title: PAO1161 PA2577-F_2_ChIP-seq

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: ChIP DNA data from PA2577-FLAG overproducer

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
PA2577 peaks were identified by comparing combined replicates of IP samples (PA2577-F) for each strain with negative control (empty vector EV-F) samples using the callpeak function of MACS2 ver 2.1.2 with default options for paired-end .BAM files, and 0.05 as false discovery rate (FDR) cut off.
Genome_build: CP032126
Supplementary_files_format_and_content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome.
Supplementary_files_format_and_content: Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed).
Supplementary_files_format_and_content: A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed).

organism: Pseudomonas aeruginosa

source_name: PA2577_FLAG overproducer (PA2577-F)

growth_protocol: P. aeruginosa PAO1161 ΔPA2577 strain carrying pMEB84 (lacIQ-tacp-PA2577-flag) as well as control strain carrying pABB28.1 (lacIQ-tacp-flag) were obtained by conjugation of PAO1161 (leu-, r-, RifR) and E. coli S-17 donor strain carrying appropriate plasmid. Conjugants were selected on L agar plates supplemented with 300 μg/mL rifampicin and 150 μg/mL chloramphenicol. Two independent overnight cultures from each strain were inoculated from single colonies and grown overnight with shaking at 37oC. After that they were diluted 1:100 in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG to induce the expression of PA2577-flag and grown with shaking at 37oC until reaching exponential phase with optical density about 0.5 (OD600).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606; Modrzejewska et al, 2021; mSystems 6:4, e0001521). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC. Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with anti-FLAG mouse antibodies (1-10 μg per reaction, 3 and 6 μL for this procedure) [DYKDDDDK Tag polyclonal  antibodies; 1 mg/mL; PA1-985B; Invitrogen] diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleared lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). All 100 μL of obtained eluates were incubated with 1 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Then, 5 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Such prepared probes were stored on ice and 3 μL of 3 M sodium acetate (pH=5) was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The DNA was stored at -20oC.
NGS library was constructed using QiaSeq Ultralow Input Library kit. Sample was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

treatment_protocol: All cultures were incubated at 37°C in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG with shaking until reaching exponential phase of growth (OD600 = 0.5).

tag: strain

value: PAO1161/pMEB84 (lacIQ-tacp-PA2577-flag)

tag: genotype

value: PA2577_FLAG overproducer (PA2577-F)

value: logarithmic phase of liquid culture

tag: antibody

value: polyclonal anti-FLAG


title: RNaseH_H3K4me3_ChRD_rep2

status: Public on Dec 10 2021

type: SRA

city: Hangzhou

first: Xingyu

last: Huang

state: Zhejiang

address: 866 Yuhangtang Road, Hangzhou, Zhejiang Province

country: China

institute: Life Sciences Institute (LSI), Zhejiang University (ZJU)

library_source: genomic

data_processing:
Library strategy: ChRD-PET
FastQC and cutadapt filtered the raw reads
Combine the R1 and R2 by FLASH, and get a "Combine" data and two "NotCombine" data
Finding the linker("CCTCGATACTTGAGCTGACT") in three file by cutadapt. And split data into DNA and RNA data
For length<70 DNA reads were aligned to MH63 genome assembly using bwa aln. For length>70 DNA reads were aligned to MH63 genome assembly using bwa mem. For RNA reads, We use a two-step comparison strategy. Firstly, RNA reads wrer aligned to MH63 using hisat2. And than, get the unmapped and multi-mapped reads and were aligned to MH63 again by bowtie2.
Remove multi-mapped reads, filtered using the SAMTOOLS MAPQ20
Remove reads aligned to rRNA, and combine DNA and RNA aligned result into a bedpe file. Merge records with similar positions(both DNA and RNA) to calculate a highly significant DNA-RNA interaction
Genome_build: MH63
Supplementary_files_format_and_content: bedpe
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Oryza sativa

source_name: MH63 seedling

growth_protocol: MH63 (one parent of one of the most widely cultivated rice hybrids in China, Shanyou 63) were used in this study. The germinating seeds were collected by soaking dry seeds in water for 72 h at 37 °C. The germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °C.

extract_protocol:
About 3 g Rice nuclei isolated from dual cross-linked rice MH63 seedlings were  lysed in Buffer S  (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1% SDS) at 4 °C for 40 min at 12 rpm. Then add 9 volume buffer F (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate) to sample and rotate at 4 °C for 40 min at 12 rpm. The chromatin were then sonicated into 1–3 kb (High level, 28 cycles, 30 s ON, and 50 s OFF) using a Bioruptor (Diagenode). The chromatin fragments were centrifuged at 2800 g for 10 min at 4 °C and the supernatant was transferred to a new tube for chromatin immunoprecipitation (ChIP). To prepare antibody-loaded beads, 40 μL antibody (H3K4me3 antibody, ABclonal cat. no. A2357；H3 antibody, ABclonal cat. no. A2348) was mixed with 750 μL of suspended protein G magnetic beads, followed by incubation at 4 °C for 8 h with rotation at 12 rpm. Then, the mixed fragmented chromatin extract was incubated with antibody-loaded beads and incubated at 4 °C overnight with rotation at 12 rpm. The supernatant was discarded and the beads were washed three times with 1 mL 0.1% SDS FA cell lysis buffer (0.05 M, HEPES-KOH, 0.15 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS), and then washed twice with 1 mL high salt ChIP buffer (0.05 M, HEPES-KOH, 0.35 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS); and once with 1 mL ChIP wash buffer (0.01 M Tris–HCl, 0.25 M LiCl, 0.001 M EDTA, 2.5% NP-40, and 0.5% sodium deoxycholate), and finally washed with 1 mL 1× TE buffer (pH 8.0, Ambion, cat. no. AM9849) twice. DNA of the ChIP complex on beads was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F), and Klenow enzyme (NEB, cat. no. M0212L). To ligate DNA and RNA, we used a specially designed single biotinylated bridge linker: forward strand: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGACT-3′; reverse strand: 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. Then, RNA ends were proximity-ligated by the single biotinylated bridge-linker with the 5′ end adenylated on the forward strand, followed by extension of the reverse strand in the linker into ligated RNA with reverse transcription as first strand cDNA synthesis. Next, the DNA ends with 3’ A-tailing were proximity-ligated by the single biotinylated bridge linker with a 3’ nucleotide T over-hang on the forward strand, followed by second strand cDNA synthesis. (For RNase H treated H3K4me3 ChRD-PET data, RNase H treatment was conducted before DNA end repair and A-tailing.)
The proximity ligation RNA-DNA fragments were reverse cross-linked and fragmented before adding sequencing adaptors simultaneously by using Tn5 transposase (VAHTS, cat. no. TD501). The fragments contained the bridge-linker at ligation junctions were captured by Streptavidin beads, and used as templates for PCR amplification. These DNA products were then subjected to size-selection and paired-end sequencing (2 × 150 bp) using Illumina Hiseq X-Ten.

treatment_protocol: Young leaves of 2-week-old seedlings were collected and immediately preserved in 1× PBS for dual crosslinking with 1% (v/v) formaldehyde (Sigma, F8775) and 1.5 mM ethylene glycol bis (EGS, Thermo Fisher Scientific, 21565). Dual cross-linked samples were rinsed three times with deionised water and immediately frozen in liquid nitrogen. Frozen tissues were kept at -80 °C for no longer than 1 month.

tag: development stage

value: seedling

tag: tissue

tag: cultivar

value: Minghui 63

tag: chip antibody

value: RNaseH and H3K4me3


title: TNBC_10

type: RNA

city: Bunkyo-ku

first: Mai

last: Onishi

state: Tokyo

department: Clinical oncology

country: Japan

institute: Juntendo university Graduated schoo;

data_processing: Raw expression data was processed using nSolverAnalysis Software 4.0.70: Background subtraction with geometric mean of negative controls; Normalization with geometric mean of positive controls and standard housekeeping genes; No ratios built

molecule: total RNA

organism: Homo sapiens

source_name: primary breast cancer

extract_protocol: Glass slide specimens with 10-µm thick sections of FFPE tissue block were prepared. Total RNA was extracted from the samples using RNeasy mini kit (Qiagen, USA) according to manufacture's instructions

value: primary breast cancer

tag: status

value: alive

tag: gender

value: female

tag: biopsy method

value: CNB

tag: er status

tag: pgr status

tag: her2 status

tag: t stage

tag: n stage


title: RNaseH_H3K4me3_ChRD_rep1


title: TNBC_9


title: MH63 seedling_ssDRIP_rep2

data_processing:
library strategy: ssDRIP-seq
Trimmomatic fitered the raw reads
ssDRIP-seq reads were aligned to the MH63 genome assembly using bwa mem
Remove multi-mapped reads, filtered using the SAMTOOLS MAPQ20 and filter the  duplication reads
Using samtools to split the filter align file into forward and reverse align file
Peak was calling using MACS2 with callpeak -t <input file> --nomodel --extsize 100 -f BAM –n <output peak file> -B -q 0.05 -g 3.6e+8
Genome_build: MH63 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001623365.1)
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

source_name: MH63 seedling_ssDRIP

extract_protocol:
Genomic DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed at 37 °C overnight using endonucleases (Ssp I, Eco RI, Hind III, Dde I, Msp I and Rsa I; New England Biolabs, Ipswich, MA, USA); the negative control was treated with RNase H (New England Biolabs) at 37 °C overnight. DRIP was performed as described previously. The S9.6 antibody was purified from HB-8730 (ATCC, Manassas, VA, USA). The DRIPed DNA samples were sonicated to a set size of 250 bp with an M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).
The sonicated DNA was denatured at 95 °C for 2 minutes and immediately placed on ice for 2 minutes to obtain ssDNA fragments. The first adapter (Adp1, GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(i7) ATCTCGTATGCCGTCTTCTGCTTG) was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences, Ann Arbor, MI, USA) via a highly efficient, proprietary reaction that tails only the 3’ ends of ssDNA and ligates the first truncated adapter to the 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequenceindependent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter (Adp2, AATGATACGGCGACCACCGAGATCTACAC(i5) ACACTCTTTCCCTACACGACGCTCTTCCGATCT) to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. The libraries were HiSeq X Ten system.

treatment_protocol: Nuclei were isolated from 3 g of 2-week-old fresh seedlings, followed by SDS/proteinase K treatment at 37℃ overnight.

