title: FWTMR(female control mice + methionine restricted feed) G6


title: RNA-Seq.MN_HD_2

status: Public on Dec 31 2021

type: SRA

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

country: USA

institute: National Institute of Health

library_source: transcriptomic

data_processing:
ChIP-Seq data were first processed using Trim Galore, then aligned to reference genome (mm10) using Bowtie2 with default settings. The PCR duplicates for each dataset were removed using the rmdup function of samtools. The reads from biological replicates were pooled together for further analysis.
The raw data for RNA-Seq were first processed with Trim Galore. TPM values for each gene were calculated using RSEM. To perform differential expression analysis, reads were aligned to reference genome using STAR, then read numbers for each gene were counted using the featureCount function from Subread, finally differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: BED files for ChIP-Seq peaks called by macs2. Tab-delimited text files contain TPM values for each gene calculated using RSEM.

molecule: polyA RNA

organism: Mus musculus

source_name: Induced motor neuron

growth_protocol: Mouse ESCs were grown in ES medium [DMEM (Gibco, 11965092) supplied with 15% FBS (HyClone, SH3007103), 1× HEPES (Gibco, 15630080), 1× NEAA (Gibco, 11140050), 1× Glutamax-I (Gibco, 35050061), 1× Anti-Anti (Gibco, 15240062), 0.1% 2-Mercaptoethanol (Gibco, 21985023) and 1 ng/μL LIF (Gibco, A35933)]. The MN induction procedure takes 6 days: 1) Trypsin treatment of mESCs to single cells, and seed ~5M cells to 15-cm Petri dish with 30 mL ADFNK medium [44% Advanced DMEM, 44% Neurobasal, 10% Knockout serum, 1× Glutamax-I (Gibco, 35050061), 1× Anti-Anti (Gibco, 15240062) and 0.1% 2-Mercaptoethanol (Gibco, 21985023)](day 0); 2) Culture with shaking in  37OC  with 5% CO2  for two days to get embryoid body (day 2); 3) Change ADFNK medium [1 μM RA, 1 μM SAG], further culture for 2 days to neuron progenitor cells (day 4); 4) change ADFNK medium [1 μM RA (), 1 μM SAG (), 1 μM DOX (), 5 μM DAPT (Sigma, D5942-5MG)], further culture for 2 days to get mature motor neurons (day 6).

extract_protocol:
Total RNA is isolated using RNeasy Mini Kit (Qiagen) followed by PolyA extraction.
RNA-Seq libraries are constructed using Illumina TruSeq Stranded mRNA Library Prep Kit.

tag: cell type

value: Motor neuron

tag: genotype


title: RNA-Seq.MN_EH_2


title: PC2606.SF

city: Stanford

first: Minyoung

last: Youn

state: CA

address: 269 Campus Drive, CCSR 1210

department: Pediatrics

institute: Stanford University

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence using Trimmomatic 0.38, then mapped to hg38 STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf provided from genecode
Sequences were imported into R , scaled, filter for low counts ( < 1 cpm) and TMM normalized using the edgeR package.
Genome_build: hg38
Supplementary_files_format_and_content: adult samples.xlsx - Matrix table with log2 counts per million reads for each adult sample
pediatric samples.xlsx - Matrix table with log2 counts per million reads for each pediatric sample.
CML.xlsx - Matrix table with log2 counts per million reads for each CML sample and log-fold changes (pediatric CML vs adult CML).

molecule: total RNA

organism: Homo sapiens

source_name: CD34+ cells

extract_protocol:
CD34+ bone marrow cells were isolated. RNAs were prepared using the RNeasy Micro Kit (Qiagen).
cDNA libraries were generated using KAPA-stranded mRNA-Seq kit (Roche), and then size selected.
Prepared libraries will be sequenced on the Illumina HiSeq 4000 (Illumina), with a minimum 30 million paired-end 75 bp reads per sample.

tag: developmental stage

value: pediatric

tag: disease

value: CML

value: CD34+ hematopoietic stem/progenitor cells


title: PC1151.SF


title: FWTMR(female control mice + methionine restricted feed) G5

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

country: China

institute: BGI

data_processing:
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:9 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the all transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .

source_name: hippocampus

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard BGI-500 protocols

tag: strain

tag: age

tag: treatment


title: Subject ID: B0507; Tissue: nasal

type: RNA

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

country: Spain

institute: GENVIP research group

hyb_protocol: We used the standard gene expression protocol for 12x RNA hybridization with 5ul of RNA as input, a hybridization time of 18h for all samples and mixing control and COVID-19 samples to avoid technical sample bias.

scan_protocol: SPRINT nCounter machine

data_processing: Normalization of the gene expression data was carried out for each tissue separately by selecting the optimal number and best reference candidate from the set of housekeeping (HK) genes included in the panel, as well as other endogenous genes that showed high levels of stability between samples. We excluded HK candidate genes with less than 50 raw counts in any of the samples compared from the reference selection analysis. Data normalization was performed through a combined approach using both DESeq2 and RUVSeq as described in Bhattacharya et al. (2021) (https://academic.oup.com/bib/article-abstract/22/3/bbaa163/5891144). Genes with counts below the background (mean + 2 standard deviations (SD) of the negative control spikes in the code set) were not included in the differential expression (DE) analysis. After data normalization and background thresholding, we eliminated lower expressed genes from the list.

source_name: nasal

extract_protocol: RNA was isolated using PAXgene blood miRNA extraction kit (Qiagen) following manufacturer recommendations and carrying out the on-column DNase I treatment during the extraction process. RNA from saliva and nasal epithelium specimens was isolated using 500ul of sample and the RNeasy microkit (Qiagen). We used Oragene RNA neutralizer solution (DNA Genotek) to precipitate impurities and inhibitors and slightly modified the protocol provided by the extraction kit as recommended by the Oragene tubes supplier

tag: subject id

tag: tissue

value: nasal

tag: gender

value: Female

value: COVID

value: Mild


title: RNA-Seq.MN_EH_1


title: Subject ID: B0511; Tissue: Blood

source_name: Blood

value: Blood

value: Control


title: RNA-Seq.MN_HD_1


title: RNA-Seq.ES_WT_1

source_name: ES cell

value: ES cell

value: WT


title: FWTMR(female control mice + methionine restricted feed) G3


title: RNA-Seq.ES_WT_2


title: ChIP-Seq.Mnx1_WT_2

library_source: genomic

molecule: genomic DNA

extract_protocol:
ChIP-Seq is performed following Ronnie Blecher-Gonen protocol (Nature Protocol, 2013. PMID: 23429716) with modifications. The antibodies used include: GFP (Invitrogen, A11122), H3K4me1 (Abcam, ab8895), H3K4me3 (Millipore, #04-745), H3K27ac (ActiveMotif, #39685), H3K27me3 (Abcam, ab6002), H3K9me3 (Abcam, ab8898).
ChIP-Seq libraries are constructed using SMARTer ThruPLEX DNA-Seq kit (Takara).

tag: chip antibody


title: Subject ID: B0506; Tissue: saliva

source_name: saliva

value: saliva

value: Male


title: Subject ID: B0506; Tissue: nasal


title: PC23866


title: Subject ID: B0506; Tissue: Blood


title: PC18142


title: FWTMR(female control mice + methionine restricted feed) G2


title: FWTMR(female control mice + methionine restricted feed) G10


title: PC739195.CG


title: PC736811.CG


title: FWTMR(female control mice + methionine restricted feed) G1


title: ChIP-Seq.Mnx1_WT_1


title: PC725028.CG


title: ChIP-Seq.K9me3_WT


title: Subject ID: B0466; Tissue: saliva

value: Hospitalized

value: Severe


title: Subject ID: B0478; Tissue: nasal


title: FAD(female AD mice + standard feed) F8

value: FAD(female AD mice + standard feed)


title: Subject ID: B0466; Tissue: nasal


title: AN55

value: adult

value: Normal


title: ChIP-Seq.K4me3_WT_2

value: Motor neuron


title: FWTMR(female control mice + methionine restricted feed) G11


title: Subject ID: B0440; Tissue: Blood


title: AN53

value: CD34+ hematopoietic stem/progenitor cells


title: FAD(female AD mice + standard feed) F7


title: FAD(female AD mice + standard feed) F6


title: AN52


title: FAD(female AD mice + standard feed) F5


title: AN369


title: Subject ID: B0428; Tissue: saliva


title: ChIP-Seq.K4me3_HD_1


title: ChIP-Seq.K4me3_HD_2


title: FAD(female AD mice + standard feed) F4


title: FAD(female AD mice + standard feed) F9


title: ChIP-Seq.K9me3_HD


title: ChIP-Seq.K4me1_WT_2


title: Subject ID: B0428; Tissue: Blood


title: Subject ID: B0428; Tissue: nasal

value: nasal


title: AN69


title: Subject ID: B0478; Tissue: Blood


title: FAD(female AD mice + standard feed) F3


title: FAD(female AD mice + standard feed) F2


title: ChIP-Seq.K4me1_WT_1


title: Subject ID: B0440; Tissue: saliva

value: Female


title: AN96


title: ChIP-Seq.K4me3_WT_1


title: ChIP-Seq.K4me1_HD_2


title: FAD(female AD mice + standard feed) F11


title: AN62.LZ


title: FAD(female AD mice + standard feed) F10


title: AN73.LZ


title: AN173


title: ChIP-Seq.K4me1_HD_1


title: FWT(female control mice + standard feed) E9


title: ChIP-Seq.K27me3_WT_1


title: ChIP-Seq.K27me3_HD_2


title: ChIP-Seq.K27me3_HD_1


title: FWT(female control mice + standard feed) E5


title: AC36.SF

value: CML


title: AN35.LZ


title: FWT(female control mice + standard feed) E4


title: AC64.SF


title: AC33.SF


title: ChIP-Seq.K27me3_WT_2


title: AC48.SF


title: AC10.SF


title: FAD(female AD mice + standard feed) F1


title: Subject ID: B0406; Tissue: saliva

value: COVID

value: Moderate


title: ChIP-Seq.K27ac_WT_2


title: ChIP-Seq.K27ac_WT_1


title: FWT(female control mice + standard feed) E7


title: Subject ID: B0415; Tissue: Blood

value: Blood


title: Subject ID: B0408; Tissue: saliva

value: Mild


title: Subject ID: B0408; Tissue: nasal


title: Subject ID: B0415; Tissue: nasal


title: Subject ID: B0415; Tissue: saliva


title: AC40


title: FWT(female control mice + standard feed) E3


title: FWT(female control mice + standard feed) E6


title: Subject ID: B0406; Tissue: Blood


title: Subject ID: B0403; Tissue: nasal


title: Subject ID: B0406; Tissue: nasal


title: Subject ID: B0403; Tissue: saliva


title: Subject ID: B0408; Tissue: Blood


title: Subject ID: B0399; Tissue: saliva


title: FWT(female control mice + standard feed) E2


title: FWT(female control mice + standard feed) E11


title: AC67


title: ChIP-Seq.Input_WT

value: WT


title: AC82


title: FWT(female control mice + standard feed) E10


title: AC88


title: FWT(female control mice + standard feed) E1


title: MADMR(male AD mice + methionine restricted feed) D8


title: AC11


title: Subject ID: B0399; Tissue: Blood


title: Subject ID: B0399; Tissue: nasal


title: ChIP-Seq.K27ac_HD_1


title: Subject ID: B0396; Tissue: saliva

value: saliva


title: N2

city: JINAN

first: XIANGYU

last: GUO

address: WENHUAXI ROAD 44

institute: SHANDONG UNIVERSITY

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

value: breast cancer

tag: metastasis status

value: no lymph node metastasis


title: E15.5_GE_neural progenitor cells

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
E15.5 GE
single cell RNA-Seq

