title: NPC H2B-Dam-NoLS repl2

description: ESCsp_to_NPC_NADs_genomic_coordinates.xlsx

data_processing:
Library strategy: DamID-seq
Fastaq files were aligned to the mm10 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
The bam files were analyzed using the damidseq pipeline script from the Brand group (http://owenjm.github.io/damidseq_pipeline) (Marshall and Brand, 2015). The pipeline bins the mapped reads into GATC-fragments according to GATC-sites indicated by a gff file for the GRCm38 mouse genome (already provided by the authors of the pipeline on the website above) and normalizes reads against the Dam control, in our case the H2B-Dam sample. The pipeline gives a bedgraph file with the log2 ratio of the m6A between H2B-Dam-NoLS and the H2B-Dam only.  The bedgraph files were processed with the find_peaks software associated with the pipeline (https://github.com/owenjm/find_peaks) adjusting the values of the FDR and the minimum quantile (FDR <0.01 and min_quant 0.70). Only the significative peaks common to both replicates were considered as NADs for further analysis. The intersection of identified NADs and previously published lamina associated domains (LADs, Peric-Hupkes et al., 2010) results in the classification of NADonly, NAD/LAD, and LAD.
for ChIP seq data,read counts were computed and normalized using “bamCoverage” from deepTools (version 3.2.1) using a bin size of 50bp.
for RNA SEQ, reads were aligned to the reference genome (ensembl version 82) with Subread (i.e. subjunc, version 1.4.6-p4; 50) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount 51 with an allocation distance of 100 bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Genome_build: mm10

extract_protocol:
DNA extracted using Quick-DNA Miniprep Plus kit (Zymo Research).
DamID seq was performed on H2B-Dam and H2B-Dam-NoLS Doxycycline and Shield1-induced samples adapting the previously described protocol to work with Next Generation sequencing (Vogel et al., 2007). Briefly, 500ng of gDNA previously extracted with Quick-DNA Miniprep Plus kit (Zymo Research) was digested for 4h at 37°C with DpnI (New England Biolabs) to cut methylated GATC sites. After heat inactivation for 20 minutes at 80°C, DamID adaptors (Vogel et al. 2007) were blunt-end ligated overnight at 16°C and then heat inactivated at 65°C for 10 minutes. In order to cut unmethylated GATC sequences, DNA was digested for 3h at 37°C with DpnII (New England Biolabs) and heat inactivated at 65°C for 20 minutes. Adaptor-ligated fragments were amplified using the Advantage® GC 2Polymerase mix (Clontech Takara) (primer described in Table MM, Vogel et al., 2007). DamID libraries were purified using Agencourt AMPure XP beads (Beckam Coulter). Since the size of fragments produced exceeded the one fitting the sequencing machine, the libraries were fragmented using the ds Fragmentase (New England Biolabs) to enrich the concentration of the libraries below 500bp and, afterwards, the libraries were purified again using the Agencourt AMPure XP beads (Beckam Coulter). The quantity and quality of the isolated DNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA). The Nugen Ovation Ultra Low Library Systems (Nugen, Inc, California, USA) to prepare the libraries for Illumina sequencing. Briefly, Nucleolar-DamID samples (1 ng) were end-repaired and polyadenylated. Then, Illumina compatible adapters, containing the index for multiplexing, were ligated. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA) the sequencing was performed as single end 150bp reads using the Illumina NovaSeq 6000.

treatment_protocol: H2B-Dam and H2B-Dam-NoLS cell lines on the 8th day of differention in NPC were harvested with 10X trypsin to get single cells from the embryoid bodies. 1 x 106 cells Neural progenitor cells were seeded in 6-well plates coated with 0.1% gelatin and treated with 100ng/ml Doxycycline and 1µM Shield1 (Clontech Takara) for 15h.

value: 100ng/mL doxycycline + 1uM Shield1 for 15h


title: X62_LCP0029_B

status: Public on Aug 11 2021

type: SRA

city: Bethesda

first: Amanda

last: Craig

state: Maryland

address: 37 Convent Dr. Bld.37/Rm.3044

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt [1] before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR [2]. Mapping statistics were calculated using Picard (2.18.26). Quantification was performed with RSEM [3]. Normalized counts were log transformed for downstream analysis.
Genome_build: HUMAN - hg38
Supplementary_files_format_and_content: csv; Gene expression matrix

molecule: total RNA

organism: Homo sapiens

source_name: Liver

extract_protocol: RNA was extracted from 58 total samples. Library preparation and sequencing were performed at the Clinical Cancer Research Sequencing Facility at the Frederick National Laboratory for Cancer Research, NCI. Libraries were constructed using TruSeq Stranded Total RNA Library Prep using the manufacturer’s recommendations. Sequencing was performed on 150bp paired end reads on an Illumina NovaSeq platform.  Libraries for four samples with low RNA concentration were constructed using NEBnext Ultra Low Input Total RNA Prep using the manufacturer’s recommendations. Sequencing was performed on 75bp paired end reads on an Illumina NextSeq platform.

tag: tag

value: Non-tumor


title: ctr9-2_NETseq

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: nascent RNA isolated by IP against Rpb3-3x FLAG affinity label

data_processing:
Library strategy: NET-seq
For NET-seq, libraries were sequenced in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts. Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. Only the position corresponding to the 5’ end of the sequencing read (after removal of the barcode), which corresponds to the 3’ end of the nascent RNA fragment, is recorded with a custom python script using HTSeq package in python.
For ChIP-nexus, all reads were filtered for the presence of the fixed barcode (CTGA), beginning at position 6 of the read. Next, the adapter sequence was trimmed using cutadapt with the following parameters: cutadapt -f fastq -a AGATCGGAAGAGCACACGTCT -O 3 -m 22 --length-tag ‘length=’. Lastly, before alignment to the genome, the molecular barcode was removed using custom python scripts. As the ChIP-nexus samples were spiked with S. pombe, the reads were aligned to a combined genome containing both the S. cerevisiae and S. pombe genomes. Reads were aligned using Bowtie version 1.1.1 (Langmead et al., 2009) with the following parameters: -v 2 -M 1 --best -S. Plus and minus strand coverage were then combined and coverage files were then generated using BEDtools version 2.23.0 with the following parameters: genomeCoverageBed -d -5. Only the 5’ end of the read, which corresponds to the point of crosslinking is recorded. The S. cerevisiae and S. pombe data were then separated and S. cerevisiae coverage files were normalized by the total number of mapped S. pombe reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph with 4 columns: Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
For NET-seq, frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). For ChIP-nexus cells were crosslinked in 1% formaldehyde, lysed by bead beating, and sonicated. Chomatin was isolated via immunoprecipitation using antibodies: for H3 (Abcam, ab1791), H4 (Abcam, ab10158), H3K23Ac (Millipore, 07-355), and H4K12Ac (Millipore, 07-595), IPs, 12 µg of each antibody were added to 100 µL of Protein G Dynabeads (Thermo Fischer Scientific) previously washed 3 times with 1 mL of 0.5% BSA in PBS.
For NET-seq, a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads. Preparation of ChIP-nexus libraries was done as described in (He et al., 2015) with the following modifications made to adapt the protocol to yeast: Frozen cell pellets were thawed on ice 1600µL of LB 140 (50 mM HEPES pH 7.4, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1X protease inhibitors (Roche, cOmplete EDTA free)) was added to the pellet. The samples were then split into two screw-cap tubes and acid-washed glass beads (Sigma) were added to the meniscus. Cells were lysed by bead beating for a total of 8 minutes, beating for 1 minute at 4˚C followed by resting for 2 minutes on ice. Chromatin was then removed from the tubes by using a 25G needle to pierce the bottom of the tube. The tubes were then placed inside a 15 mL conical and spun for 1 minute at 1000 xg at 4˚C. The samples were then transferred to a 1.5 mL eppendorf tube and spun at 14,000 rpm for 5 minutes at 4˚C. Pellets were next washed in 800 µL of LB 140 and collected again by centrifuging at 14,000 rpm for 5 minutes at 4˚C. 800 µL of LB 140 was added to the sample and the suspension was transferred to a 15 mL polystyrene tube. 600 µL of LB 140 was used to wash the empty eppendorf tube and then added to the 15 mL tube. Chromatin was then sonicated using Diagenode Bioruptor. Six cycles of sonication were done, each for 5 minutes and 30 seconds ON and 30 seconds OFF for a total sonication time of 15 minutes. After sonication, the chromatin was spun at 20,000 xg for 20 minutes at 4˚C. The supernatant was transferred to a new tube and the concentration of the chromatin was assayed by a Modified Lowry assay (Pierce). The size of the sonicated chromatin was confirmed on a 1.5% agarose gel to be between 100 - 400 bp. For each IP, 3 mg of chromatin extract was used, spiked with 5% (by protein concentration) of S. pombe chromatin. Samples were diluted up to 10 mL using WB 140 (50mM HEPES pH 7.4, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate). For H3 (Abcam, ab1791), H4 (Abcam, ab10158), H3K23Ac (Millipore, 07-355), and H4K12Ac (Millipore, 07-595), IPs, 12 µg of each antibody were added to 100 µL of Protein G Dynabeads (Thermo Fischer Scientific) previously washed 3 times with 1 mL of 0.5% BSA in PBS. After the final was, the supernatant was removed and the chromatin was added to the beads in a 15 mL conical tube. Samples were incubated overnight at 4˚C with rotation. The remainder of the library construction was done exactly as described in (He et al., 2015). The only modifications were changes made to the four wash buffers to adapt them to yeast. Wash buffer A consisted of 10mM TE and 0.1% Triton X-100. Wash buffer B consisted of 50mM HEPES pH 7.4, 140mM NaCl, 1mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate. Wash buffer C is the same as wash buffer B, but with 250mM NaCl. Wash buffer D consisted of 10mM Tris pH 7.5, 250 mM lithium chloride, 10 mM EDTA, 0.5% NP40, 0.1% sodium deoxycholate.

