title: ASC5-SISTAT33191025.5

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
STAR alignment
HTseq count
DE analysis
analysis using Degust for log fold changes and statistics (limma-voom)
batch effect removal
LogfoldChange calculations
Genome_build: GRCh38
Supplementary_files_format_and_content: STAT3genes_BatchEffect_Limma.xlsx

source_name: EndoC-bH1 cells

growth_protocol: The human β-cell line EndoC-βH1 (kindly provided by Dr. R. Scharfmann, University of Paris, France) was cultured in Matrigel-fibronectin-coated plates

extract_protocol:
RNAeqsy mini kit (Qiagen #741014)
Tru stranded mRNA kit (illumina #20020594)

treatment_protocol: EndoC-βH1 and dispersed human islets have been transfected with small interfering RNAs (siRNAs) against STAT3, STAT1 or allstars Negative Control siRNA (negative control), Qiagen, Venlo, the Netherlands) (30nM) using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA)

tag: sirna

value: STAT3 knockdown


title: RR057e_00726_SEQ003

status: Public on Nov 15 2021

type: SRA

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

country: USA

institute: University of California San Francisco

library_source: transcriptomic

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv file with genecounts

molecule: total RNA

organism: Homo sapiens

source_name: NP/OP swab

growth_protocol: Clinical naso/pharyngeal swab specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

treatment_protocol: DNAse

tag: gender

value: M

tag: age

tag: sars-cov-2 pcr

value: POS

tag: sars-cov-2 rpm

tag: infection

tag: sample type

value: Clinical naso/pharyngeal swab specimens


title: ATAC-Seq RTE_SETD2_KO_rep3

city: New York

first: Christina

middle: S

last: Leslie

state: NY

address: 417 E 68th St

department: Computational Biology Program

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Raw reads were trimmed and filtered for quality using Trimmomatic (v0.38). Trimmed reads were mapped to the mm10 genome assembly using Bowtie2 (v2.3.4.3), and non-uniquely mapping reads were removed.
Peak calling was performed on each replicate using MACS2 (v2.1.2) with ‘-p 1e-2 --extsize 200 --shift -100 --nomodel’ parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized coverage track in bigWig format

molecule: genomic DNA

organism: Mus musculus

source_name: Murine renal tubular epithelial cells

growth_protocol: Kidneys were dissected from Setd2(F/F)Ksp-Cre+ and Setd2(F/F) mice at 4-5 weeks of age. Kidney cortices were minced and digested in advanced DMEM/F12 (Thermo Fisher Scientific) containing liberase (Sigma) for 1h at 37 °C. Digested samples were filtered through 40 μm strainers (BD Biosciences) and washed with cold Hank's Balanced Salt Solution (HBSS, Thermo Fisher Scientific) twice. Finally, samples were resuspended in advanced DMEM/F12 supplemented with penicillin/streptomycin (Thermo Fisher Scientific), non-essential amino acids (NEAA, Thermo Fisher Scientific), glutamine (Thermo Fisher Scientific), 10 mM HEPES (Thermo Fisher Scientific), Insulin-transferrin-selenium (Thermo Fisher Scientific), 20 ng/ml EGF (R & D Systems), and 100 nM hydrocortisone (Sigma), and plated in dishes.

extract_protocol: 50,000 murine renal tubular epithelial cells were used for the transposition reaction at 37 °C for 30 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles as described previously (Buenrostro et al., 2013). Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by AMPure Beads at a 1.5x ratio.

tag: cell type

value: primary renal tubular epithelial (RTE) cells

tag: genotype


title: ASC6-SIQ3191025.6

value: Control


title: ATAC-Seq RTE_SETD2_KO_rep2


title: Internode explant on callus-inducing medium for 1D, biological replicate 2

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

description: Early stage of callogenesis

data_processing:
Sequences >35 bps were retained, the sequence quality score was by default 0.05, the maximum number of ambiguities was set to 0.
Adaptor trimming was performed using the Illumina adaptor sequences, then a hard trim of 15 bps at the 5′ end and 3 bps at the 3′ end was additionally carried out, resulting in a final sequence average length of 57 bps.
Mapping was performed against the previously published de novo transcriptome of nettle clone 13 with the following parameters: maximum hit per read=3, similarity and length fraction=0.95, mismatch/insertion/deletion cost=3.
The expression values were calculated using the RPKM method. An ANOVA one-way statistical test with four groups (0-1-10-34 days) was applied, each composed of 3 biological replicates and a false discovery rate (FDR) correction was thereafter applied.
Only those genes showing a corrected p-value <0.05 were retained for the bioinformatics analysis. The data were filtered by removing the genes showing a maximum value of the means <1 RPKM and a maximum FC>|4|.
Genome_build: Mapping using the de novo transcriptome assembly of Urtica dioica clone 13.
Supplementary_files_format_and_content: Tab-delimited text file includes: contig number, FDR p-value, TAIR ID,  contig size, gene annotation; unique gene reads, RPKM values for each sample, average of the three biological replicates.

organism: Urtica dioica

source_name: Internode explant

growth_protocol: Terminal shoots containing several nodes were collected from healthy vigorous nettle plants (i.e., the fibre clone 13) growing in the incubators under a cycle of 16 h light at 25° C and 8 h dark at 20° C, as previously reported. The shoots were first washed with detergent (i.e., water with a few drops of soap) for 10 min, then submerged in 50% (v/v) commercial bleach for 10 min, followed by three rinses with sterilized distilled water. Segments bearing a single node of the surface sterilized shoots were put vertically onto Murashige and Skoog (MS) basal medium containing vitamins (Duchefa Biochemie, Haarlem, The Netherlands), 3% (w/v) sucrose and 0.8% (w/v) agar and grown in a culture room under light-emitting diode (LED) lights (Philips GreenPower LED production module DeepRed/Blue) with 16/8 h light/dark cycle at constant 22° C. The obtained in vitro plantlets were sub-cultured by transferring terminal shoots to the same fresh media. The internode explants of 1 cm length were excised from 4-weeks old plantlets and used for subsequent experiments.

extract_protocol:
Total RNA extraction was performed using the RNeasy Plant Mini kit (Qiagen, Leusden, The Netherlands) according to the manufacturer’s instructions. RNA quan-tity was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Villebon-sur-Yvette, France). RNA quality was assessed with a 2100 bioana-lyzer (Agilent, Santa Clara, CA, USA). Libraries were prepared from 3µg of total RNA using the SMARTer Stranded RNA-Seq kit (Clontech). The isolation of mRNAs was performed using the Illumina beads and the TruSeq protocol (Illumina).The final elution of the mRNAs was performed using the Illumina elution buffer (19.5 µl).  The isolated mRNAs were quantified using a Qubit fluorometer.
Libraries were pooled and sequenced to generate 75 bp paired-end reads using an Illumina NextSeq500 instrument with NextSeq500/550 Mid Output Kit v2.5 (150 cycles; Illumina, San Diego, CA, USA).

treatment_protocol: The internode explants were cultured on the medium supplemented with 3 mg/L NAA and 0.01 mg/L BAP in the dark and collected at 0, 1, 10 and 34 days. Ten explants from the same plate were pooled to generate one biological replicate for each time point and three biological replicates were collected.

tag: clone

value: clone 13

tag: biological replicate

value: Callogenesis 1D repl 2

tag: stage of de-differentiation

value: Callogenesis 1d


title: Internode explant on callus-inducing medium for 34D, biological replicate 1

description: Advanced stage of callogenesis

value: Callogenesis 34D repl 1

value: Callogenesis 34d


title: ASC4-SISTAT32191018.4


title: CY708-2

city: Shenzhen

first: Conghui

last: You

state: Guangdong

address: 1068 Xueyuan Rd., Nanshan District

country: China

institute: Shenzhen University

description:
1st-round RNA-Seq Assays
CY708.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, poly-N and low-quality sequence, then mapped to NCM3722 whole genome using bowtie2 v2.2.3 with parameters -q --phred33 --sensitive -I 100 -X 500 --end-to-end --no-unal -p 4.
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. To avoid counting reads from the neighbor genes, we use TMM to normalize the read count.
Genome_build: NCM3722 (NZ_CP011495.1 and NZ_CP011496.1)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample.

organism: Escherichia coli

source_name: E. coli CY708

growth_protocol: In N-C- minimal medium supplemented with 22 mM glucose, 20 mM NH4Cl, and 0.2% (w/v) Casamino acid aerobically at 37°C water bath, 250rpm.

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extracted by RNAiso plus (Takara) and PureLink RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

tag: strain

value: clpX-V78F (spontaneous)

tag: culture conditions

value: Batch culture at 37oC, OD600~0.4


title: Internode explant on callus-inducing medium for 1D, biological replicate 1

description: Early stage of callogenesis

value: Callogenesis 1D repl 1


title: CY708-1

description:
1st-round RNA-Seq Assays
CY708.txt


title: ATAC-Seq RTE_SETD2_KO_rep1


title: ASC3-SIQ2191018.3


title: Internode explant on callus-inducing medium for 0D, biological replicate 3

description: Start of the kinetics

value: Callogenesis 0D repl 3

value: Callogenesis 0d


title: ASC2-SISTAT31191011.2


title: ATAC-Seq RTE_SETD2_wt_rep3


title: ATAC-Seq RTE_SETD2_wt_rep2


title: CY598-1

description:
1st-round RNA-Seq Assays
CY598-round1.txt

source_name: E. coli CY598

value: Wild Type


title: Internode explant on callus-inducing medium for 0D, biological replicate 2

description: Start of the kinetics

value: Callogenesis 0D repl 2


title: CY598-2


title: ASC1-SIQ1191011.1


title: ATAC-Seq RTE_SETD2_wt_rep1


title: Internode explant on callus-inducing medium for 0D, biological replicate 1

description: Start of the kinetics

value: Callogenesis 0D repl 1


title: AE17_SC_8

status: Public on Nov 14 2021

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.38 and Real Time Analysis (RTA) v1.18.61, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer.
Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Read libraries were mapped to the mouse genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of aligned reads was performed using SummerizeOverlaps
Genome_build: mm11
Supplementary_files_format_and_content: genecounts.txt file contains a matrix of raw gene counts (unfiltered and un-normalised data)

molecule: polyA RNA

source_name: Subcutaneous mesothelioma tumour

growth_protocol: AB1 and AE17 cell lines were maintained in RPMI 1640 (Invitrogen) supplemented with 10% foetal calf serum, 20 mM HEPES, 0.05 mM 2-mercaptoethanol, 60 μg/mL penicillin, 50 μg/mL gentamicin. Cells were cultured as a monolayer at 37 C in a humidified atmosphere with 5% CO2. Cells were passaged at approximately 1:10-1:5 every 2-3 days when reached 75-80% for a total of 4-5 times before tumour inoculation. Cells were trypsinized and washed two times in PBS and counted with trypan blue dye. For the subcutaneous tumour model, mice were shaved on the right-hand flank and inoculated with 5x10E5 AB1 or 1x10E6 AE17 cells suspended in 100 μL PBS. For the intrapleural tumour model, mice were anaesthetised under continuous isofluorane and inoculated with 5x10E5 AB1 or 1x10E6 AE17 cells suspended in 200 μL PBS into the pleural space.

extract_protocol:
At day 10 after tumour inoculation, mice were euthanized and the tumours and surrounding tissues were harvested. Tumours were submerged in RNAlater (Life Technologies) at 4 C overnight to allow RNAlater to penetrate the tissue. Then, tumours were removed from RNAlater and stored at –80 C until dissociation with TRIzol (Life Technologies) using a TissueRuptor (QIAGEN). RNA was extracted with chloroform and purified on RNeasy MinElute columns (QIAGEN).
Library preparation and sequencing at 50 bp single end reads with Illumina HiSeq standard protocols were performed by Australian Genome Research Facility.

