bs-seq)

description: White blood cell DNA


title: A05 (bs-seq)

description: White blood cell DNA


title: A32 (bs-seq)

description: White blood cell DNA


title: A26 (bs-seq)

description: White blood cell DNA


title: A01 (bs-seq)

description: White blood cell DNA


title: A24 (bs-seq)

description: White blood cell DNA


title: CTRL-100p00METH (bs-seq)

description: methylated control DNA

source_name: HCT116 DKO (DNMT1[-/-] and DNMT3b[-/-]) cells

growth_protocol: Described in manufacturer's data sheet

extract_protocol:
Described in manufacturer's data sheet
Libraries were prepared as outlined in the methods section. Briefly, DNA was bisulfite converted, and five DNA fragments, representing promoter regions of five established tumour suppressor genes, were amplified using custom set of primers (MLH1, chr3:36993123-36993500; CDKN2A, chr9:21974554-21974921; MGMT, chr10:129467118-129467477; CDH1, chr16:68737102-68737469; BRCA1, chr17:43125171-43125550), indexed, and sequenced on the Illumina MiSeq following the manufacturer's protocols.

value: HCT116 DKO (DNMT1[-/-] and DNMT3b[-/-]) cell DNA

tag: info

value: Enzymatically methylated at CpG sites

value: Zymo Research, catalog number D5014-2


title: A22 (bs-seq)

description: White blood cell DNA


title: A03 (bs-seq)

description: White blood cell DNA


title: pbmc,tuberculosis,rep5 [CG_R5]

city: ChongQing

first: min

last: xiao

address: xinqiao main street No.183

institute: XinQiao hospital

data_processing:
Raw data obtained from the sequencing are the image files after base calling to get the result files stored in the fastq format, called raw data or raw reads
data quality control,FastQC,0.10.1
foundation analysis,ACGT101-miR,4.2
advanced analysis,ACGTUNAfold,3.7
Target gene prediction,Targetscan,3.3a
Target gene prediction,miranda
Supplementary files format and content: In the prediction of target genes, for samples with biological duplication, the threshold  was P<=0.05. For no biology duplicate sample analysis,  | log2 (Foldchange) | > 1 multiples (double difference) and p_value < = 0.05 as the threshold.

source_name: primary mononuclear cells

extract_protocol:
Samples were separated by density gradient centrifugation by using human lymphocyte separation medium.
5 tuberculosis patients were designed as CG1-5 and 5 normal volunteers were designed as NC1-5

treatment_protocol: Peripheral venous blood was collected by using an edta anticoagulant tube.

value: primary mononuclear cells

tag: subject status

value: tuberculosis patient


title: pbmc,tuberculosis,rep1 [CG_R1]


title: pbmc,normal,rep5 [NC_R5]

value: normal volunteer


title: pbmc,tuberculosis,rep2 [CG_R2]


title: pbmc,normal,rep4 [NC_R4]


title: pbmc,tuberculosis,rep4 [CG_R4]


title: pbmc,normal,rep2 [NC_R2]


title: pbmc,tuberculosis,rep3 [CG_R3]


title: pbmc,normal,rep1 [NC_R1]


title: pbmc,normal,rep3 [NC_R3]


title: Proband

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

country: USA

institute: NIH Clinical center

data_processing:
Alignment and mapping analyses were performed by the Takara Cogent NGS Analysis Pipeline v1.5.0 (also known as CogentAP).
Differential gene expression analysis was performed by DESeq2 v1.32.0 [Bioconductor version: Release (3.15)].
Assembly: hg38
Supplementary files format and content: csv-delimited gene matrix of gene counts for each sampole, with the genes in the rows and samples in the columns

source_name: Peripheral blood

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian Components (Takara San Jose, CA) following manufacturer's protocols.

value: Peripheral blood

value: T-cell blasts

value: AIOLOS Q402* heterozygous


title: Sister


title: MiddleCerebralArtery_Epilepsi#M148

type: RNA

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

country: Japan

institute: Nagoya University Hospital

hyb_protocol: A Cy3-labeled amplified cDNA sample (2 µg), prepared without the fragmentation reaction, was used for hybridization (24 hours at 65 ℃) to the oligonucleotide spotted microarray slide (Human Whole Genome, SurePrint G3 Human GE v2 8×60K Microarray; Agilent Technologies). Subsequent washing and drying were performed according to the Agilent hybridization protocol.

scan_protocol: The slide was scanned with an Agilent Model G2505A DNA microarray scanner.

data_processing: Signal intensity was quantified from the scanned image using Feature Extraction Software version 11.0.1.1 (Agilent Technologies).

source_name: Middle Crebral Artery, Epilepsi, Patient Number M148, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 2ug cDNA using the SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.  Dye incorporation and cDNA yield were checked with the NanoDrop One Spectrophotometer.

extract_protocol: Total RNA was extracted from each MCA specimen with an RNeasy Micro Kit (Qiagen). The purified total RNA was amplified with an Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands)

treatment_protocol: We excised the vessel wall of the MCA following the reported procedure. Tissue samples were collected into RNAlater (Qiagen, Hilden, Germany) and stored at -80 °C.

value: Artery Wall

tag: gender

value: Male

tag: disease state

value: epilepsi


title: Father


title: MiddleCerebralArtery_Epilepsi#M133

source_name: Middle Crebral Artery, Epilepsi, Patient Number M133, replicate 1

value: Female


title: MiddleCerebralArtery_MoyamoyaDisease#M136

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number M136, replicate 1

value: Moyamoya desease


title: NC5 (Mother)

value: WT


title: NC4


title: P34

city: New York

first: Aditi

last: Sahu

state: NY

address: 9207-B, Dermatology Service, MSKCC, 530E, 74th street

department: Dermatology Service

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA seq reads were aligned to GRCh38 (Gencode 35) using Salmon 1.3.0
Salmon counts were imported using tximport 1.18.0 and analyzed using edgeR version 3.28.1
Raw counts were normalized using TMM method following which they were log2 transformed and filtered for lowly expressed genes ( <0 was  eliminated)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is provided in txt files as CPM and excel files as RAW counts obtained from Salmon.

source_name: basal cell carcinoma tissue

extract_protocol:
FFPE sections were deparaffinized using the mineral oil method. Briefly, 800µL mineral oil was mixed with the sections and the sample was incubated at 65°C for 10 minutes. Phases were separated by centrifugation in 360µL Buffer PKD and Proteinase K was added for digestion. After a three-step incubation (65°C for 45’, 80°C for 15’, 65°C for 30’) and additional centrifugation, the aqueous phase containing RNA was removed and DNase treated. The RNA was then extracted using the RNeasy FFPE Kit (QIAGEN catalog # 73504) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 285µL input. Samples were eluted in 13µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 356-500ng of total RNA with DV200% varying from 88-93 underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE100 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  On average, 78 million paired reads were generated per sample and 20% of the data mapped to mRNA.

treatment_protocol: tumor biopsies were formalin fixed paraffin embedded (FFPE)

tag: tissue type

value: tumor tissue

tag: tissue preservation

value: FFPE


title: NC3

tag: cell line


title: MiddleCerebralArtery_MoyamoyaDisease#M135

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number M135, replicate 1


title: NC1

tag: genotype


title: NC2


title: MiddleCerebralArtery_MoyamoyaDisease#72

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 72, replicate 1

tag: tissue


title: MiddleCerebralArtery_MoyamoyaDisease#46

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 46, replicate 1

tag: age


title: MiddleCerebralArtery_MoyamoyaDisease#68

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 68, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#62

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 62, replicate 1


title: Control, HT, E8.25, embryo

city: Beijing

first: Yaxi

last: Liu

address: 5 Yiheyuan Road

institute: Peking University

description: polyA RNA

data_processing:
Basecalls performed using CASAVA version 1.8
We used cell-specific barcode sequences attached in read 2 to separate raw reads, and then we trimmed reads by removing the template switch oligo (TSO) and polyA tail sequence.
The clean reads were aligned to the mouse genome (mm10 from UCSC) with TopHat (version 2.0.12). We used HTseq to count the unique mapped reads that were grouped by cell-specific barcode
We calculated the numbers of UMIs of each gene divided by all UMIs and then multiplied  by 1,000,000, which were used to quantify the gene expression level as TPM (transcript per million)
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include the TPM values of RefSeq genes.

source_name: heart

growth_protocol: Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory take care.

extract_protocol:
Single-cell RNA-seq libraries were prepared as described previsouly but with some modifications of  Smart-seq2 protocol(Li et.al, Cell Stem Cell, 2017). In short, cardiac cells sorted by  FACS or just trypsin digestion are picked into sc-RNA lysis buffer by mouth pipette. Then reverse transcription was performed using oligo(dT) primer which carrying a 8-nt specific barcode and a 8-nt random sequence as unique molecular identifiers (UMIs).
The second stand was synthesized using TSO oligo. After 17 cycle of PCR reaction, all synthesized cDNA was pooled together. Additional 5 cycles of PCR reaction was performed using a biotinylated primer introducing a library specific index. Then cDNA was sheared by Covaris S2 and gain average 400bp fragments and 3’ terminal fragments of the cDNA were captured by Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher). Last, RNA-seq library was constructed by NEBNext Ultra DNA Library Prep Kit for Illumina(E7370) following the manufacture’s guide. All the Single-cell RNA-seq  library are subjected to 150 bp paired-end sequencing on an Illumina High seq X ten platform.