tag: strain

tag: genotype/variation

value: RPB3::RPB3-3xFLAG NAT, CTR9::HIS3

tag: rna fraction

value: Nascent RNA

tag: ip

value: IP against 3xFLAG affinity label


title: ctr9-1_NETseq


title: pDC-depleted_H630Y_Br2_COV2

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

description:
pDC-depleted_H630Y_Br2_COV2
pDC-depleted_gene_expression.txt

data_processing:
quality check by fastqc
alignment by STAR
read count by FeatureCounts
normalization by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: text, normalized and log2-transformed read counts

source_name: pDC-depleted

extract_protocol:
RNeasy Micro kits
SMART-Seq® v4 PLUS Kit

treatment_protocol: non-stimulated, CpG-C, SARS-CoV-2

tag: age

tag: gender

value: male

value: healthy

tag: stimulation


title: NPC H2B-Dam-NoLS repl1

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Neural progenitors cells

growth_protocol: Neural progenitor cells were generated from ESCs, according to a previously established protocol (Bibel et al., 2004) using a suspension-based embryoid bodies formation (Bacteriological Petri Dishes, Bio-one with vents, Greiner). The neural differentiation media (DMEM, 10% fetal calf serum, 1× MEM NEAA, Pen/Strep, β-mercaptoethanol, Sodium Pyruvate) was filtered through 0.22 μm filters and stored at 4°C. During the 8-day differentiation procedure, media was exchanged every 2 days. In the last 4 days of differentiation, the media was supplemented with 2 μM retinoic acid to generate neural precursors that are Pax-6-positive radial glial cells.

tag: cell line

value: NPC derived in vitro from E14

tag: antibody

tag: treatment


title: X71_LCP0034_AR

value: Margin


title: NPC H2B-Dam repl2


title: pDC-depleted_H630Y_Br1_NS

description:
pDC-depleted_H630Y_Br1_NS
pDC-depleted_gene_expression.txt

value: NS


title: X57_LCP0026_AR


title: pDC-depleted_H630Y_Br1_LPS

description:
pDC-depleted_H630Y_Br1_LPS
pDC-depleted_gene_expression.txt

value: LPS


title: chd1-4_NETseq

value: RPB3::RPB3-3xFLAG NAT, CHD1::HIS3


title: NPC H2B-Dam repl1


title: chd1-3_NETseq


title: dhh1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, DHH1::HIS3


title: X55_LCP0025_AR


title: pDC-depleted_H630Y_Br2_LPS

description:
pDC-depleted_H630Y_Br2_LPS
pDC-depleted_gene_expression.txt


title: X52_LCP0024_AR


title: pDC-depleted_H630Y_Br1_COV2

description:
pDC-depleted_H630Y_Br1_COV2
pDC-depleted_gene_expression.txt


title: rd10 B6.CXB1-Pde6brd10/Jrd10+ GSK2879552 replicate2 [G764.10_rd10_GSK]

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0) allowing no mismatches in the index read. BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (release 67: "Mus_musculus.Ensembl.NCBIM37.67.gtf"). EdgeR was used to fit the read counts to the negative binomial model along with generalized linear model (GLM) and differentially expressed genes were determined by the likelihood ratio test method implemented in the edgeR package. Significance was defined to be those with q-value < 0.05 calculated by the Benjamini-Hochberg method to control the false discovery rate (FDR) and log2 fold change is greater than 1 or smaller than -1.
Genome_build: mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)
Supplementary_files_format_and_content: csv file containing raw read counts for each sample

growth_protocol: Mice were purchased from Jackson laboratory and housed in a room with an ambient temperature of 25 C, 30–70% humidity, a 12-h light–dark cycle, and ad libitum access to rodent chow

extract_protocol:
Right eye retina from each animal was flash frozen in liquid nitrogen and stored at -80oC. RNA extraction and purification was done with RNeasy Mini Kit and RNA shredder (Qiagen). RNA integrity number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit to confirm RIN above 7 for each sample.
The cDNA libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing.

treatment_protocol: Mice were treated daily with intraperitoneal injections (i.p.) of  GSK2879552 (GSK) at 4.2mg/kg or saline as control. GSK was diluted in 0.9% bacteriostatic sodium chloride (saline).

tag: strain background

value: rd10 B6.CXB1-Pde6brd10/Jrd10

value: GSK daily ip injection from PN9 till PN24

tag: tissue

value: retina at PN24


title: pDC-depleted_H630Y_Br1_CpG

description:
pDC-depleted_H630Y_Br1_CpG
pDC-depleted_gene_expression.txt

value: CpG


title: rd10 B6.CXB1-Pde6brd10/Jrd10+ GSK2879552 replicate3 [G764.11_rd10_GSK]


title: pDC-depleted_H630Y_P1_NS

description:
pDC-depleted_H630Y_P1_NS
pDC-depleted_gene_expression.txt


title: X49_LCP0023_AR


title: rd10 B6.CXB1-Pde6brd10/Jrd10+ GSK2879552 replicate1 [G764.09_rd10_GSK]


title: pDC_H781L_P1_NS

description:
pDC_H781L_P1_NS
pDC_gene_expression.txt

source_name: pDC


title: X33_LCP0017_AR


title: cdc73-4_NETseq

value: RPB3::RPB3-3xFLAG NAT, CDC73::HIS3


title: cdc73-3_NETseq


title: rd10 B6.CXB1-Pde6brd10/Jrd10 replicate3 [G764.08_rd10_cont]

source_name: rd10 B6.CXB1-Pde6brd10/Jrd10

value: saline daily ip injection from PN9 till PN24


title: pDC_H781L_P1_CpG

description:
pDC_H781L_P1_CpG
pDC_gene_expression.txt


title: X27_LCP0015_AR


title: chd1-2_NETseq


title: cdc73-1_NETseq


title: C57Bl/6J + GSK2879552 replicate 3 [G764.05_B6_GSK]

value: wild type


title: pDC_H781L_P1_COV2

description:
pDC_H781L_P1_COV2
pDC_gene_expression.txt


title: X23_LCP0014_AR


title: rd10 B6.CXB1-Pde6brd10/Jrd10 replicate2 [G764.07_rd10_cont]


title: pDC_H781L_M_NS

description:
pDC_H781L_M_NS
pDC_gene_expression.txt

value: female


title: rd10 B6.CXB1-Pde6brd10/Jrd10 replicate1 [G764.06_rd10_cont]


title: X20_LCP0013_AR


title: chd1-1_NETseq

value: Nascent RNA

value: IP against 3xFLAG affinity label


title: pDC_H781L_M_CpG

description:
pDC_H781L_M_CpG
pDC_gene_expression.txt

value: healthy


title: cdc39-1_NETseq

value: RPB3::RPB3-3xFLAG NAT, CDC39::HIS3


title: C57Bl/6J + GSK2879552 replicate 1 [G764.03_B6_GSK]


title: X18_LCP0012_AR

value: Margin


title: C57Bl/6J + GSK2879552 replicate 2 [G764.04_B6_GSK]


title: ccr4-1_NETseq

value: RPB3::RPB3-3xFLAG NAT, CCR4::HIS3


title: X14_LCP0010_AR


title: X4_LCP0007_AR


title: cbc1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, CBC1::HIS3


title: pDC_H630Y_P1_NS

description:
pDC_H630Y_P1_NS
pDC_gene_expression.txt

value: male

value: NS


title: cbc1-3_NETseq


title: pDC_H630Y_P1_CpG

description:
pDC_H630Y_P1_CpG
pDC_gene_expression.txt


title: pDC_H781L_M_COV2

description:
pDC_H781L_M_COV2
pDC_gene_expression.txt


title: controls C57Bl/6J replicate1 [G764.01_B6_cont]

source_name: controls C57Bl/6J


title: cdc39-2_NETseq


title: X39_LCP0019_AR


title: bye1-1_NETseq

value: RPB3::RPB3-3xFLAG NAT, BYE1::HIS3


title: GSK/FGF-5

city: Oklahoma City

first: Rachel

last: Sharp

state: OK

address: 975 NE 10th St.

institute: University of Oklahoma

data_processing:
Quality trim to a minimum of Q15
Map to the mm10 genome using GSNAP version 2014-12-17 using the commandline gsnap -D $GMAPDB -d mm10_total -v mm10_total.snp138 --use-splicing=mm10_total.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $file > ./${j}.sam
sort and index using SAMTOOLS
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to anti-sense genes, and sense reads to sense genes
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing FPKM values

source_name: liver tissue

extract_protocol:
Trizol was used to extract total liver mRNA
RNA seq libraries were built using Lexogen's QuantSeq 3' mRNA-Seq FWD kit and established protocols.
3' mRNA-Seq

treatment_protocol: 1X10^11 GC AAV8-TBG-FGF15 or AAV8-TBG-Null were injected via tail vein. GSK2330672 was mixed with diet to achieve a ~8 mg/kg daily dose.

value: Male C57BL/6J

tag: diet

value: 32 weeks HFCFr diet


title: GSK/FGF-4


title: pDC_H630Y_P1_COV2

description:
pDC_H630Y_P1_COV2
pDC_gene_expression.txt


title: pDC_H630Y_Br2_NS

description:
pDC_H630Y_Br2_NS
pDC_gene_expression.txt


title: cbc1-1_NETseq


title: X2_LCP0006AR


title: pDC_H630Y_Br2_CpG

description:
pDC_H630Y_Br2_CpG
pDC_gene_expression.txt

value: CpG


title: GSK/FGF-3


title: X11_LCP0009_AR


title: controls C57Bl/6J replicate2 [G764.02_B6_cont]

value: retina at PN24


title: bur2-1_NETseq

value: RPB3::RPB3-3xFLAG NAT, BUR2::HIS3


title: pDC_H630Y_Br2_COV2

description:
pDC_H630Y_Br2_COV2
pDC_gene_expression.txt


title: GSK/FGF-2


title: cdc73-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, CDC73::HIS3


title: X68_LCP0032_AR


title: X60_LCP0027_AR


title: X63_LCP0029_AR


title: Man1a2 heterozygous dead NAC liver [NHD_Liver_SIN238A15_S58]

city: La Jolla

first: Kim

last: Ngo

state: CA

address: 9500 Gilman Drive #0412

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
Illumina Novaseq reads were demultiplexed and were trimmed to filter out low-complexity reads, polyA tails, N runs
High-quality reads were then aligned to Ensembl mouse reference genome (Mouse.B38) using Omicsoft Sequence Aligner (OSA) on ArrayStudio (version 10.1), with index built to Ensembl genome for cDNA and ncRNA genome sequences.
Uniquely mapped and quantified transcript abundances from OSA output were imported into R software (version 4.0.3) for downstream differential gene expression analysis. Differential expression analysis of raw count data was performed using edgeR package (version 3.30.3) and differentially regualted genes in NAC-treated offspring were identified using two criteria: under the exactTest with dispersion set to biological coefficient of variation (bcv) to 0.2 method and absolute log2 fold-change is greater or equal to 1 compared to placebo-treated offspring.
Genome_build: mm10
Supplementary_files_format_and_content: TXT, raw non-normalized counts

molecule: polyA RNA

source_name: liver

growth_protocol: Newborn pups were monitored for survival every 8 hours for a total of 24 hours. Newborn pups that died within 24 hours were harvested immediately for liver and lung tissues. Surviving newborn pups were euthanized by decapitation with scissors. The lung and liver tissues were preserved in RNA later (Qiagen, Valencia, CA) for RNA extraction.

