title: P30 Stria Vascularis nuclei capture RNAlater

description: Single nuclei RNA-seq

tag: age

value: RNAlater treatment


title: M_FGC_17W_embryo1_sc8

status: Public on Oct 27 2020

type: SRA

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: bisulfite treated  genomic DNA

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.3.3) was used to remove the first 9 bases of random primer, adaptor sequences and low quality bases;
Clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module;
Methylation level of covered cytosines, including CpG, CHH and CHG were estimated using comstomized perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Methylation calling bed files which include the methylation level of covered cytosines, including CpG, CHH and CHG context

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Germ Cell

extract_protocol:
Pick a single cell to the lysis buffer by mouth pipette and lyse the cell at 50°C for 3 hrs. Genome DNA was bisulfite converted and purified with EZ-96 DNA Methylation-Direct™MagPrep (Zymo. D5044).
Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 13 cycles.

tag: gender

value: Male

tag: developmental stage

value: 17 week gestation


title: P8 NSC Nal

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

molecule: total RNA

organism: Mus musculus

source_name: NSC

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

tag: tissue

value: neural stem cells

tag: strain

tag: passages


title: eCLIP_rep1_INPUT

city: Wuhan

first: Jinglei

last: Xu

state: Hubei

address: Bayi road

department: The Institute of Advanced Studies

institute: Wuhan University

description: Flag-tag

data_processing:
Sequenced reads were trimmed for adaptor sequence, and segregated for repetitive elements, then mapped to hg38 whole genome using STAR (v 2.4.0i)
cluster identification was performed on usable reads using CLIPper with options -s GRCh38 -o --binomial 0.05 --save-pickle
Peak normalization vs paired SMInput datasets is run as eCLIP Standard Operating Procedure
The overlap between 2 replicates were calculated by bedtools intersect with options -wa -wb -s
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: Hela cells

growth_protocol: stable SERBP1-Flag Hela cells were grown at 37 °C and 5% CO2 in Dulbecco’s modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum (vol/vol) and 1% penicillin/streptomycin.

extract_protocol:
cells were resuspended in iCLIP buffer and sonicated in Bioruptor, lysates were digested by RNase I and RNA-RBP complexes were isolated with antibody
library construction were prepared according to eCLIP Standard Operating Procedure v1.P 20151108

treatment_protocol: UV crosslinking (254 nm, 400 mJ/cm2) in cold PBS

tag: treatment

value: UV-crosslinking

tag: clip antibody

value: ANTI-FLAG®(sigma #F7427)


title: eCLIP_rep2

description: Flag-tag

value: ANTI-FLAG®(sigma #F7428)


title: M_FGC_17W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: eCLIP_rep1

description: Flag-tag

value: ANTI-FLAG®(sigma #F7425)


title: M_FGC_17W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: CRAF KO-E rep2

city: Kunming

first: Tian-Rui

address: No.727 South Jingming Rd., Chenggong District

institute: Kunming university of science and technology

description: Processed data file: gene.description.xls

data_processing:
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 of 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 Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that because TopHat 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.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. FPKM of each gene was then 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 gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: gene.description.xls: Excel file includes read counts and FPKM values for each Sample.

source_name: human embryonic kidney cell line

extract_protocol:
Cells were sampled, and RNA was harvested using Trizol reagent. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubi 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with EGF or vehicle control.

tag: cell line

tag: cell type

value: human embryonic kidney cell line

tag: genotype/variation

value: CRAF-/-

value: EGF-activated


title: Control Rep1

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

country: USA

institute: Duke University

data_processing:
Quality of sequenced reads were assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). PolyA/T tails were trimmed using Cutadapt (Martin, 2011). Adaptor sequences were trimmed and shorter reads than 24 bp were dropped using Trimmomatic (Bolger et al., 2014). Reads were mapped to the reference genomes of human (hg38) and SARS-CoV-2 (wuhCor1) obtained from UCSC using Hisat2 (Kim et al., 2019) with default setting. Duplicate reads were removed using SAMtools (Li et al., 2009). Fragments numbers were counted using the featureCounts option of SUBREAD (Liao et al., 2014). Normalization and extraction of differentially expressed genes (DEGs) between control and treated were performed using an R package, DESeq2 (Love et al., 2014).
Genome_build: hg38 and wuhCor1
Supplementary_files_format_and_content: csv

molecule: polyA RNA

source_name: AT2 organoids without infection

growth_protocol: Human lung dissociation was as described previously (Zacharias et al., 2018).  Briefly, pleura was removed and remaining human lung tissue (approximately 2g) washed with PBS containing 1% Antibiotic-Antimycotic and cut into small pieces. Visible small airways and blood vessels were carefully removed to avoid clogging. Then samples were digested with 30 ml of enzyme mixture (Collagenase type I: 1.68 mg/ml, Dispase: 5U/ml, DNase: 10U/ml) at 37°C for 1h with rotation. The cells were filtered through a 100µm strainer and rinsed with 15ml DMEM/F12+10% FBS medium through the strainer. The supernatant was removed after centrifugation at 450g for 10 min and the cell pellet was resuspended in red blood cell lysis buffer for 10 min, washed with DMEM/F12 containing 10% FBS and filtered through a 40µm strainer. Total cells were centrifuged at 450g for 5 min at 4ºC and the cell pellet was processed for AT2 isolation. AT2 cells were isolated by Magnetic-activated cell sorting (MACS) or Fluorescence-activated cell sorting (FACS) based protocols. For mouse AT2 isolation the total lung cell pellet was resuspended in MACS buffer (1x PBS, pH 7.2, 1% BSA, and 2mM EDTA). CD31/CD45 positive cells were depleted using MACS beads according to the manufacturer’s instructions. After CD31/CD45 depletion AT2 cells were sorted based on TdTomato reporter and for AT2 cells without a reporter, cells were stained using the following antibodies: EpCAM/CD326, PDGFRα/CD140a and Lysotracker  as described previously (Katsura et al., 2019). For isolation of human AT2 cells, approximately 2-10 million total lung cells were resuspended in MACS buffer and incubated with Human TruStain FcX for 15 min at 4ºC followed by HTII-280 (1:60 dilution) antibody  for 1h at 4ºC. The cells were washed twice with MACS buffer and then incubated with anti-mouse IgM microbeads for 15 min at 4ºC. The cells were loaded into the LS column  and labeled cells collected magnetically. For FACS based purification of human AT2 cells, the total lung cell pellet was resuspended in MACS buffer. Cells were positively selected for the EpCAM population using CD326 (EpCAM) microbeads according to the manufacturer’s instructions. CD326 selected cells were stained with HTII-280 and LysoTracker at 37°C for 25min followed by secondary Alexa anti-mouse IgM-488 for 10min at 37°C. Sorting was performed using a FACS Vantage SE and SONY SH800S. HTII-280+ human AT2s (1-3 × 103) were resuspended in serum free medium and mixed with an equal amount of Matrigel and plated in 6 well plates. Human SFFF medium containing human recombinant FGF10, and human IL-1β

extract_protocol:
organoids were dissociated into single-cell suspension using TrypLE™ Select Enzyme at 37°C for 10min. The cell pellet was resuspended in 300µl of TRIzol™ LS Reagent Total RNA was extracted using the Direct-zol RNA MicroPrep kit according to the manufacturer’s instructions with DNase I treatment.
Isolated 1 µg total RNA of each sample was enriched for Poly-A RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, #E7490). Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, #E7770). Paired-end sequencing (150 bp for each read) was performed using HiSeq X ten.

treatment_protocol: Mature human AT2 organoid cultures were briefly washed twice with 500µl 1X PBS  following the removal of apical media. Cultures were then inoculated with 200µl of 1x107 PFU/ml of icSARS-CoV-2-GFP virus (1) or 200µl of 1X PBS for mock cultures. Organoids were allowed to incubate at 37C supplemented with 5% CO2 for 2h. Following incubation, the inoculum was removed, and organoid cultures were washed three times with 500ul 1X PBS. 1mL of organoid media was added to each culture. Organoids were incubated at 37C for 72h, with samples taken every 24h during infection. To sample, 100µl of media was removed. Equal volumes of fresh media were then added to the cultures to replace the sampled volume. Viral titers were ultimately determined after 72h by plaque assay on Vero E6 cells (USAMRIID).

value: Lung

value: alveolar type 2 cells

tag: infection status

value: without infection


title: CRAF KO-E rep3


title: M_FGC_17W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo2_sc7

description: bisulfite treated  genomic DNA

value: 7 week gestation


title: CRAF KO-E rep1


title: M_FGC_17W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: CRAF KO rep2

value: serum starved


title: CRAF KO rep3


title: Control Rep2


title: M_FGC_7W_embryo2_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: eCLIP_rep1_NX

description: Flag-tag

value: untreated

value: ANTI-FLAG®(sigma #F7426)


title: M_FGC_7W_embryo2_sc4

description: bisulfite treated  genomic DNA

value: Male


title: Control Rep3


title: WT-E rep3

value: wild type


title: CRAF KO rep1


title: M_FGC_7W_embryo2_sc2

description: bisulfite treated  genomic DNA


title: WT-E rep2


title: M_FGC_7W_embryo2_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo2_sc3

description: bisulfite treated  genomic DNA


title: WT rep3


title: M_FGC_7W_embryo1_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc1

description: bisulfite treated  genomic DNA

value: 17 week gestation


title: WT rep2


title: WT-E rep1


title: WT rep1


title: M_FGC_7W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo2_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc18

description: bisulfite treated  genomic DNA


title: Fresh-frozen canine healthy brain tissue - dog no. 60126

city: Bern

first: Diana

last: Solis

address: Länggassstrasse 120

department: Vetsuisse Faculty

country: Switzerland

institute: The University of Bern

data_processing:
Trimming and removal of adapters was pwrformed using fastp tool. Due to the specificity of the CORALL Total RNA-Seq Library Prep Kit, 12nt long UMIs at the beginning 5’ of the forwarding read were also removed. The fastp tool was used with following options: --umi --umi_loc read1 --umi_len 12 --trim_poly_g --trim_poly_x --cut_by_quality3 --detect_adapter_for_pe --dont_overwrite  -i input_read1.fastq.gz -I input_read2.fastq.gz -o trimmed_read1.fastq.gz -O trimmed_read2.fastq.gz
Before alignment, a STAR index was created using the full Canis lupus familiaris reference genome (Ensembl genome assembly: CanFam3.1 GCA_000002285.2) with "overhang" parameter set to 50: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir ${indexDir}/ --genomeFastaFiles Canis_lupus_familiaris.CanFam3.1.dna.toplevel.fa --sjdbGTFfile Canis_lupus_familiaris.CanFam3.1.100.gtf --sjdbOverhang 50
Reads were aligned against the full Canis lupus familiaris reference genome (Ensembl genome assembly: CanFam3.1 GCA_000002285.2) using previously created STAR index. The STAR tool was set to the following options: STAR --genomeDir ${indexDir} --sjdbGTFfile ${ref} --sjdbOverhang 50  --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM jM jI XS --readFilesIn trimmed_read1.fastq.gz trimmed_read2.fastq.gz --readFilesCommand zcat
Using Ensembl Canis_lupus_familiaris.CanFam3.1.100.gtf annotation the reads were counted at gene level using featureCounts tool with following options: featureCounts -p -C -s 1 -T 1 -Q 10 -a ${ref} -t exon -g gene_id -o FCresult.txt ${folder_with_all_BAM_files}/*bam
Genome_build: CanFam3.1 GCA_000002285.2
Supplementary_files_format_and_content: FCresult.txt file with counts at gene level for all samples

organism: Canis lupus familiaris

extract_protocol:
RNA extraction using the QIAGEN RNeasy® Mini Kit
The RNA-seq libraries were prepared using the Lexogen CORALL Total RNA-Seq Library Prep Kit which generates labelled with 12nt long Unique Molecular Identifiers (UMIs), forward stranded libraries for the transcriptome analyses. After the library preparation, the samples were amplified by PCR and finally purified to remove PCR components that could interfere with further RNA-seq quantification. Then, paired-end reads were generated by the Illumina NovaSeq 6000.

