title: DS Degradome-Seq

city: Hohhot

first: Rui

last: Shi

address: No.306, Zhaowuda Road, Saihan District, Hohhot

institute: Inner Mongolia Agricultural University

description: Degradome sequencing

data_processing:
Library strategy: Degradome-Seq
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2，3，or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Supplementary_files_format_and_content: excel,expression profiles

organism: Medicago ruthenica

source_name: Leaves

growth_protocol: Medicago ruthenica seeds were obtained from the Institute of Grassland Research, Chinese Academy of Agricultural Sciences at the Inner Mongolia Autonomous Region, China. This cultivar grows well in Inner Mongolia, with higher drought and cold resistance. The sanded Medicago ruthenica seeds were sterilized in concentrated sulfuric acid for 10 min, and then washed thoroughly with sterile water. After incubating for three days at 4 °C in dark conditions, the seeds were placed on soaked filter paper in Petri dishes, and incubated in an artificial climate chamber (temperature, 25 ± 2°C; photoperiod, 16 h light/8 h dark cycle; relative humidity, 50%). Two days later, the germinated seeds were transferred to pots (13 cm in diameter and 10 cm deep) with vermiculite and quartz sand. There were eight plants in each pot.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: Four-week-old seedlings were randomly divided into three groups: the control group (CK), the drought stress treatment group (DS), and the re-watering group (RW). The drought treatment period lasted for 15 days. During the experiment, CK plants were watered every three days, maintaining a relative soil moisture content of more than 80%, while DS and RW plants were subjected to water deprivation for 15 days, resulting in a relative soil moisture content of 20% on the 15th day. The RW plants were rehydrated to full soil saturation on the 15th day. To avoid any interference, no nutrients were added. Other growth conditions were maintained. Each treatment group had three biological replicates. Leaf samples of CK and DS were collected on the 15th day, and leaves of RW were collected 2 days after rewatering. Samples were immediately frozen in liquid nitrogen, and stored at -80 °C for later use

value: Leaves

value: Four-week-old seedlings

value: drought stress


title: nTreg_Cas9_donor4

status: Public on Aug 03 2021

type: genomic

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulfite-converted genomic DNA was amplified, fragmented, and hybridized to Illumina Infinium MethylationEPIC BeadChips per the standard Illumina protocol.

scan_protocol: BeadChips were imaged using iScan System (Illumina).

data_processing: Raw red and green intensity data (IDAT) were imported into the R statistical environment (v4.0.2) with RStudio (v1.3.1093), converted into methylated and unmethylated signals, normalized using noob and functional normalization by preprocessFunnorm in minfi (v1.34.0) and by BMIQ in wateRmelon (v1.32.0), and corrected for batch effects (BeadChip ID and position) using ComBat in sva (v3.36.0). Probes with a detection p-value > 0.01 or a bead count < 3 in at least one sample were discarded. Probes previously characterized to have low-quality genomic mapping, cross-reactive or polymorphic sequences, or type I probes targeting a common SNP that could cause a colour channel switch were discarded (https://zwdzwd.github.io/InfiniumAnnotation). Because the cohort contained a mix of males and females, probes targeting X/Y chromosomes were discarded.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood flow-sorted naive Treg

label_protocol: Standard Illumina protocol

growth_protocol: Cells were cultured at 37°C, 5% CO2 in X-VIVO 15 (Lonza) with 5% (v/v) human serum (WISENT), 1% (v/v) penicillin-streptomycin (Gibco), 2 mM GlutaMAX (Gibco), and 15.97 mg/L phenol red (Sigma-Aldrich). Media and IL-2 were replenished every 2-3 days.

extract_protocol: Genomic DNA was isolated with an AllPrep DNA/RNA Mini Kit (Qiagen) and bisulfite-converted with an EZ DNA Methylation Kit (Zymo Research) per the manufacturer's protocols.

treatment_protocol: Naive Tregs were flow-sorted (CD4+CD25hiCD127loCD45RA+) and preactivated with CD3/CD28/CD2 tetrameric antibody complexes (STEMCELL Technologies) for 5 days. Cells were CRISPR-edited by electroporation (Neon Transfection System; Invitrogen) with Cas9 or a FOXP3-targeting ribonucleoprotein, transduced with AAV6-HDR encoding sfGFP, and expanded 1:1 with 75Gy-irradiated artificial antigen-presenting cells expressing CD32, CD58, CD80 + OKT3 (0.1 μg/ml) + IL-2 (1000 IU/ml) for 7 days. Edited cells were sorted as sfGFP+ and expanded with artificial antigen-presenting cells as above for an additional 7 days. Cells were rested overnight with reduced IL-2 (100 IU/ml). In parallel, flow-sorted conventional T cells were preactivated and expanded as above except with 100U/ml IL-2, and without electroporation or CRISPR editing.

tag: experiment

tag: donor

tag: Sex

value: F

tag: age

tag: cell type

value: Naive Treg

tag: gene modification

tag: total days of expansion

tag: methylationepic beadchip id

tag: methylationepic beadchip position

tag: methylationepic technical replicate


title: Ileum Ifnrl1-/- Saline treated rep4

type: RNA

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Sample name: DS32_9
Gene expression data from ileum

hyb_protocol: 1.5µg of sample hybridized using standard illumina Protocol (55ºC High Stringency wash 100%EtOHFix Illumina BlockBuffer Block Cy3 Streptavidin Staining)

scan_protocol: Scanner : Illumina iScan. DataAcquisition software:Illumina iScan Control Software-V3. Intensity .idat files for use in downstream analysis software Genome Studio

data_processing:
The data were normalized using 75th percentile normalization in GeneSpring 11.5
Background subtracted, normalised and log2 transformed for normalised values and non-normalised values  have only had  background subtraction

molecule: total RNA

organism: Mus musculus

source_name: Ileum from Ifnrl1-/-

label_protocol: Ambion Illumina Total Prep 96 RNA Amplification Kit

extract_protocol: RNA for transcriptome analysis was isolated using the RiboPure™ Kit (Invitrogen) according to the manufacturer’s instructions

treatment_protocol: Saline control or IL-22 treated animals were sacrified 4 hours post treatment and RNA extracted from ileum

tag: genotype

tag: tissue

value: ileum

tag: treatment

value: Saline


title: 5Y_1

type: SRA

city: Lanzhou

first: Xingdong

last: Wang

address: The west lake street

country: China

institute: CAAS

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software.
HISAT2 2.0.4 software was used to compare the reference genome of valid data after preprocessing.
The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff peak calling software with the corresponding input sample serving as control.
MeTDiff was run with options (FRAGMENT_LENGTH-200, PEAK_CUTOFF_PVALUE =0.01, PEAK_CUTOFF_FDR =0.05) for peak detection.
Called peaks were annotated by intersection with gene architecture using ChlPseeker
Genome_build: LU_Bosgru_v3.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Bos grunniens

source_name: Yak testis

growth_protocol: The testis tissues of 6 healthy yaks were collected at the same location and divided into two groups: 3 of them were 1.5 years old (before sexual maturity: M), and the other 3 were 5 years old (after sexual maturity: Y).

extract_protocol:
The total RNA was isolated and purified using the TRIzol reagent . Bioanalyzer 2100 (Agilent, CA, USA) and NanoDrop 2000 (Thermo Scientific) with RIN number > 7.0 were used to evaluate the total RNA quality and quantity.
poly (A) mRNA fractions are broken using divalent cations at high temperatures (RNA solution at 94°C for exactly 5 minutes using a thermocycler). Then, the fragmentation of broken RNA were incubated with m6A-Dynabeads (Anti-m6A, Synaptic Systems, Cat. No 202003) in an m6A-binding buffer (50 mM Tris-HCl pH7.4, 150 mM NaCl2, 1%NP-40, 2 mM EDTA), Allow the fragmented RNA to bind to the m6A-Dynabeads. Then washing of m6A-Dynabeads, Elution of m6A-positive RNA. Extraction and Cleanup of the RIP, Collecting m6A “enriched RNA”. We have generally utilized 100 ng of RNA (100 ng of input and 100 ng of post m6A-IP positive fraction) for library construction utilizing Illumina TrueSeq Stranded mRNA. Afterwards, we implemented the paired-end sequencing on an Illumina HiSeq X10 system, using a suggested protocol from the manufacturer.
MeRIP-seq

treatment_protocol: The testicular tissue is immediately stored in liquid nitrogen for RNA isolation. Testicular samples of group M were obtained by castration; testicular samples of group Y were collected from slaughtered yaks within 1 hour.

tag: developmental stage

value: before sexual maturity testis

value: testis

tag: condition

value: IP


title: X129S1SvlmJ_2m_male_HC_high

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Raw sequencing read alignment and gene count summarization were performed using the bcbio-nextgen pipeline (v.19.03, https://github.com/bcbio/bcbio-nextgen). Quality encoding of sequencing reads was converted to Sanger format using seqkt (https://github.com/lh3/seqtk).
Sequencing reads were aligned to the Mus musculus genome (mm10) using HISAT2 (v.2.1.0). Sequence alignment map files were converted to binary alignment map files and indexed, and alignment statistics were determined using samtools (v.1.9).
Read count summarization at the gene level was performed using the featureCounts method of the Subread package (v.1.4.4) using the mm10 genome transcriptome annotation (v. 2018-10-10_92)
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: comma-separated value file, combining the output of featureCounts of all samples. The first column contains the Ensembl gene id, the second column contains the gene symbol, and the remaining columns contain the raw counts per sample. The strain, sex, and brain region (HC=hippocampal; CTX=cortex) are contained within column names.