data_processing:
*R1_001.fastq.gz: contain cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 101 nt RNA sequence.
*I1_001.fastq.gz: contains the 8 nt sample index.
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 1.3.1) to generate FASTQ files and aligned to mm10 genome to gene expression count
The subsequent data analysis was performed using “Seurat” package and R scripts
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output files

source_name: Ganglionic eminence

extract_protocol:
None
Cell number and viability were measured using a TC20 Automated Cell Counter (BioRad). Single-cell RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v2 User Guide (10x Genomics). Approximately 10,000 cells were loaded on a Chromium single cell Controller instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

treatment_protocol: For neural progenitor cells, heterozygous Nestin-GFP mice were bred with homozygous DCX-mRFP mice to yield GFP/RFP double positive embryos. The cortices or ganglionic eminences derived from the double positive embryos were dissociated by trituration in HBSS with 2mM of EDTA and 25 ug/ml of DNase I. Cells were washed once with HBSS and re-suspended in DMEM/F12. Fluorescence-activated cell sorting (FACS) was used to acquire neural progenitor cells (NPCs, green color).

value: Ganglionic eminence

value: neural progenitor cells (NPCs)

value: Embryonic day E15.5


title: N1


title: E18.5_GE_neural progenitor cells

description:
E18.5 GE
single cell RNA-Seq

value: Embryonic day E18.5


title: E18.5_cortex_neural progenitor cells

description:
E18.5 Cortex
single cell RNA-Seq

source_name: Cerebral cortex

value: Cerebral cortex


title: E15.5_cortex_neural progenitor cells

description:
E15.5 Cortex
single cell RNA-Seq


title: ChIP-Seq.K27ac_HD_2

value: Motor neuron


title: Subject ID: B0396; Tissue: Blood

value: Male


title: Subject ID: B0396; Tissue: nasal

value: nasal


title: MADMR(male AD mice + methionine restricted feed) D6


title: Subject ID: B0393; Tissue: saliva

value: Female


title: Subject ID: B0393; Tissue: nasal

value: COVID


title: M3

value: lymph node metastasis


title: ChIP-Seq.Input_HD


title: Dux vector with doxycycline treatment 3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Used HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data
Reads were trimmed for quality using a minimum phred value of 20 and minimum length of 20 using Fastx-Trimmer
Reads were mapped with STAR (Dobin et al, 2013) to the mouse genome downloaded from Ensembl (GRCm38).
FeatureCounts (Liao et al, 2014) was used to count reads mapped to gene bodies on the correct strand with a minimum mapping quality of 10 using Ensembl genome annotation (Mus musculus.GRCm38.85.gtf).
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression count matrix

source_name: tibialis anterior muscle

growth_protocol: C57BL/6 male mice provided by AMREP animal services, Melbourne Victoria were maintained in a 12:12 hr light:dark cycle at 22 ± 1 °C with ad libitum access to food and water.

extract_protocol:
Tibialis anterior muscle was harvested and homogenised in Trizol. RNA was isolated from Trizol homogenates using the Direct-zol™ RNA MiniPrep Kit by Zymo Research. RNA quality was assessed by MultiNA bioanalyzer.
200 ng of total RNA was subject to poly-A enrichment and library preparation using Illumina TruSeq reagents.

treatment_protocol: Intramuscular injections of AAV vectors were administered to 8 week-old Mice were placed under general anaesthesia (2 % isofluorane in molecular oxygen), then administered a subcutaneous injection of carprofen for post-operative analgesia. As a control, the tibialis anterior (TA) muscle of one limb was injected with AAV:TET and AAV:MCS (empty vector), and contralateral muscles were injected with AAV:TET and AAV:Dux vector alone, or in combination with AAV:MyoPro. Viral vector particles were diluted in 30 μl Hank’s buffered salt solution (HBSS) to a dosage of 2 × 10^8 to 5 × 10^10 vectors genomes as indicated. Animals were monitored for 7 days following injection on standard lab chow before being provided ad libitum access to standard lab chow, or lab chow containing Doxycycline (DOX, 600 mg/kg; Speciality feeds, Australia) for a further 2 or 7 days. Animals were humanely killed by cervical dislocation and tissues rapidly excised and snap-frozen.

value: tibialis anterior muscle

value: male

tag: vector

value: Dux

value: Doxycycin chow


title: Subject ID: B0393; Tissue: Blood

value: Blood

value: Mild


title: Subject ID: B0381; Tissue: saliva

value: saliva

value: Hospitalized

value: Moderate

value: Severe


title: MADMR(male AD mice + methionine restricted feed) D9


title: N3

value: breast cancer

value: no lymph node metastasis


title: s_ACs

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description:
The raw data include reads sequenced from either an Illumina HiSeq 2500 or HiSeq 4000 instrument.
s_ACs

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hybrid of both hg19 and mm10. The FASTA of the combined genome is available on the series record.  Mouse reads were discarded in downstream analysis.
Supplementary_files_format_and_content: tab-delimited file containing normalized counts for human genes.

source_name: mouse thymocytes

growth_protocol: iPSCs-derived macrophages were cultured in RPMI1640/GlutaMax medium supplemented with 10% fetal bovine serum, and 100 ng/ml human M-CSF.

extract_protocol:
RNA from cells suspended in Trizol was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated wih 75% ethonol. Sample were resuspended in RNAase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 70 000 iPSCs-derived macrophages (WT, ACK1 deficient and BRK deficient) per well in 12 well plates were washed once with PBS and incubated or not with 450 000 mouse apoptotic thymocytes in RPMI for 90 minutes. WT iPScs-derived macrophages were also pretreated for 30 minutes with AIM100 (ACK1 inhibitor; 2uM) or cpd4f (BRK inhibitor; 0.5 uM) in RPMI and then incubated or not with mouse apoptotic thymocytes. After 90 minutes incubation media was removed and macrophages were washed once with PBS. Then 1 ml trizol (15596018, Life Technology ) was added per well and cells were harvested and stored at -80C.

value: mouse thymocytes

tag: condition


title: M1


title: MADMR(male AD mice + methionine restricted feed) D4


title: MADMR(male AD mice + methionine restricted feed) D3


title: MADMR(male AD mice + methionine restricted feed) D2


title: MADMR(male AD mice + methionine restricted feed) D11


title: PC-3_shRB-Rep.3

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (GRCh38/hg38) using STAR (2.5.2b)
RseQC was used to calculate raw count, FPM, and FPKM
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
RNeasy Mini Kit (Cat No.74104, QIAGEN)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: PC-3 cells were selected by purimycin at 1ug/ml for 10 days after incubated with lentivrius carrying on shRNA

value: prostate cancer

tag: passages

tag: lentivirus

value: shRB


title: PC-3_shRB-Rep.2


title: Dux vector with doxycycline treatment 2


title: Empty vector no doxycycline 3

value: Empty vector

value: Normal chow


title: Subject ID: B0381; Tissue: Blood

value: Female

value: COVID


title: Subject ID: B0381; Tissue: nasal

value: nasal


title: MADMR(male AD mice + methionine restricted feed) D5


title: M2

value: lymph node metastasis


title: MADMR(male AD mice + methionine restricted feed) D10


title: Empty vector with doxycycline treatment 2

value: tibialis anterior muscle

value: male

value: Doxycycin chow


title: Subject ID: B0380; Tissue: saliva

value: saliva

value: Hospitalized


title: Subject ID: B0380; Tissue: nasal

value: Moderate


title: Dux vector no doxycycline 2

value: Dux


title: PC-3_NS-Rep.2

value: ns


title: PC-3_NS-Rep.3


title: MADMR(male AD mice + methionine restricted feed) D1


title: Empty vector no doxycycline 2


title: MWTMR(male control mice + methionine restricted feed) C9


title: MADMR(male AD mice + methionine restricted feed) D7


title: Dux vector no doxycycline 3


title: Subject ID: B0380; Tissue: Blood

value: Blood


title: PC-3_NS-Rep.1

value: prostate cancer


title: Subject ID: B0375; Tissue: saliva

value: Mild


title: Patient_8_pre_G207

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: Paired-end 2 x 150bp reads, Illumina HiSeq 4000

data_processing:
bcl to fastq was performed using Illumina bcl2fastq conversion software version 2.20.0.422.
Paired-end FASTQ files were used as input for Salmon version 0.9.1 (https://combine-lab.github.io/salmon/getting_started/).
The Salmon transcriptome index was prepared using the following command: "salmon index -t GRCh38_latest_rna.fna -i GRCh38_latest_rna.fna_transcripts_index -k 31"; the GRCh38_latest_rna.fna was obtained from NCBI via ftp.ncbi.nlm.nih.gov.
The following parameters were used with Salmon processing:
libType: A
numBootstraps: 100
index: GRCh38_latest_rna.fna_transcripts_index
Genome_build: GRCh38
Supplementary_files_format_and_content: *.quant.sf: Salmon output; tab-delimited text files including transcript per million (TPM) values; each sample has a separate file labeled "Sample_name.quant.sf".

source_name: glioblastoma

extract_protocol:
Covaris truXTRAC® FFPE Kit.
Illumina TruSeq Stranded total RNA kit.

