title: SeqScope_1st colon

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description:
HDMI32-DraI
1st-Seq of Seq-Scope
Extracted Barcodes

library_source: other

data_processing:
Sequencing by Illumina HiSeqX, HiSeq4000 and NovaSeq platforms .
Seq-Scope data were initially processed using the STtools package, utilizing STAR/STARsolo 2.7.5c, with a modification to use hexagonal array, instead of square array. The processed DGE matrix, pooled in non-overlapping hexagons with 12 μm sides, was analyzed in the Seurat V4 package.
First, we removed all genes starting with mt and Gm to remove mitochondrial genes and hypothetical gene models. After applying a cutoff, data were normalized using regularized negative binomial repression implemented in Seurat’s SCTransform function.
Clustering analysis was performed using the shared nearest neighbor modularity optimization implemented in Seurat’s FindClusters function. The clusters were visualized in the UMAP (uniform manifold approximation and projection) manifold or the histological space using ggplot functions. The markers for each cluster were identified through the FindAllMarkers function and used to annotate cell types.
Assembly: mm10
Supplementary files format and content: Digital expression matrix with barcode featuring spatial coordinates

molecule: other

organism: synthetic construct

source_name: Synthetic ssDNA

growth_protocol: Normal rearing condition

extract_protocol:
The Seq-Scope procedure was performed on the injured colon sample as previously described with minor modifications involving the use of the Illumina HiSeq 2500 flow cells and chemical strategies to increase RNA sequence capture.
The experimental procedures were performed as we previously described, but it was adapted to HISEQ2500 flow cell system so that Seq-Scope has wider and continuous imaging area (1.5 mm × 60 mm in HISEQ2500, compared to 1 mm-diameter circles in MISEQ). A single imaging area was used for many samples. In brief, HDMI32-Dral [Seed HDMI-oligo, containing the PCR/read adaptor sequences, the restriction enzyme-cleavable RNA-capture domain (olido-dT), the high-definition map coordinate identifier (HDMI), a spatial barcode composed of a 32 random nucleotide sequence] was amplified on a flow cell surface to generate HDMI-oligo cluster. The HDMI sequence and coordinates of each cluster were determined using the HISEQ2500 platform. Thumbnail images of clusters were visualized using Illumina Sequencing Analysis Viewer to inspect the cluster morphology and density. Next, the HISEQ2500 flow cell was processed to expose the oligo-dT and RNA-capture domain and generate an HDMI-encoded RNA-capturing array (HDMI-array). Subsequently, the HISEQ2500 flow cell was disassembled to expose the HDMI-array to the outside and used for tissue attachment. The OCT-mounted fresh frozen aortic tissue was sectioned 10 μm thickness in a cryostat (Leica CM3050S, -20°C) and the aortic sections were maneuvered onto the HDMI-array slide. After fixing in 4% formaldehyde for 10 min and incubating in isopropanol for 2 min, the tissue was stained with hematoxylin (Agilent, S3309) for 5 min, treated with bluing buffer (Agilent, CS702) for 2 min, and incubated with buffered eosin [1:9 = eosin (HT110216, Sigma): 0.45M Tris-Acetic buffer (pH 6.0)]. After mounting in 85% glycerol, the tissues were imaged under a digital imager (Keyence, BZ-X800).
Total RNAs released from the fixed tissues were performed as previously described. Briefly, the fixed tissues attached on the HDMI-array slide were treated with 0.2 U/μl collagenase I (Thermo Fisher, 17018-029) at 37 °C for 20 min, and then incubated with 1mg/ml pepsin (Sigma, P7000) in 0.1M HCl at 37 °C for 10 min. The RNAs released from the tissue sections were captured by the HDMI-array and used as a template to generate cDNA footprints on the HDMI-barcoded RNA capturing molecule by reverse transcription. After overnight reverse transcription reaction at 37 °C, the tissues were incubated in exonuclease I cocktail [1U Exo I enzyme (M2903, NEB) in 1x Exo I buffer] and subsequently digested in 1x tissue digestion buffer [100 mM Tris pH8.0, 100mM NaCl, 2% SDS, 5mM EDTA, 16 U/ml Proteinase K (P8107S, NEB)]. After tissue digestion, the secondary strand, a chimeric molecule of HDMI and cDNA sequences, is synthesized on the cDNA footprint using an adaptor-tagged random primer (Truseq Read 2-conjugated Random Primer version 2 with TCA GAC GTG TGC TCT TCC GAT CTN NNN NNN NB sequence). After removing all DNAs that did not bind to the HDMI-array, the secondary strand product was eluted using NaOH, and after neutralization, purified using AMPure XP purification kit (A63881, Beckman Coulter). The secondary strand product was used as a template to construct library using Kapa HiFi Hotstart Readymix (KK2602, KAPA Biosystems) through two rounds of library PCR. After purification using Zymoclean Gel DNA recovery Kit (D4001, Zymo Research) and AMPure XP, the pooled libraries were subjected to paired-end (100-150bp) sequencing in the Illumina platform at Psomagen lnc.