tag: development stage/tissue


title: TNBC_8

value: dead


title: lidKD_K27me3_Ov_rep1

city: Lyon

first: Guillermo

middle: A

last: Orsi

address: 46 allée d'Italie

country: France

institute: ENS Lyon/ LBMC-UMR 5239

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
fastq files were trimmered with an offset of 75 (FASTQ Trimmer Galaxy Version 1.1.5).
Trimmed fastq were then aligned to the dm6 genome using Bowtie2 (Galaxy Version 2.4.2+galaxy0) with default parameters.
bam alignments were brought down to the same readcount with the Downsample SAM/BAM tool (Galaxy Version 2.18.2.1)
bedgraph files for all fragments were generated with the bamCoverage tool (Galaxy Version 3.3.2.0.0) without normalizing, using a 25bp bin and paired-end extension.
bedgraph files for short fragments (<120bp) were generated with the bamCoverage tool (Galaxy Version 3.3.2.0.0) without normalizing, using a 10 bp bin and paired-end extension.
Genome_build: dm6
Supplementary_files_format_and_content: bedgraphs showing H3K27me3 or H3K9me3 coverage for all fragments and short fragments (<120 bp) in drosophila ovaries of different genotypes

organism: Drosophila melanogaster

source_name: Ovaries

extract_protocol:
Cut&Run in Drosophila tissues was previously described (Ahmad and Spens, 2019). Briefly, ovaries from 3-day-old flies were dissected in Wash+ Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.9 mM spermidine, 0.1% BSA with Roche cOmplete protease inhibitor) and were bound to BioMag Plus Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences, Inc). Tissue was then permeabilized for 10min in dbe+ Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.9 mM spermidine, 2 mM EDTA, 0.1% BSA, 0.05% digitonin with Roche cOmplete protease inhibitor). Samples were then incubated with gentle rocking overnight at 4°C with antibody solution (H3K27me3, Cell Signalling Technology #9733, final concentration of 1:100 in dbe+ buffer, or H3K9me3, Abcam #8898, final concentration of 1:50 in dbe+ buffer). Protein A fused to micrococcal nuclease (p-AMNase) was added in dbe+ buffer and samples were incubated with rotation at room temperature for 1 hour. Cleavage was done in WashCa+ buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.9 mM spermidine, 0.1% BSA, 2 mM CaCl2 with Roche cOmplete protease inhibitor) at 0 ̊ for 30 minutes. Digestion was stopped with addition of 2XSTOP Buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 62.5µg/mL RNaseA). Samples were incubated at 37°C for 30 min to digest RNA and release DNA fragments. Cleaved DNA was then recovered with Ampure XP beads (Beckman Coulter) immediately after protease treatment.
Cut&Run samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). Cut&Run-seq libraries were prepared from10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: ovaries

tag: genotype/variation

value: lidKD

tag: cut&run antibody

value: H3K27me3 (Cell Signaling Technology, 9733)


title: lidKD_K27me3_Ov_rep2


title: Bone marrow cells - Targeted capture DNAseq (Ph_positive_ALL_1137050-10-T)

city: Houston

first: Yuya

last: Sasaki

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: M.D. Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw-sequencing data from the Illumina platform were converted to a fastq format and aligned to the reference genome (hg19) using the Burroughs–Wheeler Aligner using MEM mode with following parameters: -k 31 -T 100 -t 8 -M.
The aligned BAM files were subjected to mark duplication, realignment, and recalibration, using Picard and GATK with default parameters.
Preprocessed BAM files were then analyzed to detect SNV and small insertions and deletions (indels), using MuTect and Pindel, respectively, against pooled unmatched normal sequences developed in house.
Genome_build: hg19
Supplementary_files_format_and_content: Mutect/Pindel calling tab-separated values matrix

source_name: Bone marrow cells

growth_protocol: Not applicable.

extract_protocol:
Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).
After sample quality control, targeted capture DNA sequencing using custom designed SureSelect panel of 295 genes (Agilent Technologies, Santa Clara, CA, USA) was performed
Targeted capture DNA sequencing

treatment_protocol: Samples were either bone marrow samples obtained from previously untreated patients.

tag: disease state

value: Ph-positive ALL

tag: treatment

value: bone marrow

tag: cell type

value: leukemic cell

tag: Sex

value: Male

tag: outcome

value: Complete Response


title: lidKD_K27me3_Ov_rep3

tag: tissue


title: Sin3aKD_K27me3_Ov_rep2


title: CD11b positive cells(PPM)

city: Suita

first: Nobuhiko

last: Shiraki

state: Osaka

address: 2-2 Yamadaoka,

department: Ophthalmology

institute: Osaka University

library_source: transcriptomic

data_processing:
FASTQ files were processed using the “cellranger count” pipeline from Cell Ranger version 3.0.2 (10× Genomics) with GRCh38 v.3.0.0 Cell Ranger reference.
The subsequent data analysis was performed using R package Seurat v3.2.1.
We followed the Seurat vignette (https://satijalab.org/seurat/pbmc3k_tutorial.html) to create the Seurat data matrix object.
We kept all genes expressed in more than three cells and cells with at least 200 detected genes.
Cells with mitochondrial gene percentages >25% and unique gene counts <1000 were discarded.
The data were normalized using Seurat’s “NormalizeData” function, in which UMI counts for each gene from each cell were divided by the total UMI counts from that cell, multiplied by the scale factor of 10,000 and natural log-transformed.
Highly variable genes were then identified using the function “FindVariableGenes” in Seurat with default parameters.
We regressed out the variation arising from the library size and percentage of mitochondrial genes using the function “ScaleData” in Seurat.
Principal component analysis (PCA) for dimensionality reduction was performed using the Seurat “RunPCA” function.
The computed PCs were used to perform unsupervised cell clustering using the functions “FindClusters” and to make UMAP results of scRNA-Seq data using the Seurat “RunUMAP” function.
The number of PCs used in each analysis is noted in the Figure legends. To identify differentially expressed genes in each cell cluster, we used the function “FindAllMarkers” in Seurat on the normalized gene expression data.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: rds

source_name: hiPS SEAM cells CD11b cells

growth_protocol: The hiPSC line 201B7 was obtained from the RIKEN Bio Resource Centre. The cells were cultured in StemFit medium on LN511E8-coated (0.5 μg/cm2) dishes. SEAMs were generated as described (Hayashi et al., 2017; Hayashi et al., 2016). The hiPS or hES cells were seeded on LN511E8-coated dishes at a density of 300–600 cells/cm2, after which they were cultured in StemFit medium for 10 days. The culture medium was then changed to differentiation medium (DM; Glasgow modified Eagle’s medium (Life Technologies) supplemented with 10% knockout serum replacement (KSR; Life Technologies), 1 mM sodium pyruvate (Life Technologies), 0.1 mM non-essential amino acids (Life Technologies), 2 mM L-glutamine (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), and 55 μM monothioglycerol (Wako, Osaka, Japan) (Hayashi et al., 2017).   Immortalised human microglia-SV40 cells were purchased from Applied Biological Materials Inc. These had been immortalised by serial passaging and transduction with recombinant lentiviruses carrying SV40 Large T antigen (Applied Biomedical Materials: abm, Richmond, QC, Canada). The cells were grown in Prigrow II media (abm) containing 10% foetal bovine serum (FBS) and 1% penicillin-streptomycin solution (abm) in T25 flasks coated with Applied Cell Extracellular Matrix (abm) and seeded at a density of 35,00040,000 cells/cm2. DMEM-F12 medium was supplemented with 10% FBS in T25 flasks coated with poly-D-lysine (1.3 μg/cm2) (Sigma-Aldrich, MO,6USA).

extract_protocol:
Cell suspension was loaded to a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions. Sample was processed using the Chromium Single Cell 3’ library and Gel Bead Kit v3 (10X Genomics) following the manufacturer’s instructions.
Single-cell library was sequenced with an 8-base index read (Chromium i7Sample Index (PN-220103, SI-GA-E3)), a 5’-CTACACGACGCTCTTCCGATCT-3’-base read1(PN-2000089), and a 5’- GATCGGAAGAGCACACGTCTGAACTCCAGTCA-3’-base read 2(PN -2000094) on an Illumina HiSeq X platform.

treatment_protocol: Samples were obtained from the cells sorted by FACS.

tag: cell line

value: iPS cell line 201B7

value: untreated


title: MH63 seedling_ssDRIP_rep1

tag: cultivar

value: Minghui 63

value: seedling


title: TNBC_7

value: primary breast cancer

tag: status

tag: gender

tag: biopsy method


title: PAO1161 EV_3_control_for_PA3458_RNA-seq_reused

description: gene expression data from empty vector control

data_processing:
base calling: bcl2fastq v2.20 (Illumina)
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Genome_build: CP032126
Supplementary_files_format_and_content: Raw counts of sequencing (FeatureCounts output summarized for all samples) (2577_Raw_counts.csv).
Supplementary_files_format_and_content: A table with DE data for all genes and normalized abundance measurements (EdgeR output) (2577_norm_counts.csv).

source_name: empty vector control (EV)

growth_protocol: The competent P. aeruginosa PAO1161 cells were prepared as described previously (Irani and Rowe, 1997) and transformed using pKKB2.11 carrying araC araBADp-PA2577 or empty vector (araC araBADp) to obtain PAO1161/pKKB2.11 and PAO1161/pKGB8, respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 g/ml chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 g/ml) and 0.02% arabinose and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from logarithmic phase cultures (OD600 = 0.5) were subjected to RNA extraction.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext® Ultra Directional RNA Library Prep Kit for Illumina® (NEB, E7420). Libraries were sequenced using standard Illumina protocols.

treatment_protocol: All cultures were incubated at 37oC in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.02% arabinose with shaking until reaching exponential phase of growth (OD600 = 0.5).

tag: strain

value: PAO1161/pKGB8 (araC araBADp)

tag: genotype

value: empty vector control (EV)

tag: growth phase

value: logarithmic phase of liquid culture


title: PAO1161 EV-F_1_ChIP-seq

description: ChIP DNA data from empty vector control

source_name: empty vector control (EV-F)

value: PAO1161/pABB28.1 (lacIQ-tacp-flag)

value: empty vector control (EV-F), replicate 1


title: PAO1161 EV_2_control_for_PA3458_RNA-seq_reused


title: Ctrl_K27me3_Ov_rep2

value: ovaries

value: control


title: Ctrl_K27me3_Ov_rep3

value: H3K27me3 (Cell Signaling Technology, 9733)


title: PAO1161 EV_1_control_for_PA3458_RNA-seq_reused


title: MH63 seedling_ATAC_rep1

data_processing:
Trimmomatic fitered the raw reads
ATAC-seq reads were aligned to the MH63 genome assembly using bwa mem
Remove multi-mapped reads, filtered using the SAMTOOLS MAPQ20 and filter the  duplication reads
Peak was calling using MACS2 with callpeak -t <input file> --nomodel --shift -100 --extsize 200 -f BAM –n <output peak file> -B -q 0.05 -g 3.6e+8
Genome_build: MH63 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001623365.1)
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

source_name: MH63 seedling_ATAC

extract_protocol:
The digested chromatin were purified by MinElute PCR Purification kit (QIAGEN; cat. no. 163038964), followed by PCR amplification.
These PCR DNA products were then subjected to size-selection and paired-end sequencing (2 × 150 bp) using Illumina Hiseq X-Ten.