source_name: sorted brain endothelial cells (CD45-, CD11b-, CD31+)

extract_protocol:
FACS sorting of endothelial cells using CD45, CD11b negative, CD31 positive endothelial cells (ARIA III, BD) with subsequent RNA isolation (Qiagen AllPrep Kit)
rRNA depletion & SMARTerStranded total RNA Pico Input Kit (Clontech Laboratories).

value: male

value: hippocampal endothelial cells

tag: strain


title: Ileum Ifnrl1-/- Saline treated rep2

description:
Sample name: DS32_7
Gene expression data from ileum


title: F-PRT treated, biological rep 4, B

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

data_processing:
Quality check and pre-processing of raw sequencing reads were conducted using FastQC and Cutadapt respectively
Alignment of pre-processed sequencing reads to the GRCm38 reference genome was performed using the STAR aligner
Quantification of expression at the gene level was conducted using RSEM
Differential expression analysis and pathway enrichment analysis were conducted using EBSeq and hypeR package repsectively.
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM quantification results at the gene level

molecule: polyA RNA

source_name: murine bone tissue

extract_protocol:
total RNA was extracted from mouse skin and bone tissues; polyA selection was conducted prior to sequencing
Illumina sequencing libraries were prepared then sequenced on a HiSeq 4000 platform (2 x 150bp)

value: bone

tag: gender

value: female

value: 10 weeks

value: F-PRT


title: F-PRT treated, biological rep 3, B


title: X129S1SvlmJ_2m_male_CTX_high

value: cortical endothelial cells


title: PDAC_FFPE_01

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Raw reads were assessed for quality using FastqQC and adapter sequences were identified and removed using Trimmomatic.
Remaining reads were aligned against the human genome (hg38) using STAR software with two-round alignment mode.
mRNAs and lncRNAs were annotated in GencodeV29 and quantified using featureCounts software.
Genome_build: hg38
Supplementary_files_format_and_content: The gene expression profiles were normalized by TPM value for each samples.

source_name: PDAC

extract_protocol:
The RNAstorm™ Kit (biotium, USA) was used to extracted and isolated total RNA fraction from FFPE Tissue Samples.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian Kit.

tag: disease

value: pancreatic ductal adenocarcinoma


title: CK Degradome-Seq

description: Degradome sequencing

value: Leaves

value: Four-week-old seedlings

value: Control


title: RW Degradome-Seq

description: Degradome sequencing

value: re-watering after drought stress


title: RW_2 miRNA-seq

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel, miRNA expression

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: RW_3 miRNA-seq


title: Col-0  cfm6-1  rep 3

city: Taipei

first: Wan-Hsing

last: Cheng

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Obtained raw sequences initially went through quality control and were trimmed. RNA-seq data were analyzed using the Galaxy, and normalized read counts were transformed into normalized RPKM values.
First step in the trim process is to convert the quality score (Q) to error probability. Next, for every base a new value is calculated: 0.05−Error probability. This value will be negative for low quality bases, where the error probability is high. For every base, we calculate the running sum of this value. If the sum drops below zero, it is set to zero. The part of the sequence to be retained is between the first positive value of the running sum and the highest value of the running sum. Everything before and after this region is trimmed off. In addition, if the read length is shorter than 35bp, the read will be discarded.
Genome_build: TAIR10
Supplementary_files_format_and_content: "expression.csv.gz" contains RPKM values for genes, "expression_feature.csv.gz" contains metadata for genes, "mapping_stats.csv.gz" contains the number and percentages of reads mapped for each sample

organism: Arabidopsis thaliana

growth_protocol: The plants were grown on a half-strength MS medium containing 1% sucrose at 22°C under long-day conditions (16-h-light/8-h-dark cycle).

extract_protocol:
Total RNA was isolated from 2-wk-old seedling grown on MS medium using RNeasy Plant Mini Kit (Qiagen), followed by TURBOTM DNase (Thermo Fisher) treatment. The quality and quantity of the RNA were assessed by NanoDrop and 2% agarose gel electrophoresis. Three biological replicates were carried out for each genotype, for a total of 6 samples.
RNA libraries were prepared for sequencing using standard Illumina protocols; Libraries were multiplexed and sequenced on Illumina HiSeqTM 2500 to generate 100bp single end reads.

value: whole seedlings

tag: Stage

value: post germination day 14

tag: background ecotype


title: X129S1SvlmJ_2m_male_HC_low

tag: Sex


title: Ileum Ifnrl1-/- IL-22 treated rep4

description:
Sample name: DS32_4
Gene expression data from ileum

value: ileum


title: Col-0  cfm6-1  rep 2


title: Ileum Ifnrl1-/- IL-22 treated rep5

description:
Sample name: DS32_5
Gene expression data from ileum


title: Col-0  cfm6-1  rep 1


title: RW_1 miRNA-seq

tag: age


title: 5Y_2

value: before sexual maturity testis

value: testis


title: F-PRT treated, biological rep 2, B


title: DS_3 miRNA-seq

value: drought stress


title: X129S1SvlmJ_2m_female_HC_high

tag: cell type

value: hippocampal endothelial cells


title: F-PRT treated, biological rep 1, B

value: bone


title: Ileum Ifnrl1-/- Saline treated rep1

description:
Sample name: DS32_6
Gene expression data from ileum

value: Saline


title: X129S1SvlmJ_2m_female_CTX_high_2

value: female


title: Canine OS primary sample 1

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre, University of Toronto

description: canine OS matched sample1

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours. After hybridization, slides were washed sequential

scan_protocol: Agilent G2565C DNA Scanner

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: Canine OS primary tumor

label_protocol: 750ng of test DNA and control DNA were double-digested and labeled by random priming (Agilent Technologies) for 2 hours using Cy5-dUTP for the test DNA and Cy3-dUTP (Agilent Technologies) for the control DNA. Labeled DNAs were incubated at 65°C for 10 minutes and then purified.

growth_protocol: Canine OS specimens were obtained from University of Guelph veterinarian clinics.

extract_protocol: Genomic DNA were extracted using phenol chloroform and treated with RNaseA (Invitrogen) for 1 hour at 37°C

tag: breed

value: Rottweiler

value: 7 yrs

value: MC

source_name: normal bone tissue


title: FM_6_1

city: College Station

first: James

last: Taylor

state: Texas

address: 2132 TAMU

department: Plant Pathology and Microbiology

country: USA

institute: Texas A&M University

data_processing:
Resulting reads were aligned to the genome with HISAT2.
The read counts were determined with Stringtie.
Differential expression analysis was performed with EdgeR.
Genome_build: Trichoderma_virens.ASM17099v1.39
Supplementary_files_format_and_content: csv file containing TMM normalized read counts from Stringtie.

organism: Trichoderma virens

source_name: Trichoderma virens tissue

extract_protocol:
Harvested tissue was frozen and ground in liquid nitrogen and extracted with a Trizol/chloroform extraction.
Illumina TruSeq RNA Library Preparation Kit v2

value: Fungus with maize


title: Col-0  WT  rep 3

value: wild type


title: X129S1SvlmJ_2m_female_CTX_high

value: cortical endothelial cells


title: FM_6_2


title: X129S1SvlmJ_2m_female_CTX_low_3


title: CK_2 miRNA-seq

value: Four-week-old seedlings

value: Leaves

value: control


title: Ribo-seq-HBEC-SARS2-96hpi-rep4

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
Library strategy: Ribo-seq
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots. Read counts per read are shown in the processed files
Supplementary_files_format_and_content: *hpi.txt: counts files for reads mapping to host cell genome/transcriptome
Supplementary_files_format_and_content: *repaired.txt: mpileup files of reads that map to the viral genomes

source_name: Primary human bronchial epithelial cells

growth_protocol: Vero E6 cells were grown in DMEM-10%FBS media. Isolation and growth of primary human bronchial epithelial cells is explained elsewhere. Primary CD4+ T-cells were isolated from PBMCs of deidentified blood donors using negative selection kit from StemCell Technologies and grown in RPMI media supplemented with 10%FBS, IL-2 and activated with CD3/CD28 conjugated Dynabeads.

extract_protocol:
Cytosolic extracts were either subjected to ribo-seq or RNA-seq as in published protocols
Infected cells were lysed and two aliquots were processed in parallel for ribo-seq and RNA-seq. For RNA-seq, total RNA was isolated using ZymoClean RNA-Clean and Concentrator kit and subjected to Illumina stranded mRNA prep. Ribo-seq libraries were prepared in house following published protocols. Both libraries were sequenced using Illumina NextSeq following the manufacturer's protocols.