treatment_protocol: The colon samples were obtained from C57BL/6 mice after 24 hrs of biopsy-induced physical wounding.

value: Synthetic ssDNA


title: NMP_021, PRE, NTP [21_S17]

status: Public on Aug 29 2024

type: SRA

city: Innsbruck

first: Theresa

last: Hautz

address: Anichstr. 45

department: Department of Visceral, Transplant and Thoracic Surgery

country: Austria

institute: Medical University of Innsbruck

library_source: transcriptomic

data_processing:
Adapters were trimmed using BBDuk according to recommendations (Lexogen, Austria) and quality checked using FastQC.
Reads were mapped to the human reference genome (GRCh38/hg38) using the splice aware aligner STAR (v2.7.1a). Note, since  the specific 3'  sequencing libraries used here, only forward reads were mapped and all reverse reads were discarded since provide only limited information.
Read counts for NCBI Gene/Refseq annotation were detrmined using featureCounts (v2.0.0)
Differentially expressed genes were determined using DESeq2 based on raw counts and a negative binomial distribution
Data were normalized using DESeq2 and log-transformed (rlog).
Assembly: hg38
Supplementary files format and content: tab delimited txt file include raw counts for each sample (raw_counts.txt)
Supplementary files format and content: tab delimited txt file include log2 transformed normalized counts adding a pseudocount of 1 (DESeq2) for each sample (log2_normalized_counts_1.txt)

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Cryopreserved liver biopsies were homogenized using the ULTRA Turrax IKA T10 basic. Total RNA was extracted according to the Rneasy Micro Kit (Qiagen, Netherlands). RNA integrity was determined using a 2100 Bioanalyzer and RNA 6000 Nano LabChip kits (Agilent Technology, USA).
QuantSeq 3'protocol (Lexogen, Austria) according to manufacturers's recommendations

treatment_protocol: Grafts were flushed with 2000 ml histidin-tryptophan-ketoglutarate, surgically prepared for NMP and connected to the OrganOc metra® device.

tag: tissue

value: liver

tag: transplantation

value: no

tag: time

value: PRE

tag: treatment

value: normothermic machine perfusion


title: NMP_019, PRE, TP [19_S15]

value: yes


title: total VisCtx RNA, Light condition, ZT7.5, biorep3

city: Rehovot

first: Daniella

last: Apelblat

address: Hertzl

department: Neuroscience

country: Israel

institute: Weizmann Institute of Science

description:
Light7.5_rep3
normalized_counts.xls, column 41

data_processing:
Data processing was performed using UTAP: User-friendly Transcriptome Analysis Pipeline (Kohen et al., 2019).
Reads were trimmed using CutAdapt (Martin 2011) [parameters: -a ADAPTER1 -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25].
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.5.2b [parameters: –alignEndsType EndToEnd –outFilterMismatchNoverLmax 0.05 –twopassMode Basic].
Reads were counted using STAR, and count normalization and differential expression was done with DESeq2 (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: excel file including DESeq2-normalized counts for each sample