extract_protocol:
Total RNA in the lung and liver tissue was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) from 3 independent experiments per for alive Wild-type, alive Man1a2 heterozygous and dead Man1a2 null, and 2 independent experiments for dead Man1a2 heterozygous pups.
Purified RNA was subjected to library synthesis using Illumina Truseq stranded mRNA kit. Purified RNA was fragmented using divalent cations under elevated temperature, and fragments copied into first stand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. Aftering adding a single 'A' base, cDNA was ligated to the adapter, purified and enriched with PCR to create the final cDNA library. Libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer. Quality of libraries was examined using Agilent Bioanalyzer Tapestation 2200 and final libraries were pooled at a final concentration of 1.8 pM. Cluster generation and 150bp paired read dual-indexed sequencing was performed on Illumina Novaseq to obtain 20 million reads.

treatment_protocol: Man1a2 heterozygous male and female mice were fed with NAC solution (1g/kg body weight) or with placebo (water) one week prior to breeding and continued until delivery of offspring.

tag: genotype

value: Man1a2 Het mutant

value: N-acetyl cysteine (NAC)

value: liver


title: GSK/FGF-1


title: bre1-2_NETseq

value: RPB3::RPB3-3xFLAG NAT, BRE1::HIS3

value: Nascent RNA

value: IP against 3xFLAG affinity label


title: bre1-3_NETseq


title: pDC_H630Y_Br1_CpG

description:
pDC_H630Y_Br1_CpG
pDC_gene_expression.txt

value: healthy


title: DNAseq of Arabidopsis: ddm1-1_nrpd1_rep2

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

data_processing:
For RNA-seq data, low-quality sequences and adaptors were trimmed using Trimmomatic. Clean reads were mapped to the reference genome by TopHat with the parameter "-g 1". The total number of reads mapping to each gene was calculated with the htseq-count script in HTSeq with the parameter “--nonunique all”, to minimize over-estimation of TE expression caused by overlapping genes; read counts for each TE were calculated by htseq-count with parameters "--nonunique all  -m intersection-strict" based on the TE-only annotation. Genes and TEs with a normalized expression level of at least one count per million mapped reads (CPM) in three or more libraries were considered as expressed. Principle component analysis (PCA) based on the transcript levels of the expressed protein-coding genes and TEs was performed using the prcomp function in R software with default settings. Differentially expressed TEs with at least a 2-fold change in expression and an FDR < 0.05 were identified by the R package edgeR using the trimmed mean of M-values (TMM) method.
For methylation data, low-quality sequences and adapters were trimmed using Trimmomatic with parameters “LEADING: 3 SLIDINGWINDOW: 4: 30 MINLEN: 36”, and clean reads were mapped to the A. thaliana TAIR 10 genome using Bisulfite Sequence Mapping Program (BSMAP) with parameters “-v 2 -S 1” which allowing 2 mismatches. The methratio.py script from BSMAP with parameters “-r -z -p -m 1” was used to extract the methylation ratio from mapping results; only mapped reads after deduplication were considered for subsequent analyses.
For ChIP-seq data analysis, around 15.2 million raw paired-end reads were obtained for each sample and subsequently cleaned by Trimmomatic. Clean reads were mapped to the reference genome by Bowtie2 using the parameter "--very-sensitive --no-unal --no-mixed --no-discordant -k 2". Subsequently, uniquely mapped reads were selected and marked as duplicates using the Picard tool followed by using the SAMtools “rmdup” command. Coverage of deduplicated reads was normalized to 1 × sequencing depth by bamCoverage in deepTools with parameters "--normalizeUsing RPGC --exactScaling -bs 10".
Identification of non-reference TE insertions with TSDs (Target Site Duplications) was conducted using SPLITREADER with some modifications.
Genome_build: TAIR10
Supplementary_files_format_and_content: methylation wig files, RNA-seq coverage bedgGraph, ChIP-seq BigWig files

organism: Arabidopsis thaliana

source_name: rosette leaf

growth_protocol: Arabidopsis seeds were plated on 1/2 Murashige and Skoog (MS) medium with 0.6% agar and 1.5% sucrose and stratified for 7 days at 4℃ in darkness before being transferred to the growth chamber (16 h light/8 h dark, 22℃). Then, the 2-week-old seedlings were transplanted to soil for growth 1 week in growth chamber (16 h light/8 h dark, 22℃).

extract_protocol:
Genomic DNA was extracted from rosette leaf of three-week-old plants using the DNeasy Plant Maxi kit (Qiagen).
Library construction and sequencing were performed at the PSC Genomics Core Facility.

value: three-week-seedling

value: rosette leaf


title: bre1-1_NETseq

description: nascent RNA isolated by IP against Rpb3-3x FLAG affinity label


title: KYSE150_siRNA1_rep2

city: Guangzhou

first: Yongsheng

last: Huang

address: 107 Yan Jiang West Road

country: China

institute: Sun Yat-Sen University

data_processing:
Reads were aligned to the genome using HISAT2 (v2.0.4),using parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000 ( Kim, D.et al., 2015), and Bowtie2 (v2.2.5) with the default parameter settings.
RSEM (v1.2.12) and DESeq (v3.4) was used for differential gene expression analysis with the default parameter settings.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files - tab-delimited files containing count and RPKM values for RefSeq genes in each sample, and fold change as well as p values relative to the control group.

source_name: Esophageal squamous cells

extract_protocol:
Total RNA was extracted from cell lines using Trizol reagent (Invitrogen) and purified using the RNAeasy Plus kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The siRNA that target CEBPG was transfected in KYSE150 cell line.

value: knockdown CEBPG by siRNA

tag: cell type

value: Esophageal squamous cells


title: X46_LCP0021_A

value: Tumor


title: X47_LCP0022_AR

value: Margin


title: KYSE150_Control_rep2

value: Negative control


title: X8_LCP0008_AR


title: X43_LCP0020_A


title: X34_LCP0017_A


title: pDC_H630Y_Br1_NS

description:
pDC_H630Y_Br1_NS
pDC_gene_expression.txt

value: male

value: NS


title: Pt21_PBMCs

first: Tim

last: Greten

address: 9000 Rockville Pike

department: National Cancer Institute

data_processing:
Targeted capture libraries were prepared using BD Rhapsody Single-cell Analysis System according to manufacturer’s recommendations ((BD Biosciences). Libraries were pooled and sequenced on NextSeq 550 using pair-end runs (R1:76bps, R2:76bps). The demultiplex of sequencing run was performed using Illumina bcl2fastq version2.17. One mismatch in sample barcodes was allowed to tolerate sequencing error or PCR errors. The average sequencing yield was about 133 million raw reads per sample and these reads were stored in FASTQ format.  The FASTQ-formatted files were processed using the standard Rhapsody analysis pipeline version 1.3 on Seven Bridges (https://www.sevenbridges.com). Mate pairs in which either read was too short or too low in sequencing quality were first removed (if Read1 <66bp or Read2 < 64bp or base call quality score is less than Q20 in either mate). In addition, reads with low complexity such as strings of identical bases and tandem repeats were removed. After filtering, the average total reads remaining per sample was about 125 million reads for scRNA-seq samples and 58 million reads for AbSeq samples. Cell barcodes and unique molecular identifiers (UMIs) were extracted from R1 reads. R2 reads were mapped to reference sequences (Immune Amplicons reference for mRNA-seq and AbSeq reference for AbSeq) using Bowtie2 [9]. The percentages of uniquely aligned reads were between 70% - 90% for each sample. A mate pair was retained if and only both reads survived the above filtering and both reads mapped uniquely.  Finally, all valid R1 and R2 reads were combined and annotated to the respective molecules by applying both recursive substation error correction (RSEC) for collapsing molecules with one base difference in UMIs as well as distribution-based error correction (DBEC) algorithms to remove PCR errors in the UMI sequences from BD Rhapsody analysis pipeline
Genome_build: HUMAN - hg38
Supplementary_files_format_and_content: csv; Gene expression matrix

extract_protocol: Single cell gene expression and protein expression analyses were done using BD Rhapsody Single cell analysis platform following manufacturer’s suggested protocol. Briefly, BD cartridge was primed with air, and washing buffers. Freshly isolated and flow sort enriched ILC populations of 1000-10000 single cells were resuspended in sample buffer (BD Biosciences) before loading onto microwells on the BD Rhapsody cartridges. Cartridge and cells were incubated for 15 minutes and cells were scanned in the cartridge. Cell capture beads were loaded onto the cartridge and incubated with the sample following the protocol. Two washing steps were performed before another imaging step. Next, cell lysis buffer was added to the samples and incubated for 2 min. After incubation on the large magnet, reverse transcription was performed (25min). A targeted panel of primers was used for library preparation