treatment_protocol: Cells were infected with SARS-CoV-2 at an MOI of 0.1 pfu/cell (low MOI) and 2 pfu/cell (high MOI) for Vero E6 cells, or MOI of 0.5 pfu/cell (low) and 1 pfu/cell (high) for primary human bronchial epithelial cells. Primary activated CD4+ T-cells were infected with HIV-1 at an MOI of 2

value: Cycloheximide

tag: agent

tag: time point


title: Ribo-seq-HBEC-SARS2-96hpi-rep3


title: Ileum Ifnrl1-/- Saline treated rep5

description:
Sample name: DS32_10
Gene expression data from ileum

value: ileum


title: DS_2 miRNA-seq


title: CK_1 miRNA-seq


title: X129S1SvlmJ_2m_female_CTX_high_3


title: Col-0  WT  rep 2

value: whole seedlings

value: post germination day 14


title: X129S1SvlmJ_2m_female_HC_high_3

value: hippocampal endothelial cells


title: 18M_2

value: after sexual maturity testis

value: testis

value: IP


title: Ribo-seq-HBEC-SARS2-96hpi-rep2


title: FM_36_3


title: Ileum Ifnrl1-/- IL-22 treated rep1

description:
Sample name: DS32_1
Gene expression data from ileum


title: Col-0  WT  rep 1


title: WSBEiJ_2m_male_CTX_high

value: male

value: WSB/EiJ


title: Ileum Ifnrl1-/- IL-22 treated rep3

description:
Sample name: DS32_3
Gene expression data from ileum


title: Ileum Ifnrl1-/- IL-22 treated rep2

description:
Sample name: DS32_2
Gene expression data from ileum


title: FM_24_1


title: DS_1 miRNA-seq

value: drought stress


title: FM_36_2

value: Fungus with maize


title: FM_24_2


title: CK_3 miRNA-seq


title: Ribo-seq-HBEC-SARS2-96hpi-rep1


title: WSBEiJ_2m_male_CTX_low


title: WSBEiJ_2m_female_CTX_high

value: female


title: Ribo-seq-HBEC-SARS2-72hpi-rep2


title: WSBEiJ_2m_female_HC_high


title: WSBEiJ_2m_male_HC_high


title: Ileum Ifnrl1-/- Saline treated rep3

description:
Sample name: DS32_8
Gene expression data from ileum

value: Saline


title: Ribo-seq-HBEC-SARS2-72hpi-rep1


title: FM_15_3


title: WSBEiJ_2m_male_HC_low


title: FM_12_3


title: FM_15_1


title: Ribo-seq-HBEC-SARS2-72hpi-rep3


title: CASTEIJ_2m_male_CTX_high

value: cortical endothelial cells

value: CAST/EiJ


title: Ribo-seq-HBEC-SARS2-72hpi-rep4


title: HMLE/ZEB2

city: Detroit

first: Guojun

last: Wu

state: MI

address: 4100 John R

department: Cancer Biology

institute: Wayne State University

hyb_protocol: Hybridized on Affymetrix array per manufacturer recommmendations.

scan_protocol: Scan protocol was performed per Affymetrix-provided methods.

data_processing:
Data was analyzed using the Transcriptome Analysis Console from Affymetrix. Analysis was performed using default settings to estimate intensity levels for each probe set.
probe group file: Clariom_D_Human.r1.pgf
meta-probeset file: Clariom_D_Human.r1.na36.hg38.a1.transcript

source_name: HMLE/ZEB2 cells

label_protocol: No labeling was performed

growth_protocol: Cells were grown according to ATCC recommendations. RNA was isolated when cells reached ~80% confluence.

extract_protocol: RNA was isolated using the Qiagen RNeasy column purification method.

treatment_protocol: No treatments were used in this study.

tag: cell line

value: HMLE

tag: genotype/variation

value: overexpressing ZEB2


title: CASTEIJ_2m_male_HC_high


title: Ribo-seq-HBEC-SARS2-48hpi-rep3

value: Cycloheximide


title: ES7_DMSO, 3 biological Rep, 72h

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: ES7 DMSO 3

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Clariom D™ Arrays. Microarrays were washed and stained with Affymetrix GeneChip® 3000 Fluidics Station.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip® 3000 Scanner.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: treated with DMSO for 72h

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip® WT PLUS Reagent Kit according to its manufacture's instruction from 6 μg total RNA.

growth_protocol: 100.000-200.000 cells were cultured in T-25 flasks over 72h.

extract_protocol: RNA was extracted with RNA isolation kits from Macherey-Nagel.

treatment_protocol: Cells were treated either triapine (440 nM for A-673, 650 nM for ES7) or equivalent volume of DMSO for 72h.

value: DMSO for 72h

value: Ewing Sarcoma


title: HMLE/LACZ

source_name: HMLE/LACZ cells

value: Control cell


title: HMLE/FOXQ1

source_name: HMLE/FOXQ1 cells

value: overexpressing FOXQ1


title: HMLE/TWIST1

source_name: HMLE/TWIST1 cells

value: overexpressing TWIST1


title: ES7_DMSO, 2 biological Rep, 72h

description: ES7 DMSO 2


title: FM_15_2


title: FM_12_2


title: F6_3

value: Fungus alone


title: FM_12_1


title: ES7_triapine, 1 biological Rep, 72h

description: ES7 Triapine

source_name: treated with triapine for 72h

value: triapine for 72h


title: Ribo-seq-HBEC-SARS2-48hpi-rep4


title: ES7_DMSO, 1 biological Rep, 72h

description: ES7 DMSO 1


title: A-673_triapine, 1 biological Rep, 72h

description: A-673 Triapine


title: HMLE/SNAI1

source_name: HMLE/SNAI1 cells

value: overexpressing SNAI1


title: CASTEiJ_2m_female_HC_high

value: hippocampal endothelial cells


title: F6_2


title: Ribo-seq-HBEC-SARS2-48hpi-rep2


title: A-673_DMSO, 2 biological Rep, 72h

description: A-673 DMSO 2


title: F36_3


title: PDAC_FFPE_04

value: pancreatic ductal adenocarcinoma


title: CASTEIJ_2m_male_CTX_low

value: male


title: CASTEiJ_2m_female_CTX_high

value: female


title: F6_1


title: F36_2


title: NODShiLtJ_2m_male_CTX_high

value: cortical endothelial cells

value: NOD/ShiLtJ


title: CASTEIJ_2m_male_HC_low

value: CAST/EiJ


title: F24_2


title: Ribo-seq-HBEC-SARS2-48hpi-rep1


title: Ribo-seq-HBEC-SARS2-24hpi-rep3


title: A-673_DMSO, 3 biological Rep, 72h

description: A-673 DMSO 3


title: ES7/TR/shControl_Dox (+), 1 biological Rep, 96h

description: ES7/TR/shControl Dox (+)

source_name: shRNA Control

growth_protocol: 100.000-200.000 cells were cultured in T-25 flasks over 72h for A-673 and 96h for ES7.

treatment_protocol: Cells were treated with/without doxycycline (0.1 μg/ml) for 72h or 96h with a refreshment after 48h.

value: dox, 96h


title: ES7/TR/shR2_3#13_Dox (+), 1 biological Rep, 96h

description: ES7/TR/shR2_3 Dox (+)

source_name: shRNA against RRM2 CDS region 2


title: A-673_DMSO, 1 biological Rep, 72h

description: A-673 DMSO 1


title: F24_1


title: ES7/TR/shControl_Dox (-), 1 biological Rep, 96h

description: ES7/TR/shControl Dox (-)

value: no dox, 96h


title: Ribo-seq-HBEC-SARS2-24hpi-rep4

value: Cycloheximide


title: NODShiLtJ_2m_male_CTX_low


title: NODShiLtJ_2m_male_HC_low


title: ES7/TR/shR2_3#13_Dox (-), 1 biological Rep, 96h

description: ES7/TR/shR2_3 Dox (-)

value: Ewing Sarcoma


title: Ribo-seq-HBEC-SARS2-4hpi-rep3


title: Ribo-seq-HBEC-SARS2-24hpi-rep1


title: NODShiLtJ_2m_female_HC_high


title: Ribo-seq-HBEC-SARS2-4hpi-rep2


title: Ribo-seq-HBEC-SARS2-24hpi-rep2


title: F15_3


title: NODShiLtJ_2m_male_HC_high


title: Ribo-seq-HBEC-mock-96hp-rep3

value: mock


title: F15_1


title: Ribo-seq-HBEC-SARS2-4hpi-rep1


title: F15_2


title: ES7/TR/shR2_1#1_Dox (+), 1 biological Rep, 96h

description: ES7/TR/shR2_1 Dox (+)

source_name: shRNA against RRM2 CDS region 1


title: F12_3


title: NODShiLtJ_2m_female_CTX_high

source_name: sorted brain endothelial cells (CD45-, CD11b-, CD31+)


title: AJ_2m_male_HC_high

value: A/J


title: Ribo-seq-HBEC-mock-96hp-rep2


title: AJ_2m_male_CTX_high


title: Ribo-seq-HBEC-mock-96hp-rep1


title: A-673/TR/shControl_Dox (+), 1 biological Rep, 72h

description: A-673/TR/shControl Dox (+)

value: dox, 72h


title: Ribo-seq-HBEC-mock-4hp-rep2


title: A-673/TR/shR2_3#7_Dox (+), 1 biological Rep, 72h

description: A-673/TR/shR2_3 Dox (+)


title: Ribo-seq-HBEC-mock-4hp-rep3


title: F12_2

value: Fungus alone


title: DBA2J_2m_male_CTX_high


title: F24_3


title: ES7/TR/shR2_1#1_Dox (-), 1 biological Rep, 96h

description: ES7/TR/shR2_1 Dox (-)


title: A-673/TR/shControl_Dox (-), 1 biological Rep, 72h

description: A-673/TR/shControl Dox (-)

value: no dox, 72h


title: AJ_2m_male_HC_low


title: A-673/TR/shR2_3#7_Dox (-), 1 biological Rep, 72h

description: A-673/TR/shR2_3 Dox (-)


title: AJ_2m_male_CTX_low


title: FM6_3

value: Fungus with maize


title: DBA2J_2m_male_HC_high

value: hippocampal endothelial cells


title: FM36_1


title: Ribo-seq-HBEC-mock-4hp-rep1


title: F12_1


title: A-673/TR/shR2_1#10_Dox (-), 1 biological Rep, 72h

description: A-673/TR/shR2_1 Dox (-)


title: DBA2J_2m_male_CTX_low


title: AJ_2m_female_HC_high


title: RNA-seq-HBEC-SARS2-96hpi-rep2

data_processing:
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots. Read counts per read are shown in the processed files
Supplementary_files_format_and_content: *hpi.txt: counts files for reads mapping to host cell genome/transcriptome
Supplementary_files_format_and_content: *repaired.txt: mpileup files of reads that map to the viral genomes


title: RNA-seq-HBEC-SARS2-96hpi-rep3


title: F36_1


title: 2.4.1 d0827 72h OG_3

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

data_processing:
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline subcommand align with the integrated mapper segemehl
READemption  was used for gene quantification with parameters gene_quanti
READemption with DESeq2 was used to perform the differential gene expression analysis, subcommand deseq
Genome_build: GCF_000012905.2 ASM1290v2
Supplementary_files_format_and_content: xlsx contain raw counts and DESeq2 analysis
Supplementary_files_format_and_content: wig files contain merged total read coverage

organism: Cereibacter sphaeroides 2.4.1

growth_protocol: All cultures were grown in malate minimal medium under microaerobic conditions (25 μM dissolved oxygen) at 32°C and 140 rpm in the dark.