value: brain tumor

tag: diagnosis

value: glioblastoma

tag: glioblastoma subtype

value: Proneural/Neural

tag: brain location

value: right frontal

tag: g207 treatment

value: pre-G207 inoculation

tag: age (years)

tag: Sex

tag: survival post g207 (days)


title: MWTMR(male control mice + methionine restricted feed) C7

tag: strain

tag: age

tag: treatment


title: Dux vector with doxycycline treatment 1

tag: tissue

tag: gender


title: Subject ID: B0375; Tissue: nasal

tag: subject id

value: nasal

value: Female

value: COVID


title: Patient_1_pre_G207

value: Mesenchymal

value: left frontal

value: male


title: Patient_5_pre_G207

value: female


title: Dux vector no doxycycline 1

value: tibialis anterior muscle

tag: vector

value: Dux

value: Normal chow


title: MWTMR(male control mice + methionine restricted feed) C6


title: Empty vector no doxycycline 1

value: Empty vector


title: Subject ID: B0375; Tissue: Blood

value: Blood

value: Mild


title: PC-3_shRB-Rep.1

tag: cell type

value: prostate cancer

value: shRB


title: MWTMR(male control mice + methionine restricted feed) C5


title: Subject ID: B0374; Tissue: nasal


title: Subject ID: B0374; Tissue: saliva

value: saliva


title: Subject ID: B0374; Tissue: Blood


title: MWTMR(male control mice + methionine restricted feed) C4


title: MWTMR(male control mice + methionine restricted feed) C3


title: HCT116_dCas9_34_2

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description: format_HCT116dCas34.10k.2.peaks.bedpe.txt

data_processing:
Library strategy: PLAC-seq
PLAC-seq data was processed with MAPS (PMID: 30986246) to normalize reads and identify long-range chromatin interactions.
MAPS aligned raw paired-end reads with BWA (version 0.7.12) to the reference genome hg38. Uniquely mapped reads were kept and split into intra-chromosomal reads and inter-chromosomal reads.
To identify intra-chromosomal chromatin interactions, each chromosome was first divided into 10 kb bins. Histone H3K4me3 ChIP-seq peaks (downloaded from ENCODE) were used as the anchor, and 10 kb bins overlapping with these ChIP-seq peaks were defined as the anchor bin.
The raw contact frequency between two 10 kb bins in the ‘XOR’ and ‘AND’ sets were then fitted into a zero-truncated Poisson model to obtain the normalized contact frequency.
Significant interactions were identified with FDR corrected p-value cutoff of 0.01. Significant interactions were further grouped together into clusters if two interactions were within 10 kb.
Genome_build: hg38
Supplementary_files_format_and_content: .bedpe format; use bedpe files to visualize chromatin interactions. Column1: bin1 chromosome, column2: bin1 start position, column3: bin1 end position, column4: bin2 location and -log10(FDR corrected P-value)

source_name: Colorectal carcinoma cell line

growth_protocol: Human chronic myeloid leukemia cell line K562 was cultured in RPMI with 10% fetal bovine serum (FBS) (Gemini). Human liver cancer cell line HepG2, lung cancer cell line A549 were cultured in DMEM/F12 media (Thermo Fisher) with 10% FBS. Human colon cancer cell line HCT116 was culture in McCoy’s 5A Modified media (Thermo Fisher) with 10% FBS.

extract_protocol:
Cells were cross-linked for 15 minutes at room temperature with 1% formaldehyde and quenched for 5 mins at room temperature with 0.2 M glycine (Thermo Fisher). The cross-linked cells were aliquot (~ 3X106 cells) and resuspended in 300 μL lysis buffer (10mM Tric-HCl pH 8.0, 10mM NaCl, 0.2% IGEPAL CA-630) and incubated on ice for 15 minutes. The suspension was then centrifuged at 2,500 xg for 5 mins and the pellet was washed by resuspending in 300 μL lysis buffer and centrifuging at 2,500 xg for 5 mins. The pellet was resuspended in 50 μL 0.5% SDS and incubated for 10 mins at 62°C. 160 μL 1.56% Triton X-100 was added to the suspension and incubated for 15 mins at 37°C.
PLAC-seq experiments were performed in biological replicates using MboI, following the protocol described by Fang, R., Yu, M., et al., Cell research 2016(PMID: 27886167).

tag: cell line

tag: genotype

value: KRAB-dCas9 clone #34

tag: chip antibody

value: H3K4me3 (Millipore, 04-745)


title: HCT116_dCas9_34_3


title: Subject ID: B0373; Tissue: saliva

value: Male

value: Hospitalized

value: Moderate


title: HCT116_dCas9_34_1


title: Empty vector with doxycycline treatment 1

value: Doxycycin chow


title: HCT116_dCas9_24_3

description: format_HCT116dCas24.10k.2.peaks.bedpe.txt

value: KRAB-dCas9 clone #24


title: MWTMR(male control mice + methionine restricted feed) C11


title: Tet-Off MLL-AF9 AML DOX treated day 4 - replicate 3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 1.24.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Tet-Off MLL-AF9 AML cells

growth_protocol: RNA sequencing analysis was performed on primary Tet-Off MLL-AF9 AML cells obtained from the spleen of leukemic animals and cultured in vitro for either 2 or 4 days in the presence of doxycycline (1μg/ml) (DOX) or left untreated (UT).

extract_protocol:
Total RNA extraction was performed using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 400 ng of total RNA using the Illumina Truseq V2 RNA-seq kit. Paired-end 50bp RNA-seq short reads were generated using HiSeq2500.

treatment_protocol: The cells were cultured in vitro in the presence or absence of doxycyline (1 μg/ml) and collected for RNA extraction at the indicated timepoints.

value: MLL-AF9 primary AML cells obtained from the spleen of terminally sick mice

tag: agent

value: DOX

tag: time point

value: 4 days

value: Female


title: Tet-Off MLL-AF9 AML DOX treated day 4 - replicate 4


title: Tet-Off MLL-AF9 AML DOX treated day 4 - replicate 2


title: MWTMR(male control mice + methionine restricted feed) C8


title: MWTMR(male control mice + methionine restricted feed) C10


title: Tet-Off MLL-AF9 AML DOX treated day 4 - replicate 1


title: Subject ID: B0372; Tissue: Blood

value: COVID


title: Subject ID: B0372; Tissue: saliva


title: Tet-Off MLL-AF9 AML untreated day 4 - replicate 4

value: Untreated


title: MWTMR(male control mice + methionine restricted feed) C1


title: HCT116_dCas9_24_2


title: HCT116_dCas9_24_1


title: Subject ID: B0369; Tissue: saliva

value: Severe


title: HCT116_WT_3

value: wild-type


title: Tet-Off MLL-AF9 AML untreated day 4 - replicate 3


title: MAD(male AD mice + standard feed) B9

value: MAD(male AD mice + standard feed)


title: Subject ID: B0369; Tissue: nasal

value: nasal


title: Tet-Off MLL-AF9 AML untreated day 4 - replicate 2


title: MAD(male AD mice + standard feed) B8


title: Subject ID: B0369; Tissue: Blood

value: Blood


title: HCT116_WT_2

value: H3K4me3 (Millipore, 04-745)


title: MAD(male AD mice + standard feed) B7


title: Tet-Off MLL-AF9 AML untreated day 4 - replicate 1


title: HCT116_WT_1


title: MAD(male AD mice + standard feed) B6


title: Tet-Off MLL-AF9 AML DOX treated day 2 - replicate 3

value: 2 days


title: A549_rep2_3

source_name: Lung carcinoma cell line


title: MAD(male AD mice + standard feed) B5


title: Tet-Off MLL-AF9 AML DOX treated day 2 - replicate 4


title: Subject ID: B0368; Tissue: saliva

value: saliva

value: Hospitalized


title: A549_rep2_2


title: Subject ID: B0368; Tissue: nasal


title: MAD(male AD mice + standard feed) B2


title: Subject ID: B0368; Tissue: Blood


title: MAD(male AD mice + standard feed) B4


title: Tet-Off MLL-AF9 AML DOX treated day 2 - replicate 1


title: Subject ID: B0361; Tissue: nasal

value: Male


title: Subject ID: B0361; Tissue: saliva


title: MAD(male AD mice + standard feed) B12


title: MAD(male AD mice + standard feed) B11


title: MAD(male AD mice + standard feed) B10


title: Tet-Off MLL-AF9 AML untreated day 2 - replicate 2


title: A549_rep1_1


title: A549_rep1_3


title: Tet-Off MLL-AF9 AML untreated day 2 - replicate 4


title: HepG2_rep2_2

source_name: Hepatocellular carcinoma cell line


title: A549_rep1_2


title: Subject ID: B0353; Tissue: saliva


title: Subject ID: B0354; Tissue: Blood

value: Mild


title: Tet-Off MLL-AF9 AML untreated day 2 - replicate 1

value: MLL-AF9 primary AML cells obtained from the spleen of terminally sick mice


title: Tet-Off MLL-AF9 AML untreated day 2 - replicate 3


title: MWT(male control mice + standard feed) A9

value: MWT(male control mice + standard feed)


title: A549_rep2_1


title: HepG2_rep1_2


title: MAD(male AD mice + standard feed) B1


title: MWT(male control mice + standard feed) A8


title: Subject ID: B0353; Tissue: nasal


title: HepG2_rep2_1


title: Subject ID: B0352; Tissue: saliva


title: Subject ID: B0361; Tissue: Blood


title: Tet-Off MLL-AF9 AML DOX treated day 2 - replicate 2

value: DOX


title: Subject ID: B0352; Tissue: nasal


title: Subject ID: B0343; Tissue: saliva

value: Female


title: 3-Day

city: Xuzhou

first: Wu

last: Dongmei

state: Jiangsu

address: 101 Shanghai Road

institute: Jiangsu Normal University

description: mixed samples from photothrombotic ischemia contralateral focal regions of 6 animals used for 3-day time point

data_processing:
Tophat(v2.1.1) used to mapping reads with default parameter.
Cufflinks(v2.2.1) used to estimate gene expression level (Fragment Per Kilobase per Million mapped reads, FPKM) with Ensembl Genes.
In all expression profile analysis, genes with average FPKM < 0.1 were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: photothrombotic ischemia focal region (caudate nucleus), 3 days

extract_protocol:
fresh freeze the brain and section the brain on cryostat with 100um thickness and punch out the ischemia focal region and the corresponding contralateral sham regions. Mix the tissue for each sample, extract total RNA by TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: photothrombotic ischemia at caudate nucleus for 10 min after 5 min 100 mg/kgrose bengal IP injection

value: male

tag: stress

value: photothrombotic ischemia focal region

value: caudate nucleus

value: adult, 8 weeks

value: 3 days


title: 10-Day

description: mixed samples from photothrombotic ischemia contralateral focal regions of 6 animals used for 10-day time point