organism: Mus musculus

source_name: visual cortex

extract_protocol:
this is an example, put the relevant info!!! ::: 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 were prepared using the MARS-Seq protocol, in the Nancy and Stephen Grand Israel National Center for Personalized Medicine (INCPM)

value: visual cortex

tag: condition

value: Light condition

tag: time point

tag: genotype

value: WT


title: total VisCtx RNA, Light condition, ZT7.5, biorep2

description:
Light7.5_rep2
normalized_counts.xls, column 40


title: NMP_012, 1H, TP [62_S51]


title: NMP_017, PRE, TP [17_S13]


title: NMP_016, PRE, TP [16_S12]


title: total VisCtx RNA, Light condition, ZT3, biorep3

description:
Light3_rep3
normalized_counts.xls, column 37


title: NMP_015, PRE, NTP [15_S11]


title: total VisCtx RNA, Light condition, ZT3, biorep2

description:
Light3_rep2
normalized_counts.xls, column 36


title: NMP_014, PRE, TP [14_S10]


title: NMP_018, PRE, NTP [18_S14]


title: ZmEIP_2_14d

city: Beijing

first: Haiyue

last: Yu

address: Yuanmingyuanxilu No.2

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
The raw reads were filtered using ht2-filter in the HTQC package (1.92.1) with default parameters to remove low-quality reads. The filtered reads were compared to the reference maize genome (Zea mays RefGen_V4) using TopHat (2.0.11) to remove host genome sequences. The mapped reads were assembled, and fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks.
Assembly: Zea mays RefGen_V4
Supplementary files format and content: FPKM

organism: Zea mays

source_name: leaves

extract_protocol:
RNA was extracted using Trizol reagent
mRNA was purified from total RNA using poly-T  oligo-attached magnetic beads. Fragmentation was carried out using  divalent cations under elevated temperature in First Strand Synthesis  Reaction Buffer(5X). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase(RNase H-).  Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and RNase H. Remaining overhangs were converted  into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments  of preferentially 370~420 bp in length, the library fragments were  purified with AMPure XP system.

value: leaves

tag: cell line

tag: cell type

value: ZmEIP


title: GFP_1_14d

value: GFP


title: EtEC81_1_10d


title: EtEC81_1_14d


title: GFP_2_14d


title: EtEC81_3_10d


title: GFP_3_14d


title: ZmEIP_3_10d


title: EtEC81_2_14d


title: ZmEIP_3_14d


title: total VisCtx RNA, Light condition, ZT7.5, biorep1

description:
Light7.5_rep1
normalized_counts.xls, column 39


title: EtEC81_2_10d


title: EtEC81_3_14d


title: ZmEIP_1_14d


title: total VisCtx RNA, Light condition, ZT3, biorep4

description:
Light3_rep4
normalized_counts.xls, column 38


title: NMP_013, PRE, TP [13_S9]


title: ZmEIP_2_10d


title: total VisCtx RNA, Light condition, ZT1, biorep4

description:
Light1_rep4
normalized_counts.xls, column 34


title: SP_D3_Inj_D45_RP2

city: Atlanta

first: James

last: Zheng

state: GA

address: 615 Michael Street

department: Cell Biology

country: USA

institute: Emory University

description:
Female mated with SP-null at D45
23123R-01-67

data_processing:
Galaxy web platform: usegalaxy.org
Quality control on the data was performed using FastQC
214 using FastQC
data was subsequently mapped using RNA STAR 35 and the Ensembl gene annotation for Drosophila genome (dm6)
Gene count was done using FeatureCount software
Assembly: Drosophila melanogaster DM6
Supplementary files format and content: raw counts