tag: cell line

value: murine mesothelioma

tag: tumour site

value: subcutaneous space

tag: disease

value: mesothelioma

tag: treatment

value: untreated

tag: sample collection day

value: day 10


title: AE17_SC_6


title: AE17_SC_5


title: Internode explant on callus-inducing medium for 34D, biological replicate 2

description: Advanced stage of callogenesis

value: clone 13

value: Callogenesis 34D repl 2


title: AE17_SC_7


title: IP_Z13_72h_H3K4ME3_1

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

data_processing:
Illumina Casava1.7 software used for basecalling.
we cleaned rawreads using Trimmomatic（version 0.30）with parameters :ILLUMINACLIP:adapters.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50
clean reads were mapped to Tibetan genome by using BWA with default parameters;
Macs2(2.1.1) were used to call peak with --broad --broad-cutoff 0.1 -q 0.05 -g 3.8e9 -m 5 50 --keep-dup 1
MEME (4.11.1) were used to find motif with para : -dna -mod zoops -maxw 12 -minw 6 -nmotifs 15 -maxsize 300000 -revcomp
Genome_build: Tibetan(url:http://show.genebang.com/project/index)
Supplementary_files_format_and_content: all processed data were peak files generated by Macs2

organism: Hordeum vulgare

source_name: Leaves

growth_protocol: The barley seeds of G7 and Z13 were disinfected with 3.5% sodium hypochlorite solution for 15 min and washed using distilled water. These clean seeds were cultivated in light culture chamber for 1-2 days (25-27℃, 60-70% relative humidity, dark culture). After germination, the barley seedlings with consistent buds were selected and transplanted to the peat. The plant cultivation was conducted in the greenhouse. When most of the plants had 4 leaves, unified white-flour pathogen infection experiment was conducted on these barley plants.

extract_protocol:
Harvesting 3g young leaves per IP, then using a final concentration at 1% formaldehyde to crosslink cells. After stop crosslink with glycine, shearing the chromatin to 100-300 bp with sonication method. With the function of protein G beads, adding specific antibody to pull down the interest protein. Antibodies used in this study are: anti-H3K4me3 (9571 CST), anti-H3K27me3 (9733 CST), anti-IgG (2729 Lot 7 CST). Then digest the protein with proteinase K, DNA which is binding to the interest protein is harvested.
Libraries were prepared according to Illumina's instructions accompanying the  NEXTflex® Rapid DNA-Seq Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The infection was performed using a method of spraying the white powder bacteria (Blumeria graminis f. sp. Hordei (Bgh)), which makes the leaves of each material plant stained with the pathogenic bacteria evenly. These plants were cultivated in a moist condition. After infection, plant samples were collected at different time points (0h, 6h, 36h, 72h, 168h).

tag: tissue

value: leaves

tag: cultivar

value: nudum

tag: substrain

tag: phenotype

value: susceptible

tag: treatment time

tag: repeat

tag: chip antibody

tag: antibody catalog # and manufacturer


title: IP_Z13_72h_H3K4ME3_2


title: AE17_SC_4

tag: cell type


title: IP_Z13_72h_H3K27ME3_2


title: AE17_SC_3


title: AE17_SC_2


title: AE17_SC_1


title: RNA-Seq RTE_SETD2_KO_rep3

data_processing:
Raw reads were trimmed and filtered for quality using Trimmomatic (v0.38). Trimmed reads were then aligned against the mm10 genome using STAR (v2.7.1a).
For each RefSeq annotated gene, reads overlapping with exon regions were counted using HTSeq (v0.11.2).
Genome_build: mm10
Supplementary_files_format_and_content: Gene quantification count in txt format

extract_protocol:
Total RNA was extracted and cleaned up using RNeasy Mini Kit (Qiagen).
The isolated RNA samples were then processed using the TruSeq RNA Sample Prep kit (Illumina).

value: primary renal tubular epithelial (RTE) cells

tag: genotype


title: IP_Z13_6h_H3K4ME3_2


title: IP_Z13_72h_H3K27ME3_1


title: IP_Z13_6h_H3K4ME3_1


title: CY598-3

tag: strain

value: Batch culture at 37oC, OD600~0.4


title: AE17_PC_8

source_name: Intrapleural mesothelioma tumour

value: pleural cavity


title: AE17_PC_7


title: IP_Z13_6h_H3K27ME3_1


title: AE17_PC_6


title: AE17_PC_5


title: IP_Z13_6h_H3K27ME3_2


title: AE17_PC_4


title: IP_Z13_36h_H3K4ME3_1


title: IP_Z13_36h_H3K4ME3_2


title: IP_Z13_36h_H3K27ME3_1


title: IP_Z13_168h_H3K4ME3_2


title: IP_Z13_36h_H3K27ME3_2


title: AE17_PC_1


title: AE17_PC_2


title: AE17_PC_3


title: IP_Z13_168h_H3K4ME3_1


title: IP_Z13_168h_H3K27ME3_2


title: AB1_SC_8

value: BALB/c


title: IP_Z13_168h_H3K27ME3_1


title: IP_Z13_0h_H3K4ME3_2


title: IP_Z13_0h_H3K4ME3_1


title: AB1_SC_6


title: AB1_SC_4


title: AB1_SC_7


title: AB1_SC_5


title: AB1_SC_2


title: AB1_SC_3


title: IP_Z13_0h_H3K27ME3_1


title: AB1_SC_1


title: IP_G7_72h_H3K4ME3_2

value: resistant


title: AB1_PC_8


title: IP_Z13_0h_H3K27ME3_2


title: IP_G7_72h_H3K4ME3_1


title: AB1_PC_7


title: AB1_PC_6


title: IP_G7_72h_H3K27ME3_2


title: AB1_PC_5


title: AB1_PC_4


title: IP_G7_6h_H3K27ME3_2


title: IP_G7_6h_H3K4ME3_2


title: IP_G7_6h_H3K4ME3_1


title: AB1_PC_3


title: AB1_PC_2


title: IP_G7_36h_H3K4ME3_2


title: IP_G7_6h_H3K27ME3_1


title: AB1_PC_1


title: IP_G7_36h_H3K4ME3_1


title: IP_G7_36h_H3K27ME3_1


title: IP_G7_36h_H3K27ME3_2


title: DroshaKO1d5_A

city: Zurich

first: Constance

last: Ciaudo

state: Zurich

address: Otto-Stern-Weg 7, HPL G.31

country: Switzerland

institute: ETH Zurich

description: reverse-stranded protocol

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR v2.4.2a allowing up to 2 mismatches
FeatureCounts V1.4.5-p1 was used to summarize reads for each gene, using -s 2 (reversely stranded) and ignoring multiple-hit reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count

source_name: Embyronic stem cells

growth_protocol: serum plus LIF

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

value: 129/Ola background

value: Blastocyst

value: Embyronic stem cells

tag: age

value: Passage 7

value: Drosha knockout 1


title: WT2_re-used sample

description: reverse-stranded protocol

value: wild type


title: WT1_re-used sample

description: reverse-stranded protocol


title: IP_G7_168h_H3K4ME3_2


title: input_glp-1-MDX53_adults_ext403_AKM143

first: Ana

middle: Karina

last: Morao

state: New York

address: 29 Washington Place

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Only reads with a minimum mapping quality of 20 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019).
Genome_build: WS220
Supplementary_files_format_and_content: ChIP-seq: bigwig coverage files for individual replicates

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. For glp-1 adult worms, gravid adults grown at the permissive temperature (15°C) were bleached and starved L1s were grown at the restrictive temperature (25°C) for three days.

extract_protocol:
ChIP-seq: embryos, L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

treatment_protocol: Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol.

tag: developmental stage

value: adults

tag: antibody target

value: input

tag: antibody (vendor, cat#, lot#)


title: input_glp-1-MDX53_adults_ext387_AM90

tag: treatment


title: IP_G7_168h_H3K4ME3_1


title: IP_G7_72h_H3K27ME3_1


title: input_MDX-53_emb_ext366_AKM20

value: MDX53 (top-2::GFP)

value: embryos


title: IP_G7_168h_H3K27ME3_1

value: leaves

value: nudum


title: IP_G7_0h_H3K4ME3_2


title: IP_G7_0h_H3K4ME3_1


title: IP_G7_168h_H3K27ME3_2


title: input_MDX-53_L2-L3_ext374_AKM41


title: IP_G7_0h_H3K27ME3_2


title: IP_G7_0h_H3K27ME3_1


title: DroshaKO2d5_B

description: reverse-stranded protocol

value: Drosha knockout 2


title: In_Z13_72h_1

value: susceptible


title: input_LS05xMDX53_L2-L3_ext462_AKM244

value: LS05 (rex-8 insertion);MDX53 (top-2::GFP)


title: input_MDX53_L2-L3_ext458_AKM234


title: In_Z13_6h_2


title: input_LS05xMDX53_L2-L3_ext461_AKM243


title: input_SEA03xMDX53_L2-L3_ext463_AKM245

value: SEA03 (rex-41 deletion);MDX53 (top-2::GFP)


title: In_Z13_6h_1


title: RB4: dKO_E6

city: Bethesda

first: Remy

last: Bosselut

state: Maryland

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

data_processing:
Basecalling was performed using RTA 2.11.3 for WT/dKO_E5, using RTA 2.4.11 for WT/dKO_E6 and using RTA 3.9.2 for WT/dKO_E7.
Barcode was demultiplexed with mkfastq in Cellranger 6.0.0 for WT/dKO_E5. Barcode was demultiplexed allowing 1 mismatch with Bcl2fastq 2.20 for WT/dKO_E6/E7.
Alignment, tagging and gene counting were done with Cellranger 6.0.0 for WT/dKO_E5 and with Cellranger 5.0.0.for WT/dKO_E6/E7.
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files of raw/filtered gene-by-barcode matrces

source_name: spleen

extract_protocol: WT/dKO_E5: Single Cell 5' Reagent Kits v1.1 per the manufacturer instructions (10X genomics). Two libraries were sequenced on NextSeq 550 (HighOutput Kit V2.5, 75 cycle, parameter: R1: 26bp, I1: 8bp and R2: 55 bp). WT/dKO_E6: Two 10x Genomics Single Cell Chromium 5' mRNA libraries were made and sequenced on one NextSeq run. Read length: R1: 26bps, R2: 8bps, R3: 91bps (NextSeq). WT/dKO_E7: 2 10x Genomics Single Cell Chromium mRNA libraries were sequenced on one NextSeq 2000 P2 run. Read length: R1: 26, R2: 91.

value: C57BL/6 chimera

tag: population

value: GP66:I-Ab+ Rosa26YFP+ CD4+ spleen T cells

value: dKO

tag: infection

value: LCMV Arm >= d30pi


title: In_Z13_36h_2

tag: tissue

tag: cultivar


title: RB2: dKO_E5

value: Smarta cells

value: LCMV Arm d7 pi


title: input_CA1200_L2-L3_ext467_AKM249

value: auxin


title: RB1: WT_E5

value: WT


title: leukemia cell-K562-Bort

city: Wenzhou

first: Jinglai

last: Dong

address: Life and healthy town

institute: The First Affiliated Hospital of Wenzhou Medical University

data_processing:
Solexa pipeline version 1.8 ( Off-Line Base Caller software, version 1.8 ) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 using Hisat2
FPKM calculations of gene level and transcription level were performed using R software Ballgown
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: leukemia cell

