title: Midlog_H3K56ac_ChIPreadsFig3GEO

description:
H3K56ac ChIP in log phase
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,log phase, H3K56ac on bulk DNA.paired end reads


title: G1_inputreadsFig3GEO

status: Public on Dec 17 2021

type: SRA

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
Input DNA from MNAse digested chromatin after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,alpha factor arrest in G1, input DNA.paired end reads

library_source: genomic

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
time points and time point fractions  were separated either by in line barcodes and the 5bp barcode were removed from the read sequence and saved into separate fastq files from a unique fastq file obtained from the sequencing service using a custom perl script, or with Illumina unique indexes (Set A and B) and demultiplexed after sequencing into separate fastq files by the sequencing facility
reads were mapped to the yeast S288C genome using BLAT
Paired end read count distribution in 50bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands
the genome average read count value was calculated and the data were normalized to one
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: tab-delimited text files of indicated feature enrichment (columns) normalized to the average genome read count and distributed in 50bp bins. 50bp bins marked with R indicate repetitive sequences.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2)

growth_protocol: Cells were grown overnight at 30°C in SCD-URA. The culture was diluted to OD600 ~0.3 the next morning and grown to OD600 ~0.65 and re-diluted to OD600 ~0.3  in fresh media. The culture was synchronized with the addition of 0.15 μg/ml α factor for 3h30min at 30°C. Cells were released from arrest in preheated (SCD-URA) + 10 μM EdU and grown at 30°C for indicated times before fixation with formaldehyde.

extract_protocol:
Cross-linked frozen cell pellets were re-suspended in 1.5 ml NP lysis buffer (100 mM NaCl, 10 mM Tris 7.4, 5 mM MgCl2, 1 mM CaCl2, 10% NP-40, 50 mM EDTA, 0.1 % SDS (optional), 1 mM PMSF and 1xEDTA-free protease inhibitor cocktail (Roche)). The suspension was then split into aliquots each containing ~billion cells. Zirconium Sillicate beads (400 μl, 0.5 mm) were then added to each aliquot and cells were mechanically disrupted using a bullet blender (Next Advance) for 4 times x 3 min (intensity 8). Spheroplasts were treated with micrococcal nuclease or sonicated. Sonicated or digested chromatin was subject to ChIP with the indicated antibody. An aliquot was set aside for the input DNA fraction prior to ChIP. EdU incorporated into ChIPed and Input DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads (ChIP-NChAP and NChAP fractions, respectively). The supernatant after binding to  streptavidin beads was kept for the unreplicated ChIP fraction and an input DNA and a bulk ChIP DNA aliquot were set aside prior to biotinylation for the Input and ChIP fractions.
DNA samples from all fractions were treated with calf intestinal phosphatase (NEB). NGS libraries were constructed either with costum enzymes( blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read)) or using the TrueSeq V2 LT Sample prep kit (Illumina) with the Illumina unique multiplexing indexes Set A and B. The custom library samples were amplified with the Phusion enzyme (NEB) for 18 PCR cycles with Illumina PE1 and PE2 primers.  The primer mix from the kit was  used in the PCR amplification step (also with Phusion) for the samples prepared with  TrueSeq V2 LT (15 cycles). For nascent (replicated NChAP and ChIPNChAP fractions) libraries, the nascent 'EdU containing) strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidine coated magnetic beads.
Strand specific MNase-CHIP-seq  or strand specific sonicated-ChIP-seq  of replicated DNA fragments. The method which we call ChIP-NChAP (Nascent Chromtin Avidin Pulldown) was developed in the Radman-Livaja group.

treatment_protocol: cell aliquots  were fixed with 1% (w/v) formaldehyde for 15 min at 30°C followed by 5 min of quenching in 125 mM Glycine. Cell pellets were then washed with cold PBS and flash frozen in liquid nitrogen and kept at -80°C until further processing.

tag: genotype/variation

value: wt

tag: cell cycle

value: G1 arrest with alpha factor

tag: edu incubation

tag: antibody


title: 4_CAMHB + PBT2

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

description: A. baumannnii MS14413 RNAseq data

library_source: transcriptomic

data_processing:
HiSeq 2500 ultra-high-throughput sequencing system was used for base-calling
Samples were uploaded to the Galaxy web platform (public server at usegalaxy.org), trimmed and mapped to the reference genome (A. baumannii MS14413 accession number: NZ_CP054302) using bowtie2 with default parameters
Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0
Genome_build: NZ_CP054302
Supplementary_files_format_and_content: xlsx files

molecule: total RNA

organism: Acinetobacter baumannii

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth (CA-MHB) as per CLSI guidelines at 37°C under aerobic conditions.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 + ZnSO4 + tetracycline. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNASeq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared using a Ribo-zero stranded protocol. In brief, rRNA was depleted with Ribo Zero, RNA was fragmented (heat and divalent cations) and 1st strand cDNA synthesis was done with SuperScript II Reverse Transcriptase (Invitrogen). For the 2nd strand cDNA synthesis, the strand was “marked” with dUTP.  A 3’ adenylation of DNA fragments was performed followed by sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments). The library was amplified by PCR (amplification of “unmarked” 1st strand only). Libraries were assessed using either Agilent’s Bioanalyzer DNA 1000 chip or TapeStation D1K TapeScreen system. qPCR was used to quantify individual libraries before normalizing (2 nM) and pooling. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents followed by sequencing on the Illumina HiSeq 2500 system with TruSeq SBS Kit v3 reagents with 110 (101 read 1, 9 cycles index read). Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 50-base-single end reads. An average of 30 million reads per sample were generated, uploaded to the Galaxy web platform (public server at usegalaxy.org), and mapped to the reference genome (S. pneumoniae ATCC 700669 accession number: NC_011900) using bowtie2 with default parameters. Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0. Figures were generated using ggplot2 and ggpubr packages in R-studio

treatment_protocol: Bacteria were grown to  OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 (64 µM), ZnSO4 (8 µM) and tetracycline (1 µg/mL).

tag: strain

tag: treatment condition

value: CAMHB + 64 uM PBT2


title: Mycn mutant  zebrafish embryos 72 hpf

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

country: China

institute: Zhejiang University

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Genome_build: GRCz11
Supplementary_files_format_and_content: tar archive included filtered_gene_bc_matrices after running CellRanger pipeline

organism: Danio rerio

source_name: zebrafish cells

growth_protocol: embryos were cultured in a Petri dish filled with 0.3X Danieau buffer

extract_protocol: Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000074) according to the manufacturer’s protocol for 10000 cells recovery.

treatment_protocol: WT and Mycn mutant zebrafish embryos were collected for RNA sequencing at 72 hpf

value: Mycn mutant

tag: tissue

value: embryonic cells

tag: age

value: 72 hpf


title: wild-type  zebrafish embryos 72 hpf

value: AB


title: G1_H3K56ac_ChIPreadsFig3GEO

description:
H3K56ac ChIP after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,alpha factor arrest in G1, H3K56ac on bulk DNA.paired end reads


title: Mycn mutant zebrafish embryos 72hpf rep3

data_processing:
The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package.
Genome_build: GRCz11
Supplementary_files_format_and_content: comma-delimited csv files included read counts  of each sample and each gene

extract_protocol:
Total RNAs was extracted using TRIzol following the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and Mycn mutant zebrafish embryos were collected for RNA sequencing at 48 hpf and 72 hpf


title: RNA-Seq of HEK293 cells expressing GFP alone, replicate 2

city: Toronto

first: Jack

last: Greenblatt

address: 160 College Street

country: Canada

institute: University of Toronto

description:
pau_results_QAPA.txt
diff_table_N_noAr_vs_GFP_noAr.tab
groups_N_noAr_GFP_noAr_deseq2_results.tab

data_processing:
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 1.0 (Tapial et al., (2017))
Alternative splicing analysis: From primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Significantly differential AS was assessed with the diff module of vast-tools under development and were additionally required to have a PSI difference >10.
Expression analysis: Expression differences were calculated based on vast-tools raw read counts per gene using the R package edgeR.
For differential mRNA expression analysis, gene-level read counts were quantified using Salmon (version 0.8.2) and normalized by variance-stabilizing transformation using DESeq2.
To estimate the differential poly(A) site usage, we used QAPA with default settings, essentially as previously described (Ha KCH et. al. 2018. Genome Biology). To quantify the relative usage of proximal poly(A) sites, QAPA calculates the percentage of expression of a single 3′ UTR over the total expression level of all 3′ UTRs for a given gene. Lengthening events were defined as those with percentage of proximal Poly(A) Usage Index (PAU) group difference between N andGFP (PAU_Group_diff) < −20% and shortening events with PAU_Group_diff > 20%.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for PAU from QAPA analysis, PAU difference between N and GFP from QAPA analysis, and differential gene expression from DESeq2 analysis

molecule: polyA RNA

organism: Homo sapiens

source_name: Human embryonic kidney cells

growth_protocol: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with the Qiagen RNasy Mini kit.
1000 ng per sample was used in the library preparation. To obtain larger insert size (540 nt on average after size selection), Illumina’s TruSeq Stranded mRNA sample preparation protocol was modified as follows: 1) fragmentation time and temperature was reduced from 8 minutes at 98 C to 2 minutes at 80 C. Average size distribution prior to library preparation was 232 nt versus 740 nt, respectively; 2) after the final library was generated, the samples were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100 V. The libraries were size selected between 400 and 600 bp. Excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). The rest of the protocol was adapted as described in Illumina’s TruSeq Stranded mRNA sample preparation guide (Part# 15031047 Rev. E, Illumina).

treatment_protocol: GFP-N or GFP alone was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to UV crosslinking.Cells were treated with Sodium Arsenite for 1hour prior to harvesting.