source_name: photothrombotic ischemia focal region (caudate nucleus), 10 days

value: 10 days


title: HepG2_rep1_1

value: wild-type


title: 1-Day

description: mixed samples from photothrombotic ischemia contralateral focal regions of 6 animals used for 1-day time point

source_name: photothrombotic ischemia focal region (caudate nucleus), 1 day

value: 1 day


title: MWT(male control mice + standard feed) A7

source_name: hippocampus


title: K562_rep2_2

source_name: Chronic myelogenous leukemia cell line

value: H3K4me3 (Millipore, 04-745)


title: K562_rep2_3


title: MWT(male control mice + standard feed) A6


title: K562_rep1_3


title: MWT(male control mice + standard feed) A5


title: MWT(male control mice + standard feed) A4


title: K562_rep2_1


title: K562_rep1_2


title: K562_rep1_1


title: MWT(male control mice + standard feed) A2


title: A3_3_R1

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

country: Germany

institute: DKFZ

data_processing:
Raw reads data are mapped to mm9 transcriptome with Bowtie1.0.0. Default paramters are used
TPM were generated by RSEM (1.2.15) with default parameters
Cells were filtered basing on the number of genes detected, cells have more than 4500 genes are discarded for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: geneTPM.txt includes TPM values for each Sample

source_name: neural stem cells

extract_protocol:
Briefly, single cells were lysed in 5 μl lysis buffer and 1 μl of 3’ SMART CDS primer (24 μM) was added and incubated at 72°C for 3 min.
SMARTer Ultra Low Input RNA- High Volume kit was used to prepare amplified cDNA. We added 50 μl of nuclease-free H2O to the amplified cDNA to make a total volume of 60 μl. The cDNA was sheared in a microtube (6x 16mm) with 10% duty cycle, 5% intensity and 200 burst cycle for 5 min in the frequency sweeping mode with Covaris S2 machine. We got the average of 180 bp cDNA fragments after sonication. The illumina sequencing libraries were prepared using NEBNext Ultra DNA library prep kit.

value: subventricular zone

tag: sample type

value: Bulk (500 cells)

value: neural stem cells (NSCs)

tag: Stage

value: Bulk, no stage properties


title: A3_3_R3


title: A3_3_R2


title: Subject ID: B0343; Tissue: nasal

source_name: nasal

value: nasal

value: COVID

value: Hospitalized

value: Severe


title: Subject ID: B0343; Tissue: Blood

source_name: Blood

value: Blood

value: Female


title: Subject ID: B0338; Tissue: Blood

value: Moderate


title: Subject ID: B0342; Tissue: nasal


title: MWT(male control mice + standard feed) A11

value: MWT(male control mice + standard feed)


title: WT_input

data_processing:
Fastq file was aligned using bowtie2 (Version 2.3.4.3).
SAMtools (Version 1.9) and MarkDuplicates (Picard) were used to filter (MAPQ < 30) and clean data post alignment.
The reads were then converted to reads per kilobase per million in 200 bp bins using deepTools2 (Version 3.5.0)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig format; normalized signal

growth_protocol: Human colon cancer cell line HCT116 was culture in McCoy’s 5A Modified media (Thermo Fisher) with 10% FBS.

extract_protocol:
The cells from ∼80% confluent 10 cm dishes were crosslinked by adding fixation solution (1% formaldehyde, 0.1M NaCl, 1 mM EDTA, 50 mM HEPES⋅KOH pH 7.6) for 10 min at room temperature. Crosslinking was quenched with 125 mM Glycine for 5 min. We used 1.0 million cells for each ChIP sample
Shearing of chromatin was performed using truChIP Chromatin Shearing Reagent Kit (Covaris) according to the manufacturer's instructions. Covaris M220 was used for sonication with following parameters: 410 seconds duration at 20.0% duty factor, 75.0 peak power, 200 cycles per burst at 5-9°C temperature range. For immunoprecipitation, we used 50 μL Protein A or Protein G Magnetic beads (NEB) and washed twice with PBS with 5 mg/ml BSA and 4 μg of antibody coupled in 500 μl PBS with 5 mg/ml BSA overnight at 4°C. The magnetic beads were washed twice with ChIP buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), once with ChIP buffer including 500 mM NaCl, four times with RIPA buffer (10 mM Tris-HCl pH8.0, 0.25M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na⋅Deoxycholate), and once with TE buffer (pH 8.0). Chromatin was eluted twice from washed beads by adding elution buffer (20 mM Tris-HCl pH8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS) and incubating for 15 min at 65°C. The crosslinking was reversed at 65°C for 6 hr and RNase A (Sigma) was added for 1 hr at 37°C followed by proteinase K (Ambion) treatment overnight at 50°C. ChIP-enriched DNA was purified using Phenol/Chloroform/Isoamyl alcohol extractions in phase-lock tubes. ChIP samples were end-repaired, A-tailed, and adaptor-ligated using QIAseq ultralow input library kit (Qiagen) according to the manufacturer's instructions. Size selection using AMpure beads (Beckman Coulter) was performed to get 300-500 bp DNA and PCR amplification (8-10 cycles) were performed. Library quality and quantity were measured using TapeStation (Agilent) and Qubit (Thermo Fisher).


title: Subject ID: B0342; Tissue: Blood


title: A3_2_R3


title: 4-Hour

description: mixed samples from photothrombotic ischemia contralateral focal regions of 6 animals used for 4 hours time point

source_name: photothrombotic ischemia focal region (caudate nucleus), 4hr

value: male

value: photothrombotic ischemia focal region

value: caudate nucleus

value: adult, 8 weeks

value: 4 hours


title: MWT(male control mice + standard feed) A10


title: A3_2_R2

value: subventricular zone


title: Sham

description: mixed samples from photothrombotic ischemia contralateral sham regions of 24 animals used for all time points

source_name: photothrombotic ischemia contralateral sham region (caudate nucleus)

value: sham

value: Sham


title: WT_H3K27ac

value: H3K27ac (Diagenode, C15200184)

value: wild-type


title: Subject ID: B0335; Tissue: nasal

value: nasal

value: Male

value: COVID


title: Subject ID: B0335; Tissue: saliva

source_name: saliva

value: saliva

value: Hospitalized

value: Severe


title: MWT(male control mice + standard feed) A3

value: MWT(male control mice + standard feed)


title: dCas9_clone34_H3K27ac

value: KRAB-dCas9 clone #34


title: A3_2_R1

value: Bulk (500 cells)

value: neural stem cells (NSCs)

value: Bulk, no stage properties


title: Subject ID: B0335; Tissue: Blood

value: Blood


title: MWT(male control mice + standard feed) A1


title: Empty vector with doxycycline treatment 3

source_name: tibialis anterior muscle

value: tibialis anterior muscle

value: male

value: Empty vector

value: Doxycycin chow


title: MWT8

data_processing:
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:9 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the all transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .
Genome_build: GCF_000001635.26_GRCm38
Supplementary_files_format_and_content: FPKM

value: hippocampus

value: WildType

tag: Sex


title: dCas9_clone24_H3K27ac

value: H3K27ac (Diagenode, C15200184)

value: KRAB-dCas9 clone #24


title: dCas9_clone6_H3K27ac

value: KRAB-dCas9 clone #6


title: Subject ID: B0334; Tissue: saliva

value: saliva

value: Female

value: COVID

value: Hospitalized

value: Moderate


title: A3_1_R2

value: subventricular zone

value: Bulk (500 cells)

value: neural stem cells (NSCs)


title: Subject ID: B0334; Tissue: Blood

value: Blood


title: Subject ID: B0333; Tissue: saliva


title: A2_3_R1

value: Bulk, no stage properties


title: A3_1_R1


title: MWT4

tag: strain

value: male


title: MWT6

tag: age


title: input_H3K9me3_451Lu_vector_NT_rep2

first: Steven

last: Offer

address: 200 First Street Southwest

data_processing:
Realtime base calling was performed on the instrument
Bowtie2 was used to align ChIP-seq reads to the genome
Dulicate reads were filtered using Picard
MACS2 was used for peak calling in H3K27ac and ATAC data
SICER was used for peakcalling in H3K9me3 data
STAR v2.5.3 was usedfor RNAseq alignment and annotation
deepTools was used to transform mapped reads to BigWig files for visualization
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (.bw) files were generated using deepTools
Supplementary_files_format_and_content: .bed files contain peak data for ATAC and ChIP

source_name: Melanoma cell line

extract_protocol: Chromatin was crosslinked, sheared by sonication, and treated with RNase and Proteinase K. Libraries were prepared using NEBNext Ultra II and sequenced. Input control for associated H3K9me3 ChIP-seq.

value: vector; NT control

tag: antibody


title: Subject ID: B0331; Tissue: nasal

tag: tissue

value: nasal

value: Severe


title: H3K9me3_451Lu_vector_NT_rep2

extract_protocol: Chromatin was crosslinked, sheared by sonication, incubated with H3K9me3 antibody, eluted, and crosslinking reversed. DNA was treated with RNase and Proteinase K. Libraries were prepared using NEBNext Ultra II and sequenced.


title: MWT2

value: hippocampus

value: WildType

tag: treatment


title: input_H3K9me3_451Lu_vector_NT_rep1


title: A1_2_R1


title: Subject ID: B0331; Tissue: saliva

tag: subject id

tag: gender


title: A2_2_R1

tag: cell type


title: A3_1_R3


title: MWT10


title: H3K9me3_451Lu_vector_NT_rep1

tag: cell line


title: MWT9


title: MWT1


title: A1_1_R1


title: Subject ID: B0331; Tissue: Blood


title: input_H3K9me3_451Lu_shp150_AP1_rep2

tag: genotype

value: over-expressing AP-1 components c-JUN and c-FOS; shRNA against p150


title: A3_1_S9

value: Single cell

value: filtered out


title: Subject ID: B0329; Tissue: Blood

value: Male

value: COVID


title: MWF8


title: MWF7


title: Subject ID: B0329; Tissue: saliva

value: saliva

value: Hospitalized

value: Moderate


title: A3_1_S8

value: subventricular zone

value: neural stem cells (NSCs)


title: A3_1_S7


title: Subject ID: B0328; Tissue: Blood

value: Blood

value: Female


title: A3_1_S13


title: H3K9me3_451Lu_shp150_AP1_rep1


title: input_H3K9me3_451Lu_resistant_rep2

tag: parental or resistant

value: Vemurafenib-resistant


title: MWF5

value: male


title: MWF3


title: H3K9me3_451Lu_resistant_rep2


title: A3_1_S12


title: Subject ID: B0319; Tissue: saliva

value: Severe


title: input_H3K9me3_451Lu_parental_rep2

value: parental


title: MWF10

value: hippocampus

value: WildType


title: Subject ID: B0319; Tissue: Blood


title: A3_1_S11

value: Single cell


title: H3K9me3_451Lu_parental_rep2


title: MWF1


title: A3_1_S10

value: filtered out


title: H3K9me3_451Lu_shp150_AP1_rep2

value: over-expressing AP-1 components c-JUN and c-FOS; shRNA against p150


title: Subject ID: B0318; Tissue: nasal

value: nasal

value: Male

value: COVID


title: input_H3K9me3_451Lu_resistant_rep1


title: Subject ID: B0318; Tissue: Blood

value: Hospitalized


title: Subject ID: B0317; Tissue: saliva

value: saliva


title: MAF9


title: A1_1_S18

value: subventricular zone

value: neural stem cells (NSCs)


title: Subject ID: B0317; Tissue: nasal


title: MWF2


title: MAF7


title: MAF5


title: A1_1_S16


title: H3K9me3_451Lu_parental_rep1


title: Subject ID: B0318; Tissue: saliva


title: H3K27ac_WM983B_resistant_rep2

extract_protocol: Chromatin was crosslinked, sheared by sonication, incubated with H3K27ac antibody, eluted, and crosslinking reversed. DNA was treated with RNase and Proteinase K. Libraries were prepared using NEBNext Ultra II and sequenced.