treatment_protocol: All brain tissues samples during necropsy, and collection time varied from 1 to 18 hours after death. Samples were either frozen at -80 ° C (FF); or/and immersion-fixed in 10% neutral buffered formalin and paraffin-embedded fixation as tissue blocks.

value: control

tag: tissue status

value: Fresh-frozen

tag: breed

value: Bolonka Swetna

tag: age of dog


title: Fresh-frozen canine healthy brain tissue - dog no. 60462

value: French Bulldog


title: Fresh-frozen canine healthy brain tissue - dog no. 60629

value: Berner sennenhund


title: Fresh-frozen canine healthy brain tissue - dog no. 60516

value: Mongrel


title: Fresh-frozen canine healthy brain tissue - dog no. 60460


title: M_FGC_7W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: Fresh-frozen canine healthy brain tissue - dog no. 60459

value: Hovawart


title: M_FGC_7W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: Fresh-frozen canine oligodendroglioma - dog no. 60461

source_name: Fresh-frozen canine oligodendroglioma

value: Oligodendroglioma Grade III

value: Boxer


title: M_FGC_7W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: Fresh-frozen canine oligodendroglioma - dog no. 60127

value: Pomerian


title: M_FGC_7W_embryo1_sc10

description: bisulfite treated  genomic DNA

value: 7 week gestation


title: M_FGC_7W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: Fresh-frozen canine oligodendroglioma - dog no. 60749


title: M_FGC_7W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: Fresh-frozen canine oligodendroglioma - dog no. 60631

value: Border Terrier


title: FFPE canine healthy brain tissue - dog no. 60462

source_name: FFPE canine healthy brain tissue

value: FFPE


title: Fresh-frozen canine oligodendroglioma - dog no. 60679

value: Oligodendroglioma Grade II


title: Fresh-frozen canine oligodendroglioma - dog no. 60636


title: FFPE canine healthy brain tissue - dog no. 61478


title: FFPE canine healthy brain tissue - dog no. 60126


title: M_FGC_7W_embryo1_sc5

description: bisulfite treated  genomic DNA

value: Male


title: M_FGC_7W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: FFPE canine healthy brain tissue - dog no. 60460


title: M_FGC_7W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: FFPE canine healthy brain tissue - dog no. 50315


title: M_FGC_7W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: FFPE canine healthy brain tissue - dog no. 50276


title: M_FGC_7W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: FFPE canine healthy brain tissue - dog no. 47198


title: M_FGC_6W_embryo2_sc7

description: bisulfite treated  genomic DNA

value: 6 week gestation


title: FFPE canine healthy brain tissue - dog no. 45726


title: FFPE canine healthy brain tissue - dog no. 43323


title: M_FGC_6W_embryo2_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo2_sc5

description: bisulfite treated  genomic DNA


title: FFPE canine healthy brain tissue - dog no. 36808


title: M_FGC_6W_embryo2_sc4

description: bisulfite treated  genomic DNA


title: FFPE canine oligodendroglioma - dog no. 60127

source_name: FFPE canine oligodendroglioma


title: FFPE canine oligodendroglioma - dog no. 60792


title: M_FGC_6W_embryo2_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo2_sc2

description: bisulfite treated  genomic DNA


title: FFPE canine oligodendroglioma - dog no. 60749


title: M_FGC_6W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: FFPE canine oligodendroglioma - dog no. 60679


title: M_FGC_6W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: FFPE canine oligodendroglioma - dog no. 60636


title: FFPE canine oligodendroglioma - dog no. 60461


title: FFPE canine oligodendroglioma - dog no. 51234


title: M_FGC_6W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo2_sc1

description: bisulfite treated  genomic DNA


title: FFPE canine oligodendroglioma - dog no. 60177


title: FFPE canine oligodendroglioma - dog no. 50416


title: M_FGC_6W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: FFPE canine oligodendroglioma - dog no. 43917


title: FFPE canine oligodendroglioma - dog no. 44331


title: M_FGC_6W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: VPC3

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

description: cell line

data_processing:
The sequenced data were mapped to the hg38 genome using STAR RNA-seq aligner. Uniquely mapped sequencing reads were assigned to hg38 refGene genes using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: text file, featureCounts

source_name: Ventricule cardio-myofibroblast + high phosphate and calcium

extract_protocol:
Explanted whole human hearts were transported on ice to the Massachusetts General Hospital. Organs underwent gross pathologic examination, including measurements of heart weight, left atrial and left ventricular wall thickness. Left ventricular free wall was excised and total RNA was extracted using the Nucleospin RNA isolation kit (Clontech).
cDNA libraries were generated using SMART-seq2 and NExtera XT (Illumina). Sequencing was performed with paired-end configuration on Nextseq 500.

value: fibroblast

tag: patient diagnosis


title: VPC2

description: cell line


title: M_FGC_6W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_6W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: VPC1_2

description:
cell line
excluded from analysis


title: VP1_2

description:
cell line
excluded from analysis

source_name: Ventricule cardio-myofibroblast + high phosphate


title: VN3

description: cell line

source_name: Ventricule cardio-myofibroblast + vehicle


title: VN2

description: cell line


title: VN1

description: cell line


title: Kc167_ModKD_neuRNAseq_R2

city: bethesda

first: Elissa

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

description: nascent EU RNAseq

data_processing:
removing adapter sequences with cutadapt v2.7
aligning the reads with hisat2 v2.1.0 against Drosophia melanogaster whole genome, multimapping reads were filtered using samtools 1.9
using featurecounts v1.6.4 to estimate the number of gene reads
using DESeq2 v1.22.1 in v3.5.1 R version to perform differential expression analysis
Genome_build: Flybase r6.24
Supplementary_files_format_and_content: featurecounts output and bigWig files

organism: Drosophila melanogaster

growth_protocol: Kc167 cells-derived from Drosophila embryo, were routingly maintained in CCM3 (Thermo Scientific HyClone, Logan, UT). The cells were maintained in monolayer at 25°C.

extract_protocol:
Nascent EU RNA seq (neuRNA-seq) labeling and capture were done by using Click-iT Nascent RNA Capture Kit (Thermo Fisher Scientific) according to manufacturer’s protocol. Kc- cells were incubated with 0.2mM EU for 1 h and RNA was extracted with Trizol (Thermo Fisher Scientific). Next RNA was chemical fragmentated for 5 min at 70C with RNA Fragmentation Reagents (Thermo Fisher Scientific), followed by DNase I treatment (Roche). Then RNA was precipitated using Phenol:Chloroform (Thermo Fisher Scientific) purification. The Click-iT reaction was performed with 0.5 mM biotin azide using 5 µg of EU-RNA and biotinylated RNA was captured with 12 μL T1 beads. After that nascent EU-RNA was used to generate RNA-seq libraries with Ovation RNA-seq Systems 1–16 for Model Organisms (Nugen). Samples were sequenced with HiSeq2500 (Illumina) by 50 bp single-end sequencing at the NIDDK Genomics Core Facility.
RNA-seq libraries were prepared with Ovation RNA-seq Systems 1–16 for Model Organisms (Nugen) according to manufacturer's protocol.
neuRNA-seq

treatment_protocol: 10 million Kc167 cells were transfected with 20 ug of dsRNA against M1BP, 12 µg of dsRNA  against Cp190, 5 µg of dsRNA against Mod(mdg4)67.2 or no RNA (mock) by using Amexa cell line Nucleofector kit V (Lonza) and electroporated using G-30 program. Cells were incubated for 5 d at 25°C to obtain efficient depletion of each protein.

value: Kc167 cells

value: embryo

tag: Sex

value: female

value: ModKD


title: Kc167_M1BPKD_neuRNAseq_R3

description: nascent EU RNAseq


title: VC2

description: cell line

source_name: Ventricule cardio-myofibroblast + high calcium


title: RF8

source_name: Human Hemodialysis

value: heart tissue

value: CKD


title: Kc167_ModKD_neuRNAseq_R1

description: nascent EU RNAseq


title: VC1

description: cell line


title: Kc167_mock_neuRNAseq_R4

description: nascent EU RNAseq

value: mock


title: RF9


title: Kc167_M1BPKD_neuRNAseq_R1

description: nascent EU RNAseq


title: Kc167_Cp190KD_neuRNAseq_R2

description: nascent EU RNAseq


title: RF7

description: excluded from analysis


title: RF6

description: excluded from analysis


title: PS19 rep3

city: atlanta

first: David

middle: J

last: Katz

state: ga

address: 615 Michael st

institute: Emory University

data_processing:
FASTQ files were quality assessed using FASTQC (v.0.11.7), trimmed using Trimmomatic (v.0.36.5) and minimum QC score of 20 and minimum read length of 36bp.
Paired-end reads were subsequently mapped to the GRCm38 genome using HISAT2 (v.2.1.0). Unmapped, unpaired and multiply mapped reads were removed using Filter SAM or BAM (v.1.1.2).
Assignment of transcripts to GRCm38 genomic features was performed using Featurecounts (v.1.6.0.6) and the Ensembl GRCm38.93 gtf file
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) ((46)). For all datasets, a cutoff of adjusted p-value < 0.1 and abs (log2 fold change) > 0.58 was applied
Genome_build: GRCm38.93
Supplementary_files_format_and_content: tab-delimited text files include raw count data for each sample

source_name: Hippocampus

extract_protocol:
hippocampi were dissected and snap frozen with liquid nitrogen in 1mL Trizol, and stored at -80°C. For RNA isolation, samples were thawed at 37°C then kept on ice prior to homogenization with Polytron homogenizer with a 5 second pulse. After a 5 minute incubation at room temperature, one tenth the sample volume of 1-bromo-3chloropropane was added, mixed by inversion and incubated for 3 minutes at room temperature. Samples were then centrifuged at 13,000 X g for 15 minutes at 4°C to separate the aqueous and organic layers. As much of the aqueous layer was recovered as possible, then RNA was precipitated with isoproponal. Pellets were then washed with 75% ethanol and resuspended in 50μL of dionized water.
RNA library preparation and sequencing were performed by HudsonAlpha Genomic Services Lab. RNA was Poly(A) selected and 300bp size selected

value: hippocampus

tag: genotype

value: PS19 tg ; LSD1 +/+

value: PS19 transgene


title: Kc167_mock_neuRNAseq_R2

description: nascent EU RNAseq


title: Kc167_mock_neuRNAseq_R1

description: nascent EU RNAseq


title: RF5

description: excluded from analysis


title: Kc167_Cp190KD_M1BP_R2

data_processing:
ChIP-seq reads were aligned to the Flybase r6-24 genome assembly  using Bowtie2 v2.3.5
Multimapping reads removed with samtools v1.9 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.20.2
peaks were called using  MACS2 version 2.2.5
Genome_build: Flybase r6-24 genome

extract_protocol:
ChIP-seq was performed as described previously (Bag et al., 2019).
ChIP-seq library was performed as described previously (Bag et al., 2019, Matzat et al., 2012).