treatment_protocol: Rice nuclei isolated from formaldehyde-fixed rice MH63 seedling were permeabilized by 0.3% triton X-100 for 10min on ice, then ready for in situ chromatin digestion by Tn5 transposase (VAHTS; cat. no. TD501) (8μl 5X TTBL, 4μl TTE mix, 0.45μl 2% triton X-100, add H2O to 50μl) for 30min at 37℃ at 400RPM.

tag: development stage/tissue


title: TNBC_6

value: alive

value: female

value: CNB

tag: er status

tag: pgr status

tag: her2 status

tag: t stage

tag: n stage


title: MH63 seedling_totalRNA_rep2

data_processing:
Trimmomatic fitered the raw reads.
The cleaned reads were mapped to the MH63 reference genome using Hisat2.
Gene raw count was quantified using HTSeq
Gene FPKM was converted by gene raw count
Genome_build: MH63 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001623365.1)
Supplementary_files_format_and_content: FPKM values or  raw count values for each sample.

source_name: MH63 seedling_totalRNA

extract_protocol:
RNA was isolated from leaves using RNeasy Plant Mini Kit (QIAGEN, 74904) according to the manufacturer’s instructions.
2 µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions.

treatment_protocol: Seedlings of 2-week-old MH63  were collected at 8:00 and immediately processed to RNA insolation.


title: PAO1161 PA2577_3_RNA-seq

description: gene expression data for a PA2577 overproducer

source_name: PA2577 overproducer (PA2577)

growth_protocol: The competent P. aeruginosa PAO1161 cells were prepared as described previously (Irani and Rowe, 1997) and transformed using pMEB12 carrying araC araBADp-PA2577 and pKGB8 empty vector (araC araBADp) to obtain PAO1161/pMEB12 and PAO1161/pKGB8, respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 g/ml chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 g/ml) and 0.02% arabinose and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from logarithmic phase cultures (OD600 = 0.5) were subjected to RNA extraction.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero™ rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, E7420). Libraries were sequenced using standard Illumina protocols.

value: PA2577 overproducer (PA2577)

tag: cell type


title: PAO1161 PA2577-F_1_ChIP-seq

value: PAO1161/pMEB84 (lacIQ-tacp-PA2577-flag)

value: PA2577_FLAG overproducer (PA2577-F)

tag: antibody

value: polyclonal anti-FLAG


title: Ctrl_K27me3_Ov_rep1

tag: tissue

tag: genotype/variation

tag: cut&run antibody


title: TNBC_5

tag: status


title: TNBC_4

tag: gender


title: MH63 seedling_totalRNA_rep1

value: Minghui 63

value: seedling


title: Ctrl_K27me3_Ov_rep4


title: TNBC_3

value: primary breast cancer

tag: biopsy method


title: PAO1161 PA2577_1_RNA-seq

tag: strain


title: H3K4me3_ChRD_rep2

data_processing:
library strategy: chromatin associated RNA-DNA interactions followed by paired-end-tag sequencing (ChRD-PET)
FastQC and cutadapt filtered the raw reads
Combine the R1 and R2 by FLASH, and get a "Combine" data and two "NotCombine" data
Finding the linker("CCTCGATACTTGAGCTGACT") in three file by cutadapt. And split data into DNA and RNA data
For length<70 DNA reads were aligned to MH63 genome assembly using bwa aln. For length>70 DNA reads were aligned to MH63 genome assembly using bwa mem. For RNA reads, We use a two-step comparison strategy. Firstly, RNA reads wrer aligned to MH63 using hisat2. And than, get the unmapped and multi-mapped reads and were aligned to MH63 again by bowtie2.
Remove multi-mapped reads, filtered using the SAMTOOLS MAPQ20
Remove reads aligned to rRNA, and combine DNA and RNA aligned result into a bedpe file. Merge records with similar positions(both DNA and RNA) to calculate a highly significant DNA-RNA interaction
Genome_build: MH63 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001623365.1)
Supplementary_files_format_and_content: bigWig

source_name: MH63 seedling_H3K4me3_ChRD

extract_protocol:
About 5 g of samples were ground in liquid nitrogen into fine powder and then lysed in 7 ml of Buffer S (50 mM HEPES-KOH (pH7.5), 150 mM NaCl, 1 mM Ethylene Diamine Tetraacetic Acid (EDTA), 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) at 4 °C for 40 min with rotation at 12 rpm. The homogenate, containing the entire chromatin from the ground sample, was mixed with 30 ml of Buffer F (50 mM HEPES-KOH (pH7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and Sonicate chromatin solution into 1–3 kb (High level, 36 cycles, 30 s ON, and 50 s OFF) using a Bioruptor (Diagenode). Centrifuge the chromatin fragments at 12,000 rpm for 10 min at 4 °C and transfer the supernatant to a new tube for chromatin immunoprecipitation (ChIP). To prepare antibody-loaded beads, 40 μl antibody (H3K4me3, ABclonal cat. no. A2357) was mixed with 750 μL suspended protein G magnetic beads (~1:100 dilution) followed by incubation at 4 °C for 8 h with rotation at 12 rpm. Then, mixed fragmented chromatin extract with antibody-loaded beads and incubated it at 4 °C for overnight with rotation at 12 rpm. The supernatant was discarded and the beads were washed using 5 mL 0.1% SDS FA cell lysis buffer (0.05 M, HEPES-KOH, 0.15 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) for three times, then followed by washing with 5 mL High salt ChIP buffer (0.05 M, HEPES-KOH, 0.35 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) twice; the beads were washed with 5 mL ChIP wash buffer (0.01 M Tris–HCl, 0.25 M LiCl, 0.001 M EDTA, 2.5% NP-40, and 0.5% sodium deoxycholate) once and finally followed washing with 5 mL 1× TE buffer (pH 8.0, Ambion, cat. no. AM9849) twice. DNA of ChIP complex on beads was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F) and Klenow enzyme (NEB, cat. no. M0212L). To ligate DNA and RNA, we use specially designed single biotinylated bridge-linker: Forward strand: 5′-[5APP] CCTCGATAC/iBIOdT/TGAGCT GACT-3′, Reverse strand: 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG -3′. Then the RNA ends were proximity-ligated by the single biotinylated bridge-linker with 5’ adenylated on forward strand and followed by extending the Reverse strand in linker into ligated RNA with reverse transcription as first strand cDNA synthesis. Next, the DNA ends, with 5’ A-tailing, were proximity-ligated by the single biotinylated bridge-linker with 3′ nucleotide T over-hanging on forward strand and followed by second strand cDNA synthesis.
The proximity ligation RNA-DNA fragments were reverse cross-linked and fragmented before adding sequencing adaptors simultaneously by using Tn5 transposase (VAHTS, cat. no. TD501). The fragments contained the bridge-linker at ligation junctions were captured by Streptavidin beads, and used as templates for PCR amplification. These DNA products were then subjected to size-selection and paired-end sequencing (2 × 150 bp) using Illumina Hiseq X-Ten.

treatment_protocol: Seedlings of 2-week-old MH63  were collected at 8:00 and preserved immediately in 1× PBS. Specimens were then fixed at room temperature with 1% (v/v) formaldehyde (SIGMA, F8775) and vacuumed for 5 min. The vacuum was then turned off and released, and samples were further incubated for 25 min. Formaldehyde was quenched by adding glycine to a final concentration of 0.2 M. Subsequently, Specimens were rinsed thrice with deionized water, and incubated in 1.5 mM ethylene glycol bis(EGS, Thermo Fisher Scientific, 21565) for 45 min under vacuum. EGS fixative solution was prepared by dissolving 0.06 g EGS in 600 μL DMSO at 37 °C for 5 min, mixed with 89.4 mL 1× PBS, and incubated at 37 °C before use. Dual Cross-linked samples were rinsed thrice with deionized water and immediately frozen in liquid nitrogen. Frozen tissues were kept at -80 °C no longer than 1 mouth.

tag: cultivar

tag: development stage

tag: chip antibody


title: H3K4me3_ChRD_rep1


title: TNBC_2

value: dead

tag: er status


title: MH63 seedling_ATAC_rep2

tag: development stage/tissue


title: E17.5

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

data_processing:
Sequencing and making Fastq files by illumina HiSeq X Ten. Read length: Read1:26, Index read 1(i7):8, Read2:98.
Cell Ranger v2.0.0 software was used to perform alignment and gene and UMI counting each cell.
Genome_build: GRCm38_93
Supplementary_files_format_and_content: tab-delimited text files and comma-separated value files

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: ICR

value: Kidney

tag: genotype

value: Wild type

tag: developmental stage


title: TNBC_1

tag: pgr status

tag: her2 status

tag: t stage

tag: n stage


title: PAO1161 PA2577_2_RNA-seq

tag: cell type

value: logarithmic phase of liquid culture


title: p325-A7

status: Public on Dec 09 2021

city: York

first: Dimitris

last: Lagos

address: YBRI, Wentworth Way,

department: The Hull York Medical School

country: United Kingdom

institute: University of York

hyb_protocol: Hybrdisation of fluorescent reporter and capture probes was performed according to the Nanostring nCounter™ platform and the human v3 miRNA panel

scan_protocol: Nanostring FLEX system

data_processing: Extraction of raw reads and analysis of the individual datasets was carried out using the nSolver™ Analysis Software. For each miRNA the mean plus one standard deviation of negative controls from all counts was subtracted. The spike-in count (osa-miR414) was used to normalise miRNA counts.

label: not provided

source_name: plasma

label_protocol: Nanostring human v3 miRNA panel (catalog number CSO-MIR3-12)

extract_protocol: Whole venous blood was collected in EDTA tubes and diluted 1:1 with PBS. Blood plasma was separated following centrifugation, and stored at -80oC until usage. 5 µl of a synthetic spike-in control RNA target, osa-miR-441 (sequence 3’-UCAUCCUCAUCAUCAUCGUCC-5’) was added to 800 µl isolated plasma prior to extraction using the Norgen plasma/serum RNA purification midi kit (Norgen Biotech Corp.).