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
Injured and sham flies were injured at 3 days post-eclosion. At 1 day and 6 weeks post-injury, brains from males, wildtype-mated females, virgin females, and SP0-mated females were collected, resulting in 16 conditions, each condition containing three independent cohorts of n=40 flies. RNA from brain tissue was extracted by TRIzol®/Chloroform extraction (ThermoFisher, 15596026) and further clean-up with the Zymo DNA Clean & Concentrator-5 kit (D4004) with on column DNase treatment (ThermoFisher, AM1907). Once obtained, RNA samples were transferred on dry ice to Admera Health for library preparation and sequencing. Total RNA integrity was checked by BioAnalyzer. QIAseq FastSelect rRNA Fly + NEB Ultra II Directional kit was used to deplete rRNA and prepare stranded cDNA libraries. Samples were sequenced on NextSeq High Output Flow Cell (Illumina) for 150 cycles to generate a total of 60M paired-ended, 101 base-pair reads.
Once obtained, RNA samples were transferred on dry ice to Admera Health for library preparation and sequencing. Total RNA integrity was checked by BioAnalyzer. QIAseq FastSelect rRNA Fly + NEB Ultra II Directional kit was used to deplete rRNA and prepare stranded cDNA libraries.

treatment_protocol: Adult flies were exposed to mild head injury on day 3 aftere eclosion or ctrl. Brains were dissect on day 4 or day 45 for RNA extraction

value: brain


title: M_D3_Inj_D45_RP3

description:
Male at D45
23123R-01-76


title: F_sham_D4_RP3

description:
Female at D4
23123R-01-84

value: CTRL (Sham)


title: total VisCtx RNA, Light condition, ZT3, biorep1

description:
Light3_rep1
normalized_counts.xls, column 35


title: SP_D3_Inj_D45_RP1

description:
Female mated with SP-null at D45
23123R-01-66


title: M_sham_D45_RP3

description:
Male at D45
23123R-01-69


title: F_sham_D4_RP2

description:
Female at D4
23123R-01-77


title: ZmEIP_1_10d


title: SP_D3_Inj_D45_RP3

description:
Female mated with SP-null at D45
23123R-01-68


title: M_D3_Inj_D4_RP3

description:
Male at D4
23123R-01-70


title: total VisCtx RNA, Light condition, ZT1, biorep3

description:
Light1_rep3
normalized_counts.xls, column 33


title: NMP_011, PRE, TP [11_S7]


title: M_D3_Inj_D4_RP2

description:
Male at D4
23123R-01-63


title: NMP_010, PRE, TP [10-3_S6]


title: NMP_007, PRE, TP [7_S5]


title: GFP_3_10d


title: F_D3_Inj_D45_RP3

description:
Female at D45
23123R-01-62


title: GFP_1_10d


title: NMP_005, PRE, TP [5_S4]


title: NMP_012, PRE, TP [12_S8]


title: total VisCtx RNA, Light condition, ZT1, biorep1

description:
Light1_rep1
normalized_counts.xls, column 31


title: SP_sham_D45_RP3

description:
Female mated with SP-null at D45
23123R-01-61


title: SP_sham_D45_RP2

description:
Female mated with SP-null at D45
23123R-01-60


title: GFP_2_10d


title: total VisCtx RNA, Light condition, ZT1, biorep2

description:
Light1_rep2
normalized_counts.xls, column 32


title: total VisCtx RNA, Dark condition, ZT18, biorep4

description:
Dark18_rep4
normalized_counts.xls, column 30

value: Dark condition


title: CUT&RUN in EGR2 knock-out mouse alveolar macrophages, BRD4 (rep2)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

library_source: genomic

data_processing:
nfcore/cutandrun pipeline version 1.1 default settings
adapter and quality trimming with Trim Galore!
alignment to both target and spike-in genomes with Bowtie2
filter on quality, sort and index alignemtns with samtools
duplicate read marking with picard
create bedgraph files with bedtools
create bigWig coverage files with bedGraphToBigWig
peak calling for low background noise experiments with SEACR
consensus peak merging and reporting with bedtools
Assembly: mm10
Supplementary files format and content: bedgraph
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: mouse alveolar macrophage

growth_protocol: We applied primary mouse alveolar macrophages from C57BL6 background control and EGR2 myeloid-specific conditional knock out mice.