treatment_protocol: 10 million Kc167 cells were transfected with 20 ug of dsRNA (Li and Gilmour, 2013) against M1BP and 12 µg of dsRNA (Moshkovich et al., 2011) against Cp190 by using Amexa cell line Nucleofector kit V (Lonza) and incubated 5 days at 25°C to obtain significant knockdown of M1BP and CP190.

tag: chip antibody


title: RF4


title: Kc167_mock_neuRNAseq_R3

description: nascent EU RNAseq

tag: developmental stage


title: Kc167_Cp190KD_input_R2


title: Kc167_M1BPKD_neuRNAseq_R2

description: nascent EU RNAseq


title: RF3

tag: tissue


title: RF19


title: VC3

description: cell line


title: RF2


title: Kc167_Cp190KD_M1BP_R1


title: RF18


title: Kc167_Cp190KD_CP190_R1


title: Kc167_Cp190KD_CP190_R2


title: Kc167_Cp190KD_input_R1


title: RF17


title: Kc167_mock2_CP190_R2


title: Kc167_Cp190KD_neuRNAseq_R1

description: nascent EU RNAseq


title: Kc167_mock2_M1BP_R2


title: RF16


title: VP3

description: cell line


title: RF15_2

description: excluded from analysis


title: Kc167_mock2_CP190_R1


title: Kc167_mock2_M1BP_R1


title: Kc167_mock2_input_R1


title: RF12


title: PD3

description: excluded from analysis

source_name: Human Peritoneal dialysis


title: PD1

description: excluded from analysis


title: Kc167_M1BPKD_MOD_R2

value: MOD


title: Kc167_M1BPKD_CP190_R2


title: PD2

description: excluded from analysis


title: N8

description: excluded from analysis

source_name: Human healthy control

value: healthy


title: Kc167_M1BPKD_input_R2


title: Kc167_M1BPKD_M1BP_R2


title: N15


title: Kc167_mock2_input_R2


title: RF13


title: N14


title: Kc167_M1BPKD_CP190_R1


title: Kc167_M1BPKD_SuHw_R1

value: SuHw


title: N9

description: excluded from analysis


title: N12


title: Kc167_M1BPKD_SuHw_R2


title: MPC3

description: cell line


title: Kc167_M1BPKD_M1BP_R1


title: N10


title: Kc167_mock_MOD_R2


title: RF11


title: MPC2

description: cell line


title: Kc167_mock_SuHw_R2


title: MP3

description: cell line


title: MP2

description: cell line


title: Kc167_mock_M1BP_R2


title: N7

description: excluded from analysis


title: Kc167_mock_input_R2


title: Kc167_M1BPKD_MOD_R1


title: Kc167_mock_MOD_R1


title: MN3

description: cell line


title: Kc167_mock_CP190_R1


title: MN2

description: cell line


title: Kc167_mock_SuHw_R1


title: N13


title: Kc167_M1BPKD_input_R1


title: MN1

description: cell line


title: MC3

description: cell line


title: Kc167_mock_M1BP_R1


title: Kc167_mock_CP190_R2


title: Kc167_mock_input_R1


title: CAD7

description: excluded from analysis

source_name: Human Hypertension

value: hypertension


title: Sample_103951

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description:
∆CXCL12
FACS-sorted

data_processing:
We downloaded the reads files and concatenated those into a single .fastq.gz file for each sample.
We checked the quality of the raw reads data for each sample using FastQC [1] (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference genome including both mRNAs and lncRNAs (UCSC mm10) [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We ran two different, popular techniques for differential expression analysis: Cufflinks/CuffDiff and HTSeq/DESeq2 [9], using UCSC mm10.fa as the reference genome sequence.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2: depth_normalized_counts, raw_counts, rlog_normalized_counts, Tuxedo: Fpkm, RawCounts, ScaledCounts

source_name: Bone/bone marrow (femur)

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated by collagenase. GFP+ cells (Control) or GFP+tdTomato+ cells (∆CXCL12) were FACS-isolated. ~20,000 cells were used for subsequent steps.
Nextera XT DNA Library Preparation Kit

value: Bone/bone marrow (femur)

value: delta-CXCL12 bone marrow stromal cells (Cxcl12-GFP+tdTomato+)

tag: age

value: Postnatal day 21


title: MC2

description: cell line

value: fibroblast


title: Sample_103949

description:
∆CXCL12
FACS-sorted


title: Sample_103950

description:
∆CXCL12
FACS-sorted


title: Sample_103948

description:
Control
FACS-sorted

value: Cxcl12(GFP/fl); R26R(tdTomato/+)

value: CXCL12+ bone marrow stromal cells (Cxcl12-GFP+)


title: CAD8

description: excluded from analysis


title: CAD6


title: Sample_103947

description:
Control
FACS-sorted


title: MP1

description: cell line


title: CAD5


title: CAD4


title: MC1

description: cell line


title: CAD3


title: CAD2


title: CAD1


title: CAD11


title: CAD10


title: Tcells_gut_steadystate_R2

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

data_processing:
A high read quality (mean score above 28) in all samples was confirmed using FastQC. Reads were aligned to the mouse genome (GRCm38) using Star (v2.6.0c) (Dobin et al. 2013) with the parameters --quantMode GeneCounts, --outFilterMultimapNmax 1 and --outFilterMatchNmin 35. The Star index was generated with the parameters --sjdbGTFfile (transcriptome version 93) and --sjdbOverhang 74. The mean alignment rate was above 85% per sample.  Read counting was performed by star using unstranded counting for both datasets. For both datasets normalised counts and differential expression values were generated using DESeq2 (Love et al. 2014) under default settings. Genes with an adjusted p-value of less than 0.01 and an absolute fold change of greater than 2 were considered significant.
The RNA-seq data was explored using Searchlight 2 (v2.0.0a) (Cole et al. n.d.) and R (version 3.4.4). Specifically, enrichment of gene ontologies was generated using a standard hypergeometric test with Benjamini-Hochberg multisample correction, and the gene-set database Gene Ontologies Molecular Function (GO_MF) (as downloaded from MsigDB collections (Subramanian et al. 2005).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include per gene read counts for each sample

source_name: T cells

extract_protocol:
Cells were isolated from C57BL/6 mice that previously underwent complete mesenteric lymphadenectomy. ILCs were identified as live, single, CD45+ IL-7Rα+ lineage- (CD3, CD5, CD11b, CD11c, B220) cells and T cells as live, single, CD45+ CD11b- CD11c- B220- CD3+ CD5+ CD4+ CD44high CD25- cells. Cells for RNA seq were purified by flow cytometric sorting, collected into 350 μl RLT plus buffer (Qiagen) and stored at -80°C until further processing. Samples were sorted in quadruplicates and isolated cell types included migratory ILCs (n = 15) and T cells (n = 8) from afferent lymph of thoracic duct cannulated mice in steady state, ILCs (n = 4) and T cells (n = 4) from the colonic and small intestinal lamina propria at similar proportions, and migratory ILCs (n = 25) from afferent lymph of Salmonella infected mice that underwent thoracic duct cannulation. RNA was isolated according to the manufacturer’s protocol (RNAeasy plus micro kit, Qiagen). CD11b+ CD103- and CD11b+ CD103+ DCs (live, single, CD45+, CD64- MHCIIhigh CD11c+) were isolated from the small intestinal lamina propria of C57BL/6 mice after removal of Peyer’s Patches. The migratory DC counterparts were isolated by thoracic duct cannulations of mice that previously underwent complete mesenteric lymphadenectomy. RNA was isolated according to the manufacturer’s protocol (RNAeasy kit, Qiagen).
The ILC and T-cell sequencing libraries were prepared according to published protocols (Bar-Ephraim et al. 2017), using a TAKARA SMART-seq v4 ultra low input library preparation kit with 15 cycles of amplification, and were sequenced to a mean depth of 5.1 million read pairs per sample using an Illumina HiSeq 2500. The DC sequencing libraries were prepared using a TAKARA SMART-seq v4 ultra low input library preparation kit, and were sequenced to a mean depth of 37.5 million read pairs per sample using an Illumina HiSeq 4000. The read length for both libraries was 75bp.

treatment_protocol: C57BL/6 mice were either used at steady state or infected with Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344. For S. Typhimurium infections,  mice received 20 mg streptomycin (Sigma) in 100 μl PBS via oral gavage 24h before infection with Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344. S. Typhimurium was grown in luria broth (LB) at 37°C for 5h at 180 rpm. After incubation, the cultures were diluted 1:2 in LB and further kept in a static incubator overnight. The following day, bacterial cell density was adjusted to an OD600 of 0.75. Intact or lymphadenctomised mice received 5-8 x 107 colony forming units (CFU) bacteria in 100μl PBS via oral gavage.

value: T cells

tag: strain

value: small intestinal and colonic lamina propria


title: Tcells_gut_steadystate_R3


title: Tcells_gut_steadystate_R1


title: Tcells_gut_steadystate_R4


title: Tcells_lymph_steadystate_R4

value: intestinal lymph


title: APC3

description: cell line

source_name: atrial cardio myofibroblast + high phosphate and calcium


title: APC1

description: cell line


title: APC2

description: cell line


title: Tcells_lymph_steadystate_R1


title: ILC_gut_steadystate_R4

source_name: Innate lymphoid cells

value: Innate lymphoid cells


title: ILC_gut_steadystate_R2


title: ILC_gut_steadystate_R3


title: Tcells_lymph_steadystate_R3


title: AP2

description: cell line

source_name: atrial cardio myofibroblast + high phosphate


title: AP3

description: cell line


title: AP1

description: cell line


title: Sample_103946

description:
Control
FACS-sorted


title: AN3

description: cell line

source_name: atrial cardio myofibroblast + vehicle


title: AN2

description: cell line


title: ILC_lymph_steadystate_R4


title: ILC_gut_steadystate_R1


title: AN1

description: cell line


title: ILC_lymph_steadystate_R3


title: WT - Col-0 [Sample_Col_w_4]

city: Tel - Aviv

first: Alin

last: Finkelshtein

state: Israel

address: Haim levanon st. 30, Britania building, room 407

department: Plant sciences

country: Israel

institute: Tel Aviv university

data_processing:
The reads were mapped to the TAIR10 genome using Tophat2 version 2.1.0 with up to 3 mismatches allowed per read.
Only uniquely mapped reads were counted to exons, using 'HTSeq-count' package version 0.6.1 with ‘union’ mode.
Normalization and differential expression analyses were conducted using DESeq2 R package version 1.18.1.
Genome_build: TAIR10
Supplementary_files_format_and_content: all data.xlsx: Excel file that concentrates all the raw data before any analysis is done.
Supplementary_files_format_and_content: Primed genes.xlsx: Excel file that summarizes all primed genes. We have defined genes as primed if they were significantly misregulated in WT plants following I3C treatment and showed similar misregulation in untreated ICT1 samples.
Supplementary_files_format_and_content: heatmap_wt. xlsx: Excel file that analyses the genes affected in WT following I3C treatment.
Supplementary_files_format_and_content: I3C_TREATED.xlsx: Excel file that contains only the I3C treated samples for easier understanding of genes and pathways affected by the treatment.