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

tag: morphology

value: lymphoblast

value: treated with Bortezomib for 24 hours


title: RB3: WT_E6

value: GP66:I-Ab+ CD4+ spleen T cells

value: LCMV Arm >= d30 pi


title: input_CA1200_L2-L3_ext466_AKM248

value: input

value: no-auxin


title: In_Z13_168h_2

value: leaves

value: nudum

tag: substrain

tag: phenotype

value: susceptible

tag: treatment time


title: input_CA1200_L2-L3_ext441_AKM197


title: Fast Food Slurry Antibiotic Drinking Water Replicate 4

city: Cleveland

first: Lucas

last: Osborn

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic Foundation

description:
FF_Abx_4
MB-LO33

data_processing:
Basecalls performed using Illumina HiSeq 4000 platform
Single 50 bp reads were controlled for quality with FastQC
Reads were trimmed from the 3' ends to remove Illumina adapters using cutadapt
Reads were aligned to the Mus musculus reference genome (NCBI GRCm38.p6) using STAR aligner
Reads were counted using HTSeq
Counts were loaded into R (http://www.R-project.org/) (R Development Core Team, 2015) and DESeq2 [Love et al., 2014] (v.1.28.1, https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was used to perform differential expression (DE) analysis on genes with 1 counts per sample with alpha set to 0.05. P-values were adjusted using the Benjamini-Hochberg method and genes with p<0.05 were considered statistically significant.
Heat maps were generated of top 50 differentially expressed transcripts using pheatmap [Kolde 2012] and RColorBrewer [Neuwirth, 2011]. Non-metric multidimensional scaling (NMDS) analysis was performed using the plotMDS function of edgeR [Robinson et al., 2010] using the top 500 DE genes as sorted by log2 fold change. Pathway analysis on the top 150 DE genes was performed using Metascape [Zhou et al., 2019].
Genome_build: NCBI GRCm38.p6
Supplementary_files_format_and_content: .txt file containing counts

source_name: Liver tissue

growth_protocol: Murine Hepatic Tissue

extract_protocol:
QIAGEN Rneasy
First, RNA quality was checked using a Bio-analyzer (Agilent). Then, libraries were prepared using the Illumina mRNA TruSEQ library kit. Sequencing was performed using an Illumina HiSeq 4000
Single read RNA Sequencing 50 bp

treatment_protocol: Mice randomly assigned to normal drinking water or antibiotic drinking water were given a single oral gavage of chow or fast food slurries and the liver was harvested four hours later

tag: diet

value: Fast Food

value: Antibiotic Drinking Water

value: Liver


title: input_SEA03xMDX53_L2-L3_ext464_AKM246

value: SEA03 (rex-41 deletion);MDX53 (top-2::GFP)


title: input_MDX-53_embryo_ext390_AKM91

value: MDX53 (top-2::GFP)

value: embryos


title: input_CA1200_L2-L3_ext440_AKM196


title: In_Z13_36h_1

tag: repeat

tag: chip antibody

tag: antibody catalog # and manufacturer


title: Fast Food Slurry Antibiotic Drinking Water Replicate 3

description:
FF_Abx_3
MB-LO15

tag: strain


title: In_Z13_72h_2


title: Fast Food Slurry Antibiotic Drinking Water Replicate 2

description:
FF_Abx_2
MB-LO16


title: Fast Food Slurry Antibiotic Drinking Water Replicate 1

description:
FF_Abx_1
MB-LO05


title: Chow Slurry Antibiotic Drinking Water Replicate 4

description:
Chow_Abx_4
MB-LO14

value: Chow


title: In_Z13_168h_1


title: Chow Slurry Antibiotic Drinking Water Replicate 3

description:
Chow_Abx_3
MB-LO17


title: input_CA1200_L2-L3_ext438_AKM195

tag: developmental stage

value: auxin


title: Chow Slurry Antibiotic Drinking Water Replicate 1

description:
Chow_Abx_1
MB-LO30


title: Chow Slurry Antibiotic Drinking Water Replicate 2

description:
Chow_Abx_2
MB-LO26


title: In_Z13_0h_2


title: input_CA1200_L2-L3_ext437_AKM194

tag: antibody target


title: In_Z13_0h_1


title: leukemia cell-K562-NC

value: lymphoblast

value: untreated


title: Fast Food Slurry Control Drinking Water Replicate 4

description:
FF_4
MB-LO46

value: Control Drinking Water


title: Fast Food Slurry Control Drinking Water Replicate 2

description:
FF_2
MB-LO27


title: Fast Food Slurry Control Drinking Water Replicate 3

description:
FF_3
MB-LO22


title: Chow Slurry Control Drinking Water Replicate 4

description:
Chow_4
MB-LO21


title: input_AM05_L2-L3_ext454_AKM241

value: AM05 (top-1::degron::GFP)

tag: antibody (vendor, cat#, lot#)


title: Fast Food Slurry Control Drinking Water Replicate 1

description:
FF_1
MB-LO32

tag: treatment


title: In_G7_72h_1

value: resistant


title: In_G7_6h_2


title: Chow Slurry Control Drinking Water Replicate 2

description:
Chow_2
MB-LO52


title: input_AM05_L2-L3_ext402_AKM142

value: input


title: Chow Slurry Control Drinking Water Replicate 1

description:
Chow_1
MB-LO36


title: input_AM05_L2-L3_ext401_AKM141


title: In_G7_36h_2

value: leaves


title: In_G7_6h_1

value: nudum


title: input_AM01_L2-L3_ext460_AKM236

value: AM01 (dpy-27::degron::GFP)


title: In_G7_36h_1


title: input_AM05_L2-L3_ext469_AKM265


title: In_G7_168h_2


title: In_G7_72h_2


title: input_AM05_L2-L3_ext455_AKM242


title: input_AM01_L2-L3_ext459_AKM235

value: no-auxin


title: wild type EZH2, Input

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq raw reads from fastq files were aligned to the hg19 genome assembly using bwa 0.7.17 using default settings to SAM files.
SAM files were converted to BAM files using samtools then sorted and indexed.
ChIP-seq peaks were called using Homer 4.10 findpeaks function with factor and histone settings.
BigWig files were generated from sorted BAM files using deeptools 3.1.3.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files for visualizing ChIPseq peaks using IGV browser.

source_name: Human cancer cell MDA-MB-231

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, #SH3007103).

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-Pol II antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: cell line

tag: genotype

value: EZH2 wild-type


title: EZH2 YF mutation, Input

value: EZH2 knockout, re-expressing EZH2 Y696F mutation


title: EZH2 knockout, Pol II IP

value: EZH2 knockout

value: Pol II


title: EZH2 YF mutation, IgG IP

value: IgG


title: EZH2 YF mutation, Pol II IP


title: wild type EZH2, Pol II IP


title: wild type EZH2, IgG IP


title: Chow Slurry Control Drinking Water Replicate 3

description:
Chow_3
MB-LO43

value: Chow

tag: tissue

value: Liver


title: EZH2 knockout, IgG IP


title: TOP2_AM01_1h-no_auxin_L2-L3_ext459_AKM232_input_AKM235_ChIP-seq

value: Maddox lab (Ladouceur et al, 2017)


title: input_SS02_L2-L3_ext457_AKM223

organism:
Caenorhabditis briggsae
Caenorhabditis elegans

value: auxin


title: EZH2 knockout, Input


title: input_SS02_L2-L3_ext456_AKM222


title: input_SS02_L2-L3_ext428_AKM181


title: TOP2-GFP_SEA03xMDX53_L2-L3_ext463_AKM252_AKM245_ChIP-seq

value: SEA03 (rex-41 deletion);MDX53 (top-2::GFP)

value: GFP

value: Abcam, ab290


title: TOP2_AM01_1h_auxin_L2-L3_ext460_AKM233_input_AKM236_ChIP-seq


title: TOP2-GFP_MDX53_emb_ext390_AKM98_input_AKM91_ChIP-seq

value: MDX53 (top-2::GFP)

value: embryos


title: Hi-C-dnaA_ex

city: Amsterdam

first: Gaurav

last: Dugar

address: Science Park 904

department: Bacterial Cell Biology

country: Netherlands

institute: University of Amsterdam

data_processing:
RNA-seq and sedimentation assay (DNA-seq) files were then trimmed using Trimmomatic (Galaxy Version 0.36.5) before mapping them to the Bacillus subtilis subsp. subtilis str. 168 reference genome (NC_000964.3)  using Bowtie2 (Galaxy version 2.3.4.2). The BAM files were converted to bigwig using the tool bamCoverage (Galaxy version 3.0.2.0)
Paired end reads generated for Hi-C were mapped separately to B. subtilis genome (NCBI Reference Sequence NC_000964.3) using very sensitive local setting mode in Bowtie2. The mapped files were used to build the contact matrix using the tool hicBuildMatrix using a bin size of 10 Kb, HindIII restriction site (AAGCTT) and AGCT as the dangling sequence. The contact matrix (.cool format) was then used for further analysis and visualization
Genome_build: NC_000964.3
Supplementary_files_format_and_content: BigWig, cool matrix file

organism: Bacillus subtilis

growth_protocol: B. subtilis strains were inoculated from an overnight culture and grown at 37°C in Luria broth (LB) media  prior to sample collection

extract_protocol:
Total RNA was extracted using PCI followed by ribosomal RNA removal using NEBNext® rRNA Depletion Kit for bacteria (E7850S). Standard protocol with HindIII digestion was used for Hi-C.
libraries were constructed using the NEBNext® Ultra™ II DNA (NEB#E7103) and Ultra™ II Directional RNA (NEB#E7765) Library Prep kits

tag: growth phase

value: Exponential


title: input_SS01A_L2-L3_ext406_AKM155

value: SS01A (top-2::degron::GFP)

value: input


title: input_SS02_L2-L3_ext427_AKM180

value: no-auxin


title: In_G7_0h_2

value: leaves

tag: cultivar

value: nudum

value: resistant


title: In_G7_168h_1

tag: substrain


title: In_G7_0h_1

tag: phenotype


title: TOP2-GFP_MDX53_emb_ext366_AKM17_input_AKM20_ChIP-seq


title: TOP2-GFP_MDX53_L2-L3_ext458_AKM231_input_AKM234_ChIP-seq


title: TOP2-GFP_SEA03xMDX53_L2-L3_ext464_AKM253_AKM246_ChIP-seq


title: input_SS01A_L2-L3_ext397_AKM97


title: input_SS01A_L2-L3_ext394_AKM94


title: RC8+RC8S_2

value: Stationary


title: RC8_2


title: input_SS01A_L2-L3_ext392_AKM92


title: TOP2-GFP_MDX53_L2-L3_ext374_AKM40_input_AKM41_ChIP-seq


title: Hi-C-dnaA_st


title: TOP2-GFP_LS05xMDX53_L2-L3_ext461_AKM250_input_AKM243_ChIP-seq

value: LS05 (rex-8 insertion);MDX53 (top-2::GFP)


title: wt_st_RNA_2


title: input_CA1200_L2-L3_ext415_AKM173


title: RB6: dKO_E7

value: C57BL/6 chimera

tag: population

value: GP66:I-Ab+ Rosa26YFP+ CD4+ spleen T cells

value: dKO

tag: infection

value: LCMV Arm >= d30 pi


title: TOP2-GFP_AM09_adults_ext403_AKM140_input_AKM143_ChIP-seq

value: adults

value: GFP


title: RB5: WT_E7

value: GP66:I-Ab+ CD4+ spleen T cells

value: WT


title: input_SS01A_L2-L3_ext404_AKM153


title: Hi-C-wt_HU


title: Hi-C-RC8+RC8R

description: Chromosome conformation capture using Hi-C

growth_protocol: B. subtilis strains were inoculated from an overnight culture and grown at 37°C in Luria broth (LB) media or Spizizen minimal medium (SMM) prior to sample collection