title: A1_1_S15


title: MAF3

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard BGI-500 protocols


title: MAF2


title: Subject ID: B0317; Tissue: Blood

extract_protocol: RNA was isolated using PAXgene blood miRNA extraction kit (Qiagen) following manufacturer recommendations and carrying out the on-column DNase I treatment during the extraction process. RNA from saliva and nasal epithelium specimens was isolated using 500ul of sample and the RNeasy microkit (Qiagen). We used Oragene RNA neutralizer solution (DNA Genotek) to precipitate impurities and inhibitors and slightly modified the protocol provided by the extraction kit as recommended by the Oragene tubes supplier

value: Blood


title: Subject ID: B0315; Tissue: saliva


title: Subject ID: B0315; Tissue: nasal


title: A1_1_S14


title: A1_1_S12


title: A1_2_S10


title: Subject ID: B0315; Tissue: Blood


title: H3K27ac_WM983B_resistant_rep1

value: Vemurafenib-resistant


title: MAF10

value: male


title: A1_1_S11


title: MAF1


title: H3K27ac_WM983B_parental_rep1


title: H3K9me3_451Lu_resistant_rep1


title: input_H3K9me3_451Lu_parental_rep1


title: A3_3_S24

value: aNSC


title: MAD8


title: Subject ID: B0314; Tissue: saliva

value: Severe

value: Death


title: H3K27ac_451Lu_resistant_rep2


title: MAD7

value: hippocampus


title: A3_3_S21

value: Single cell

value: qNSC


title: Subject ID: B0314; Tissue: Blood


title: H3K27ac_WM983B_parental_rep2

value: parental


title: Subject ID: B0250; Tissue: saliva

value: Female

value: Moderate


title: Subject ID: B0314; Tissue: nasal

value: nasal

value: Male

value: COVID


title: MAD4


title: A3_3_S18

value: subventricular zone


title: MAD3


title: H3K27ac_451Lu_parental_rep1


title: ATAC_451Lu_AP1_rep2

extract_protocol: Nuclear DNA underwent tagmentation by Tn5 transposase. Tagged fragments were purified, amplified, and sequenced.

value: over-expressing AP-1 components c-JUN and c-FOS


title: Subject ID: B0250; Tissue: nasal

value: Hospitalized


title: MAD2


title: Subject ID: B0250; Tissue: Blood

value: Blood


title: A3_3_S15

value: neural stem cells (NSCs)


title: MAD10

value: male


title: ATAC_451Lu_AP1_rep1


title: ATAC_451Lu_vector_rep2

value: vector


title: Subject ID: B0248; Tissue: saliva

value: saliva


title: Subject ID: B0248; Tissue: nasal


title: A3_3_S14


title: A3_3_S22

value: aNSC


title: H3K27ac_451Lu_parental_rep2


title: ATAC_451Lu_vector_rep1


title: MAD6

value: hippocampus


title: Subject ID: B0248; Tissue: Blood


title: A3_3_S13

value: Single cell


title: H3K27ac_451Lu_resistant_rep1

value: Vemurafenib-resistant


title: FWT9

value: WildType

value: female


title: FWT7


title: ATAC_451Lu_shp150_rep2

value: shRNA against p150


title: A3_3_S17


title: A3_3_S11


title: FWT6


title: A3_3_S16


title: FWT5


title: A3_3_S12


title: ATAC_451Lu_shp150_rep1


title: FWT4


title: ATAC_451Lu_NT_rep1

value: NT control


title: FWT2


title: ATAC_451Lu_vector_NT_rep2

value: vector; NT control


title: A3_3_S7

value: subventricular zone

value: qNSC


title: FWT10


title: A3_3_S6


title: FWT1


title: ATAC_451Lu_shp150_AP1_rep2

value: over-expressing AP-1 components c-JUN and c-FOS; shRNA against p150


title: ATAC_451Lu_vector_NT_rep1


title: FWF9


title: A3_3_S4


title: FWF7


title: A3_3_S3


title: ATAC_WM983B_resistant_rep2


title: A3_3_S2


title: ATAC_451Lu_shp150_AP1_rep1


title: FWF6


title: ATAC_WM983B_parental_rep2

value: parental


title: A3_3_S1

value: neural stem cells (NSCs)


title: FWF4


title: ATAC_451Lu_NT_rep2


title: A3_3_S9


title: FWF3


title: A3_2_S23


title: A3_3_S8


title: FWF10


title: A3_2_S22


title: ATAC_451Lu_Resistant_Rep2


title: ATAC_451Lu_Parental_Rep2


title: A3_2_S21


title: FAF7


title: ATAC_451Lu_Resistant_Rep1


title: A3_2_S20


title: FAF6


title: ATAC_451Lu_Parental_Rep1


title: A3_2_S19


title: FAF5


title: RNA-seq_NEG004

city: Jinan

last: Wang

state: China

address: No.2,  Jianguo xiaojing road, Jinan City, Shandong Province, PR China

institute: Jinan Maternal and Child Health Care Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: placenta

extract_protocol:
The placenta was 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.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

value: placenta

tag: gestational age

tag: patient diagnosis

value: healthy control


title: A3_2_S16


title: A3_2_S18


title: A3_2_S24


title: FAD9


title: ATAC_WM983B_resistant_rep1


title: FAF1


title: A3_2_S15


title: RNA-seq_NEG003


title: RNA-seq_NEG002


title: ATAC_WM983B_parental_rep1


title: A3_2_S14


title: FAD8


title: FAF9


title: Bacillus subtilis BJ3-2 37℃

city: Guiyang

first: Yongjun

state: Guizhou

address: JiaXiu South Road

department: College of Life Sciences

institute: Guizhou University

data_processing:
Illumina Hiseq software used for Base-calling.
Perform sequencing-related quality evaluation for the original sequencing data of each sample, as follows: (1) A/T/G/C base content distribution statistics; (2) base quality distribution statistics; (3) base error rate distribution statistics.
Use SeqPrep and Sickle software to filter the original sequencing data to obtain high-quality sequencing data (clean data)
Use short sequence alignment software (Bowtie2) to compare the high-quality sequences (clean reads) obtained after quality control with the designated reference genome.
Overall quality assessment of the transcriptome,as follows: (1)Ribosomal RNA contamination rate assessment; (2)Sequencing saturation analysis; (3)duplicate reads analysis; (4)Gene coverage analysis
Use RSEM software to analyze gene expression
Genome_build: mm9
Supplementary_files_format_and_content: text files include FPKM and count values for each sample

organism: Bacillus subtilis

source_name: Bacillus subtilis

extract_protocol:
Using TRIzol® Reagent to extract total RNA from tissue samples, Nanodrop2000 detects the concentration and purity of the extracted RNA, agarose gel electrophoresis to detect RNA integrity, and Agilent 2100 to determine the RIN value. A single library construction requires a total amount of RNA of 5ug, concentration ≥200ng/μL, and an OD260/280 between 1.8 and 2.2.
The sequencing experiment uses the Illumina TruseqTM RNA sample prep Kit for library construction

value: Prokaryotic cell

tag: growth temperature


title: A3_2_S13

tag: sample type

value: aNSC


title: Bacillus subtilis BJ3-2 45℃


title: RNA-seq_GDM004

value: gestational diabetes mellitus


title: FAD7

value: hippocampus


title: RNA-seq_NEG005


title: RNA-seq_GDM003


title: FAF3


title: A3_2_S9

value: Single cell

tag: Stage


title: FAD5

tag: Sex


title: non-viviparous species N. colorata as L, Leaf L4 rep2 [L4-2]

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference  N. colorata genome using hisat2(v2.1.0) with parameters -p 8 --fr --dta-cufflinks
FPKM value of each gene was calculated using cufflinks(v2.2.1) with parameters --no-update-check -u -p 8 --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count(version 0.7.2) with parameters -i gene_id -f bam -s reverse -r name.
DEGs were identified using the Deseq library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Genome_build: Nymphaea_colorata_Nym_GWHAAYW00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Nymphaea colorata

growth_protocol: The plants of two Nymphaea species N. micrantha (X) and N. colorata (L) (Figure 1A and 1B) were grown in a planting container of 100 cm diameter and 60 cm depth, with 30 cm soil thickness at Water Lily Resource Garden of the Floriculture Institute of Guangxi Academy of Agricultural Sciences, Guangxi, China during the growth season of 2019. Six disease free plants with robust growth for each genotype were selected for the transcriptome study

extract_protocol:
The total RNA was extracted by CTAB method from leaf tissues of each sample using the three biological repeats.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

treatment_protocol: The harvested leaves were immediately frozen in liquid nitrogen and stored at -80 °C.