organism: Arabidopsis thaliana

source_name: plant

growth_protocol: The seedlings were grown hydroponically for 10 days. In MS liquid medium, long day light, 21 Celsius degrees, 50% humidity.

extract_protocol:
Roots were cut and the RNA was extracted with Trizol following zymo RNA mini prep quick (DNase treatment was also performed).
27 RNA libraries were generated using 'Illumina TruSeq RNA Library Preparation Kit v2' according to manufacturer's protocol.

treatment_protocol: 20 seedlings were used for each treatment. In case of wounding, each leaf was wounded with thin tweezers 3 times and incubated in room temperature for 8 hours (to allow the signal to reach the root tissue). In all other treatments, solutions of DMSO, 200 & 400µM of I3C were prepared in MS medium, added to the liquid medium of hydroponic growth and incubated for 2 hours. All samples were collected at once (to eliminate the circadian clock effect).

tag: strain/ecotype

value: WT

value: 10-day-old seedling

value: root

tag: treatment

value: w (wounded)


title: ILC_lymph_steadystate_R1


title: ILC_lymph_steadystate_R2


title: WT - Col-0 [Sample_Col_w_2]


title: ILC_lymph_Salmonella_R3


title: WT - Col-0 [Sample_Col_w_1]


title: ILC_lymph_Salmonella_R4


title: WT - Col-0 [Sample_Col_NT_5]

value: NT (No Treatment) - DMSO


title: WT - Col-0 [Sample_Col_NT_4]


title: ILC_lymph_Salmonella_R1


title: Tcells_lymph_steadystate_R2


title: ILC_lymph_Salmonella_R2


title: Double+DC_node_steadystate_R3

source_name: CD103+ CD11b+ dendritic cells

value: CD103+ CD11b+ dendritic cells

value: intestinal lymph node


title: WT - Col-0 [Sample_Col_NT_3]


title: WT - Col-0 [Sample_Col_400_5]


title: WT - Col-0 [Sample_Col_400_4]


title: Double+DC_duct_steadystate_R2

value: intestinal lymph duct


title: CD103b+DC_duct_steadystate_R5

source_name: CD103+ dendritic cells

value: CD103+ dendritic cells


title: WT - Col-0 [Sample_Col_200_5]


title: Double+DC_duct_steadystate_R3


title: CD11b+DC_duct_steadystate_R2

source_name: CD11b+ dendritic cells

value: CD11b+ dendritic cells


title: CD11b+DC_duct_steadystate_R1


title: WT - Col-0 [Sample_Col_200_4]


title: WT - Col-0 [Sample_Col_200_1]


title: ICT1_8098 (S30 overexpressing mutant) [Sample_8098_NT_5]

value: s30 overexpression (under s35 promoter)


title: Dvir_zebrafish_Light_7_010919

city: Ashburn

first: Dvir

last: Gur

state: VA

address: 19700 Helix Dr

institute: HHMI Janelia Research Campus

data_processing:
The libraries were pooled and sequenced on an Illumina NextSeq 550 high-output flowcell with 26 base pair read1, 50 base pair read 2, 8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings.
Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 (Zorita et al., 2015) with the following additional parameters: “-d 1 -q --print_clusters”. Read 2 sequences were renamed using the error-corrected barcode from starcode and UMI sequences from read 1, and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl (ensemble.org) using STAR (Dobin et al., 2013) with the following additional parameters: “--alignIntronMax 200000 --outSAMattributes All --outSAMunmapped Within --outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene-level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request.
Genome_build: Danio rerio GRCz11.94 genome assembly from Ensembl.org
Supplementary_files_format_and_content: single Microsoft Excel file that includes counts per million (CPM) and correct p-values for each sample and gene

organism: Danio rerio

source_name: Flank dermis

growth_protocol: Zebrafish were housed at ~28 °C, 14L:10D, fed rotifers, Artemia and flake food

extract_protocol:
Fish were euthanized in MS222 and the stripe and interstiped regions were micro-dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase (0.25 mg/ml in dPBS) at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re-suspended in 1% BSA / 5% FBS in dPBS before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter (BD Biosciences, San Jose, CA, USA) coupled with BD FACSDiva software (BD Biosciences) for instrument operation, data acquisition, and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore-excitation and a 100-μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter (FSC) detector photomultiplier tube (PMT) gain setting = 80 V with a 1.5 neutral density filter; side light scatter (SSC) detector PMT gain setting = 90 V; FSC threshold = 10,000; PE-Texas Red (PE TX Red) channel PMT gain setting = 280 V; fluorescein isothiocyanate (FITC) channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts (below 500 processed events per sec). The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back-gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled (PNP4-mCherry-Eos) from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart-scrb lysis buffer (0.2% Triton X-100 [Sigma], 0.1 U/ul RNAse inhibitor [NEB]) using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. After sorting, the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge (Eppendorf AG, Hamburg, Germany) and stored at -80ºC until further processing.
Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously (Cembrowski et al., 2018) with minor modifications to the sequencing configuration.  Reverse transcription, PCR, purification, tagmentation, and library quantification were performed as described.

treatment_protocol: Untreated fish

value: Flank dermis

tag: stripe pattern

value: light

tag: reporter

value: Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells


title: Dvir_zebrafish_Dark_9_010919

value: dark


title: Dvir_zebrafish_Light_6_010919


title: Dvir_zebrafish_Dark_2_010919


title: ICT1_8098 (S30 overexpressing mutant) [Sample_8098_200_4]

tag: genotype/variation


title: ICT1_8098 (S30 overexpressing mutant) [Sample_8098_NT_1]


title: Dvir_zebrafish_Light_5_010919


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_NT_2]


title: ICT1_8098 (S30 overexpressing mutant) [Sample_8098_200_2]


title: WT - Col-0 [Sample_Col_400_1]


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_NT_1]


title: Dvir_zebrafish_Dark_3_010919


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_400_4]


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_NT_5]


title: ICT1_8098 (S30 overexpressing mutant) [Sample_8098_200_3]


title: Dvir_zebrafish_Light_4_010919


title: Dvir_zebrafish_Dark_1_010919


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_400_3]


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_200_5]


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_200_4]


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_400_5]


title: ICT1_8098 (S30 overexpressing mutant) [Sample_8098_NT_4]


title: ICT1_2 (S30 overexpressing mutant) [Sample_2_200_2]


title: 4340.V SC_Root_N_1

city: Cologne

first: Thorsten

last: Thiergart

address: Carl-con-Linne-Weg 40

country: Germany

institute: MPIPZ cologne

description:
4340.V
SC_Root_N_1

data_processing:
FastQC suite was used to check the quality of the reads
RNA-seq reads were mapped to the annotated genome of A. thaliana (TAIR10) using Tophat2
Mapped RNA-seq reads were subsequently transformed into a fragment count per gene per sample using Htseq
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw count data

source_name: Root

growth_protocol: Shoots and roots of five-week old A. thaliana Col-0 grown in FlowPot system

extract_protocol: Total RNA from all samples were extracted using the RNeasy® Plant Mini Kit (Qiagen, Germany)

treatment_protocol: Roots were washed quickly (< 1 min) to detach the surrounding peat matrix using 10% RNAlater (Qiagen, Valencia, CA) in 1X PBS as the capture buffer to mitigate RNA degradation

tag: inculated with microbes

value: No

tag: condition

value: Shade


title: 4340.U SC_Root_Y_3

description:
4340.U
SC_Root_Y_3

value: Yes


title: 4340.S SC_Root_Y_1

description:
4340.S
SC_Root_Y_1


title: 4340.T SC_Root_Y_2

description:
4340.T
SC_Root_Y_2


title: 4340.X SC_Root_N_3

description:
4340.X
SC_Root_N_3


title: 4340.P NC_Root_N_1

description:
4340.P
NC_Root_N_1

value: Normal


title: 4340.Q NC_Root_N_2

description:
4340.Q
NC_Root_N_2


title: K_2_C_NS

type: RNA

city: Beijing

first: Fengyang

last: Shi

address: No. 7 Beinong Road, Changping District

institute: Beijing University Of Agriculture

description: Gene expression at 21dpi without PCV2 infection

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=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

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.

organism: Sus scrofa

source_name: Ileum, 21dpi, control, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, 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 using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: mucosal epithelial and lamina propria

tag: gender

value: male


title: 4340.O NC_Root_Y_3

description:
4340.O
NC_Root_Y_3


title: K_3_C_NS


title: K_2_NS

value: Peyer's patches and mesenteric lymph nodes


title: K_1_C_NS


title: chorionic villus, 300M82

city: Stanford

first: Amy

middle: Elizabeth

last: Braun

state: California

address: 300 Pasteur Dr., Grant Building, S365

department: OBGYN

institute: Stanford

data_processing:
fastq files were aligned to a unique index composed of a human reference transcriptome (Ensembl GRCh38) using the Lexogen Bluebee integrated data analysis pipeline
Counts produced by htseq-count (v0.7.2) were then downloaded and imported into R for further analysis.
Expression data was normalized using the voom() function in the Limma package in R (v3.38.3) to transform raw count data into log2-counts per million (logCPM)
Statistically significant differences between male (M) and female (F) gene expression were identified using an empirical Bayes approach. p values were produced by the moderated t-statistic underwent Benjamini-Hochberg correction for multiple comparisons, and those smaller than a significance threshold (alpha = 0.05) were called differentially expressed.
Genome_build: human reference transcriptome (Ensembl GRCh38)
Supplementary_files_format_and_content: tab-delimited text file includes log2 counts per million (CPM) values for each Sample

source_name: chorionic villus

extract_protocol:
RNA was extracted from frozen chorionic villi samples using Trizol fractionation [57], followed by ethanol precipitation, and collection by column centrifugation (QIAGEN midi-prep for human, Germantown, MD)
Single-stranded 3′-Seq libraries were chosen were prepared using a Lexogen QuantSeq FWD kit (Lexogen, SKU #015.96)
3' RNA-seq

