title: heavy-poly

city: Nagoya

first: Koichi

last: Ogami

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University

description: 5’capped 3’ polyA RNA

data_processing:
Base-callingg: Guppy 2.3.1
Quality check: MinIONQC 1.3.5
Alignment: minimap2 2.15 with parameters  -ax splice -uf -k 12 -c -L -N 5 —secondary=no
Poly(A) tail analysis: nanopolish 1.18.2
Read counts: FeatureCounts (Subread 1.6.2)
Genome_build: hg38
Supplementary_files_format_and_content: Counts.txt (raw counts for all features in all samples)

source_name: cultured HEK293T cells

growth_protocol: HEK293T cells were cultured in somplete DMEM

extract_protocol:
[RNA prep] HEK293T cells seeded at 3.0 × 10^6 cells grown in three 10cm dishes were treated with 100 ug/mL cycloheximide (CHX) for 10 min at 37 °C. Cells were washed once with ice-cold PBS containing 100 ug/mL CHX and then resuspended in 450 uL of polysome lysis buffer (20 mM HEPES-KOH (pH 7.5), 150 mM KCl, 5 mM MgCl2, 0.5 mM EGTA, 0.5 % NP-40, 1×Protease inhibitor cocktail) containing 100 g/mL CHX. After 10 min of incubation on ice, the lysates were mixed with 50 uL of 1:1 mixture of 10 % Triton X-100/ 10 % Na-deoxycholate and then centrifuged at 204,000 × g for 10 min at 4 °C. The RNA concentration was quantified using QuantiFluor RNA System (Promega), and diluted supernatant containing the same amount of RNA was loaded onto 10-50 % sucrose gradients (20mM HEPES-KOH (pH 7.5), 150 mM KCl, 5 mM MgCl2, 1 mM EGTA, 100 ug/mL CHX) and separated into fractions by centrifugation at 37,000 rpm for 90 min using an SW41Ti rotor. Ten percent of the diluted supernatant was used as an input. Fractions were collected using piston gradient fractionator (Biocomp) while measuring A254. Collected fractions were mixed with 1 volume of Solution D and isopropanol precipitated in the presence of glycogen.   [Library prep]GST-eIF4Ek119A (100 μg) was immobilized on 50 μL of MagneGST Glutathione Particles (Promega) at 10 °C for 2 hr in 200 μL of 4E pull-down (4E-PD) buffer (10 mM Tris-HCl (pH 8.0), 100 mM KCl, 2 mM EDTA, 2.5 % glycerol, 1.3 % polyvinylalcohol (polymerization degree about 500), 0.005 % Triton X-100, 1mM DTT) and unbound protein was removed by washing three times with 200 μL of 4E-PD buffer. Prior to the cap-purification, total RNA was first subjected to LiCl-precipitation twice to remove abundant 5' capped small ncRNAs. The LiCl-precipitated RNA (30 μg) was heat-denatured at 65 °C for 10 min and mixed with GST-eIF4Ek119A-bound MagneGST particles in 200 μL of 4E-PD buffer supplemented with 25 μg yeast tRNA and 40 U recombinant RNase inhibitor (TaKaRa) for 2 hr at 25 °C. After washing three times with 500 μL of 4E-PD buffer, GST-eIF4Ek119A was eluted in 100 μL of elution buffer (100 mM Tris-HCl (pH 8.6), 1 mM EDTA, 0.005 % Triton X-100, 150 mM NaCl, 40 mM glutathione, 1 mM DTT, 5 U/mL Turbo3C protease) at r.t. for 10 min. The elution was repeated four times, and the eluate was combined and phenol-chloroform extracted followed by EtOH precipitation in the presence of glycogen (Roche). The precipitated RNA was dissolved in 10 μL of QW and further purified using 1.8 volume of Agencourt RNAClean XP (Beckman). After elution in 10 μL of QW, RNA concentration was determined using QuantiFluor RNA System (Promega).
Library preparation for nanopore sequencing was performed using the Oxford Nanopore’s direct RNA sequencing kit (SQK-RNA001 or SQK-RNA002) according to the manufacturer’s instruction except that we used 1μg of the cap-purified RNA and 0.5 μL of RNA calibration strand (RCS) for adapter ligation. To improve throughput, we performed reverse transcription using SuperScript III (Thermo Scientific) after the adapter ligation. All the procedures above were performed in DNA LoBind tubes (Eppendorf).
Nanopore direct RNA-sequencing

treatment_protocol: HEK293T cells were treated with 100ug/mL cycloheximide for 10min before harvesting

tag: fraction

value: heavy polysome


title: light-poly

status: Public on Sep 22 2022

type: SRA

country: Japan

description: 5’capped 3’ polyA RNA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

value: light polysome


title: mono

description: 5’capped 3’ polyA RNA

value: monosome


title: WT_rep2_SATB1_HiChIP

city: Tampa

first: Tomas

last: Zelenka

state: Florida

address: 12902 Magnolia Drive

department: Immunology

country: USA

institute: H. Lee Moffitt Cancer Center & Research Institute

library_source: genomic

data_processing:
Raw reads were mapped with bowtie2 (version 2.3.4.3; Langmead and Salzberg, 2012) to the mm10 genome and fully processed using the HiC-Pro pipeline (version 2.11.1; Servant et al., 2015) with default parameters. Biological replicates were processed individually to assess their quality and then combined for downstream analyses and visualization. The Hi-C and HiChIP matrices are provided as individual replicates and also as a single file representing merged biological replicates. All matrices are in hic format (Juicer Tools, version 1.8.9; Durand et al., 2016) and include multiple resolutions from 5 kbp to 2 mbp as well as DpnII restriction fragment based resolutions. They were produced by the following command utilizing a HiC-Pro script: bash hicpro2juicebox.sh -i xxx.allValidPairs -g chrom_mm10.sizes -j juicer_tools.1.8.9_jcuda.0.8.jar -o -r DpnII_resfrag_mm10.bed.
The HiChIP datasets were used to identify binding sites of the targeted factors. The SATB1 binding sites were extracted from an unsuccessful HiChIP experiment with >60% Dangling End Pairs (~280 million reads; here referred to as rep3 and rep4), using PeakInferHiChIP.sh script from FitHiChIP (version 6.0; Bhattacharyya et al., 2019), with MACS2 (version 2.1.2) parameters: --nomodel --extsize 147; filter peaks with >2.5 enrichment. The peaks were called separately for two biological replicates and then merged. Raw data of the unsuccessful HiChIP as well as called peaks are provided. The H3K27ac peaks were derived similarly but from the HiChIP datasets that were also used for the chromatin interaction analysis. The CTCF peaks were also derived the same way and motif analysis with MEME (Bailey and Elkan, 1994) validated the high enrichment of the CTCF binding motif in the HiChIP derived peaks, confirming its specificity. However, due to a relatively low number of HiChIP-derived CTCF binding sites, for FitHiChIP loop calling we employed a CTCF ChIP-seq dataset from the ENCODE project (ENCFF714WDP; Dunham et al., 2012).
We used the described peaks and the allValidPairs HiChIP output from the HiC-Pro pipeline (biological replicates were combined) to identify HiChIP loops by FitHiChIP (Bhattacharyya et al., 2019) with the following parameters: 5,000 kbp resolution, 20000-2000000 distance threshold, FDR 0.01, coverage specific bias correction, merged nearby peak to all interactions. Resulting HiChIP loops are provided here.  For the differential analysis of H3K27ac WT and Satb1 cKO HiChIP datasets, we utilized the differential analysis pipeline from FitHiChIP (Bhattacharyya et al., 2019) and only utilized loops that were classified as differential in 3D but not in 1D. These were loops that showed differences in interaction counts but no significant differences in H3K27ac occupancy at loop anchors. We divided the loops into two categories depending if they evinced decreased (referred to as underinteracting loops) or increased interaction in Satb1 cKO (referred to as overinteracting loops). Loops from both categories are provided in the excel file. Some regions contained H3K27ac loops from both under- and over-interacting categories, hence we further calculated a difference between the number of under- and over-interacting loops and this score including the affected genes are also provided.
Genome_build: mm10
Supplementary_files_format_and_content: hic files are interaction matrices produced by Juicer Tools
Supplementary_files_format_and_content: narrowPeak files contain HiChIP-inferred binding sites (peaks) of targeted factors in HiChIP experiments
Supplementary_files_format_and_content: bed files contain coordinates of chromatin loops identified from the HiChIP experiments
Supplementary_files_format_and_content: xlsx is a Microsoft Excel file containing results of the differential analysis of H3K27ac loops – showing H3K27ac loops that are over- and underinteracting in Satb1 cKO and also the genes affected by these differential loops