tag: cell line

tag: overexpression

value: GFP alone


title: RNA-Seq of HEK293 cells expressing GFP alone, replicate 1

description:
pau_results_QAPA.txt
diff_table_GFP_Ar_vs_GFP_noAr.tab
groups_GFP_Ar_GFP_noAr_deseq2_results.tab


title: 3_control

description: A. baumannnii MS14413 RNAseq data

value: Treatment with CAMHB (reference sample)


title: iCLIP-seq of N in oxidatively stressed cells, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt2clip/5Phos/NNACAANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNACAANNN, where N are random bases.
N_Ar.bed

data_processing:
Raw reads were demultiplexed,  XXXNNNNXX barcode where X is a random basepair and N is the barcode, and trimmed using cutadapt (2.10)
Barcodes were moved to the fastq header using UMI-tools (1.0.0) extract
Reads were mapped using STAR (2.7.1a) to GENCODE GRCh37 (hg19)
Peaks were called using Pureclip (1.0.0) with both replicates and input
Genome_build: hg19
Supplementary_files_format_and_content: BED file; peaks were called using Pureclip(1.0.0)

extract_protocol:
Cells were crosslinked (0.4 J/cm2) at 254 nm with a Stratalinker 1800. Three independent replicates were used for generating iCLIP samples. Lysates generated from the crosslinked cells were treated with Turbo DNAse (Ambion) and diluted RNAse I (Ambion) for 5 minutes at 37°C to digest the genomic DNA and trim the RNA to short fragments of an optimal size range. RNA-protein complexes were immunoprecipitated using 100 μL of protein G Dynabeads (Life Technologies) and 10 μg of anti-Flag (Sigma) antibody. Following stringent high salt washes, the immunoprecipitated RNA was 3´ end dephosphorylated and a pre-adenylated adaptor was ligated at the 3´ end as described for a previously described enhanced CLIP ligation method (Van Nostrand et al., Nat. Methods 2016) for adaptor ligation. After additional washes, the immunoprecipitated RNA was 5´ end-labeled using radioactive 32P isotopes. The immunoprecipitated complexes were separated with SDS-PAGE and transferred to a nitrocellulose membrane (Protran). RNA was recovered by digesting proteins using proteinase K.
RNA was reverse transcribed into cDNA using reverse transcription primers that include barcode sequences to enable multiplexing,  a unique molecular identifier, and a BamHI restriction site. The cDNA was size selected (low: 70 to 85 nt, middle: 85 to 110 nt, and high: 110 to 180 nt), circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR amplified using AccuPrime SuperMix I (Life Technologies). The final PCR libraries were purified by agarose gel electrophoresis using gel extraction columns (QIAGEN), eluted DNA was mixed at a ratio of 1:5:5 from the low, middle, and high fractions and submitted for sequencing.

treatment_protocol: Crosslinking (0.4 J/cm2) was done at 254 nm with a Stratalinker 1800.

value: HEK293 treated with Sodium arsenite (1hour)


title: earlyS-phase-24min_inputreadsFig3GEO

description:
Input DNA from MNAse digested chromatin early S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,24min after release into S phase,input DNA.paired end reads

value: early S-phase (60% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: earlyS-phase-24min_NChAPreadsFig3GEO

description:
nascent DNA purification by EdU-biotin pulldown from Mnase digested chromatin in early S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,24min after release into S phase, replicated DNA.paired end reads


title: Mycn mutant zebrafish embryos 72hpf rep2


title: 1_control

description: A. baumannnii MS14413 RNAseq data


title: iCLIP-seq of N in oxidatively stressed cells, replicate A

description:
Extracted RNA was reverse transcribed using primer Rt6clip/5Phos/NNCCGGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNCCGGNNN, where N are random bases.
N_Ar.bed

tag: treatment

value: GFP-N was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to UV crosslinking.Cells were treated with Sodium Arsenite for 1hour prior to harvesting.


title: Mycn mutant zebrafish embryos 48hpf rep3

value: 48 hpf


title: earlyS-phase-24min_H3K56ac_ChIPreadsFig3GEO

description:
H3K56ac ChIP from early S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,24min after release into S phase, H3K56ac on bulk DNA.paired end reads


title: earlyS-phase-24min_H3K56ac_ChIPNChAPreadsFig3GEO

description:
H3K56ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from early S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig3GEO.txt
MNase digested chromatin,24min after release into S phase, H3K56ac on replicated DNA.paired end reads


title: Mycn mutant zebrafish embryos 48hpf rep2


title: iCLIP-seq of N, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt14clip/5Phos/NNTGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTGCCNNN, where N are random bases.
N.bed


title: Size matched input for N (related to A+B replicates)

description:
Extracted RNA was reverse transcribed using primer Rt12clip/5Phos/NNGTGGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGTGGNNN, where N are random bases.
N.bed


title: Mycn mutant zebrafish embryos 48hpf rep1


title: G1_RNAP2Chip_rep2readsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,alpha factor arrest in G1, RNAPol2 on bulk DNA.paired end reads, replicate 2


title: G1_RNAP2Chip_rep1readsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,alpha factor arrest in G1, RNAPol2 on bulk DNA.paired end reads, replicate 1


title: wild-type zebrafish embryos 72hpf rep3


title: iCLIP-seq of N, replicate A

description:
Extracted RNA was reverse transcribed using primer Rt9clip/5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGCCANNN, where N are random bases.
N.bed

value: GFP-N was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to UV crosslinking.

value: GFP monoclonal antibody  (Invitrogen)


title: Size matched input for N in oxidatively stressed cells (related to A+B replicates)

description:
Extracted RNA was reverse transcribed using primer Rt13clip/5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTCCGNNN, where N are random bases.
N_Ar.bed


title: Size matched input for G3BP1 in N-expressing oxidatively stressed cells

description:
Extracted RNA was reverse transcribed using primer Rt13clip/5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTCCGNNN, where N are random bases.
G3BP1_N_Ar.bed

value: HEK293 cells overexpressing SARS-CoV-2 N treated with Sodium arsenite (1hour)


title: AR167_2667_ASC_7

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

data_processing:
Bases were trimmed to remove bases with low PHRED scores in Partek Genomics Suite.
Trimmed bases were then aligned to human genome hg38 using Partek Genomics Suite.
Gene counts were quantified using HTSeq algorithm with union model in Partek Genomics Suite.
Gene counts were library size and log normalized using the rlog function in DESeq2 (v1.28.1; default parameter) in R.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: InVitro_GeneCounts.normalized.txt: Tab-delimited text file of log2 normalized read counts.

source_name: In vitro differentiated plasma cells

extract_protocol:
Cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research).
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: subject id

tag: culture day

tag: gender

value: Female

tag: race

value: African American + Caucasian

tag: ethnicity

value: Non-Hispanic

value: Blood

tag: cell subset

value: Antibody-secreting cells (ASC)


title: AR165_2667_ASC_1


title: AR166_2667_ASC_3


title: 2_control

description: A. baumannnii MS14413 RNAseq data


title: Mycn mutant zebrafish embryos 72hpf rep1

value: Mycn mutant

value: embryonic cells

value: 72 hpf


title: G1_input_rep2readsFig2GEO

description:
Input DNA from sonicated chromatin after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,alpha factor arrest in G1, input DNA.paired end reads, replicate 2

tag: genotype/variation

value: wt

value: G1 arrest with alpha factor


title: AR157_2665_ASC_7

value: Male

value: Asian


title: iCLIP-seq of G3BP1 in N-expressing oxidatively stressed cells, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt10clip/5Phos/NNGACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGACCNNN, where N are random bases.
G3BP1_N_Ar.bed


title: wild-type zebrafish embryos 72hpf rep2

value: AB


title: G1_input_rep1readsFig2GEO

description:
Input DNA from sonicated chromatin after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,alpha factor arrest in G1, input DNA.paired end reads, replicate 1

tag: cell cycle


title: AR156_2665_ASC_3


title: iCLIP-seq of G3BP1 in N-expressing oxidatively stressed cells, replicate A

description:
Extracted RNA was reverse transcribed using primer Rt9clip/5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGCCANNN, where N are random bases.
G3BP1_N_Ar.bed


title: 32min_10prcnt_unreplicated_Sphase_unreplicatedRNAP2ChIP_rep2readsFig2GEO

description:
Early-mid S-phase (32min after release) RNAPol2 (Rpb3HA) ChIPed unreplicated DNA separated from ChIPed replicated EdU labeled biotinylated DNA after binding to streptavidin magnetic beads.
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, RNAPol2 on unreplicated DNA.paired end reads, replicate 2

value: early-mid S-phase (10% of the genome is unreplicated)

tag: edu incubation

value: from beginning of release from G1 arrest


title: wild-type zebrafish embryos 48hpf rep3

value: 48 hpf


title: AR155_2665_ASC_1


title: wild-type zebrafish embryos 48hpf rep2


title: AR154_2665_ASC_0


title: wild-type zebrafish embryos 72hpf rep1


title: 32min_10prcnt_unreplicated_Sphase_RNAP2ChIP_rep1readsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP from early-mid S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, RNAPol2 on bulk DNA.paired end reads, replicate 1

tag: antibody


title: 32min_10prcnt_unreplicated_Sphase_RNAP2ChIPNChAP_rep2readsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from early-mid S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 2


title: iCLIP-seq of G3BP1 in N-expressing cells, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt15clip/5Phos/NNTATTNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTATTNNN, where N are random bases.
G3BP1_N.bed

value: HEK293 cells overexpressing SARS-CoV-2 N


title: AR164_2667_ASC_0

value: Female


title: iCLIP-seq of G3BP1 in N-expressing cells, replicate A

description:
Extracted RNA was reverse transcribed using primer Rt14clip/5Phos/NNTGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTGCCNNN, where N are random bases.
G3BP1_N.bed

value: GFP-N was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to UV crosslinking.