extract_protocol:
Total RNA was isolated using the hot phenol method and remaining DNA was removed by a DNaseI treatment (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested during indicated growth phases (exponential, 72h, 72h outgrowth, 144h, 144h outgrowth).

tag: genotype

value: StsR deletion


title: DBA2J_2m_male_HC_low

value: male


title: A-673/TR/shR2_1#10_Dox (+), 1 biological Rep, 72h

description: A-673/TR/shR2_1 Dox (+)

tag: treatment


title: 2.4.1 d0827 72h OG_2


title: RNA-seq-HBEC-SARS2-96hpi-rep4


title: RNA-seq-HBEC-SARS2-96hpi-rep1


title: FM24_3


title: C57BL6J_2m_male_CTX_high


title: 2.4.1 d0827 72h OG_1


title: RNA-seq-HBEC-SARS2-72hpi-rep3


title: 2.4.1 d0827 72h_3


title: RNA-seq-HBEC-SARS2-72hpi-rep4


title: 2.4.1 d0827 72h_2


title: C57BL6J_2m_male_CTX_low


title: C57BL6J_2m_male_HC_high


title: RNA-seq-HBEC-SARS2-72hpi-rep1


title: DBA2J_2m_female_HC_high

value: female


title: C57BL6J_2m_male_HC_low


title: 2.4.1 d0827 72h_1


title: RNA-seq-HBEC-SARS2-72hpi-rep2


title: RNA-seq-HBEC-SARS2-48hpi-rep3


title: 2.4.1 d0827 exp_3

source_name: d0827 exp


title: C57BL6J_2m_female_HC_high


title: 2.4.1 d0827 exp_2


title: RNA-seq-HBEC-SARS2-48hpi-rep2


title: 2.4.1 d0827 exp_1


title: Wild type skin

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description: Healty control skin cells

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 2.1.1 mkfastq
Demultiplexed data was then processed using the Cell Ranger 2.1.1 count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: h5 files including counts (output CellRanger Count) for each sample

source_name: Skin

growth_protocol: Mice were housed in individually-ventilated cages at the VIB Center for Inflammation Research, in a specific pathogen-free animal facility. All experiments on mice were conducted according to institutional, national and European animal regulations. Animal protocols were approved by the ethics committee of Ghent University.

extract_protocol:
Single cell suspensions were obtained from total skin following trypsin digestion for 1 hour at 37ºC and subsequent digestion with collagenase type-1 (1,25 mg/ml), type-2 (0,5 mg/ml) and type-4 (0,5 mg/ml) for 30 to 45 minutes. Live cells were sorted on FACS and resuspended in PBS with 0.04% BSA at a final concentration of 1000 cells/ml.
Cellular suspensions were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton) to generate single-cell Gel Bead-in-Emulsion (GEMs). Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell V2 3’Gel Bead and Library kit (10x Genomics) according to the manufacturer’s instructions.

value: Wild type

tag: platform

value: 10x Genomics – v2


title: RNA-seq-HBEC-SARS2-48hpi-rep1


title: RNA-seq-HBEC-SARS2-48hpi-rep4


title: 2.4.1 wildtype 144h OG_3

source_name: wildtype 144h OG

value: wildtype


title: normal healthy skin tissues NO.3

city: Jinan

first: chen

last: cheng

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

description: Gene expression in normal healthy skin tissues

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: normal healthy skin tissues

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 3 psoriatic lesions and 3 normal healthy skin tissues were collected from the Department of Dermatology. All psoriatic lesions were consistent with the diagnostic criteria for psoriasis vulgaris and scored by the psoriasis area and severity index (PASI). The normal control group comprised healthy adult volunteers, whose age, sex, and site of extraction were matched with the psoriasis group.

tag: tissue

value: skin

tag: sample type

value: normal healthy skin tissues

value: man


title: 2.4.1 wildtype 144h OG_2

tag: strain


title: C57BL6J_2m_female_CTX_high

value: cortical endothelial cells


title: NC2_BCR

city: Beijing

first: Hui

last: Xu

address: Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases

department: Department of neurology

institute: Xuanwu Hospital

description:
APOE ε3/3
Processed data not yet produced for this sample.
NC2_BCR

data_processing:
Library strategy: BCR-seq
The Cell Ranger software pipeline (version3.0.2) provided by 10X Genomics.We performed barcode counting and unique molecular identifier counting   after filtering and alignment to the GRCh37 (hg19) reference genome to generate the   feature-barcode matrix and determine clusters. Dimensionality reduction was   performed using principal component analysis, and the first ten principal components   were used to generate clusters by graph-based algorithm.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

source_name: Homo sapiens mononuclear cells

extract_protocol:
We collected the Homo sapiens of all the participants at 7 a.m., and PBMCs were isolated by density-gradient centrifugation. After the PBMC suspension was resuspended in phosphate-buffered saline, followed by incubation at 4°C with CD45 antibodies for 20 minutes and 7-aminoactinomycin D for 10 minutes. MoFlo XDP (Beckman Coulter) was used for cell sorting. CD45+ cells were selected by gating on the basis of CD45 high, side-scatter low populations for subsequent single-cell RNA sequencing.
RNA libraries were prepared with Chromium Single Cell 5' Library & Gel Bead Kit, Chromium Single Cell V(D)J Enrichment Kit, Human T Cell, and Chromium Single Cell V(D)J Enrichment Kit, Human B Cell according to the manufacturer’s protocol.

value: Homo sapiens mononuclear cells

tag: disease state

value: normal control

tag: apoe genotype

value: APOE e3/3


title: Lesional OTULIN KO skin rep3

description: Lesional skin cells

tag: condition

value: KO Lesional


title: normal healthy skin tissues NO.1

tag: gender


title: psoriatic lesions NO.3

description: Gene expression in psoriatic lesions

source_name: psoriatic lesions

value: psoriatic lesions


title: psoriatic lesions NO.2

description: Gene expression in psoriatic lesions


title: normal healthy skin tissues NO.2


title: Lesional OTULIN KO skin rep2

description: Lesional skin cells


title: psoriatic lesions NO.1

description: Gene expression in psoriatic lesions


title: 2.4.1 wildtype 144h_2

source_name: wildtype 144h


title: Lesional OTULIN KO skin rep1

description: Lesional skin cells


title: Non-Lesional OTULIN KO skin rep2

description: Non-lesional skin cells

value: KO Non-Lesional


title: NC2_TCR

description:
APOE ε3/3
Processed data not yet produced for this sample.
NC2_TCR

data_processing:
Library strategy: TCR-seq
The Cell Ranger software pipeline (version3.0.2) provided by 10X Genomics.We performed barcode counting and unique molecular identifier counting   after filtering and alignment to the GRCh37 (hg19) reference genome to generate the   feature-barcode matrix and determine clusters. Dimensionality reduction was   performed using principal component analysis, and the first ten principal components   were used to generate clusters by graph-based algorithm.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

tag: Sex

tag: age


title: Non-Lesional OTULIN KO skin rep1

description: Non-lesional skin cells


title: RNA-seq-HBEC-SARS2-24hpi-rep4

source_name: Primary human bronchial epithelial cells

value: Cycloheximide


title: NC1_TCR

description:
APOE ε3/4
Processed data not yet produced for this sample.
NC1_TCR

value: APOE e3/4


title: RNA-seq-HBEC-SARS2-24hpi-rep3


title: 2.4.1 wildtype 144h OG_1


title: 2.4.1 wildtype 144h_3


title: RNA-seq-HBEC-SARS2-24hpi-rep1


title: HE002_NS

city: Tianjin

first: shusen

last: wang

address: No.24, Fukang Road

department: Organ Transplant Center

institute: Tianjin First Central Hospital

description: Gene expression in human non-diabetic islets

hyb_protocol: Cy3-labelled cRNA was fragmented following the manufacturers instructions (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US). After hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat.# G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution= 3 μm, PMT 100%, 20 bit.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: human non-diabetic islets, replicate 1

label_protocol: Total RNA was amplified and labeled with a Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US). Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, Dusseldorf, Germany). mbion, Austin, TX, USA) according to the manufacturer’s instructions and then evaluated for its

growth_protocol: Human islets (> 90% purity) were collected and cultured in CMRL-1066 medium (Corning, Manassas, VA, USA), supplemented with 10% Human Serum Albumin (Baxter, Vienna, Austria), 100 U/mL penicillin and 100 μg/mL streptomycin at 37 ℃ in 5% CO2.