molecule: genomic DNA

organism: Mus musculus

source_name: thymus

extract_protocol:
Both Hi-C and HiChIP experiments were performed identically until the chromatin immunoprecipitation step. Aliquots of 10 million isolated thymocytes resuspended in 1X PBS were fixed by adding 1/10th sample volume of fixation butter [11% methanol-free formaldehyde (Pierce, 28908), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM Hepes pH 8.0] and rocking at RT for 10 minutes. To quench the reaction, glycine was added to 0.125 M final concentration and incubated at RT for 5 minutes, while rocking. After two washes with 1X PBS, cell pellet was resuspended in 500 μl of ice-cold Hi-C Lysis Buffer (10 mM Tris-HCl – pH 8, 10 mM NaCl, 0.2% NP40, 0.5 mM PMSF) and rotated at 4°C for 1.5 hours. Cells were centrifuged at 2,500 g, at 4°C for 5 minutes and the supernatant was discarded. The cell pellet was washed once with 500 μl of ice-cold Hi-C Lysis Buffer and then resuspended in 100 μl of 0.5% SDS. Cells were incubated at 62 °C for 10 minutes and then combined with 296 μl of H2O and 50 μl of 20% Triton X-100. Samples were incubated at 37°C for 15 minutes and then combined with 50 μl of 10X DpnII Buffer and 200 U of DpnII restriction enzyme (NEB, R0543M) and digested for additional 16 hours at 37 °C while shaking (160 rpm). The restriction enzyme was inactivated at 62°C for 20 minutes and the nuclei were centrifuged at 2,500 g, at 4 °C for 6 minutes. The supernatant was discarded and the nuclei were resuspended in 300 μl Fill-in Buffer [30 μl Klenow Buffer 10X (NEB, M0210L), 238.5 μl water, 15 μl 1 mM Biotin-16-dCTP (Jena Bioscience, NU-809-BIO16-L), 1.5 μl of each 10 mM dATP, dGTP, dTTP (Promega, U1240), 12 μl 5 U/μl DNA Polymerase I, Klenow Fragment (NEB, M0210L)].  The biotinylation mixture was incubated at 37°C for 30 minutes with rotation. SDS was added to a final concentration of 0.5% to inactivate the Klenow enzyme. Triton X-100 was added to 1% final concentration and samples were incubated at 37°C for 5 minutes. Samples were centrifuged at 2,500 g, at 4 °C for 10 minutes and the supernatant was discarded. The nuclei pellet was resuspended in the Ligation Buffer [120 μl 10X NEB T4 DNA Ligase Buffer with 10 mM ATP (NEB, B0202), 60 μl 20% Triton X-100 (1% final), 6 μl 2% (20 mg/ml) BSA, 40 μl 30% PEG 6,000 (1% final), 5 μl 400 U/μl T4 DNA Ligase (NEB, M0202L), 969 μl water]. Samples were incubated for 6 hours at RT with rotation. Nuclei were centrifuged at 2,400 g, at RT for 15 minutes and the supernatant was discarded. The pellet was resuspended in 60 μl Lysis Buffer (1% SDS, 50 mM Tris-HCl – pH 8, 20 mM EDTA, 1X protease inhibitors) and incubated at RT for 15 minutes. The lysate was diluted to 600 μl using ice cold TE Buffer supplemented with protease inhibitors and then sonicated with a Labsonic M – Tip sonicator for 3 cycles (30 seconds ON/OFF, 40% power). The sonicated material was centrifuged at 16,000 g, at RT for 15 minutes and the supernatant was collected into a new tube. Samples from the same genotype were merged and then split again: separately 100 μl for Hi-C and 450 μl for HiChIP.  Hi-C samples were combined with two volumes of Hi-C Elution Buffer (10 mM Tris-HCl – pH 8, 5 mM EDTA, 300 mM NaCl, 1% SDS) and incubated at 65°C overnight. De-crosslinked material was diluted to 500 μl with TE Buffer and treated with RNase A and Proteinase K. DNA was purified using a ChIP DNA Clean & Concentrator kit following the manufacturer’s instructions (Zymo Research, D5205). Purified DNA was quantified using Qubit dsDNA BS Assay Kit (Invitrogen, Q32853) checked on an agarose gel for shearing efficiency and 100 μg were used for library construction.  HiChIP samples were combined with Triton X-100 to 1% final concentration and samples were incubated at 37°C for 15 minutes. Samples were combined with an equal volume of 2X ChIP Binding Buffer (20 mM Tris-HCl – pH 8, 2 mM EDTA, 0.2 % sodium deoxycholate, 2X protease inhibitors). Chromatin preclearing and antibody binding to magnetic beads were performed as described in the ChIP protocol. The following antibodies were used for the immunoprecipitation step: SATB1 long isoform (8 μg, custom-made from Davids Biotechnologies), CTCF (7 µg, Abcam, ab70303), H3K27ac (2 µg, Abcam, ab4729). Antibody-coupled beads were incubated with chromatin at 4°C with rotation for 16 hours. Beads were washed five times with ice cold RIPA Buffer (50 mM Hepes pH 8, 1% NP-40, 0.70% Na-Deoxycholate, 0.5 M LiCl, 1 mM EDTA, protease inhibitors) and then twice with TE Buffer. After the first wash with TE Buffer, resuspended beads were transferred into a new tube. Immune complexes bound to beads were eluted in 125 μl Hi-C Elution Buffer (10 mM Tris-HCl – pH 8, 5 mM EDTA, 300 mM NaCl, 1% SDS) at 65°C for 16 hours. De-crosslinked material was diluted to 250 μl with TE Buffer and treated with RNase A and Proteinase K as previously described. DNA was purified using a ChIP DNA Clean & Concentrator kit following the manufacturer’s instructions (Zymo Research, D5205). Purified DNA was quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and used for library construction.
Samples were brought to 25 μl with water. 5 μl and 20 μl for HiChIP / Hi-C samples, respectively, of Dynabeads MyOne Streptavidin C1 beads (Invitrogen, 65001) were washed with 500 μl Tween Wash Buffer (5 mM Tris-HCl – pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20). Beads were resuspended in 25 μl of 2X Biotin Binding Buffer (10 mM Tris-HCl – pH 7.5, 1 mM EDTA, 2M NaCl) and combined with samples. Samples were incubated at RT for 20 minutes. Beads were separated on a magnet and washed twice with 400 μl of Tween Wash Buffer. Beads were washed by 100 μl of 1X TD Buffer (10 mM Tris-HCl – pH 7.5, 5 mM MgCl2, 10% Dimethylformamide). Beads were resuspended in 25 μl of 2X TD Buffer and combined with Tn5 enzyme from the Nextera DNA Sample Preparation Kit (Illumina, FC-121-1030) and water to final volume 50 μl. The amount of Tn5 enzyme was adjusted according to the input DNA amount: 4.5 μl for Hi-C libraries, 1.5 μl for SATB1 HiChIP and 1 μl for other HiChIP libraries. The reaction was incubated at 55°C for 10 minutes. The beads were collected with a magnet and the supernatant was discarded. Beads were resuspended in 300 μl of Strip Buffer (0.15% SDS, 10 mM Tris-HCl – pH 8, 50 mM EDTA) and incubated for 5 minutes at RT to strip off and deactivate Tn5. Beads were washed once with 400 μl of Tween Wash Buffer and once with 500 μl of 10 mM Tris-HCl (pH 8.0).  The beads were resuspended in 50 μl of the following PCR master mix with indexed primers from the Nextera DNA Sample Preparation Index Kit (Illumina, FC-121-1011): 25 μl Phusion HF 2X (NEB, M0531L), 1 μl (1.5 for Hi-C) Nextera Index 1 N7XX, 1 μl (1.5 for Hi-C) Nextera Index 2 N5XX, 23 μl (22 for Hi-C) water. The PCR reaction was performed according to the following program: initial incubation at 72°C for 5 min and 98°C for 1 min, then x cycles of 98°C for 15 s, 63°C for 35 s and 72°C for 60 s. The number of PCR cycles was estimated based on post-ChIP quantification and amplification was 6 cycles for Hi-C libraries, 11 cycles for SATB1 HiChIP and 13 cycles for the other HiChIP libraries. DNA libraries were purified and size-selected using AMPure XP beads, quantified by Qubit and analyzed on a Bioanalyzer. The DNA Libraries were sequenced on an Illumina® HiSeq 4000 2x 75 bp platform.

tag: cell type

value: thymocytes

tag: strain

tag: age

value: 4-8 weeks

tag: genotype

value: wild type

tag: chip antibody

value: extra exon of long SATB1 isoform (Davids Biotechnologies, custom-made)


title: free

description: 5’capped 3’ polyA RNA

value: free


title: Satb1_cKO_rep3_ATACseq

data_processing:
To acquire BAM files and ATAC-seq peaks, raw data were fully processed by the complete esATAC pipeline (version 1.4.2; Wei et al., 2018). The esATAC uses F-seq (Boyle et al., 2008) to call peaks and these peak files are provided here. To identify the regions with differential accessibility between genotypes, all esATAC called peaks across samples and replicates were pooled and tested for differences in accessibility levels. ATAC-seq counts were calculated for each peak, each replicate and each condition using FeatureCounts function from Rsubread package (version 1.32.4; Liao et al., 2019) and used as an input for edgeR (version 3.24.3; Robinson et al., 2010) with the standard parameters. A cutoff of |logFC|≥1 and p-value ≤0.01 was used to determine the differentially accessible regions.
BigWig files were generated separately from the BAM file output of esATAC. Mitochondrial reads and PCR duplicates were removed from all BAM files using samtools (Li et al., 2009) and Picard MarkDuplicates (version 2.21.3; http://broadinstitute.github.io/picard/), respectively. Low quality and unmapped reads were removed using the following samtools command: samtools view h -b -F 1804 -f 2 -q 30. The final bam files were merged for the two conditions using samtools and RPKM normalized BigWig files were generated using deeptools (version 3.3.1; Ramírez et al., 2016) with the following parameters: -of bigwig --effectiveGenomeSize 2652783500 --normalizeUsing RPKM -bl mm10.blacklist.bed -bs 1. The blacklisted regions were downloaded from ENCODE (ENCFF547MET).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with ATAC-Seq signal for individual replicates and for merged replicates
Supplementary_files_format_and_content: bed files with ATAC-Seq peaks, the fourth column represents the score from F-seq

extract_protocol:
The ATAC-seq experiment was performed according to the Omni-ATAC protocol previously published (Corces et al., 2017), with modifications. Freshly isolated murine female thymocytes were separated using Lympholyte®-M (Cedarlane, CL5030) according to the manufacturer’s protocol, to ensure the presence of only viable cells. Isolated cells were washed twice with 1X PBS and aliquots of 10,000 cells were used for analysis. The cell pellet was gently resuspended by pipetting up and down three times in 50 µl of ice cold ATAC-RSB-NTD Buffer (10 mM Tris-HCl – pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 0.01% Digitonin) and incubated on ice for 3 minutes. Cell lysis was stopped by adding 1 ml of cold ATAC-RSB-T Buffer (10 mM Tris-HCl – pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and inverting the tube three times to mix. Nuclei were centrifuged at 1,000 g, at 4°C for 10 minutes. The pellet was resuspended in 50 µl of Transposition Mix [25 µl 2X TD buffer (20 mM Tris-HCl – pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide – before adding DMF, the pH was adjusted to 7.6 with 100% acetic acid), 2.5 µl transposase (100 nM final), 16.5 µl PBS, 0.5 µl 1% digitonin, 1 µl 5% Tween-20, 4.5 µl H2O] by pipetting up and down six times. The reaction was incubated at 37°C for 30 minutes with occasional pipetting. DNA was purified with a DNA Clean & Concentrator-5 Kit (Zymo Research, D4013) according to the manufacturer’s protocol. DNA was eluted in 20 µl of Elution Buffer.
All the material was used in a PCR reaction, together with 25 µl Phusion HF 2X Master Mix (NEB, M0531L) and 2.5 µl of each Nextera Index 1 (N7XX) and Nextera Index 2 (N5XX) primers from a Nextera DNA Sample Preparation Index Kit (Illumina, FC-121-1011). PCR was performed according to the following protocol: initial incubation at 72°C for 5 min and 98°C for 1 min, then 5x cycles of 98°C for 15 s, 63°C for 35 s and 72°C for 60 s. Samples were put on ice and 5 µl of the pre-amplified mixture was combined with 15 µl of qPCR Master Mix using the following set-up: 3.25 µl water, 0.5 µl primer FWD, 0.5 µl primer REV, 0.75 µl 20X SYBR Green, 5 µl Phusion HF 2X Master Mix, 5 µl pre-amplified sample. The qPCR reaction was run for additional 20 cycles following the program: initial incubation at 98°C for 1 min, then 20x cycles of 98°C for 15 s, 63°C for 35 s and 72°C for 60 s. Based on the Rn (Fluorescence) vs Cycle linear plot, a cycle with 1/4 up to 1/3 of the maximum fluorescence level was determined. This was the number of additional PCR cycles to run on the pre-amplified libraries which were stored on ice until this point. The final amplified libraries were purified using a DNA Clean & Concentrator-5 Kit (Zymo Research, D4013) according to the manufacturer’s protocol and eluted in 20 µl of Elution Buffer. Libraries were quantified by Qubit and analyzed on a Bioanalyzer as previously described, followed by two-sided size selection using AMPure Beads. Libraries were sequenced on an Illumina® HiSeq 4000 2x 75 bp platform.