value: G3BP1 monoclonal antibody (SANTA CRUZ  Biotechnology)


title: Size matched input for G3BP1 in N-expressing cells

description:
Extracted RNA was reverse transcribed using primer Rt12clip/5Phos/NNGTGGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGTGGNNN, where N are random bases.
G3BP1_N.bed


title: 32min_10prcnt_unreplicated_Sphase_RNAP2ChIPNChAP_rep1readsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from early-mid S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, RNAPol2 on replicated DNA.paired end reads, replicate 1


title: Sample 5: Src_CD_2

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE, Foege Building, S041

department: Genome Sciences

institute: University of Washington

description:
Targeted barcode amplification from extracted plasmid DNA
Src_1_8000_Score.csv, Src_2_2000_Score.csv, Src_4_800_Score.csv

data_processing:
Sample 1 was sequenced on MiSeq (Illumina). Samples 2-5 were sequenced on NextSeq 500 (Illumina).
All reads were processed using  bcl2fastq v.2.16 and ea-utils v.1.1.2-537.
Sample 1: Custom scripts were used to process these reads. R2 files were trimmed to 230bp.
Samples 2-5: Functional scores were calculated using Enrich2 v1.2 software and Src_Barcode_Map.txt.
Genome_build: NA
Supplementary_files_format_and_content: Src_Barcode_Map.txt provides the linkage between the barcode sequence (first column) and the full length variant sequence of Src's catalytic domain (second column). This document was generated through the following steps: 1)Custom subassembly scripts to link barcode sequence with full length catalytic domain sequence. 2) Custom subassembly filtering script for high quality reads. 3) Filtering out  WT barcodes with aberrant activity score using 2x Std. Dev. of WT barcode mean activity score. 4) Spike in of 6 barcode sequences of control Src variants (3 each for K298M and T341I).
Supplementary_files_format_and_content: Src_Das_25_Score.csv, Src_DAS_100_Score.csv, Src_1_8000_Score.csv, Src_2_2000_Score.csv, and Src_4_800_Score.csv are the output of Enrich2 v1.2. The inputs for Enrich2 v1.2 were the corresponding "Raw Files" (Input, A, B, and C) that share the same Src Inhibitor and concentration. Variants are denoted by their amino acid level changes and each has a calculated functional score from Enrich2.

molecule: other

source_name: Synthetic sequence

growth_protocol: TOP10 E.coli were grown in LB supplemented with 100 ug/mL Ampicillin. BY4741 ∆PDR5 or BY4741 Green Monster S. cerevisiae were grown in C-Leu media supplemented with 2% galactose.

extract_protocol:
Harvested cells (4 OD units worth) at each sampled time point were pelleted and stored at -20ºC. Plasmid DNA was extracted using Zymogen Yeast Miniprep Kit I following supplied protocol.
Extracted barcodes were amplifed and sample indices appended using 2x KAPA2G Robust HotStart ReadyMix with Thermocycler conditions of: Initial denaturation at 95ºC for 3 min, followed by 17 cycles of 95ºC for 15s, 60ºC for 15s, and 72ºC for 15s. Amplicons were quantified using KAPA Library Quantification Kit.
DNA amplicon sequencing using custom primers

treatment_protocol: S. cerevisiae harboring Src variant library were grown in 2% galactose containing media to induce Src expression and in varying concentrations of indicated Src kinase inhibitor. Library was grown and 4 OD unit timepoints were harvested throughout growth. The indicated concentration of Src inhibitor was added at the same time Src kinase expression was induced by galactose.

tag: strain

value: Green Monster BY4741

value: Src Inhibitor:1,2,4

tag: treatment concentration

tag: molecule

value: Plasmid DNA


title: wild-type zebrafish embryos 48hpf rep1

tag: tissue

value: embryonic cells

tag: age


title: Size matched input for G3BP1 in oxidatively stressed cells

description:
Extracted RNA was reverse transcribed using primer Rt13clip/5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTCCGNNN, where N are random bases.
G3BP1_Ar.bed

tag: cell line

value: HEK293 treated with Sodium arsenite (1hour)


title: AR142_2598_ASC_3

value: Caucasian

value: Non-Hispanic

value: Blood

value: Antibody-secreting cells (ASC)


title: AR143_2598_ASC_7


title: 32min_10prcnt_unreplicated_Sphase_NChAP_rep1readsFig2GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in early-mid- S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, replicated DNA.paired end reads, replicate 1

value: wt


title: iCLIP-seq of G3BP1 in oxidatively stressed cells, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt12clip/5Phos/NNGTGGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGTGGNNN, where N are random bases.
G3BP1_Ar.bed


title: Sample 4: Src_CD_1

tag: treatment


title: AR141_2598_ASC_1

tag: subject id


title: Sample 2: Src_CD_1

description:
Targeted barcode amplification from extracted plasmid DNA
Src_DAS_25_Score.csv, Src_DAS_100_Score.csv

value: BY4741 {delta}PDR5

value: Src Inhibitor:Dasatinib


title: 32min_10prcnt_unreplicated_Sphase_input_rep2readsFig2GEO

description:
Input DNA from sonicated chromatin from early-mid S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, input DNA.paired end reads, replicate 2

value: early-mid S-phase (10% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: AR140_2598_ASC_0

tag: culture day

value: Female


title: Size matched input for G3BP1

description:
Extracted RNA was reverse transcribed using primer Rt14clip/5Phos/NNTGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTGCCNNN, where N are random bases.
G3BP1.bed


title: AR128_2588_ASC _14

tag: gender

value: African American


title: iCLIP-seq of G3BP1, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt10clip: /5Phos/NNGACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGACCNNN, where N are random bases.
G3BP1.bed


title: smRNA-seq_HCT15-FR_2

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

data_processing:
Reads from all RNA-seq experiments were aligned to zebrafish genome build hg19 using STAR. All ATAC-Seq data sets were trimmed and aligned to zebrafish genome build hg19 genome using Bowtie2.
Duplicate reads of all RNA-seq and ATAC-seq data were removed with SAMtools.
The mRNA and lncRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff. SPAR and DEseq2 were used to quantify small RNA expression. MACS2 was used to identify regions of ATAC-seq peaks.
The ATAC-seq peaks were used for known motif enrichment analysis of each sample, which were performed using HOMER (v4.9).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (bw) files were generated using deepTools.

source_name: colon cancer cell line

growth_protocol: The HCT15 and 5-fluorouracil-resistant HCT15 (HCT15-FR) cell lines were purchased from the iCell Bioscience Inc (Shanghai, China) and cultured in RPMI-1640 medium (KEL Biotech, China) with 10% fetal bovine serum (KEL Biotech, China), 2 mM L-Glutamine (Gibco, USA), 0.1 M sodium pyruvate (Gibco, USA), 50 units/mL penicillin and 50 µg/mL streptomycin (Sangon Biotech, China). All cells were grown to 80% confluence in 10 cm culture dishes in a humidified atmosphere with 5% CO2 at 37 °C, refreshing culture medium every 2-3 days.

extract_protocol:
Total RNA was isolated from samples using TRIzol Reagent (Invitrogen, USA) and purified using RNeasy Mini Kit (QIAGEN, Germany). Agilent Bioanalyzer 2100 was used to assess RNA integrity.
The mRNA and lncRNA‐seq library preparation from 3 μg of total RNA was performed with NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer's instructions. PE150 sequencing was performed on the Illumina HiSeq X Ten platform (Novogene Biotech, China). A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) was used to generate the sequencing libraries following the manufacturer’s instructions. library quality was assessed on the Agilent Bioanalyzer 2100 system and then sequenced on an Illumina Hiseq 2500 platform (Novogene Biotech, China). 50bp single-end reads were generated for each sample. The ATAC-seq libraries were prepared using a total of 50,000 fresh cells were washed twice with 100 μl of cold PBS (KEL Biotech, China) and resuspended in 100 μl of lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 0.1% IGEPAL CA-630 (Sigma-Aldrich) and 3 mM MgCl2] for 10 min on ice to prepare the nuclei. Immediately after lysis, the suspension of nuclei was spun at 500 g at 4°C for 5 min to remove the supernatant. Nuclei were then incubated with the 50 μl of Tn5 transposition reaction mix (DIATRE Biotech, China) at 37 °C for 30 min. The stop buffer was then added directly into the reaction to end the tagmentation. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Germany). PCR was performed to amplify the library for 12 cycles. Libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers.

treatment_protocol: The parental HCT15 cells were grown in a drug-free medium, resistant-derived cells were maintained in 5-FU at a concentration of 20 μg/mL.