value: non-viviparous species

value: wild type

tag: developmental stage

value: Maturity stage

value: the leaves are fully unfolded with obvious viviparous traces/mark in the center of X-species while absent in L-species

value: leaf


title: A3_2_S7

value: subventricular zone

tag: age


title: FAD4

tag: strain

value: female


title: non-viviparous species N. colorata as L, Leaf L3 rep2 [L3-2]

value: Development stage

value: the leaves are half rolled and the with tip is in contact with water surface

tag: tissue


title: RNA-seq_GDM001


title: FAD3

tag: treatment


title: meRIP-seq_NEG005_IP

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter,trimmed adaptor bases by cutadapt) were aligned to genome sequences from Ensembl using HISAT2 software (v2.1.0).
Aligned reads were used for peak calling by exomePeak, statistically significant MeRIP enriched regions (peaks) were also identified for each compare by exomePeak.
The MeRIP enriched regions (peaks)were annotated by the overlapped gene using the newest Ensembl database.
Then the statistic of peak in each transcript region was done.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The read Numbers at each position of chromosomes in the comparison results were calculated, and the results were saved as UCSCbedgraph.gz format after being standardized（RPM）

extract_protocol:
Total RNA samples are qualified by agarose gel electrophoresis and quantified using Nanodrop
mRNA was isolated and then fragmented to 100-nucleotide-long fragments. m6A methylated mRNAs were enriched with anti-N6-methyadenosine(m6A) antibody. We use commercial kit for RNA-seq library preparation of m6A mRNA and input samples.
Completed libraries were qualified and then sequenced on Hiseq 4000 platform.

tag: rip antibody


title: non-viviparous species N. colorata as L, Leaf L3 rep1 [L3-1]


title: non-viviparous species N. colorata as L, Leaf L4 rep1 [L4-1]


title: RNA-seq_GDM002


title: O9

description:
V300026139_L04_530
V300026139_L04_531

data_processing:
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:9 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the 31 transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: FPKM


title: meRIP-seq_NEG005_input

value: none (input)


title: FAD10


title: A3_2_S3

value: neural stem cells (NSCs)


title: non-viviparous species N. colorata as L, Leaf L2 rep2 [L2-2]

value: the leaves are submerged and completely rolled leaves with 4-6 cm length


title: meRIP-seq_NEG004_IP

value: placenta

value: healthy control


title: A3_2_S2

value: aNSC


title: non-viviparous species N. colorata as L, Leaf L2 rep1 [L2-1]


title: A3_2_S4


title: non-viviparous species N. colorata as L, Leaf L1 rep2 [L1-2]

value: the leaves are submerged and completely rolled with 1-2 cm length


title: O8

description:
V300026139_L04_527
V300026139_L04_529

value: hippocampus


title: O7

description:
V300026139_L04_525
V300026139_L04_526


title: A3_2_S1

value: Single cell

value: qNSC


title: meRIP-seq_NEG003_IP


title: non-viviparous species N. colorata as L, Leaf L1 rep1 [L1-1]

value: non-viviparous species

value: wild type


title: O6

description:
V300026139_L03_523
V300026139_L03_524


title: meRIP-seq_NEG003_input


title: A3_1_S24


title: A3_2_S5


title: O4

description:
V300026139_L03_521
V300026139_L03_522


title: A3_1_S23


title: meRIP-seq_NEG002_IP


title: A3_1_S22


title: Ferret lung tissues - young adult - control - 3

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

country: South Korea

institute: GENOME INSIGHT

data_processing:
Raw reads were assembled and low-quality reads were filtered using Cutadapt (version 2.8).
Filtered reads were aligned on a reference genome downloaded from Ensembl (MusPutFur1.0, Accession number: GCF_000215625.1) using STAR (version 2.7.1a).
Genome_build: MusPutFur1.0, Accession number: GCF_000215625.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mustela putorius furo

source_name: Lung tissues

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer‟s instructions.
Extracted RNAs were processed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer‟s instructions.

treatment_protocol: Ferrets were infected through the intranasal route with the PBS or NMC-nCoV02 strain (GISAID accession number: EPI_ISL_1069194) at a dose of 105.8 TCID50 per ferret

value: Lung tissues

tag: age group

value: young adult (1 ≤ Age ≤ 2 years)

value: PBS

tag: time

value: uninfected


title: meRIP-seq_NEG004_input


title: A3_1_S21

value: subventricular zone

tag: cell type


title: meRIP-seq_NEG002_input

value: none (input)


title: A3_1_S20

value: neural stem cells (NSCs)


title: meRIP-seq_GDM004_IP

value: gestational diabetes mellitus


title: O2

address: Beishan road

description:
V300026139_L03_517
V300026139_L03_518


title: O3

description:
V300026139_L03_519
V300026139_L03_520


title: A3_1_S19


title: Ferret lung tissues - juvenile - 5dpi - 3

value: juvenile (Age ≤ 6 months)


title: M8

description:
V300026139_L04_551
V300026139_L04_552


title: Ferret lung tissues - juvenile - 5dpi - 2


title: meRIP-seq_GDM003_IP

value: placenta


title: meRIP-seq_GDM004_input


title: Ferret lung tissues - young adult - control - 1


title: O1

description:
V300026139_L03_515
V300026139_L03_516


title: Ferret lung tissues - juvenile - 5dpi - 1


title: A3_1_S18

value: aNSC


title: M7

description:
V300026139_L04_548
V300026139_L04_550


title: meRIP-seq_GDM003_input


title: Ferret lung tissues - juvenile - 2dpi - 3


title: A3_1_S17


title: M6

description:
V300026139_L04_545
V300026139_L04_546


title: meRIP-seq_GDM002_IP


title: Ferret lung tissues - juvenile - 2dpi - 2


title: A3_1_S16


title: Ferret lung tissues - young adult - control - 2


title: M5

description:
V300026139_L04_543
V300026139_L04_544


title: meRIP-seq_GDM002_input


title: Ferret lung tissues - juvenile - 2dpi - 1


title: A3_1_S15


title: Ferret lung tissues - juvenile - control - 3


title: A3_1_S14


title: M3

description:
V300026139_L04_539
V300026139_L04_540


title: M4

description:
V300026139_L04_541
V300026139_L04_542


title: meRIP-seq_GDM001_IP


title: meRIP-seq_GDM001_input


title: Ferret lung tissues - juvenile - control - 1


title: Ferret lung tissues - juvenile - control - 2


title: A3_1_S2


title: A2_3_S16


title: Ferret lung tissues - aged - 5dpi - 3

value: aged (3 years ≤ Age)


title: huvec_3

city: Hong Kong

first: Baicheng

last: Yi

address: 34 Hospital Road, Sai Ying Pun, Hong Kong

department: Faculty of Dentistry

institute: The University of Hong Kong

data_processing:
Illumina Casava1.8 software was used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie. Then all transcriptomes from samples were merged to reconstruct a comprehensive transcriptome. After the final transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts by calculating FPKM.
Genome_build: Homo_sapiens Ensembl release-96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample of SCAP, SCAP-ECs and HUVECs

source_name: huvec

growth_protocol: SCAP were cultured and expanded in α-MEM supplemented with 10% FBS, 100 g/L streptomycin and 100000 U/L penicillin. When reaching 80% confluence, the cells were trypsinized using 0.25% trypsin, harvested and serially passaged. HUVECs were cultured in endothelial cell medium (ECM) at 37°C with 5% CO2. SCAP and HUVECs from 3rd to 6th passage were utilized for experiments.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SCAP (3×10e5) were seeded on 0.1% gelatin-coated 6-well plates in α-MEM and incubated at 37°C in a humidified atmosphere with 5% CO2. At 40-50% cell confluence, the culture medium was changed to EGM-2 plus 50 ng/mL rhVEGF165, 20 ng/ml BMP-4 the chemical cocktails for a 4-day induction, and then BMP-4 was replaced by 100 μM 8-Br-3,5-cAMP in the next 4 days. The medium was changed every 2 days.

value: human umbilical vein

value: human umbilical vein endothelial cells


title: M2

city: Shenzhen

first: Jin

last: Xin

institute: BGI

description:
V300026139_L04_532
V300026139_L04_538

value: hippocampus


title: M15

description:
V300026139_L04_553
V300026139_L04_554


title: F8

description:
V300026139_L03_513
V300026139_L03_514


title: huvec_2


title: Ferret lung tissues - aged - 5dpi - 2


title: huvec_1


title: F7

description:
V300026139_L03_511
V300026139_L03_512


title: scap-ec_3

source_name: scap-ec

value: dental papilla

value: small molecules induced endothelial cells of stem cells from apical papilla


title: A2_3_S13

value: Single cell

value: qNSC


title: F6

description:
V300026139_L03_509
V300026139_L03_510


title: Ferret lung tissues - aged - 5dpi - 1

value: Lung tissues


title: scap-ec_2


title: A2_3_S11


title: Ferret lung tissues - aged - 2dpi - 3


title: A2_3_S9


title: F5

description:
V300026139_L03_507
V300026139_L03_508


title: scap-ec_1


title: Ferret lung tissues - aged - 2dpi - 2


title: F4

description:
V300026139_L03_505
V300026139_L03_506


title: A2_3_S8


title: A2_3_S7


title: scap_3

source_name: scap

value: stem cells from apical papilla


title: scap_2


title: F2

description:
V300026139_L01_545
V300026139_L01_546


title: F1

description:
V300026139_L03_503
V300026139_L03_504


title: Ferret lung tissues - aged - control - 3

value: PBS

value: uninfected


title: Ferret lung tissues - aged - control - 2


title: A2_3_S5

value: subventricular zone

value: neural stem cells (NSCs)


title: Ferret lung tissues - aged - control - 1


title: E8

description:
V300026139_L02_594
V300026139_L02_595


title: A2_3_S6


title: E9

description:
V300026139_L03_501
V300026139_L03_502


title: E7

description:
V300026139_L02_590
V300026139_L02_591


title: Ferret lung tissues - young adult - 5dpi - 3

value: young adult (1 ≤ Age ≤ 2 years)


title: Ferret lung tissues - young adult - 5dpi - 2


title: CBF_Pt4_3'READS

city: La Jolla

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Drive #0815

institute: UC San Diego Moores Cancer Center

description:
CBF04
processed data file: clusters.using.all.reads.primarysamples.csv

data_processing:
Library strategy: 3'READS
3'READS: The libraries were sequenced from 3' to 5' end with respect to the RNA sequence.
3'READS: Nucleotides corresponding to the 5′ adapter was first removed from raw 3′READS+ reads using cutadapt (version 2.6).
3'READS: The 5′ random nucleotides and 5′T's in the reads were trimmed before the reads were mapped to the human (hg19) genome using STAR (version 2.7.3a) with the following parameters: "--alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMmultNmax 1 --alignIntronMin 20 --alignIntronMax 1000000". Only reads with a mapping quality score (MAPQ) ≥10 were used for further analysis.
3'READS: The trimmed 5′T's of each read were then compared to the genomic region downstream from the last aligned position of the read to identify 5′T's that cannot be aligned to the genome. Reads with ≥2 unaligned 5′T's after this process were called polyA site supporting (PASS) reads. Cleavage sites within 24 nt of each other (due to microheterogeneity) were clustered into pAs as previously described (Hoque et al. Nature Methods, 2013).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The csv file, 'clusters.using.all.reads.primarysamples.csv', contains reads per poly(A) peak for 3'READS analysis.