tag: patient number

tag: sample number

tag: covid-19 severity

value: Severe

tag: molecule subtype

value: Circulating RNA


title: E13.5

tag: strain

tag: tissue


title: p325-R1


title: p318-A6


title: p325-A1


title: p325-A30


title: p318-A1


title: p318-A4


title: p325-A3


title: p305-A1


title: p300-A7


title: p300-A3


title: p300-A22


title: p305-A14


title: p300-A1


title: p300-A10


title: p305-A19


title: p298-A7


title: p290-A2

value: Moderate


title: p281-A9


title: p298-A12


title: p298-A26


title: p298-A4


title: p298-A1


title: p262-A1


title: p251-A8


title: p281-A2


title: p305-A2


title: p251-A10


title: p251-A4


title: p247-A15


title: p247-A13


title: p247-A1


title: p225-A5


title: p097-A5

value: Mild


title: p232-A1


title: p222-A1


title: p225-A3


title: p232-A7


title: p097-A7


title: p232-A3


title: p097-A1


title: p097-A2


title: p097-A26


title: p097-A13


title: p096-A6


title: p095-A58


title: p096-A1


title: p095-A5


title: p096-A2


title: p095-A6


title: p095-A7


title: p096-A4


title: p095-A14


title: p095-A4


title: p232-A5


title: p225-A8


title: p095-A12


title: p090-A4


title: p095-A11


title: p088-A1


title: p082-A3


title: p091-A1


title: p088-A2


title: p090-A3


title: p090-A1


title: p090-A2


title: p082-A11


title: p082-A2


title: p087-A1


title: p082-A8


title: p082-A10


title: p082-A18


title: p095-A1


title: p068-A4


title: p068-A2


title: p068-A1


title: p067-A5


title: p067-A4


title: p067-A3


title: p068-A6


title: p068-R1


title: p082-A12


title: p067-A2


title: p065-A3


title: p067-A6


title: p068-A5


title: p063-A2


title: p062-A7


title: p062-A6


title: p063-A1


title: p064-A2


title: p064-A1


title: p082-A1


title: p062-A1


title: p062-A5


title: p062-A4


title: p061-A5


title: p061-A4


title: p061-A2


title: p060-A8


title: p300-A17


title: p060-A7


title: p067-A1


title: p065-A2


title: p062-A2


title: p050-A9


title: p051-A2


title: p049-A4


title: p049-A8


title: p050-A2


title: p050-A3


title: p049-A6


title: p051-A5


title: p060-A6


title: p049-A5


title: p049-A14


title: p050-A5


title: p047-A4


title: p039-A8


title: p050-A4


title: p045-A3


title: p037-A9


title: p042-A1


title: p039-A4


title: p035-A4


title: p045-A5


title: p049-A2


title: p049-A11


title: p034-A5


title: p035-A2


title: p035-A6


title: p044-A1


title: p035-A5


title: p034-A1


title: p034-A3


title: p031-A2


title: p026-A3


title: p030-A5


title: p030-A4


title: p029-A4


title: p026-A2


title: p031-A3


title: p033-A3


title: p050-A6


title: p025-A5


title: p024-A1


title: p025-A4


title: p025-A12


title: p023-A1


title: p023-A3


title: p030-A7


title: p021-A1


title: p025-A3


title: p027-A2


title: p016-A2


title: p017-A1


title: p017-A4


title: p020-A5


title: p028-A2


title: p020-A2


title: p018-A2


title: p025-A6


title: p034-A6


title: p012-A3


title: p010-A58


title: p015-A3


title: p014-A3


title: p010-A25


title: p010-A30


title: p010-A52


title: KO for single-cell RNA-seq

city: nantong

first: hong

last: shihao

address: 19 Qixiu Road

institute: Nantong university

data_processing:
Libraries were sequenced on the Illumina HiSeq X using 150 bp paired end reads. Raw data were processed by: FastQC (V0.11.7) (FastQC, RRID:SCR_014583) for quality evaluation, fastp (v1) (fastp, RRID:SCR_016962) for trimming, STAR aligner (v2.5.3a) (STAR, RRID:SCR_015899) for alignment, and featureCounts (v1.6.2) (featureCounts, RRID:SCR_012919) for transcript counting.
Cells were integrated and filtered under Seurat 3.2.2n(Feature_RNA>500). Batch effects were removed by sctransform 0.3.1 in Seurat.

source_name: testis

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
Single-cell suspensions were prepared in phosphate-buffered saline at 1 × 105 cells/ml and loaded onto microfluidic devices .We constructed the sequencing libraries with GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies) according to the manufacturer instructions. After constructing the library, we used the Qubit2.0 fluorometer for preliminary quantification. The library was diluted to 1.5 ng/μl, and then we used the Agilent 2100/4200 bioanalyzer to detect the insert size of the library. After confirming that the insert size met the expectation, the effective concentration of the library was measured with quantitative polymerase chain reaction. Accurate quantification (the effective concentration of the library was higher than 2 nM) ensured the quality of the library. The different libraries were pooled according to the effective concentration and target offline data volume for Illumina sequencing. We applied the sequencing-by-synthesis principle. We added fluorescently labeled dNTP and DNA polymerase to the flow cell for sequencing and adaptor primers were used for amplification. After each sequencing cluster extended the complementary strand, each time a fluorescently labeled dNTP was added to release the corresponding fluorescence, the sequencer captured the fluorescent signal and converted the light signal into a sequencing peak through computer software to obtain the sequence information of the fragment to be tested.

value: testis

tag: age


title: p010-A11


title: WT for single-cell RNA-seq

value: WT


title: CON1_m6a_MeRIPseq

city: Beijing

first: Zihui

last: Yu

address: 2 Yabao Road, Chaoyang District, Beijing

institute: Capital Institute of Pediatrics

data_processing:
m6A-enriched genes were obtained by calling significant peaks form the BAM files with MACS2 (v2.1.2) with a q-value < 1e-5 for each individual biological replicate.
CpGs, differentially methylated loci (DMLs) and differentially methylated regions (DMRs) were called using DSS v_2.30.1 with default parameters
R package Seurat (v.2.3.4) was used for gene cell data matrices.
Genome_build: mm10
Supplementary_files_format_and_content: MeRIP peaks, DMRs and scRNA marker genes expression

source_name: kidney

extract_protocol:
Genomic DNA was extracted by using QIAamp DNA Mini Kits (Qiagen, 51306) according to the manufacturer’s instructions. A Qubit Fluorometer (Life Technology, Q32856) was used to quantify the DNA concentration. Total RNA was analyzed using TRIzol reagent (Invitrogen, 15596018). A Qubit Fluorometer (Life Technology, Q32856) was used to quantify the RNA concentration and evaluate RNA quality.
After chopping and mixing, the kidneys were divided into three parts: one part for single-cell RNA-seq, one part for WGBS, and the last part for MeRIP-seq, avoiding the problem of different cell types composition in each sample.

tag: starin

value: kidney

value: wild type


title: CON1_m6a_RNAseq


title: CON2_m6a_RNAseq


title: fat-1 transgenic bovine fetal fibroblast cell

city: Hohhot

first: xueqiao

last: wang

address: No.24，zhaojun Street

institute: Inner Mongolia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ARS-UCD1.2 whole genome using WALT with parameters -u -m 2
After alignment, reads were further deduplicated use samtools
For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated) using per scripts in house and MethPipe
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information:  mC postion and methylation level (#methylated cytosines sequenced/#total cytosines sequenced)

organism: Bos taurus

source_name: fetal fibroblast cell

extract_protocol:
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany). The quantity of DNA was measured by reading A260/280 ratios by spectrophotometer. When A260/280 ratios located range 1.8 to 2.0, DNA was available. The fragmented DNA samples by using sonication were subjected to bisulfite conversion. The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments.  Bead-based SPRI clean-ups are used to remove both oligonucleotides and small fragments, as well as to change enzymatic buffer composition. Finally, we performed the pair-end 2×150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences
DNA libraries were prepared for sequencing using standard Illumina protocols

value: 50-60 days after pregnancy

value: fetus

value: fibroblast

tag: treatment

value: Primary culture to obtain fetal fibroblasts

value: fat-1 transgenic


title: WT bovine fetal fibroblast cell

value: wild-type


title: CON2_m6a_MeRIPseq


title: CON1_WGBS


title: VCD1_m6a_MeRIPseq

value: Gulo-/-


title: VCD1_WGBS


title: VCD2_m6a_MeRIPseq


title: VCD2_m6a_RNAseq


title: CON2_WGBS


title: VCD2_WGBS


title: VCD1_singlecell

description: scRNA-markergenes.csv


title: VCD2_singlecell

description: scRNA-markergenes.csv


title: PTBP1 iCLIP KO2

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
library strategy: iCLIP
Fastq files were uploaded to the Genialis iMaps platform (without first demultiplexing), and demultiplexed based on the constant sequence in their 5' barcode.
Reads were trimmed with cutadapt (v2.4) and mapped to the GRCm38 genome using STAR (v2.7.0f).
Reads were deduplicated using the random portion of their 5' barcodes, and crosslink sites for individual replicates were determined as described in PMID:20601959 with iCOUNT: https://icount.readthedocs.io/en/latest/cite.html. In the provided fastq files, the random, constant and biased portions of the 5' barcodes are tagged to the end of the header lines; these 5' barcodes have been removed from the reads themselves.
Significant crosslink binding sites (FDR<0.05) were identified with iCOUNT (https://icount.readthedocs.io/en/latest/cite.html), for each replicate independently.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNAseq_raw_counts.tsv: tab-delimited text file containing gene names and IDs together with raw counts for all RNAseq samples, generated with Seqmonk.
Supplementary_files_format_and_content: RNAseq_FPKM.tsv: tab-delimited text file containing gene names and IDs together with FPKM values for all RNAseq samples, generated with cuffnorm from Cufflinks.
Supplementary_files_format_and_content: iCLIP processed data files: bedgraph files for each replicate containing significant xlink-binding sites (FDR<0.05) identified with iCOUNT

source_name: Activated CD8 T cells

growth_protocol: Single cell suspensions were prepared from spleen and lymph nodes by passing the organs through 70 and 40 mm cell strainers consecutively. Negative naïve CD8 T cell isolation was achieved by depletion of cells bound by biotinylated antibodies: CD4 (GK1.5), CD11b (M1/70), CD11c (N418), CD19 (1D3), B220 (A3-6B3), CD105 (MJ7/18), TER-119, gamma/delta TCR (GL3), Gr1 (RB6-8C5), NK1.1 (PK136), F4/80 (BM8), CD44 (1M7) and magnetic Dynabeads™ M-280 Streptavidin (Thermofisher cat#:11206D), except for iCLIP experiments where the anti-CD44 antibody was omitted.