value: treated with 20microg/mL 5-FU

value: HCT15 cell line


title: AR144_2598_ASC _14

tag: race


title: 25min_21prcnt_unreplicated_Sphase_RNAP2ChiPreadsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP from mid-early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on bulk DNA.paired end reads

value: mid-early S-phase (21% of the genome is unreplicated)


title: iCLIP-seq of G3BP1, replicate A

description:
Extracted RNA was reverse transcribed using primer Rt1clip/5Phos/NNAACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNAACCNNN, where N are random bases.
G3BP1.bed

tag: growth protocol

value: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

value: WT cells were UV crosslinked prior to harvesting

value: G3BP1 monoclonal antibody (SANTA CRUZ  Biotechnology)


title: AR127_2588_ASC _7

tag: ethnicity

tag: cell subset


title: AR126_2588_ASC _3


title: smRNA-seq_HCT15_2

value: untreated


title: SEM-R2-T0

city: San Francisco

first: Matthew

last: Nix

state: CA

address: 185 Berry St

department: Laboratory Medicine

institute: UCSF

description: Replicate 2, collected at the start of screen

data_processing:
Reads were mapped to a gene reference library that contained all sgRNA guides and the genes they targeted that were used in the screen. The mapping and counting of sgRNAs  was performed using custom Python scripts.
The calculation of sgRNA-level and gene-level phenotype scores and p-values was calculated using custom python scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file that includes gene phenotype scores and p-values for all sgRNA's and targeted genes

source_name: B-ALL cell line

growth_protocol: Cells were grown in standard culture conditions with RPMI + 20% FBS and 1% pen-strep

extract_protocol:
Cell pellets were harvested in biological duplicates and flash frozen. Genomic DNA  was harvested using Machery Nagel Blood XL kit.
Illumina sequencing library was generated using custom PCR primers to amplify the sgRNA sequences from total isolated genomic DNA.  sgRNA sequences served as barcodes for analysing the changes in guide abundance during the course of the experiments

treatment_protocol: Cells were not treated. Aliqouts of cells were isolated at T=0 time point shortly after sgRNA library transduction of the cells(T0), and again after 12 passages (End) to allow for depletion of cells harboring sgRNA's targeting essential genes

tag: b-all type

value: MLLr

tag: time point


title: 25min_21prcnt_unreplicated_Sphase_RNAP2ChIPNChAPreadsFig2GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on replicated DNA.paired end reads

tag: genotype/variation

tag: cell cycle

tag: edu incubation

tag: antibody


title: smRNA-seq_HCT15_1


title: Sample 3: Src_CD_2

tag: strain

tag: treatment concentration

tag: molecule

value: Plasmid DNA


title: AR125_2588_ASC _1

tag: age

value: Non-Hispanic

tag: tissue

value: Blood

value: Antibody-secreting cells (ASC)


title: 25min_21prcnt_unreplicated_Sphase_NChAPreadsFig2GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in mid-early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads

value: wt


title: SEM-R2-End

description: Replicate 2, collected at the end of the screen, 12 passages

value: end


title: 32min_10prcnt_unreplicated_Sphase_NChAP_rep2readsFig2GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in early-mid S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, replicated DNA.paired end reads, replicate 2

value: early-mid S-phase (10% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: 32min_10prcnt_unreplicated_Sphase_input_rep1readsFig2GEO

description:
Input DNA from sonicated chromatin from early-mid S-phase 32min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,32min after release into S phase, input DNA.paired end reads, replicate 1


title: bulk DNA from mid-log cultures 15min after the EdU pulse bound with RNAPII replicate 2

description:
RNApol2 (Rpb3HA) ChIP from a midlog culture 15 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin,15min after the EdU pulse, RNAPol2 on bulk DNA.paired end reads 2, replicate 2
15-Rpb3ChIP-2reads2FigS3BGEO

growth_protocol: Mid-log cells (grown o/n in SCD-URA at 30°C, OD600 ~0.68) were treated with 10µM EdU for 1min by mixing equal volumes of culture and preheated (30°C) premixed media containing 20µM EdU. EdU incorporation was stopped with the addition of Thymidine (Acros Organics , previously mixed into preheated SCD-URA media) to a final concentration of 10mM (1000 fold excess) to the culture. The culture was divided into two flasks and the ½ cultures were fixed with formaldehyde 7 or 15 minutes after EdU addition. Cell pellets were washed with cold PBS and flash frozen in liquid nitrogen and kept at -80°C until further processing.

extract_protocol:
Cross-linked frozen cell pellets were re-suspended in 1.5 ml NP lysis buffer (100 mM NaCl, 10 mM Tris 7.4, 5 mM MgCl2, 1 mM CaCl2, 10% NP-40, 50 mM EDTA, 0.1 % SDS (optional), 1 mM PMSF and 1xEDTA-free protease inhibitor cocktail (Roche)). The suspension was then split into aliquots each containing ~billion cells. Zirconium Sillicate beads (400 μl, 0.5 mm) were then added to each aliquot and cells were mechanically disrupted using a bullet blender (Next Advance) for 4 times x 3 min (intensity 8). Spheroplasts were treated with micrococcal nuclease or sonicated. Sonicated or digested chromatin was subject to ChIP with the indicated antibody. An aliquot was set aside for the input DNA fraction prior to ChIP. EdU incorporated into ChIPed and Input DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads (ChIP-NChAP and NChAP fractions, respectively). The supernatant after binding to  streptavidin beads was kept for the unreplicated ChIP fraction and an input DNA and a bulk ChIP DNA aliquot were set aside prior to biotinylation for the Input and ChIP fractions.
DNA samples from all fractions were treated with calf intestinal phosphatase (NEB). NGS libraries were constructed either with costum enzymes( blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read)) or using the TrueSeq V2 LT Sample prep kit (Illumina) with the Illumina unique multiplexing indexes Set A and B. The custom library samples were amplified with the Phusion enzyme (NEB) for 18 PCR cycles with Illumina PE1 and PE2 primers.  The primer mix from the kit was  used in the PCR amplification step (also with Phusion) for the samples prepared with  TrueSeq V2 LT (15 cycles). For nascent (replicated NChAP and ChIPNChAP fractions) libraries, the nascent 'EdU containing) strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidine coated magnetic beads.
Strand specific sonicated-ChIP-seq  of replicated DNA fragments. The method which we call ChIP-NChAP (Nascent Chromtin Avidin Pulldown) was developed in the Radman-Livaja group.

value: mid-log 15min after an EdU pulse chased with excessed Thymidine

value: 1min EdU pulse


title: iCLIP-seq of G3BP1 in oxidatively stressed cells, replicate A

description:
Extracted RNA was reverse transcribed using primer Rt16clip/5Phos/NNTTAANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTTAANNN, where N are random bases.
G3BP1_Ar.bed

tag: cell line

value: HEK293 treated with Sodium arsenite (1hour)

tag: treatment

value: Cells were treated with Sodium Arsenite for 1hour prior to harvesting


title: SEM-R1-T0

description: Replicate 1, collected at the start of screen


title: s2

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
3'-mRNA
10X Genomics single-cell seq. 10X Chromium v3 kit (NextGEM) was used for library prep.

data_processing:
Cellranger-4.0.0 mkfastq was used for adapter trimming and converting the base calls.
Cellranger-4.0.0 counts was used to align the reads on the pre-mRNA and create the read count matrices.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: matrix.mtx: count matrix; barcodes.tsv: barcode table; features.tsv: feature table.

organism: Mus musculus

source_name: Adult mice brain hippocampus

extract_protocol:
Mice were sacrificed by cervical dislocation. Tissue were immediately frozen in liquid nitrogen. Nuclei from frozen mouse brain tissues were isolated according to previously published protocol with modifications. Isolated total nuclei were stained with 7AAD (Invitrogen, Cat: 00-6993-50) and single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter.
Around 5000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3′ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei.

tag: genotype

value: WT

value: Hippocampus

tag: stimulation


title: SEM-R1-End

description: Replicate 1, collected at the end of the screen, 12 passages


title: AR124_2588_ASC _0

tag: subject id

tag: culture day

tag: gender

value: Female

tag: race

value: African American

tag: ethnicity


title: s1


title: bulk DNA from mid-log cultures 15min after the EdU pulse bound with RNAPII replicate 1

description:
RNApol2 (Rpb3HA) ChIP from a midlog culture 15 min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin, 15 min after the EdU pulse, RNAPol2 on bulk DNA.paired end reads 1, replicate 1
15-Rpb3ChIP-1reads1FigS3BGEO

tag: cell cycle


title: s3


title: smRNA-seq_HCT15-FR_1

value: treated with 20microg/mL 5-FU

value: HCT15 cell line


title: Input DNA from mid-log cultures 15min after the EdU pulse replicate 2

description:
Input DNA from sonicated chromatin from midlog cultures 15min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin,15min after the EdU pulse, input DNA.paired end reads 2, replicate 2
15-Inpt-2reads2FigS3BGEO

tag: edu incubation


title: AR111_2585_ASC _7

value: Non-Hispanic

tag: cell subset


title: EBV B-cell Rep1

data_processing:
Reads were mapped to the reference human (hg19) genome sequence, using Tophat2 aligner(Kim et al., 2013) with the default parameters.
The mRNA expression level for each gene was represented as FPKM, called by Cufflinks(Trapnell et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file that includes FPKM for all samples

extract_protocol:
Cell pellets were harvested in biological replicates and flash frozen. RNA was harvested using Qiagen Rneasy Kit. mRNA was purified from total RNA using Oligo (dT)25 magnetic beads ( NEB, S1550S)
Illumina sequencing library prep was performed using using KAPA Stranded RNAseq it with riboerase (Kapa Biosystems, KK8483)

tag: b-all type

value: non-MLLr


title: RNASET2HippocampusControl5000nucleiSakib [C4]

tag: strain


title: AR110_2585_ASC _1

value: Blood

value: Antibody-secreting cells (ASC)


title: TOM1 Rep2


title: AR109_2585_ASC _0


title: Input DNA from mid-log cultures 15min after the EdU pulse replicate 1

description:
Input DNA from sonicated chromatin from midlog cultures 15min after the EdU pulse
all_readsFandR_norm_50bpbins_FigS3BGEO.txt
Sonicated chromatin 15 min after the EdU pulse, input DNA.paired end reads 1, replicate 1
15-Inpt-1reads1FigS3BGEO


title: RNASET2HippocampusControl5000nucleiSakib [C3]


title: TOM1 Rep1


title: WT log phase cells reads, replicate 2

description:
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
all_readsFandR_norm_50bp_Fig_S5GEO.txt
WT log phase cells reads, replicate 2