value: PBMCs


title: Pt63_Tumor


title: KYSE150_Control_rep1


title: FGF-5

value: Male C57BL/6J

value: 32 weeks HFCFr diet


title: pDC_H630Y_Br1_COV2

description:
pDC_H630Y_Br1_COV2
pDC_gene_expression.txt


title: FGF-1


title: KYSE150_siRNA1_rep1


title: X61_LCP0027_A


title: X15_LCP0010_A


title: GSK-4

value: AAV8-TBG-Null + GSK2330672


title: Pt21_Non-tumor

value: Non-tumor


title: FGF-2


title: Pt21_Margin


title: GSK-2


title: X3_LCP0006_A


title: Pt21_Tumor


title: Pt20_PBMCs


title: FGF-4


title: GSK-5


title: Null-5


title: Pt20_Margin


title: Pt20_Tumor


title: GSK-3


title: GSK-1


title: X64_LCP0029_A


title: Pt19_Non-tumor


title: Null-3


title: Pt19_PBMCs


title: X69_LCP0032_A


title: X12_LCP0009_A


title: Null-4


title: OMO+DOX_4

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

data_processing:
RNA-Seq reads were trimmed using Trim Galore software to remove adapter sequences and low-quality end bases; the minimum read length after trimming was set to 20
STAR was employed to align reads to Genecode Human release 32 primary assembly. More than 90% of the reads were successfully mapped to the human genome most of them were aligned to unique locations
The --quantMode TranscriptomeSAM option was used to generate alignments translated into transcript coordinates. The expression levels of transcripts and genes were quantified by using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each Sample

source_name: medulloblastoma-derived cell line

growth_protocol: culture medium for D283 Med

extract_protocol:
Qiagen miRNeasy mini kit
TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: OMOMYC induction by doxycycline treatment for 72hrs

value: D283 Med medulloblastoma cell line

value: MYC-inhibited

tag: myc inhibitor

value: OMOMYC


title: X21_LCP0013_A

tag: tag


title: X9_LCP0008_A


title: FGF-3

tag: strain


title: OMO+DOX_2


title: Null-2


title: Pt19_Tumor


title: Pt17_PBMCs


title: Pt20_Non-tumor


title: Pt19_Margin


title: Pt17_Margin


title: OMO_3

value: untreated


title: OMO+DOX_1


title: OMO+DOX_3


title: Chow-3

value: 32 weeks chow diet


title: OMO_4


title: Null-1


title: Chow-5


title: OMO_2


title: Chow-1


title: Pt10_Non-tumor


title: Pt17_Tumor


title: Chow-2


title: OMO_1


title: Chow-4


title: Pt10_PBMCs


title: Pt17_Non-tumor


title: Hypothalamus, control rep4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.39 parameters:ILLUMINACLIP:PE_adapters.fa:2:30:10 RAILING:20
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 95 derived splice sites (--known-splicesite-infile)
mapped read were stired as position sorted bam files by directly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb95.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed file is a count matrix containing the counts output from featurecounts for all samples

source_name: hypothalamus

growth_protocol: Mice were housed in a temperature-controlled, specific pathogen free (SPF) air-conditioned animal house with 14 and 10h light/dark cycles and received food and water ad libitum

extract_protocol:
Total RNA was isolated with Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
The 2h library was constructed using the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: mice were placed in a hypoxic chamber end exposed to 7% oxygen (93% nitrogen) for 2 hours (hypoxia group), or kept in normal conditions (normoxia group). Mice were sampled after 2 hours.

value: 21% O2 for 2 hours

value: hypothalamus


title: RNA-seq_INH-treated_rep2

city: Beijing

first: Hongquan

last: Zhang

address: #38 Xue Yuan Road

department: Human Anatomy, Histology and Embryology

institute: Peking University

data_processing:
The library preparations were sequenced on an illumina NovaSeq 6000 platform and 150bp paired-end reads were generated.
Align Reads to the Reference Genome, we took the GRch38 genome as the reference genome for this project. Sequencing reads were aligned to the reference genome sequence using Tophat2 (v2.1.1) and bowtie2 (v2.2.2) in default parameter.
Genes and isoforms expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization v1.3.0).
RSEM computes maximum likelihood abundance estimates using the Expectation-Maximization (EM) algorithm as its statistical model.
EdgeR (v3.6.8) package method was used for screening differentially expressed genes. GSEA analysis of KEGG pathway was implemented using the Diamond (v0.8.33) package.
Genome_build: GRch38
Supplementary_files_format_and_content: CSV files include FPKM values for each Sample is provided in expresion_matrix.csv.

source_name: Cultured cells

growth_protocol: Cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNAs were extracted by TRIZOL reagent (Invitrogen) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the treatment group, cells were treated with 10 mM INH for 12 hours before harvesting

value: treated with 10mM INH for 12 hours


title: Pt10_Margin

value: Margin


title: Hypothalamus, control rep2


title: RNA-seq_INH-treated_rep3


title: RNA-seq_control_rep3


title: Pt10_Tumor

value: Tumor


title: Hypothalamus, control rep1


title: Pt06_Margin


title: RNA-seq_control_rep1


title: X59_LCP0027_B


title: Pt06_Tumor


title: Dual-RNA-48hr-4

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

description:
mRNA after ribo zero gold rRNA depletion
OA31

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped  to the reference genome Mouse: UCSC/mm10 using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
Reads were mapped  to the reference genome Yersinia pestis CO92 (NC_003143,NC_003131, NC_003132, NC_003134) using bowtie2 (2.2.0) and htseq-count 0.6.1
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

source_name: Mouse lungs collected 48 hour post intranasal infection

growth_protocol: Yersinia pestis Kimberly53 strain were used for intranasal infection. Bacterial cultures were grown at 28◦C overnight in HIB (BD, MD USA), supplemented with 0.2% (+) xylose and 2.5 mM CaCl2 (Sigma-Aldrich). The bacteria were used for intranasal infection of mice (OF1 strain).

extract_protocol:
One, 24 and 48 hours post infection, mice were sacrificed, lungs were removed and used for RNA extraction. RNA was also extracted from bacteria grown in culture (at 28° and 37° C) and naive mice, as control. Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen). In order to enrich the mRNA bacteria grown in culture (In vitro) we used riboZiro rRNA removal kit for depletion of rRNA, in each sample and ribozero gold rRNA depletion for dual RNA samples (mouse and Y. pestis).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice (OF1)  were infected intranasally with 800,000 cfu/mouse (~1500 LD50).

value: OF1 strain

tag: agent

value: Yersinia pestis Kimberley53

tag: time point

value: 48 hours


title: Hypothalamus, 2h of hypoxia rep4

value: 7% O2 for 2 hours


title: X70_LCP0034_B


title: Hypothalamus, 2h of hypoxia rep1


title: RNA-seq_INH-treated_rep1


title: Dual-RNA-48hr-2

description:
mRNA after ribo zero gold rRNA depletion
OA29


title: Dual-RNA-48hr-3

description:
mRNA after ribo zero gold rRNA depletion
OA30


title: RNA-seq_control_rep2


title: 18_Adult dermal fibroblast

city: Madison

first: Martha

last: Floy

state: Wi

address: 1415 Engineering Hall

institute: University of Wisconsin-Madison

data_processing:
Raw FASTQ files were mapped to the human genome (hg38) using RNA STAR (version 2.7.5b) implemented on the Galaxy public server at usegalaxy.org
Gene-level transcript abundances were calculated using featureCounts (version 1.6.4+galaxy2) in Galaxy
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw counts for every gene for every sample, matrix table with TPM for every gene for every sample

source_name: Adult dermal fibroblast

growth_protocol: Cardiac fibroblasts were grown in TCPS in FibroGRO medium until reaching 80-90% confluency. Primary cell samples were between P1-5. hPSC cardiac fibroblasts were at P1 and the three samples were from three independent differentiations.

extract_protocol:
Cells were singularized in Accutase, quenched, and centrifuged for 5 min at 200g. Cell pellets were snap-frozen at -80°C until mRNA extraction. Total RNA was isolated using the RNeasy mini kit (Qiagen) and treated with DNase (Qiagen).
Quality and quantity of RNA samples was first analyzed using Nanochip to confirm presence of 18S and 28S ribosomal RNA with appropriate A260/A280 and A260/A230 ratios. Then, RNA was quantified on an Agilent 2100 Bioanalyzer using Qubit prior to library construction and sequencing. Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA kit (polyA enrichment).

tag: stem cell line

value: Adult dermal fibroblast

tag: cardiac fibroblast differentiation lineage

tag: sample name

value: dFB 18


title: ESC RNA-seq repl2

data_processing:
Fastq files were aligned to the mm10 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
for RNA SEQ, reads were aligned to the reference genome (ensembl version 82) with Subread (i.e. subjunc, version 1.4.6-p4; 50) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount 51 with an allocation distance of 100 bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Genome_build: mm10
Supplementary_files_format_and_content: ESC_RNAseq_RPKM.csv (RPKM files for each gene of the three relpicates of the RNA seq)

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells were cultured in either 2i media composed of DMEM-F12 and Neurobasal medium (1:1, Life Technologies), supplemented with 1× N2/B27 (Life Technologies), 1× penicillin/streptomycin/l-glutamine (Life Technologies), 50 μM β-mercaptoethanol (Life Technologies), recombinant leukemia inhibitory factor, LIF (Polygene, 1,000 U/ml) and MEK and GSK3β inhibitors, 2i (Sigma CHIR99021 and PD0325901, 3 and 1 μM, respectively). ESCs were seeded at a density of 50,000 cells/cm2 in culture dishes (Corning® CellBIND® surface) coated with 0.1% gelatin without feeder layer. Propagation of cells was carried out every 2 days using enzymatic cell dissociation.

extract_protocol:
Total RNA from three independent mouse ESC colture dishes was purified with TRIzol reagent (Life Technologies). In order to remove DNA contaminants, the samples were treated with 1U DNaseI (Thermo Scientific) for 1h at 37°C and the RNA samples were re-purified using TRIzol. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany).
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit HS4000 (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the NovaSeq 6000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).