value: M

value: gestational day 82

value: chorionic villus

tag: index

value: GCGAAT


title: chorionic villus, 291F86

value: F

value: gestational day 86

value: GCTCGA


title: chorionic villus, 307M109

value: gestational day 109

value: CGAAGG


title: chorionic villus, 287F110

value: gestational day 110

value: CAAGCA


title: 4340.W SC_Root_N_2

description:
4340.W
SC_Root_N_2

value: No

value: Shade


title: chorionic villus, 303F106

value: gestational day 106

value: TGGATT


title: 4340.N NC_Root_Y_2

description:
4340.N
NC_Root_Y_2

value: Yes

value: Normal


title: K_1_NS

value: Peyer's patches and mesenteric lymph nodes

value: male


title: chorionic villus, 305F98

value: gestational day 98

value: chorionic villus

value: ACCTAC


title: G_3_C_NS

description: Gene expression at 21dpi after PCV2 infection

source_name: Ileum, 21dpi, infection, replicate 1

value: mucosal epithelial and lamina propria


title: G_2_NS


title: K_3_NS


title: 4340.R NC_Root_N_3

description:
4340.R
NC_Root_N_3


title: G_3_NS


title: chorionic villus, 270F87

value: F

value: gestational day 87

value: TTTATG


title: chorionic villus, 269F101

value: gestational day 101

value: CCGCAA


title: 4340.M NC_Root_Y_1

description:
4340.M
NC_Root_Y_1


title: G_1_C_NS


title: G_2_C_NS


title: chorionic villus, 285M101

value: M

value: AACGCC


title: chorionic villus, 268F98

value: CACACT


title: 4340.H SC_Shoot_N_2

description:
4340.H
SC_Shoot_N_2

source_name: Shoot

value: No

value: Shade


title: chorionic villus, 265M88

value: gestational day 88

value: TATGTC


title: 4340.G SC_Shoot_N_1

description:
4340.G
SC_Shoot_N_1


title: chorionic villus, 266F95

value: gestational day 95

value: GAGTCC


title: 4340.D NC_Shoot_Y_1

description:
4340.D
NC_Shoot_Y_1

value: Yes

value: Normal


title: chorionic villus, 264F86

value: gestational day 86

value: chorionic villus

value: ATACTG


title: 4340.E NC_Shoot_Y_2

description:
4340.E
NC_Shoot_Y_2


title: chorionic villus, 263M85

value: gestational day 85

value: GTCAGG


title: 4340.C NC_Shoot_N_3

description:
4340.C
NC_Shoot_N_3


title: chorionic villus, 256M94

value: gestational day 94

value: GGCTGC


title: chorionic villus, 258F110

value: F

value: gestational day 110

value: TACCTT


title: chorionic villus, 251M91

value: M

value: gestational day 91

value: CCTAAG


title: 4340.B NC_Shoot_N_2

description:
4340.B
NC_Shoot_N_2

value: No


title: chorionic villus, 238M81

value: gestational day 81

value: ATGAAC


title: 4340.L SC_Shoot_Y_3

description:
4340.L
SC_Shoot_Y_3

value: Yes

value: Shade


title: 4340.A NC_Shoot_N_1

description:
4340.A
NC_Shoot_N_1

value: Normal


title: 4340.K SC_Shoot_Y_2

description:
4340.K
SC_Shoot_Y_2


title: 4339.X NC_Root_Y_3

description:
4339.X
NC_Root_Y_3


title: 4340.J SC_Shoot_Y_1

description:
4340.J
SC_Shoot_Y_1


title: chorionic villus, 267M105

value: gestational day 105

value: chorionic villus

value: GGAGGT


title: 4339.W NC_Root_Y_2

description:
4339.W
NC_Root_Y_2


title: 4340.I SC_Shoot_N_3

description:
4340.I
SC_Shoot_N_3


title: 4339.V NC_Root_Y_1

description:
4339.V
NC_Root_Y_1


title: chorionic villus, 223M82

value: gestational day 82

value: CGGTTA


title: chorionic villus, 212F82

value: F

value: TCAGGA


title: chorionic villus, 233M83

value: gestational day 83

value: TTAACT


title: 4340.F NC_Shoot_Y_3

description:
4340.F
NC_Shoot_Y_3


title: chorionic villus, 259M83

value: M

value: TCTTAA


title: 4339.T SC_Root_Y_2

description:
4339.T
SC_Root_Y_2


title: 4339.S SC_Root_Y_1

description:
4339.S
SC_Root_Y_1


title: 4339.R SC_Root_N_3

description:
4339.R
SC_Root_N_3

value: No


title: 4339.Q SC_Root_N_2

description:
4339.Q
SC_Root_N_2


title: 68D_SK_KD

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

data_processing:
Quality control performed using fastQC, fastQScreen
RNA-seq reads were aligned to the hg38 genome assembly using STAR version 2.6.0a
RNA-seq reads were mapped to v29 genomic feature using featureCounts, the package version 1.6.4 (Y.Liao, GK.Smyth, and W.Shi 2014)
Differential gene expression analysis (DEG) was assessed with voom+limma in the limma package version 3.40.2 (ME.Ritchie and GK.Smyth 2015) and using R version 3.6.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes counts values

source_name: tumor sample

extract_protocol:
Rneasy kit (Qiagen)
TruSeq stranded mRNA Library Prep (Illumina)

tag: cell line

value: SK-ES1 xenograft

value: Knock-down for RING1B

value: Ewing sarcoma


title: 68E_SK_KD


title: 67D_SK_KD


title: 67E_SK_KD


title: 62E_SK_CTRL

value: wild-type


title: 4339.P SC_Root_N_1

description:
4339.P
SC_Root_N_1

value: Shade


title: 64E_SK_CTRL


title: 4339.O NC_Root_N_3

description:
4339.O
NC_Root_N_3

value: Normal


title: 4339.N NC_Root_N_2

description:
4339.N
NC_Root_N_2


title: 65D_SK_KD


title: 4339.M NC_Root_N_1

description:
4339.M
NC_Root_N_1


title: 62D_SK_CTRL


title: 4339.U SC_Root_Y_3

description:
4339.U
SC_Root_Y_3

value: Yes


title: 4339.L NC_Shoot_Y_3

description:
4339.L
NC_Shoot_Y_3


title: 61E_SK_CTRL


title: 4339.K NC_Shoot_Y_2

description:
4339.K
NC_Shoot_Y_2


title: 4339.J NC_Shoot_Y_1

description:
4339.J
NC_Shoot_Y_1


title: 60E_SK_CTRL


title: 60D_SK_CTRL


title: 4339.I NC_Shoot_N_3

description:
4339.I
NC_Shoot_N_3


title: 4339.H NC_Shoot_N_2

description:
4339.H
NC_Shoot_N_2


title: 4339.G NC_Shoot_N_1

description:
4339.G
NC_Shoot_N_1


title: 66D_SK_KD


title: ChIPseq_RING1B-shRING1B

description: ChIPseq experiment

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Human genome (hg19, February 2009) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIPseq peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of reads of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIPseq)
Supplementary_files_format_and_content: ChIPseq_BMI1.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_CBX7.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_EWSR1-FLI1.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_INPUTforEWSR1-FLI1.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_RING1B-shCTRL.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_EWSR1-FLI1-shCTRL.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_INPUT-shCTRL.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_RING1B-shRING1B.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_EWSR1-FLI1-shRING1B.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_INPUT-shRING1B.bedgraph.gz
Supplementary_files_format_and_content: Files .bed (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIPseq_EWSR1-FLI1.bed.gz

source_name: Ewing sarcoma cell line

growth_protocol: RPMI 1640 media (Gibco®) supplemented with 10% FBS,  L-Glutamine and penicillin/streptomycin. Cells were cultured at 37ºC with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina instructions.


title: ChIPseq_INPUT-shRING1B

description: ChIPseq experiment


title: ChIPseq_EWSR1-FLI1-shRING1B

description: ChIPseq experiment

value: Abcam ab15289


title: 4339.F SC_Shoot_N_3

description:
4339.F
SC_Shoot_N_3


title: ChIPseq_INPUT-shCTRL

description: ChIPseq experiment


title: 4339.E SC_Shoot_N_2

description:
4339.E
SC_Shoot_N_2


title: ChIPseq_EWSR1-FLI1-shCTRL

description: ChIPseq experiment


title: ChIPseq_RING1B-shCTRL

description: ChIPseq experiment


title: 4339.D SC_Shoot_N_1

description:
4339.D
SC_Shoot_N_1


title: 4339.C SC_Shoot_Y_3

description:
4339.C
SC_Shoot_Y_3


title: Long read Control-AA rep2

city: New Haven

first: Tara

middle: Diane

last: Alpert

state: CT

address: 333 Cedar St.

department: Molecular Biophysics and Biochemistry

institute: Yale University

description:
ControlAA
processed data file: longread_fractionspliced.txt

data_processing:
library strategy: SMIT and long read sequencing of nascent RNA
For SMIT, data processing was completed as previously published (Carrillo et al. 2016) with the exception that reads were mapped with Hisat2 (v2.1.0). First, fastq files are filtered for quality with the Fastx Toolkit (v 0.0.14) fastq_quality_filter function (-Q 33 -q 20 -p 90). 3′ end adapter and Illumina adapter sequences were trimmed using Cutadapt (v1.9.1). For R1: -g CATTGATGGTGCCTACAG -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n 2 -O 18 -m 23 -e 0.11 --match-read-wildcards --discard-untrimmed. For R2: -a CTGTAGGCACCATCAATG -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -n 2 -m 28 -M 76 -e 0.11 --match-read-wildcards. Prinseq-lite (v0.20.4) removed PCR duplicates (-out_format 3 -qual_noscale -ns_max_p 1 -derep 1). The resulting reads had a remaining 5 N bases from the SMIT primer which aid in deduplication. These bases were trimmed with the FastX Toolkit fastx_trimmer tool (for R1: -Q 33 -f 6; for R2: -Q 33 -t 5). Reads were then mapped to the SacCer3 genome annotation using Hisat2 (v2.1.0) (--phred33 --no-mixed --min-intronlen 30 --max-intronlen 1010 -p 5). PolyA sequences were removed from the SAM file with a custom script. Custom R scripts compiled the number of spliced and unspliced reads for every position in the second exon of intron-containing genes. Fraction spliced values were normalized to correct for an insert length bias introduced by the PCR (https://github.com/carrillo/SMITproject/blob/master/smit_r/insert_length_model.R). Fraction spliced values were modeled with ggplot2 (v 3.2.1) geom_smooth function using the loess method (span = 0.15). The distance matrix between the fraction spliced of Control and Sample (considering only the first 300 nt after the 3′ SS) was generated for each gene using the R stats dist function (v3.6.1) using the Euclidean method. The matrix was collapsed into a single value by finding the median which is assigned as the ΔSMIT value for that gene.
For long read sequencing, the raw fast5 files were basecalled with Guppy (v3.3.0) with default quality filter parameters and basecalled reads were demultiplexed with Qcat (v1.1.0). Nanopore adapters were trimmed with Cutadapt (v1.9.1) and 3′ end adapter sequence was removed with the following parameters (cutadapt -a CTGTAGGCACCATCAATG -e 0.17 -O 6 -m 5 --match-read-wildcards --discard-untrimmed). Reads which had 3′ end adapter on 5′ end (cutadapt -g AAGCAGTGGTATCAACGCAGAGTAC -e 0.17 -O 6 -m 5 --match-read-wildcards) were reverse complemented using a custom script. Trimmed reads were then mapped to the sacCer3 genome with minimap2 (v2.17) (-ax splice -k 10 -G 2000 –secondary=no). Reads with polyA tails were removed using a custom script. Reads with 30 or more soft-clipped bases which contain a stretch of 10 A’s were removed. Reads with less than 30 soft-clipped bases which contain 6 A’s were removed. Bam and bed files were generated using Samtools (v1.9) and BEDTools (v 2.29.2) respectively. Custom R scripts were written identify intrusive and readthrough reads using transcript start and end positions defined by Nagalakshmi et al 2008. Fraction spliced of reads with 3′ ends downstream of the 3′ SS was determined using the DescTools (v0.99.30) Overlap function.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files with fraction spliced for each gene
Supplementary_files_format_and_content: tab-delimited text files with the deltaSMIT value for each gene
Supplementary_files_format_and_content: .bed file for mapped long read data filtered for reads overlapping intron-containing genes only; BED12 file with extra column to identify gene.
Supplementary_files_format_and_content: longread_fractionspliced.txt