extract_protocol:
The mice were euthanized by CO2 inhalation. Cells were isolated from bronchoalveolar lavage and cryopreserved until experiment
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina acording to the manufacter protocol

treatment_protocol: We did not apply any treatment.

value: alveolar macrophage

tag: strain

tag: organ

value: lung


title: total VisCtx RNA, Dark condition, ZT18, biorep3

description:
Dark18_rep3
normalized_counts.xls, column 29


title: SP_sham_D45_RP1

description:
Female mated with SP-null at D45
23123R-01-59


title: NMP_003, PRE, NTP [3_S3]


title: CUT&RUN in EGR2 knock-out mouse alveolar macrophages, BRD4 (rep1)


title: M_sham_D4_RP2

description:
Male at D4
23123R-01-49


title: M_sham_D4_RP3

description:
Male at D4
23123R-01-56


title: IL-2 + IL-15 + TGFb + RA 001

city: Melbourne

first: Luke

middle: C

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

country: Australia

institute: WEHI

description: Biological replicate 1

data_processing:
FASTQ files were produced using standard Illumina protocols and software
FASTQ files were analysed using the RNAsik pipeline (Tsyganov et al., 2018) using STAR aligner (Dobin et al., 2013) with Mus musculus GRCm38.
Reads were quantified using featureCounts (Liao, et al., 2014) producing the raw gene count matrix
Assembly: Mus_musculus/Ensembl/GRCm38
Supplementary files format and content: Tab-delimited text files; columns are Ensembl gene ID, gene symbol, and number of reads mapping to each gene

source_name: Spleen

extract_protocol:
RNA was isolated from cutured CD8 T cells with the RNeasy Micro kit (Qiagen).
Illumina Truseq stranded mRNA sample preparation kit

value: Spleen

value: CD8 T cell

value: IL-2 + IL-15 + TGFb + RA


title: NMP_002, PRE, TP [2_S2]

value: liver

value: PRE


title: CUT&RUN in wild type mouse alveolar macrophages, BRD4 (rep1)


title: total VisCtx RNA, Dark condition, ZT18, biorep2

description:
Dark18_rep2
normalized_counts.xls, column 28


title: Proliferative dCas9 HepaRG cells @ Day 5

city: Stockholm

first: Peter

middle: Daniel

last: Saliba Gustafsson

state: Stockholm

address: C2:94, Karolinska Universitetssjukhuset Huddinge

department: Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation was carried out using Cell Ranger v. 6
Assembly: hg38
Supplementary files format and content: Complete Cell Ranger output; web-summaries, bam-files etc.

source_name: HepaRG

growth_protocol: Standard maintenance media; Williams E, supplemented with 50uM hydrocortisone, 5ug/ml insulin, 10% FBS, 1X Glutamax

extract_protocol:
Freshly harvested control or differentiated HepaRG cells, sorted on Sytox Green negativity. Both Wt HepaRG and dCas9-expressing cells were captured.
Library was prepared by the Stanford functional genomics core facility according to the manufacturers instruction (single cell 3' v2 protocol, 10X Genomics).

treatment_protocol: With or without DMSO-induced differentiation

value: HepaRG

value: Hepatocyte

value: Control


title: CUT&RUN in wild type mouse alveolar macrophages, BRD4 (rep2)


title: V_D3_Inj_D4_RP3

description:
Virgin female at D4
23123R-01-42

value: WT


title: Differentiated @ D28 WT HepaRG cells according to standard protocols using DSMO

description: 10X Genomics

value: Differentiated


title: total VisCtx RNA, Dark condition, ZT18, biorep1

description:
Dark18_rep1
normalized_counts.xls, column 27

value: visual cortex


title: total VisCtx RNA, Dark condition, ZT15, biorep3

description:
Dark15_rep3
normalized_counts.xls, column 25


title: IL-2 + IL-15 + TGFb + RA 003

description: Biological replicate 3


title: Differentiated @ D28 dCas9 HepaRG cells according to standard protocols using DSMO