extract_protocol:
Total RNA was extracted using PCI followed by ribosomal RNA removal using MICROBExpress™ Bacterial mRNA Enrichment Kit (AM1905). Standard protocol with HindIII digestion was used for Hi-C.
libraries were constructed using the NEBNext® Ultra™ II DNA (NEB#E7103) and Ultra™ II Directional RNA (NEB#E7765) Library Prep kits

tag: growth media

value: Luria broth

value: delta{RC8} with RC8 complementation in reverse orientation


title: input_CA1200_L2-L3_ext414_AKM172

value: input


title: Hi-C-RC8+RC8S

value: delta{RC8} with RC8 complementation in sense orientation


title: RB14: dKO_E7

data_processing:
Basecalling was done with RTA 3.9.2 for WT/dKO_E4/E5, with RTA 3.7.17 for WT/dKO_E6 and with RTA 2.4.11 for WT/dKO_E7.
Barcode was demultiplexed allowing 1 mismatch with Bcl2fastq 2.20.
Alignment, tagging and accessibility counting were done with Cellranger ATAC 1.2.0.
Genome_build: mm10

extract_protocol: WT/dKO_E4: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 P3 run and combined with a previous NextSeq 2000 P2 run. The sequencing run was setup as a 2x51 cycles symmetric run. R1: 51bp, Index1: 8bp, Index2: 16bp, R2: 51bp. WT/dKO_E5/E6/E7: 2 10x Genomics Single Cell Chromium ATAC libraries were sequenced on one NextSeq 2000 run. The sequencing run was setup as a 50 cycles + 50 cycles symmetric run. R1: 50bp, Index1: 8bp, Index2: 16bp, R2: 50bp.


title: RC8+RC8R_2


title: TOP2-GFP_AM09_adults_ext387_AM89_input_AM90_ChIP-seq

value: Abcam, ab290


title: mouse 1 wildtype

type: RNA

city: Edinburgh

first: Emily

last: Gwyer Findlay

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing: NanoString data were normalised using internal reference (housekeeping) genes

label: Nanostring oligonucleotide probes

source_name: inguinal lymph node CD4+ T cells, day 7 EAE

extract_protocol: inguinal lymph nodes were removed from mice on day 7 of EAE. Samples were strained through a 100uM sieve and washed. Live CD4+ T cells were isolated by FACS and total RNA purified on the same day using Qiagen microRNA kits.

tag: Sex

value: Female

value: wildtype

tag: age

value: 8 weeks


title: mouse 2 wildtype


title: mouse 1 knockout

value: cathelicidin knockout


title: mouse 3 knockout


title: mouse 2 knockout


title: mouse 3 wildtype


title: TOP2-GFP_LS05xMDX53_L2-L3_ext462_AKM251_input_AKM244_ChIP-seq

tag: strain

value: LS05 (rex-8 insertion);MDX53 (top-2::GFP)


title: RB13: WT_E7

value: C57BL/6 chimera


title: input_AM05_L2-L3_ext425_AKM178

value: AM05 (top-1::degron::GFP)

tag: developmental stage

value: no-auxin


title: Hi-C-RC8

value: Stationary

value: delta{RC8} (Rok cluster 8 deletion)


title: input_AM01_L2-L3_ext411_AKM157

value: AM01 (dpy-27::degron::GFP)

tag: antibody target

value: auxin


title: TOP1-GFP_AM05_L2-L3_AKM137_ext401_input_AKM141_ChIP-seq

value: GFP

tag: antibody (vendor, cat#, lot#)


title: TOP1-GFP_AM05_L2-L3_AKM138_ext402_input_AKM142_ChIP-seq

tag: treatment


title: Hi-C-scpB_min

value: Spizizen minimal medium

value: delta{scpB} (scpB deletion)


title: RB12: dKO_E6

value: GP66:I-Ab+ Rosa26YFP+ CD4+ spleen T cells

value: LCMV Arm >= d30 pi


title: IgG_LS05xMDX53_L2-L3_ext462_AKM277_input_AKM244_ChIP-seq

value: IgG

value: Abcam, ab46540


title: Hi-C-wt_min

value: wild type


title: RB11: WT_E6

value: GP66:I-Ab+ CD4+ spleen T cells


title: RB10: dKO_E5

value: Smarta cells

value: LCMV Arm d7 pi


title: input_AM05_L2-L3_ext426_AKM179

value: AM05 (top-1::degron::GFP)

value: input


title: TOP2_AM01_1h-no_auxin_L2-L3_ext410_AKM149_input_AKM156_ChIP-seq

value: Maddox lab (Ladouceur et al, 2017)

value: no-auxin


title: Hi-C-rok+rok95

value: Stationary

value: Luria broth

value: delta{rok} with rok95 muant complementation


title: Hi-C-rok+rok45

value: delta{rok} with rok45 mutant complementation


title: TOP2_AM01_1h_auxin_L2-L3_ext411_AKM150_input_AKM157_ChIP-seq

value: AM01 (dpy-27::degron::GFP)

value: auxin


title: RB9: WT_E5


title: Hi-C-rok+rok

value: delta{rok} with rok_wt complementation


title: RB7:  WT_E4

source_name: Spleen

value: C57BL/6 chimera


title: Hi-C-wt_st_2


title: Hi-C-rok_st_2

value: delta{rok} (rok deletion)


title: Hi-C-rok_st_1

data_processing:
SECO-seq and RNA-seqfiles were then trimmed using Trimmomatic (Galaxy Version 0.36.5) before mapping them to the B. subtilis subsp. subtilis str. 168 reference genome (NC_000964.3) using Bowtie2 (Galaxy version 2.3.4.2). The BAM files were converted to bigwig using the tool bamCoverage (Galaxy version 3.0.2.0)
Paired end reads generated for Hi-C were mapped separately to B. subtilis genome (NCBI Reference Sequence NC_000964.3) using very sensitive local setting mode in Bowtie2. The mapped files were used to build the contact matrix using the tool hicBuildMatrix using a bin size of 10 Kb, HindIII restriction site (AAGCTT) and AGCT as the dangling sequence. The contact matrix (.cool format) was then used for further analysis and visualization
Genome_build: NC_000964.3
Supplementary_files_format_and_content: BigWig, cool matrix file

growth_protocol: B. subtilis cultures were grown in LB media and harvested at the given growth phase.


title: dendritic cells - high tension rep3

city: Novato

first: Daniel

last: Winer

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
Data quality was assessed using FastQC v.0.11.2
Trimmed reads were screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.4.3
RSeQC package v.2.3.7 was used to assess read distribution, positional read duplication and confirm strandedness of alignments
Raw trimmed reads were aligned to the reference genome hg19 using Tophat v.2.0.11
Tophat alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Raw gene counts loading, sample-normalization and two-condition differential expression was performed with the edgeR R package, v.3.16.5.
Two-condition differential expression was done with the edgeR R package, v.3.8.6
The method used for normalizing the data was TMM, implemented by the calcNormFactors(y) function
The test for differential expression was done using the quasi-likelihood F-test functionality in edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: bone marrow

growth_protocol: Bone marrow cells were collected from the femurs and tibia of C57BL/6 and plated at a density of 4 x 106 /3mL per well on 6-well plates. Cultures were fed on day 3,6 and 10 with 1 mL cell culture medium containing fresh GM-CSF.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (50) from qiagen (Sku: 74104)
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep for Illumina

treatment_protocol: The cells were grown under different tensions (2 and 50 kPa)  with GM-CSF (20ng/ml, Biolegend) in cell culture medium

value: cells grown at 50kPa


title: dendritic cells - high tension rep2


title: IgG_LS05xMDX53_L2-L3_ext461_AKM275_input_AKM243_ChIP-seq

value: LS05 (rex-8 insertion);MDX53 (top-2::GFP)

value: IgG

value: Abcam, ab46540


title: DPY27_SS02_1h_auxin_L2-L3_ext428_AKM221_input_AKM181_ChIP-seq

value: Covance Research Products Inc, JL00001_DPY27


title: DPY27_AM05_1h-no_auxin_L2-L3_ext454_AKM239_input_AKM241_ChIP-seq

value: AM05 (top-1::degron::GFP)


title: DPY27_CA1200_1h-no_auxin_L2-L3_ext440_AKM210_input_AKM196_ChIP-seq


title: DPY27_SS02_1h_auxin_L2-L3_ext457_AKM219_input_AKM223_ChIP-seq


title: DPY27_CA1200_1h-no_auxin_L2-L3_ext437_AKM188_input_AKM194_ChIP-seq


title: DPY27_SS02_1h-no_auxin_L2-L3_ext456_AKM218_input_AKM222_ChIP-seq


title: DPY27_AM05_1h_auxin_L2-L3_ext455_AKM240_input_AKM242_ChIP-seq


title: dendritic cells - high tension rep1


title: input_AM01_L2-L3_ext410_AKM156

value: input


title: Hi-C-wt_st_1

value: wild type


title: DPY27_SS01A_1h_auxin_L2-L3_ext406_AKM148_input_AKM155_ChIP-seq

value: SS01A (top-2::degron::GFP)


title: RB8: dKO_E4

value: GP66:I-Ab+ Rosa26YFP+ CD4+ spleen T cells

value: LCMV Arm d7 pi


title: Hi-C-rok_le_1

value: Late Exponential

value: Luria broth


title: DPY27_CA1200_1h_auxin_L2-L3_ext438_AKM189_input_AKM195_ChIP-seq

value: auxin


title: DPY27_CA1200_1h_auxin_L2-L3_ext441_AKM211_input_AKM197_ChIP-seq


title: dendritic cells - low tension rep3

value: cells grown at 2kPa


title: dendritic cells - low tension rep2


title: DPY27_SS01A_1h_auxin_L2-L3_ext394_AKM104_input_AKM94_ChIP-seq


title: DPY27_SS01A_1h-no_auxin_L2-L3_ext404_AKM147_input_AKM153_ChIP-seq

value: no-auxin


title: Hi-C-wt_le_1


title: Hi-C-rok_ex_1

value: Exponential

value: delta{rok} (rok deletion)


title: dendritic cells - low tension rep1


title: DPY27_SS02_1h-no_auxin_L2-L3_ext427_AKM220_input_AKM180_ChIP-seq


title: DPY27_SS01A_1h-no_auxin_L2-L3_ext392_AKM102_input_AKM92_ChIP-seq


title: Hi-C-wt_ex_1


title: DPY27_AM01_1h-no_auxin_L2-L3_ext459_AKM229_input_AKM235_ChIP-seq

value: AM01 (dpy-27::degron::GFP)


title: DPY27_AM01_1h_auxin_L2-L3_ext411_AKM152_input_AKM157_ChIP-seq


title: wt_st_RNA

description: RNA-seq

value: Stationary


title: DPY27_AM05_1h_auxin_L2-L3_ext426_AKM171_input_AKM179_ChIP-seq


title: DPY27_AM01_1h-no_auxin_L2-L3_ext410_AKM151_input_AKM156_ChIP-seq


title: 8WG16_LS05xMDX53_L2-L3_ext462_AKM276_input_AKM244_ChIP-seq

value: LS05 (rex-8 insertion);MDX53 (top-2::GFP)

value: Millipore 05-952-I-100UG


title: 8WG16_LS05xMDX53_L2-L3_ext461_AKM274_input_AKM243_ChIP-seq


title: rok_st_RNA

description: RNA-seq


title: DPY27_AM01_1h_auxin_L2-L3_ext460_AKM230_input_AKM236_ChIP-seq

value: Covance Research Products Inc, JL00001_DPY27


title: DPY27_AM05_1h-no_auxin_L2-L3_ext425_AKM170_input_AKM178_ChIP-seq

value: AM05 (top-1::degron::GFP)


title: BS IFE 1

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13)
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
read counts from the featureCounts in the subread package (v1.4.6)
DESeq2 (v1.6.3) was used to determine differentially expressed genes
genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (read counts from featureCounts)

source_name: Skin epidermis

extract_protocol:
Newborn P0 back skins and paw skin were collected and subjected to 0.25% collagenase digestion for 60 minutes at 37ºC with 80 rpm shaking, followed by 0.25% trypsin treatment for 15 minutes at 37ºC. The cell suspension was washed twice with 1x PBS, stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend) and 1:200 EpCAM-APC (Biolegend) for 30 minutes on ice, and washed twice with 1x HBSS prior to cell sorting. We sorted IFE as GFP(-), EPCAM(+), and SCA1(+). We sorted Merkel cells as GFP(+), EPCAM(+), and SCA(-). FACS-purified cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform, obtaining 150-nucleotide paired-end reads.