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the yeast S288C and the S.pombe genomes using BLAT
The read density distribution was determined for each species in each dataset separately. The average S.pombe genomic read density per bp (F and R reads were processed together) was determined for each dataset. For spike-in normalization, S.cerevisiae read densities per bp were then divided with the corresponding S.pombe average genomic read density. For internal normalization S.cerevisiae read densities were divided with its average genomic read density as described above.
Normalized read densities for each gene were aligned by the transcription start site and divided into sense and antisense transcripts. The median read density for each gene (from the tss to the end of the coding sequence) was then determined for each transcript. Intron regions were excluded from the calculation.
Genome_build: Saccer1 and Schizosaccharomyces pombe (assembly ASM294v2)
Supplementary_files_format_and_content: tab-delimited text files of mRNA enrichment (columns) normalized either  to the average genome read count or the S.pombe "spike in" and distributed in 50bp bins. 50bp bins marked with R indicate repetitive sequences.

source_name: MATa ade2-1::ADE2 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100  Rpb3-3HA::TRP URA3::GDP-TK(7x) AUR1c::ADH-Hent1 ∆bar1::HIS3

growth_protocol: S. cerevisiae and S.pombe cells were grown in YPD and YES respectively.

extract_protocol:
Cells were resuspended in Trizol, cell walls were broken with bead beating and total RNA was extracted and DNAseI treated. Extracted total RNA amounts were measured with  the Qubit fluorimeter and the Nanodrop spectrophotometer and the quality was checked by a Bioanalyzer scan (Agilent). Each S.cerevisiae total RNA extract was mixed with the S.pombe total RNA extract at a mass ratio of 10:1.
The mixed RNA samples were then used for NGS library preparation using the Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol.

treatment_protocol: Exponentially growing S.cerevisiae and S. pombe (strain FY2319, courtesy of S. Forsburg) cells were flash frozen in liquid N2.

value: exponential growth


title: RNASET2HippocampusControl5000nucleiSakib [C2]


title: REH Rep2


title: WT log phase cells reads, replicate 1

description:
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
all_readsFandR_norm_50bp_Fig_S5GEO.txt
WT log phase cells reads, replicate 1


title: 25min_21prcnt_unreplicated_Sphase_inputreadsFig2GEO

description:
Input DNA from sonicated chromatin from mid-early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig2GEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads

tag: genotype/variation

value: wt

value: mid-early S-phase (21% of the genome is unreplicated)

tag: antibody


description:
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
all_readsFandR_norm_50bp_Fig_S5GEO.txt
rtt109D log phase cells reads, replicate 2

source_name: MATa ade2-1 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100 GAL psi+ RAD5+ URA3::GDP-TK(7x) AUR1c::ADH-hENT1 ∆rtt109::Kan ∆bar1::His3


title: AR96_2578_ASC_14

tag: age

value: Asian

tag: tissue


title: AR95_2578_ASC_7


title: AR94_2578_ASC_3


title: WT4monthsHippocampus [A3]


title: RNASET2HippocampusControl5000nucleiSakib [C1]


title: REH Rep1


title: AR112_2585_ASC _14


title: BV173 Rep2


description:
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
all_readsFandR_norm_50bp_Fig_S5GEO.txt
rtt109D log phase cells reads, replicate 1


title: WT4monthsHippocampus [A1]


description:
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
all_readsFandR_norm_50bp_Fig_S5GEO.txt
hst3,4DD log phase cells reads, replicate 2

source_name: MATalpha ade2-1::ADE2 his3-11 15 leu2-3 112 trp1-1 ura3-1 can1-100  Rpb3-3HA::TRP URA3::GDP-TK(7x) AUR1c::ADH-Hent1 ∆bar1::HIS3 Δhst3::HygMX Δhst4::NatMX


title: AR93_2578_ASC_1


title: BV173 Rep1


title: WT4monthsHippocampus [A2]


title: AR92_2578_ASC_0


description:
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
all_readsFandR_norm_50bp_Fig_S5GEO.txt
hst3,4DD log phase cells reads, replicate 1


title: AR81_2577_ASC_14

value: Male


title: SUP-B15 Rep2


title: 4C_Muscle_CTCFbs

city: Paris

first: Matthieu

last: Dos Santos

state: Paris

address: 24 rue du Faubourg Saint Jacques

institute: Institut Cochin

description: 4C–seq libraries were constructed according to Matelot and Noordermeer, Meth Mol Biol 2016. 4C-seq libraries were prepared from indicated tissue samples. The primary restriction enzyme used was DpnII (New England Biolabs, R0543M) and the secondary restriction enzyme was NlaIII (New England Biolabs, R0125L). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Tru-seq adapters. Illumina adapters (single end reads) were included in the inverse 4C PCR primers used for 4C-seq library preparation. Multiplexed samples were sequenced on the Illumina NextSeq 550 system using 86 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (David et al., 2014 Plos ONE). Samples were mapped to the ENSEMBL Mouse assembly NCBIM38 (mm10).

data_processing:
Library strategy: 4C-seq
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 PLoS ONE).
Reads were mapped to the mm10 (NCBIM38) mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009 Genome Biology) with parameters -n 2 --best -strata -m 5.
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 PLoS ONE).
4C figures were made using a running mean algorithm with a window size of eleven fragments (mappable restriction fragments with 0 values included).
Genome_build: mm10
Supplementary_files_format_and_content: Signal/restriction fragment (bw) and smoothed signal/restriction fragment (bedGraph), one per viewpoint, per cell type.

source_name: Muscle

extract_protocol:
Muscle nuclei were isolated with hypotonic buffer (25mM Hepes-KOH pH 7.8, 10mM KCL, 1.5mM MgCl2, 0.1% NP40, PIC 1X (complete protease inhibitor Roche), PMSF 1mM). Muscles were sliced with a scissor and then homogenized with an Ultra-Turrax. The solution was transferred in a 15 ml Falcon tube and crosslinked with 2% formaldehyde at room temperature during 10 min. 1,43 ml of cold glycine (1M) was added to quench the formaldehyde for 5 min at +4°C while shaking. The crosslinked nuclei were dounced 10 times with a loose pestle and then centrifuged at 1000 Rcf for 10 min at +4°C. The nuclear pellet was resuspended in 5ml of hypotonic buffer and filtered with 70µm and 40µm cells strainers. The nuclei were pelleted with centrifugation at 1000 rcf for 10 min, snap frozen into liquid nitrogen and stored at -80°C.
PCR amplification using primers with included Tru-seq adapter sequences and indexes.

treatment_protocol: Circular Chromosome Conformation Capture (4C) technique was performed as described (Matelot and Noordermeer, 2016 Meth Mol Biol). Cross-linked chromatin was digested with DpnII, ligated under diluted conditions, cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions.

value: Gastrocnemius+Tibialis+Quadriceps

value: 8 weeks


title: AR80_2577_ASC_7


title: BEL1 Rep2

value: MLLr


title: 4C_Muscle_EnhancerLincRNA


title: BEL1 Rep1


title: Rpb3ChIPNChAP_52percentunreplicatedreadsFigS4GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,20min after release into S phase, RNAPol2 on replicated DNA.paired end reads

value: early S-phase (52% of the genome is unreplicated)

value: from beginning of release from G1 arrest


title: AR79_2577_ASC_3


title: Rpb3ChIPNChAP_38percentunreplicatedreadsFigS4GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 26min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,26min after release into S phase, RNAPol2 on replicated DNA.paired end reads

value: early S-phase (38% of the genome is unreplicated)


title: 4C_Muscle_Myh8


title: KOPN8 Rep2


title: Rpb3ChIP_52percentunreplicatedreadsFigS4GEO

description:
RNApol2 (Rpb3HA) ChIP from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,20min after release into S phase, RNAPol2 on bulk DNA.paired end reads


title: AR77_2577_ASC_0


title: KOPN8 Rep1


title: Rpb3ChIP_45percentunreplicatedreadsFigS4GEO

description:
RNApol2 (Rpb3HA) ChIP from S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,24min after release into S phase, RNAPol2 on bulk DNA.paired end reads

value: early S-phase (45% of the genome is unreplicated)


title: 4C_Muscle_Myh4


title: AR67_2576_ASC_14

value: Female


title: 4C_Muscle_Myh3


title: RS411 Rep2


title: Rpb3ChIP_38percentunreplicatedreadsFigS4GEO

description:
RNApol2 (Rpb3HA) ChIP from S-phase 26min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,26min after release into S phase, RNAPol2 on bulk DNA.paired end reads


title: AR66_2576_ASC_7

value: Non-Hispanic


title: RS411 Rep1


title: 4C_Muscle_Myh2


title: SUP-B15 Rep1

value: non-MLLr


title: AR65_2576_ASC_3

value: Blood


title: 4C_Quadriceps_Myh4

source_name: Quadriceps

value: Quadriceps


title: Rpb3ChIPNChAP_45percentunreplicatedreadsFigS4GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,24min after release into S phase, RNAPol2 on replicated DNA.paired end reads


title: NChAP_45percentunreplicatedreadsFigS4GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,24min after release into S phase, replicated DNA.paired end reads


title: 4C_Muscle_Myh13


title: SEM Rep2


title: SEM Rep1


title: AR64_2576_ASC_1

value: Antibody-secreting cells (ASC)


title: AR63_2576_ASC_0


title: Inpt_52percentunreplicatedreadsFigS4GEO

description:
Input DNA from sonicated chromatin from S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,20min after release into S phase, input DNA.paired end reads