title: ALS patient 7

city: Moncton

first: Rodney

last: Ouellette

address: 35 Providence St.

country: Canada

institute: ATLANTIC CANCER RESEARCH INSTITUTE

description: ALS patient plasma

data_processing:
RNA-seq reads were mapped using bowtie2 (version 2.2.6)  using hg19 version of index files.
parameters used are as follows with Bowtie2: --local --very-sensitive-local -q -mm
Counts were extracted with different tools such as: FeatureCounts (version 1.4.6-p4) : parameters -t gene -largestOverlap “ignoreDup -minOverlap 5 -C -M -O -o; HTSeq: parameters -f bam -a 0 -q -r pos -s no -t gene“idattr gene_id “nonunique all; ShortStack: --mincov1; snardiff   and derfinder (using our pipeline at https://github.com/acri-nb/derfinder-pipe) Bioconductor packages.
We calculated normalized TMM values using edgeR  ( version 3.18.1)
Genome_build: hg19
Supplementary_files_format_and_content: Csv file with normalized counts from 14 samples for each one of the 5  tools used to extract counts: FeatureCounts (_FC suffix), HTSeq (_HTS suffix); Derfinder (_DF suffix) ; srnadiff(_SRNA suffix); ShortStack (_SS suffix).

molecule: total RNA

source_name: Vn96-plasma Evs

extract_protocol:
RNA was extracted with miRVana Total RNA kit
RNA quality was assayed on Agilent Tape Station 2200 using RNA HS screen tape assay. RNA (25 ng) was used to prepare a small RNA library using Clean Tag Small RNA library kit (TriLink biotech). For each individual library, RNA was ligated to chemically modified adapters to suppress adaptor dimer formation. Modified adapters were added to both 3â€² and 5â€² ends following manufacturer recommended conditions. Adapter ligated RNA was reverse transcribed using Ion Torrent specific primer. cDNA was then amplified using Ion convert barcode primers containing a unique index to allow libraries to be pooled during Ion Torrent sequencing (Life Technologies). Library QC was assayed on Agilent Tape Station using D1000 screen tape. Equally-pooled libraries (pmol) were clonally amplified onto Ion Sphereâ„¢ Particles (ISPs) supplied by Ion Pi HiQ OT2 kit. ISPs were then loaded onto Ion PI chip and sequenced using Ion Torrent Proton Sequencer.

value: Plasma Evs

value: ALS


title: ALS patient 16

description: ALS patient plasma


title: WT_rep3_ATACseq


title: Satb1_cKO_rep1_ATACseq


title: WT_rep1_SATB1_HiChIP


title: ALS patient 5

description: ALS patient plasma


title: WT_rep1_ATACseq


title: WT_rep2_ATACseq


title: ALS patient 2

description: ALS patient plasma


title: ALS patient 4

description: ALS patient plasma


title: ALS patient 3

description: ALS patient plasma


title: sample 6119 count

city: Rochester

first: ARIJIT

last: PANDA

state: MINNESOTA

address: 200 1st street SW

institute: MAYO CLINIC

data_processing:
Raw sequences were mapped to reference genome (hg38) using STAR (v2.6.1)
Feature counts were calculated using subread (v1.5.1)
Genome_build: hg38
Supplementary_files_format_and_content: txt

source_name: Glioma Tissue

extract_protocol:
Samples were extracted with Qiazol Lysis Reagent prior to use of the Rneasy Lipid Tissue Mini Kit (Qiagen)
Samples were treated with Dnase, and ribodepleted with the Ribo-Zero rRNA removal kit (Illumina).  Samples were sequenced on the Illumina HiSeq in a 2x150bp configuration

tag: tissue

value: glioma


title: sample 6080 count


title: sample 5568 count


title: ALS patient 1

description: ALS patient plasma


title: Satb1_cKO_rep2_ATACseq


title: Healthy donor D

description: Healthy donor plasma

value: Normal


title: sample 5669 count


title: sample 3456 count


title: Healthy donor C

description: Healthy donor plasma


title: sample 5552 count


title: sample 5510 count


title: Healthy donor A

description: Healthy donor plasma


title: sample 5345 count


title: ALS patient 6

description: ALS patient plasma


title: sample 5154 count


title: Brain, THC, LPS3

city: Irvine

first: Daniele

last: Piomelli

address: 837 Health Sciences Road

institute: University of California, Irvine

data_processing:
Reads were mapped to the reference genome using STAR (v2.5) and HTSeq. STAR used the method of Maximal Mappable Prefix (MMP); STAR parameter mismatch of 2; HTSeq parameter of negative m union
STAR counted the number of reads per gene while mapping, and then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. This method was used to quantify the gene expression level.
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: abundance measurements (Normalized, Raw reads, fpkm)

source_name: brain

extract_protocol:
RNA was extracted using TRIzol reagent followed by PureLink RNA mini kit (Invitrogen). RNA was rendered genomic DNA free by running the samples through a genomic DNA shredder column (Qiagen).
Total RNA was extracted, library was constructed, and sequenced.

treatment_protocol: Male mice were administered THC (5 mg/kg, i.p.) or the vehicle (Veh, 8 % Tween-80 in saline) once daily from PND30-PND44 and when they reached adulthood (PND70) they were administered with LPS (0.33 mg/kg, i.p.) or saline (Ctrl). After 24 hours, mice were sacrificed and brain tissue was collected.

value: brain

tag: Sex

value: male

tag: treatment

value: THC followed by LPS


title: Healthy donor F

description: Healthy donor plasma


title: Brain, THC, LPS1


title: Healthy donor E

description: Healthy donor plasma


title: sample 5243 count


title: Brain, THC, LPS2


title: Brain, Veh, LPS3

value: vehicle followed by LPS


title: sample 5422 count


title: sample 5141 count


title: sample 5466 count


title: Brain, Veh, LPS2


title: sample 4136 count


title: Healthy donor B

description: Healthy donor plasma


title: Brain, THC, Ctrl2

value: THC followed by control


title: Brain, Veh, LPS1


title: sample 4055 count


title: sample 4002 count


title: sample 4050 count


title: Brain, THC, Ctrl1


title: sample 4059 count


title: sample 3999 count


title: Brain, Veh, Ctrl2

value: vehicle followed by control


title: Brain, Veh, Ctrl3


title: sample 3957 count


title: sample 3868 count


title: Brain, Veh, Ctrl1


title: TG mice 3

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

country: China

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hippocampal

value: TG

value: genotype


title: sample 3734 count


title: TG mice 2


title: sample 3470 count


title: Wildtype mice 3

value: Wild type


title: Brain, THC, Ctrl3


title: Wildtype mice 2


title: Wildtype mice 1


title: sample 3706 count


title: sample 3605 count


title: TG mice 1


title: sample 3693 count


title: sample 3430 count


title: sample 3436 count


title: sample 3599 count


title: sample 3607 count


title: sample 3278 count


title: sample 3524 count


title: sample 3269 count


title: sample 3258 count


title: sample 3284 count


title: sample 3034 count


title: sample 2911 count


title: sample 3089 count


title: sample 2986 count


title: sample 3074 count


title: sample 2874 count


title: sample 5385 count


title: sample 3678 count


title: sample 2737 count


title: sample 3139 count


title: sample 2683 count


title: sample 2475 count


title: Math1-Cre_SmoM2_Piezo2KO_MB_rep2

city: Changsha

first: Siyi

last: Wanggou

state: Hunan

address: Xiangya Road, No.87

department: Departmeng of Neurosurgery

institute: Xiangya Hospital, Central South University

data_processing:
The Illumina sequencer’s base call files (BCls) were demultiplexed into FASTQ files using cellranger mkfastq.
The FASTQ files were aligned to GRCm38 (mm10) mouse genome reference to generate barcode-labeled sparse matrices individually by cellranger count.
Genome_build: mm10

source_name: Medulloblastoma tissue

growth_protocol: Mice were maintained in specific pathogen-free conditions in the animal facility with 12:12 h light/dark cycles.

extract_protocol:
Math1-Cre; SmoM2 medulloblastoma and Math1-Cre; SmoM2; Piezo2fl/fl medulloblastoma from P21 mice were harvested followed by mechanical and enzymatic dissociation using the Papain Dissociation System (Worthington Biochemical Corporation). Single cell suspension was assessed by Trypan blue. Approximately 5,000 cells at a concentration of ~1,000 cells/μl were loaded onto the Chromium Controller.
Library generation for 10X Genomics v3 chemistry was performed using the Chromium Single Cell 3ʹ Reagents Kit. Quantifications of cDNA libraries were performed using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) and the high-sensitivity DNA chips. 10X libraries were sequenced using the Illumina 2500 sequencing platform to achieve ~25,000 reads per cell.
Two biological replicates of Math1-Cre; SmoM2 medulloblastoma. Two biological replicates of Math1-Cre; SmoM2; Piezo2fl/fl medulloblastoma. Four libraries in total.

treatment_protocol: Math1-Cre; SmoM2 mice vs Math1-Cre; SmoM2; Piezo2fl/fl mice

value: Math1-Cre; SmoM2; Piezo2fl/fl

value: post natal day 21


title: sample 3097 count


title: sample 3300 count


title: Math1-Cre_SmoM2_Piezo2KO_MB_rep1


title: Math1-Cre_SmoM2_MB_rep2

value: Math1-Cre; SmoM2


title: Math1-Cre_SmoM2_MB_rep1


title: sample 3105 count


title: sample 5829 count


title: sample 2443 count


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Euploid _2

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: processed file: annotated_WT_DP_peaks.txt

data_processing:
RNA-seq: Raw sequencing reads from mouse embryonic forebrain or adult hippocampus were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts against Ensembl v90 annotation.
Differential expression analysis was done using the DESeq2 package27 (v1.6.3) for both one-way ANOVA and pairwise comparisons at FDR (embryonic)/p-value (adult) cutoffs of 0.05.
For Smarca2/4 ChIP-seq and neuronal ATAC-seq from adult mouse hippocampus, raw sequencing reads were aligned to the mouse genome (mm10) using default settings of HISAT2.
For ATAC-seq, peak calling was performed using MACSv2.1.124 with settings --nomodel --shift -100 --extsize 200. For both ChIP-seq and ATAC-seq datasets, peaks were filtered for FDR < 0.05 and fold change > 1.2.
For ChIP-seq, peak-calling–normalized to respective inputs–was performed using MACSv2.1.124 with default settings; the window size was set as 300 bp.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file
Supplementary_files_format_and_content: bigWig file