tag: cell type

value: IFE

value: Epidermis

value: Postnatal day 0

tag: skin source

value: back skin


title: BS MC 2

value: merkel cells

tag: tissue

tag: genotype


title: 8WG16_CA1200_1h_auxin_L2-L3_ext467_AKM256_input_AKM249_ChIP-seq


title: 8WG16_SS01A_1h_auxin_L2-L3_ext406_AKM146_input_AKM155_ChIP-seq

value: SS01A (top-2::degron::GFP)

value: Abcam, ab817


title: BS IFE 2


title: rok_ex_RNA

description: RNA-seq

tag: growth phase

value: Luria broth


title: BS MC 1


title: wt_ex_RNA

description: RNA-seq

value: wild type


title: PAW IFE 2

value: paw


title: 8WG16_SS01A_1h_auxin_L2-L3_ext394_AKM101_input_AKM94_ChIP-seq

value: auxin


title: 8WG16_CA1200_1h-no_auxin_L2-L3_ext466_AKM255_input_AKM248_ChIP-seq

value: no-auxin


title: 8WG16_AM05_1h_auxin_L2-L3_ext469_AKM262_input_AKM265_ChIP-seq


title: 8WG16_SS01A_1h_auxin_L2-L3_ext397_AKM107_input_AKM97_ChIP-seq


title: rok_top

description: DNA coverage from top fraction from sedimentation assay

data_processing:
Library strategy: SECO-seq
SECO-seq and RNA-seqfiles were then trimmed using Trimmomatic (Galaxy Version 0.36.5) before mapping them to the B. subtilis subsp. subtilis str. 168 reference genome (NC_000964.3) using Bowtie2 (Galaxy version 2.3.4.2). The BAM files were converted to bigwig using the tool bamCoverage (Galaxy version 3.0.2.0)
Paired end reads generated for Hi-C were mapped separately to B. subtilis genome (NCBI Reference Sequence NC_000964.3) using very sensitive local setting mode in Bowtie2. The mapped files were used to build the contact matrix using the tool hicBuildMatrix using a bin size of 10 Kb, HindIII restriction site (AAGCTT) and AGCT as the dangling sequence. The contact matrix (.cool format) was then used for further analysis and visualization
Genome_build: NC_000964.3
Supplementary_files_format_and_content: BigWig, cool matrix file

value: Exponential

value: delta{rok} (rok deletion)


title: 8WG16_CA1200_1h_auxin_L2-L3_ext415_AKM159_input_AKM173_ChIP-seq


title: PHH cells infected with HBV - H3K79succ_input

city: Chongqing, China

first: yi ping

last: Qin

address: Room 617, College of Life Sciences Building, 1 YiXueYuan Road, YuZhong District, Chongqing

institute: Chongqing Medical University

data_processing:
ChIP-seq reads were aligned to the HBV genotype D reference genome using Bowtie2 (2.4.1).
Genome_build: HBV genotype D
Supplementary_files_format_and_content: bigwig files were generated using Deeptools (3.5.0).
Supplementary_files_format_and_content: Complete_genome_sequence_of_HBV_genotype_D.txt

source_name: PHH cells

growth_protocol: PHH cells were acquired from ScienCell Research Laboratories. The PHH cell line was maintained in hepatocyte medium (ScienCell, 5210) and cultured in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
HBV-infected PHHs were resuspended in cold nuclei isolation buffer (PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM DTT, 10 mM sodium butyrate, 1× protease inhibitor) for 15 min on ice with gentle mixing every 5 min. After centrifugation at 1000×g at 4◦C for 5 min, the nuclei was pelleted and fixed in 1% formaldehyde for 30 min at 4◦C. Cross-linked nuclei were washed and resuspended in MNase digestion buffer (50 mM Tris-HCl pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% glycerol, 10 mM sodium butyrate, 1× protease inhibitor). The nuclei was cut into mainly single nucleosome-sized pieces by digesting with 500 U/ml MNase (New England Biolabs, U.S.A.) at 37◦C for 10 min and ultrasonic crushing on ice. The sample was centrifugated at 6500×g for 5 min and the supernatant was applied to 5–30% sucrose (sucrose, 50 mM Tris-HCl pH 7.5, 50 mM NaCl, 5 mM EDTA pH 8.0, 0.01% NP-40, 10 mM sodium butyrate, 1× protease inhibitor) gradient centrifuge at 40000 rpm at 4◦C for 4 h. Mononucleosome containing fractions were pooled and subjected to ChIP assay. The immuno-enriched DNA sample was then used for sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: PHH cells were infected with 2000 genome equivalents/cell of HBV particles in the presence of 4% PEG8000. Seven days after HBV infection, ChIP-Seq analysis of cccDNA in HBV-infected PHHs was carried out.

value: Normal human hepatocytes

value: Infection with HBV

tag: chip antibody


title: PAW MC 2


title: wt_dense

description: DNA coverage from dense fraction from sedimentation assay


title: 8WG16_CA1200_1h-no_auxin_L2-L3_ext414_AKM158_input_AKM172_ChIP-seq


title: PAW MC 1


title: wt_top


title: tpm_CA1586932

status: Public on Nov 13 2021

city: Changsha

first: Hu

last: Jiao

address: No.87 Xiangya Road, Changsha, Hunan

institute: Xiangya hospital，Central South University

data_processing:
Reads were aligned to genome GRCh38  with  bowtie2-2.2.5  and  counted with the software rsem.
DESeq
Genome_build: GRCh38

source_name: bladder cancer

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Biotinylated RNA were prepared with MGIEasy RNA Library Prep Kit

value: bladder cancer cell


title: tpm_CA1568599


title: tpm_CA1590649


title: tpm_CA1589810


title: tpm_CA1580755


title: tpm_CA1586396


title: tpm_CA1589480


title: tpm_CA1554315


title: tpm_CA1587363


title: tpm_CA1559012


title: tpm_CA1532452


title: PAW IFE 1

value: IFE


title: tpm_CA1533024


title: tpm_CA1528542


title: tpm_CA1521373


title: tpm_CA1520663


title: tpm_CA1526051


title: tpm_CA1522117


title: tpm_CA1517987


title: tpm_CA1511992


title: tpm_CA1510351


title: tpm_CA1506424


title: PHH cells infected with HBV - H3K79succ_rep1

value: H3K79succ (PTM-412, PTM-bio)


title: tpm_CA1505875


title: 8WG16_AM05_1h_auxin_L2-L3_ext455_AKM163_input_AKM178_ChIP-seq

value: AM05 (top-1::degron::GFP)