value: wt


title: 4C_Soleus_Myh4

source_name: Soleus

value: Soleus


title: AR78_2577_ASC_1

value: Asian


title: LSK cells, DPL-MLN-Input

city: Bethesda

first: Yang

last: Du

state: MD

address: 4301 Jones Bridge Road

department: Pediatrics

institute: Uniformed Services University of the Health Sciences

data_processing:
RNA-seq: Raw sequencing data were demuxed using bcl2fastq2 conversion software.
RNA-seq: Raw paired-end sequencing reads were aligned to the mouse reference genome (mm10) using MapSplice version 2.2.1.
RNA-seq: Gene read counts against UCSC mouse gene models (obtained on February 21, 2016) were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s reverse
RNA-seq: Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
ChIP-seq: Raw sequencing data were demuxed using bcl2fastq2 conversion software.
ChIP-seq: Raw reads were aligned to the mouse genome (mm10) using the BWA mem algorithm (version 0.7.12-r1039)
ChIP-seq: Histone mark peaks were called with the MACS2 (version 2.1.1.20160309) callpeak function using the standard model building procedure and additional parameters: -g mm --call-summits -B
ChIP-seq: M2 and MLL1 peaks were called with the MACS2 (version 2.1.1.20160309) callpeak function with a fixed shift size (i.e. no model building, d = 284): -g mm --call-summits -B --nomodel --extsize 284
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts_table.txt - tab-delimited text file of gene raw counts for all samples
Supplementary_files_format_and_content: bigWig files were generated from MACS2 output bedGraph files using bdg2bw
Supplementary_files_format_and_content: peaks.txt files contain MACS2 peak calling ouput

source_name: Lin-Sca-1+c-kit+ cells

growth_protocol: Transduced LSK cells were expanded for 5 days in methylcellulose medium supplemented with 15% fetal bovine serum, 1X penicillin/streptomycin, mouse SCF (100ng/ml), mouse IL-3 (6ng/mL), and mouse IL-6 (10ng/mL) before harvesting.

extract_protocol:
RNA-seq: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germantown, MD).
ChIP-seq: ChIP reactions were performed using the iDeal ChIP-seq kit for transcription factors or histones (C01010054 and C01010051, respectively; Diagenode, Denville, NJ).
RNA-seq: Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Samples were sequenced using NextSeq 500 (Illumina, San Diego, CA) with ~25-45 million 75bp, paired-end reads.
ChIP-seq: Sequencing libraries were produced using DNA SMART ChIP-Seq kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions.

value: Bone marrow

tag: cell type

value: LSK cells

tag: condition

tag: chip antibody


title: LSK cells, 2PL-MLN-Input


title: AR51_2574_ASC_14

tag: subject id

value: Male


title: Inpt_45percentunreplicated_readsFigS4GEO

description:
Input DNA from sonicated chromatin from S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,24min after release into S phase, input DNA.paired end reads


title: 4C_Soleus_Myh2

value: 8 weeks


title: AR50_2574_ASC_7

tag: culture day


title: Inpt_38percentunreplicatedreadsFigS4GEO

description:
Input DNA from sonicated chromatin from S-phase 26min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,26min after release into S phase, input DNA.paired end reads


title: H3K56acChIPNChAP_52percentunreplicatedreadsFigS4GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K56Ac on replicated DNA.paired end reads

value: early S-phase (52% of the genome is unreplicated)


title: NChAP_52percentunreplicatedreadsFigS4GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,20min after release into S phase, replicated DNA.paired end reads

value: from beginning of release from G1 arrest


title: LSK cells, DPL-MLN-3

value: MLL1 (Bethyl Laboratory, A300-086A)


title: LSK cells, 2PL-MLN-3


title: AR49_2574_ASC_3

tag: gender


title: H3K56acChIPNChAP_45percentunreplicatedreadsFigS4GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,24min after release into S phase, H3K56Ac on replicated DNA.paired end reads

value: early S-phase (45% of the genome is unreplicated)


title: LSK cells, DPL-M2-Input


title: AR48_2574_ASC_1

tag: race


title: 4C_Quadriceps_Myh2


title: AR47_2574_ASC_0

tag: ethnicity


title: H3K56acChIPNChAP_38percentunreplicatedreadsFigS4GEO

description:
H3K56Ac ChIP followed by nascent DNA purification by EdU-biotin pulldown from S-phase 26min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,26min after release into S phase, H3K56Ac on replicated DNA.paired end reads

tag: cell cycle

value: early S-phase (38% of the genome is unreplicated)


title: LSK cells, 2PL-M2-Input


title: NChAP_38percentunreplicatedreadsFigS4GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in S-phase 26min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,26min after release into S phase, replicated DNA.paired end reads

tag: edu incubation


title: AR46_2574_ASC_0

value: Non-Hispanic

tag: cell subset


title: LSK cells, DPL-M2-2

value: Anti-FLAG M2 (Sigma, F1804, Lot SLBX2256)


title: H3K56acChIP_52percentunreplicatedreadsFigS4GEO

description:
H3K56Ac ChIP from S-phase 20min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,20min after release into S phase, H3K56Ac on bulk DNA.paired end reads


title: AR31_2573_ASC_14

value: Female

value: Blood


title: H3K56acChIP_45percentunreplicatedreadsFigS4GEO

description:
H3K56Ac ChIP from S-phase 24min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,24min after release into S phase, H3K56Ac on bulk DNA.paired end reads


title: LSK cells, 2PL-M2-2


title: AR30_2573_ASC_7

value: Antibody-secreting cells (ASC)


title: LSK cells, DPL-Histone-Input


title: AR28_2573_ASC_1


title: AR29_2573_ASC_3


title: LSK cells, 2PL-Histone-Input


title: rat vascular smooth muscle cells_PDGF-BB_20ng/ml_24h_circRNA 2

type: RNA

city: Xi'an

first: Bo

last: Yuan

address: No. 229, Taibai North Road, Beilin District

institute: Northwest University

description: circRNA expression data from PDGF-BB induced rat vascular smooth muscel cells

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

organism: Rattus norvegicus

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Rat vascular smooth muscle cells

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

treatment_protocol: The rat vascular smooth muscle cells were inoculated with DMEM  supplemented with 10% (v/v) fetal bovine serum and kept in a humidified incubator at 37°C with 5% CO2

value: vascular smooth muscle cells (VSMCs)

tag: treatment

value: induced with 20ng/ml PDGF-BB

tag: molecule subtype

value: circRNA


title: H3K56acChIP_38percentunreplicatedreadsFigS4GEO

description:
H3K56Ac ChIP from S-phase 26min after G1 arrest with alpha factor
all_readsFandR_norm_50bp_Fig_S4BGEO.txt
Sonicated chromatin,26min after release into S phase, H3K56Ac on bulk DNA.paired end reads

extract_protocol:
Cross-linked frozen cell pellets were re-suspended in 1.5 ml NP lysis buffer (100 mM NaCl, 10 mM Tris 7.4, 5 mM MgCl2, 1 mM CaCl2, 10% NP-40, 50 mM EDTA, 0.1 % SDS (optional), 1 mM PMSF and 1xEDTA-free protease inhibitor cocktail (Roche)). The suspension was then split into aliquots each containing ~billion cells. Zirconium Sillicate beads (400 μl, 0.5 mm) were then added to each aliquot and cells were mechanically disrupted using a bullet blender (Next Advance) for 4 times x 3 min (intensity 8). Spheroplasts were treated with micrococcal nuclease or sonicated. Sonicated or digested chromatin was subject to ChIP with the indicated antibody. An aliquot was set aside for the input DNA fraction prior to ChIP. EdU incorporated into ChIPed and Input DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads (ChIP-NChAP and NChAP fractions, respectively). The supernatant after binding to  streptavidin beads was kept for the unreplicated ChIP fraction and an input DNA and a bulk ChIP DNA aliquot were set aside prior to biotinylation for the Input and ChIP fractions.
DNA samples from all fractions were treated with calf intestinal phosphatase (NEB). NGS libraries were constructed either with costum enzymes( blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read)) or using the TrueSeq V2 LT Sample prep kit (Illumina) with the Illumina unique multiplexing indexes Set A and B. The custom library samples were amplified with the Phusion enzyme (NEB) for 18 PCR cycles with Illumina PE1 and PE2 primers.  The primer mix from the kit was  used in the PCR amplification step (also with Phusion) for the samples prepared with  TrueSeq V2 LT (15 cycles). For nascent (replicated NChAP and ChIPNChAP fractions) libraries, the nascent 'EdU containing) strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidine coated magnetic beads.
Strand specific MNase-CHIP-seq  or strand specific sonicated-ChIP-seq  of replicated DNA fragments. The method which we call ChIP-NChAP (Nascent Chromtin Avidin Pulldown) was developed in the Radman-Livaja group.

tag: genotype/variation

value: wt


title: 25minSphase_unreplicatedRNApol2ChIPreadsFig1GEO

description:
Early S-phase (25min after release) RNAPol2 (Rpb3HA) ChIPed unreplicated DNA separated from ChIPed replicated EdU labeled biotinylated DNA after binding to streptavidin magnetic beads.
all_readsFandR_norm_50bpbins_Fig1BGEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on unreplicated DNA.paired end reads

value: early S-phase (54% of the genome is unreplicated)

tag: antibody


title: Spleen TRC WT rep2

city: Melbourne

first: Hyun Jae

last: Lee

address: 792 Elizabeth Street

institute: University of Melbourne

description:
TRCs from wild type mice, replicate 2
WT-2_S20

data_processing:
First 5bp from the 5' end of the forward sequenced reads were trimmed using trimmomatic v0.39 and then mapped to mm10 gnome using STAR v2.7.3a with default parameters.
HTSeq-Count v0.11.2 was used to count the reads overlapping exons with the parameter “-m union”. Only uniquely mapping reads were counted to generate the raw counts matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Spleens were disgested with Collagenase D + Dispase II and TRCs sorted using FACS Aria III. Total RNA was extracted using Qiagen RNeasy plus microkit
Library was constructed by using the Ribosomal RNA depletion using Nugen Ovation SoLo RNA-Seq system and Nugen Ovation SoLo library construction chemistry

tag: strain

value: Spleen

tag: genotype

value: SpiB Flox/Flox


title: 25minSphase_RNApol2ChIPNChAPreadsFig1GEO

description:
RNApol2 (Rpb3HA) ChIP followed by nascent DNA purification by EdU-biotin pulldown from early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bpbins_Fig1BGEO.txt
Sonicated chromatin,25min after release into S phase, RNAPol2 on replicated DNA.paired end reads