value: Embryonic stem cells


title: HTR5-GFP-seedling-GFP

first: Fengyue

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Duplicated reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, bigwig coverage files of HTR5-GFP relative to input (log2 ratio) were generated using deepTools utility bamCoverage with a bin size of 10bp.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw: Normalized HTR5-GFP coverage relative to input (log2 ratio)

source_name: 10-day-old seedlings

growth_protocol: 10-day-old seedlings grown at ~22°C under long-day conditions

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde, followed by nuclei extraction and micrococcal nuclease (MNase) (Sigma,N5386) digestion to generate mononucleosomes. Immunoprecipitation was performed with GFP-trap agarose beads (Chromotek, gta-20).
Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture’s instruction

tag: ecotype

tag: chip antibody


title: Hypothalamus, 2h of hypoxia rep3


title: HTR5-GFP-seedling-Input


title: Pt06_Non-tumor

source_name: Liver

value: Non-tumor


title: 17_Adult dermal fibroblast

value: dFB 17


title: Hypothalamus, 2h of hypoxia rep2


title: X16_LCP0011_B


title: HK-2_RPTEC_24h

city: Kaohsiung

first: Yi-Chun

last: Tsai

address: No.100 , Tzyou 1st Road

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
For small RNA sequencing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
Supplementary_files_format_and_content: excel files include miRNA, raw read counts and normalized values for samples 1 and 2.

source_name: proximal tubular epithelial cells

growth_protocol: HK-2 cells were grown under normoxia and hypoxia conditions and maintained in 37 °C incubator containing 5% CO2 until confluence.

extract_protocol:
total RNAs from HK-2 cells were extracted by Trizol Reagent according to the manufacturer’s instructions.
Small RNA library construction and deep sequencing was carried out using Illumina sample preparation kit, according to the TruSeq Small RNA Sample Preparation Guide.

value: Kidney

tag: cell line

value: proximal tubular epithelial cells

tag: treatmment

value: normoxia


title: X38_LCP0019_B

first: Amanda

address: 37 Convent Dr. Bld.37/Rm.3044

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt [1] before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR [2]. Mapping statistics were calculated using Picard (2.18.26). Quantification was performed with RSEM [3]. Normalized counts were log transformed for downstream analysis.
Genome_build: HUMAN - hg38
Supplementary_files_format_and_content: csv; Gene expression matrix

extract_protocol: RNA was extracted from 58 total samples. Library preparation and sequencing were performed at the Clinical Cancer Research Sequencing Facility at the Frederick National Laboratory for Cancer Research, NCI. Libraries were constructed using TruSeq Stranded Total RNA Library Prep using the manufacturer’s recommendations. Sequencing was performed on 150bp paired end reads on an Illumina NovaSeq platform.  Libraries for four samples with low RNA concentration were constructed using NEBnext Ultra Low Input Total RNA Prep using the manufacturer’s recommendations. Sequencing was performed on 75bp paired end reads on an Illumina NextSeq platform.


title: ESC RNA-seq repl3

tag: treatment


title: 16_Adult dermal fibroblast

value: dFB 16


title: Dual-RNA-48hr-1

description:
mRNA after ribo zero gold rRNA depletion
OA28


title: 14_Adult left ventricular cardiac fibroblast

value: aCFB 14


title: Dual-RNA-24hr-4

description:
mRNA after ribo zero gold rRNA depletion
OA23

source_name: Mouse lungs collected24 hour post intranasal infection

value: 24 hours


title: ESC RNA-seq repl1


title: HK-2_Hypo_R_24h

tag: tissue

value: hypoxia


title: Hypothalamus, control rep3

value: 21% O2 for 2 hours

value: hypothalamus


title: ESC H2B-Dam-NoLS repl2

data_processing:
Library strategy: DamID-seq
Fastq files were aligned to the mm10 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
The bam files were analyzed using the damidseq pipeline script from the Brand group (http://owenjm.github.io/damidseq_pipeline) (Marshall and Brand, 2015). The pipeline bins the mapped reads into GATC-fragments according to GATC-sites indicated by a gff file for the GRCm38 mouse genome (already provided by the authors of the pipeline on the website above) and normalizes reads against the Dam control, in our case the H2B-Dam sample. The pipeline gives a bedgraph file with the log2 ratio of the m6A between H2B-Dam-NoLS and the H2B-Dam only.  The bedgraph files were processed with the find_peaks software associated with the pipeline (https://github.com/owenjm/find_peaks) adjusting the values of the FDR and the minimum quantile (FDR <0.01 and min_quant 0.70). Only the significative peaks common to both replicates were considered as NADs for further analysis. The intersection of identified NADs and previously published lamina associated domains (LADs, Peric-Hupkes et al., 2010) results in the classification of NADonly, NAD/LAD, and LAD.
Genome_build: mm10
Supplementary_files_format_and_content: Coordinates_NADonly_NADsLADs_LADonly.xlsx (coordinates NAD-only, NAD/LAD and LAD-only sequences based on the intersection of NADs identified in this study and LADs identified in Peric-Hupkes et al., 2010), ESC_NADs_Nucleolar-DamID_score.csv (ESC NADs identified with log2 ratio H2B-Dam-NoLS vs H2B-Dam)

extract_protocol:
DNA extracted using Quick-DNA Miniprep Plus kit (Zymo Research).
DamID seq was performed on H2B-Dam and H2B-Dam-NoLS Doxycycline and Shield1-induced samples adapting the previously described protocol to work with Next Generation sequencing (Vogel et al., 2007). Briefly, 500ng of gDNA previously extracted with Quick-DNA Miniprep Plus kit (Zymo Research) was digested for 4h at 37°C with DpnI (New England Biolabs) to cut methylated GATC sites. After heat inactivation for 20 minutes at 80°C, DamID adaptors (Vogel et al. 2007) were blunt-end ligated overnight at 16°C and then heat inactivated at 65°C for 10 minutes. In order to cut unmethylated GATC sequences, DNA was digested for 3h at 37°C with DpnII (New England Biolabs) and heat inactivated at 65°C for 20 minutes. Adaptor-ligated fragments were amplified using the Advantage® GC 2Polymerase mix (Clontech Takara) (primer described in Table MM, Vogel et al., 2007). DamID libraries were purified using Agencourt AMPure XP beads (Beckam Coulter). Since the size of fragments produced exceeded the one fitting the sequencing machine, the libraries were fragmented using the ds Fragmentase (New England Biolabs) to enrich the concentration of the libraries below 500bp and, afterwards, the libraries were purified again using the Agencourt AMPure XP beads (Beckam Coulter). The quantity and quality of the isolated DNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA). The Nugen Ovation Ultra Low Library Systems (Nugen, Inc, California, USA) to prepare the libraries for Illumina sequencing. Briefly, Nucleolar-DamID samples (1 ng) were end-repaired and polyadenylated. Then, Illumina compatible adapters, containing the index for multiplexing, were ligated. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA) the sequencing was performed as single end 150bp reads using the Illumina NovaSeq 6000.

treatment_protocol: 7 x 104 H2B-Dam and H2B-Dam-NoLS mouse ES cell lines were seeded in 6-well plates (Corning® CellBIND® surface) coated with 0.1% gelatin without feeder layer. Two days after seeding half of the cells were treated with 100ng/mL Doxycycline () and 1uM Shield1 (Clontech Takara) for 15h to induce the expression of Dam-fusion proteins.

value: 100ng/mL doxycycline + 1uM Shield1 for 15h


title: input from cells treated with TM

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: input.TM

data_processing:
Library strategy: CUT&RUN
Cut-and-run data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files with default normalization parameters
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain alignment tracks in bigwig format

source_name: A1847 cells

extract_protocol:
cells were harvested by trypsinization, and gently washed twice using wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and EDTA free Protease Inhibitor Cocktail). Cells were then incubated with the antibody at 4°C overnight in antibody buffer (Wash buffer supplemented with 0.05% digitonin and 2 mM EDTA). The next day, supernatant was removed by centrifuge and cell pellets were washed once with Dig-wash buffer (Wash buffer containing 0.05% digitonin). Cell pellets were then incubated with Protein A MNase (700 ng/ml in Dig-wash buffer) for 1 hour by rotation at 4°C. After three times of wash, cell pellets were resuspended in 100 μl Dig-wash buffer with 2 μl 100 mM CaCl2, incubated at 0°C for 30 mins, reactions were stopped by addition of 100 μl 2 x STOP buffer (340 mM NaCl, 20 mM EDTA pH 8.0, 4 mM EGTA, 0.05% digitonin, 50 μg/ml RNase A, 50 μg/ml glycogen). The supernatant DNA was collected after centrifuge and further purified using phenol-chloroform-isoamyl alcohol (Sigma, #145 p3803) extraction and ethanol precipitation.
Purified DNA was used for library construction using NEBNext Ultra DNA Library Prep Kit (NEB, E7645) following the manufacturer’s instructions

value: A1847 cells

tag: factor

value: input

value: TM


title: 11_Fetal cardiac fibroblast

source_name: Fetal cardiac fibroblast

value: Fetal cardiac fibroblast

value: fCFB 11


title: XBP1 binding in cells treated with TM


title: 12_Fetal cardiac fibroblast

value: fCFB 12


title: input from cells in control (TM minus) condition

description: input.ctr

value: control (TM minus) condition


title: Dual-RNA-24hr-3

description:
mRNA after ribo zero gold rRNA depletion
OA22

source_name: Mouse lungs collected 24 hour post intranasal infection

value: OF1 strain

value: Yersinia pestis Kimberley53


title: ESC H2B-Dam repl2

description: Coordinates_NADonly_NADsLADs_LADonly.xlsx

value: Embryonic stem cells


title: Dual-RNA-24hr-1

description:
mRNA after ribo zero gold rRNA depletion
OA20


title: Dual-RNA-24hr-2

description:
mRNA after ribo zero gold rRNA depletion
OA21


title: 15_Adult left ventricular cardiac fibroblast

value: aCFB 15


title: 9_Pluripotent stem cell derived cardiac fibroblast

value: epicardial cell derived

value: EpiC-FB 9


title: XBP1 binding in control (TM minus) condition


title: ESC H2B-Dam-NoLS repl1


title: 10_Fetal cardiac fibroblast

value: fCFB 10


title: CARM1 binding in control (TM minus) condition


title: Dual-RNA-1hr-3

description:
mRNA after ribo zero gold rRNA depletion
OA19

source_name: Mouse lungs collected 1 hour post intranasal infection

value: 1 hours


title: 8_Pluripotent stem cell derived cardiac fibroblast

value: EpiC-FB 8


title: Dual-RNA-1hr-2

description:
mRNA after ribo zero gold rRNA depletion
OA18


title: W-VE-2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3  whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and HISAT software (Kim D, Langmead B and Salzberg SL, Nature Methods, 2015).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium sample

growth_protocol: Strains were grown at 30 °C in Minimal Medium (MM) or Compete Medium (CM) prepared as described previously. All liquid cultures were incubated in the rotary shaker at 250 rpm. In transfer experiment, freshly harvested spores were pre-grown for 16h in CM with 2% (w/v) glucose. The mycelium was then harvested by filtration over sterile cheesecloth, washed with MM andwas transferred to 50 mL MM with 0.02 % (w/v) aromatic compound. After 2h of incubation, the mycelium was harvested by vacuum filtration, dried between two sheets of paper and frozen in liquid nitrogen. The culture filtrate was harvested, centrifuged and frozen. All samples were stored in -20°C until being processed.