extract_protocol:
Cells were collected and irradiated 1x with 254 nm UV light (150 mJ/cm2). Cells extracts were prepared with 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630 (Sigma I8896), 0.1% SDS and 0.5% sodium deoxycholate lysis buffer.
iCLIP libraries were carried out following the improved iCLIP protocol (Lee et al, bioRxiv, 2021; doi: https://doi.org/10.1101/2021.08.27.457890). After sonication between 0.5 mg – 0.2 mg protein lysates in 1 ml were incubated with low amounts of RNAse I (0.05 – 0.01 units, ThermoFisher cat#: EN0602) and 4 units Turbo DNAse (Ambion cat#:AM2238) for 3 minutes at 37 oC. PTBP1-RNA complexes were precipitated with 2 µg of anti-PTBP1 antibody (ThermoFisher clone 1 cat#:32-4800) and 20 µl of Protein A/G beads (Pierce cat#:88802) overnight rotating at 4 oC. Immuno precipitates were stringently washed with high High-salt Wash buffer and with PNK buffer as described in doi: https://doi.org/10.1101/2021.08.27.457890. Libraries were amplified with the P3 Solexa (CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT) and P5 Solexa (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) primers, with the indicated 5' barcode introduced at the end of the P5 primer, thus comprising the first 12 bases of each read.

treatment_protocol: Naïve cells were either used unstimulated, or were activated ex vivo for 24h by culturing in RPMI 1640 Medium (Dutch modification) with 20 mM HEPES (ThermoFisher cat#:22409-015), 50 μM b-Mercaptoethanol, 100 units/ml penicillin and streptomycin, GlutaMAX and 10% FCS on 96 flat-bottom well plates precoated with 5μg/ml anti-CD3 (2C11) and 1μg/ml anti-CD28 (37.51) antibodies, in the presence of 20ng/ml murine IL2.

value: Spleen + LN

value: 24h activation, anti-CD3 + anti-CD28 + IL2

value: CD4-CreTg Ptbp1-fl/fl

tag: Sex

value: Female

value: 14-15 weeks

tag: 5' barcode

value: NNNNCAAGTWWW


title: PTBP1 iCLIP WT2

tag: genotype

value: NNNNATACGWWW


title: PTBP1 iCLIP KO1

value: 11-15 weeks

value: NNNNCCTGCWWW


title: PTBP1 iCLIP WT3

value: 8-9 weeks

value: NNNNTGTGGWWW


title: PTBP1 iCLIP WT4

value: NNNNCATACWWW


title: CON1_singlecell

description: scRNA-markergenes.csv

value: kidney

value: wild type


title: PTBP1 iCLIP WT1

data_processing:
library strategy: iCLIP
Fastq files were uploaded to the Genialis iMaps platform (without first demultiplexing), and demultiplexed based on the constant sequence in their 5' barcode.
Reads were trimmed with cutadapt (v2.4) and mapped to the GRCm38 genome using STAR (v2.7.0f).
Reads were deduplicated using the random portion of their 5' barcodes, and crosslink sites for individual replicates were determined as described in PMID:20601959 with iCOUNT (v2.0.1.dev): https://icount.readthedocs.io/en/latest/cite.html. In the provided fastq files, the random, constant and biased portions of the 5' barcodes are tagged to the end of the header lines; these 5' barcodes have been removed from the reads themselves.
Significant crosslink binding sites (FDR<0.05) were identified with iCOUNT (https://icount.readthedocs.io/en/latest/cite.html), for each replicate independently.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNAseq_raw_counts.tsv: tab-delimited text file containing gene names and IDs together with raw counts for all RNAseq samples, generated with Seqmonk.
Supplementary_files_format_and_content: RNAseq_FPKM.tsv: tab-delimited text file containing gene names and IDs together with FPKM values for all RNAseq samples, generated with cuffnorm from Cufflinks.
Supplementary_files_format_and_content: iCLIP processed data files: bedgraph files for each replicate containing significant xlink-binding sites (FDR<0.05) identified with iCOUNT

value: NNNNGATCGWWW


title: VCD1_m6a_RNAseq


title: CON2_singlecell

description: scRNA-markergenes.csv


title: Homozygous (Lepr -/-) Day3wound-derived Gr-1+ cell pool 2

city: Manchester

first: Kimberly

last: Mace

address: Michael Smith Building, Oxford Road

department: Division of Cell Matrix Biology & Regenerative Medicine

institute: University of Manchester

data_processing:
RNA-Seq reads were aligned to mouse genome mm9 release 64 and transcriptome ensembl release 64 using TopHat (Trapnell et al., 2009).
Cufflinks was used to analyse the aligned reads (Trapnell et al., 2010). Reads were normalised using the trimmed means method (Robinson and Oshlack, 2010).
Reads mapped to multiple gene transcription units or reads mapped more than once to the same transcription unit were removed from the list.
Genome_build: mm9, release 64
Supplementary_files_format_and_content: Combined table of FPKM for each sample with chomosome location in excel format

source_name: cutaneous wound (Day 3)

extract_protocol:
RNA was isolated using Trizol, checked for quality using Bioanalyzer (RIN>7), and shipped on dry ice to GATC (Konstanz, Germany) for sequencing on an Illumina HiSeq2000.
1 mg RNA was used to generate cDNA libraries, which were sequenced using 1 lane per sample

treatment_protocol: All procedures were approved by the UK Home Office and ethical committee. Mice (age, 8-16 weeks, and sex-matched, both males and females) were anaesthetised, given buprenorphine analgesia and wounded on the dorsum (2x 8mm-diameter excisional wounds). Mice were housed individually. On day 3 following wounding, mice were sacrificed and wounds were collected, including a 2-mm border of peri-wound skin. Tissue was enzymatically dissociated as previously described (Mahdipour E. et al., 2011) and Gr-1+ cells isolated using magnetic bead separation (Stem Cell Technologies).

value: Day3wound-derived Gr-1+ cell pool

tag: genotype/variation

value: Homozygous (Lepr -/-)


title: Heterozygous (Lepr +/-) Day3wound-derived Gr-1+ cell pool 2

value: Heterozygous (Lepr +/-)


title: Homozygous (Lepr -/-) Day3wound-derived Gr-1+ cell pool 1


title: treatment32

city: 南京

first: qian

last: li

address: 仙林大道

institute: 南京中医药大学

hyb_protocol: After cleavage, 10 micrograms of mRNA were hybridized on the microarray rat genome array at 45 ℃ for 16 hours. The gene chips were cleaned and stained in Affymetrix fluid workstation 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: biotin

organism: Rattus norvegicus

label_protocol: According to the standard Affymetrix scheme, from 6 μ G preparation of biotinylated mRNA from total RNA (Technical Manual for expression analysis, Affymetrix, 2001)

growth_protocol: After acclimatization for seven days, the 18 female rats were randomly and equally divided into three groups (n = 6 for each group): control group, model group and treatment group. The female rats in the treatment group before modeling were electro-acupunctured at Guanyuan and Sanyinjiao points for 15 minutes each time, and for 7 consecutive days; and after treatment, the rats were used for modeling (continue to acupuncture). The establishment method of an ovulation induction model was shown as follows: the female rats were injected with pregnant horse serum gonadotropin (PMSG, 0.5U/rat, Ningbo Second Biological Pharmaceutical Factory, Zhejiang, China) intraperitoneally, and then after 48 h, the female rats were injected with the same amount of HCG

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The female rats in the model and treatments groups were used to establish an ovulation induction model, and the rats in the control group were without treatment. The female rats in the treatment group before modeling were electro-acupunctured at Guanyuan and Sanyinjiao points for 15 minutes each time, and for 7 consecutive days; and after treatment, the rats were used for modeling (continue to acupuncture).

value: female

value: Uterine tissue

tag: condition

value: treatment


title: control 42

source_name: control 42

value: control


title: Homozygous (Lepr -/-) bone marrow-derived Gr-1+ cell pool 2

source_name: bone marrow Gr-1+ cells

value: bone marrow-derived Gr-1+ cell pool


title: model 23

source_name: model 23

value: model


title: Heterozygous (Lepr +/-) bone marrow-derived Gr-1+ cell pool 2


title: control 43

source_name: control 43


title: Cortical neuron-CDH12 siRNA

city: Nantong

first: tuchen

last: guan

institute: Nantong University

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so  we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISA T2 v2.0.5
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Genome_build: Ensembl RGSC 3.4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Cortical neuron

growth_protocol: Cortical neurons were collected from Sprague-Dawley rats at the age of embryonic fetuses 18 days (E18). Bilateral cerebral cortex was put into the culture dish containing ice-cold Hank’s buffer (Cat# C0218, Beyotime), followed by removal of the meninges. Brain tissues treated with 0.25% trypsin-EDTA for 12 min at 37℃ to prepare cell suspension. The single cells obtained by centrifugation were resuspended in DMEM/F-12 (Cat# 10-092-CV, Thermo Fisher Scientific) containing 10% FBS, and plated into the petri dishes precoated with Poly-L-Lysine (PLL) to allow incubation in a humidified atmosphere of 5% CO2 at 37℃ for 5 h. Subsequently, the culture medium was replaced by Neurobasal medium supplemented with 2% B27, 0.5 mM glutamine, and 1% penicillin-streptomycin (Thermo Fisher Scientific).

extract_protocol:
Total RNA was collected and purified on the Illumina TruSeq Stranded mRNA LT sample preparation kit (Illumina Inc.) per manufacturer’s instructions. The RNA integrity and quantity was mea_x0002_sured by Nanodrop (Thermo Scientific)
For this mRNA enrichment, the rRNA removal kit was used to interrupt all se_x0002_quences into 200–300 bp. Complementary DNA was synthesized from enriched and fragmented RNA using Super Script II Reverse Transcriptase (Invitrogen Corp.) and random primers. After the library was constructed using the dsDNA converted from cDNA, RNA-Seq libraries were qualified by the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: RNA interferenced with CDH12 siRNA or NC siRNA for 36h.

value: Sprague Dawley

value: brain

value: Cortical neuron

tag: treament

value: CDH12 siRNA

value: E18 fetal


title: Heterozygous (Lepr +/-) Day3wound-derived Gr-1+ cell pool 1


title: Cortical neuron-NC siRNA

value: NC siRNA


title: treatment33


title: treatment31


title: Homozygous (Lepr -/-) bone marrow-derived Gr-1+ cell pool 1


title: model 22

source_name: model 22


title: model 21

source_name: model 21


title: Heterozygous (Lepr +/-) bone marrow-derived Gr-1+ cell pool 1


title: control 41

source_name: control 41


title: MELA_0228

type: genomic

city: Herston

first: Felicity

last: Newell

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

hyb_protocol: Illumina protocol

scan_protocol: iScan Illumina

data_processing: The raw data in the form of IDAT files for 43 samples were imported filtered and normalized using the ChAMP package implemented in R .  Probes were primarily filtered out if detection p-value > 0.01 or there were fewer than three beads in 5% or more of samples.  A β-mixture quantile normalisation (BMIQ) was performed to account for probe type 1 and type 2 biases, followed by a quantile normalisation.  Further filtering was performed to remove probes if they were located in non-CpG sites, X and Y chromosomes, single nucleotide polymorphism-related polymorphisms and probes that map to multiple locations .  A total of 136,444 probes were removed during the filtering process, leaving 729,474 probes for further analyses.