source_name: Brain

extract_protocol:
RNA: RNA was isolated on RNeasy Microcolumns (Qiagen) following the manufacturer’s instructions; ChIP: Hippocampal tissues (unilateral hippocampus from two animals were pooled/biological replicate; Euploid, Ts65Dn and Ts65Dn; BRWD1+/-, 6-8 wk old) were crosslinked, quenched and processed, as previously described. Briefly, samples were washed thoroughly, lysed and sonicated. Samples were then incubated with a custom anti-Smarca2/4 antibody provided by the Crabtree lab (15) (7.5 ug/sample) bound to sheep anti-rabbit M-280 Dynabeads (Invitrogen) on a rotator at 4°C O/N. The following day, immunoprecipates were washed, eluted and reverse-crosslinked in elution buffer O/N. DNA was purified using a PCR purification kit (Qiagen); ATAC: Nuclei Isolation for (Fluorescence Activated Nuclear Sorting) FANS
Frozen whole hippocampus was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) by douncing 50x in a 10ml dounce homogenizer and filtered through a 40 µm cell strainer to isolate nuclei. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Mg(Ace)2, 1 mM DTT, 10 mM Tris-HCl, pH8) and subjected to centrifugation at 4,000 rpm for 15 minutes at 4°C to remove cellular debris. Pellets were thoroughly resuspended in 500 µl DPBS and incubated in BSA (final concentration 0.1%) and anti-NeuN antibody (1:1000, Alexa488 conjugated, Millipore, cat#: MAB377X) under rotation for 1 hour at 4 °C in the dark. Prior to FANS, DAPI (Sigma cat#: MBD0015) was added to a final concentration of 1 µg/ml. Unstained nuclei and nuclei stained with only secondary antibody served as negative controls. DAPI positive neuronal (NeuN+) nuclei were sorted into tubes using a BD-FACSAria flow cytometer (BD Biosciences) equipped with a 70μm nozzle.
RNA-seq and ChIP-seq: Following RNA purifications, libraries were prepared according to Illumina protocols and sequenced on an Illumina HiSeq 4000 sequencer; ATAC-seq: ATAC-seq reactions were performed using an established protocol (16) with minor modifications. Following FANS, 50,000 sorted nuclei were centrifuged at 500 × g for 10 min, 4°C. Pellets were re-suspended in transposase reaction mix [25 μL 2x TD Buffer (Illumina Cat #FC-121-1030), 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O] on ice. Samples were incubated at 37 °C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204) according to manufacturer’s instructions. Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011), under the following cycling conditions: 72 °C for 5 minutes, 98 °C for 30 seconds, followed by thermocycling at 98 °C for 10 seconds, 63 °C for 30 seconds and 72 °C for 1 minute for a total of 5 cycles. In order to prevent saturation due to over-amplification, a 5 µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 μL reaction. The additional number of cycles was determined as follows: (1) Plot linear Rn vs. Cycle, (2) Calculate the # of cycle that is corresponded to 1⁄4 of maximum fluorescent intensity. In general, we found adding 4-6 cycles to this estimate yielded optimal ATAC-seq libraries. Libraries were amplified for a total of 13–19 cycles. Following PCR, ATAC-seq libraries were purified and double-end size-selected by (.5x ratio and 1.8x ratio) Ampure XP bead purification (Beckman Coulter cat#; A63881) to remove primer-dimers (<100bp) and large fragments (>1000bp). Library size was quantified using Bioanalyzer High Sensitivity DNA Chips (Agilent technologies Cat#5067-4626). Libraries were quantified by quantitative PCR (KAPA Biosystems Cat#KK4873) prior to sequencing. Libraries were sequenced on NovaSeq 6000 System (Illumina) obtaining 2 x 50 paired-end reads.

treatment_protocol: Genotypes compared: euploid vs. Ts65Dn vs. Ts65Dn; Brwd1+/–

tag: gender

value: Male

tag: region

value: Hippocampus

value: WT

tag: Stage

value: Adult

tag: experiment

value: ATAC-seq

tag: sample type

value: IP

value: Neuron


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Euploid _3


title: sample 5149 count

value: glioma


title: sample 2403 count


title: sample 1634 count


title: sample 3790 count


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Ts65Dn _3

description: processed file: annotated_TS_DP_peaks.txt

value: Trisomic


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Euploid _1


title: sample 3110 count


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Ts65Dn _2


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Ts65Dn _1


title: sample 2436 count


title: sample 1182 count


title: sample 5558 count


title: sample 2507 count


title: sample 2897 count


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Ts65Dn; Brwd1+/– _2

description: processed file: annotated_CR_DP_peaks.txt

value: Brwd1 Rescue


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Ts65Dn; Brwd1+/– _1


title: sample 3331 count


title: sample 2307 count


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_Input_4

description: processed file: annotated_WT_peaks_1e-4.txt

value: ChIP-seq

value: Input


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_Input_4

description: processed file: annotated_cross_peaks_1e-4.txt


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_Input_2


title: sample 4042 count


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_Input_3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_Input_1


title: sample 2549 count


title: sample 3413 count


title: Adult_Hippocampus_Male_Neuronal ATAC-Seq_Ts65Dn; Brwd1+/– _3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_Input_4

description: processed file: annotated_Ts_peaks_1e-4.txt


title: sample 3653 count


title: sample 5572 count


title: sample 3842 count


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_Input_2


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_Input_1


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_Input_3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_Input_3


title: sample 2470 count


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_Input_2


title: sample 6119 K4me3

data_processing:
Raw sequences were mapped to reference genome (hg38) using BWA (v0.7.17-r1194-dirty) sampe with the following parameters -n 10 -a 500 -o 10000 -N 10
Narrow Peak calling was performed using MASC2 (v2.0.10.20120913 tag:beta). Parameters: effective genome size = 2.70e+09  band width = 123  model fold = [5, 50]  qvalue cutoff = 1.00e-02
Board Peak calling was performed using SICER (v1.1)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Glioma tissue

extract_protocol:
Frozen tissue was homogenized and fixed with 1% formaldehyde.  Lysates were sonicated and Histone associated DNA were isolated with antibodies.
Libraries were prepared with the ThruPLEX DNA-seq Kit (Rubicon Genomics) per the manufactures guidelines.

value: K4me3 (Mayo Clinic Epigenomics Development Laboratory, Lot 1)


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_Input_1


title: sample 5568 K4me3


title: sample 6080 K4me3


title: sample 5243 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_IP_4


title: sample 3456 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_IP_4


title: sample 2462 count


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_IP_2


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_IP_1


title: sample 5669 K4me3


title: sample 5552 K4me3


title: sample 5510 K4me3


title: sample 5345 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_IP_3


title: sample 5154 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_IP_2


title: sample 5422 K4me3


title: sample 5141 K4me3


title: sample 4055 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_IP_1


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_IP_2


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn; Brwd1+/–_IP_3


title: sample 3999 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_IP_3


title: sample 4002 K4me3


title: sample 4050 K4me3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Ts65Dn_IP_4


title: E16_FB-derived_neuronal_culture_RNA-Seq_Ts65Dn_2

data_processing:
RNA-seq: Raw sequencing reads from mouse embryonic forebrain or adult hippocampus were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts against Ensembl v90 annotation.
Differential expression analysis was done using the DESeq2 package27 (v1.6.3) for both one-way ANOVA and pairwise comparisons at FDR (embryonic)/p-value (adult) cutoffs of 0.05.
For Smarca2/4 ChIP-seq and neuronal ATAC-seq from adult mouse hippocampus, raw sequencing reads were aligned to the mouse genome (mm10) using default settings of HISAT2.
For ATAC-seq, peak calling was performed using MACSv2.1.124 with settings --nomodel --shift -100 --extsize 200. For both ChIP-seq and ATAC-seq datasets, peaks were filtered for FDR < 0.05 and fold change > 1.2.
For ChIP-seq, peak-calling–normalized to respective inputs–was performed using MACSv2.1.124 with default settings; the window size was set as 300 bp.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

value: pooled male and female

value: Forebrain-derived primary neuronal cultures

value: Embryonic

value: RNA-seq


title: sample 3957 K4me3


title: E16_FB-derived_neuronal_culture_RNA-Seq_Ts65Dn_3


title: sample 4059 K4me3


title: E16_FB-derived_neuronal_culture_RNA-Seq_Ts65Dn_1


title: sample 3868 K4me3


title: E16_FB-derived_neuronal_culture_RNA-Seq_Euploid _2


title: sample 3470 K4me3


title: E16_FB-derived_neuronal_culture_RNA-Seq_Ts65Dn; Brwd1+/– _2


title: E16_FB-derived_neuronal_culture_RNA-Seq_Ts65Dn; Brwd1+/– _3


title: Adult_Hippocampus_Male_Smarca2/4 ChIP-Seq_Euploid_IP_1

value: Male


title: E16_FB-derived_neuronal_culture_RNA-Seq_Ts65Dn; Brwd1+/– _1


title: sample 3706 K4me3


title: sample 3607 K4me3


title: sample 3653 K4me3


title: sample 3693 K4me3


title: sample 3605 K4me3


title: E16_FB-derived_neuronal_culture_RNA-Seq_Euploid _3


title: Myocarditis patient blood 7374-MA-1

city: Nashville

first: Margaret

middle: L

last: Axelrod

state: TN

address: 2200 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt University

description:
Myocarditis patient blood
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
CD45+ cells were FACS sorted and prepapred as single cell suspensions
Library was performed according to the manufacter’s instructions (single cell 5’ RNA + VDJ protocol, 10x Genomics).
scRNA-seq and scTCR-seq

value: CD3+ PBMC

value: Blood


title: lungs of COVID-19 patient 4

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq550 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: human lung

growth_protocol: Total RNA was isolated from the lungs of control patients and COVID-19 patients.

extract_protocol:
RNA-seq in human lungs: Total RNA was isolated from the lungs of control patients and COVID-19 patients using an RNeasy Protect Mini Kit (Qiagen).
RNA-seq in human lungs: Library preparation was performed using a Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: lung

tag: disease

value: COIVD-19 patient


title: sample 3524 K4me3


title: lungs of COVID-19 patient 3

treatment_protocol: Total RNA was isolated from the lungs of control patients and COVID-19 patients.


title: lungs of COVID-19 patient 2


title: lungs of COVID-19 patient 1


title: E16_FB-derived_neuronal_culture_RNA-Seq_Euploid _1

value: WT


title: sample 3269 K4me3


title: sample 3284 K4me3


title: sample 3339 count


title: lungs of healthy donor

value: healthy donor


title: OVCAR-5 shSCD rep 3

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-analyzed using FastQC (0.11.5)
Reads were aligned to the ENSEMBL human genome GRCh38 (release 91) using STAR (2.5.2)
BAM files from STAR alignment were sorted by name using Samtools (1.6)
HTSeq-count (anaconda 3.6) was used to generate raw counts for each BAM file
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: ascites

growth_protocol: OVCAR-5 shCtrl and shSCD ovarian cancer cells were routinely cultured and maintained in their required medium.

extract_protocol:
RNA was harvested using TRI Reagent (Sigma Aldrich). gDNA was removed using QIAGEN RNeasy MinElute Cleanup Kit. Then mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep kit for Illumina.

treatment_protocol: OVCAR-5 shCtrl and shSCD cells were cultured in low serum condition (1% FBS) for 48 hours; then the cells were harvested for RNA extraction.