tag: embryonic stage


title: DKO, HT, E8.25, embryo

description: polyA RNA


title: P23


title: P22


title: Control, OFT, E8.25, embryo, 2

description: polyA RNA


title: P27


title: P20


title: P21


title: MiddleCerebralArtery_MoyamoyaDisease#118

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 118, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#70

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 70, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#58

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 58, replicate 1


title: Control, OFT, E8.25, embryo, 1

description: polyA RNA


title: P29


title: P26


title: P7


title: P17


title: P6


title: P14


title: P5


title: BR014

city: New Haven

first: Jonas

last: Schupp

state: CT

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

description: 10x Genomics

data_processing:
fastq read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
Downstream processing was conducted with zUMIs v2.0 with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample.
Cells being accepted had to pass the following filters: between 3000  and 50000 transcripts profiled, having at least 12% of transcripts arising from intron spanning or unspliced reads, less than 20% of their transcriptome of mitochondrial origin, doublets are removed
Genome_build: Ensembl GRCh38 release 91
Supplementary_files_format_and_content: gene vs barcode sparse matrix of all samples
Supplementary_files_format_and_content: Brushes.processed.mtx: sparse matrix file of processed counts
Supplementary_files_format_and_content: Brushes.processed.genes.tsv: gene IDs to sparse matrix file of processed counts
Supplementary_files_format_and_content: Brushes.processed.barcodes.tsv: barcode IDs to sparse matrix file of processed counts

source_name: bronchial brush cells

extract_protocol:
Bronchial epithelial cells were harvested by bronchial brushes of sub-segmental bronchi of the right lower lobe during flexible bronchoscopy.
Single-cell libraries were prepared using the standard 10x Genomics single cell 3' reagent kits v2 processing workflow.
Standard10x genomics single cell 3' reagent kits v2 library preparation. Sequencing on Illumina HiSeq 4000 sequencer, aiming for 150 million reads per sample. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.

tag: group

value: UIP

tag: Sex

value: m

tag: smoking

value: never

tag: fvc % predicted

tag: dlco % predicted


title: BR015

description: 10x Genomics

value: ex


title: DKO, OFT, E8.25, embryo, 1

description: polyA RNA


title: Control_Mouse3

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

data_processing:
Transcripts were aligned using STAR and counted using the SummarizedExperiment package with default settings
Assembly: GRCh38/hg38
Supplementary files format and content: Raw counts

source_name: CD4+ CAR-T

growth_protocol: Peripheral blood was obtained from healthy donors who provided informed consent to participate in a blood donation protocol approved by the Fred Hutchinson Cancer Research Center Institutional Review Board. T-cell subsets were isolated using EasySep CD4+ Naïve T-cell negative selection kits (Stemcell). Non–tissue-culture-coated plates were coated overnight at 4˚C with phosphate-buffered saline (PBS) plus 5 mg/mL RetroNectin (Takara) and either 2.5 mg/mL Ultra-LEAF-Purified aNOTCH1 mAb (MHN1-519, BioLegend) for NOTCH1 (N1) culture or 2.5 mg/mL mouse IgG1k isotype (BioLegend) for control culture. Coating solution was aspirated and plates washed twice with PBS before T-cell plating. On day 0, 2x10^5 T cells and 6x10^5 Human T-Activator CD3/CD28 Dynabeads (ThermoFisher) in 1 ml T-cell culture medium including IL-2 were plated per N1/control-coated 24-well. On day 1, T cells were transduced with CAR lentivirus. T cells were expanded in N1/control-coated wells for 7 days before transfer to uncoated flasks. DynaBeads were removed at day 5.

extract_protocol:
8 days post-transfer, 300 CD4+ EGFRt+ CAR-T cells were FACS-sorted from peripheral blood of tumor-bearing mice into SMART-Seq HT lysis buffer (Takara).
cDNA was generated using 13 amplification cycles and purified using AMPure XP beads (Agencourt). Libraries were prepared using the Nextera XT kit (Illumina) and sequenced on a HiSeq (Illumina) to read depths >10x106 per sample.

treatment_protocol: 6- to 8-week-old NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice were engrafted IV with 5x105 CD19+/GFP+/firefly luciferase+ Raji lymphoma. One week later, mice were treated IV with 2.5x106 N1 or control CD19-specific CD4+ CAR-T.

value: CD19-specific CD4+ CAR-T

tag: treatment

value: Control culture

tag: time point

value: Day 8 Post-Transfer

value: NSG bearing CD19+ Raji lymphoma


title: DKO, OFT, E8.25, embryo, 2

description: polyA RNA


title: BR013

description: 10x Genomics

value: nonUIP


title: BR012

description: 10x Genomics


title: P33


title: N1_Mouse2

value: NOTCH1 agonism


title: BR011

description: 10x Genomics


title: MiddleCerebralArtery_MoyamoyaDisease#76

source_name: Middle Crebral Artery, Moyamoya Disease, Patient Number 76, replicate 1

value: Artery Wall

value: Male


title: N1_Mouse1


title: 24hrRestim_Control_donor3

growth_protocol: Peripheral blood was obtained from healthy donors who provided informed consent to participate in a blood donation protocol approved by the Fred Hutchinson Cancer Research Center Institutional Review Board. T-cell subsets were isolated using EasySep CD4+ Naïve T-cell negative selection kits (Stemcell). Non–tissue-culture-coated plates were coated overnight at 4˚C with phosphate-buffered saline (PBS) plus 5 mg/mL RetroNectin (Takara) and either 2.5 mg/mL Ultra-LEAF-Purified aNOTCH1 mAb (MHN1-519, BioLegend) for NOTCH1 (N1) culture, 2.5 mg/mL mouse IgG1k isotype (BioLegend) for control culture, or various concentrations of DLL1-Fc. Coating solution was aspirated and plates washed twice with PBS before T-cell plating. On day 0, 2x10^5 T cells and 6x10^5 Human T-Activator CD3/CD28 Dynabeads (ThermoFisher) in 1 ml T-cell culture medium including IL-2 were plated per N1/control-coated 24-well. On day 1, T cells were transduced with CAR lentivirus. T cells were expanded in N1/control-coated wells for 7 days before transfer to uncoated flasks. DynaBeads were removed at day 5. For restimulation, day 11 CAR-T were co-cultured with CD19+ K562 tumor for 24hr.

extract_protocol:
300 CD4+ EGFRt+ CAR-T cells were FACS-sorted into SMART-Seq HT lysis buffer (Takara).
cDNA was generated using 13 amplification cycles and purified using AMPure XP beads (Agencourt). Libraries were prepared using the Nextera XT kit (Illumina) and sequenced in an SP flow cell on a NovaSeq 6000 (Illumina) to read depths >10x106 per sample.

tag: cell type

tag: culture time point

value: 24hr restimulation with CD19+ K562


title: BR009

description: 10x Genomics


title: H3K27ac, E8.25, WT, SHF, rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad".
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Assembly: mm10
Supplementary files format and content: The processed files were bigwig files.

source_name: E8.25 second heart field

extract_protocol:
The E8.25 hearts were firstly fixed with 0.25% formaldehyde, then FHF/SHF were separated by forceps followed by methyl alcohol fixation.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

tag: strain

value: E8.25 second heart field

value: wildtype

tag: chip antibody


title: 24hrRestim_N1_donor3


title: BR008

description: 10x Genomics


title: RNA-seq_ARPE-19 cells, sh-METTL3,rep3

city: Chongqing

first: 刘

middle: 先

last: 洋

address: Medical road

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
We used Hisat2 v2.0.5 and hg38 for read alignment and read quantification
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Retinal pigment epithelium

growth_protocol: ARPE-19 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction.
RNA libraries for RNA-seq were prepared using standard illumina protocols.

treatment_protocol: Inflammation was induced by treatment of sh-Control and sh-METTL3 cells with 1ug/ml lipopolysaccharide.

value: Retinal pigment epithelium cells

value: METTL3 knockdown

value: LPS stimulated for 24h


title: H3K27ac, E8.25, WT, SHF, rep1


title: RNA-seq_ARPE-19 cells, sh-METTL3,rep2


title: Control_Mouse2


title: Control_Mouse1


title: 24hrRestim_Control_donor2


title: H3K27ac, E8.25, WT, FHF, rep1

source_name: E8.25 first heart field

value: E8.25 first heart field


title: BR007

description: 10x Genomics

value: UIP

value: m


title: H3K27ac, E8.25, WT, FHF, rep2


title: 24hrRestim_N1_donor2

value: CD19-specific CD4+ CAR-T


title: RNA-seq_ARPE-19 cells, sh-METTL3,rep1


title: RNA-seq_ARPE-19 cells, sh-Control,rep3

value: Scramble


title: 24hrRestim_Control_donor1


title: A22 (array)

type: genomic

hyb_protocol: Each sample was hybridized to an Illumina Infinium MethylationEPIC BeadChip

scan_protocol: Array was scanned using the Illumina iScan system

data_processing: IDAT files were processed (normalized and annotated) with the minfi Bioconductor package using the preprocessQuantile method with outlier thresholding enabled

label: Cy3, Cy5

source_name: White blood cells

label_protocol: 500 ng of genomic DNA was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, cat.no. D5001). The samples were further processed following Illumina’s Infinium HD Assay Methylation Protocol Guide

extract_protocol: Genomic DNA was extracted from EDTA-whole blood using QIAamp DNA Mini kit (Qiagen, cat.no. 51304) according to the manufacturer’s instructions

tag: gender

value: male

value: blood


title: BR004

description: 10x Genomics

value: f

value: ex


title: BR006

description: 10x Genomics


title: NKX2-5, E9.5 heart, DKO, rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad".
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files.