source_name: Tumour

label_protocol: Illumina protocol

extract_protocol: All prep DNA/RNA/miRNA Universal kit

tag: tisue

value: melanoma


title: MELA_0388


title: MELA_0384


title: MELA_0421


title: MELA_0386


title: MELA_0395


title: MELA_0391


title: MELA_0433


title: MELA_0377


title: MELA_0434


title: MELA_0447


title: MELA_0381


title: MELA_0255


title: MELA_0385


title: MELA_0379


title: MELA_0393


title: MELA_0425


title: MELA_0387


title: MELA_0444


title: MELA_0458


title: MELA_0562


title: MELA_0376


title: MELA_0374


title: TOP1cc CAD-seq MYC-mAID auxinole rep 1

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

data_processing:
library strategy: Covalent Adduct Detection coupled to ChIP-seq
FastQC and MultiQC were used for quality control of the .fastq-files
Adapter and poor quality read trimming was performed with cutadapt
The ChIP-seq data was mapped using bowtie2.
Aligned files were sorted, deduplicated and indexes using SortSam, MarkDuplicates and BuildBamIndex from Picard package.
Merging of duplicates for visualization was performed using MergeSamFiles from Picard package.
Genome_build: hg38
Supplementary_files_format_and_content: Bam coverage BigWig files generated from merged replicas, normalized to RPM.

source_name: K562 MYC-mAID

growth_protocol: K562 MYC-mAID cells were grown in RPMI media containing 10%FBS and supplemented with l-glitamine, sodium pyruvate and 1x pen/strep.

extract_protocol:
Cells in suspension were collected by centrifugation and adherent cells were scraped in M buffer (9.3mM 870 Tris-HCl pH6.5, 18.6 mM EDTA, 5.59M guanidine thiocyanate, 0.93% DTT, 0.93% Sarcosyl, 3.72% Triton) to a final concentration of 5x106cells/ml and briefly sonicated with Bandelin probe sonicator at 20% amp for 3 cycles 30sec ON, 30 sec OFF. 2.5 ml DNA and bound proteins were precipitated with 1.25 ml EtOH at -20°C, washed thrice in wash buffer (20mM Tris-HCl pH7.5, 50mM NaCl, 1mM EDTA, 50% EtOH). The resulting pellet was dried for 5 minutes and resuspended in TE-SDS (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 0.1% SDS) and sonicated with Covaris ME220 sonicator for 5 minutes at High Cell protocol in milliTUBE–1 mL with AFA Fiber. For immunoprecipitation 1.5 μg anti-TOP1 (ab109374) or 3 μg of 1:1 mixture of anti-TOP2A (sc166934 and ab52934) antibodies were mixed with 30 μl Protein A/G magnetic beads (Pierce, 88803) and incubated at 40C for 6 hrs with controlled rotation. DNA and bound complexes from 1×107 cells were added to the Protein A/G-antibody complexes and incubated overnight at 40C with rotation. Washing was performed as described above but only once with every buffer and always in presence of 0.1% SDS. The beads were then resuspended in 100 μl TE plus 0.25% SDS supplemented with proteinase K (500 μg/ml, Roche) and incubated for 4 hrs at 60ºC. Samples were then purified by PCR purification Kit (Qiagen).
DNA from CAD-seq samples was quantified with the Qubit dsDNA HS Assay Kit. To cleave off covalently bound tyrosyl residues from TOP2cc CAD-seq DNA samples, the samples were additionally treated with ExoVII (0.5U per 10 ng of DNA) and purified by AMPure XP beads. Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara). Size selection was performed in the range of 200-700bp with AMPure XP beads and confirmed using the Agilent High Sensitivity DNA Kit on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina). The sequencing run was Single End and Dual Index with 75 bp reads.

treatment_protocol: To induce rapid protein degradation cells were treated for 30 minutes (MYC-mAID) with 500 µM auxin final concentration in the respective growth media. Treatment with 100 µM auxinole for 24 hours was performed as a control for auxin experiments. Cells were treated with 10 µM MG-132 for 30 min before addition of 20 µM CPT and further incubation for 5 min to trap TOP1cc.

tag: cell type

value: Human immortalised myelogenous leukemia cells

tag: chip antibody

value: MYC-mAID

value: 100 µM auxinole


title: TOP1cc CAD-seq MYC-mAID auxinole rep 2


title: MELA_0430


title: TOP1cc CAD-seq MYC-mAID auxin rep 1

value: 500 µM auxin


title: RNAPII ChIP-seq TOP2A-mAID auxinole rep 2

data_processing:
FastQC and MultiQC were used for quality control of the .fastq-files
Adapter and poor quality read trimming was performed with cutadapt
The ChIP-seq data was mapped using bowtie2.
Aligned files were sorted, deduplicated and indexes using SortSam, MarkDuplicates and BuildBamIndex from Picard package.
BigWig files were generated with bamCoverage from Deeptools package.
Merging of duplicates for visualization was performed using MergeSamFiles from Picard package.
Peak calling was performed using SICER2 and MACS3.
Genome_build: hg38
Supplementary_files_format_and_content: Aligned bam files, deduplicated and sorted.
Supplementary_files_format_and_content: Bam coverage BigWig files generated from merged replicas, normalized to RPM.
Supplementary_files_format_and_content: Bam coverage Spike-In normalized BigWig files generated by merging independently Spike-In normalized BigWigs of two replicas.

source_name: HCT116 TOP2A-mAID

growth_protocol: Human colon carcinoma HCT116WT and HC116 TOP2A-FLAG cells were grown in high glucose (4.5g/L) DMEM containing 10% FBS in a 37ºC incubator supplied with 5% CO2. HCT116 TOP1-mAID cells were grown in media containing selection antibiotics: 1µg/ml puromycin (Thermo Fisher, A11138-03) and 125µg/ml hygromycin B (Thermo Fisher, 10687010), HCT116 TOP2A-mAID were grown in media containing 7.5 ug/ml blasticidine (Thermo Fisher, A1113903) in addition to the aforementioned antibiotics.

extract_protocol:
For RNAPII and MYC, fter harvesting cells by scraping, the pellet was washed once with PBS plus 0.5% BSA and resuspended in RIPA buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na-Deoxycholate, 0.1% SDS, 200mM NaCl, with the addition of protease inhibitor cocktail) to a final concentration of 1x107 cells/ml. For TOP2A cells were directly scapred in TE-SDS 0.25%. Samples were sonicated with a Bandelin probe sonicator to produce chromatin fragments of 400 bps on average. For normalization of RNAPII and MYC ChIP-seq 20 ng spike-in chromatin (Active Motif, 53083) was added per 1x107 cells. After centrifugation, extracts were immunoprecipitated wtih 2 μg of anti-MYC antibody (ab32072) or 2 μg of anti-RNAPII (ab5408) antibody and 1 μg of spike-in antibody (Active Motif, 61686) or 2 μg of anti-FLAG (F1804) antibody were mixed with 35 μl Protein A/G magnetic beads (Pierce, 88803) and incubated at 40C for 6 hrs with controlled rotation. Chromatin from 1x107 cells was added to the Protein A/G-antibody complexes and incubated with rotation overnight at 40C. Samples were washed twice with RIPA buffer, twice with RIPA buffer containing 300 mM NaCl, twice with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-Deoxycholate) and twice with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). The beads were then resuspended in 125 μl TE plus 0.25% SDS supplemented with proteinase K (500 μg/ml, Roche) and incubated overnight at 65ºC. DNA was recovered from the elute by phenol:chloroform (25:24:1) (Sigma) extraction followed by ethanol (100%) precipitation in the presence of 20 μg of GlycoBlue (Invitrogen) and dissolved in TE.
To cleave off covalently bound tyrosyl residues from TOP2A ChIP samples, the samples were additionally treated with ExoVII (1U per 10 ng of DNA) and purified by PCR purification Kit (Qiagen). DNA from ChIP was quantified with the Qubit dsDNA HS Assay Kit. Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara). Size selection was performed in the range of 200-700bp with AMPure XP beads and confirmed using the Agilent High Sensitivity DNA Kit on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina). The sequencing run was Single End and Dual Index with 75 bp reads.

treatment_protocol: To induce rapid protein degradation cells were treated for 1.5hrs (TOP1-mAID and TOP2A-mIAD) with 500 µM auxin final concentration in the growth media. Treatment with 100 µM auxinole for 24 hours was performed as a control for auxin experiments. For RNAPII and MYC cells were crosslinked with 1% formaldehyde for 5 minutes. Cross-linking was stopped by the addition of glycine (125 mM) and cells were washed twice with cold PBS. For TOP2A cells were treated with 100 μM Etoposide for 4 min and crosslinked with formaldehyde for 5 min. Cross-linking was stopped by the addition of glycine (125 mM).  stopped by the addition of glycine as described above.

value: Human colon carcinoma

value: RNAPII (Abcam 5408)


title: RNAPII ChIP-seq TOP2A-mAID auxin rep 2


title: RNAPII ChIP-seq TOP2A-mAID auxinole rep 1


title: TOP1cc CAD-seq MYC-mAID auxin rep 2


title: RNAPII ChIP-seq TOP2A-mAID auxin rep 1


title: MELA_0418


title: RNAPII ChIP-seq TOP1-mAID auxinole rep 2

source_name: HCT116 TOP1-mAID


title: RNAPII ChIP-seq TOP1-mAID auxinole rep 1


title: MELA_0392


title: RNAPII ChIP-seq TOP1-mAID auxin rep 2


title: RNAPII ChIP-seq TOP1-mAID auxin rep 1


title: MYC ChIP-seq TOP2A-mAID auxinole rep 2

value: MYC (Abcam 32072)


title: MYC ChIP-seq TOP2A-mAID auxinole rep 1


title: MYC ChIP-seq TOP2A-mAID auxin rep 2


title: MYC ChIP-seq TOP2A-mAID auxin rep 1


title: MYC ChIP-seq TOP1-mAID auxinole rep 2


title: MYC ChIP-seq TOP1-mAID auxinole rep 1


title: MYC ChIP-seq TOP1-mAID auxin rep 1


title: MYC ChIP-seq rep 2

value: Wild type


title: biofilm_48h

city: Jouy en JOsas

first: romain

last: briandet

address: Domaine de Vilvert

institute: INRAE

description: Sample of B. subtilis NDmed, 48 hour after adhesion.

hyb_protocol: 1200 ng of Cy3-labeled cDNA were hybridized to the tiling array following Agilent’s hybridization, washing and scanning protocol (One-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray (BaSysBio Bacillus subtilis T3 array, 2x400K [Agilent-044473]) was scanned with Agilent Technologies Scanner, model G2505C. Grid: 044473_D_F_20121025. Protocol: GE1_107_Sep09.