value: ovarian cancer cell

tag: tumor stage

value: high grade serous

tag: shRNA

value: unknown

tag: passage

value: shSCD


title: sample 3339 K4me3

value: glioma


title: Myocarditis patient blood 7374-MA-1 TCR

description:
Myocarditis patient blood
10x Genomics

tag: cell type


title: sample 3258 K4me3

value: K4me3 (Mayo Clinic Epigenomics Development Laboratory, Lot 1)


title: OVCAR-5 shSCD rep 1


title: OVCAR-5 shSCD rep 2


title: sample 3034 K4me3


title: sample 3074 K4me3


title: OVCAR-5 shCtrl rep 3

value: shCtrl


title: sample 2911 K4me3


title: sample 3089 K4me3


title: sample 3105 K4me3


title: OVCAR-5 shCtrl rep 2


title: sample 3436 K4me3


title: OVCAR-5 shCtrl rep 1


title: LNCaP_OGT Si2_INPUT

city: Oxford

first: Ninu

last: Poulose

state: Oxfordshire

address: Headley Way

department: Nuffield Department of Surgical Sciences

country: United Kingdom

institute: University of Oxford

data_processing:
Fastq files were generated with Illumina pipeline software (bcl2fastq version 2.19 using the default thresholds).
Reads were mapped to the GRCh37/hg19 reference genome using bowtie2 (version 2.2.6) and subsequently filtered to remove PCR duplicates.
Prior to peak calling, Encode curated blacklisted genomic regions were removed from bam files.
Fastq files were aligned to hg19 using bowtie2.
The MACS algorithm (version 2.1.2) was used to analyse the resulting alignments and identify transcription factor binding regions.
Supplementary_files_format_and_content: bed

source_name: LNCaPs

growth_protocol: Prostate cancer cells (LNCaPs) were cultured in RPMI media supplemented with 10% FBS and pencillin-streptomycin.

extract_protocol:
After 24h nutlin-3a treatment or 3 days post transfection, cells were fixed with 1% formaldehyde and chromatin prepared by sonication in Bioruptor plus. Fragmentation efficiency was analysed using fragment analyser and ChIP carried out using diagenode iDeal ChIP-seq kit for transcription factors (Cat# C01010170).
Libraries were prepared using Diagenode MicroPlex Library Preparation Kit v2 (Cat# C05010014) and purified and purified/size selected using Agencourt® AMPure® XP beads (Beckman Coulter, Cat. No. A63881)

treatment_protocol: LNCaPs were treated 2.5uM nutlin-3a for 24h. For siRNA transfections, forward transfection was performed the following day using Lipofectamine RNAiMAX Transfection Reagent in OPTI-MEM with 30 pmol of siRNA/well according to the manufacturer’s instructions. After overnight incubation, media was changed to RPMI with 10% FBS.

tag: agent

value: OGT Si2


title: sample 2683 K4me3


title: LNCaP_OGT Si1_INPUT

value: OGT Si1


title: sample 3300 K4me3


title: sample 4090 K4me3


title: LNCaP_Scr Si_INPUT

value: Scr Si


title: LNCaP_OGT Si2_p53


title: sample 2475 K4me3


title: LNCaP_OGT Si1_p53


title: sample 4090 count


title: sample 2436 K4me3


title: sample 2443 K4me3


title: LNCaP_VPRBP Si2_p53

value: VPRBP Si2


title: sample 5829 K4me3


title: sample 5385 K4me3


title: LNCaP_VPRBP Si2_INPUT


title: LNCaP_VPRBP Si1_p53

value: VPRBP Si1


title: LNCaP_Nutlin 3A_p53

value: Nutlin 3A


title: sample 2403 K4me3


title: LNCaP_VPRBP Si1_INPUT


title: LNCaP_Scr Si_p53


title: sample 5558 K4me3


title: sample 3331 K4me3


title: sample 1182 K4me3


title: LNCaP_Nutlin 3A_Input


title: sample 2307 K4me3


title: sample 3413 K4me3


title: sample 4028 K4me3


title: sample 3790 K4me3


title: sample 3842 K4me3


title: sample 6119 K4me1

value: K4me1 (Cell Signaling Technology, Cat# 5326, Lot 1)


title: sample 2462 K4me3


title: sample 6080 K4me1


title: sample 2897 K4me3


title: CFA/IFA-treated  MLNs

type: RNA

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

description:
CFA/IFA-treated
Gene expression data from MLNs

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 Array at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT).

label: biotin

source_name: MLNs

label_protocol: The sense cDNA was then fragmented and biotin-labeled with terminal deoxynucleotidyl transferase using the GeneChip WT Terminal labeling kit.

growth_protocol: The epithelial cells were isolated from large intestines of mice treated with PBS or CFA/IFA on day 5.

extract_protocol: Using Qiagen Rneasy, kits the total RNA extraction was performed according to the manufacturer's protocol instructions

treatment_protocol: Mice were subcutaneously injected with PBS or CFA (Chondrex, Cat# 7009)/IFA (Chondrex, Cat# 7001).

value: mesenteric lymph nodes


title: Vehice-treated PPs

description:
Vehice-treated
Gene expression data from PPs

source_name: PPs

value: Peyer's patches


title: SJLB800

city: Chapel Hill

first: Federico

last: Innocenti

state: North Carolina

address: 120 Mason Farm  Road, CB7361

department: Eshelman School of Pharmacy

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-Seq reads were trimmed of adapter and for quality using Trimmomatic v0.35 leaving paired reads with a minimum length of 20 bp
Trimmed RNA-Seq reads were mapped to the human genome reference hg19/GRCh37 via HiSat2
Alignment files were sorted and converted into bam files and Picard Tools used to mark duplicates in the alignments
Counts for exons, genes and TPMs (Transcripts per Kilobase Million) were generated with RNASeqC v2.1 in “legacy” mode with the Gencode.v19.gene.v7.patched_contigs.gtf annotation file as a guide.  The 29,245 gene transcripts with expression thresholds of >0.1 TPM and ≥6 reads in at least ten individuals were selected for analysis.
The distribution of TPMs in each sample was quantile normalized to the average empirical distribution observed across all samples.  The normalized TPMs for each gene were subsequently transformed to the quantiles of the standard normal distribution.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: gene_reads.txt.gz - gene read counts
Supplementary_files_format_and_content: gene_tpm_normalized.txt.gz - normalized TPM counts
Supplementary_files_format_and_content: exon_reads.txt.gz - exon fractional read counts (These are NOT integers. Counts are distributed based on the mappings to exons such that if a read maps to more than one exon, a fractional value is assigned to that exon equal to the percentage of the read contained within that exon); subset of exons within the 29,245 genes

source_name: liver tissue

extract_protocol:
 Total RNA was extracted from tissue homogenized in TRIzol reagent, followed by Qiagen RNAeasy cleanup
mRNA libraries were prepared using the Illuminia TruSeq Stranded Total RNA with Ribo-Zero protocol

value: liver

value: female

tag: age


title: CFU-E_Epo_KO_3h

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Gene expression data from CFU-E KO mouse

hyb_protocol: 15 µg labelled cRNA were hybridized onto the Mouse Genome 2.0 GeneChip® Arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix)

data_processing: CEL files were analysed using the affy R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: CFU-E cells, Epo KO, 3 hours

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix)

growth_protocol: Fetal livers from EpoR-/- BALB/c mice embryos at 13.5 gestational day were dissected and fetal liver cells were negatively sorted to obtain CFU-E cells.

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Freshly extracted EpoR-/- CFU-E cells were washed three times and deprived from growth factors in Panserin 401 (Pan Biotech) supplemented with 50 mM 2-mercaptoethanol and 1% BSA at 37°C for 1 h.The cells were washed once and re-suspended in Panserin 601 at a density of 1×10^6 cells/replicate. EpoR-/- CFU-E cells were cultivated in PANSERIN 601 without addition of supplemental growth factors for three hours (KO_3) or lysed immediately (KO_0) by the addition of an equal volume of ice cold lysis buffer (2x 1% Nonidet P-40 lysis buffer supplemented with 2 μg/ml aprotinin and 200 μg/ml AEBSF).

tag: developmental stage

tag: genotype

value: Epo KO

value: supplemental growth factors


title: SJLB798

tag: tissue

value: male


title: CFA/IFA-treated  PPs

description:
CFA/IFA-treated
Gene expression data from PPs


title: sample 5243 K4me1

tag: chip antibody

value: glioma


title: CFU-E_Epo_KO_0h

source_name: CFU-E cells, Epo KO, 0 hour

tag: background strain

value: BALB/c

tag: treatment

value: control


title: SJLB796

tag: Sex


title: Vehice-treated MLNs

description:
Vehice-treated
Gene expression data from MLNs


title: sample 3456 K4me1


title: sample 5568 K4me1


title: CFA/IFA-treated  S-IECs

description:
CFA/IFA-treated
Gene expression data from S-IECs

source_name: S-IECs

value: small intestinal epithelial cells


title: Vehice-treated L-IECs

description:
Vehice-treated
Gene expression data from L-IECs

source_name: L-IECs

value: large intestinal epithelial cells


title: CFA/IFA-treated  L-IECs

description:
CFA/IFA-treated
Gene expression data from L-IECs


title: sample 5669 K4me1


title: sample 5552 K4me1


title: sample 5572 K4me3

value: K4me3 (Mayo Clinic Epigenomics Development Laboratory, Lot 1)