extract_protocol:
RNA was extracted from grinded mycelia using TRIzol® reagent (Invitrogen, Breda, the Netherlands) and purified with NucleoSpin® RNA II Clean-up kit (Macherey-Nagel) with rDNase treatment. The RNA quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 2h incubation on veratric acid

tag: genotype


title: Dual-RNA-1hr-1

description:
mRNA after ribo zero gold rRNA depletion
OA17


title: CARM1 binding in cells treated with TM

value: A1847 cells


title: input DNA from untreated cells

description: input

value: input

value: untreated cells


title: W-VA-2

value: 2h incubation on vanillic acid


title: W-VE-1


title: Slc4a4_bKO_HFD_Rep3

city: Cambridge

first: Matthew

middle: R

last: Brown

address: 75 Ames St

institute: Broad Institute

data_processing:
Illumina's RTA version 2.7.7. for basecalling
Fragment reads were aligned using TopHat version 2.0.6 (Trapnell et al., 2012), assembled using StringTie version 2.1.3 (Pertea et al., 2015), and counted using StringTie’s script (PrepDE.py) via Python version 3.6, all with default settings. The count matrix was then imported into R version 3.6.1 and differentially expressed genes were identified using edgeR version 3.1.1 (Robinson et al., 2010).
Genome_build: mm10

source_name: Islet

extract_protocol:
Islets were hand-picked and RNA was isolated using the Rneasy Plus Minikit (Qiagen). RNA libraries were prepared using 200 ng of total RNA.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 according to manufacturer's instructions (Illumina).

value: Pancreatic islets

tag: age

value: 20 weeks

value: 8 weeks 60% high fat diet


title: 7_Pluripotent stem cell derived cardiac fibroblast

tag: cell type

value: EpiC-FB 7


title: W-VA-1


title: 13_Adult left ventricular cardiac fibroblast

value: aCFB 13


title: 5_Pluripotent stem cell derived cardiomyocyte

value: CM 5


title: W-CO-2

value: 2h incubation on coniferyl alcohol


title: XBP1 knock-down cells treated with tunicamycin, replicate 2

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

extract_protocol:
Total RNA was extracted using RNeasy mini Kit (Qiagen, 74106) and digested with DNase I (Qiagen, 79254)
RNA-Seq libraries were constructed using 3’mRNA-seq Library Prep Kit (Lexogen) and sequenced with Illumina NextSeq 500 using 75 nt single read

tag: condition

tag: carm1 status

value: WT

tag: xbp1 status

value: KD

value: TM

tag: replicate


title: 6_Pluripotent stem cell derived cardiomyocyte

tag: stem cell line

value: CM 6


title: W-CI-2

tag: strain

value: 2h incubation on cinnamic acid


title: XBP1 knock-down cells treated with tunicamycin, replicate 3


title: Control_HFD_Rep1


title: Slc4a4_bKO_HFD_Rep2


title: 1_Pluripotent stem cell derived cardiac fibroblast

tag: cardiac fibroblast differentiation lineage

value: second heart field derived

tag: sample name

value: SHF-FB 1


title: 3_Pluripotent stem cell derived cardiac fibroblast

value: SHF-FB 3


title: 4_Pluripotent stem cell derived cardiomyocyte

value: CM 4


title: Control_HFD_Rep2


title: XBP1 knock-down cells under control condition, replicate 3

value: A1847 cells

value: ctr


title: W-CI-1


title: Control_HFD_Rep3

value: Pancreatic islets

value: 20 weeks


title: XBP1 knock-down cells treated with tunicamycin, replicate 1


title: 2_Pluripotent stem cell derived cardiac fibroblast

value: SHF-FB 2


title: XBP1 knock-down cells under control condition, replicate 1


title: Irisin group mouse 5

city: Charlestown

first: Christiane

last: Wrann

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Per-sample transcript-level quantifications (read counts) are processed and aggregated to the gene-level using tximport [PMID:26925227], a R/Bioconductor package. Gene-level counts are filtered to retain contributions from more useful biotypes (which may be named differently depending on the species), broadly these include: protein_coding, lncRNA, macro_lncRNA, miRNA, antisense, pseudogene, processed_pseudogene, processed_transcript, transcribed_processed_pseudogene, transcribed_unprocessed_pseudogene.
Per-sample gene-level read counts for genes surviving the above filters are normalized using the DESeq2 [PMID:25516281] R/Bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts for all mice in different groups and all genes

source_name: microdisected hippocampus sample

extract_protocol:
Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.

value: APP/PS1 mice (34832-JAX)

value: tail vein injected AAV8-Irisin-FLAG

value: Hippocampus


title: XBP1 knock-down cells under control condition, replicate 2

value: WT


title: Irisin group mouse 4


title: Control

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

description:
scRNA-seq
mRNA Expression Profiling

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner.
The unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.1.1).
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were log transformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (gene-barcode counts), barcodes.tsv (cell barcodes), features.tsv (genes) files.

source_name: blood

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp paired-end reads were generated.
RNA libraries were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Blood


title: Slc4a4_bKO_HFD_Rep1

value: 8 weeks 60% high fat diet


title: W-CO-1

value: 2h incubation on coniferyl alcohol


title: Irradiated patient

description:
scRNA-seq
mRNA Expression Profiling

value: Radiation


title: ESC H2B-Dam repl1

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

institute: University of Zurich

value: Embryonic stem cells

value: 100ng/mL doxycycline + 1uM Shield1 for 15h


title: CARM1 knock-out cells treated with tunicamycin, replicate 3

value: KO

value: TM


title: Irisin group mouse 3


title: aorta_A+M_rep2

type: RNA

city: BeiJing

last: Tan

address: No. 38 Xue Yuan Road

institute: Peking University Health Science Center

description: Gene expression in aortae of AngⅡ-infused mice with MK-626

hyb_protocol: 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 × GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with the Gene Spring GX v12.1 software package (Agilent Technologies).

source_name: aorta_Ang II+MK-626

label_protocol: The mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). 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.

extract_protocol: After mice were sacrificed, aortae were removed, cleaned of adhering tissue in sterilized PBS, and then stored in liquid nitrogen for total RNA extraction. Total RNA from each sample was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA quantity and quality were measured by NanoDrop ND-1000 to make sure the high purity of the isolated RNA.

treatment_protocol: Under ketamine/xylazine anesthesia (75 and 6 mg/kg), AngⅡ - or PBS-loaded osmotic pumps were implanted in Male C57BL/6J mice (8-10 weeks old). Then the mice received MK-626 administration (3 mg/kg/day) or vehicle for 2 weeks.

value: 8-10 weeks old

tag: Sex

value: male

value: oral MK-626 treatment (3 mg/kg/d) (Ang II+ MK-626)

value: aorta


title: Irisin group mouse 1


title: GFP group mouse 5

value: tail vein injected AAV8-GFP


title: CARM1 knock-out cells under control condition, replicate 3

tag: cell line

value: A1847 cells

value: ctr


title: warm control 6 hr replicate 2 [W2-6hr_S7_L001]

city: Brisbane

first: Peter

middle: A

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

country: Australia

institute: The University of Queensland

data_processing:
bcl2fastq2 Conversion Software v2.20 was used to convert bcl to fastq files and remove adapter sequences
Quality control was performed with FastQC v.0.11.2. Adapters were removed using scythe v.0.991 with flags -p 0.01 for the prior and reads were quality trimmed with sickle v.1.33 with flags -q 20 (quality threshold) -l 20 (minimum read length after trimming). The trimmed and quality filtered reads were aligned to the rice reference genome Os-Nipponbare-Reference-IRGSP-1.0 from the MSU Rice Genome Annotation Project Database v7 (http://rice.plantbiology.msu.edu/) using the subjunc aligner v1.5.0-p1 with -u and -H flags to report only reads with a single unambiguous best mapping location, -P 3 for phred+33 encoding (Liao et al., 2013). Reads were then sorted, indexed and compressed using samtools v1.1-26-g29b0367 (Li et al., 2009) and strand-specific bigwig files were generated using bedtools genomecov v2.16.1 (Quinlan and Hall, 2010) and the UCSC utility bedGraphToBigWig for viewing in IGV (Robinson et al., 2011). Summary statistics for each sample are provided in Supplementary Dataset S1: Summary of transcriptomic datasets.
For standard differential gene expression testing, the number of reads mapping per IRGSP-1.0 gene loci was summarised using featureCounts v1.5.0-p1(Liao et al., 2014) with flags -P and -c to discard read pairs mapping to different chromosomes and the -s flag set to 2 for strand specificity for a strand specific library, multimapping reads and multioverlapping reads were not counted. Reads were summarised to parent IRGSP-1.0 gene loci rather than individual splice variants by summarising to the genomic coordinates defined by the feature "gene" in the IRGSP-1.0.gff reference (last modified 7/2/2012 ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.gff3). Only loci with an abundance of at least 1 CPM (approximately 5 reads) in at least 4 samples were retained. Statistical testing for relative gene expression was performed in R following the “edgeR-limma-voom” approach (https://www.bioconductor.org/help/workflows/RNAseq123/); using, edgeR v.3.4.2(McCarthy et al., 2012; Robinson and Oshlack, 2010; Robinson et al., 2010; Robinson and Smyth, 2007, 2008), and voom in the limma package 3.20.1(Law et al., 2014; Smyth, 2005, 2004).
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: Gene expression counts were normalised using limma-voom and are provided as a normalised counts per million per gene locus matrix.