organism: Saccharomyces cerevisiae

source_name: MATa tor1-1 fpr1Δ::loxP-LEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP

growth_protocol: Yeast cells were grown in YPAD medium at 30°C into log phase (OD600 = 0.5-0.8). For Nab2-AA and Control-AA strains, rapamycin was added at a final concentration of 1 ug/ml for either 10 or 30 minutes. Cells were pelleted at 4°C and washed with cold 1x PBS before snap freezing.

extract_protocol:
Nascent RNA was extracted as previously described (Carrillo et al 2010). Briefly, chromatin isolated from frozen cell pellets is incubated with phenol-chloroform to extract nucleotides. DNA is digested with DNase and polyA sequences are depleted using oligo(dT) beads. For long read sequencing, ribosomal RNA was depleted using a cap-dependent exonuclease.
SMIT library construction was performed as described previously (Carrillo et al. 2016). Briefly, a 3′ end adapter (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) was ligated to nascent RNA and samples were reverse transcribed. Gene-specific forward primers were used to amplify the cDNA and a second PCR added Illumina library adapters. Long read sequencing utilized the same adapter ligation strategy used in SMIT. Strand-switching reverse transcription created full length double-stranded cDNA molecules with common 5′ and 3′ ends. An initial PCR of 12-15 cycles amplified product for input into the ONT PCR Barcoding kit (SQK-PBK004) which includes dA-tailing and barcode adapter ligation. A final PCR of 8-10 cycles enriched for successful ligation and AMPure XP bead purification removes products under 250 bp. The final library was loaded onto an Oxford Nanopore MinION flow cell and sequenced for 48 hours.

treatment_protocol: Rapamycin was added to exponentially growing cells to a final concentration of 1 ug/ml for either 10 or 30 minutes.

value: MATa tor1-1 fpr1{delta}::loxP-LEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP

value: rapamycin (1 ug/ml) for 10 min

tag: molecule subtype

value: nascent RNA


title: Long read Nab2-AA rep2

description:
Nab2AA
processed data file: longread_fractionspliced.txt

source_name: MATα tor1-1 fpr1Δ::loxP-LEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP NAB2-FRB::HIS

tag: genotype

value: MATalpha tor1-1 fpr1{delta}::loxP-LEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP NAB2-FRB::HIS


title: Long read Control-AA rep1


title: Long read Nab2-AA rep1


title: ChIPseq_INPUTforEWSR1-FLI1

description: ChIPseq experiment

tag: chip antibody


title: 4339.B SC_Shoot_Y_2

description:
4339.B
SC_Shoot_Y_2


title: dex treated callus LFY ChIP-seq Rep3

city: Philadelphia

first: Doris

last: Wagner

state: PA

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Base-calling was performed automatically in Illumina BaseSpace
FASTQ reads were trimmed using TRIMMOMATIC v0.36 (SE -phred33 ILLUMINACLIP:adapters.fasta:2:30:10 LEADING:3 TRAILING:3 MINLEN:50 TOPHRED33)
Sequencing quality metrics were obtained for the raw and trimmed FASTQ files with FASTQC v0.11.5
Trimmed sequencing reads were mapped to Release 10 of the Arabidopsis Genome (TAIR10) using Bowtie2 v2.3.1 with the `--no-unal` parameter
Using samtools v1.7 with the parameters `-F 1804 -q 30 `, reads with a mapping quality score ≧30 were selected that passed Bowtie2 quality checks, and were not called a PCR or optical duplicate by Bowtie2
Duplicated reads were marked using the MarkDuplicates function in Picard tools 2.9.4 (VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=false ASSUME_SORTED=true)
Regions of the Arabidopsis genome which that have high signal/read counts independent of experiment (i.e noise defined as signal present in the input) were identified using MACS2 (2.1.1.20160309) callpeak with parameters `--keep-dup auto --nomodel --extsize138 --gsize 101274395` on our input samples using q-value ≤10-65. These regions and regions between two such peaks that were ≤2kb apart,were removed from the mapping files using samtools.
Read coverage of each biological replicate was calculated and normalized to 10 million reads mapped per million reads sequenced (10RPM) and coverage was averaged using bedtools.
Peak calling was performed on the ChIP samples using MACS2 callpeak parameters `--keep-dup auto --nomodel --extsize 138 --gsize 101274395` and the input samples controls , using a a summit q-value ≤ 10^-10.
Genome_build: TAIR10
Supplementary_files_format_and_content: sample-specific *bigwig: bigwig normalized to 10RPKM for single replicates
*pooled.bigwig: Bigwig showing 10RPM-normalized coverage after masking of signicant input regions, mean of three replicates
*narrowPeak: BED file in narrowPeak format showing peaks with summit MACS2 Q<1e-10 for Dex treated vs. Mock treated

source_name: callus on CIM for 5 days with dex treatment

growth_protocol: Plants were grown on 1/2MS plates for 3 weeks. Roots were harvested from 3-week-old seedlings and put on CIM for up to 5 days with either 1hr of mock or dex treatment

extract_protocol:
ChIP assay was performed according to Yamaguchi et al., 2014. N. Yamaguchi et al., PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues. Arabidopsis Book 12, e0170 (2014).
DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406) and quantified by the NEBNext Library Quant Kit (cat. E7630L). Equal amounts of DNA were pooled from each library with different dual indexing primers and sequenced on a Next seq 500

treatment_protocol: 5uM of Dexamathasone or mock treatment on the last hour of 5 day CIM incubation was performed

value: callus

tag: cultivar

tag: transgenics

tag: mutant

value: WT

tag: antibody

value: anti-LFY antibody


title: ChIPseq_EWSR1-FLI1

description: ChIPseq experiment


title: 4339.A SC_Shoot_Y_1

description:
4339.A
SC_Shoot_Y_1


title: dex treated callus LFY ChIP-seq Rep1

tag: tissue


title: ChIPseq_CBX7

description: ChIPseq experiment

value: Sigma 7981


title: mock treated callus LFY ChIP-seq Rep3

source_name: callus on CIM for 5 days with mock treatment


title: mock treated callus LFY ChIP-seq Rep2


title: mock treated callus LFY ChIP-seq Rep1


title: SC_Shoot_Y_3

description: X

tag: ecotype

tag: inoculated with microbes

value: shade


title: SC_Shoot_Y_1

description: V


title: ChIPseq_BMI1

description: ChIPseq experiment

value: Abcam ab14389


title: dex treated callus LFY ChIP-seq Rep2


title: callus Input Rep1

source_name: callus on CIM for 5 days without treatment

value: no antibody


title: callus Input Rep3


title: callus Input Rep2


title: RAD6BKOM14 3: RAD6B knockout M14

city: Detroit

first: Malathy

middle: P

last: Shekhar

state: MI

address: 421 East Canfield Avenue

department: Oncology

institute: Wayne State University

data_processing:
Data were demultiplexed using Illumina's CASAVA 1.8.2 software.
After quality was assessed using FastQC, reads were aligned to the human reference genome using STAR before tabulation using htseq-count.
RNA-seq data were analyzed using the R/Bioconductor package edgeR.
Read counts within and between samples were normalized using the trimmed mean of M-values (TMM) method.
Genome_build: hg38
Supplementary_files_format_and_content: Melanoma_melanocyte_.csv contains counts and differential expressions between isogenic RAD6BKO and control M14 cells, M14 and HEMa-LP normal melanocytes, and RAD6BKO M14 and HEMa-LP cells.

source_name: RAD6B gene disrupted M14 cells

growth_protocol: HEMa-LP cells were cultured in Dermal cell basal medium supplemented with insulin, ascorbic acid, L-glutamine, epinephrine, calcium chloride and M8 supplement (ATCC). RAD6B knockout and parental control M14 cells were cultured in DMEM/F12 supplemented with 5% fetal bovine serum.

extract_protocol:
Total RNA was isolated from cell lines using RNA later followed by purification with RNeasy mini kit (Qiagen) using the manufacturer’s recommended in-solution DNase digestion.
RNA-seq libraries were prepared using Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina) from 200 ng of DNAse I treated total RNA. Libraries were quantified using Qubit 2.0 dsDNA HS kit and the size distribution determined on a Fragment Analyzer.

treatment_protocol: RAD6B was knocked out from M14 cells using CrispR/Cas9.

value: RAD6B gene disrupted M14 cells


title: MCF7_MeCP2

city: Lubbock

first: Kevin

last: Pruitt

address: 3601 4th Street

department: Immunology & Molecular Microbiology

institute: Texas Tech University Health Sciences Center

data_processing:
Preprocessing: Qseq with DNASTAR/ArrayStar software from Lasergene genomics.
ChIP-seq reads were aligned to the Human (GRCh38.p13) genome assembly using DNASTAR from Lasegene genomics.
Peak detection: MACS method; p value cut off: 0.05; Mfold: 2; Lambsa set: 1000, 5000, 10000.
Read assignment qualification options: Require at least 20 bases and at least 80% of the bases matching within each read. Mer length 15. Read technology Illumina.
Filter out reads that match more than 25 places equally.
Genome_build: Human (NCBI Genome Reference GRCh38.p13)
Supplementary_files_format_and_content: bigWig files were generated using DNASTAR/ArrayStar software from Lasergene genomics.

growth_protocol: MDA-MB-468 cells were cultured in RPMI 1640 (Gibco) supplemented with 1% pen-strep and 10% fetal bovine serum (GIBCO) and MCF7 cells were cultured in MEM (Gibco) media supplemented with 0.1% insulin, 1% pen-strep and 10% fetal bovine serum (GIBCO). Cells were plated for 72 hrs and the media was changed 24 hrs prior to the experiment.