title: SJLB795


title: SJLB794


title: sample 5510 K4me1


title: SJLB793


title: sample 5345 K4me1


title: SJLB791


title: sample 5154 K4me1


title: SJLB788


title: Vehice-treated S-IECs

description:
Vehice-treated
Gene expression data from S-IECs


title: SJLB786


title: sample 5141 K4me1


title: SJLB783


title: sample 5422 K4me1


title: SJLB778


title: SJLB780


title: SJLB770


title: sample 4002 K4me1


title: sample 3999 K4me1


title: sample 4050 K4me1


title: sample 4055 K4me1


title: SJLB779


title: sample 4059 K4me1


title: SJLB775


title: sample 3957 K4me1


title: SJLB759


title: SJLB765


title: sample 3868 K4me1


title: SJLB763


title: sample 3706 K4me1


title: SJLB757


title: sample 3470 K4me1


title: SJLB767


title: SJLB754


title: SJLB755


title: SJLB753


title: sample 3607 K4me1


title: sample 3653 K4me1


title: sample 3605 K4me1


title: sample 3524 K4me1


title: SJLB773


title: sample 3693 K4me1


title: SJLB751


title: sample 3436 K4me1


title: SJLB750


title: sample 3339 K4me1


title: sample 3284 K4me1


title: sample 3269 K4me1


title: SJLB744


title: SJLB741


title: SJLB732


title: sample 3258 K4me1


title: SJLB749


title: sample 2911 K4me1


title: SJLB745


title: SJLB730


title: SJLB742


title: sample 3034 K4me1


title: sample 3105 K4me1


title: sample 3074 K4me1


title: SJLB727


title: sample 2683 K4me1


title: SJLB733


title: sample 3300 K4me1


title: SJLB728


title: sample 4090 K4me1


title: SJLB722


title: sample 2475 K4me1


title: SJLB724


title: SJLB720


title: sample 3089 K4me1


title: sample 5385 K4me1


title: SJLB716


title: SJLB725


title: SJLB713


title: SJLB711


title: SJLB669


title: SJLB687


title: sample 2443 K4me1


title: sample 3790 K4me1


title: SJLB665


title: sample 1182 K4me1


title: SJLB671


title: sample 2307 K4me1


title: SJLB657


title: sample 2403 K4me1


title: sample 3331 K4me1


title: sample 5558 K4me1


title: sample 4028 K4me1


title: SJLB662


title: SJLB644


title: sample 3413 K4me1


title: SJLB643


title: sample 3842 K4me1


title: sample 5829 K4me1


title: sample 2436 K4me1


title: sample 2462 K4me1


title: SJLB642


title: SJLB639


title: sample 5572 K4me1


title: sample 2897 K4me1


title: sample 6119 K36me3


title: SJLB659


title: SJLB636


title: SJLB634


title: sample 6080 K36me3


title: sample 5243 K36me3


title: sample 5568 K36me3


title: SJLB633


title: SJLB630


title: SJLB627


title: sample 3456 K36me3


title: sample 5669 K36me3


title: sample 5552 K36me3


title: sample 5154 K36me3


title: sample 5510 K36me3


title: SJLB623


title: SJLB624


title: SJLB620


title: SJLB629


title: SJLB619


title: SJLB493


title: sample 5422 K36me3


title: SJLB617


title: sample 5141 K36me3


title: sample 4055 K36me3


title: SJLB618


title: SJLB491


title: SJLB492


title: sample 3999 K36me3


title: sample 4050 K36me3


title: sample 4002 K36me3


title: SJLB489


title: SJLB632


title: sample 3957 K36me3


title: sample 4059 K36me3


title: SJLB485


title: sample 5345 K36me3


title: SJLB479


title: sample 3693 K36me3


title: SJLB476


title: sample 3470 K36me3


title: sample 3706 K36me3


title: SJLB470


title: SJLB465


title: SJLB466


title: sample 3653 K36me3


title: sample 3607 K36me3


title: SJLB464


title: sample 3605 K36me3


title: sample 3524 K36me3


title: sample 3436 K36me3


title: SJLB484


title: SJLB461


title: SJLB458


title: SJLB459


title: SJLB457


title: sample 3284 K36me3


title: SJLB450


title: sample 3339 K36me3


title: sample 3258 K36me3


title: sample 3269 K36me3


title: SJLB444


title: sample 3868 K36me3


title: SJLB440


title: SJLB439


title: sample 3034 K36me3


title: sample 3089 K36me3


title: sample 3105 K36me3


title: sample 3074 K36me3


title: SJLB438


title: SJLB437


title: SJLB436


title: sample 2911 K36me3


title: SJLB433


title: sample 2683 K36me3


title: sample 3300 K36me3


title: SJLB431


title: sample 2475 K36me3


title: sample 4090 K36me3


title: SJLB424


title: SJLB426


title: SJLB423


title: sample 2436 K36me3


title: sample 5829 K36me3


title: SJLB421


title: SJLB419


title: sample 2403 K36me3


title: sample 2443 K36me3


title: SJLB417


title: sample 1182 K36me3


title: SJLB418


title: sample 3790 K36me3


title: SJLB435


title: sample 5558 K36me3


title: SJLB416


title: SJLB434


title: sample 5385 K36me3


title: sample 2897 K36me3


title: SJLB414


title: sample 4028 K36me3


title: SJLB413


title: sample 3331 K36me3


title: SJLB411


title: sample 2307 K36me3


title: SJLB407


title: SJLB406


title: sample 3413 K36me3


title: SJLB415


title: sample 5572 K36me3


title: SJLB403


title: SJLB404


title: sample 3842 K36me3


title: SJLB400


title: SJLB393


title: SJLB399


title: sample 6119 K27ac

value: K27ac (Cell Signaling Technology, Cat# 8173, Lot 1)


title: SJLB387


title: sample 6080 K27ac


title: sample 5568 K27ac


title: sample 3456 K27ac


title: sample 2462 K36me3


title: sample 5669 K27ac


title: sample 5552 K27ac


title: SJLB382


title: sample 5510 K27ac


title: SJLB390


title: SJLB383


title: SJLB381


title: SJLB380


title: sample 5154 K27ac


title: sample 5141 K27ac


title: SJLB379


title: sample 5422 K27ac


title: SJLB378


title: SJLB388


title: sample 4055 K27ac


title: SJLB376


title: sample 5243 K27ac


title: SJLB374


title: sample 4050 K27ac


title: sample 5345 K27ac


title: sample 4002 K27ac


title: SJLB369


title: SJLB372


title: sample 3999 K27ac


title: SJLB368


title: SJLB365


title: SJLB363


title: sample 3957 K27ac


title: sample 3868 K27ac


title: sample 3706 K27ac


title: sample 3470 K27ac


title: SJLB360


title: sample 3653 K27ac


title: sample 3605 K27ac


title: SJLB356


title: Amygdala Ethanol 2 RNA-seq

first: Subhash

middle: C

last: Pandey

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

data_processing:
Sequence quality control using FASTQC (v0.11.8) and processing, reads were aligned to the reference Rattus Norvegicus Rnor 6.0 genome from NCBI (release 106) and counted using STAR (v2.7.0f).
Read counts per gene were generated using the featureCounts function from Subread v1.6.3 with default parameters.
We used R (v3.6.2) (R Core Team, 2019-12-12) for all statistical analyses. The TMM (trimmed mean of M-values) normalization method in the edgeR package was used to normalize reads to account for differences arising from total number of reads and RNA composition differences.
We estimated sample-specific quality weights and observational (gene)-level weights using the voomWithQualityWeights function in the limma package, which also transformed the counts appropriately for linear modeling. The transformed values and weights were tested for differential expression using an empirical Bayes method and false discovery rates evaluated.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: featCounts file (.txt) signifying gene read counts

organism: Rattus norvegicus

source_name: Ethanol injected (i.p 1g/kg)

extract_protocol:
Brains were collected for the dissection of amygdala and following total RNA extraction, RNA integrity numbers (RIN) for each RNA sample were determined using an Agilent Tapestation and were all above 8.0. Samples were then used for RNA-sequencing (single-end) using the Illumina platform.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit'.
The libraries were pooled in equimolar concentration, quantitated by qPCR and sequenced on three lanes for 101 cycles from one end of the fragments on a HiSeq2500 using a HiSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina). Reads are  100nt in length. Adaptors have been trimmed from the 3'-end of the reads.

treatment_protocol: Adult male Sprague Dawley rats received either saline or ethanol (1g/kg) intraperitoneal injections and after 1 h animals were sacrificed and amygdala tissue collected for RNA-seq. Treatment protocol is as described in "Pandey et al., 2008, Journal of Neuroscience 28 (14), 3729-3737". A total of 6 controls (saline-treated) and 6 ethanol treated (1g/kg; IP) rats were used for the experiment and total RNA from 2 animals was pooled to obtain n=3 for RNA-seq.

tag: strain

value: Sprague Dawley/WT

value: Amygdala

tag: treatment group

value: Acute Ethanol


title: Amygdala Ethanol 3 RNA-seq


title: SJLB366


title: Amygdala Ethanol 1 RNA-seq


title: Amygdala Control 2 RNA-seq

source_name: Saline injected

value: Control


title: Amygdala Control 3 RNA-seq


title: SJLB355


title: sample 3524 K27ac


title: SJLB357


title: sample 4059 K27ac


title: Amygdala Control 1 RNA-seq


title: sample 3436 K27ac


title: sample 3693 K27ac


title: SJLB352


title: SJLB353


title: SJLB358


title: SJLB351


title: SJLB359


title: sample 3607 K27ac


title: left ventricel, PGC-1α4 overexpression, 4-week-old, rep2

city: Kuopio

first: Tomi

last: Tuomainen

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Base calling was performed with bcl2fastq software (Illumina) with automatic adapter trimming.
Sequencing reads were aligned to genomic DNA with Hisat2 software using indexes for mouse GRCm38 genome builds
Total gene counts were achieved from alignments stored in bam file format with QoRTs software against Ensembl’s gene annotation release version 92.
Assembly: GRCm38

source_name: left ventricle

extract_protocol:
TissueLyzer II (Qiagen) with TRI reagent
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047 rev E)

value: left ventricle

value: floxed Pgc-1{alpha}4 + Myh6-cre


title: left ventricel, PGC-1α4 overexpression, 4-week-old, rep1


title: left ventricel, control, 4-week-old, rep3

value: floxed Pgc-1{alpha}4


title: left ventricel, PGC-1α4 overexpression, 4-week-old, rep4


title: sample 3269 K27ac


title: left ventricel, PGC-1α4 overexpression, 4-week-old, rep3


title: left ventricel, control, 4-week-old, rep4


title: left ventricel, control, 4-week-old, rep2


title: sample 3339 K27ac


title: SJLB349

value: liver


title: sample 3284 K27ac


title: venticles, PGC-1α4 overexpression, neonatal, rep4

source_name: ventricles

value: ventricles


title: sample 3258 K27ac


title: venticles, PGC-1α4 overexpression, neonatal, rep3

value: male


title: venticles, PGC-1α4 overexpression, neonatal, rep2


title: SJLB348


title: sample 3034 K27ac

value: glioma


title: venticles, PGC-1α4 overexpression, neonatal, rep1


title: SJLB347

value: female


title: SJLB350


title: sample 3074 K27ac


title: venticles, control, neonatal, rep3


title: venticles, control, neonatal, rep4


title: sample 3089 K27ac


title: venticles, control, neonatal, rep2


title: SJLB346


title: sample 2911 K27ac


title: SJLB345


title: SJLB344


title: SJLB343


title: NC-2_input

city: Shanghai

first: Xiang

last: Gu

address: Zhizaoju Road

institute: shanghai ninth people hospital

data_processing:
The harvested paired-end reads were subjected to quality control using Q30 and 3’ adaptor trimming by cutadapt software (v1.9.3) to remove low-quality reads.
Clean reads of all libraries were aligned to the reference genome (HG19) using HISAT2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified through MACS software and differentially methylated sites were identified by diffReps.
The peaks identified overlapping with exons of mRNA were chosen.
GO and pathway enrichment analyses were performed using the differentially methylated protein coding genes.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: MeRIP-seq

growth_protocol: 92.1 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
RNA was randomly fragmented to approximately 200 nt through RNA Fragmentation Reagents and protein A/G beads were connected to an m1A antibody (202003, Synaptic Systems, Germany) by rotating at RT for 1 h. The RNA fragments were incubated with the beads at 4 °C for 4 h. Then, the captured RNA was eluted from the beads and extracted with TRIzol Reagent (Invitrogen, USA). Both the input sample and the m1A IP sample were subjected to library generation with the NEBNext Ultra RNA Library Prep Kit (New England Biolab, UK).