source_name: E9.5 heart

extract_protocol:
The hearts of E9.5 mouse embryo were isolated and directly used for ChIP-seq.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

tag: strain background

tag: genotype/variation

value: DKO

tag: developmental stage

value: heart

tag: chip anitbody


title: N1_Mouse3

value: NOTCH1 agonism

value: Day 8 Post-Transfer

value: NSG bearing CD19+ Raji lymphoma


title: BR005

description: 10x Genomics

tag: age

value: never


title: NKX2-5, E9.5 heart, DKO, rep1

tag: tissue


title: RNA-seq_ARPE-19 cells, sh-Control,rep1

tag: cell line

value: Retinal pigment epithelium cells

tag: genotype


title: RNA-seq_ARPE-19 cells, sh-Control,rep2

value: LPS stimulated for 24h


title: 24hrRestim_N1_donor1

value: 24hr restimulation with CD19+ K562


title: D11_Control_donor3

value: Control culture

value: Day 11


title: ATAC, E16.5 ventricle, U2KO, rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files.

source_name: E16.5 ventricle

extract_protocol:
The ventricles of E16.5 mouse embryo were isolated and directly used for ChIP-seq.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.


title: ARPE-19 cells, sh-METTL3,rep3

data_processing:
Base calling were performed with Illumina CASAVA pipeline
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
Reference genome and gene model annotation files were downloaded from genome website directly.
Peak finding algorithm to indentify regions of IP enrichment over background used the MACS2 version 2.1.0.
Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: hg38

extract_protocol:
In brief, purified mRNAs were fragmented into approximately 100 nt of length by a 45 s incubation at 94 °C in RNA fragmentation reagent (AM8740, Life Technologies). Then, the fragmented mRNAs were collected and incubated with anti-m6A antibody or IgG in immunoprecipitation buffer containing RNase inhibitor at 4 °C overnight. Methylated RNAs were immunoprecipitated with protein A/G beads (Life Technologies, 10013D), eluted by competition with free m6A and for library construction or qPCR analysis.
Libraries for Methyl-seq were prepared using standard illumina protocols.

value: METTL3 knockdown

tag: rip antibody

value: anti-m6a antibody (synaptic systems #202003)


title: A29 (array)

value: male


title: D11_N1_donor3

value: CD19-specific CD4+ CAR-T


title: BR003

description: 10x Genomics

tag: group

value: nonUIP

tag: Sex

value: m

tag: smoking

tag: fvc % predicted

tag: dlco % predicted


title: BR002

description: 10x Genomics

value: UIP


title: B13 (array)

value: blood


title: ARPE-19 cells, sh-METTL3,rep2

tag: cell type

tag: treatment


title: ATAC, E16.5 ventricle, U2KO, rep1

tag: strain


title: BR001

description: 10x Genomics


title: ATAC, E16.5 ventricle, Control, rep2

value: control


title: ARPE-19 cells, sh-METTL3,rep1


title: D11_N1_donor2

value: NOTCH1 agonism

tag: culture time point


title: D11_Control_donor2


title: ATAC, E16.5 ventricle, Control, rep1

tag: genotype/variation


title: A45 (array)

tag: gender


title: ARPE-19 cells, sh-Control,rep3

value: Scramble


title: infected group,rep3,miRNAseq

city: Guangzhou

first: yuyou

last: lu

address: Xiaoguwei street

institute: Sun Yat-sen university

data_processing:
Raw small RNA sequencing reads s including dirty reads containing adapters or low quality bases were filtered to get clean tags.
All of the clean tags were aligned with small RNAs in GeneBank database(Release 209.0) and Rfam database (Release 11.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA.
The remaining sequences were searched against miRBase database to identify known (Species studied) miRNAs, and the unannotated tags were aligned with reference genome to predict novel miRNA candidates by software MIREAP_v0.2
The novel miRNAs were named miR-x (processed from the 5 '-region of pre-miRNA) or miR-y (processed from the 3 '-region of pre-miRNA), which distinguished from miR-5p and miR-3p in known miRNAs.
Assembly: E. coioides (the data is not published)
Supplementary files format and content: tab-delimited text files include count and TPM values for each Sample

organism: Epinephelus coioides

source_name: spleen

extract_protocol:
Total RNA was extracted from the samples with a Trizol reagent kit (Invitrogen, USA), amd small RNA (molecules in a size range of 18–30nt) were obtained  via polyacrylamide gel electrophoresis (PAGE).
The 3’ adapters were added and the 36-44nt RNAs were enriched, after which the 5’ adapters were connected as well. The ligation products were reverse transcribed by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library, which were subjected to Illumina HiSeqTM 2500.

value: spleen

value: Vibrio parahaemolyticus infection

tag: time

value: Day 1


title: A26 (array)


title: H3K27ac, E16.5 ventricle, U2KO, rep2

tag: chip antibody


title: D11_Control_donor1


title: infected group,rep2,miRNAseq

tag: tissue


title: A05 (array)


title: ARPE-19 cells, sh-Control,rep2

tag: cell line

value: Retinal pigment epithelium cells

value: LPS stimulated for 24h


title: B32 (array)


title: A02 (array)


title: D11_N1_donor1

value: Day 11


title: H3K27ac, E16.5 ventricle, U2KO, rep1


title: infected group,rep1,miRNAseq


title: D3_Control_donor3

value: Control culture

value: Day 3


title: H3K27ac, E16.5 ventricle, Control, rep2


title: ARPE-19 cells, sh-Control,rep1

tag: genotype

value: anti-m6a antibody (synaptic systems #202003)


title: ARPE-19 cells, sh-METTL3,input

value: METTL3 knockdown

tag: rip antibody

value: none (input)


title: H3K27ac, E16.5 ventricle, Control, rep1


title: ARPE-19 cells, sh-Control,input


title: control group,rep3,miRNAseq

value: control (PBS)

value: Day 0


title: BR010

description: 10x Genomics

tag: group

value: nonUIP

tag: age

value: m

value: ex


title: D3_N1_donor3

value: CD19-specific CD4+ CAR-T


title: D3_Control_donor2


title: control group,rep1,miRNAseq

value: spleen


title: IgG, E16.5 ventricle, Control

value: control


title: CAL27 cells Metformin 30mM replicate 3

city: Huhhot

first: shanchun

last: hou

address: Xinhua Street

institute: inner Mongolia medical university

data_processing:
the next-generation libraries were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme,nanjing,China).
The Library quality was determined by Bioanalyzer 2100 (Agilent, santa Clara, CA, USA)
Then the RNA-seq libraries was sequenced in HiSeq X10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Tongue

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from treated cells using the Trizol reagent and further purified using the Qiagen miRNeasy Micro Kit and assessed with Bioanalyzer 2100.
RNA libraries for RNA-seq were prepared using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: The cells were treated for 48 hours with either PBS vehicle or 30 mM metformin

value: Tongue

value: epithelial cell

tag: disease

value: Squamous Cell Carcinoma

value: Metformin 30mM


title: infected group,rep3,mRNAseq

data_processing:
fastp (version 0.18.0) , Bowtie2 (version 2.2.8),  HISAT2. 2.4, StringTie v1.3.1
Reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.18.0) (parameter- containing more than 10% of unknown nucleotides/more than 50% of low quality bases)
The short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database and the rRNA mapped reads were removed
Read count extraction and normalization were performed using CLC genomic benchwork
The HISAT2. 2.4  was used to align paired-end clean reads to the reference genome of E. coioidesand the mapped reads were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: Epinephelus coioides (the data is not published)
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

extract_protocol:
Total RNA was extracted from the samples with a Trizol reagent kit (Invitrogen, USA). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

value: Vibrio parahaemolyticus infection

value: Day 1


title: CAL27 cells Metformin 30mM replicate 1


title: CAL27 cells Metformin 30mM replicate 2


title: D3_Control_donor1

value: NOTCH1 agonism

value: Day 3


title: D3_N1_donor1


title: H3K27ac, E9.5 heart, DKO, rep2

value: E9.5 heart

value: DKO


title: infected group,rep2,mRNAseq


title: H3K27ac, E9.5, OFT

source_name: E9.5 heart Outflow Tract

value: wildtype


title: infected group,rep1,mRNAseq


title: control group,rep3,mRNAseq

value: control (PBS)

value: Day 0


title: CAL27 cells Control PBS replicate 3

value: Control PBS


title: H3K27ac, E9.5 heart, DKO, rep1


title: H3K27ac, E9.5 heart, Control, rep2


title: control group,rep2,miRNAseq


title: control group,rep2,mRNAseq


title: D3_N1_donor2

value: CD19-specific CD4+ CAR-T


title: H3K27ac, E9.5 heart, Control, rep1


title: control group,rep1,mRNAseq

value: spleen


title: LY8sh1

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

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 hg38 whole genome using Hisat2
Gene annotated in NCBI were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: FPKM values for each Sample

growth_protocol: OCI-LY8 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol: Total RNA was extracted from cell lines using Trizol®reagent (Invitrogen; Thermo Fisher Scientific, Inc.).