title: tpm_CA1505257


title: tpm_CA1503628


title: tpm_CA1534929


title: tpm_CA1502698


title: tpm_CA1474792


title: tpm_CA1485034


title: tpm_CA1502091


title: tpm_CA1481665


title: tpm_CA1481528


title: tpm_CA1501158


title: tpm_CA1463949


title: tpm_CA1466950


title: tpm_CA1473520


title: tpm_CA1456349


title: tpm_CA1460006


title: tpm_CA1461830


title: tpm_CA1443723


title: tpm_CA1456774


title: tpm_CA1513247


title: tpm_CA1443189


title: tpm_CA1445125


title: tpm_CA1442434


title: tpm_CA1436303


title: tpm_CA1435228


title: tpm_CA1382793


title: tpm_CA1409255


title: tpm_CA1427893


title: tpm_CA1430225


title: tpm_CA1455582


title: tpm_CA1474704


title: tpm_CA1375590


title: tpm_CA1366278


title: tpm_CA1315330


title: X1481665_BA.TPM

source_name: normal bladder

value: bladder


title: tpm_CA1308866


title: tpm_CA1277013


title: X1474704_BA.TPM


title: X1466950_BA.TPM


title: X1474792_BA.TPM


title: X1460006_BA.TPM


title: X1456774_BA.TPM


title: X1445125_BA.TPM


title: X1443723_BA.TPM


title: X1443189_BA.TPM


title: X1375590_BA.TPM


title: X1277013_BA.TPM


title: X1442434_BA.TPM


title: X1455582_BA.TPM


title: genomic DNA from glioblastoma 98

type: genomic

city: Hamburg

first: Richard

last: Drexler

address: Martinistraße 52

department: Neurosurgery

country: Germany

institute: Medical Center Hamburg-Eppendorf

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: glioblastoma 98

label_protocol: Standard Illumina EPIC Protocol

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

treatment_protocol: Standard Illumina EPIC Protocol

tag: diagnosis

value: glioblastoma

tag: gender

value: female

tag: idh

value: wildtype


title: genomic DNA from glioblastoma 107

source_name: glioblastoma 107

value: male


title: genomic DNA from glioblastoma 104

source_name: glioblastoma 104


title: genomic DNA from glioblastoma 99

source_name: glioblastoma 99


title: genomic DNA from glioblastoma 89

source_name: glioblastoma 89


title: genomic DNA from glioblastoma 105

source_name: glioblastoma 105


title: genomic DNA from glioblastoma 110

source_name: glioblastoma 110


title: genomic DNA from glioblastoma 85

source_name: glioblastoma 85


title: genomic DNA from glioblastoma 109

source_name: glioblastoma 109


title: genomic DNA from glioblastoma 94

source_name: glioblastoma 94


title: genomic DNA from glioblastoma 97

source_name: glioblastoma 97


title: genomic DNA from glioblastoma 101

source_name: glioblastoma 101


title: genomic DNA from glioblastoma 83

source_name: glioblastoma 83


title: genomic DNA from glioblastoma 91

source_name: glioblastoma 91


title: genomic DNA from glioblastoma 111

source_name: glioblastoma 111


title: genomic DNA from glioblastoma 92

source_name: glioblastoma 92


title: genomic DNA from glioblastoma 95

source_name: glioblastoma 95


title: genomic DNA from glioblastoma 88

source_name: glioblastoma 88


title: genomic DNA from glioblastoma 102

source_name: glioblastoma 102


title: genomic DNA from glioblastoma 106

source_name: glioblastoma 106


title: genomic DNA from glioblastoma 96

source_name: glioblastoma 96


title: genomic DNA from glioblastoma 90

source_name: glioblastoma 90


title: genomic DNA from glioblastoma 100

source_name: glioblastoma 100


title: genomic DNA from glioblastoma 108

source_name: glioblastoma 108


title: genomic DNA from glioblastoma 112

source_name: glioblastoma 112


title: genomic DNA from glioblastoma 87

source_name: glioblastoma 87


title: genomic DNA from glioblastoma 86

source_name: glioblastoma 86


title: genomic DNA from glioblastoma 93

source_name: glioblastoma 93


title: genomic DNA from glioblastoma 103

source_name: glioblastoma 103


title: genomic DNA from glioblastoma 84

source_name: glioblastoma 84


title: genomic DNA from glioblastoma 80

source_name: glioblastoma 80


title: genomic DNA from glioblastoma 77

source_name: glioblastoma 77


title: genomic DNA from glioblastoma 73

source_name: glioblastoma 73


title: genomic DNA from glioblastoma 81

source_name: glioblastoma 81


title: genomic DNA from glioblastoma 75

source_name: glioblastoma 75


title: genomic DNA from glioblastoma 67

source_name: glioblastoma 67


title: genomic DNA from glioblastoma 70

source_name: glioblastoma 70


title: genomic DNA from glioblastoma 82

source_name: glioblastoma 82


title: genomic DNA from glioblastoma 79

source_name: glioblastoma 79


title: genomic DNA from glioblastoma 72

source_name: glioblastoma 72


title: genomic DNA from glioblastoma 76

source_name: glioblastoma 76


title: genomic DNA from glioblastoma 65

source_name: glioblastoma 65


title: genomic DNA from glioblastoma 59

source_name: glioblastoma 59


title: genomic DNA from glioblastoma 60

source_name: glioblastoma 60


title: genomic DNA from glioblastoma 58

source_name: glioblastoma 58


title: genomic DNA from glioblastoma 62

source_name: glioblastoma 62


title: genomic DNA from glioblastoma 57

source_name: glioblastoma 57


title: genomic DNA from glioblastoma 64

source_name: glioblastoma 64


title: genomic DNA from glioblastoma 69

source_name: glioblastoma 69


title: genomic DNA from glioblastoma 54

source_name: glioblastoma 54


title: genomic DNA from glioblastoma 66

source_name: glioblastoma 66


title: genomic DNA from glioblastoma 74

source_name: glioblastoma 74


title: genomic DNA from glioblastoma 53

source_name: glioblastoma 53


title: genomic DNA from glioblastoma 61

source_name: glioblastoma 61


title: genomic DNA from glioblastoma 56

source_name: glioblastoma 56


title: genomic DNA from glioblastoma 78

source_name: glioblastoma 78


title: genomic DNA from glioblastoma 63

source_name: glioblastoma 63


title: genomic DNA from glioblastoma 71

source_name: glioblastoma 71


title: genomic DNA from glioblastoma 55

source_name: glioblastoma 55


title: genomic DNA from glioblastoma 52

source_name: glioblastoma 52


title: genomic DNA from glioblastoma 68

source_name: glioblastoma 68


title: genomic DNA from glioblastoma 49

source_name: glioblastoma 49


title: genomic DNA from glioblastoma 50

source_name: glioblastoma 50


title: genomic DNA from glioblastoma 51

source_name: glioblastoma 51


title: genomic DNA from glioblastoma 46

source_name: glioblastoma 46


title: genomic DNA from glioblastoma 45

source_name: glioblastoma 45


title: genomic DNA from glioblastoma 48

source_name: glioblastoma 48


title: genomic DNA from glioblastoma 47

source_name: glioblastoma 47


title: genomic DNA from glioblastoma 44

source_name: glioblastoma 44


title: genomic DNA from glioblastoma 38

source_name: glioblastoma 38


title: genomic DNA from glioblastoma 41

source_name: glioblastoma 41


title: genomic DNA from glioblastoma 40

source_name: glioblastoma 40


title: genomic DNA from glioblastoma 36

source_name: glioblastoma 36


title: genomic DNA from glioblastoma 34

source_name: glioblastoma 34


title: genomic DNA from glioblastoma 39

source_name: glioblastoma 39


title: genomic DNA from glioblastoma 37

source_name: glioblastoma 37


title: genomic DNA from glioblastoma 43

source_name: glioblastoma 43


title: genomic DNA from glioblastoma 42

source_name: glioblastoma 42


title: genomic DNA from glioblastoma 29

source_name: glioblastoma 29


title: genomic DNA from glioblastoma 27

source_name: glioblastoma 27


title: genomic DNA from glioblastoma 26

source_name: glioblastoma 26


title: genomic DNA from glioblastoma 31

source_name: glioblastoma 31


title: genomic DNA from glioblastoma 30

source_name: glioblastoma 30


title: genomic DNA from glioblastoma 33

source_name: glioblastoma 33


title: genomic DNA from glioblastoma 28

source_name: glioblastoma 28


title: genomic DNA from glioblastoma 24

source_name: glioblastoma 24


title: genomic DNA from glioblastoma 32

source_name: glioblastoma 32


title: genomic DNA from glioblastoma 23

source_name: glioblastoma 23


title: genomic DNA from glioblastoma 22

source_name: glioblastoma 22


title: 5480-890

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

institute: Erasmus MC

description: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of serial dilutations and post-treatment samples from CLL patients enrolled in the CLL11 trial

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

source_name: BMMCs

extract_protocol:
gDNA was available from the CLL11 trial. 1-27 ug DNA was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the EC-NGS leader primer protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