data_processing:
An aggregated expression value was computed for each GenBank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region as described in (Nicolas et al., 2012 PMID: 22383849).
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347). Data were quantile normalized using LIMMA package. To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis

source_name: Bacillus subtilis NDmed

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D (final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye, GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: 200 µL of an overnight culture of Bacillus subtilis NDmed in TSB (adjusted to an OD 600nm of 0.02) were added in each well of 96-well microtiter plates, incubated at 30°C for 90 min to allow the bacteria to adhere to the bottom of the wells.

extract_protocol: Total RNA was extracted as described by Nicolas et al., (2012) Science 335, 1103–1106 (PMID:22383849). RNA concentration was measured using a NanoDrop spectrophotometer; RNA quality was checked by analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Wells were then rinsed with TSB to eliminate non-adherent bacteria and refilled with 200 µL of sterile TSB. For each time point (1h, 3h, 4h, 5h, 7h, 24h and 48h) 96-well plates were prepared.

value: NDmed

value: Wild-type, undomesticated

value: Adhesion

tag: time point


title: MYC ChIP-seq rep 1


title: TOP2A ChIP-seq rep 2

source_name: HCT116 TOP2A-FLAG

value: FLAG (Sigma-Aldrich F1804)


title: MYC ChIP-seq TOP1-mAID auxin rep 2


title: biofilm_24h

description: Sample of B. subtilis NDmed, 24 hour after adhesion.


title: biofilm_7h

description: Sample of B. subtilis NDmed, 7 hour after adhesion.


title: Cy325-1

city: Shenzhen

first: Xian

last: Ju

state: Guangdong province

address: 1066 Xueyuan Avenue, Fuguang Community, Taoyuan Street, Nanshan District, Shenzhen

department: College of Life Sciences and Oceanology

institute: Shenzhen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, unknown bases(N) are more than 10% and low-quality sequence, then mapped to NCM3722 whole genome using bowtie2 v2.3.2 with parameters --sensitive -I 100 -X 500 --end-to-end --no-unal
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using a protocol from Trapnell, et al., 2010. In short,the number of reads falling in each gene were counted and normalized by the size of the library.
Genome_build: NCM3722 (NZ_CP011495.1 and NZ_CP011496.1) with minor updates following MG1655 (NC_000913.3)
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and FPKM values for every gene and every sample

organism: Escherichia coli

source_name: E. coli

growth_protocol: in N-C- minimal medium plus NH4Cl and glucose aerobically at 37°C in water bath shaker, 250rpm or in nitrogen source limited chemostat with a dilute rate of 0.2/h.

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extract 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: culture

value: Batch culture in glucose minimal medium at 37°C, OD600≈0.4

value: gcvB deletion


title: TOP2A ChIP-seq rep 1


title: MELA_0436


title: wt-2

value: Wild Type


title: wt-1


title: biofilm_4h

description: Sample of B. subtilis NDmed, 4 hour after adhesion.


title: CD8_Naive_Unstim_HIV_GU1136

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: CD8 Naive T-Cell

data_processing:
Illumina’s bcl2fastq2.17 software was used to de-multiplex the reads into individual fastq files for each sample.
Reads were mapped to human genome GRCh38, Ensemble version 91, using CLC Genomics Workbench v20 (QIAGEN) and “total exon reads” counted for each gene.
Genome_build: GRCh38, Ensemble version 91
Supplementary_files_format_and_content: table of raw counts of "total exon reads"

source_name: PBMC

growth_protocol: PBMCs were thawed with X-Vivo media (Lonza, MD) containing Benzonase nuclease (50 U/ml; Millipore Sigma, MO) and cultured in the absence or presence of rhIL-27 (100 ng/ml).

extract_protocol:
Total RNA extraction from approx. 50,000 sorted cells of each sample was performed using Qiagen RNeasy Plus Universal mini kit (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, CA) and RNA integrity was analyzed using Agilent TapeStation 4200 (Agilent Technologies, CA).
cDNA was converted by using SMARTer kit (Clontech, CA), and sequencing libraries were prepared using Illumina Nextera XT Library Preparation Kit (NEB, MA).

treatment_protocol: After overnight culture, PBMCs from HIV infected participants were stimulated with HIVGag peptide pool (2 ug/ml, NIH AIDS Reagent Program), and PBMCs from healthy donors were stimulated with the CMV, EBV and Influenza (CEF) peptide pools (5ug/ml, NIH AIDS Reagent Program). DMSO was used as control in the unstimulated culture condition. After 2 hours of stimulation, Brefeldin A (10 ug/ml, Calbiochem, CA) was added and cultured for additional 4 hours. Cells were harvested and stained with Live/Dead staining (Invitrogen, CA). Cells were incubated with human IgG (10 ug/ml, Sigma, MO) to block Fc receptors followed by a cocktail of mAbs as described in manuscript Table S2, Panel 2.  T cell sorting and mRNA-Seq analysis: T cell subsets were sorted based on surface expression of CD45RA and CD27. Naïve (CD45RA+CD27+) and Memory (CD45RA-CD27+) CD4 and CD8 T cell subsets from PLWH (n= 5) and healthy controls (n= 3) were sorted in BD FACS Aria based on surface staining with antibody cocktail of mAbs (Table S2, Panel 3). Sorted cells were spun down and rested 3 hours for subsequent in vitro simulation for 90 minutes at 37°C and 5% CO2 with rhIFN-α (100 U/ml, PBL Biomedical Laboratories, N), rhIL-6 (100 ng/ml, PeproTech, NJ), rhIL-27 (100 ng/ml; PeproTech, NJ) or media as unstimulated control. After stimulation, the cells were washed with cold PBS, resuspended in TRIzol (Invitrogen, CA) and stored at -80°C.

tag: t-cell type

tag: ex-vivo stimulation

value: Unstim

tag: donor hiv status

value: HIV

tag: donorid


title: CD8_Memory_Unstim_HIV_GU1136

description: CD8 Memory T-Cell


title: Cy325-2

tag: strain


title: MELA_0378

value: melanoma


title: MELA_0380


title: MELA_0413


title: biofilm_1h

description: Sample of B. subtilis NDmed, 1 hour after adhesion.


title: MELA_0369


title: MELA_0382


title: CD4_Naive_Unstim_HIV_GU1136

description: CD4 Naive T-Cell


title: 20120a056_01

city: Tuebingen

first: Christoph

last: Trautwein

address: Roentgenweg 13

department: Werner Siemens Imaging Center

country: Germany

institute: University of Tuebingen

data_processing:
Read quality of RNA-seq data in FASTQ files was assessed using ngs-bits (v.2020_06), to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR v2.7.3a (Dobin et al., 2013) to the GRCh37 and alignment quality was analyzed using ngs-bits and visually inspected in the Integrative Genome Viewer (v2.7.2).
Normalized read counts for all genes were obtained using Subread (v2.0.0).
The distribution of logarithmized cpm-normalized expression values shows similar characteristics over all samples. Based on the filtered data set, samples were investigated with respect to their pairwise similarity. Spearman’s rank correlation coefficient was calculated for each pair of samples.
A hierarchical clustering was performed on the resulting similarity values. Differential gene expression analysis was conducted based on the filtered gene expression data set. A statistical model incorporating the group property of samples was tested by fitting a negative binomial distribution using a generalized linear model (GLM) approach.
Genome_build: GRCh37
Supplementary_files_format_and_content: The full processed and annotated gene expression values are given in the file "Processed_Data_Spreadsheet_Glioma_Study.xlsx". Simple boxplots between genes and groups of interest were used for the publication.

source_name: glioma tissue

extract_protocol:
Tissue collection: Archival tumor samples were available after tissue acquisition according to a standardized routine bio banking procedures. In brief, after removal of tumor tissue from the resection cavity in the operating room, samples were immediately frozen in liquid nitrogen, the tumor content was assessed on a cryo-slide by a neuropathologist, and only tissue samples with sufficient tumor content (> 70-80%) were stored as bio samples in the biobank at -80°C.
Tissue homogenization: Tissue samples were cryogenically pulverized (Covaris CryoPREP CP02) and aliquots of 5 mg used for RNA analysis.
RNA was purified from lyophilized tissue using the QIAsymphony RNA kit (Qiagen). More precisely, tissue was thawed at room temperature and 800 µl of Buffer RTL Plus was added to the tissue. Homogenization was performed twice for 2 minutes at 25 Hz using the TissueLyser II (Qiagen). Resulting homogenates were centrifuged for 3 minutes at maximum speed in a microcentrifuge and 400 µl of the resulting lysate was loaded on the QIAsymphony SP (Qiagen) using the RNA CT 400 protocol. At the end of the protocol, the RNA was eluted in 35 µl of RNase-free water.
For library preparation, mRNA fraction was enriched using polyA capture from 200ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) using the liquid handler Biomek i7 (Beckman). Next, mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Library molarity was determined by measuring the library size (approximately 400 bp) using the Fragment Analyzer with the High NGS Fragment 1-6000bp assay (Agilent) and the library concentration (approximately 5 ng/µl) using the Infinite 200Pro (Tecan) and the Quant-iT HS Assay Kit (Thermo Fisher Scientific).
The libraries were denatured, diluted to 270 pM and sequenced as paired-end 100bp reads on an Illumina NovaSeq6000 (Illumina, San Diego, CA, USA) with a sequencing depth of approximately 25 million clusters per sample.

tag: diagnosis

value: Diffuse glioma

tag: tissue

value: Glioma

tag: histology

value: Glio

tag: treatment

value: Treated (Radiochemotherapy)

tag: paired patient


title: MELA_0370


title: CD4_Memory_Unstim_HIV_GU1136

description: CD4 Memory T-Cell


title: CD4_Naive_IL27_HIV_GU1136

description: CD4 Naive T-Cell


title: 20120a055_01

tag: genotype

value: Untreated


title: CD8_Memory_IL27_HIV_GU1136

description: CD8 Memory T-Cell


title: CD4_Memory_IL27_HIV_GU1136

description: CD4 Memory T-Cell


title: CD8_Naive_IL27_HIV_GU1136

description: CD8 Naive T-Cell


title: CD8_Naive_Unstim_HIV_GU1125

description: CD8 Naive T-Cell


title: CD8_Naive_IL27_HIV_GU1125

description: CD8 Naive T-Cell


title: 20120a054_01


title: biofilm_3h

description: Sample of B. subtilis NDmed, 3 hour after adhesion.

tag: condition


title: 20120a053_01


title: CD8_Memory_Unstim_HIV_GU1125

description: CD8 Memory T-Cell


title: CD4_Naive_Unstim_HIV_GU1125

description: CD4 Naive T-Cell


title: CD8_Memory_IL27_HIV_GU1125

description: CD8 Memory T-Cell


title: biofilm_5h

description: Sample of B. subtilis NDmed, 5 hour after adhesion.