extract_protocol: Total RNA was extracted and purified using the mirVana™ miRNA Isolation Kit (Cat.# AM1561, Ambion, Austin, TX, USA) according to the manufacturer’s instructions and then evaluated for its RIN number to determine RNA integration with an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

value: human non-diabetic islets

tag: bmi


title: HE005_Islets__NS

description: Gene expression in human type 2 diabetic islets

source_name: human type 2 diabetic islets, replicate 1

value: human type 2 diabetic islets

value: male


title: RNA-seq-HBEC-SARS2-24hpi-rep2

tag: agent


title: NC2_GEX

description:
APOE ε3/3
NC2_GEX

data_processing:
The Cell Ranger software pipeline (version3.0.2) provided by 10X Genomics.We performed barcode counting and unique molecular identifier counting   after filtering and alignment to the GRCh37 (hg19) reference genome to generate the   feature-barcode matrix and determine clusters. Dimensionality reduction was   performed using principal component analysis, and the first ten principal components   were used to generate clusters by graph-based algorithm.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell


title: NC1_BCR

description:
APOE ε3/4
Processed data not yet produced for this sample.
NC1_BCR

value: female


title: RNA-seq-HBEC-SARS2-4hpi-rep2

tag: time point


title: 2.4.1 wildtype 72h OG_2

source_name: wildtype 72h OG

value: wildtype


title: H046_NS


title: mteclo_wildtype_R1

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

description:
Salmon_gene_tpm_uq.csv.gz
Salmon_transcript_tpm_uq.csv.gz
mTT_assembly.gtf.gz

data_processing:
The mTEC data was processed together with the ENCODE mouse tissues (GSE36025, only the colon samples were kept to represent the large intestine).
Sequence reads were trimmed to 76 bp (fastx trimmer v0.0.14) and mapped with Hisat2 (v2.1.0; mouse genome plus known splice junctions; Ensembl mm10-v91; settings:”–dta –score -min L,0.0,-0.2 –rna-strandness RF”). To generate a single high-depth sample for each tissue and mTEC population replicate samples were combined and downsampled to 200M reads (samtools v1.3.1).
The mT&T transcriptome assembly was constructed as follows: (1) Separate reference-guided assemblies were then constructed for each ENCODE tissue or TEC population using the high-depth samples (StringTie v1.3.3b; Ensembl mm10-v91). (2) To identify transcripts that were reproducibly detected we  prepared biological replicate samples (n=2; 60M reads/samples) for each tissue and TEC population. Expression of the transcripts present in each of the assemblies was  quantified in the relevant tissue or TEC population using the two 60M replicates (Salmon, with parameters: “--incompatPrior=0 --validateMappings  --rangeFactorizationBins=4  --seqBias --gcBias  -x 0.66”). The non-parametric Irreproducibility Discovery Rate (npIDR) was then calculated. Prior to npIDR analysis data were log-transformed and extreme expression values removed to avoid issues arising from data sparsity (<5th or >95th expression quantile). To determine TPM thresholds above which transcripts could be reproducibly detected (npIDR ≤ 0.1) we modelled the TPM vs npIDR relationship for each tissue or TEC population using a LOESS regression curve. (3) The reproducibly detected transcripts from each tissue or TEC population were then merged into a single unified assembly (StringTie, Ensembl reference annotation guided merge). (4) Transcripts contained in reference introns, possible polymerase run-on fragments, repeats, transcripts overlapping opposite-strand exons or introns and possible pre-mRNA fragments were removed (gffcompare v.0.10.6, class codes ‘irpxse’). (5) To be included in the final mT&T assembly, the merged transcript models were required to be reproducibly detected (npIDR ≤ 0.1; analysis performed as above) in at least one tissue or TEC population.
The  mT&T assembly was used as the annotation for the Salmon quantification at the gene and transcript level.
Genome_build: mm10
Supplementary_files_format_and_content: [Salmon_transcript_tpm_uq.csv.gz]  Comma-separated file containing TPM abundances for all transcripts in each Sample (mT&T assembly as annotation)
Supplementary_files_format_and_content: [Salmon_gene_tpm_uq.csv.gz]  Comma-separated file containing TPM abundances for all genes in each Sample (mT&T assembly as annotation)
Supplementary_files_format_and_content: [mTT_assembly.gtf.gz]  Gene Transfer Format (GTF) file containing the mT&T transcriptome assembly

source_name: immature mTEC

extract_protocol:
Thymi were dissected from 4-week old mice, enriched for CD45- cells (AutoMACS) and cells sorted by FACS (MHCII low immature versus MHCII high mature mTEC; GFP positive cells for Aire knockout samples). RNA was extracted using QUIAGEN RNeasy kit.
A minimum of 1 μg of total RNA was used to generate Ribo-depleted directional (i.e. stranded) libraries. 100bp paired-end sequencing was performed with an Illumina HiSeq 4000.

value: 4 weeks

value: thymus

tag: cell type

value: immature medullary thymic epithelial cell (mTEC)

tag: aire locus

tag: facs phenotype

value: CD45- EpCAM+  Ly51- UEA+  MHCII low


title: RNA-seq-HBEC-mock-96hp-rep3

tag: treatment

value: mock


title: RNA-seq-HBEC-SARS2-4hpi-rep3


title: 2.4.1 wildtype 72h OG_1

tag: genotype


title: 2.4.1 wildtype 72h_3

source_name: wildtype 72h


title: 2.4.1 wildtype 144h_1


title: HE003_Islets__NS

tag: tissue


title: RNA-seq-HBEC-mock-4hp-rep3


title: AD2_TCR

description:
APOE ε3/3
Processed data not yet produced for this sample.
AD2_TCR

value: Homo sapiens mononuclear cells

value: Alzheimer's disease


title: mteclo_wildtype_R2


title: AD2_BCR

description:
APOE ε3/3
Processed data not yet produced for this sample.
AD2_BCR

value: APOE e3/3


title: 2.4.1 wildtype 72h OG_3


title: RNA-seq-HBEC-mock-4hp-rep2


title: RNA-seq-HBEC-SARS2-4hpi-rep1


title: 2.4.1 wildtype exp_3

source_name: wildtype exp


title: NC1_GEX

description:
APOE ε3/4
NC1_GEX

value: normal control


title: AD3_TCR

description:
APOE ε2/4
Processed data not yet produced for this sample.
AD3_TCR

value: APOE e2/4


title: mtechi_gfpposko_R2

source_name: mature Aire-knockout mTEC

value: mature medullary thymic epithelial cell (mTEC)

value: GFP/GFP (GFP +ve)

value: CD45- EpCAM+  Ly51- UEA+ MHCII high GFP+


title: AD2_GEX

description:
APOE ε3/3
AD2_GEX


title: mtechi_wildtype_R2

source_name: mature mTEC

value: CD45- EpCAM+  Ly51- UEA+  MHCII high


title: mtechi_gfpposko_R1

value: CD45- EpCAM+  Ly51- UEA+  MHCII high GFP+


title: 2.4.1 wildtype exp_2


title: AD3_BCR

description:
APOE ε2/4
Processed data not yet produced for this sample.
AD3_BCR

value: male


title: Rbfox2_SKO2_mteclo

data_processing:
Reads were mapped using HISAT (v2.1.0, mm10)
Bam files were deduplicated using Picard (v2.10.9).
Bam files were subsampled to a common read depth separately for the immature (10M reads/replicate) and mature mTEC (14.5M reads/replicate) samples.
Gene expression levels were quantified using featurecounts (v.1.6.0)
Genome_build: mm10
Supplementary_files_format_and_content: [Rbfox1_Rbfox2_SKO_featurecounts.txt]  tab-delimited file including gene counts

extract_protocol:
Thymi were dissected from mice, enriched for CD45- cells (AutoMACS) and 10,000 cells sorted per-population by FACS. RNA was extracted using QUIAGEN RNeasy micro plus kit.
Libraries were prepared using a stranded, paired-end protocol including polyA-enrichment (NEB) and sequenced on an Illumina HiSeq 4000.

value: 4-6 weeks

value: female

value: Rbfox2 lox/lox :Foxn1 wildtype/cre

value: immature medullary thymic epithelial cell


title: Tconv_donor7

city: Vancouver

first: Megan

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

data_processing:
Demultiplexed FASTQ files generated with BCL Convert (v1.2.0), aligned with STAR (v2.5.0b), gene expression quantified as raw counts by Illumina’s RnaReadCounter within  Illumina BaseSpace RNA-Seq Alignment App (v1.1.0) to generate the processed data files.
From raw counts, DESeq2 (v1.28.1) within R (v4.0.2) used to identify differentially expressed genes by pairwise comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: Per sample: raw counts of all genes, generated by RnaReadCounter

source_name: Peripheral blood flow-sorted conventional T cell

extract_protocol:
Total RNA isolated with RNeasy Micro Kit. All samples had an RNA integrity number of 9.4-10.
mRNA enrichment and library preparation with NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNExt Ultra II Directional RNA Library Prep Kit for Illumina.

tag: experiment

tag: donor

value: M

value: Conventional T Cell

tag: gene modification

tag: total days of expansion


title: mtechi_wildtype_R1

tag: strain

value: 4 weeks

value: thymus

value: wildtype


title: Rbfox2_SKO1_mteclo

value: CD45- EpCAM+  Ly51- UEA+  MHCII low


title: RNA-seq-HBEC-mock-96hp-rep1

value: Cycloheximide

value: mock


title: 2.4.1 wildtype 72h_1


title: nTreg_FOXP3-HDR-KO_donor7

source_name: Peripheral blood flow-sorted naive Treg

value: Naive Treg

value: CRISPR/HDR-mediated FOXP3 KO, GFP sort-purified


title: AD3_GEX

description:
APOE ε2/4
AD3_GEX

value: Homo sapiens mononuclear cells

tag: disease state

value: Alzheimer's disease

tag: apoe genotype

value: APOE e2/4


title: Embryo WT Rep 2

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

data_processing:
The raw fastq files were aligned to the dm6 genome (Ensembl v97) using STAR v2.7.1a
The reads were then quantified using RSEM v1.3.1
Genome_build: dm6
Supplementary_files_format_and_content: raw counts of sequencing reads; genes.results were generated using RSEM v1.3.1 and includes the quantified reads for each sample

organism: Drosophila melanogaster

source_name: Embryo WT

growth_protocol: For each cross, flies were housed in cages with a grape juice agar plate containing yeast paste. Females were allowed to lay eggs at 25°C for 24h, after which the agar plates were changed to harvest the mixed stage embryos.