value: Diffuse large B-cell lymphoma cells

value: SMYD3 knockdown


title: LY8NC

value: WT


title: LY8sh2


title: CAL27 cells Control PBS replicate 1

value: Tongue

value: epithelial cell

value: Squamous Cell Carcinoma


title: EHT, Day 5 mRNA cDNA

status: Public on Jul 02 2022

city: Vancouver

first: Peter

last: Zandstra

state: British Columbia

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description: poly A RNA

data_processing:
The Cell Ranger function mkfastq was used for FASTQ generation, and Cell Ranger count was applied using default parameters for trimming, alignment and counting using hg19 as the reference genome. (cellranger v6.0.1) ; (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files, comma-separated values files and matrix files

source_name: Hematopoietic

extract_protocol:
EHT cultures were initiated and carried out as described above. Three wells of a 96 well flat bottom TC-treated plate were prepared for each coating condition and cells were cultured in EHT media for 5 days. On day 5, non-adherent cells were harvested by gentle pipetting. Well replicates were pooled for each condition and pelleted by centrifugation at 300xg for 5 minutes. Samples were washed with 200 uL HF buffer (HBSS, Thermo Fisher Scientific, 14175103, supplemented with 2% Fetal bovine serum, Thermo Fisher Scientific, 12483020). Cells were stained with 0.1ug TotalSeq-B anti-human Hashtag antibody (Biolegend, 394633, 394635, 394637 or 394639) per sample diluted in 100uL HF buffer for 30 minutes on ice. Cells were washed 3 times with HF buffer. Cell density was determined by hand counting using a hemocytometer and samples were pooled at equal cell ratios per sample. The pooled sample was counted and loaded on the chromium controller as per the manufacturer’s instructions aiming for a target cell capture of 5,900 cells.
scRNAseq libraries were prepared using the 10x Chromium Single Cell 3' Capture v3.1 kit following the manufacturer's protocol

value: Hematopoietic

value: Hematopoietic stem and progenitor cells (HSPC), Myeloid progenitors, erythroid and megakaryocyte progenitors

value: Four plating conditions:Uncoated, VCAM1, DLL4, DLL4+VCAM1


title: C28PLT_12_Exp3

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

data_processing:
Sequences smaller than 80 bp and adapter were removed with trimmomatic
Reads were mapped with STAR 2.7.9a
Raw counts were extracted from STAR output (--geneCounts) and raw count table created
Differential gene expression analysis was performed with DESeq2 using raw counts
Genome_build: Arabidopsis thaliana TAIR10 version 51/Araport11 March 2020
Supplementary_files_format_and_content: raw counts

organism: Arabidopsis thaliana

source_name: whole rosettes

growth_protocol: The A. thaliana accessions Columbia-0 (Col-0), an accession with intermediate freezing tolerance (Zuther et al., 2012), was used for the experiment. Plants were grown on soil in a climate chamber at 20°C day and 6 °C night temperature in a 14 h/10 h- light/dark cycle with a light intensity of 180 µmol quanta m-2 s-1 and a relative humidity (RH) of 60 % and 70 % respectively. After one week the conditions were changed to 20 °C/16 °C day/night temperature with an 8 h day length and a light intensity of 180 µmol quanta m-2 s-1 with 60 %/75 % RH for another week before plants were pricked (10 plants per 10-cm-diameter pot). Plants were kept at the previously mentioned conditions for a further week before being transferred to long-day conditions with a 16 h day length and a light intensity of 200 µmol quanta m-2 s-1 for an additional week.

extract_protocol:
Homogenized plant material of five replicate samples per condition was pooled to reach 100 mg separately for each of the three independent experiments resulting in 54 samples. Total RNA was isolated using a “single step” Trizol based method (Chomczynski and Sacchi, 2006) with modifications as previously described (Sprenger et al., 2016). Four µg of RNA were treated with DNAse (RapidOut DNA-removal Kit, Thermo Fisher Scientific, Schwerte, Germany) and the absence of genomic DNA in the samples was confirmed using qPCR using intron-specific primers (Zuther et al., 2012). The RNA quality and integrity was verified by the Agilent 2100 Bionalyzer (Agilent Technologies, Santa Clara, CA).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: For cold priming 28 day old plants were transferred to a chamber with constant 4 °C and a 16 h day length with light intensity of 90 µmol quanta m-2 s-1 and 70-80 % RH for three days of cold priming. After three days of cold treatment the plants were returned to the previously described long-day conditions for a 7 day lag/deacclimation phase. Part of the plants was transferred to cold conditions as mentioned above for one further day (cold triggering). In order to compensate for the additional week of growth during the lag phase a developmental control was introduced. These plants grew an additional week at long day conditions before being moved to cold conditions for cold priming (35-day old developmental control).

tag: ecotype

value: whole rosette

tag: condition

tag: time point


title: IgG, E9.5 heart, Control

value: E9.5 heart

value: IgG, AB donal, WH086883, AC005


title: C28PLT_2_Exp3


title: C28PLT_4_Exp3


title: C28PLT_0_Exp3


title: C35P_24_Exp3


title: C35P_12_Exp3


title: CAL27 cells Control PBS replicate 2

tag: cell type

tag: treatment


title: C35P_6_Exp3


title: C35P_2_Exp3


title: C28P_24_Exp3


title: C35P_0_Exp3


title: C28P_12_Exp3


title: EHT, Day 5 HTO cDNA

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein


title: C28PLT_6_Exp3


title: C28P_4_Exp3


title: C28PLT_6_Exp2


title: C28PLT_24_Exp3


title: C28P_0_Exp3


title: C28PLT_24_Exp2


title: C28PLT_4_Exp2


title: C28PLT_12_Exp2


title: C28PLT_2_Exp2


title: C28PLT_0_Exp2


title: C35P_6_Exp2


title: C35P_4_Exp3


title: C35P_2_Exp2


title: C28P_6_Exp3


title: C35P_12_Exp2


title: C35P_24_Exp2


title: C35P_4_Exp2


title: ipsc_human_hepatocyte_tnt_0.3125_2

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

hyb_protocol: All samples were completely randomized using a random number generator and hybridized to Agilent 8 x 60K, human microarrays (AMADID #39494).

scan_protocol: Microarray slides were scanned using an Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C, Agilent Technologies) at 2 μm resolution.  Data were extracted from microarray images using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies).  Analysis of internal control spikes added prior to complementary RNA (cRNA) synthesis indicated that signal data were within the linear range of detection.

data_processing: Microarray data were read in, normalized and analyzed in R (version 3.4.1). Data were normalized using robust quantile normalization (preprocessCore package) on log2 intensity values.

source_name: human hepatocytes derived from inducible pluripotent stem cells (iCell Hepatocytes 2.0)

label_protocol: The Agilent Low-Input Quick Amp, One Color Microarray Hybridization protocol (Agilent Technologies) was utilized following manufacturer’s recommendations where 50 ng of total RNA served as the starting material for each exposure replicate.

growth_protocol: Human hepatocytes derived from inducible pluripotent stem cells (iCell Hepatocytes 2.0) were purchased from Cellular Dynamics (PHC-100-020-001).  Cells were thawed, plated and grown per manufacturer’s recommendations.  Briefly, cells were thawed in plating media consisting of RPMI 1640 (ThermoFisher 11875093) containing 1x B27 Supplement (ThermoFisher 17504044), 20ng/mL Oncostatin M (R&D Systems 295-OM), 0.1µM Dexamethasone (Fisher Scientific ICN19456125), 25µg/mL Gentamicin (ThermoFisher 15750) and 1x iCell Hepatocytes 2.0 Medium Supplement (Cellular Dynamics HCS-100-021-001). Cells were pelleted at 200xg for 3 minutes and then resuspended in plating media and plated out at 9.6x104 cells per well on Biocoat Collagen I 96-well plates (Becton Dickson 354407).  Cells were then incubated at 37ºC, 5% CO2 for 3-4 hours before aspirating plating media and cell debris from unattached cells and replacing it with fresh plating media.  Media was then replaced with fresh plating media at 24 hours post thawing. Media was exchanged with plating media then continued daily until day 5 post plating.   On day 5 post plating, plating media was exchanged for maintenance media consisting of RPMI 1640 (ThermoFisher 11875093) containing 1x B27 Supplement (ThermoFisher 17504044), 0.1µM Dexamethasone (Fisher Scientific ICN19456125), 25µg/mL Gentamicin (ThermoFisher 15750) and 1x iCell Hepatocytes 2.0 Medium Supplement (Cellular Dynamics HCS-100-021-001).  Media was then exchanged every other day with maintenance media until day 10 post plating when cells were used in experiments.