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
time points and time point fractions  were separated either by in line barcodes and the 5bp barcode were removed from the read sequence and saved into separate fastq files from a unique fastq file obtained from the sequencing service using a custom perl script, or with Illumina unique indexes (Set A and B) and demultiplexed after sequencing into separate fastq files by the sequencing facility
reads were mapped to the yeast S288C genome using BLAT
Paired end read count distribution in 50bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands
the genome average read count value was calculated and the data were normalized to one
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: tab-delimited text files of indicated feature enrichment (columns) normalized to the average genome read count and distributed in 50bp bins. 50bp bins marked with R indicate repetitive sequences.

source_name: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and HA tagged Rpb3 (subunit of RNAPol2)


title: AR27_2573_ASC_0

tag: age

value: Asian

tag: tissue


title: Spleen TRC WT rep1

description:
TRCs from wild type mice, replicate 1
WT-1_S19


title: 25minSphase_NChAPreadsFig1GEO

description:
nascent DNA purification by EdU-biotin pulldown from sonicated chromatin in early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bpbins_Fig1BGEO.txt
Sonicated chromatin,25min after release into S phase, replicated DNA.paired end reads

value: from beginning of release from G1 arrest


title: AR15_2568_ASC_14

value: Male


title: Spleen TRC SpiB KO rep2

description:
SpiB-deficient TRCs, replicate 2
SpiB-2_S23

value: CCL19-Cre SpiB Flox/Flox


title: Spleen TRC SpiB KO rep1

description:
SpiB-deficient TRCs, replicate 1
SpiB-1_S22


title: LSK cells, DPL-K4me3

value: Bone marrow

tag: cell type

value: LSK cells

tag: condition

tag: chip antibody


title: AR14_2568_ASC_7

tag: subject id

tag: culture day

tag: gender

value: Non-Hispanic


title: 25minSphase_Input_readsFig1GEO

description:
Input DNA from sonicated chromatin from early S-phase 25min after G1 arrest with alpha factor
all_readsFandR_norm_50bpbins_Fig1BGEO.txt
Sonicated chromatin,25min after release into S phase, input DNA.paired end reads

tag: cell cycle


title: LSK cells, 2PL-K16Ac


title: rat vascular smooth muscle cells_PDGF-BB_20ng/ml_24h_circRNA 3


title: rat vascular smooth muscle cells_circRNA 2

description: circRNA expression data from rat vascular smooth muscel cells

source_name: VSMCs


title: rat vascular smooth muscle cells_circRNA 1


title: LSK cells, 2PL-K4me3


title: Spleen TRC WT rep3

description:
TRCs from wild type mice, replicate 3
WT-3_S21


title: rat vascular smooth muscle cells_circRNA 3


title: LSK cells, DPL-K16Ac


title: LSK cells, DN-3


title: Hk2 cKO repopulated microglia

city: Hangzhou

first: weiying

last: wu

state: Zhejiang

address: 866 Yuhangtang Rd

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology Co. Ltd., (HangZhou, China) at a minimum depth of 20,000 reads per cell.
Raw sequencing data demultiplexing and converting were carried out by Illumina bcl2fastq software.
Sample demultiplexing, barcode processing and single-cell 3’ gene counting were included in the preprocessing steps of Cell Ranger pipeline (version 3.1.0).
Data were aligned to Ensembl genome GRCm38 reference genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression matrices output by Cellranger are provided as mtx files. The gene and cell barcode name files that accompany the mtx files are provided as tsv files (.tsv) for each sample.

source_name: Brain

growth_protocol: Cx3cr1CreER mice were purchased from the Jackson Laboratory. hk2 floxed (hk2 fl/fl) mice and Hk2CreER-tdTomato mice were generated by Biocytogen Company (China). hk2 fl/fl mice were crossed with the Cx3cr1CreER/+mice to generate the Cx3cr1CreER::hk2 fl/fl or hk2 fl/fl animals. All animals were housed under a 12-h light/dark cycle with food and water available.

extract_protocol:
Mice were anesthetized with sodium pentobarbital and perfused with ice-cold 0.9% NaCl solution. Brains were rapidly dissected and transferred to a pre-chilled dish with cold PBS on ice. The brains were minced and dissociated in DMEM medium (Fischer Scientific) containing 0.5 mg/ml collagenase IV (Sigma) and 10 U/ml DNase I (Roche). Myelin and tissue debris were removed by centrifuging through a 37-70% (v/v) Percoll gradient (GE Healthcare BioSciences) density. Mononuclear cells were collected and incubated with different antibodies as indicated, and microglia were purified as a CD11b+CD45low populations on a BD FACSAria II using the 80 μm micron nozzle.
Single-cells were captured and libraries were prepared following the manufacturer’s instructions of 10x Chromium Next GEM Single Cell 3' GEM and Library & Gel Bead Kit v3.

treatment_protocol: For induction of the Cre-dependent recombination in postnatal mice, 100 μg tamoxifen (TAM, Sigma) dissolved in corn oil was injected intraperitoneally for 2 consecutive days at postnatal day 1-2 or as indicated.

value: Hk2 cKO

value: isolated CD11b high CD45 low cells


title: Hk2 fl/fl repopulated microglia

value: Hk2 fl/fl


title: AR12_2568_ASC_1

tag: race

tag: ethnicity

value: Blood

value: Antibody-secreting cells (ASC)


title: AR13_2568_ASC_3

tag: cell subset


title: Roots, IP ammonium 2

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

description:
ammoniu_peak.txt
N2

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The root transcriptome from maritime pine (GJFX00000000.1) was used as the reference for the read mapping that was performed with BWA using the MEM option. The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The m6A peak identification was made using MeTPeak software using the root transcriptome from maritime pine (GJFX00000000.1) as reference.
Genome_build: NCBI TSA: GJFX00000000.1
Supplementary_files_format_and_content: Tab-delimited text file include raw counts for each sample.The column ID is the sequence identifier. Tab-delimited text file including peak information for each transcript.

organism: Pinus pinaster

source_name: Roots from one-month-old seedlings

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a light intensity of 100 μmol m−2 s−1, constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
Total root RNA from maritime pine seedlings was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology, 34: 209-214) and modified by Canales et al. (2012, Frontiers in Plant Science; 3:100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK). Samples with a RIN value > 7 were selected to mRNA isolation. The poly(A)-RNA isolation was performed using Dynabeads™ mRNA Purification Kit (Invitrogen, Paisley, UK) following the manufacturer’s instructions. This process was carried out twice per sample to avoid rRNA contamination. poly(A)-RNA quality was determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA HS, High Sensitivity, Assay Kit (Invitrogen, Paisley, UK). To perform the N6-methyladenosine (m6A) RNA immunoprecipitation, fragmented polyA mRNA in a range of 3.15 - 6 µg was used. Samples were precipitated with 1/10 of the total volume of sodium acetate (3M, pH5.2), 1/14 of the total volume of molecular grade glycogen (5mg/mL) (Invitrogen, Paisley, UK) and 2.5 volumes of cold molecular grade absolute ethanol. Subsequently, samples were incubated at -80 ºC overnight. After that, samples were centrifuged at 14.000 rpm for 30 minutes on a precooled ultra-centrifuge. Pellets were washed with 70% ethanol. The final pellets obtained were dried at room temperature for 10 minutes and resuspended in molecular grade distilled water (10 µL of molecular grade distilled water (Ambion, Austin, TX, USA) per 1 µg of polyA mRNA used). Samples were mixed with 10 µL of RNaseOUT (Life Technologies, Carlsbad, CA, USA), 200 µL 5X IP buffer (50 mM Tris HCl pH7.4, 750 mM NaCl, 0.5% vol/vol Igepal[CA-6300]) and 5 μL of m6A antibody (ab151230, Abcam, Cambridge, UK). The volume of the samples was brought up to 1 mL with molecular grade distilled water. Then, samples were incubated at 4ºC for 3 hours. During the time of the immunoreaction, Dynabeads™ protein-A beads (Invitrogen, Paisley, UK) were prepared using 1X IP buffer supplemented with molecular grade BSA (0.5 mg/mL) (Sigma, San Luis, MO, USA). Protein-A beads solution was rotated at 4ºC for 2 hours. Then, 100 µL of protein-A beads was added to each immunoreaction tube and incubated at 4ºC for 2 hours. Subsequently, samples were spin down, and the resulting pellets were washed three times with 1X IP buffer. For each pellet, 95 µL of proteinase K buffer (5 mM Tris pH 7.5, 1 mM EDTA, 0.25% SDS) and 5 µL of molecular grade proteinase K (Invitrogen, Paisley, UK) was added. Proteinase K reactions were incubated at 50ºC for 45 minutes and mixed every 10 minutes. Afterwards, samples were spun down, and pellets were washed twice with 300 µL of 1X IP buffer. The resulting mixtures were precipitated (as described above). Finally, pellets were resuspended in 20 µL of molecular grade distilled water. Final m6A-RNA immunoprecipitation yield was quantified using Qubit RNA HS, High Sensitivity, Assay Kit (Invitrogen, Paisley, UK). Total amount from 80 up to 130 ng were obtained.
The RIP sample sequencing was carried out by Novogen (HK). The cDNA synthesis and amplification, and the library preparation was made with the SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara, Mountain View, CA, USA) following the manufacturer’s instructions. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads and final reads of 150 bp length (Illumina, San Diego, CA, USA).

treatment_protocol: One-month old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into two different groups, relocated into forestall seedbeds and watered with 80 mL distilled water. After three days of acclimation, the control group was irrigated with 80 mL of water (C) and the experimental group with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times.