growth_protocol: Neither the healthy HSPCs nor the patient blasts were cultured. RNA was extracted immediately after thawing (healthy HSPCs) or immediately following CD34-enrichment (patient samples).

extract_protocol:
RNA was extracted using Trizol reagent per the manufacturer's instructions.
The protocol for 3'READS library preparation is described in detail in (Hoque et al. Nature Methods, 2013).

treatment_protocol: Patient samples were blast-enriched using the Miltenyi CD34+ magnetic bead enrichment kit.

tag: diagnosis

value: AML

tag: mutations

tag: cell surface marker

value: Blasts


title: CBF_Pt3_3'READS

description:
CBF03
processed data file: clusters.using.all.reads.primarysamples.csv


title: A2_3_S15

value: aNSC


title: Ferret lung tissues - aged - 2dpi - 1

value: aged (3 years ≤ Age)


title: A2_3_S4


title: CBF_Pt2_3'READS

description:
CBF02
processed data file: clusters.using.all.reads.primarysamples.csv

value: t(8;21), cKIT mut


title: A2_3_S3


title: E6

description:
V300026139_L02_588
V300026139_L02_589

value: hippocampus


title: CBF_Pt1_3'READS

description:
CBF01
processed data file: clusters.using.all.reads.primarysamples.csv


title: A2_2_S16


title: Ferret lung tissues - young adult - 5dpi - 1


title: E5

description:
V300026139_L02_583
V300026139_L02_587


title: AML_Pt4_3'READS

description:
AML04
processed data file: clusters.using.all.reads.primarysamples.csv


title: Ferret lung tissues - young adult - 2dpi - 3


title: A2_2_S14


title: scap_1

value: dental papilla


title: E3

description:
V300026139_L02_581
V300026139_L02_582


title: AML_Pt3_3'READS

description:
AML03
processed data file: clusters.using.all.reads.primarysamples.csv

value: del(5q), gain(11q)


title: A2_2_S13

value: Single cell


title: E2

description:
V300026139_L02_579
V300026139_L02_580


title: Ferret lung tissues - young adult - 2dpi - 2


title: Ferret lung tissues - young adult - 2dpi - 1


title: A2_3_S1

value: qNSC


title: A2_2_S11


title: AML_Pt2_3'READS

description:
AML02
processed data file: clusters.using.all.reads.primarysamples.csv

value: trisomy 13, trisomy 19, i(17q)


title: E1

description:
V300026139_L02_577
V300026139_L02_578


title: A2_2_S9


title: B8

description:
V300026139_L02_573
V300026139_L02_574


title: xpo-1_D5_Rep4

city: Providence

first: Louis

last: Lapierre

address: 185 Meeting St.

institute: Brown

data_processing:
 Illumina HiSeq, 2x150bp configuration, single index, per lane
Sequences were trimmed using Trimmomatic and mapped to the Caenorhabditis elegans reference genome available on ENSEMBL  using the STAR aligner
Unique gene hit counts were calculated by using feature Counts from the Subread package. Only unique reads that fell within exon regions were counted.
Genome_build: WBcel235 (Ensembl Release 67)
Supplementary_files_format_and_content: Normalized counts are TMP

organism: Caenorhabditis elegans

source_name: N2 (WT) Day5 on xpo-1 RNAi

growth_protocol: Wildtype C. elegans (N2 Bristol) were synchronized using hypochlorite and eggs were seeded on nematode growth media plates with E. coli OP50 and developed at 20°C

extract_protocol:
Total RNA was extracted from approximately 3000 Day 5 worms after exposure to RNAi or control empty vector using Trizol Reagent (Invitrogen) followed by purification using Qiagen RNeasy kit according to the manufacturers' protocols
Standard Illumina protocols were used for RNA library preparations

treatment_protocol: At Day 1 of adulthood, the N2 worms were transfererred onto nematode growth media plates with E. coli HT115 expressing dsRNA to xpo-1 or empty vector (L4440) for 96h at 20°C with daily transfers using M9 buffer

value: N2 (Bristol)

value: E. coli HT115 expressing dsRNA to xpo-1


title: xpo-1_D5_Rep2


title: AML_Pt1_3'READS

description:
AML01
processed data file: clusters.using.all.reads.primarysamples.csv

value: inv(16), trisomy 2, trisomy 8


title: B6

description:
V300026139_L02_569
V300026139_L02_570


title: A2_2_S8

value: subventricular zone


title: CBF_Pt4_RNA-seq

description:
CBF04
processed data file: normalized_counts_mapped_Norm_T821.txt

data_processing:
RNA-seq: Raw RNA-sequencing reads were aligned and mapped using HISAT2.
RNA-seq: FeatureCounts on the usegalaxy public supercomputing platform was used for quantification.
RNA-seq: Reads were normalized using the DESeq2 software package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The two text files (normalized_counts_mapped*.txt) contain normalized reads per gene as is conventional for RNA-sequencing analysis.

extract_protocol:
RNA was extracted using Trizol reagent per the manufacturer's instructions.
For RNA-sequencing library preparation, the Illumina TruSeq Stranded mRNA kit was used following the manufacturer's instructions.


title: A2_2_S5

extract_protocol:
Briefly, single cells were lysed in 5 μl lysis buffer and 1 μl of 3’ SMART CDS primer (24 μM) was added and incubated at 72°C for 3 min.
SMARTer Ultra Low Input RNA- High Volume kit was used to prepare amplified cDNA. We added 50 μl of nuclease-free H2O to the amplified cDNA to make a total volume of 60 μl. The cDNA was sheared in a microtube (6x 16mm) with 10% duty cycle, 5% intensity and 200 burst cycle for 5 min in the frequency sweeping mode with Covaris S2 machine. We got the average of 180 bp cDNA fragments after sonication. The illumina sequencing libraries were prepared using NEBNext Ultra DNA library prep kit.

value: neural stem cells (NSCs)


title: B5

description:
V300026139_L02_567
V300026139_L02_568


title: CBF_Pt3_RNA-seq

description:
CBF03
processed data file: normalized_counts_mapped_Norm_T821.txt


title: xpo-1_D5_Rep1


title: A2_2_S4


title: N2_D5_Rep3

source_name: N2 (WT) Day5 on L4440

value: E. coli HT115 expressing L4440


title: B4

description:
V300026139_L01_565
V300026139_L01_566


title: A2_2_S10


title: N2_D5_Rep2


title: CBF_Pt2_RNA-seq

description:
CBF02
processed data file: normalized_counts_mapped_Norm_T821.txt

value: AML


title: HSPC_7_3'READS

description:
HSPC_2
processed data file: clusters.using.all.reads.primarysamples.csv

value: Healthy

value: Hematopoietic stem and progenitor cells (HSPCs)


title: B10

description:
V300026139_L02_575
V300026139_L02_576


title: xpo-1_D5_Rep3


title: HSPC_6_3'READS

description:
HSPC_1
processed data file: clusters.using.all.reads.primarysamples.csv


title: A2_2_S2

value: aNSC


title: B7

description:
V300026139_L02_571
V300026139_L02_572


title: B2

description:
V300026139_L01_560
V300026139_L01_563


title: N2_D5_Rep1


title: A2_2_S1


title: A9

description:
V300026139_L04_555
V300026139_L04_556


title: AML_Pt4_RNA-seq

description:
AML04
processed data file: normalized_counts_mapped_Norm_AML.txt

value: Blasts


title: A2_1_S16


title: xpo-1_Polysome RNA_1

extract_protocol:
Total, monosome, and polysome mRNA were extracted from nematodes fed xpo-1 RNAi or control bacteria that were subjected to solubilization and sucrose gradient centrifugation fractionation to separate ribosomal fractions. RNA extraction was carried out using Trizol Reagent (Invitrogen) as per manufacturer's protocol.
Standard Illumina protocols were used for RNA library preparations

tag: rna fraction

value: Polysome RNA


title: AML_Pt3_RNA-seq

description:
AML03
processed data file: normalized_counts_mapped_Norm_AML.txt


title: AML_Pt2_RNA-seq

description:
AML02
processed data file: normalized_counts_mapped_Norm_AML.txt


title: A8

description:
V300026139_L01_555
V300026139_L01_556

value: hippocampus


title: Control_Polysome RNA_2


title: A2_1_S15


title: CBF_Pt1_RNA-seq

description:
CBF01
processed data file: normalized_counts_mapped_Norm_T821.txt


title: Control_Polysome RNA_1


title: AML_Pt1_RNA-seq

description:
AML01
processed data file: normalized_counts_mapped_Norm_AML.txt


title: A2_1_S14


title: A4

description:
V300026139_L01_551
V300026139_L01_552


title: xpo-1_Polysome RNA_2


title: HSPC_5_RNA-seq

description:
Norm05
processed data file: normalized_counts_mapped_Norm_AML.txt
processed data file: normalized_counts_mapped_Norm_T821.txt


title: xpo-1_Monosome RNA_1

value: Monosome RNA


title: A2

description:
V300026139_L01_548
V300026139_L01_550


title: A2_1_S13

value: Single cell


title: HSPC_4_RNA_seq

description:
Norm04
processed data file: normalized_counts_mapped_Norm_AML.txt
processed data file: normalized_counts_mapped_Norm_T821.txt


title: A2_1_S12


title: A10

description:
V300026139_L01_557
V300026139_L01_559


title: HSPC_3_RNA-seq

description:
Norm03
processed data file: normalized_counts_mapped_Norm_AML.txt
processed data file: normalized_counts_mapped_Norm_T821.txt


title: A2_2_S3

value: qNSC


title: A2_1_S10


title: Control_Monosome RNA_1


title: Total iBAT_KO_3

city: Minneapolis

first: Hai-Bin

last: Ruan

department: Integrative Biology and Physiology

institute: University of Minnesota

data_processing:
Sequencing Reads Filtering using SOAPnuke: v1.5.2
Genome Mapping using HISAT2: v2.0.4
Mapping clean reads to reference using Bowtie2: v2.2.5
DEG detection using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: interscapular brown adipose tissue

extract_protocol:
RNA extracted from total iBAT
RNA-Seq Quantification Library (Normal Library)

value: interscapular brown adipose tissue

tag: genotype

value: Myf5-Fstl1 KO

value: Newborn


title: HSPC_2_RNA_seq

description:
Norm02
processed data file: normalized_counts_mapped_Norm_AML.txt
processed data file: normalized_counts_mapped_Norm_T821.txt


title: Total iBAT_KO_1


title: A2_1_S9

source_name: neural stem cells

tag: sample type


title: xpo-1_Total RNA_2

value: N2 (Bristol)