extract_protocol: Total RNA was extracted from approximately 1.92x105 iPSC hepatocytes per replicate (4 replicates per TNT concentration and vehicle control, 1%DMSO) using Clontech Nucleospin RNA XS kits (catalog no. 740900; Takara Bio USA, Inc., Mountain View, CA). RNA quality was assessed using Agilent RNA 6000 Nano Kits (Agilent Technologies, Santa Clara, CA) run on an Agilent Bio-Analyzer (Agilent Technologies) and using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific).  Criteria for acceptable RNA included an RNA integrity number >7.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading >2.0.

treatment_protocol: On day 10 post plating, media was aspirated from individual wells and replaced with treatment media.  Treatment consisted of: untreated control, solvent treated control, and a logarithmic range of 5 TNT doses (1000, 100, 10, 1 and 0.1ppm) in maintenance media.  Military grade TNT (≥98% purity) was obtained from the Naval Surface Warfare Center, Indian Head Division, Indian Head, MD, USA.  TNT was dissolved in DMSO (Sigma D2650-5x10mL) and serially diluted in DMSO to make up 100x concentrations of dose to ensure final solvent concentration was always 1%. Four replicates were performed for each dose.  Cell viability was determined 24 hours post exposure using a neutral red assay.  The highest concentration of TNT with 80% or better viability was chosen as the high dose for subsequent exposures. Exposures were performed using the same method as in the Range Finder.  Starting with the high dose identified in the range finder, the dose was decreased by half for a total of 5 doses (5, 2.5, 1.25, 0.625, and 0.3125ppm) plus untreated control and solvent treated control.  Each dose had four replicates with each replicate consisting of cells harvested from two individual wells to ensure sufficient cells for RNA isolation.  After 24 hours of exposure, media was aspirated and cells were harvested off of each plate with 1x trypsin-EDTA (ThermoFisher 15400-054). Trypsin-EDTA was then inactivated using an equal volume of Dulbecco’s phosphate buffered saline containing 1% fetal bovine serum (ThermoFisher 16000044).  Cells solution was transferred from wells to a cryovial (Sigma V3881) and centrifuged at 400xg for 5 minutes.  Supernate was aspirated and the cell pellet was flash frozen in liquid nitrogen. Cryovials containing cell pellets were stored at -80ºC until RNA isolation.

tag: concentration group

value: TNT 0.3125 ppm


title: C35P_0_Exp2


title: ipsc_human_hepatocyte_tnt_1.25_3

value: human hepatocytes derived from inducible pluripotent stem cells (iCell Hepatocytes 2.0)

value: TNT 1.25 ppm


title: ipsc_human_hepatocyte_tnt_5.00_1

value: TNT 5 ppm


title: ipsc_human_hepatocyte_tnt_0.625_3

value: TNT 0.625 ppm


title: ipsc_human_hepatocyte_tnt_0.3125_4


title: C28P_24_Exp2


title: ipsc_human_hepatocyte_tnt_0.625_2


title: ipsc_human_hepatocyte_tnt_1.25_4


title: IAEAR9_MDL1-IL-23 (Rep3)

city: Sacramento

first: Cuong

middle: T

last: Nguyen

state: CA

address: 2425 Stockton Blvd

department: Internal Medicine

institute: University of California, Davis

data_processing:
RNA-Seq reads for the 9 individual samples (e.g. 3 groups of control, treatment, and mutant, 3 replicates each, barcoded and run on a single lane) were independently aligned to the mouse genome (ref. ID: GRCh38.p6) using the STAR v2.7.0a alignment software
The featureCounts package was used to count the mapped reads
For differential expression analysis, the edgeR package was used
Supplementary_files_format_and_content: featurecount_*_csv files were generated using the featrueCounts package to count the mapped reads. edgeR_*_csv files were generated using the EdgeR package.
Supplementary_files_format_and_content: The columns of the featurecount_*_csv files represent the number of mapped reads per gene of each sample
Supplementary_files_format_and_content: The columns of the edgeR_*_csv files are the log fold change (logFC), the log counts per gene per million mapped reads (logCPM), p-value (Pvalue) and false discovery rate (FDR) values of each gene in the comparison group

extract_protocol:
RNA was isolated from murine ears of WT or Mdl-1-/- mice injected with GFP MC either IL-23 MC using RNeasy Plus mini kit (Qiagen) and analyzed with Bioanalyzer. Purified total RNA (RIN value >5) was used for library preparation. The 3'Tag RNA-Seq run was performed on an Illumina HiSeq 4000 and generated an average of 600,000 reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fifteen micrograms of IL-23 or GFP MC DNA was injected hydrodynamically into mice via tail vein delivery

tag: strain

value: 10 weeks

tag: genotype/variation

value: MDL1-/- (mutant)

value: IL-23 MC DNA

value: Ear


title: ipsc_human_hepatocyte_tnt_0.00_1

value: 1% DMSO


title: C28P_12_Exp2


title: ipsc_human_hepatocyte_tnt_0.00_3


title: IAEAR8_MDL1-L-23 (Rep2)


title: ipsc_human_hepatocyte_tnt_2.50_1

value: TNT 2.5 ppm


title: ipsc_human_hepatocyte_tnt_0.00_2


title: ipsc_human_hepatocyte_tnt_2.50_4


title: IAEAR6_WT-IL-23 (Rep3)

value: wild type (treatment)


title: C28P_2_Exp3


title: ipsc_human_hepatocyte_tnt_2.50_2


title: ipsc_human_hepatocyte_tnt_0.00_4


title: ipsc_human_hepatocyte_tnt_5.00_3


title: ipsc_human_hepatocyte_tnt_0.625_1


title: IAEAR5_WT-IL-23 (Rep2)


title: C28P_4_Exp2


title: C28P_6_Exp2


title: C28P_2_Exp2


title: IAEAR7_MDL1-IL-23 (Rep1)


title: IAEAR4_WT-IL-23 (Rep1)


title: IAEAR3_WT-GFP (Rep3)

value: wild type (control)

value: GFP MC DNA


title: Tbx3_S5_R1_001.fastq

city: Palo Alto

first: Roel

last: Nusse

address: 265 Campus Drive

department: Developmental biology

institute: Stanford University, School of Medicine

data_processing:
Raw reads were aligned to the UCSC mm10 genome using Bowtie 2,  and processed and sorted with Samtools to bamfile.
Peaks file with p-values were generated using MACS2  from advance peakcalling subcommands and ChIP signals and local lambda stored in BEDGRAPH file.
Peaks were called using MACS2 with the significance cut-off p-value <=0.0001
Assembly: UCSC mm10 genome
Supplementary files format and content: peaks

organism: Mus

source_name: Primary mouse hepatocytes

extract_protocol: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a S220 focused-ultrasonicator (Covaris).

value: Primary mouse hepatocytes

value: anti-HA antibody (Roche Sigma 11867423001)


title: Tbx3_S4_R1_001.fastq


title: IAEAR2_WT-GFP (Rep2)


title: C28PLT_24_Exp1

value: whole rosette


title: ipsc_human_hepatocyte_tnt_5.00_4


title: ipsc_human_hepatocyte_tnt_0.3125_1

value: TNT 0.3125 ppm


title: C28P_0_Exp2


title: C28PLT_12_Exp1


title: ipsc_human_hepatocyte_tnt_5.00_2

value: human hepatocytes derived from inducible pluripotent stem cells (iCell Hepatocytes 2.0)


title: IAEAR1_WT-GFP (Rep1)


title: ipsc_human_hepatocyte_tnt_1.25_2

value: TNT 1.25 ppm


title: ipsc_human_hepatocyte_tnt_0.625_4


title: Input1_S1_R1_001.fastq


title: BRC2174_human foetal lung organoid cells_CRISPRi_ETV4_ETV5_gRNA2-RNA-Seq

city: Cambridge

first: Dawei

last: Sun

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

data_processing:
Illumina software used for conventional basecalling
Reads were aligned to GRCh38 genome assembly (hg38) using STAR version 2.7.1a
Reads were summarised using featureCounts
Differentially gene expression analysis was performed using DESeq2
Assembly: GRCh38 genome assembly (hg38)
Supplementary files format and content: DESeq2 output file with log2(normalised read count+1), log2(fold change between selected groups) and adjusted p-value

source_name: human feotal lung organoid cells

growth_protocol: Organoids were maintained with self-renewing medium, conatining EGF, FGF10, FGF7, Noggin, TGFb inhibitor, R-spondin1 and GSK3b inhibitor (detailed protocol in Nikolic et al., 2017).