organism: Oryza sativa

source_name: warm control 6 hr_leaf tissue

growth_protocol: Rice (Oryza sativa) cultivar IR64 plants were grown hydroponically in a glasshouse facility at the Research School of Biology, Australian National University between October and December 2015. Seeds were initially incubated at 40-42°C for two days before soaking in water for eight hours, placed on wet Whatman filter papers in Petri dishes and kept in the dark at 30°C for five days. The germinated seedlings were then transferred to trays of vermiculite and placed in temperature-controlled glasshouses (30°C day and 25°C night) under natural sunlight and photoperiod with photosynthetically active radiation (PAR) between 400 and 1200 µmol m-2 s-1.   When the third leaf had emerged, seedlings were transplanted from vermiculite to a hydroponic system. Individual plants were placed within PVC tubes with a 3.7 cm diameter and 13 cm height. Tubes were then suspended at the top of 20 L capacity hydroponic tanks (12 tanks in total), with each tank holding a maximum of 20 plants. Each tank was filled with hydroponic solution (Table S1) (Hubbart et al., 2007). The nutrient solution was replaced weekly and sulphuric acid or sodium hydroxide were used to adjust the pH to between 5-6, with pH monitored using a portable pH meter (Rowe Scientific Pty. Ltd., NSW, Australia). The hydroponic solution was aerated continuously using Infinity AP-950 air pumps (Kong’s Pty. Ltd., Ingleburn, Australia). After two weeks of hydroponic growth at 30/25°C, the most recently fully-expanded leaves were labelled as pre-existing (PE) leaves. Following labelling, four tanks were randomly chosen and shifted to an adjacent glasshouse room set to 25°C day and 20°C night (25/20°C), and four tanks to a room set at 40°C day and 35°C night (40/35°C) temperature regime, while four tanks were retained at 30/25°C as controls. Newly-developed (ND) leaves that emerged in each thermal regime were labelled, with all measurements reported on ND leaves being made 21-days after T transfer. For all experiments, four separate leaves from separate plants, one from each hydroponic tank (pot replicates) per T treatment were sampled.

extract_protocol:
For each time point and temperature treatment, approximately 8 cm of middle leaf section (less than 100 mg) were sampled by immediately freezing leaf material in liquid N2 and storing at -80°C until RNA extraction. Total RNA was extracted using the RNeasy plant mini protocol (Qiagen, Doncaster, VIC, AU) and treated with DNase I (Qiagen, Doncaster, VIC, AU) to remove any contaminating DNA.
RNAseq libraries were prepared using the Illumina Stranded Total RNAseq kit with RiboZero rRNA depletion as per the manufacturer's guidelines (Illumina). Libraries were pooled and sequenced on a HiSeq1500 for 61 cycles in single end mode at the Centre for AgriBioscience, LaTrobe University, Melbourne, Australia.

treatment_protocol: To quantify transcript abundance following changes in thermal regimes, the labelled pre-existing (PE) leaves were harvested 2, 6 and 24 h after the shifting of the plants 3 h into the day period so that all sample points were collected during the day.

tag: cultivar

tag: treatment teperature

value: warm

tag: timepoint

value: leaf tissue


title: CARM1 knock-out cells under control condition, replicate 1

value: WT

tag: treatment


title: MS19024_GT19_07837_SI-NA-A7_S9

city: Farmington

first: Duygu

last: Ucar

state: Connecticut

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
snATAC-seq reads were processed by using 10x's cellranger-atac software, version 1.2.0, with default parameters. Hg19 was used as the reference genome
Doublet cells were identified by using the novel ATAC-DoubletDetector method
Single cells were processed using the Seurat(version 3.2) and Signac(version 1.1) packages on R.
Genome_build: hg19
Supplementary_files_format_and_content: snATAC-seq peaks, cell barcodes and matrix showing the number of reads for a particular cell at a particular peak, aggregate reads for the clusters identified on the same peaks

source_name: Pancreatic Islet

extract_protocol:
Human islets were obtained through partnerships with the Integrated Islet Distribution Program (IIDP, http://iidp.coh.org/). Assessment of human islet function was performed by islet GSIS static incubation assay on the day after arrival, following the IIDP protocol. Primary human islets were cultured in Prodo media (PIM-S + supplements PIM-G + PIM-ABS) in 5% CO2 at 37oC for ∼24 hours prior to beginning studies. In preparation of single cell suspension for 10x platform, human islets were dispersed with StemPro Accutase (Thermo Fisher Scientific) 1ml/1000IEq for 10min at 37oC. Islet single cell suspension was washed three times in PBS-0.03% BSA and cell number determined using Countess II FL Automated Cell Counter (Life Tech). Nuclei isolation for single cell ATAC sequencing was performed following the 10x protocol (https://assets.ctfassets.net/an68im79xiti/5g035d2ngCW1aB9DFqPphO/71445a59fb282ea273a866c26cb5d319/CG000169_DemonstratedProtocol_NucleiIsolation_ATAC_Sequencing_RevD.pdf, based on the OMNI nucleiprep by Corces et al.13).
For single nucleus ATAC sequencing (snATACseq) experiments, viable single cell suspensions from each sample were used to generate snATACseq data using the 10X Chromium platform according to the manufacturer’s protocols (Demonstrated Protocol Nuclei Isolation for ATAC Sequencing Document CG000169; Chromium Single Cell ATAC_User Guide RevB Document CG000168). Briefly, >100,000 cells of interest were centrifuged, the supernatant was removed without disrupting the cell pellet, Lysis Buffer was added for 5 minutes on ice to generate isolated and permeabilized nuclei, followed by quenching by dilution with Wash Buffer. After centrifugation to pellet the washed nuclei, Diluted Nuclei Buffer was used to re-suspend nuclei at the desired nuclei concentration as determined using a Countess II FL Automated Cell Counter and combined with ATAC Buffer and ATAC Enzyme to form a Transposition Mix. Transposed nuclei were immediately combined with Barcoding Reagent, Reducing Agent B and Barcoding Enzyme and loaded onto a 10X Chromium Chip E for droplet generation, followed by library construction. The barcoded sequencing libraries were subjected to bead clean-up and checked for quality on an Agilent 4200 TapeStation, quantified by qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms), and pooled for sequencing on an Illumina NovaSeq 6000 S2 flow cell (paired-end libraries 2×50bp).

tag: tissue

value: Pancreatic Islet

value: F

tag: race

value: White

tag: bmi


title: GFP group mouse 4

value: APP/PS1 mice (34832-JAX)

value: Hippocampus


title: aorta_A+M_rep3

tag: age


title: warm control 6 hr replicate 1 [W1-6hr_S3_L001]


title: GFP group mouse 3


title: CARM1 binding in untreated cells

tag: factor

value: untreated cells


title: aorta_A+M_rep1


title: Irisin group mouse 2

value: tail vein injected AAV8-Irisin-FLAG


title: SLE-1

first: Yiyao

last: Deng

state: China

address: Department of Nephrology

department: Department of Nephrology

institute: Chinese PLA General Hospital

description: one PBMC sample from SLE

data_processing:
The Cell Ranger software pipeline (version 3.1.0) were used for genome alignment, calling Cell Barcodes and estimating multiplet rates .
Genome_build: Homo_sapiens.GRCh38.93.chr
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: PBMC

extract_protocol:
1. After collection of cells, centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types). Carefully discard the supernatant and retain the cell precipitation.  2. The  cell  pellet  was  resuspended  by  1mL 1X  PBS  containing  0.04%  BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. If necessary, cell filter should be applied to remove cell debris and clusters (eg. 30µm MACS SmartStrainers and 40µm FlowmiTM Cell Strainer). 3.Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. If the calculated concentration is too high, adjust the liquid volume to the appropriate concentration and repeat counting once more. Once the desired cell suspension was obtained, immediately place the samples on ice for subsequent GEMs preparation and reverse transcription.
1. Interrupt, end repair and add A base. Finally the SPRIselect beads was used to purify the product.  2. Adaptor ligation and SPRIselect purification.  3. Index PCR and SPRIselect purification.  4. Qubit® 3.0 Flurometer (Life Technologies, CA, USA) was used to determine the library concentration.  5. Agilent 2100 High Sensitivity DNA Assay Kit (Agilent Technologies, CA, USA)    was used to determine the distribution of library product fragments.

tag: subject status

value: systemic lupus erythematosus (SLE) patient

value: female

value: 45 years old


title: CARM1 knock-out cells treated with tunicamycin, replicate 1

tag: condition

tag: carm1 status

value: KO

tag: xbp1 status

value: TM

tag: replicate


title: warm control 24 hr replicate 3 [W3-24hr_S2_L002]

source_name: warm control 24 hr_leaf tissue


title: MS19025_GT19_07838_SI-NA-A8_S13

value: M

value: African American


title: GFP group mouse 2

tag: strain

value: tail vein injected AAV8-GFP


title: warm control 6 hr replicate 4 [W4-6hr_S15_L002]

value: warm

value: leaf tissue


title: 786-O shRARRES2_3 rep3

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
Raw image data file from high-throughput sequencing(like Illumina) was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base  Calling).
The raw reads were trimmed for adaptor sequence with TrimGalore version 0.6.1
The data was later aligned to the human genome hg38/GRCh38 and gene quantified with the STAR algorithm v2.5.2
The differential expression analysis was performed using the quasi-likelihood function implemented in edgeR
The calcNormFactors function in edgeR was used to normalizes the library sizes across samples by finding a set of scaling factors for the library sizes that minimizes the log-fold changes between the samples for most genes using the trimmed mean of M-values (TMM) between each pair of samples.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file containging matrix of TMM normalized counts per million for each gene in each sample

source_name: Clear cell renal cell carcinoma cell line

growth_protocol: 786-O cells were maintained in DMEM media supplemented with 10% FBS