title: MELA_0360

tag: tisue


title: CD4_Memory_IL27_HIV_GU1125

description: CD4 Memory T-Cell


title: CD8_Memory_Unstim_HD_GU1118

description: CD8 Memory T-Cell

value: HD


title: MELA_0368


title: MELA_0367


title: 20120a050_01


title: 20120a052_01


title: 20120a051_01


title: MELA_0407


title: MELA_0359


title: CD8_Memory_IL6_HD_GU1118

description: CD8 Memory T-Cell


title: CD8_Memory_IL27_HD_GU1118

description: CD8 Memory T-Cell


title: CD8_Memory_IFNa_HD_GU1118

description: CD8 Memory T-Cell

value: IFNa


title: 20120a048_01


title: 20120a049_01


title: CD4_Naive_Unstim_HD_GU1118

description: CD4 Naive T-Cell


title: CD4_Naive_IL6_HD_GU1118

description: CD4 Naive T-Cell


title: MELA_0365


title: CD8_Naive_IL27_HD_GU1118

description: CD8 Naive T-Cell


title: CD4_Naive_IFNa_HD_GU1118

description: CD4 Naive T-Cell


title: CD4_Naive_IL27_HD_GU1118

description: CD4 Naive T-Cell


title: MELA_0398


title: MELA_0364


title: 20120a045_01

value: Astro


title: CD4_Memory_Unstim_HD_GU1118

description: CD4 Memory T-Cell


title: CD4_Memory_IL6_HD_GU1118

description: CD4 Memory T-Cell


title: CD8_Naive_Unstim_HD_GU1111

description: CD8 Naive T-Cell


title: CD8_Naive_IL6_HD_GU1111

description: CD8 Naive T-Cell


title: CD4_Memory_IFNa_HD_GU1118

description: CD4 Memory T-Cell


title: CD8_Naive_IL27_HD_GU1111

description: CD8 Naive T-Cell


title: CD8_Naive_IFNa_HD_GU1111

description: CD8 Naive T-Cell


title: CD4_Naive_IL27_HIV_GU1125

description: CD4 Naive T-Cell


title: MELA_0357


title: 20120a024_01

value: Oligo


title: 20120a043I2_01


title: 20120a046_01


title: 20120a014_01

value: Treated (Chemotherapy)


title: MELA_0361


title: CD8_Memory_Unstim_HD_GU1111

description: CD8 Memory T-Cell


title: CD4_Naive_Unstim_HD_GU1111

description: CD4 Naive T-Cell


title: 20120a028_01

value: Treated (Radiotherapy)


title: CD4_Memory_IL27_HD_GU1118

description: CD4 Memory T-Cell


title: CD4_Naive_IL6_HD_GU1111

description: CD4 Naive T-Cell


title: CD4_Naive_IL27_HD_GU1111

description: CD4 Naive T-Cell


title: 20120a042_01


title: CD4_Memory_Unstim_HD_GU1111

description: CD4 Memory T-Cell


title: 20120a026_01


title: 20120a020_01


title: CD4_Memory_Unstim_HIV_GU1125

description: CD4 Memory T-Cell


title: CD4_Memory_IL27_HD_GU1111

description: CD4 Memory T-Cell


title: CD4_Memory_IL6_HD_GU1111

description: CD4 Memory T-Cell


title: 20120a012_01

value: Treated


title: CD8_Naive_Unstim_HIV_GU1103

description: CD8 Naive T-Cell


title: CD4_Memory_IFNa_HD_GU1111

description: CD4 Memory T-Cell


title: CD8_Memory_IL27_HD_GU1111

description: CD8 Memory T-Cell


title: CD8_Naive_IL27_HIV_GU1103

description: CD8 Naive T-Cell


title: 20120a023_01


title: 20120a019_01


title: CD8_Memory_IL27_HIV_GU1103

description: CD8 Memory T-Cell


title: CD8_Memory_Unstim_HIV_GU1103

description: CD8 Memory T-Cell


title: 20120a025_01


title: pDC

city: NEW DELHI

first: Prafullakumar

last: Tailor

state: DELHI

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Immunology

data_processing:
Basecalling was performed using CASAVA v1.8 software.
The reads produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software using the parameter (SLIDING WINDOW: 4:15; LEADING:3, TRAILING:3; ILLUMINACLIP: adapter.fa: 2:30:7; MINLEN:36).
The clean reads obtained after trimming were mapped to a reference Mus musculus genome (mm10 assembly) by using Bismark software.
The Bismark program (bismark_methylation_extractor, -no_overlap) was run to extract the DNA methylation level.
DMRs were identified using DSS v2.12.0 software with the raw methylation data with methylated and unmethylated read counts as input.
Genome_build: mm10
Supplementary_files_format_and_content: wig files

source_name: Spleen

extract_protocol:
Pure B220+CD11clowpDC, CD8α+CD11chighcDC1 and CD4+CD11chighcDC2 splenic subsets were obtained by FACS sorting. The sorted cells were lysed and genomic DNA was extracted using Dneasy Blood and Tissue kit from Quiagen (Cat#69504).
Libraries for sequencing were prepared using the standard illumina protocols.

value: Spleen

tag: cell type

value: pDC


title: CD4_Naive_Unstim_HIV_GU1103

description: CD4 Naive T-Cell

value: Unstim


title: L11_IL5Crecontrol  PBS

city: San Francisco

first: Kelly

middle: M

last: Cautivo

state: California

address: 513 Parnassus Av

institute: UCSF

data_processing:
FastQC v0.72
Umi-tools extract umi
Trimmomatic v0.38.1
HISAT2 v2.1.0
Umi-tools deduplicated
HTSeq-count v0.91
DESeq2 v2.11.40
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: Normalized Raw Count

source_name: Lung

extract_protocol:
Approximately 10,000-20,000 ILC2s from lungs and adipose tissue were sorted int0 100-200ul of lysis/binding buffer (Qiagen) using a BD FACSAria II sorting system with a 70um nozzle size and 4 way-purity sort mode. ILC2 were sorted from IL5Cre-Tdtomato Red5 mice as live, lineage negative, CD45+,Thy1.2+, Tdtomato+. Total RNA was isolated using QIAGEN RNeasy Plus Micro kit
Gene expression profiling was carried out using a 3' Tag-RNA-Seq protocol. Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer (Lexogen). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. Up to forty-eight libraries per lane were sequenced on a HiSeq 4000 sequencer (Illumina, San Diego, CA).

treatment_protocol: Mice treated with recombinat cytokines: 500ng IL-33  +/- 10µg IFNγ  (three i.p doses, every other day)

value: Lung

value: Innate Lymphoid cells (ILC2)

value: Red5 (Il5-Tdtomato-Cre)


title: 20120a032_01

value: Diffuse glioma

value: Glioma


title: CD4_Naive_IFNa_HD_GU1111

description: CD4 Naive T-Cell


title: cDC2

value: cDC


title: L10_IL5Crecontrol  IL33


title: 20120a027_01

value: Untreated


title: CD4_Memory_Unstim_HIV_GU1103

description: CD4 Memory T-Cell

value: HIV


title: 20120a034_01


title: CD4_Naive_IL27_HIV_GU1103

description: CD4 Naive T-Cell


title: L9_IL5Crecontrol  IL33


title: CD4_Memory_IL27_HIV_GU1103

description: CD4 Memory T-Cell


title: L7_IL5Crecontrol  IL33 + IFNγ


title: 20120a030_01


title: 20120a022_01


title: CD8_Naive_Unstim_HIV_GU1076

description: CD8 Naive T-Cell


title: CD8_Naive_IL27_HIV_GU1076

description: CD8 Naive T-Cell


title: CD8_Memory_Unstim_HIV_GU1076

description: CD8 Memory T-Cell


title: L6_IL5Crecontrol  IL33 + IFNγ


title: 20120a009_01


title: 20120a031_01


title: L5_IL5Crecontrol  IL33 + IFNγ


title: L4_IL5CreΔIfnγr1  IL33 + IFNγ


title: L3_IL5CreΔIfnγr1  IL33 + IFNγ


title: 20120a010_01


title: cDC1


title: 20120a011_01


title: CD8_Memory_IL27_HIV_GU1076

description: CD8 Memory T-Cell


title: L2_IL5CreΔIfnγr1  IL33 + IFNγ


title: 20120a021_01


title: CD4_Naive_IL27_HIV_GU1076

description: CD4 Naive T-Cell


title: 20120a013_01


title: L1_IL5CreΔIfnγr1  IL33 + IFNγ


title: L8_IL5Crecontrol  IL33


title: 20120a033_01


title: CD4_Memory_IL27_HIV_GU1076

description: CD4 Memory T-Cell


title: CD4_Memory_Unstim_HIV_GU1076

description: CD4 Memory T-Cell


title: 20120a002_01


title: CD8_Naive_Unstim_HIV_GU1053

description: CD8 Naive T-Cell


title: 20120a029_01


title: 20120a040_01


title: CD4_Naive_Unstim_HIV_GU1076

description: CD4 Naive T-Cell


title: CD8_Naive_IL27_HIV_GU1053

description: CD8 Naive T-Cell


title: 20120a016_01

value: Treated (Radiochemotherapy)


title: F7_IL5Crecontrol  IL33

source_name: Gonadal adipose tissue

value: Fat


title: F5_IL5Crecontrol  IL33 + IFNγ


title: F6_IL5Crecontrol  IL33 + IFNγ


title: CD8_Memory_IL27_HIV_GU1053

description: CD8 Memory T-Cell


title: 20120a008_01

value: Oligo


title: 20120a006_01


title: F4_IL5Crecontrol  IL33 + IFNγ


title: CD8_Memory_Unstim_HIV_GU1053

description: CD8 Memory T-Cell


title: CD4_Naive_IL27_HIV_GU1053

description: CD4 Naive T-Cell


title: CD4_Naive_Unstim_HIV_GU1053

description: CD4 Naive T-Cell


title: 20120a004_01


title: F2_IL5CreΔIfnγr1  IL33 + IFNγ


title: CD4_Memory_Unstim_HIV_GU1053

description: CD4 Memory T-Cell


title: F9_IL5Crecontrol  PBS


title: F1_IL5CreΔIfnγr1  IL33 + IFNγ


title: F8_IL5Crecontrol  IL33


title: F3_IL5CreΔIfnγr1  IL33 + IFNγ


title: CD4_Memory_IL27_HIV_GU1053

description: CD4 Memory T-Cell


title: CD8_Memory_Unstim_HD_GU0003

description: CD8 Memory T-Cell

value: HD


title: 20120a035_01

value: Astro


title: 20120a039_01


title: CD8_Memory_IL27_HD_GU0003

description: CD8 Memory T-Cell