extract_protocol:
mRNA was extracted using Qiagen RNeasy Mini Kit (74104)
Library was constructed using Eukaryotic RNA-seq (lib prep) service from Novogene (UK)

treatment_protocol: Organoids infected with inducible CRISPRi and the relevant gRNAs were treated with Dox and TMP for 5 days before harvetsed for RNA-Seq (detailed infection and treatment protocol in Sun et al., 2021)

value: human feotal lung tissue derived organoid cells

tag: developmental stage

value: 8 pcw human foetal lung

value: Dox and TMP


title: Input2_S2_R1_001.fastq


title: ipsc_human_hepatocyte_tnt_2.50_3


title: D5, scRNAseq

first: Lei

last: Yue

state: Beijing

address: 8th Xishiku AVe, Peking University First Hospital

department: Orthopaedics

institute: Peking University First Hospital

data_processing:
We used PerkinElmer LabChip Touch and StepOnePlusTM Real-Time PCR Systems for library quality assessment after library preparation. The Illumina Hiseq platform was used to load the qualified libraries for PE150 sequencing.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lumbar intervertebral disc

extract_protocol:
There was a lysis component and an enzyme inhibitor in the tubes used to collect single cell samples.
We then used the Smart Seq2 technique for amplification. The initial strand of cDNA was synthesized using an Oligo dT primer, which was then amplified using PCR and purified using magbeads. Qubit 3.0 Fluorometer and Agilent 2100 Bioanalyzer were used to verify that the predicted 1–2kbp cDNA synthesis had occurred. Ultrasonic waves were used to randomly shear the cDNA in preparation for the Illumina library preparation technique, which includes DNA fragmentation, end repair, 3' end A tailing, adaptor ligation, PCR amplification, and library validation.

value: Nucleus pulposus cell

value: Lumbar intervertebral disc

value: normal degeneration


title: D2, scRNAseq


title: D4, scRNAseq


title: C28PLT_6_Exp1


title: D1, scRNAseq


title: ipsc_human_hepatocyte_tnt_0.3125_3


title: ipsc_human_hepatocyte_tnt_1.25_1


title: BRC2174_human foetal lung organoid cells_CRISPRi_ETV4_ETV5_gRNA1-RNA-Seq


title: M4, scRNAseq

value: degeneration with modic change


title: BRC2174_human foetal lung organoid cells_CRISPRi_NT2-RNA-Seq


title: M5, scRNAseq


title: M3, scRNAseq


title: D3, scRNAseq


title: C28PLT_2_Exp1


title: M2, scRNAseq


title: C28PLT_0_Exp1


title: BRC1915_human foetal lung organoid cells_CRISPRi_ETV4_ETV5_gRNA2-RNA-Seq


title: BRC2174_human foetal lung organoid cells_CRISPRi_NT1-RNA-Seq


title: M1, scRNAseq


title: kanamycin 2

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2  --local using Bacillus subtilis 168 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Assembly: Bacillus_subtilis_168_ASM904v1
Supplementary files format and content: Tab delimited text file

organism: Bacillus subtilis

source_name: Bacterial

growth_protocol: Bacterial cells were grown in Spizizen minimal medium (SMM) supplemented with 0.5% (w/v) glucose and 1% (v/v) trance elements at 37 degees celcius. Cultures were aerated with shaking 220rpm.

extract_protocol:
Cell were lysed using glassbead and total RNA was isolated using TRIzol/chlorophorm extraction followed by ethanol and isopropanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: Bacterial cells were grown in SMM untill reached OD600 0.3 and 0.6 M NaCl was added to the treated culture. After 90 minutes of osmotic upshift, the cells were washed and resuspended in SMM without salts. After the washing step, 62.5 ug/ml of kanamycin was added to the culture. Cultures were grown with or without the antibiotic for 1 hour prior to cell collection for the RNA extraction. Subsequently cells were harvested by centrifugation at 10.000 x g for 1 minute, snap-frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.

value: kanamycin


title: BRC1915_human foetal lung organoid cells_CRISPRi_NT2-RNA-Seq


title: C28PLT_4_Exp1


title: C35P_12_Exp1


title: C35P_24_Exp1


title: kanamycin 3


title: BRC1915_human foetal lung organoid cells_CRISPRi_ETV4_ETV5_gRNA1-RNA-Seq


title: C35P_6_Exp1


title: kanamycin 1


title: BRC1915_human foetal lung organoid cells_CRISPRi_NT1-RNA-Seq


title: C35P_4_Exp1


title: siFAM-2

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

data_processing:
Sequencing reads were trimmed for bases with base quality score less than 20
Trimmed sequencing reads were aligned to human transcriptome hg38 using HISAT2
Transcript abundances were estimated by StringTie2
Assembly: hg38
Supplementary files format and content: comma-separated file

source_name: LAM 621-101 cells, siFAM120A 3 day siRNA transfection + 24 hour serum-starvation

growth_protocol: LAM 621-101 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using PureLink RNA isolation kit (Life Technologies). 1 ug of total RNA was removed rRNA using NEBNext® rRNA Depletion Kit (New England Biolabs) and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
After 2 days of siRNA transfection, cells were serum starved for 24 hours.
Serum depleted media (only DMEM without FBS) was treated for 24hours.

value: angioleiomyoma patient-derived cell line

value: FAM120A knockdown

value: 24hour serum starvation


title: T13_1, normal tissue

city: Tehran

first: Ali Mohammad

last: Alizadeh

state: Tehran

address: Keshavarz Blvd, Cancer Institute, Imam Khomeini Hospital

department: Cancer institute

country: Iran

institute: Tehran University of Medical Sciences

data_processing:
Trim data: cutadapt (sequence: TGGAATTCTCGGGTGCCAAGG)
Reads with adapters: 50,772,655 (97.0%), Reads that were too short: 3,511,739 (6.7%), Reads written (passing filters): 48,823,422 (93.3%)
Mirdeep tool to quantify the expression of known miRNA and discovery of novel ones
The reads that have the exact same sequence in the raw files were clustered together in a .fa file. This is to speed up the mapping. Then the data was mapped to human genome version hg38. The clustered files were also mapped to the latest release of known mature and precursor sequences from miRbase.
Differential expression analysis was performed using DESeq2 on the data. Unfortunately because there are no technical or biological replicates we can not draw powerful results and  small p-values. Also some types of analysis like correlation matrix heatmap and hierarchical clustering are absent because they depend on replicates being present in the sample.
For each microRNA the amount of expression in both samples along with log2 of fold change and raw and adjusted p-values is reported.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include counts

source_name: epithelial tissue

extract_protocol:
RNA was harvested using TRIzol (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for Small RNA sequencing (RNA-Seq) were prepared using TruSeq Small RNA Library Prep Kit following manufacturer's protocols.

value: epithelial tissue

tag: tissue type

value: normal

tag: subject status

value: gastric cancer patient


title: siNTC-1

source_name: LAM 621-101 cells, siNTC (Control) 3 day siRNA transfection + 24 hour serum-starvation

tag: cell line

value: WT


title: siFAM-3

tag: genotype


title: siNTC-2


title: CPH303_LPMC_CD4

city: Oxford

first: Carl-Philipp

last: Hackstein

address: 3 South Parks Road

department: NDM Experimental Medicine

institute: University of Oxford

description: BD Rhapsody (targeted mRNA and Abseq)

data_processing:
Raw data files were uploaded to the 7 bridges genomics platform (https://www.sevenbridges.com) and processed in the BD Rhapsody Targeted analysis pipeline to obtain gene/protein counts per cell (Combined_CPH303-1stSeq-2_DBEC_MolsPerCell.csv) and the information about the sample tags (CPH303-1stSeq-2_Sample_Tag_Calls.csv) required for further analysis in SeqGeq (BD)
Assembly: hg38
Supplementary files format and content: Tab-separated values files

source_name: colonic lamina propria

extract_protocol:
Stimulated LPMCs from three donors (141, 194 and 267) were washed with ice-cold BD stain buffer, resupended in stain buffer containing Fc-block for 10 min at RT and then washed again. Staining with with BD sample tags and a panel of 50 BD Abseq antibodies was performed in BD stain buffer on ice for 1 hour. Cells were washed with addtional staining buffer and resuspended in a Mastermix containing near-infraread fluorescent LIVE/DEAD dye and flurecently labelled antibodies (CD4, CD8, CD45, TCRgd, Va7.2, Va24-Ja18, TCRgd) for sorting. Live CD45+CD4+ cells negative for all other markers were sorted RPMI containing 20% FCS. After the sort, cells were washed and equal cell numbers form each sample (3 donors, 4 condtions = 12 samples) were pooled together to 20.000 cells and loaded onto a BD Rhapsody cartridge.
Libraries for the targeted mRNA, sample Tags and Abseq were constructed using the BD Rhapsody Targeted mRNA and Abseq Amplification kit using the recommended reagents and manufacturer's instructions (Protocol Doc IDs: 210967 Rev. 1.0 and 214508 Rev. 3.0). Briefly, single cells were captured  with beads on a BD Rhapsody cartridge, lysed, beads were recovered , cDNA synthesis and an exonuclease I treatment were performed to obtain cDNA containing the information about the cells mRNA, sample Tags , Abseq barcodes and unique molecular identifiers. cDNA was subjected to several PCR-amplification and clean-up steps using AMPure beads to obtain the three different libraries. In a final OCR step a Illumina i7 sequences was added, library size and concentration were controled  using a Tapestation and Qubit respectively and libraries were pooled together for sequecing.