tag: sequencing run number

tag: rearrangement/patient number

value: BMMCs

tag: sample type

value: CLL11  EOT patient sample


title: 7530-890


title: 5603-854

source_name: PBMCs

value: PBMCs


title: genomic DNA from glioblastoma 21

source_name: glioblastoma 21

tag: age


title: genomic DNA from glioblastoma 19

source_name: glioblastoma 19


title: genomic DNA from glioblastoma 25

source_name: glioblastoma 25


title: 5209-890


title: 5219-854


title: 5124-854


title: 2221-890


title: 2161-890


title: 1841-890


title: 1643-854


title: genomic DNA from glioblastoma 35

source_name: glioblastoma 35


title: 5109-890


title: 4523-890


title: 4463-890


title: cPT-QC_run15

source_name: thymus, tonsil and PBMCs

value: cPT-QC

value: thymus, tonsil and PBMCs

value: quality control


title: 4387-890


title: genomic DNA from glioblastoma 18

source_name: glioblastoma 18


title: 7520-854


title: genomic DNA from glioblastoma 17

source_name: glioblastoma 17


title: 7753-854 13


title: 6826-854


title: 5109-854


title: 4387-854 15


title: 2126-890


title: cPT-QC_run14


title: 4523-854


title: 2181-890


title: 7753-890


title: genomic DNA from glioblastoma 13

source_name: glioblastoma 13


title: 5481-854


title: cPT-QC_run13


title: 5216-854


title: genomic DNA from glioblastoma 10

source_name: glioblastoma 10


title: 5124-890


title: 6826-890


title: 5216-890


title: 5481-890


title: 5215-854


title: 5219-890


title: genomic DNA from glioblastoma 15

source_name: glioblastoma 15


title: genomic DNA from glioblastoma 14

source_name: glioblastoma 14


title: 1607-854 13


title: 6827-854


title: 4387-854 13


title: 4462-890


title: 5171-890


title: 5203-890


title: genomic DNA from glioblastoma 4

source_name: glioblastoma 4


title: genomic DNA from glioblastoma 8

source_name: glioblastoma 8


title: 7753-854 12


title: genomic DNA from glioblastoma 7

source_name: glioblastoma 7


title: 5480-854


title: 7530-854


title: genomic DNA from glioblastoma 16

source_name: glioblastoma 16


title: 5209-854


title: 5203-854


title: 5120-890

source_name: BMMCs


title: genomic DNA from glioblastoma 12

source_name: glioblastoma 12


title: 4462-854

source_name: PBMCs


title: 4382-854


title: 2200-854


title: genomic DNA from glioblastoma 11

source_name: glioblastoma 11


title: 2141-854


title: 2101-890


title: 1981-854


title: 1607-854 12


title: 1742-854


title: 7520-890


title: 1260-890


title: genomic DNA from glioblastoma 20

source_name: glioblastoma 20


title: 6280-854


title: 5700-854


title: 5120-854


title: 5401-854


title: 5160-854


title: 5171-854


title: 1300-854


title: genomic DNA from glioblastoma 6

source_name: glioblastoma 6


title: genomic DNA from glioblastoma 9

source_name: glioblastoma 9


title: genomic DNA from glioblastoma 3

source_name: glioblastoma 3


title: 2221-854


title: 1020-854


title: 1261-854


title: 5163-854


title: cPT-QC_run12

source_name: thymus, tonsil and PBMCs


title: cPT-QC_run9


title: MRD6-3-3

value: Serial dilution


title: MRD5.5-1


title: MRD6-3-2


title: MRD6-3


title: MRD5.5-2


title: MRD5.5-3


title: MRD6-2


title: 4_MRD5.8-2


title: MRD6-3-1


title: genomic DNA from glioblastoma 5

source_name: glioblastoma 5


title: 4_MRD5.5-2


title: cPT-QC_run11


title: 4_MRD5.5-4


title: genomic DNA from glioblastoma 1

source_name: glioblastoma 1


title: 4_MRD5.8-3


title: 4_MRD5-3


title: 4_MRD5.8-1


title: 4_MRD5-4


title: 4_MRD5.5-1


title: 4_MRD5.5-3


title: 4_MRD5-2


title: 4_MRD5-1


title: cPT-QC_run8


title: MRD6-1


title: 5401-890


title: 1686_MRD4-2


title: 5450-890


title: 1686_MRD4-3


title: 1686_MRD3-4


title: 1686_MRD4-1


title: 1686_MRD3-2


title: 1686_MRD3-1


title: 1686_MRD2-4


title: 1686_MRD5.5-2


title: 1686_MRD2-2


title: 1686_MRD5.5-3


title: 1686_MRD5.5-1


title: 1686_MRD3-3


title: cPT-QC_run7


title: 1686_MRD5-4


title: 1686_MRD5.8-2


title: 1686_MRD2-1


title: 1686_MRD5.8-3


title: 1686_MRD5-3


title: 1686_MRD5.8-1


title: 1686_MRD4-4


title: 2142-854


title: 1686_MRD5-1


title: 1559_MRD4-4


title: 1686_MRD2-3


title: 1559_MRD4-2


title: 1559_MRD4-3


title: 1559_MRD3-4


title: 1559_MRD3-3


title: 1559_MRD4-1


title: 1559_MRD3-1


title: 1559_MRD3-2


title: 1559_MRD2-4


title: 1686_MRD5.5-4


title: 4_MRD4-1


title: 1559_MRD2-3


title: 1559_MRD2-2


title: 4_MRD4-3


title: 1559_MRD2-1


title: 4_MRD4-4


title: cPT-QC_run6


title: 4_MRD3-3


title: 4_MRD2-3


title: 4_MRD2-4


title: 4_MRD3-1


title: 4_MRD2-2


title: 1686_MRD5-2


title: 1559_MRD5.8-3


title: 1559_MRD5.5-3


title: 1559_MRD5.8-2


title: 1559_MRD5.8-1


title: 1559_MRD5.5-4


title: 4_MRD4-2


title: 4_MRD3-4


title: 1559_MRD5-4


title: 4_MRD2-1


title: 4_MRD3-2


title: 1559_MRD5.5-1


title: 1559_MRD5-3


title: 1559_MRD5-2


title: 1559_MRD5-1


title: genomic DNA from glioblastoma 2

source_name: glioblastoma 2


title: 805_MRD3_6


title: 805_MRD5_3


title: 805_MRD4_5


title: 805_MRD4_6


title: 764_MRD3_6


title: 805_MRD2_5


title: 764_MRD4_5


title: 764_MRD2_5


title: 764_MRD2_6


title: 764_MRD5_4


title: 805_MRD3_5


title: 764_MRD3_5


title: 764_MRD4_6


title: 805_MRD5_4


title: 1559_MRD5.5-2


title: 112_MRD4_6


title: 112_MRD5_4


title: cPT-QC_run5


title: 112_MRD4_5


title: 805_MRD5_2


title: 112_MRD2_5


title: 112_MRD3_6


title: 112_MRD2_6


title: 112_MRD3_5


title: 805_MRD2_6


title: 805_MRD5_1


title: 805_MRD4_3


title: 805_MRD3_4


title: 805_MRD3_3


title: 805_MRD4_4


title: 805_MRD2_4


title: 764_MRD4_3


title: 764_MRD5_3


title: 764_MRD2_4


title: 764_MRD4_4


title: 805_MRD2_3


title: 764_MRD2_3


title: 764_MRD3_3


title: cPT-QC_run4


title: 112_MRD5_3


title: 112_MRD4_3


title: 112_MRD3_4


title: 112_MRD4_4


title: BMDCs_FliC_24h_rep3

city: Yangzhou

first: Xilong

last: Kang

state: Jiangsu

address: 48 East Wenhui Road

institute: Yangzhou University

description: miRNA expression after 24 h in flagellin-stimulated BMDCs

hyb_protocol: Samples in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was performed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent) software was used to extract all features of the data obtained from the scanned images and genespring software (Agilent) was used to analyze the raw data, which are normalized by quantile normalization.

source_name: BMDCs, FliC, 24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Murine BMDCs were generated from C3H/HeJ murine bone marrow in vitro cultured in presence of rmGM-CSF and rmIL-4. The CD11c+ BMDCs were sorted using anti-CD11c-coated magnetic beads with the auto-MACS system. The purified BMDCs were incubated at 37°C in a 5% CO2 atmosphere.

extract_protocol: RNA was extracted using the mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations.

treatment_protocol: The purified BMDCs were stimulated with 100 ng/mL flagellin or medium and incubated 24 h at 37°C in a 5% CO2 atmosphere.

tag: strain

value: bone marrow-derived dendritic cells

value: flagellin-stimulated


title: BMDCs_FliC_24h_rep1


title: 112_MRD2_4


title: ESC Diff input rep1

city: Boston

first: Hye Ji

last: Cha

state: MA

address: 1 Blackfan Circle

institute: Boston Children’s Hospital

data_processing:
ChIP sequencing was performed using Illumina HiSeq2500 or NextSeq500.
Sequencing reads were aligned to the assembly of the mouse genome mm10 using Bowtie2 with the default parameters.
Duplicate reads were removed using Picard Tools (http://broadinstitute.github.io/picard/).
Peaks were called using Model-based Analysis of ChIP-Seq (MACS2).
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: Mouse embryonic stem cell

growth_protocol: MEL cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal calf serum, 1% L-glutamine, and 2% penicillin/streptomycin at 37 °C in a humidified. atmosphere of 5% CO2. Mouse ES cells were maintained on mouse embryonic fibroblasts (Gibco MEFs) feeders in standard ES medium supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix, 50 U/ml Penicillin/Streptomycin, 1000U/ml recombinant leukemia inhibitory factor(LIF/ESGRO).

extract_protocol:
Cells were crosslinked and nuclei were prepared using truChIP Chromatin Shearing Reagent Kit (Covaris).
Purified ChIP DNA was processed to generate libraries using the NEBNext ChIP-seq Library Prep Master Mix, NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs), ThruPLEX DNA-Seq Kit (Rubicon Genomics), or Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer’s instructions.

treatment_protocol: Mouse ES cells were differentiated in Iscove’s Modified Dulbecco Media (IMDM) supplemented with 10% heat-inactivated fetal calf serum, 2mmol L-glutamine, 4.5x10-4mol/L monothioglycerol, 0.5 mmol/L ascorbic acid, 200 μg/mL transferrin, 5% protein free hybridoma media (PFHM-II) and 50 U/ml Penicillin/Streptomycin.

value: Embryonic stem cell

value: wild type

value: differentiated


title: ESC Matr3KO input rep2

value: Matr3 -/-

value: untreated


title: ESC Diff input rep2


title: 112_MRD3_3


title: BMDCs_FliC_24h_rep2


title: BMDCs_mock_24h_rep1

description: miRNA expression after 24 h in mock BMDCs

source_name: BMDCs, mock, 24h

value: mock


title: BMDCs_mock_24h_rep2


title: 764_MRD3_4


title: ESC Matr3KO input rep1


title: ESC parental input rep3


title: ESC parental input rep2


title: cPT-QC_run3


title: 112_MRD2_3


title: IRI-Ctrl-3_S6_R1_001

city: Münster

first: Jan

last: Rossaint

address: Albert-Schweitzer-Campus 1, Bldg. A1

department: Dpt. of Anesthesiology

institute: University of Münster

description: TECs IRI Vehicle

data_processing:
quality control was performed with FastQC and MultiQC and adapter trimming was performed with trim-galore (v0.6.4).
Read-mapping and quantification with Salmon (v1.0.0) using the Gencode mouse reference transcriptome vM23
The transcript counts where summarized to gene-level with tximport and supplementary annotation data from Ensembl
The differential expression analysis was carried out by DESeq2 on gene level counts
The reported log foldchanges where shrunk with apeglm and s-values where calculated for statistical significance filtering. For a significant differential gene we require a s-value below 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated matrix of quantification counts of each gene per sample.

source_name: kidney lysate of mice

extract_protocol:
RNA was extracted from the sorted cells using a RNeasy Mini Kit (Qiagen).
Reverse transcription into cDNA was performed based on polyA tail. For library construction, PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The single strand circle DNA (ssCirDNA) were formatted as the final library. The library was amplified to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: IRI-induced AKI was induced in wildtype mice by temporal clamping of the renal pedicals. Cells were isolated from the blood (neutrophils) and kidney tissue (renal tubular epithelial cells) 24 hours after the procedure.

value: kidney

value: renal tubular epithelial cells

value: Vehicle

value: cells isolated 24 hours afer induction of IRI-induced AKI


title: IRI-Gln-3_S11_R1_001

description: TECs IRI Glutamine

value: Glutamine


title: Dicer clone_me3_ChIP_1

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
RNA-seq: Reads were trimmed for adapters and quality with Trimmomatic. Mapping to the mm10 genome was performed with the STAR aligner with --winAnchorMultimapNmax and --outFilterMultimapNmax set to 100 in order to allow reads to multimap for downstream analysis. The analysis of differential expression of both genes and repetitive elements was performed with TEtranscripts and DESeq2. Gene set enrichment analysis was performed with GSEA. Intersections between RNA-seq data sets and ChIP-seq datasets were performed with custom scripts. For strand-specific analysis, trimmed reads were mapped with bowtie2 with default settings and -k 5 to allow for multimapping. Normalized, strand-specific coverage was generated using deepTools.
small RNA: Raw reads were first trimmed with Cutadapt to clip Illumina 3’ adapters, while retaining the 4nt-long degenerate sequences at the 5’ and 3’ end of each insert. Reads with an insert size between 12-60 nt were subsequently filtered using Gordon Assaf’s FASTX-Toolkit to discard low-quality reads with Phred scores less than 20 in 10% or more nucleotides. PCR duplicates were removed using PRINSEQ (derep option 1) and degenerate sequences were extracted and appended to the name of each read using UMI-tools. Preprocessed reads were first aligned to calibrator sequences and then either to Mus musculus mm10 UCSC genome using Bowtie2, which assigns multi-mapping reads in an unbiased way. Aligned reads were filtered for 0-2 mismatches using Samtools and BamTools. For ERV and GSAT (major satellite) analysis, aligned reads were intersected with RepeatMasker annotation (http://www.repeatmasker.org) using BEDtools. Read counts were normalized to total calibrator per library.
ChIP-seq: Reads were trimmed for adapters and quality with Trimmomatic. Bowties was used for mapping with default settings and –dovetail, -X 600, and -k 5. The resulting SAM files were converted, sorted, and indexed with SAMtools. Normalized coverage was calculated for library size for each sample and a relative normalized coverage was calculated for IP over input using deepTools. Peaks were called with default settings with MACS2. Differential peaks were called with default settings with MAnorm. Peaks were assigned to underlying or nearby features and a functional enrichment analysis of these features was performed with ChIP-Enrich.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq/sRNA-seq: counts table contains all features (genes and repetitve elements) as rows with individual samples as the columns.; ChIP-seq: peak files generated by MACS2 contain all relevant peak location, magnitude, and significance information

source_name: Dicer clone_me3_ChIP

growth_protocol: Mouse embryonic stem cells, including Dicer1 flx/flx lines, were grown in 2i conditions. The 2i medium consists of : 250 mL Neurobasal medium (Gibco 21103-049), 250 mL DMEM/F12 (Gibco 11320-033), 2.5 mL N2 supplement (Gibco 17502-048), 5 mL B27 supplement (Gibco 17504-044), 5 mL GlutaMAX (Gibco 35050-061) and 3.3 mL 7.5% BSA Fraction V (Gibco 15260-037). Just prior to adding the media to the cells, the following additional supplements were added: PD0325901 to 1 M (Stemgent 04-0006), CHIR99021 to 3 M (Stemgent 04-0004), 2-Mercaptoethanol to 100 M (Gibco 21985-023), and Mouse LIF to 103 units/mL (EMD Millipore ESG1106). Culture dishes were coated with gelatin (1X Attachment Factor – ThermoFisher S006100) for a minimum 15 minutes, gelatin was removed, and dishes were allowed to dry before cells were plated. Cells were split with TrypLE Express Enzyme (Gibco 12605-010) for 5 minutes at 37 degrees Celsius. Cells were collected in enough media for a 10-fold dilution of the TrypLE Express and pipetted up and down a minimum of 10 times to achieve a single cell suspension. Cells were then spun for 5 minutes at 150 x g and resuspended in media for counting and plating. Cells were frozen in freezing media: 10% DMSO (Sigma D2650), 50% ES-FBS (Gibco 16141-002), and 40% cells in media. Inducible Dicer1 knockout cells were treated with hydroxytamoxifen (OHT – Sigma H7904) at a final concentration of 1 M.

extract_protocol: Cells were grown in 2i conditions as detailed on 15 centimeter plates. 37% formaldehyde is added to a final concentration of 1% in the media and incubated at room temperature for 10 minutes. The reaction was quenched with for 5 minutes at room temperature with the 10X glycine buffer from the SimpleChIP Kit (Cell Signaling 56383). The protocol for the SimpleChIP Kit was followed as directed. Chromatin was fractionated using the 1 mL millitubes on the Covaris with optimized custom settings to achieve an average size of 250 basepair fragments. ChIP was performed with recommended dilutions of antibodies and control H3 antibodies. An input control was also generated for each sample. ChIP-sequencing libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit (NEB E7645S). Libraries were quantified with the KAPA Illumina Quantification Kit (KAPA KK4824) and checked for quality on the Agilent Bioanalyzer.