value: E. coli HT115 expressing dsRNA to xpo-1

value: Total mRNA


title: xpo-1_Total RNA_1


title: A6

description:
V300026139_L01_553
V300026139_L01_554


title: HSPC_1_RNA-seq

description:
Norm01
processed data file: normalized_counts_mapped_Norm_AML.txt
processed data file: normalized_counts_mapped_Norm_T821.txt


title: shFIP1L1-2_rep3_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP2_3

data_processing:
RNA-sequencing
First, raw RNA-sequencing reads without adaptors or those containing greater than 10% undetermined bases were removed.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using the DESeq2 software.
3'READS
The libraries were sequenced from 3' to 5' end with respect to the RNA sequence.
Nucleotides corresponding to the 5′ adapter was first removed from raw 3′READS+ reads using cutadapt (version 2.6).
The 5′ random nucleotides and 5′T's in the reads were trimmed before the reads were mapped to the human (hg19) genome using STAR (version 2.7.3a) with the following parameters: "--alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMmultNmax 1 --alignIntronMin 20 --alignIntronMax 1000000". Only reads with a mapping quality score (MAPQ) ≥10 were used for further analysis.
The trimmed 5′T's of each read were then compared to the genomic region downstream from the last aligned position of the read to identify 5′T's that cannot be aligned to the genome. Reads with ≥2 unaligned 5′T's after this process were called polyA site supporting (PASS) reads. Cleavage sites within 24 nt of each other (due to microheterogeneity) were clustered into pAs as previously described (Hoque et al. Nature Methods, 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Both files contain read counts in each analyzed sample. The text file, 'readcount.txt', contains reads per gene as is conventional for RNA-sequencing analysis. The csv file, 'clusters.using.all.reads.csv', contains reads per poly(A) peak for 3'READS analysis.

source_name: Kasumi-1 AML Cell Line

growth_protocol: Kasumi-1 cells were maintained in RPMI supplemented with 10% FBS.

extract_protocol:
RNA was extracted using Trizol reagent per the manufacturer's instructions.
RNA-seq: For RNA-sequencing library preparation, the NEBNext® UltraTM RNA Library Prep Kit was used following the manufacturer's instructions.
3'READS: The protocol for 3'READS library preparation is described in detail in (Hoque et al. Nature Methods, 2016).

treatment_protocol: Kasumi-1 cells were transduced with lentivirus containing control shRNAs or shRNAs targeting FIP1L1. Transduced cells were selected with puromycin.

tag: cell line

value: Kasumi-1 AML Cell Line

tag: cell culture conditions

value: RPMI + 10percent FBS

tag: lentiviral shrna for transduction

value: shRNA targeting FIP1L1 #2


title: Control_Total RNA_1

value: E. coli HT115 expressing L4440


title: A2_1_S6

value: subventricular zone

tag: age

value: neural stem cells (NSCs)

tag: Stage

value: aNSC


title: Total iBAT_WT_3

tag: tissue

tag: developmental stage


title: shFIP1L1-2_rep2_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP2_2


title: Total iBAT_WT_2


title: Control_Monosome RNA_2

tag: strain

tag: treatment


title: shFIP1L1-2_rep1_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP2_1


title: sBAT SVF_12Weeks_3

description: Rabbit.SVF.GeneExpression.FPKM.xls

data_processing:
Sequencing Reads Filtering using SOAPnuke: v1.5.2
Genome Mapping using HISAT2: v2.0.4
Mapping clean reads to reference using Bowtie2: v2.2.5
Gene expression cluster analysis using Cluster v3.0
DEG detection using DEseq2
Genome build: OryCun2.0
FPKM

organism: Oryctolagus cuniculus

source_name: subscapular brown adipose tissue

extract_protocol:
RNA extracted from total or the SVF fraction of BAT
RNA-Seq Quantification Library (Normal Library)

value: subscapular brown adipose tissue

value: New Zealand White

value: 12 weeks

tag: fraction

value: stromal vascular fraction


title: Total iBAT_WT_1

value: interscapular brown adipose tissue


title: shFIP1L1-1_rep4_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP1_4

value: shRNA targeting FIP1L1 #1


title: A2_1_S11

data_processing:
Raw reads data are mapped to mm9 transcriptome with Bowtie1.0.0. Default paramters are used
TPM were generated by RSEM (1.2.15) with default parameters
Cells were filtered basing on the number of genes detected, cells have more than 4500 genes are discarded for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: geneTPM.txt includes TPM values for each Sample

value: Single cell

tag: cell type

value: qNSC


title: A2_1_S5


title: Total iBAT_KO_2

value: Myf5-Fstl1 KO

value: Newborn


title: sBAT SVF_12Weeks_2

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: A2_1_S4


title: A2_1_S3


title: control3

city: Beijing

first: Miao

last: Yu

address: 22 Zhongguancun South Avenue

institute: Peking University

data_processing:
SOAPnuke was employed to filtrate low-quality reads and obtain high-quality clean reads.
The alignment was acquired through comparing the clean reads to the reference gene sequence using Bowtie 2 software.
The gene expression levels were counted and normalized to fragments per kilobase of exon model per million mapped reads (FPKM) by RESM software.
Genome_build: mm10
Supplementary_files_format_and_content: text files include RPKM values for all Samples

source_name: first mandibular molar

extract_protocol:
First mandibular molars at PN4 were separated and sent to the Beijing Genomic Institution (BGI, Shenzhen, China, www.genomics.org.cn) for mRNA enrichment
cDNA library construction and sequencing was performed using the BGISEQ-500 platform.

value: first mandibular molar

value: post natal day 4


title: sBAT SVF_12Weeks_1

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: shFIP1L1-1_rep2_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP1_2

value: Kasumi-1 AML Cell Line

value: RPMI + 10percent FBS


title: control2


title: shFIP1L1-1_rep1_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP1_1


title: control1


title: Control_Total RNA_2

value: N2 (Bristol)

value: E. coli HT115 expressing L4440

value: Total mRNA


title: sBAT SVF_6Weeks_2

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: subscapular brown adipose tissue

value: 6 weeks


title: shFIP1L1-1_rep3_3'READS

description:
3'READS
clusters.using.all.reads.csv
shFIP1_3


title: A2_1_S1

value: subventricular zone

value: neural stem cells (NSCs)

value: aNSC


title: A2_1_S7


title: shControl_rep3_3'READS

description:
3'READS
clusters.using.all.reads.csv
shCtrl_3

value: shControl


title: sBAT SVF_6Weeks_1

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: New Zealand White

value: stromal vascular fraction


title: shControl_rep2_3'READS

description:
3'READS
clusters.using.all.reads.csv
shCtrl_2


title: case2

value: K14-Cre; Wnt10aflox/flox


title: A1_3_S14

value: Single cell

value: qNSC


title: case1

value: first mandibular molar

value: post natal day 4


title: sBAT SVF_3Weeks_3

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: 3 weeks


title: sBAT SVF_3Weeks_2

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: sBAT SVF_3Weeks_1

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: A1_3_S13


title: sBAT SVF_6Weeks_3

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: CT_HIV_CD4_2

city: Guangzhou

first: Emmanuel

last: Dzakah

address: Lujing Lu, Yuexiu District

institute: Dermatology Hospital

description:
processed data file:
CT_HIV_CD4.xls.xlsx

data_processing:
Zebra call 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 bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200, and RSEM v1.2.12  with parameters --forward-prob 0.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from   Langmead and Salzberg, Nat Methods, 2012. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.  Li and Dewey， BMC Bioinformatics, 2011.Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: read count values for each Sample

source_name: C. trachomatis and HIV-1-coinfected CD4 T cells

growth_protocol: PBMCs were cultured in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% heat-inactivated fetal bovine serum (Sigma-Aldrich, USA) and  10 µg/ml gentamycin at 37℃ with 5% CO2. Cells were stimulated with C. trachomatis lysate for 3 days followed by HIV-1 infection for additional 3 days.

extract_protocol:
Cells 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 protocols for BGISEQ-500

treatment_protocol: PBMCs were stimulated with or without elementary bodies of C. trachomatis serovar E for 3 days followed by HIV-1 infection (50ng p24) for additional 3 days. CD4+ T cells were isolated using the EasySep human CD4+ T cells isolation kit (Stemcell Technologies, Canada) according to the manufacturer’s instruction. Total RNA was extracted using the TriZol method.

tag: tissue source

value: blood

value: PBMCs

value: C. trachomatis stimulation and HIV-1 coinfection

tag: cell subtype

value: CD4+ T cells


title: shFIP1L1-2_rep4_RNA-seq

description:
readcount.txt
FIP2_4

value: Kasumi-1 AML Cell Line

value: RPMI + 10percent FBS

value: shRNA targeting FIP1L1 #2


title: A2_1_S2

value: subventricular zone

value: neural stem cells (NSCs)

value: aNSC


title: shControl_rep1_3'READS

description:
3'READS
clusters.using.all.reads.csv
shCtrl_1

value: shControl


title: A1_3_S12


title: CT_HIV_CD4_1


title: A1_3_S11


title: HIV_CD4_2

description:
processed data file:
HIV_CD4.xls.xlsx

source_name: HIV-1-infected CD4 T cells

value: HIV-1 infection


title: case3

value: K14-Cre; Wnt10aflox/flox


title: shFIP1L1-2_rep3_RNA-seq

description:
readcount.txt
FIP2_3


title: A1_3_S10

value: Single cell

value: qNSC


title: HIV_CD4_1

description:
processed data file:
HIV_CD4.xls.xlsx


title: sBAT SVF_Day1_2

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: subscapular brown adipose tissue

value: New Zealand White

value: 1 day

value: stromal vascular fraction


title: sBAT SVF_Day1_1

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: A1_3_S16


title: shFIP1L1-2_rep2_RNA-seq

description:
readcount.txt
FIP2_2


title: NC_CD4_2

description:
processed data file:
NC_CD4.xls

source_name: CD4 T cells, NC represents negative control

value: blood

value: PBMCs

value: none; untreated


title: iBAT SVF_12Weeks_3

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: interscapular brown adipose tissue

value: 12 weeks


title: A1_3_S9

value: subventricular zone


title: shFIP1L1-1_rep4_RNA-seq

description:
readcount.txt
FIP1_4

value: Kasumi-1 AML Cell Line

value: RPMI + 10percent FBS

value: shRNA targeting FIP1L1 #1


title: NC_CD4_1

description:
processed data file:
NC_CD4.xls

value: CD4+ T cells


title: iBAT SVF_12Weeks_2

description: Rabbit.SVF.GeneExpression.FPKM.xls