extract_protocol:
The embryos were dechorionated in bleach, washed in water and 100% ethanol prior to RNA extraction using the ISOLATE II RNA Mini Kit’s protocol (Bioline, UK).
The extracted RNA was quantified using Nanodrop (Thermo Fisher Scientific). Library preparation was performed using 1µg of total RNA and sequencing was performed using Illumina HiSeq 4000 System (2 × 151 bp read length, 40 million reads per sample).

value: embryo

value: wild type


title: AD1_GEX

description:
APOE ε2/4
AD1_GEX

tag: Sex

value: male

tag: age


title: RNA-seq-HBEC-mock-4hp-rep1

tag: agent


title: Rbfox1_SKO3_mteclo

value: 4-6 weeks

value: Rbfox1 lox/lox :Foxn1 wildtype/cre

value: immature medullary thymic epithelial cell


title: Tconv_donor4

value: F

value: Conventional T Cell


title: mtechi_gfpposhet_R1

source_name: mature Aire-positive mTEC

value: 4 weeks

value: female

value: thymus

value: mature medullary thymic epithelial cell (mTEC)

value: GFP/Aire (GFP +ve)

value: CD45- EpCAM+  Ly51- UEA+  MHCII high GFP+


title: 2.4.1 wildtype 72h_2

value: wildtype


title: Embryo WT Rep 1


title: Rbfox1_SKO3_mtechi

value: mature medullary thymic epithelial cell

value: CD45- EpCAM+  Ly51- UEA+  MHCII high


title: nTreg_Cas9_donor4

value: Naive Treg


title: RH4_si-circVAMP3_1

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description: Total cell lysate

data_processing:
Raw sequencing data processing (format conversion and demultiplexing) was performed using Bcl2Fastq version 2.20.0.422.
Due to a laser intensity drop in the last cycles of the sequencing reaction, the last 20 based of reverse reads exhibited low Phred quality scores. Trimmomatic software was employed to cut reverse reads down to 130 nucleotides; a second Trimmomatic run, with parameters ILLUMINACLIP:path/to/adapter:2:30:10:8:true  MINLEN:35, allowed to remove adapter sequences (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/).
Alignment to human GRCh38 genome and Ensembl 99 transcriptome was performed using STAR aligner version 2.5.2b with parameters --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMattrIHstart 0 --outSAMtype BAM SortedByCoordinate  --outFilterType BySJout –outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04.
Reads mapping to each gene were counted using htseq-count software with parameters -m intersection-strict -f bam -s reverse. Read count files were combined into a count matrix file, which was given as input to edgeR R package, after removing genes with a CPM value (Counts Per Million) less than 1 in at least 3 samples.
Gene-level FPKM values were calculated using rpkm function from the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values of expressed genes in each sample.

source_name: Alveolar rhabdomyosarcoma cell line (RH4)

growth_protocol: RH4 cells are cultured in DMEM high-glucose supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1x penicillin-streptomycin.

extract_protocol:
Total RNA was extracted with Direct-zol RNA Miniprep kit (Zymo Research) with a 30-minute DNase-I treatment according to the manufacturer’s protocol.
TruSeq Stranded mRNA kit

treatment_protocol: RH4 cells were transfected with 30 nM (final concentration) siRNA (Dharmacon) and Dharmafect-1 Transfection Reagent (Dharmacon) according to the manufacturer’s instructions. The medium was replaced 24 h after the transfection and cells were harvested after another 24 h.

value: Alveolar rhabdomyosarcoma cancer cells


title: mtechi_gfpposhet_R2


title: 2.4.1 wildtype exp_1


title: Embryo Raf926 KO Rep 3

source_name: Embryo Raf926 KO

value: embryo


title: RH4_si-circVAMP3_2

description: Total cell lysate


title: RNA-seq-HBEC-mock-96hp-rep2

value: Cycloheximide

value: mock

tag: time point


title: Rbfox2_SKO2_mtechi

value: 4-6 weeks

value: Rbfox2 lox/lox :Foxn1 wildtype/cre

tag: cell type


title: nTreg_Cas9_donor7

value: M


title: AD1_BCR

description:
APOE ε2/4
Processed data not yet produced for this sample.
AD1_BCR

source_name: Homo sapiens mononuclear cells

value: Homo sapiens mononuclear cells

value: Alzheimer's disease

value: male

value: APOE e2/4


title: Tconv_donor3

value: Conventional T Cell


title: Rbfox1_SKO2_mtechi

value: female

value: Rbfox1 lox/lox :Foxn1 wildtype/cre

value: thymus


title: Rbfox1_SKO2_mteclo

value: immature medullary thymic epithelial cell

value: CD45- EpCAM+  Ly51- UEA+  MHCII low


title: Embryo WT Rep 3

value: wild type


title: AD1_TCR

description:
APOE ε2/4
Processed data not yet produced for this sample.
AD1_TCR


title: Rbfox2_WT2_mteclo

value: Rbfox2 lox/lox :Foxn1 wildtype/wildtype


title: LF4

city: changsha

first: Wu

last: Cichun

address: Xiangya Road Street, Kaifu District

institute: Cichunwu

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gene_fpkm.txt: Tab-delimited file includes FPKM values for each Sample.

source_name: Liver

extract_protocol:
RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. 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 (RNase H -). 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 of preferentially 250~300 bp in 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 m in 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, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

tag: group

value: Liver fibrosis


title: Tconv_donor5


title: Rbfox2_SKO1_mtechi

value: 4-6 weeks

value: mature medullary thymic epithelial cell

tag: facs phenotype

value: CD45- EpCAM+  Ly51- UEA+  MHCII high


title: nTreg_FOXP3-HDR-KO_donor4

value: F

value: Naive Treg

value: CRISPR/HDR-mediated FOXP3 KO, GFP sort-purified


title: LF2


title: LF1


title: Embryo Raf926 KO Rep 1

value: embryo


title: Rbfox1_WT3_mteclo

value: male

value: Rbfox1 lox/lox :Foxn1 wildtype/wildtype


title: human_smallRNA_ishi_44_5

city: Indianapolis

first: Shannon

last: Hawkins

state: Indiana

institute: Indiana University School of Medicine

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version unknown pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:16. Custom perl scripts along with FASTX-Toolkit version 0.0.14 with the following parameters, “-l 17 -v -M 1 -i “, were used to look for partial adapters within the reads
PolyA reads were mapped against GRCm38 or GRCh38 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100
PolyA read counts for each gene were created using HTSeq-Count from the HTSeq package version 0.6.1p1 and Gencode v24 as the annotation for human reads and Gencode M9 as the annotation for mouse
smallRNA reads were mapped against GRCm38 or GRCh38 and also miRbase version 21 as reference using miRDeep2 version 2.0.0.7 to identify and quantify known microRNA’s.
Genome_build: GRCh38
Genome_build: GRCm38
Genome_build: miRbase version 21
Supplementary_files_format_and_content: humanCounts.polyA.tsv - Gene counts for each sample in tab-delimited format
Supplementary_files_format_and_content: human_mirna.counts.tsv - miRNA counts for each sample in tab-delimited format
Supplementary_files_format_and_content: mouseCounts.polyA.tsv - Gene counts for each sample in tab-delimited format
Supplementary_files_format_and_content: mouse_mirna.counts.tsv - miRNA counts for each sample in tab-delimited format

source_name: Endometrial adenocarcinoma cell line

extract_protocol:
Total RNA was extracted from mouse uterus ( three mice per genotype) and ishikawa cells (duplicate per phenotype) using the mirVana miRNA isolation kit. RNA quality control was performed on an Agilent 2100 bioanalyzer
Poly-A RNA libraries were constructed using mRNA Stranded TruSeq protocol (Illumina, San Diego, CA). Small RNA library construction was performed using the TruSeq Small RNA kit (Illumina). Purified libraries were visualized and quantified using a TapeStation HSD1000 (Agilent, Santa Clara, CA).

value: ishikawa

value: Uterus

value: female

value: DICER1 -/-


title: Rbfox1_WT3_mtechi

value: thymus


title: human_smallRNA_ishi_44_4


title: Rbfox1_WT2_mteclo

value: immature medullary thymic epithelial cell

value: CD45- EpCAM+  Ly51- UEA+  MHCII low


title: human_smallRNA_ishi_33_5

value: DICER1 +/-


title: NC1

value: Liver

value: Normal control


title: Rbfox1_WT2_mtechi

value: 4-6 weeks

value: mature medullary thymic epithelial cell

value: CD45- EpCAM+  Ly51- UEA+  MHCII high


title: LF3

value: Liver fibrosis


title: nTreg_Cas9_donor3

value: M

value: Naive Treg


title: nTreg_FOXP3-HDR-KO_donor3

value: CRISPR/HDR-mediated FOXP3 KO, GFP sort-purified


title: Rbfox2_WT2_mtechi

value: Rbfox2 lox/lox :Foxn1 wildtype/wildtype


title: Rbfox2_WT1_mteclo

value: male


title: nTreg_Cas9_donor5


title: Rbfox2_WT1_mtechi


title: NC3


title: nTreg_FOXP3-HDR-KO_donor5


title: human_smallRNA_ishi_control_6

value: ishikawa

value: Uterus

value: female

value: DICER1 +/+


title: NC4


title: RNA_shPAX9_2_H1963_Rep2

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
ChIP-seq ATAC-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 and STAR version 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
ATAC-seq reads were aligned to UCSC hg19 using BWA version 0.7.12. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: cells were maintained with DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

treatment_protocol: Cells were treated with either DMSO or HDAC1/2 inhibitor MERCK60 or EZH2 inhibitior GSK126 for 24 to 96 hours.