extract_protocol:
The cells were subjected to 1% formaldehyde cross-linking (Sigma) for 8 minutes at room temperature. The cross-linking reaction was quenched by adding glycine (Sigma) to a final concentration of 0.125M for 5 minutes at room temperature. The medium was then removed and cells were washed twice with cold PBS containing protease inhibitor cocktail (Thermo Fisher Scientific). Cells were scraped in PBS and pelleted. Pellet was resuspended in SDS Lysis buffer (50mM Tris-HCl pH 8.0, 10mM 0.5M EDTA, and 1% SDS) with protease inhibitor cocktail and sonicated in a Diagenode Bioruptor sonicator. The soluble chromatin fraction was collected and incubated for 2 hrs at 4°C with antibody. Dynabeads Protein A (Invitrogen) were washed and then added to the chromatin-antibody mixture and rotated for 2 hrs at 4°C. Beads were washed with a low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH 8.1, and 150mM NaCl), a high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH 8.1, and 500mM NaCl), and TE (1mM EDTA and 10mM Tris HCl pH 8). Reverse-crosslinking was performed at 65°C overnight followed by treatment with RNaseA (Invitrogen) for 2 hrs at 37°C and proteinase K (Invitrogen) at 55°C for 2 hrs. The chromatin was eluted and purified using Qiaquick PCR purification kit (Qiagen).
Purified DNA were extracted and sent to GENEWIZ company for library construction and sequencing. Instrument/Configuration: Illumina HiSeq 2x150bp SR.

tag: cell type

value: Breast cancer cell line

tag: treatment

value: untreated

value: MeCP2 (Sigma, M9317)


title: RAD6BKOM14 2: RAD6B knockout M14


title: SC_Root_Y_3

description: U

value: Yes


title: RAD6BKOM14 1: RAD6B knockout M14


title: SC_Shoot_Y_2

description: W


title: MDAMB468_IgG

value: IgG (Sigma I5006)


title: SC_Root_Y_2

description: T


title: SMIT Control-AA 30 min

value: MATa tor1-1 fpr1{delta}::loxP-LEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP

value: rapamycin (1 ug/ml) for 30 min


title: HEMaLP 2: HEMa-LP normal melanocytes

source_name: Normal epidermal melanocytes

value: Normal epidermal melanocytes


title: MDAMB468_MeCP2


title: SMIT Control-AA 10 min

value: rapamycin (1 ug/ml) for 10 min

value: nascent RNA


title: SMIT Control-AA 0 min

value: rapamycin (1 ug/ml) for 0 min


title: HEMaLP 3: HEMa-LP normal melanocytes


title: MCF7_IgG


title: NC_Shoot_Y_3

description: R

value: normal


title: SMIT Nab2-AA 30 min

value: MATalpha tor1-1 fpr1{delta}::loxP-LEU2-LoxP RPL13A-2xFKBP12::LoxP-TRP1-LoxP NAB2-FRB::HIS


title: SC_Root_Y_1

description: S

value: shade


title: SMIT Nab2-AA 10 min


title: NC_Shoot_Y_2

description: Q


title: HEMaLP 1: HEMa-LP normal melanocytes


title: CtrlM14 3: Control M14 melanoma

source_name: Metastatic melanoma line

value: Metastatic melanoma line


title: SMIT Nab2-AA 0 min


title: NC_Shoot_Y_1

description: P


title: CtrlM14 2: Control M14 melanoma


title: NC_Root_Y_3

description: O


title: SMIT Htz1-KO rep2

description:
SMIT-rep-3_TTAGGC_L001
processed data file: dSMIT_deletions_rep2.txt

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 htz1Δ::KanMX

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 htz1{delta}::KanMX

value: none (untreated)


title: SMIT Htz1-KO rep1

description:
SMIT_MM_1345_TA_004_TGACCA_L001
processed data file: dSMIT_deletions_rep1.txt


title: SMIT Pub1-KO rep2

description:
SMIT-rep-5_ACAGTG_L002
processed data file: dSMIT_deletions_rep2.txt

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pub1Δ::KanMX

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 pub1{delta}::KanMX


title: CtrlM14 1: Control M14 melanoma


title: hCD45pos_TRC105_treated_rep4

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

institute: University of Minnesota

description:
9525
TRC105_vs_IgG_all_transcripts.xlsx

data_processing:
RNA-seq analysis:Paired-end reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via Hisat2 (v2.0.2) using the human genome (hg19) as reference. Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: processed file containing tab-delimited expression values following analysis using EdgeR.

source_name: human CD45+ cells

growth_protocol: FACS: bone marrows were collected from xenotransplanted mice. Cells were lysed with ACK lysing solution and incubated for on ice for 30 minutes with PE-Cy7-conjugated human CD45 (clone HI30; BD Biosciences). After washing, cell pellets were resuspended in 7AAD-containing buffer for analysis and cell sorting. hCD45+7AAD- cells were sorted using a FACSAria II cytometer (BD Biosciences)

extract_protocol:
RNA-isolation: 50,000 sorted cells were subjected for RNA isolation using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) following the manufacturer’s instructions for “RNA Extraction from Cell Pellets” (including DNase Treatment).
RNA-seq libraries were generated using the Clontech SMARTer Stranded RNA-seq kit and dual-index adapter-barcodes following manufacturer's instructions.

tag: time

value: one month treatment

value: Human CD45+ cells


title: SMIT Pub1-KO rep1

description:
SMIT_MM_2678_006_GCCAAT_L001
processed data file: dSMIT_deletions_rep1.txt


title: NC_Root_Y_2

description: N

source_name: Root

value: Yes

tag: condition


title: SMIT Tho2-KO rep1

description:
SMIT_MM_2678_008_ACTTGA_L001
processed data file: dSMIT_deletions_rep1.txt

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 tho2Δ::KanMX

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 tho2{delta}::KanMX


title: SC_Shoot_N_3

description: L

value: No


title: hCD45pos_TRC105_treated_rep3

description:
9524
TRC105_vs_IgG_all_transcripts.xlsx


title: SMIT Rtt103-KO rep2

description:
SMIT-rep-7_CAGATC_L002
processed data file: dSMIT_deletions_rep2.txt

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rtt103Δ::KanMX

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rtt103{delta}::KanMX


title: SMIT Gbp2-KO rep2

description:
SMIT-rep-2_CGATGT_L001
processed data file: dSMIT_deletions_rep2.txt

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 gbp2Δ::KanMX

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 gbp2{delta}::KanMX


title: hCD45pos_TRC105_treated_rep2

description:
9522
TRC105_vs_IgG_all_transcripts.xlsx


title: NC_Root_Y_1

description: M


title: SMIT Rtt103-KO rep1

description:
SMIT_MM_2678_007_CAGATC_L001
processed data file: dSMIT_deletions_rep1.txt


title: SMIT Npl3-KO rep2

description:
SMIT-rep-4_TGACCA_L001
processed data file: dSMIT_deletions_rep2.txt

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 npl3Δ::KanMX

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 npl3{delta}::KanMX


title: SMIT Gbp2-KO rep1

description:
SMIT_MM_1345_TA_003_TTAGGC_L001
processed data file: dSMIT_deletions_rep1.txt

value: nascent RNA


title: SC_Shoot_N_2

description: K

source_name: Shoot


title: hCD45pos_TRC105_treated_rep1

description:
9521
TRC105_vs_IgG_all_transcripts.xlsx


title: SMIT WT rep2

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: SC_Shoot_N_1

description: J


title: SMIT WT rep1


title: SMIT Npl3-KO rep1

description:
SMIT_MM_1345_TA_005_ACAGTG_L001
processed data file: dSMIT_deletions_rep1.txt


title: hCD45pos_IgG_treated_rep4

description:
9523
TRC105_vs_IgG_all_transcripts.xlsx

value: IgG


title: Nd-218_KO_HFD_eWAT

city: Davis

first: Michael

middle: L

last: Goodson

state: CA

address: One Shields Ave

institute: University of California Davis

data_processing:
Base calling was done using Illumina Casava
Aligned to GRCM38 (mm10) genome using Tophat /Bowtie2
Transcript assemblies created using Cufflinks/cuffmerge v. 2.1.1
Differential gene expression computed using Cuffdiff
Genome_build: mm10/Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: Normalized count (FPKM) tables (_FPKM_matrix.txt) and differential gene expression lists (_gene_exp.diff) for HFD and LFD WT vs KO samples in Liver and eWAT

source_name: eWAT

growth_protocol: Adult  NCoR-omega KO and C57BL/6N (WT) adult mice were fed HF (Research Diets Cat#D12492; 60% kcal fat) or LF (Research Diets Cat#D12450B;10%kcal fat) diet for 10 weeks.

extract_protocol:
Qiagen RNeasy Mini Kit
Nugen Encore Complete RNA-Seq Library System

treatment_protocol: LFD/HFD

tag: strain

tag: Sex

value: male

value: eWAT

tag: age

value: 17 weeks

tag: diet

value: HFD

value: KO


title: SC_Root_N_3

description: I

value: shade


title: SMIT Tho2-KO rep2

description:
SMIT-rep-8_ACTTGA_L002
processed data file: dSMIT_deletions_rep2.txt

tag: genotype

value: none (untreated)

tag: molecule subtype


title: hCD45pos_IgG_treated_rep3

description:
9519
TRC105_vs_IgG_all_transcripts.xlsx

value: one month treatment

value: Human CD45+ cells


title: SC_Root_N_2

description: H


title: Nd-216_KO_HFD_eWAT


title: Nd-209_KO_LFD_eWAT

value: LFD


title: Nd-208_KO_LFD_eWAT


title: SC_Root_N_1

description: G

value: No


title: Nd-207_KO_LFD_eWAT


title: hCD45pos_IgG_treated_rep1

description:
9516
TRC105_vs_IgG_all_transcripts.xlsx


title: NC_Shoot_N_3

description: F

value: normal


title: B6-109_WT_HFD_eWAT

value: WT


title: ChIPseq_INPUTforH2Aub1_Replicate1

description: ChIPseq experiment

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Human genome (hg19, February 2009) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIPseq peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIPseq)
ChIPseq_RING1B_Replicate1.bedgraph.gz
ChIPseq_RING1B_Replicate2.bedgraph.gz
ChIPseq_INPUTforRING1B_Replicate1.bedgraph.gz
ChIPseq_INPUTforRING1B_Replicate2.bedgraph.gz
ChIPseq_H2Aub1_Replicate1.bedgraph.gz
ChIPseq_H2Aub1_Replicate2.bedgraph.gz
ChIPseq_INPUTforH2Aub1_Replicate1.bedgraph.gz
ChIPseq_INPUTforH2Aub1_Replicate2.bedgraph.gz
Files .bed (BED, signal enriched regions)
ChIPseq_RING1B_Replicate1.bed.gz
ChIPseq_RING1B_Replicate2.bed.gz
ChIPseq_H2Aub1_Replicate1.bed.gz
ChIPseq_H2Aub1_Replicate2.bed.gz