tag: cell line

value: Ocular melanoma cells

value: WT

tag: rip antibody

value: none (input)


title: SH-2_input

value: ALKBH3 knockdown


title: left ventricel, control, 4-week-old, rep1


title: sample 3105 K27ac

value: K27ac (Cell Signaling Technology, Cat# 8173, Lot 1)


title: NC-1_input


title: sample 5385 K27ac


title: sample 2683 K27ac


title: SJLB342


title: sample 3300 K27ac


title: 92.1-2_input


title: 92.1-1_input


title: venticles, control, neonatal, rep1


title: SJLB341


title: SH-2_IP


title: Pig1-1_input

value: melanocyte


title: SH-1_IP


title: SH-1_input


title: SJLB340


title: NC-2_IP


title: Pig1-2_input


title: sample 4090 K27ac


title: NC-1_IP


title: SJLB338


title: sample 2475 K27ac


title: Pig1-2_IP


title: Pig1-1_IP


title: 92.1-2_IP


title: SJLB337


title: 92.1-1_IP


title: SJLB336


title: SJLB335


title: sample 2436 K27ac


title: sample 5829 K27ac


title: SJLB334


title: sample 2443 K27ac


title: SJLB333


title: sample 3790 K27ac


title: sample 2403 K27ac


title: SJLB332


title: sample 1182 K27ac


title: SJLB331


title: sample 5558 K27ac


title: sample 2897 K27ac


title: SJLB328


title: NB4-Input Sample

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.3.5)
Peaks were identified using MACS2 (v2.0.9)
Assembly: hg38
Supplementary files format and content: peak text files

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


title: SJLB325


title: HC9 control monocytes

city: Yokohama-shi

first: Yukie

last: Yamaguchi

state: Kanagawa-Ken

address: 3-9 Fukuura Kanazawa-ku

institute: Yokohama City University Graduate School of Medicine

data_processing:
HISAT2 version 2.1.0, Bowtie2 2.3.4.1
Transcript is assembled by StringTie version 2.1.3b with aligned reads.
DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (Periostin_vs_Control) as requested using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Normalization values are provided as FPKM  / RPKM and TPM for each sample.

source_name: monocytes

growth_protocol: Monocytes isolated from blood samples obtained from three HCs were seeded in 12-well multi-dishes in RPMI1640 supplemented with 1% penicillin–streptomycin and 10% FBS.

extract_protocol:
About 0.5-1μg of total RNA was extracted from the six samples (3 PBS controls and 3 rPn-stimulated)  using the IllustraTM RNAspin Mini RNA Isolation Kit.
Total RNA was used to prepare sequencing libraries with the TruSeq stranded mRNA kit  in accordance with the manufacturer’s instructions. .

treatment_protocol: Two hours after isolation, monocytes were stimulated by 10 μL/mL of PBS or 1000 ng/mL of human recombinant periostin. Cells were harvested 16 hours after stimulation.

tag: individual

value: Healthy control HC9

value: monocytes

value: control


title: HC1 Periostin-stimulated monocytes

value: Healthy control HC1

value: rPeriostin-stimulated


title: HC12 Periostin-stimulated monocytes

value: Healthy control HC12


title: HC9 Periostin-stimulated monocytes


title: sample 3331 K27ac

first: ARIJIT

last: PANDA

address: 200 1st street SW

institute: MAYO CLINIC

source_name: Glioma tissue


title: HC12 control monocytes


title: HC1 control monocytes


title: SJLB321

value: liver


title: sample 2307 K27ac


title: SJLB323


title: sample 4028 K27ac


title: SJLB320


title: SJLB319


title: sample 3413 K27ac


title: sample 5572 K27ac


title: SJLB318


title: sample 2462 K27ac


title: NB4-LDB1


title: Youth pulp, scRNAseq

city: Beijing

first: Huihui

last: Ren

address: No.22, Zhongguancun Nandajie, Haidian District

institute: Peking University School and Hospital of Stomatology

description: 10x Genomics

data_processing:
The cell Ranger software pipeline (version 4.0.0) provided by 10XGenomics was used to demultiplex, barcoded process, gene count and aggregation.(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: dental pulp

extract_protocol:
The tissue was extracted and transported to laboratory in 4℃ α-MEM with 10% penicillin-streptomycin solution immediately. Soft dental pulp tissue was  washed in Mg2+/Ca2+ free phosphate-buffered saline (PBS)  following enamel and dentin was broken by sterilized pliers in super clean bench. Subsequently, the pulp tissue was shred into small pieces (<1 mm3) and centrifuged. The precipitation was digested for 40 min in 3mg/ml Type 1 Collagenase at 37℃, under agitation at 300 rpm in oscillation box, and blew by pipette gun 8-10 times every 8-10 min. The digestion was stopped by 2% FBS  and then filtered through a 40 μm cell strainer. After centrifuged, the pellet was re-suspended in PBS including 2% FBS and re-sieved through a 40 μm cell strainer.
RNA libraries were prepared with Chromlum Single cell 3' Reagent Kits v3 according to the manufacture's protocol

value: dental pulp

value: dental pulp cells

tag: development stage

value: human dental pulp of third molar less than 1/3 root completed

value: no


title: ICC7_TCR

first: Hong Yuen

last: Wong

state: Tennessee

address: 2220 Pierce Ave # PRB648, Preston Research Building

institute: VUMC

description: Paired ICC/IDC-enriched and adjacent benign-enriched tissues

data_processing:
10x Genomics Cell Ranger 5.0.0 was used to build reference genome index
Reads were mapped to reference genome and then quantified
Cells labeled with sample-specific hashtags (feature barcoding antibodies) were demultiplexed
scRNABatchQC was used for quality control
Cells were removed if they had unique features counts of less than 200 or larger than 8000, had fewer than 500 read counts and/or had greater than 40% mitochondrial read counts
Seurat was used for sctransform-based normalization, dimension reduction, and clustering
Cell type annotation was cell activity database-based cell type classification and manual annotation
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: rds file that contains metadata of filtered and analyzed single cells; csv file (rename_cluster) that contains final (auto+manual) cell type for clusters; csv file (TCRresult) tha contains final TCR analysis.

source_name: ICC/IDC Prostate 7

extract_protocol:
Tissues were dissociated with the Tumor Dissociation Kit (Miltenyi Biotec Cat# 130-095-929), flow sorted for DAPI-EpCAM+, DAPI-CD45+, and DAPI-EpCAM-CD45- populations, then loaded onto the Chromium Controller for single cell RNA-sequencing.
Libraries were prepared with standard 10X Genomics protocols (v1 user guide CG000186 Rev D for ICC1-5; v2 user guide CG000330 Rev A for ICC6-7)

value: Prostate

tag: feature barcoding ab 1

value: ICC/IDC-enriched cells tagged with TotalSeq™-C0252 anti-human Hashtag 2 Antibody (Clones LNH-94; 2M2) (BioLegend, Cat# 394663)

tag: feature barcoding ab 2

value: Benign-enriched cells tagged with TotalSeq™-C0251 anti-human Hashtag 1 Antibody (Clones LNH-94; 2M2) (BioLegend, Cat# 394661)


title: SJLB253

value: female


title: ICC6_TCR

source_name: ICC/IDC Prostate 6


title: sample 3842 K27ac

city: Rochester

value: K27ac (Cell Signaling Technology, Cat# 8173, Lot 1)

value: glioma


title: ICC5_TCR

source_name: ICC/IDC Prostate 5


title: SJLB251

value: male


title: NC_control plasmid 2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (TP53TG1-AS) and regulated alternative splicing events (TP53TG1-RAS) between TP53TG1-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hela cells

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: Hela cells

tag: cell type

value: Hela  cell (control plasmid)


title: OE_TP53TG1_2

value: TP53TG1 overexpressed  in Hela cell


title: NC_control plasmid 3


title: hESCs, Day0, Bio rep 1

first: Ting

last: Xu

address: 1239 Siping Road

institute: Tongji University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < hESCs_1, hESCs_2, Day21_1, Day21_2, Day21_3, Day42_1, Day42_2, Day42_3> samples of homo sapiens was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: homo_sapiens GRCh38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Approximately 10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina（NEB，UK）following manufacturer's protocols.

value: Human embryonic stem cells

value: TPH2-EGFP knockin

value: induced serotonin neuron differentiation


title: NC_control plasmid 1


title: OE_TP53TG1_3


title: OE_TP53TG1_1


title: ICC4_TCR

source_name: ICC/IDC Prostate 4


title: SJLB238

source_name: liver tissue

value: liver

tag: age


title: SJLB223


title: ICC3_TCR

source_name: ICC/IDC Prostate 3


title: P6 iAT 1, 2, 3

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

description: inguinal adipose tissue at postnatal day 6

data_processing:
assembled clean reads into Unigenes: using HISAT2: Version: v2.0.4 Parameters: -p 8 --phred64 --sensitive -I 1 -X 10000
map the clean reads to reference using Bowtie2: Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
calculate the Unigene expression levels using RSEM : Version: v1.2.12 Parameters: default
DEG Detection using DEGseq: Parameters: Fold Change >= 2 and Adjusted Pvalue <= 0.001

extract_protocol:
Tri Reagent (phenolic extarction) according to Sigma-Aldrich protocol
RNA libraries were prepared for sequencing using standard BGISEQ protocols: mRNA enrichment-RNA fragmentation and reverse transcription-End repair, add A tailing and adaptor ligation-PCR amplification-Denature and cyclization-Sequencing

value: postnatal day 6 (P6)

value: inguinal adipose tissue (iAT)


title: SJLB221


title: Differentiated cells, Day42, Bio rep 1

value: TPH2+ serotonin neurons


title: Differentiated cells, Day42, Bio rep 2


title: Differentiated cells, Day21, Bio rep 1

value: Neural progenitor cells


title: SJLB220


title: Differentiated cells, Day21, Bio rep 3


title: Differentiated cells, Day21, Bio rep 2


title: ICC7_GEX

value: Prostate

value: ICC/IDC-enriched cells tagged with TotalSeq™-C0252 anti-human Hashtag 2 Antibody (Clones LNH-94; 2M2) (BioLegend, Cat# 394663)


title: SJLB217


title: ICC2_TCR

source_name: ICC/IDC Prostate 2

value: Benign-enriched cells tagged with TotalSeq™-C0251 anti-human Hashtag 1 Antibody (Clones LNH-94; 2M2) (BioLegend, Cat# 394661)


title: ICC1_TCR

source_name: ICC/IDC Prostate 1


title: SJLB216


title: ICC6_GEX


title: hESCs, Day0, Bio rep 3


title: hESCs, Day0, Bio rep 2


title: ICC5_GEX


title: ICC4_GEX


title: SJLB204

value: female


title: SJLB201


title: ICC3_GEX


title: ICC2_GEX


title: SJLB202


title: Differentiated cells, Day42, Bio rep 3


title: SJLB200


title: ICC1_GEX


title: SJLB177


title: Hfq-deletion strain Sample 2C

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

institute: University Of Miami

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned using Bowtie 2
Reads were counted using htseq-count
Assembly: NC_000913.3
Supplementary files format and content: Read counts per gene

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria

growth_protocol: Wild-type and mutant cells were grown at 37C in rich defined medium to mid log phase then harvested for RNA preparation

extract_protocol:
RNA was isolated using the hot phenol method
Libraries were constructed using NEBNext Small RNA prep kit (New England Biolabs) using the manufacturer's protocol.