tag: strain background

value: mouse embryonic stem cells


title: Dicer clone_me3_ChIP_2


title: IRI-Gln-2_S10_R1_001

description: TECs IRI Glutamine


title: 805_MRD4_1

value: PBMCs


title: Tissue_ypT+N+_replicate 2

city: Jinan

first: Zhao

last: Bi

address: Jiyan Road 440

institute: Shandong Cancer Hospital

description:
lncRNA
Gene expression in ypT+N+ tissue

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tissue_ypT+N+_replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.  The protocol includes Mix the following in a microcentrifuge tube; Incubate at 37°C for 30 minutes; Add 350 μl Buffer RLT, and mix well; Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting; Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through; Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through; Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane; Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min; Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA; RNA quantification and quality control(Passed-please see report ”RNA-QC”).

treatment_protocol: Cryopulverization of tissue using the Biopulverizer, homogenization using the Mini-Bead-Beater-16.

tag: disease state

value: HER-2 positive breast cancer

tag: disease subgroup

value: ypT+N+

value: Core biopsies tissues


title: Tissue_ypT0N0_replicate 3

description:
lncRNA
Gene expression in ypT0N0 tissue

source_name: Tissue_ypT0N0_replicate 1


title: Dicer timecourse_me3_ChIP_2

source_name: Dicer timecourse_me3_ChIP

tag: cell type


title: Dicer timecourse_me3_ChIP_1


title: 805_MRD3_2

source_name: PBMCs

value: Serial dilution


title: IRI-Gln-1_S9_R1_001

description: TECs IRI Glutamine

tag: treatment


title: Tissue_ypT+N+_replicate 1

description:
lncRNA
Gene expression in ypT+N+ tissue

tag: tissue


title: Dicer clone_me2_ChIP_1

source_name: Dicer clone_me2_ChIP


title: Dicer clone_me2_ChIP_2


title: wild type_me3_ChIP_1

source_name: wild type_me3_ChIP


title: 805_MRD3_1


title: IRI-Ctrl-4_S7_R1_001

description: TECs IRI Vehicle


title: IRI-Ctrl-5_S8_R1_001

description: TECs IRI Vehicle


title: Tissue_ypT0N0_replicate 1

description:
lncRNA
Gene expression in ypT0N0 tissue


title: Tissue_ypT+N+_replicate 3

description:
lncRNA
Gene expression in ypT+N+ tissue


title: Tissue_ypT0N0_replicate 2

description:
lncRNA
Gene expression in ypT0N0 tissue


title: CL100148065_L1_RDWHMOUynoEABOAA-547

description: PMNs IRI Vehicle

source_name: murine peripheral whole blood

value: blood

value: neutrophils


title: Dicer timecourse_me2_ChIP_1

source_name: Dicer timecourse_me2_ChIP


title: ESC parental input rep1

value: Embryonic stem cell

tag: genotype

value: wild type


title: Dicer timecourse_me2_ChIP_2


title: 805_MRD2_2


title: CL100148065_L1_RDWHMOUynoEABNAA-546

description: PMNs IRI Vehicle


title: 805_MRD4_2


title: wild type_me3_ChIP_2


title: 805_MRD2_1


title: wild type_me2_ChIP_2

source_name: wild type_me2_ChIP


title: Dicer clone_H3_ChIP_2

source_name: Dicer clone_H3_ChIP


title: wild type_me2_ChIP_1


title: Dicer timecourse_H3_ChIP_2

source_name: Dicer timecourse_H3_ChIP


title: 764_MRD5_2


title: CL100148065_L1_RDWHMOUynoEABMAA-544

description: PMNs IRI Vehicle


title: Dicer timecourse_H3_ChIP_1


title: CL100148065_L1_RDWHMOUynoEABQAA-550

description: PMNs IRI Glutamine


title: CL100148065_L1_RDWHMOUynoEABRAA-551

description: PMNs IRI Glutamine


title: CL100148065_L1_RDWHMOUynoEABPAA-548

description: PMNs IRI Glutamine


title: 764_MRD4_2


title: wild type_H3_ChIP_2

source_name: wild type_H3_ChIP


title: wild type_H3_ChIP_1


title: Dicer clone_H3K9_ChIP_input_2

source_name: Dicer clone_H3K9_ChIP


title: 764_MRD3_2


title: Dicer clone_H3K9_ChIP_input_1


title: Dicer timecourse_H3K9_ChIP_input_1

source_name: Dicer timecourse_H3K9_ChIP


title: Dicer timecourse_H3K9_ChIP_input_2


title: Dicer timecourse_BRD4_ChIP_2

source_name: Dicer timecourse_BRD4_ChIP


title: Dicer timecourse_BRD4_ChIP_1


title: Dicer clone_H3_ChIP_1


title: Dicer clone_BRD4_ChIP_2

source_name: Dicer clone_BRD4_ChIP


title: Dicer clone_BRD4_ChIP_1


title: 764_MRD2_2


title: 764_MRD3_1


title: wild type_BRD4_ChIP_2

source_name: wild type_BRD4_ChIP


title: 764_MRD5_1


title: 1559-2

city: Fuzhou

first: Liman

last: Qiu

address: Xihong Road 312, Fuzhou 350025, Fujian, P. R. China.

institute: Mengchao Hepatobiliary Hospital of Fujian Medical University

data_processing:
The sequencing reads that meet any of the following criteria were removed: (1) containing adaptor sequence; (2) with >10% ambiguous bases (N) of total read length; (3) containing >20% low quality bases (base quality ≤ 20) of total read length
Qualified reads were aligned to ribosomal rRNA sequences download from RNAcentral database to remove possible rRNA inference.
The unmapped reads were aligned to UCSC human genome reference (GRCh37/hg) using TopHat2
All the reads that could not align to the genome were extracted to identify the potential back-spliced junction reads by TopHat-Fusion. The identified potential candidate reads that could be mapped to the same chromosome but in reverse order were further considered as the candidate back-spliced junction reads
After removing any circular RNA with less than two unique back-spliced reads in one tissue sample, the expression levels for each circular RNA were calculated, according to reads Per Million mapped reads (RPM) using all the junction reads within the circular RNA region
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

source_name: HCC peritumor tissues

extract_protocol:
Total RNA from HCC tumor and peritumor tissue samples were extracted using TransZol reagents. rRNAs were removed by a Ribo-Zero Magnetic kit, and linear RNA was digested by RNase R before construction of the RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient diagnosis

value: hepatocellular carcinoma (HCC)

tag: subject id

value: Male

value: liver

tag: tissue region

value: peritumor


title: 1522-2

tag: gender


title: 1497-2


title: wild type_H3K9_ChIP_input_1

source_name: wild type_H3K9_ChIP


title: 764_MRD4_1


title: 1517-2


title: 764_MRD2_1


title: 112_MRD5_2


title: 1340-2


title: Dicer timecourse_BRD4_ChIP_input_1


title: Dicer timecourse_BRD4_ChIP_input_2


title: 1329-2


title: 1495-2

value: Female


title: 112_MRD5_1


title: 112_MRD4_2


title: wild type_H3K9_ChIP_input_2


title: Dicer clone_BRD4_ChIP_input_1


title: Dicer clone_BRD4_ChIP_input_2


title: wild type_BRD4_ChIP_input_2


title: 1302-2


title: 112_MRD4_1


title: wild type_BRD4_ChIP_input_1


title: Dicer timecourse_sRNAseq_3 [OHT3]

description:
OHT3
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt

source_name: Dicer timecourse_sRNAseq

extract_protocol:
Small RNAs were isolated from total RNA using Novex TBE-Urea Gels (ThermoFisher EC6885BOX). Libraries were constructed with the TruSeq Small RNA Kit (Illumina RS-200-0012). Libraries were quantified with the KAPA Illumina Quantification Kit (KAPA KK4824).
extracted from total RNA by TBE PAGE size selection 14-60 nt

tag: extraction

value: Trizol


title: wild type_BRD4_ChIP_1


title: Dicer timecourse_sRNAseq_2 [OHT2]

description:
OHT2
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: 1263-2


title: 112_MRD3_2

source_name: PBMCs

tag: sequencing run number


title: 1559-1

source_name: HCC tumor tissue

value: tumor


title: Dicer timecourse_sRNAseq_1 [OHT1]

description:
OHT1
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt

value: mouse embryonic stem cells


title: Dgcr8 knockout_sRNAseq_3 [Dgcr8_2]

description:
Dgcr8_2
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt

source_name: Dgcr8 knockout_sRNAseq


title: 112_MRD2_2

tag: rearrangement/patient number

value: PBMCs


title: Dgcr8 knockout_sRNAseq_2 [Dgcr8_1]

description:
Dgcr8_1
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: 1232-2


title: 112_MRD2_1

tag: sample type


title: 1522-1

tag: age


title: Dicer clone_sRNAseq_2 [Dcr_A6]

description:
Dcr_A6
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt

source_name: Dicer clone_sRNAseq


title: Dicer clone_sRNAseq_3 [Dcr_C8]

description:
Dcr_C8
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: Dicer clone_sRNAseq_1 [Dcr_A4]

description:
Dcr_A4
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: wild type_sRNAseq_3 [WT3]

description:
WT3
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt

source_name: wild type_sRNAseq


title: 1517-1


title: cPT-QC_run2

source_name: thymus, tonsil and PBMCs

value: cPT-QC

value: thymus, tonsil and PBMCs

value: quality control


title: wild type_sRNAseq_2 [WT2]

description:
WT2
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: wild type_sRNAseq_1 [WT1]

description:
WT1
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: 1497-1


title: 1495-1


title: 24_Dicer/Elp3 mutant clone_RNAseq_2

description:
24_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Dicer/Elp3 mutant clone_RNAseq

extract_protocol:
RNA was isolated with TRIzol as described and DNase treated. When total RNA was sequenced, 1 microgram RNA was first depleted for ribosomal RNA using the rRNA Depletion Kit (NEB E6310). Total RNA libraries were then prepared using the NEBNext Ultra II Directional Kit (NEB E7760). Libraries were quantified with the KAPA Illumina Quantification Kit (KAPA KK4824).
For ChIP the following primary antibodies were used: H3K9me3 (Abcam, ab1769916), H3K9me2 (Cell Signaling Technology, 4658s), BRD4 (Active Motif, 39910), and H3 (Cell Signaling Technology, 4620s).
Illumina stranded


title: 23_Dicer/Elp3 mutant clone_RNAseq_1

description:
23_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 1340-1


title: 112_MRD3_1

value: Serial dilution


title: Dgcr8 knockout_sRNAseq_1 [Dgcr8_0]

description:
Dgcr8_0
processed data file: sRNAseq_overall_summary_counts_mm10_mapped.txt


title: 22_Dicer/Brd4 mutant clone_RNAseq_4

description:
22_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Dicer/Brd4 mutant clone_RNAseq


title: 344-MRD4_2

description: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of serial dilutations and post-treatment samples from CLL patients enrolled in the CLL11 trial


title: 21_Dicer/Brd4 mutant clone_RNAseq_3

description:
21_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 20_Dicer/Brd4 mutant clone_RNAseq_2

description:
20_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 344-MRD2_2


title: 1302-1


title: 19_Dicer/Brd4 mutant clone_RNAseq_1

description:
19_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 18_Dicer/Brd4 mutant timecourse_RNAseq_3

description:
18_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Dicer/Brd4 mutant timecourse_RNAseq


title: 1329-1


title: 216-MRD5_2


title: 344-MRD5_2


title: 1232-1


title: 15_Elp3 mutant_RNAseq_2

description:
15_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Elp3 mutant_RNAseq