source_name: Ewing sarcoma cell line

tag: cell line

value: Ewing sarcoma cell line

tag: chip antibody


title: B6-092_WT_LFD_eWAT


title: NC_Shoot_N_2

description: E


title: 337

city: Shanghai

first: Honggang

last: Xiang

address: No. 490, South Chuanhuan Road

department: Department of General Surgery

institute: Pudong New Area People’s Hospital affiliated to Shanghai University of Medicine & Health Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Homo

source_name: cell line

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

value: pancreas ductal adenocarcinoma

tag: origin

value: pancreas

tag: classification

value: overespressing 337


title: B6-107_WT_HFD_eWAT

value: male

tag: tissue


title: B6-093_WT_LFD_eWAT

value: eWAT


title: ChIPseq_INPUTforH2Aub1_Replicate2

description: ChIPseq experiment


title: ChIPseq_H2Aub1_Replicate2

description: ChIPseq experiment

value: H2Aub (Cell Signalling, D27C4, lot 2)


title: EV

value: control


title: NC_Shoot_N_1

description: D

tag: ecotype


title: Nd-217_KO_HFD_eWAT

value: 17 weeks

value: HFD

value: KO


title: sh337

value: silencing 337


title: B6-091_WT_LFD_eWAT


title: hCD45pos_IgG_treated_rep2

description:
9517
TRC105_vs_IgG_all_transcripts.xlsx

value: one month treatment

value: IgG

value: Human CD45+ cells


title: NC_Root_N_2

description: B

tag: inoculated with microbes

value: No

value: normal


title: Nd-218_KO_HFD_Liver

source_name: Liver

value: Liver


title: shNC

value: pancreas ductal adenocarcinoma


title: NC_Root_N_3

description: C


title: ChIPseq_INPUTforRING1B_Replicate2

description: ChIPseq experiment

tag: cell type

value: Ewing sarcoma cell line


title: Nd-217_KO_HFD_Liver


title: Nd-216_KO_HFD_Liver


title: ChIPseq_INPUTforRING1B_Replicate1

description: ChIPseq experiment


title: NC_Root_N_1

description: A


title: B6-108_WT_HFD_eWAT

value: WT


title: ChIPseq_RING1B_Replicate2

description: ChIPseq experiment


title: Patient 3, CD2-high

city: Seattle

first: Xia

last: Wu

state: WA

address: 750 Republican St., E650

institute: University of Washington

description:
ex vivo human specimens
PT3_CD32-high

scan_protocol: Data was obtained with BioMark HD.

data_processing:
Four arrays were performed.  The data of the four arrays were combined to present in one worksheet Normalized Ct values and one worksheet Fold Change
The Fluidigm Real-Time PCR Analysis software was used to calculate Ct thresholds, using the settings of quality threshold 0.65, baseline correction linear, Ct threshold method auto detection.  Gene abundance in individual liver slices was normalized to the arithmetic mean values of ACTB, HPRT, and GAPDH.
Kupffer cell enriched genes were defined as two-fold or greater in abundance in CD32-mid or CD32-high populations, compared with total liver samples.
Fold Change of CD32-mid versus CD32-high is reported.

label: FAM-MGB

source_name: CD32-high Kupffer cells

label_protocol: Taqman primers with FAM-MGB labled was used in fluidigm assays with 48x48 platform.

extract_protocol: RNA was extracted from the cell pellets with populations with TRIzol and the Direct-zol RNA MiniPrep Kit of Zymo Research.

tag: individual

value: Patient 3

value: liver

value: CD32-high Kupffer cells


title: ChIPseq_H2Aub1_Replicate1

description: ChIPseq experiment

value: H2Aub (Cell Signalling, D27C4, lot 2)


title: ChIPseq_RING1B_Replicate1

description: ChIPseq experiment


title: G_1_NS

source_name: Ileum, 21dpi, infection, replicate 1

value: Peyer's patches and mesenteric lymph nodes

tag: gender

value: male


title: Nd-208_KO_LFD_Liver

value: 17 weeks

value: LFD

value: KO


title: Patient 3, CD32-mid

description:
ex vivo human specimens
PT3_CD32-mid

source_name: CD32-mid Kupffer cells

value: CD32-mid Kupffer cells


title: Patient 3, total liver

description:
ex vivo human specimens
PT3_total_liver

source_name: Total livers

value: Total livers


title: Nd-207_KO_LFD_Liver


title: Patient 2, CD2-high

description:
ex vivo human specimens
PT2_CD32-high

value: Patient 2


title: B6-108_WT_HFD_Liver

value: HFD


title: B6-113_WT_HFD_Liver

value: Liver


title: Patient 2, CD32-mid

description:
ex vivo human specimens
PT2_CD32-mid


title: Patient 2, total liver

description:
ex vivo human specimens
PT2_total_liver


title: Patient 1, CD32-high

description:
ex vivo human specimens
PT1_CD32-high

value: Patient 1


title: B6-107_WT_HFD_Liver


title: Nd-209_KO_LFD_Liver


title: Patient 1, CD32-mid

description:
ex vivo human specimens
PT1_CD32-mid


title: SARS-CoV-2 infected 48 hrs Rep3

city: Durham

first: Yoshihiko

last: Kobayashi

address: 307 Research Dr

institute: Duke University

data_processing:
Quality of sequenced reads were assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). PolyA/T tails were trimmed using Cutadapt (Martin, 2011). Adaptor sequences were trimmed and shorter reads than 24 bp were dropped using Trimmomatic (Bolger et al., 2014). Reads were mapped to the reference genomes of human (hg38) and SARS-CoV-2 (wuhCor1) obtained from UCSC using Hisat2 (Kim et al., 2019) with default setting. Duplicate reads were removed using SAMtools (Li et al., 2009). Fragments numbers were counted using the featureCounts option of SUBREAD (Liao et al., 2014). Normalization and extraction of differentially expressed genes (DEGs) between control and treated were performed using an R package, DESeq2 (Love et al., 2014).
Genome_build: hg38 and wuhCor1
Supplementary_files_format_and_content: csv

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: AT2 organoids infected SARS-CoV-2

extract_protocol:
organoids were dissociated into single-cell suspension using TrypLE™ Select Enzyme at 37°C for 10min. The cell pellet was resuspended in 300µl of TRIzol™ LS Reagent Total RNA was extracted using the Direct-zol RNA MicroPrep kit according to the manufacturer’s instructions with DNase I treatment.
Isolated 1 µg total RNA of each sample was enriched for Poly-A RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, #E7490). Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, #E7770). Paired-end sequencing (150 bp for each read) was performed using HiSeq X ten.

value: Lung

value: alveolar type 2 cells

tag: infection status

value: infected SARS-CoV-2


title: Patient 1, total liver

description:
ex vivo human specimens
PT1_total_liver

value: liver


title: SARS-CoV-2 infected 48 hrs Rep2


title: p14 Mertk KO-4

city: Charlottesville

first: Stephen

last: Turner

address: 1670 Discovery Drive

institute: Signature Science, LLC

description:
p14 Mertk KO-4
21-4

data_processing:
align to genome with STAR
count reads mapping to genes with featureCounts
Genome_build: grcm38
Supplementary_files_format_and_content: gene counts, txt

source_name: retinal pigmented epithelial cells

extract_protocol:
RNA was extracted with RNeasy qiagen kit per kit protocol starting at 2 hour post-light onset.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Library Prep. Briefly, total RNA  is used to purify the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. RNA is fragmented into small pieces. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Then, second strand cDNA is synthesized using DNA Polymerase I and RNase H. cDNA fragments then have a single "A" base added along with ligation of adapters. The products are then purified using magnetic beads and then PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

tag: strain

value: mixed c57Bl/6J and B6;129-Mertktm1Grl/J

value: retinal pigment epithelium

value: female

tag: genotype/variation

value: Mertk KO


title: SARS-CoV-2 infected 48 hrs Rep1


title: Sample 16-3_skin_lesional_nb-UVB x 3

first: Astrid

middle: Haaskjold

last: Lossius

state: Oslo

address: Sognsvannsveien 20

department: Dermatology/Pathology

country: Norway

institute: University of Oslo

hyb_protocol: The final target were hybridized Clariom S human Array in Gene Chip Hybridization Oven. The arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G

data_processing: The data were processed with Transcriptomic Analysis Console (SST-RMA)

label: biotin

source_name: Skin_lesional_nb-UVB x 3

label_protocol: Fragmented and biotinylated ssDNA were prepared according to the standard Affymetrix protocol

growth_protocol: 4 mm skin biopsies were bisected and immidiately fixated in RNAlater

extract_protocol: RNA was isolated with Rneasy kit from Qiagen according to protocol

treatment_protocol: 1 & 4: untreated lesional skin; 2: untreated non-lesional skin; 3: nb-UVB x 3, 5: 6-8 weeks of treatment, lesional skin; 6: 6-8 weeks of treatment, non-lesional skin

tag: subject status

value: Atopic dermatitis (AD) patient

value: Female

tag: treatment

value: nb-UVB x 3

value: Skin


title: Sample 16-2_skin_non-lesional_untreated

value: untreated


title: PT4-S2: Parental tumor 4 (sample 2)

type: genomic

city: Bethesda

first: Daniela

last: Hirsch

address: 50 South Drive

department: National Cancer Institute

institute: National Institutes of Health

description: aCGH

hyb_protocol: Combined samples were hybridized at 65 °C and 20 rpm for 24-48 hours to the CGH microarrays.

scan_protocol: Scanned with microarray scanner G2565BA (Agilent)

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

source_name: Parental tumor

label_protocol: Parental tumor DNA was extracted from FFPE tissue and labeled with the Genomic DNA ULS Labeling Kit (Agilent); cell line DNA was enzymaticall labeled using the SureTag Labeling System (Agilent). Tumor and cell line DNA was labeled with Cy-3, genomic reference DNA (Promega) with Cy-5.

growth_protocol: Cell were cultured in DMEM - high glucose (CL1, CL2, CL3) or DMEM/KSFM (2:1; CL4) supplemented with fetal bovine serum (20% v/v), penicillin (100 U/ml) and gentamicin (2.5 mg/ml) at 37 °C in a humidified atmosphere of 5% CO2. Medium was replaced every third day.

extract_protocol: DNA was isolated using the DNeasy Blood and Tissue Mini Kit (Qiagen).

value: male

tag: tumor type

value: Pancreatic ductal adenocarcinoma

source_name: Genomic reference DNA


title: Sample 16-1_skin_lesional_untreated


title: B6-092_WT_LFD_Liver

tag: Sex

value: Liver

tag: age

value: 17 weeks

tag: diet

value: LFD

tag: genotype

value: WT


title: Sample 15-4_skin_lesional_untreated


title: Sample 16-4_skin_lesional_untreated


title: CL4: Derived cell line 4

description: aCGH

source_name: Cell line


title: p14 Mertk WT-4

description:
p14 Mertk WT-4
21-3

value: Mertk WT


title: Sample 15-3_skin_lesional_nb-UVB x 3


title: Sample 15-1_skin_lesional_untreated


title: CL3: Derived cell line 3

description: aCGH

value: Colorectal adenocarcinoma