treatment_protocol: LPMCs were isolated from colonic tissue by digestion and gradient centrifugation, washed, counted and stimulated with human recombinant IL12 and IL18 (C), plate-bound aCD3 antibodies and soluble aCD28 antibodies (T) or a combination (TC) overnight.

tag: tissue

value: colonic lamina propria

value: CD4 T cells


title: siFAM-1


title: siNTC-3


title: C35P_2_Exp1

value: whole rosette


title: T18_1, tumor tissue

value: cancer


title: VBNC 3

value: osmotic stress and aminoglycoside treatment


title: C28P_24_Exp1


title: VBNC 1


title: C35P_0_Exp1


title: Sample_O3

first: Dongyoun

last: Lee

address: 81, Irwon-ro, Gangnam-gu

institute: Samsung Medical Center

description: RNA-Seq

data_processing:
After cluster amplification of denatured templated, the prepared libraries were sequenced using Illumina Novaseq6000 (Illumina Technologies., San Diego, CA, USA). ScRNA-seq: System targeting 50,000 raw reads per cell.
BulkRNA-seq: The RNA-sequencing reads were mapped to the human reference genome (hg19) using the STAR (Spliced Transcripts Alignment to a Reference). Gene expression level quantification was performed using RSEM (RNA-seq by Expectation–Maximization). ScRNA-seq: The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Assembly: hg19 (Bulk RNA-seq), hg38 (ScRNA-seq)
Supplementary files format and content: Tab-delimited text file includes counts per million (CPM) for each sample

source_name: Nail matrix keratinocytes

growth_protocol: Bulk RNA-seq: After removing the lower portion from nail matrix tissue, primary NMKs were harvested from nail matrix biopsy specimens. NMKs were isolated after 0.25% trypsin–EDTA treatment for 30 min and cultured in Keratinocyte Growth Media (KGM, Lonza) and maintained at 37 °C with 5% CO2. We checked no fibroblast growth under an inverted microscope. The cells which are passage three were plated in triplicate in six-well plates.

extract_protocol:
Bulk RNA-seq: After 24h or 48 h of culture, NMK was treated with 1 ml of Trizol to isolate RNA for further bulk RNAseq experiments. ScRNA-seq: Single-cell suspensions were generated immediately after manual isolation of the human scalp specimens.  Briefly, the scalp tissue for scRNA-seq was washed in phosphate-buffered saline (PBS) and cut into small pieces. After chopping the HF and DP with a scalpel in a Petri dish, samples were transferred to prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) and incubated for 60 min at 37ºC for digestion. The residual tissue was transferred into a dissociation solution containing 0.05% Trypsin and incubated for 30 min at 37ºC for a second round of dissociation. Then dissociated samples was filtered out using a 70-μm cell strainer (#352340, Corning). Following centrifugation (300 x g for 5 min), the supernatant was decanted, and the live cells were resuspended in PBS-0.04% bovine serum albumin (Sigma Aldrich). The samples were centrifuged (200 x g for 5 min) and then resuspended in 1ml PBS-0.04% bovine serum albumin. Live cells were counted and confirmed using LUNA-FL dual fluorescence cell counter (Logos Biosysteomics).
Bulk RNA-seq: Libraries preparation for 150bp paired-end sequencing was processed using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero H/M/R (Illumina Technologies., San Diego, CA, USA), following the protocol. The integrity and overall quality of the total RNA was quantified using a Nanodrop 8000 UV- Vis spectrometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and checked with a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). After cluster amplification of denatured templated, the prepared libraries were sequenced using Illumina Novaseq6000 (Illumina Technologies., San Diego, CA, USA). ScRNA-seq: To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 10,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA)  targeting 50,000 raw reads per cell.

treatment_protocol: Bulk RNA-seq: Recombinant human  BMP5  were treated at 500ng/ml and 100ng/ml in KGM without rhEGF, respectively.

value: Control

tag: cell source

value: Nail matrix


title: Sample_O2

description: RNA-Seq


title: LIPUS-induced EVs b

first: Tingwei

last: Zhang

address: 426# Songshibei Rd., Yubei District,

institute: Stomatological Hospital affiliated to Chongqing Medical University

data_processing:
The library preparations were sequenced on an Illumina Novaseq 6000 platform, and 50 bp single-end reads were generated.
The small RNA tags were mapped to the reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
The miRNA expression levels were estimated by transcript per million (Zhou et al., 2010).
All the procedures for small-RNA library preparation and sequencing analysis were accomplished by Novogene (Beijing, China).
Genome_build: Homo_sapiens
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: stem cells from the apical papilla

growth_protocol: SCAPs were routinely maintained in Alpha-minimum essential medium (Hyclone) containing 10% fetal bovine serum (Biological Industries，South America). Cells at passages 4-6 were used for EV isolation. After the cell density reaches 70%-80%, SCAPs was washed with PBS 3 times, and changed to EV-free medium (bovine serum EVs were removed by 16 hours centrifugation at 110,000×g). Culture medium was collected after 48 hours. EVs were isolated and purified based on the established differential centrifugation protocol.

extract_protocol:
RNA was isolated by Trizol extraction from EVs of con- and LIPUS-induced SCAPs. Agilent Bioanalyzer small RNA assay kit (Novogene) was used to quantify the samples. All samples were transported to the Novogene Experimental Department in dry ice box
Small-RNA cDNA libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina® (NEB, United States) following the manufacturer’s recommendations.

treatment_protocol: SCAPs were treated with LIPUS (90mW/cm2, 0.5 h) right after changing to EV-free medium

value: the apical papilla

tag: passage

value: treated with LIPUS (90mW/cm2, 0.5 h)

tag: molecule subtype

value: extracellular miRNA


title: C28P_12_Exp1

tag: ecotype


title: Sample_O1

description: RNA-Seq

tag: condition


title: control 2

value: control


title: LIPUS-induced EVs a


title: LIPUS-induced EVs c


title: Control EVs c

value: untreated


title: control 3


title: C28P_4_Exp1

tag: time point


title: Sample_B3

description: RNA-Seq

value: BMP 500ng/ml treated


title: Sample_B1

description: RNA-Seq


title: Sample_B2

description: RNA-Seq


title: Control EVs a


title: SG200-dsu-2

city: Taian

first: Ru Chang

last: Ren

address: Daizong

department: College of Life Sciences

institute: Shandong Agricultural University

data_processing:
We use internal software to filter reads, fllowed as:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases(N) are more than 10%;  3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 20 is greater than 50% in a read).
We use HISAT2 to perfrom genome mapping
we mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

source_name: dsu mutant

extract_protocol:
Total RNA was isolated from leaves of WT and dsu seedling leaves through an Ultrapure RNA Kit (catalog no. CW0581, CWBIO, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf blade

tag: cell type

value: leaf cell

value: ZmADT2 mutation

value: SG200 strains infection


title: SG200-dsu-1

tag: treatment


title: C28P_2_Exp1


title: C28P_6_Exp1


title: HF3

description: scRNA-seq

source_name: Hair follicle

value: Normal skin

value: Scalp


title: SG200-dsu-3


title: VBNC 2


title: C28P_0_Exp1

value: whole rosette


title: SIM1 ARNT2 round 3

city: Adelaide

first: David

middle: C

last: Bersten

state: SA

address: Victoria Drive

department: Molecular and Biomedical Sciences

institute: The University of Adelaide

data_processing:
Library strategy: SELEX-seq
base-calling and demultiplexing was achieved with bcl2fastq,
fastq files were analysed for quality using Fastx toolkit (Hannon Lab, version 0.0.13). In some analysis, Kmer enrichment and transcription factor binding models were generated with filtered fastq data to remove more than one “Core” binding site per read.
One Core motif per read was filtered using fastq-tools (version 0.8) fast-grep -v function. Kmer counting and relative enrichments were analysed using the SELEX-seq R package (version 1.2), transcription factor binding motif models generated using No Read Left Behind (NRLB) https://github.com/BussemakerLab/NRLB. Demultiplexing and trimming of primers and barcode sequences were removed using SELEX-seq or NRLB during analysis by specifying flanks and barcodes.
Supplementary_files_format_and_content: read count of kmers