extract_protocol:
RNA was extracted using TRIzol reagent and Rneasy Mini Kit (Qiagen) according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentivirals encoding either control shGFP or shRARRES2 (3 types of shRARRES2)

tag: cell type

value: Clear cell renal cell carcinoma

value: shRARRES2_3 knockdown


title: Wild type CARM1/XBP1 cells treated with tunicamycin, replicate 2

tag: cell line

value: A1847 cells

value: WT


title: SLE-2

description: one PBMC sample from SLE

tag: Sex

value: 37 years old


title: CARM1 knock-out cells under control condition, replicate 2

value: ctr


title: Wild type CARM1/XBP1 cells treated with tunicamycin, replicate 3


title: CARM1 knock-out cells treated with tunicamycin, replicate 2


title: warm control 24 hr replicate 2 [W2-24hr_S8_L001]

tag: cultivar

tag: treatment teperature


title: C-1

description: one PBMC sample from healrh volunteer

value: health volunteer

value: 25 years old


title: 786-O shRARRES2_3 rep2

tag: treatment


title: 786-O shRARRES2_3 rep1


title: 786-O shRARRES2_2 rep3

value: shRARRES2_2 knockdown


title: Wild type CARM1/XBP1 cells under control condition, replicate 2


title: 786-O shRARRES2_2 rep1


title: warm control 24 hr replicate 4 [W4-24hr_S16_L002]

tag: timepoint

tag: tissue


title: warm control 6 hr replicate 3 [W3-6hr_S1_L002]


title: Naive-Animal 10

city: Houston

first: Angelique

last: Regnier-Golanov

state: United States of America

address: 6560 Fannin St #900

department: Neurosurgery

institute: The Houston Methodist Neurological Institute

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
DNA sequencing reads were aligned with default parameters to the mouse reference genome (mm9) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models from the UCSC Known Genes dataset.
Differentially expressed genes (DEG) were determined with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts per gene per sample

source_name: whole bilateral hippocampus

growth_protocol: mice fed ad libitum

extract_protocol:
Bilateral whole hippocampus of SAH (n=4), Sham (n=3), and Naïve (n=3) groups were manually collected by an experimenter blinded to the specific group and total RNA was extracted immediately after using QIAzol reagent (RNeasy Mini Kit, Qiagen Inc, Hilden, Germany).
RNA-seq was performed by the Genomics Core Laboratory of Weill Cornell University Medical College (New York, NY). Total RNA integrity was evaluated with the Agilent Bioanalyzer 2100 (Agilent Biotechnologies, Santa Clara, CA) and only samples with an RNA integrity number (RIN) >9.0 were further processed for RNA-seq.  RNA concentrations were measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA). All RNA-seq libraries were prepared using 100ng of total RNA with the TruSeq Stranded Total RNA sample preparation kit (ribosomal RNA depletion and stranded RNA-Seq) with Ribo-Zero according to manufacturer’s specified protocol (Illumina, San Diego, CA). Samples were multiplexed and sequenced across multiple lanes of a HiSeq 4000 Sequencing System (Illumina) using 50-base paired-end reads to achieve a minimum depth of 30 million aligned read-pairs

treatment_protocol: no drug treatment

value: naive


title: warm control 2 hr replicate 2 [W2-2hr_S6_L001]

source_name: warm control 2 hr_leaf tissue


title: warm control 24 hr replicate 1 [W1-24hr_S4_L001]


title: Wild type CARM1/XBP1 cells under control condition, replicate 3


title: Wild type CARM1/XBP1 cells treated with tunicamycin, replicate 1


title: Sham-Animal 6

value: sham


title: 786-O shRARRES2_1 rep2

value: shRARRES2_1 knockdown


title: warm control 2 hr replicate 4 [W4-2hr_S14_L002]


title: Sham-Animal 7


title: Naive-Animal 8


title: GFP group mouse 1

value: APP/PS1 mice (34832-JAX)

value: Hippocampus


title: 786-O shRARRES2_1 rep1


title: Wild type CARM1/XBP1 cells under control condition, replicate 1


title: APECED_rep 3 (human)

city: Gaithersburg

first: Timothy

last: Break

address: 16020 Industrial Dr.

institute: MesoScale Diagnostics

description:
HD-APECED_CPM_TMM_counts.txt
HD-APECED_RawCountFile.txt

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25 human genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCh38 v25 genome annotation GTF which included ERCCs.
An expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: GRCh38.v25
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Oral mucosal tissue

extract_protocol:
Oral mucosal tissue was homogenized using Miltenyi Gentlemacs M tube and total RNA was extracted from whole tissue using Trizol Reagent
Sequencing libraries were prepared by the Illumina Nextera method, following manufacturer's recommendations and sequenced in a NextSeq500 instrument in 150 bp end mode

value: Oral mucosal gingival tissue

value: 65 years old

value: Male

tag: disease state

value: APECED patient


title: APECED_rep 5 (human)

tag: age

value: 36 years old

value: Female


title: warm control 0 hr replicate 3 [W3-0hr_S9_L001]

source_name: warm control 0 hr_leaf tissue

value: warm

value: leaf tissue


title: 786-O shRARRES2_1 rep3

value: Clear cell renal cell carcinoma


title: 786-O shRARRES2_2 rep2


title: Naive-Animal 9


title: warm control 0 hr replicate 4 [W4-0hr_S3_L002]


title: SAH-Animal 4

value: subarachnoid hemorrhage


title: Sham-Animal 5


title: APECED_rep 2 (human)

value: 53 years old


title: warm control 2 hr replicate 3 [W3-2hr_S10_L001]


title: APECED_rep 4 (human)

value: 21 years old


title: 786-O shGFP rep3

value: shGFP control


title: warm control 2 hr replicate 1 [W1-2hr_S2_L001]


title: warm control 0 hr replicate 2 [W2-0hr_S5_L001]


title: APECED_rep 1 (human)

value: 41 years old


title: warm control 0 hr replicate 1 [W1-0hr_S1_L001]


title: SAH-Animal 2


title: 786-O shGFP rep2


title: SAH-Animal 1


title: SAH-Animal 3


title: 786-O shGFP rep1


title: hot  treated 6 hr replicate 3 [H3-6hr_S24_L003]

source_name: hot  treated 6 hr_leaf tissue

value: hot


title: drug_normoxia_rep3

city: Oxford

first: Adrian

middle: L

last: Harris

address: John Radcliffe Hospital

department: Department of Medical Oncology

country: United Kingdom

institute: University of Oxford

data_processing:
Cutadapt was used to trim low quality sequences
STAR was used to align the reads to genome and counts per gene was calculated using featurecounts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix containing raw gene counts for 786-0 cells upon knockout of HIF2α & upon treatment with PT2385 (drug) in normoxia

source_name: 786-0 cells

growth_protocol: cells were grown in DMEM 5mM glucose supplemented with 10% FBS

extract_protocol:
RNA was extracted using Tri-Reagent following the manufacturer´s instructions
libraries were prepared using Illumina’s instructions

treatment_protocol: 786-0 WT and 786-0 KO cells were cultured under normoxia (21% O2) for 48h. 786-0 WT cells were additionally treated with 10uM PT2385 for 48h.

value: clear cell renal cell carcinoma

tag: genotype

value: WT


title: drug_normoxia_rep2


title: HD_rep 4 (human)

value: Oral mucosal gingival tissue

value: 25 years old

value: Healthy donor


title: Lin-  eCLIP for IGF2BP3 rep6

city: Los Angeles

first: Dinesh

last: Rao

address: 650 Charles E Young Dr S

department: Pathology & Lab Medicine

institute: UCLA

description:
technical rep
bm_linms_jd133e

data_processing:
Library strategy: eCLIP-Seq
mapping to mm10 with STAR (v 2.5.3a)
repeatmasking with bowtie2
peak calling - CLIPper with default parameters
differential expression with DESeq2 on all genes with non-zero counts
Genome_build: mm10

source_name: Lin- cells

growth_protocol: Lin- cells were obtained by harvesting the BM from mice, lysing in red blood cell lysis buffer, and staining with a cocktail of biotinylated antibodies for lineage depletion by MACS (Miltenyi). Lin- cells were spin-infected with the MSCV-MLL-flag-Af4 retroviral supernatant four times at 30°C for 45 minutes in the presence of polybrene. Cells were selected with 400 μg/ml of G418 for 7 days.

extract_protocol:
CD11b+ cells were obtained by harvesting the splenic tumors from the WT/MLL-Af4 or I3/MLL-Af4 mice, lysing in red blood cell lysis buffer, and staining with a CD11b biotinylated antibody for positive selection by MACS (Miltenyi). RNA from both cell types was collected using QIAzol Lysis Reagent and purified using the miRNeasy Mini Kit (217004; Qiagen). The Agilent 2100 Bioanalyzer using RNA pico chip was utilized to quality check total RNA. The Nugen Universal plus mRNA-Seq Kit was used to generate strand-specific RNA-seq libraries. Samples were subjected to poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming. The cDNA samples were then subjected to end repair to generate blunt ends, adapter ligation, strand selection, and PCR amplification to generate the final library. To mulitplex samples in one sequencing lane, different index adapters were used. Single-end, strand-specific RNA sequencing was performed on the Illumina HiSeq3000 system for the Lin- and CD11b+ samples, resulting in 15-20 million reads per sample, at the the UCLA Technology Center for Genomics & Bioinformatics.
Nugen Universal plus mRNA-Seq Kit (RNA-seq) and Eclipse BioInnovations Inc eCLIP kit (eCLIP)

value: Lin- cells

tag: eclip antibody

value: MBL IGF2BP3 antibody (RN009P)

value: no treatment


title: Lin- size-matched input rep6

value: input


title: hot  treated 6 hr replicate 1 [H1-6hr_S18_L002]

value: leaf tissue


title: HD_rep 1 (human)

value: 27 years old

value: Female


title: drug_normoxia_rep1


title: hif2aKO_normoxia_rep3

value: hif2a KO


title: hot  treated 24 hr replicate 4 [H4-24hr_S28_L003]

source_name: hot  treated 24 hr_leaf tissue


title: hot  treated 24 hr replicate 2 [H2-24hr_S22_L003]