tag: cell line

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: treatment

value: cells transduced with PAX9 shRNA #2

value: PAX9 depletion


title: NC2

tag: tissue

value: Liver

value: Normal control


title: human_smallRNA_ishi_33_2

tag: genotype

value: DICER1 +/-


title: Embryo Raf926 KO Rep 2

value: embryo


title: human_smallRNA_ishi_control_5


title: human_polyA_ishi_44_5

value: DICER1 -/-


title: RNA_shPAX9_2_H1963_Rep1


title: SAMPLE 24_genomic DNA from fetal tissues

city: Shanghai

first: Ye

last: Liu

state: Shanghai

address: No. 1961, Huashan Road

department: School of Medicine

institute: The International Peace Maternity and Child Health Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K  Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2; the 'signal intensities.txt' contains unmethylated and methylated signal intensities.

source_name: fetal tissues

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fetal tissues samples using Qiagen DNeasy Kit according to standard instructions

tag: sample group

value: MFPR

tag: gender


title: E_Spinal Cord FTY720

city: Cornella de Llobregat

first: Tamara

last: Maes

state: Barcelona

address: Carrer Sant Ferran 74

department: R&D

country: Spain

institute: Oryzon Genomics S.A.

hyb_protocol: Cy3 and Cy5 labeled cRNA for the control probes (Zea mays Zmmyb42 and Expansin) were added to the Cy3- and Cy5-labelled sample cRNA mixes and hybridized to microarrays according to the manufacturer’s instruction.

scan_protocol: Raw data were obtained using Agilent's DNA Microarray Scanner G2505B. Images were quantified using Agilent Feature Extraction software (v10.1).

data_processing: The raw fluorescence intensity data were processed using proprietary Oryzon Genomics SA Polyphemus software, which involves the following steps: 1. Spatial data compensation of the signals in the 2 channels based on the spike probes distributed over the array and generating signal at several discrete levels. 2. Noise filtering based on negative controls.  3. Data normalization by modified nonlinear Q-splines normalization method (Workman et al., 2002) and Log2(sample/control) value calculation without background correction. Differential expression assessment using robust statistics on the average of 3 technical replicates per gene oligo after removal of eventual outlier points (caused by dust or array imperfections). Criteria for outlier elimination are established automatically based on the intra-array technical variability of the signal distribution of the controls probes. The p-values are calculated after outlier elimination based on the absolute value of the regularized t-statistics (Baldi et al., 2001), which uses a Bayesian framework to derive the algorithm. Control probes have SPOTID ORY_C* and each is present in 2103 copies; gene oligos have SPOTID ORY_P* and each is present in triplicate, respectively, in the crossref file. The Agilent design file and AgilentOryzonRrossRef file are provided.

source_name: E_Pool Spinal Cord EAE mice FTY720

label_protocol: Total RNA from the spinal cord of 5 mice or the brain of 10 mice was pooled for the survey. Total RNA (0.5 μg) amplification and labeling with Cy3 or Cy5 was carried out using a modified Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy extraction kit. Evaluation of RNA quality was performed with the Agilent 2100 bioanalyzer and NanoDrop™ ND-1000 (Thermo Scientific).

treatment_protocol: Experimental Immune Encephalomyelitis (EAE) was induced in female C57BL/6 by administration of MOG following a standard protocol. Treatment with vehicle or compounds was started at onset of symptoms (day 12 after immunization). Mice were sacrificed on day 26 in the subchronic phase (SC) or on day 17 in the effector phase (E). Tissue samples were obtained for RNA extraction.

value: Female

value: Spinal Cord

tag: strain

source_name: E_Pool Spinal Cord EAE mice vehicle


title: human_polyA_ishi_44_4


title: RNA_shPAX9_1_H1963_Rep2

value: cells transduced with PAX9 shRNA #1


title: RNA_shPAX9_1_H1963_Rep1


title: SAMPLE 21_genomic DNA from fetal tissues


title: human_polyA_ishi_33_5

value: ishikawa


title: SAMPLE 19_genomic DNA from fetal tissues

value: male


title: SAMPLE 20_genomic DNA from fetal tissues

value: female


title: SAMPLE 22_genomic DNA from fetal tissues


title: RNA_shNONT_H1963_Rep1

value: cells transduced with non-targeting shRNA

value: control


title: SAMPLE 18_genomic DNA from fetal tissues


title: E_Spinal Cord Vehicle


title: RNA_shNONT_H1963_Rep2

value: small cell lung cancer

value: Low passages (6-10)


title: human_polyA_ishi_33_2

value: Uterus


title: SAMPLE 23_genomic DNA from fetal tissues


title: E_Spinal Cord ORY-2001

source_name: E_Pool Spinal Cord EAE mice ORY-2001


title: E_Brain FTY720

source_name: E_Pool Brain EAE mice vehicle FTY720

value: Brain

source_name: E_Pool Brain EAE mice vehicle


title: human_polyA_ishi_control_6

value: DICER1 +/+


title: RNA_GSK126_H1963_Rep2

value: cells treated with GSK126


title: E_Brain ORY-2001

source_name: E_Pool Brain EAE mice vehicle ORY-2001


title: SAMPLE 17_genomic DNA from fetal tissues

value: embryo


title: SC_Spinal Cord ORY-LSD1

source_name: SC_Pool Spinal Cord EAE mice ORY-LSD1

source_name: SC_Pool Spinal Cord EAE mice vehicle


title: RNA_GSK126_H1963_Rep1


title: Treg_NSD2_cKO_rep2

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

data_processing:
Sequence reads were mapped to mm10 reference genome using Hisat2
Differential gene expression analysis was detected using Bioconductor DESeq2 package with a threshold of RPKM 5 and fold change 1.5.
Genes with reads per kilobase of transcript per million mapped reads 1 were not included for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Treg cells were sorted out for RNA extraction and library construction at RiboBio Co., Ltd.Each sample combined a mixture of RNA from at least three mice.Sequencing was done on an Illumina Hiseq 2500 platform and SE50 single-end module.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Nsd2 Treg conditional knock out

value: spleen

value: Treg cells


title: RNA_MERCK60_H1963_Rep1

value: cells treated with MERCK60


title: Treg_WT_rep2

value: wild type (WT)


title: Treg_NSD2_cKO_rep1


title: human_polyA_ishi_control_5

value: ishikawa


title: E_Brain Vehicle

value: Female


title: RNA_DMSO_H1963_Rep2

value: cells treated with DMSO


title: RNA_MERCK60_H1963_Rep2


title: SAMPLE 14_genomic DNA from fetal tissues

value: MFPR

value: female


title: SC_Spinal Cord ORY-2001

source_name: SC_Pool Spinal Cord EAE mice ORY-2001

value: Spinal Cord


title: RNA_DMSO_H1963_Rep1

value: small cell lung cancer

value: Low passages (6-10)

value: control


title: 2P24-invF-3-12h

first: Jing

state: Not applicable

address: 12 Zhongguancun South St

institute: Chinese Academy of Agricultural Sciences

data_processing:
The sequencing data quality was evaluated by FastQC (V0.10.1).
The Cutadapt (version 1.9.1) is used to preprocess the original data, filter the low quality data, remove the pollution and the joint sequence.
The Clean Data and the reference genome were compared and analyzed by using BowtiE2 (V2.1.9) software with default parameters.
Samtools (V0.1.18) software was used for MPileup processing, so as to obtain the possible SNV results of each sample, and then Annovar (V2013.02.11) software was used for annotation.
Htseq software (V 0.6.1) was used to calculate gene expression levels.
DESeq2 (V1.6.3) of Bioconductor software package was used to analyze the genetic differences.
Genome_build: GenBank: CP025542.1
Supplementary_files_format_and_content: Gene counts and FPKM of all samples at 6 h and 12 h
Supplementary_files_format_and_content: Differentially expressed genes (DEGs) of 2P24ΔinvF compared with 2P24 at 6 h and 12 h

organism: Pseudomonas fluorescens

source_name: Bacterial cells

growth_protocol: Strains 2P24 and 2P24ΔinvF were grown on KB plates with 50 μg/mL ampicillin at 28℃. Fresh lawns were suspended in 5 mL of KB and incubated at 28℃ overnight with 200 rpm shaking. Bacterial suspension was diluted in 50 mL of MG medium in flasks to a final OD600 of 0.1. The cultures were incubated at 28°C at 200 rpm on a rotary shaker for 6 h/12 h.

extract_protocol:
The cell fractions were separated by centrifugation at 10, 000 rpm for 5 min at 4°C. Total RNA was isolated using a E.Z.N.A.® Bacterial RNA Kit (Omega Bio‐tek, USA) as described by the manufacturer for RNA-seq. A prokaryotic chain specific sequencing library was constructed using a NEBNext Ultra Directional RNA Library Prep Kit and then sequenced on an Illumina HiSeq platform.
RNA libraries were prepared for sequencing using standard protocols of NEBNext Ultra Directional RNA Library Prep Kit.

value: invF deficient mutant


title: SAMPLE 15_genomic DNA from fetal tissues


title: SAMPLE 16_genomic DNA from fetal tissues

value: male


title: SC_Spinal Cord Vehicle


title: Treg_WT_rep1


title: Bregs-TLR_2

city: Boston

first: Qiang

last: Fu

state: Massachusetts

address: 55 Fruit St.