organism: synthetic construct

source_name: Synthetic

growth_protocol: We purified full length human ARNT (1-774) or ARNT2 (1-717) homodimers from Expi293 cells, bHLH-PAS (PAS A and PAS B, N-terminus) heterdimers (human HIF1a(1-375)/ARNT(1-474), human HIF2a(1-353)/ARNT(1-474), human SIM1(1-348)/ARNT2(1-439) and mouse NPAS4(1-329)/ARNT2(1-481)) from baculovirus infected Sf9 insect cells or human AhR(1-287)/ARNT(1-364) from bacteria.    Baculoviral expression and purification  MultiBAC-LoxP-EYFP was generated by recombination of pUDCM-EYFP into the MultiBAC genome by Cre transposition as described Berger I et al, Nature Biotechnology 2004. With the exception of NPAS4 all truncated bHLH-PAS (A and B) heterodimers were incorporated into the MultiBAC-LoxP-EYFP baculoviral genome by pFBDM Tn7 transposition as described in Berger I et al, Nature Biotechnology 2004. Truncated mNPAS4 (1-329)/mARNT2 (1-481)/mnucTomato (monomeric nuclear) were recombined into MultiBAC by Tn7 transposition. All expression constructs Class I bHLH-PAS transcription factors were N-terminally tagged with a 6xHis-TEV tag immediately leading the endogenous start codon and class II ARNT or ARNT2 were untagged and expressed under the Polh and p10 baculoviral promoters.  Virus production and protein expression was carried out in Sf9 insect cells cultured in SF900III media essentially as described in Fitzgerald et al, Nature Methods 2006, with protein expression monitored by EYFP or nucTomato fluorescent protein expression.     Bacterial AhR expression and purification  BL21(DE3) (LysS) bacterial cells were co-transformed with pET16b-6xHis-TEV-hAhR(1-287) (AmpR) pAC28-hARNT(1-362) (KanR) (Ref). Bacteria was grown in Luria Broth to an OD600 of 0.6 and protein expressed was induced by the addition of 1mM IPTG at 16oC for 18hrs.     Insect or bacterially expressed proteins were purified by His-tag purification, followed by His tag removal by Tobacco Etch Virus (TEV) protease cleavage, ion-exchange, and size-exclusion chromatography. Protein purity was assessed by SDS-PAGE and coomassie staining and concentrations estimated by A280. Purified proteins were stored in a buffer containing (20mM Hepes pH 8.0, 300mM NaCl, 5% Glycerol, 10mM DTT), and flash frozen in LiN2, for long term storage at -80oC. This approach left untagged heterodimeric bHLH-PAS transcription factor complexes.     Expi293 mammalian expression and purification    C-terminal Twin strep tagged full-length ARNT or ARNT plasmids (pEFIRES-Puro-hARNT-2xStrep or  pEFIRES-Puro-hARNT2-2xStrep) were transiently transfected into Expi293 cells (Life Technologies) grown in Expi293SF media using PEI Polyethylenimine (PolySciences). ~60hrs post-transfection, Expi293 cells were harvested by centrifugation, and washed with PBS. ARNT-2xStrep  or ARNT2-2xStrep were purified by strep-tactin XT resin (IBA-LifeSciences) and homodimers enriched using 100KDa mwco filters. The concentration and purity of ARNT-2xStrep or ARNT2-2xStrep was estimated by SDS-PAGE and commassie staining with BSA standards.

extract_protocol:
~250nM of purified transcription factor and 200nM (1.5μl of 5μM of DNA library (Random 18mer or FixedCore 18/22mer) , ~ 7x 1010 DNA molecules) of Round 0 library were incubated at room temperature in buffer containing ~20mM Tris-HCl pH 8.0, 3mM MgCl2, ~200-300mM NaCl, 8% Glycerol, 50 μg/ml polydI-dC, 0.2 mg/ml BSA. + 10mM DTT in a 30μl for 20mins. DNA was extracted, amplified as described in Riley et al 2014.
DNA isolated from SELEX Round 0 (initial Library), Round 1 and Round 2 (FixedCore 8NCGTG10N), or Round 3 (Random 18mer) were barcoded as described in Riley et al, Methods Mol Biol 2014 and illumina compatible adapters added by limited cycle PCR and cleaned up by PAGE purification. FixedCore 18/22mer SELEX samples from each round (Round 0, Round 1 , Round 2) of were quantified, pooled and run on separate lanes of a Hiseq2500 run. Random 18mer SELEX samples (Round 0 and Round 3) were barcoded by limited cycle PCR, quantified, pooled and sequenced on a NEXTSeq500 using a single end 1x75bp High Output mode.
SELEX-Seq Random 18mer –   GTTCAGAGTTCTACAGTCCGACGATC(N18)CTGTCTCTTATACACATCTCCG  SELEX-Seq FixedCore 18/22mer –  SELEX_18/22mer_Multiplex1: NPAS4/ARNT2  GTTCAGAGTTCTACAGTCCGACGATCTGGNNNNNNNNCGTGNNNNNNNNNNCCAgcTgTCGTATGCCGTCTTCTGCTTG  SELEX_18/22mer_Multiplex3:SIM1/ARNT2  GTTCAGAGTTCTACAGTCCGACGATCTGGNNNNNNNNCGTGNNNNNNNNNNCCAGAACTCGTATGCCGTCTTCTGCTTG  SELEX_18/22mer_Multiplex4:HIF2a/ARNT  GTTCAGAGTTCTACAGTCCGACGATCTGGNNNNNNNNCGTGNNNNNNNNNNCCAAGAGTCGTATGCCGTCTTCTGCTTG  SELEX_18/22mer_Multiplex5:AhR/ARNT  GTTCAGAGTTCTACAGTCCGACGATCTGGNNNNNNNNCGTGNNNNNNNNNNCCAACCTTCGTATGCCGTCTTCTGCTTG

tag: protein source

value: human

tag: protein


title: MOCK-dsu-3

value: mock


title: DT_AB2_5

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

data_processing:
Basecalling was performed using Illumina Casava v.1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequences.
Read quality was accessed using FASTQC.
Read counts were estimated at the transcript level using kallisto: kallisto quant -i /$input_directory/transcripts.idx -o /$output_directory/$sample_name -b 100 -t 6 --single -l 180 -s 20 $sample_name.
Assembly: mm10

source_name: distal colon

extract_protocol:
Colon samples were stored in RNAlater (Ambion) at -80˚C until further use. Colonic samples were homogenized using bead-beating system (Precellys) for total RNA purification using RNAeasy kit (Qiagen) following manufacturers recommendations. RNA purity and quantity was measured by NanoDrop spectrophotometer (ThermoFisher). All samples were screened for RNA integrity check and presented RIN values above 8 on 2100 Bioanalyzer instrument (Agilent).
Samples were submitted to Novogene for library preparation using TruSeq Stranded mRNA Library Prep Kit (poly-A selection) and sequencing using HiSeq-2500 platform (Illumina). Samples were sequenced using single-end 50bp sequencing, aiming a minimum coverage of 20M reads.

value: distal colon

value: CD19-cre x iDTR

value: diphtheria toxin


title: DT_AB2_4


title: HF2

description: scRNA-seq


title: HF1

description: scRNA-seq


title: NPAS4 ARNT2 round 3

value: mouse


title: AhR ARNT round 3


title: MOCK-dsu-2


title: ARNT2 round 3

description: ARNT2 (1-717)


title: control_AB3_5


title: Control EVs b

city: Chongqing

value: the apical papilla

value: extracellular miRNA


title: control 1

tag: strain

value: control


title: control_AB2_7


title: C6

data_processing:
After cluster amplification of denatured templated, the prepared libraries were sequenced using Illumina Novaseq6000 (Illumina Technologies., San Diego, CA, USA)
The RNA-sequencing reads were mapped to the human reference genome (hg19) using the STAR (Spliced Transcripts Alignment to a Reference). Gene expression level quantification was performed using RSEM (RNA-seq by Expectation–Maximization).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes counts per million (CPM) for each sample

growth_protocol: After removing the lower portion from nail matrix tissue, primary NMKs were harvested from nail matrix biopsy specimens. NMKs were isolated after 0.25% trypsin–EDTA treatment for 30 min and cultured in Keratinocyte Growth Media (KGM, Lonza) and maintained at 37 °C with 5% CO2. We checked no fibroblast growth under an inverted microscope. The cells which are passage three were plated in triplicate in six-well plates.

extract_protocol:
After 24h or 48 h of culture, NMK was treated with 1 ml of Trizol to isolate RNA for further bulk RNAseq experiments
Libraries preparation for 150bp paired-end sequencing was processed using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero H/M/R (Illumina Technologies., San Diego, CA, USA), following the protocol. The integrity and overall quality of the total RNA was quantified using a Nanodrop 8000 UV- Vis spectrometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and checked with a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). After cluster amplification of denatured templated, the prepared libraries were sequenced using Illumina Novaseq6000 (Illumina Technologies., San Diego, CA, USA).

treatment_protocol: Recombinant human  BMP5  were treated at 500ng/ml and 100ng/ml in KGM without rhEGF, respectively.

value: Control

value: Nail matrix


title: MOCK-dus-1

value: leaf blade

value: leaf cell


title: C5


title: SG200-WT-3

source_name: wild-type

value: wild-type

value: SG200 strains infection


title: ARNT round 3

description: ARNT (1-774)


title: C4


title: HIF2a ARNT round 3


title: SG200-WT-2


title: SG200-WT-1


title: Y2_M1

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

data_processing:
Illumina sequencing and conventional base calling.
Sequenced reads were quality-controlled by FASTQC and trimmed by Trimmomatic v.0.36 for adaptor sequence (if present).
Clean sequences were mapped to the mm10 whole genome using STAR v2.7.
The uniquely-mapped reads aligned to exons were counted with HTSeq v.0.6.1, then tested for the presence of differentially expressed genes (DEGs) by the DESeq2 R package v.1.22.2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_htseq-count.txt: Tab-delimited text files with the raw counts for each sample.

source_name: Brain

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

value: Brain

tag: age

value: 1 month

tag: genotype/variation

value: 3' Homozygous


title: C3