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: 1 month-old seedling

tag: treatment time

value: 24 hours

tag: treatment

value: 3mM ammonium

value: root

tag: type

value: immunoprecipitated (m6A)

tag: rip antibody


title: Roots, IP ammonium 1

description:
ammoniu_peak.txt
N1

tag: tissue

value: m6A antibody (ab151230, Abcam, Cambridge, UK)


title: Roots, IP ammonium 3

description:
ammoniu_peak.txt
N3


title: Roots, IP control 3

description:
control_peak.txt
C3

value: water


title: rat vascular smooth muscle cells_PDGF-BB_20ng/ml_24h_circRNA 1

tag: cell type

value: vascular smooth muscle cells (VSMCs)

value: induced with 20ng/ml PDGF-BB

tag: molecule subtype

value: circRNA


title: Roots, IP control 2

description:
control_peak.txt
C2


title: LSK cells, DN-1

tag: strain

value: Bone marrow

value: LSK cells

tag: condition


title: Peritoneal macrophages, SHP099_3

city: Nanjing

first: Yuyu

last: Zhu

address: Xianlin

institute: Nanjing University of Chinese Medicine

data_processing:
Basecalls performed using Illumina Casava 1.8
Index of the reference genome was built using Hisat2 v2.0.4 and pairedend clean reads were aligned to the reference genome using Hisat2 v2.0.4.
Data were filtered using the following specifications…
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Mus_musculus_Ensemble_92
Supplementary_files_format_and_content: fpkm.txt includes FPKMs for each Sample

source_name: Peritoneal macrophages

growth_protocol: Wild-type and SHP2lyz2-/- mice were intraperitoneally injected with 1 ml starch broth per mice, after 3 days, peritoneal cells were harvested by lavaging the peritoneal cavity . Adherent peritoneal macrophages were cultured in DMEM media containing 10% FBS and  at 37°C.

extract_protocol:
Peritoneal macrophages were used for total RNA isolation with Trizol (TaKaRa)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H ）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: peritoneal macrophages

tag: age

value: 8 weeks

tag: genotype

value: wild type


title: Peritoneal macrophages, SHP099_2


title: Peritoneal macrophages, SHP099_1


title: LSK cells, WT-3


title: REH_HiChIP

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
HiChIP data were processed and analyzed using MAPS41 v1.9 as implemented within the Arima Genomics bioinformatics pipeline available at https://github.com/ijuric/MAPS
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file for coverage and bedpe file for interaction loops

source_name: cell line

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine.

extract_protocol:
Freshly cultured cells were counted using trypan blue and a cell suspension volume corresponding to 6 million live cells was washed once with PBS (-Ca2+ -Mg2+) and then crosslinked in a volume of 5 mL PBS with 2% formaldehyde for 10 minutes at room temperature, followed by quenching with Stop Solution 1 according to the Arima protocol.
All H3K27ac HiChIP experiments were performed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ Document numbers A160168 v00 (HiChIP) and A160169 v00 (library preparation)),
HiChIP

treatment_protocol: no treatment

value: leukemia

tag: chip antibody

value: H3K27ac (Active Motif am91193 lot#22420004)

value: untreated

tag: cell line

value: REH


title: Roots, IP control 1

description:
control_peak.txt
C1

value: Segura-Alcaraz

value: 1 month-old seedling

value: 24 hours


title: LSK cells, WT-2


title: Roots, Input ammonium 3

description:
ammoniu_peak.txt
a3N

value: 3mM ammonium

value: root

value: input


title: LSK cells, WT-1


title: Nalm-16_HiChIP


title: LSK cells, 2105-3

value: Control


title: LSK cells, DN-2


title: Roots, Input ammonium 1

description:
ammoniu_peak.txt
a1N


title: Roots, Input ammonium 2

description:
ammoniu_peak.txt
a2N


title: Roots, Input control 3

description:
control_peak.txt
a3C

value: water


title: C42 iDA + EMF treated 2

city: São Paulo

first: Lygia

last: da Veiga Pereira Carramaschi

state: São Paulo

address: Rua Ana Moreira dos Santos Mattos, 208

department: Depto. Genética e Biologia Evolutiva

country: Brazil

institute: Universidade de São Paulo

description: induced dopaminergic neuron (iDA) + 0,4 Telsa EMF

data_processing:
Sickle software was used to trim the reads that had bases with a quality less than 30 or size smaller than 50 bp
The reads were aligned against the human transcriptome, using the STAR software with the default settings
Non-coding transcripts, including long noncoding RNAs, antisense transcripts and pseudogenes were excluded from further analysis
Quantification of readings was performed with the Salmon software in quantification mode
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text file containing gene expression quantification of all samples
Supplementary_files_format_and_content: Space-separated text file containing one list of transcripts IDs

source_name: induced dopaminergic neurons

growth_protocol: Three iPSC samples (Tofoli et al., 2019a) were differentiated into midbrain dopaminergic neurons (or iDA = induced dopaminergic neurons) following Kriks et al., 2011 protocol (as described in Tofoli et al., 2019b) until 35 days.

extract_protocol:
RNA was isolated using RNAeasy columns (Qiagen) and libraries prepared by Macrogen Ink. (Korea)
The libraries were prepared with the 42 TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). sequenced using the Illumina Novaseq 6000 (150PE). The read count was approximately 50,000 readings/ sample (~ 7.5 Gb)
RNA-seq libraries were prepared by Macrogen Ink. (korea). The quality control of the RNA was carried out with the Agilent 2100 Bioanalyzer equipment. The total RNA of the hiPSC-derived DA neurons/ sample was sequenced using the Illumina Novaseq 6000 (150PE). The libraries were prepared with the 42 TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). The read count was approximately 50,000 readings/ sample (~ 7.5 Gb) and the quality control of the readings was done using the FastQC tool.

treatment_protocol: Same samples also were differentiated into iDA under EMF (0,4 Telsa) since day 0 of the dopaminergic differentiation.

value: IDA derived from hiPSC

value: with EMF


title: LSK cells, 2105-1

value: Bone marrow

value: LSK cells


title: Peritoneal macrophages, WT_3

value: peritoneal macrophages

value: 8 weeks

value: wild type


title: LSK cells, 2105-2


title: C41 iDA + EMF treated 1


title: H54 iDA control 3

description: induced dopaminergic neuron (iDA)

value: without EMF


title: AR11_2568_ASC_0

data_processing:
Bases were trimmed to remove bases with low PHRED scores in Partek Genomics Suite.
Trimmed bases were then aligned to human genome hg38 using Partek Genomics Suite.
Gene counts were quantified using HTSeq algorithm with union model in Partek Genomics Suite.
Gene counts were library size and log normalized using the rlog function in DESeq2 (v1.28.1; default parameter) in R.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: InVitro_GeneCounts.normalized.txt: Tab-delimited text file of log2 normalized read counts.

source_name: In vitro differentiated plasma cells

extract_protocol:
Cells were FACS sorted into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research).
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: subject id

tag: culture day

tag: gender

value: Male

tag: race

value: Asian

tag: ethnicity

value: Non-Hispanic

value: Blood

value: Antibody-secreting cells (ASC)


title: Peritoneal macrophages, KO_1


title: Spleen reticular cells from naïve CCL19-EYFP mice

first: Scott

last: Mueller

state: Victoria

address: 792 Elizabeth street

institute: The University of Melbourne

data_processing:
Fastq files were processed using the standard pipeline within Cell Ranger version 3.0.2
Processed in R (version 3.6.3) using edgeR (version 3.28.1) and Seurat (version 3.2.0). Ribosomal genes and retired Entrez Gene IDs were removed and cells expressing Ptprc were filtered out using edgeR. Cells with at least 500 genes and less than 10% mitochondrial genes were retained using edgeR for further analysis in Seurat.
Data were normalized using the SCTransform() function in Seurat. Dimensionality reduction was performed by PCA and UMAP and cell clusters identified using FindNeighbors() and FindClusters() at default resolution. Differentially expressed genes per cluster were identified using FindAllMarkers() or FindMarkers().
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell cluster

source_name: spleen

extract_protocol: Spleen CD45- CD31- Ter119- cells that expressed at least one of the markers CD157, PDPN and EYFP were flow cytometrically sorted and encapsulated into emulsion droplets using a Chromium Controller (10x Genomics) and libraries prepared. scRNA-seq libraries were constructed using Chromium Single Cell 3' v3 Reagent Kit according to the manufacturer’s protocol. Cells were examined under a microscope and counted with a hemocytometer before loading. Libraries were run on the HiSeq2500 for 100 bp paired end Illumina sequencing.

tag: strain background

tag: genotype/variation

value: Ccl19-cre x R26R-EYFP

value: spleen


title: H42 iDA control 2

description: induced dopaminergic neuron (iDA)

tag: treatment


title: Peritoneal macrophages, WT_2


title: Peritoneal macrophages, KO_3


title: Roots, Input control 1

description:
control_peak.txt
a1C

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: 1 month-old seedling

tag: treatment time

value: 24 hours

tag: tissue

value: root

tag: type

value: input

tag: rip antibody


title: Peritoneal macrophages, KO_2

tag: strain

tag: cell type

tag: age

tag: genotype


title: H41 iDA control 1

description: induced dopaminergic neuron (iDA)

value: IDA derived from hiPSC


title: Roots, Input control 2

description:
control_peak.txt
a2C

value: water


title: C54 iDA + EMF treated 3

value: with EMF