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: Read counts, CPMs

source_name: Bregs-TLR

growth_protocol: CpG-B cells and TLR-Bregs were obtained by giving isolated C57BL/6 splenic B cells either CpG ODN1668 stimulation for 3 days, or CpG stimulation with LPS, PMA, and ionomycin over the last 5 hours. RNA was extracted from all groups and analyzed using RNA-Sequencing and R.

extract_protocol:
Total RNA was extracted from five million cells using RNeasy Plus Mini Kit (Qiagen, Cat# 74134) as well as on-column DNAse digestion.
NEBNExt Ultra Directional RNA Library Prep for Illumina (New England Biolabs)
polyA selection followed by strand-specific library construction

value: Bregs-TLR


title: SC_Brain ORY-LSD1

source_name: SC_Pool Brain EAE mice ORY-LSD1

value: Brain

source_name: SC_Pool Brain EAE mice vehicle


title: SC_Brain Vehicle


title: Input_DMSO

library_source: genomic

tag: chip antibody

value: cells treated with DMSO, spiked in with 10% drosophila S2 cell chromatin


title: SC_Brain ORY-2001

source_name: SC_Pool Brain EAE mice ORY-2001


title: Input_MERCK60

value: cells treated with MERCK60, spiked in with 10% drosophila S2 cell chromatin


title: SAMPLE 11_genomic DNA from fetal tissues

value: ETP

value: embryo


title: 2P24-2-12h

value: wild type


title: Input_shPAX9_2

value: cells transduced with PAX9 shRNA #2

value: PAX9 depletion


title: SAMPLE 10_genomic DNA from fetal tissues


title: Bregs-CpG_1

source_name: Bregs-CpG

value: Bregs-CpG


title: SAMPLE 8_genomic DNA from fetal tissues

value: female


title: Naive B cells_3

source_name: Naive B cells

value: Naive B cells


title: Bregs-CpG_3


title: Bregs-TLR_1


title: SAMPLE 7_genomic DNA from fetal tissues

source_name: fetal tissues


title: H3K27Ac_DMSO

value: small cell lung cancer

value: anti-H3K27Ac (CST #8173)


title: 2P24-invF-1-12h


title: H3K27Ac_MERCK60

value: Low passages (6-10)

value: control


title: 2P24-invF-2-12h

value: invF deficient mutant


title: Bregs-CpG_2


title: Naive B cells_2


title: 2P24-invF-2-6h

value: 6 h


title: SAMPLE 4_genomic DNA from fetal tissues

value: male


title: SAMPLE 13_genomic DNA from fetal tissues

value: MFPR


title: FFPE_ATAC_on_FFPE_kidney_rep1

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
Reads were aligned to the mm9 genome/hg19 genome using bowtie2
duplicate reads were removed with Picard
MACS2  was used call narrow peak
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: peak text files

source_name: Kidney

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA with T7-Tn5. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

value: FVBN

value: FFPE


title: SAMPLE 12_genomic DNA from fetal tissues

value: ETP

value: embryo


title: SAMPLE 6_genomic DNA from fetal tissues


title: HDAC2_H1963

value: anti-HDAC2 (abcam ab7029)

value: normal cells


title: Naive B cells_1


title: SAMPLE 3_genomic DNA from fetal tissues


title: 2P24-invF-1-6h


title: 2P24-3-12h

value: wild type


title: FFPE_ATAC_on_FFPE_liver_rep2

source_name: Liver


title: FFPE_ATAC_on_FFPE_liver_rep1


title: HDAC1_H1963

value: anti-HDAC1 (activemotif 40967)


title: K14Cre/+ Il12rb2fl/fl Aldara rep2

city: Zürich

first: Pascale

last: Zwicky

address: Wintherturerstrasse 190

institute: University of Zurich

data_processing:
The raw reads were aligned to mouse genome build GRCm38 using the STAR aligner, with FeatureCounts (part of Subread package) used to calculate read counts per gene based on GENCODE gene annotation version M16
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: skin

extract_protocol:
Total RNA of IF keratinocytes was isolated using the Qiagen RNeasy Micro kit according to the manufacturers’ protocol.
Library preparation was performed according to illumina`s “smartseqII” protocol (Picelli et al., 2014). The Novaseq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocols. Sequencing was single end 100bp.

value: skin

value: interfollicular keratinocytes

value: K14Cre/+ Il12rb2fl/fl

value: Aldara (topical) - day 1


title: 2P24-1-12h


title: BAZ1B KO Rep3 - D6

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCh39/hg38 + Gencode 31
Supplementary_files_format_and_content: raw gene counts

growth_protocol: Cells were grown in expansion media and the cells were allowed to mature in differentiation media. Cells were taken at D0 and D6 of differentiation.

extract_protocol: The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

tag: differentiation day

value: BAZ1B KO


title: SAMPLE 9_genomic DNA from fetal tissues


title: S_exo2

city: Jinan

first: Huiqiang

last: Sun

state: Shandong

address: #44-1 wenhuaxilu Road

department: Prosthodontics

institute: Shandong school and hospital of stomatology

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: Rattus_norvegicus Ensembl release96
Supplementary_files_format_and_content: excel,expression profiles

source_name: Supernatant of RAW264.7 cell culture medium cultured on smooth titanium plate

growth_protocol: Culturing cells in exosome-free medium

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: RAW264.7 cells are stimulated by smooth titanium disks and micro-/nano-texture hierarchical topography titanium disks

value: Mouse-derived RAW264.7 cells

value: cultured on smooth titanium plate


title: SAMPLE 5_genomic DNA from fetal tissues

value: male


title: BAZ1B KO Rep2 - D6


title: 2P24-invF-3-6h

city: Beijing

tag: age

value: 6 h

value: invF deficient mutant


title: 2P24-1-6h


title: SAMPLE 2_genomic DNA from fetal tissues

value: female


title: MN_exo3

source_name: Supernatant of RAW264.7 cell culture medium cultured on micro-/nano- titanium plate

value: Mouse-derived RAW264.7cells

value: cultured on micro-/nano- titanium plate


title: BAZ1B KO Rep1 - D6


title: Input_shVT

value: small cell lung cancer

value: Low passages (6-10)

value: cells transduced with non-targeting shRNA

value: control


title: MN_exo2


title: Il12rb2fl/fl Aldara rep1

value: skin


title: S_exo3


title: K14Cre/+ Il12rb2fl/fl Aldara rep1

value: interfollicular keratinocytes


title: MN_exo1


title: AgNPs-2

city: haikou

first: zhang

last: chuanling

address: renmin Road NO.58

institute: Hainan University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Hisat2 mapping to reference genome
count counting
Genome_build: Tair10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: leaves

growth_protocol: Six days in MS medium

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: silver nanoparticles and silver ions

tag: ecotype

value: Columbia

value: six days

tag: agent

value: AgNPs

tag: adenovirus

value: leaves


title: 2P24-2-6h

value: wild type


title: K14Cre/+ Il12rb2fl/fl Aldara rep3

tag: cell type

value: K14Cre/+ Il12rb2fl/fl

value: Aldara (topical) - day 1


title: AgNPs-3


title: BAZ1B WT Rep1 - D6

value: BAZ1B WT


title: 2P24-3-6h

value: 6 h


title: K14Cre/+ Il12rb2fl/fl naive rep4

value: untreated


title: Il12rb2fl/fl Aldara rep3


title: BAZ1B KO Rep1 - D0

value: BAZ1B KO


title: BAZ1B WT Rep2 - D6


title: FFPE_ATAC_on_FFPE_kidney_rep2

value: FVBN

value: FFPE


title: K14Cre/+ Il12rb2fl/fl naive rep3


title: S_exo1

value: Mouse-derived RAW264.7 cells

value: cultured on smooth titanium plate


title: BAZ1B WT Rep3 - D0


title: Il12rb2fl/fl naive  rep2

value: skin


title: WT rep2

city: London

first: Yi-Fang

address: Du Cane Road

institute: MRC LMS

description:
Expression profile of WT E14 ES cells
Gene_featurecounts.txt

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat2 (2.0.11) with parameters -r 100 --library-type fr-firststrand -N 2 --b2-very-sensitive --b2-L 25 -p 8
Gene annotations were obtained from Ensembl Mouse genome (NCBIM37). Gene-based read count and ERCC count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes Gene counts for each Sample

source_name: WT E14 ES cells

growth_protocol: Cells were grown in 15% FBS

extract_protocol:
Cells were collected and counted. RNA was extracted from 2 million cells using Trizol (ThermoFisher), 2 ul of a 1:10 dilution of ERCC Spike-in Mix (ThermoFisher) were added to each sample.
500 ng of RNA were used to prepare a polyA RNA library using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Embryonic stem cells


title: CK-2

value: Columbia

value: CK


title: K14Cre/+ Il12rb2fl/fl naive rep2

value: interfollicular keratinocytes


title: Ag+-3

value: six days

value: Ag+

value: leaves


title: AgNPs-1

value: AgNPs


title: Ag+-2


title: S138A rep2

description:
Expression profile of S138A mutant E14 ES cells
Gene_featurecounts.txt

source_name: S138A mutant E14 ES cells

value: S138A, UBE2D3 ser to ala mutant


title: S138A rep1


title: BAZ1B WT Rep2 - D0

value: BAZ1B WT


title: S138A rep3