value: MG1655 rph+

value: Bacteria

value: hfq deletion


title: Hfq-deletion strain Sample 2D


title: Hfq-deletion strain Sample 2A


title: Hfq-deletion strain Sample 2B


title: ICC6_feature_barcoding


title: SJLB175

value: male


title: SJLB174


title: WT strain Sample 1D

value: Wild-type


title: WT strain Sample 1A


title: WT strain Sample 1C


title: WT strain Sample 1B


title: ICC5_feature_barcoding


title: ICC7_feature_barcoding


title: SJLB172


title: ICC3_feature_barcoding


title: mPFC-SI-rep3

data_processing:
The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, should be processed to be removed before downstream analyses.
After reads filtering, we map clean reads to reference genome using HISAT
We map clean reads to reference transcripts using Bowtie2, then calculate gene expression level for each sample with RSEM .
Genome_build: mm10

source_name: medial prefrontal cortex

extract_protocol:
Total RNA from the mPFC was extracted with RNAiso Plus (Takara, #9109) according to the manufacturer’s instructions. The RNA quality and quantity were measured using NanoDrop 2000 (Thermo Scientific)
RNA library was constructed using the BGISEQ-500 platform according to the manufacturer's instruction; after that, adapters were ligated to each end of the RNAs and subsequently reverse transcribed to create single-stranded cDNA and sequenced on the BGISEQ-500 platform with a read length of 50 bps

value: medial prefrontal cortex

value: Post-weaning social isolation for 3 weeks

value: 6 weeks


title: mPFC-Control-rep3

value: control


title: mPFC-Control-rep1


title: mPFC-Control-rep2


title: mPFC-SI-rep1


title: 3D6_7

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Salmon was used to map reads to the transcriptome
Assembly: Ensembl Mus musculus GRCm38.99 transcriptome
Supplementary files format and content: Count matrix

growth_protocol: Male C57BL6 mice were obtained from the Animal Resources Centre (Perth, WA, Australia) and were group housed with a 12 hr light/dark cycle at 22oC. Animals had ad libitum access to food and water. All procedures involving animals were approved by The Deakin University Animal Welfare Committee (A58-2010, G15-2017 and G08-2020), which is subject to the Australian Code for the Responsible Conduct of Research.  High fat feeding: At 12 weeks of age, mice were randomly assigned to regular chow or high fat diet (HFD; 43% digestible energy from fat, 20% from sucrose; SF04-001 Specialty Feeds). Throughout the diet period, mice were weight weekly. After three months of the diet period, mice underwent body composition assessment using EchoMRI. Two days later, mice were fasted for 5 hrs before being humanely killed by cervical dislocation. Epididymal and inguinal adipose tissues were carefully excised and weighted and were either immediately frozen and stored at -80oC for later analysis or were used for ex vivo adipose explant experiments.

extract_protocol:
Bulk RNA was isolated from LV tissue by homogenisation using a hand-held homogeniser in Trizol and RNA was isolated using RNeasy kits (Qiagen), according to manufacturer’s instructions.
Sequencing libraries were generated from 0.5 µg of total RNA using TruSeq Stranded Total RNA preparation kit (Illumina) as per manufacturer’s instructions.

treatment_protocol: Ab peptide administration: Lyophilised recombinant Aβ42 (#AG912, Millipore) and scrambled control peptide (ScrAβ42; #AG916, Millipore) were resuspended in 1% NH4OH and aliquoted at 200ng/ml in H2O and stored at -80◦C for no longer than 4 weeks. Recombinant human Aβ42 was used as it has a greater propensity to aggregate than the mouse sequence65 and peptides appeared as low molecular weight aggregates of Aβ42 by SDS-PAGE (data not shown). Peptide administration began when male C57BL6J mice were 12 weeks of age and involved daily i.p. injection of 1mg of peptide. Throughout the peptide administration period, body weight was measured daily and food intake was measured twice weekly, and body composition was measured weekly by EchoMRI. After two weeks, plasma Aβ42 was determined from samples collected 5 hr after recombinant ScrAβ42 or Aβ42 administration. After 3 weeks, an insulin tolerance test (ITT; i.p. 0.75U/kg) was performed following a 5 hr fast. Blood glucose was measured at baseline and after 20, 40, 60, 90 and 120 min after glucose administration. One week later, a glucose tolerance test (GTT; i.p 2g/kg with 5μCi 3H-2-deoxyglucose and 5μCi 14C-glucose) was performed. Blood glucose was measured at baseline and after 15, 30, 45, 60 and 90 min after glucose administration. Plasma was obtained at 0, 15, 30, 60 and 90 min for insulin determination and the measurement of tracer specific activity. Mice were humanely killed by cervical dislocation immediately after the GTT. Blood was collected for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis. Another cohort of mice were administered ScrAβ42 or Aβ42 for four weeks, as described above. After four weeks of peptide administration, mice were anaesthesia by isoflurane inhalation before undergoing echocardiography. Two days later, mice were humanely killed by cervical dislocation and blood was obtained for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis. Another cohort of mice were administered ScrAβ40 or Aβ40 (Millipore) for four weeks, as described above. After four weeks of peptide administration, mice were anaesthesia by isoflurane inhalation before undergoing echocardiography. Two days later, mice were humanely killed by cervical dislocation and blood was obtained for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis.  3D6 administration: For the 3D6 prevention study, 12-week-old mice were assessed for baseline cardiac structure and function by echocardiography and were assigned to one of two groups such that deceleration time was matched. One week later, mice were fed a high fat diet (as described above) and then received control antibody (IgG2a isotype antibody, #BE-0085 BioXCell) or 3D6 antibody (#TAB-0809CLV, Creative Biolabs) weekly via i.p. injection (0.75mg/kg). Body weight was measured twice per weekly, while body composition was measured every two weeks throughout the study. After 10 weeks of high fat feeding, mice underwent an ITT and a GTT after 11 weeks of high fat feeding. After 12 weeks of high fat feeding mice underwent echocardiography and two weeks later were humanely killed by cervical dislocation following a 5 hr fast.  Blood was collected for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis. In the 3D6 reversal study, 12-week-old mice were assessed for baseline cardiac structure and function by echocardiography and were assigned to one of three groups such that deceleration time was matched. One week later, one group of mice remained on standard chow, while the other two groups were fed a high fat diet. Body weight was measured twice per week throughout the study. After 13 weeks of high fat feeding, mice underwent echocardiography for pre-treatment assessment of cardiac function and morphology. Mice were then administered control antibody or 3D6 antibody weekly via i.p. injection (0.75mg/kg) for the remainder of the study. Four weeks later, mice underwent pre-treatment assessment of cardiac function and morphology, followed by assessment of body composition by EchoMRI two days later. One week later, mice were humanely killed by cervical dislocation following a 5 hr fast.  Blood was collected for plasma and tissues were dissected, rapidly frozen and stored at -80oC for later analysis.

value: left ventricle

value: wild type


title: 3D6_20


title: 3D6_4


title: mPFC-SI-rep2


title: Con_23

value: 3D6 control antibody


title: 3D6_24


title: Con_8


title: Con_19


title: Con_3


title: 3D6_21


title: Con_22


title: SJLB162

value: liver


title: SJLB157


title: ICC1_feature_barcoding

city: Nashville

value: Prostate


title: Con_18


title: ICC2_feature_barcoding

value: ICC/IDC-enriched cells tagged with TotalSeq™-C0252 anti-human Hashtag 2 Antibody (Clones LNH-94; 2M2) (BioLegend, Cat# 394663)


title: SJLB156


title: P56 iAT 1, 2, 3

description: inguinal adipose tissue at postnatal day 56

value: postnatal day 56 (P56)

value: inguinal adipose tissue (iAT)


title: ICC4_feature_barcoding

value: Benign-enriched cells tagged with TotalSeq™-C0251 anti-human Hashtag 1 Antibody (Clones LNH-94; 2M2) (BioLegend, Cat# 394661)


title: SJLB85

value: female


title: SJLB151


title: SJLB152


title: SJLB122


title: 3D6_12


title: 3D6_16


title: 3D6_17


title: mCherry RNAi replicate 3

city: Caparica

first: Daniel

last: Sobral

address: Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa, Campus de Caparica

department: Life Sciences

country: Portugal

institute: UCIBIO - FCT NOVA

data_processing:
RNA sequencing reads were aligned against the Drosophila melanogaster BDGP release 6 genome using the STAR aligner (2.7.2a)
Gene-level counts were obtained using featureCounts (v1.6.3); parameters: -s 2 -p -B -P -C
bigWig files were obtained from the RNA-Seq alignments transformed with the deeptools (3.5.0) bamcoverage tool with CPM normalization
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig

organism: Drosophila melanogaster

source_name: ovaries from 2 days old females (after pupae eclosion)

growth_protocol: Ovaries from 2 days old females (after pupae eclosion) were isolated

extract_protocol:
Total RNA was extracted using standard procedures
The cDNA library was made using the TruSeq Stranded mRNA sample prep kit for Illumina

treatment_protocol: For negative control or Sfmbt depleted ovaries, we used the nanos-Gal4 driver for germ line-specific expression of, respectively, UAS-mCherry RNAi (negative control) or UAS-Sfmbt RNAi (Sfmbt RNAi-1)

value: mCherry RNAi

tag: replicate


title: SJLB66

value: male


title: S855Nr48_PANC1_C3

city: Warszawa

first: AKANKSHA

last: JAISWAR

address: ul. Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Institute

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.19).
Quality check of the reads has been performed by FastQC and adapters were trimmed with trimmomatic toolkit,then trimmed raw reads were aligned to the human reference genome (hg38) using HISAT2.
Differential Gene Expression Analysis were performed with DESeq2 also we calculate exon gene sizes with the GenomicFeatures Package in R and FeaturesCount which are required to calculate FPKM values in DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic Cancer

growth_protocol: Standard, ATCC-derived protocls for 2D in vitro growth for each cell line.

extract_protocol:
Qiazol reagent extraction from PBS-washed cell line pellets, followed by an isopropanol RNA precipitation and RNA quality control.
RNA libraries were prepared for sequencing using TruSeq Stranded TotalRNA (Illumina) protocols

treatment_protocol: Cell lines indicated in the file names were either treated with carfilzomib (C) for 24h at concentrations at the IC50 of proteasome activity (see the associated manuscript for exact carfilzomib concentrations for each cell line), or with DMSO (D) as a control, in biological triplicates (numbers 1-3).

value: Carfilzomib

value: Pancreatic Cancer


title: S855Nr47_PANC1_C2


title: S855Nr45_PANC1_D3

value: DMSO


title: mCherry RNAi replicate 1


title: mCherry RNAi replicate 2


title: S855Nr46_PANC1_C1


title: Con_11

source_name: left ventricle

tag: genotype


title: S855Nr44_PANC1_D2

tag: tissue


title: ScrAbeta42_3449

value: Ab42 scrambled control


title: Sfmbt RNAi replicate 3

value: Sfmbt RNAi


title: Con_15

value: left ventricle