description: 10X Genomics


title: M_sham_D45_RP2

description:
Male at D45
23123R-01-44


title: total VisCtx RNA, Dark condition, ZT15, biorep2

description:
Dark15_rep2
normalized_counts.xls, column 24


title: Differentiated @ Day42 WT HepaRG cells according to standard protocols using DSMO

description: 10X Genomics


title: F_D3_Inj_D45_RP2

description:
Female at D45
23123R-01-55


title: IL-2 + IL-15 + TGFb + RA 002

description: Biological replicate 2


title: F_sham_D45_RP2

description:
Female at D45
23123R-01-40


title: Proliferative WT HepaRG cells @ Day 5

description: 10X Genomics


title: IL-2 + IL-15 + TGFb 002

description: Biological replicate 2

value: IL-2 + IL-15 + TGFb


title: F_sham_D45_RP3

description:
Female at D45
23123R-01-48

value: brain


title: total VisCtx RNA, Dark condition, ZT13, biorep2

description:
Dark13_rep2
normalized_counts.xls, column 21


title: total VisCtx RNA, Dark condition, ZT15, biorep1

description:
Dark15_rep1
normalized_counts.xls, column 23


title: NMP_001, PRE, TP [1_S1]

value: yes

value: normothermic machine perfusion


title: total VisCtx RNA, Dark condition, ZT15, biorep4

description:
Dark15_rep4
normalized_counts.xls, column 26

value: Dark condition


title: SP_D3_Inj_D4_RP3

description:
Female mated with SP-null at D4
23123R-01-39


title: total VisCtx RNA, Dark condition, ZT13, biorep3

description:
Dark13_rep3
normalized_counts.xls, column 22


title: Patient NB006 snRNA-seq, snap-frozen

city: Gent

first: Noah

last: Bonine

state: -- SELECT --

address: Technologiepark-Zwijnaarde 75

country: Belgium

institute: Ghent University

description:
Patient NB006 snRNA-seq from snap-frozen tissue.
Bonine2023_nucleus_NBO006

data_processing:
The sequenced libraries were quantified with Cell Ranger software (version 6.1.2) with default parameters. For snRNA-seq, the option include-introns = T was added.
The reference genome GRCh38 (Ensembl v99) was used.
In addition, for CITE-seq, surface antibodies were quantified with the Cell Ranger count feature reference option.
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated values and matrix files.

molecule: nuclear RNA

source_name: neuroblastoma

extract_protocol:
For scRNA-seq, tumor specimens were minced into small pieces digested into single-cell suspensions using 1 mg/mL Collagenase A and 10 U/mL DNAse in RPMI at 37°C for 30 mins at the most with agitation until a turbid solution was obtained. Next, cells were pelleted by centrifugation (5 mins at 400 g). If a red cell pellet was obtained, indicating a large number of red blood cells, RBC lysis buffer was added followed by repeating cell pelleting. For CITE-seq, an Fc receptor block 2.4G2 antibody was added together with CITE-seq antibodies (as described in Guilliams et al. 2022 40). Following 20 mins of incubation at 4°C, the cells were washed with PBS with 2% FCS and 2mM EDTA. For regular single-cell RNA, this step was omitted. Approximately 160,000 live cells (APCcy7+) were sorted with FACS per sample (using BD FACSAria III). After sorting, cells were pelleted by centrifugation at (5 mins at 400 g). For snRNA-seq, snap or viably frozen neuroblastoma tissues were dounce homogenized in a homogenization buffer. The homogenate was filtered over a 70 µm cell strainer. Next, the nuclei were pelleted using a sucrose density gradient ultracentrifugation (7,700 rpm for 30 min at 4°C). Thereafter, 100,000 to 400,000 DAPI-positive nuclei were sorted by flow cytometry (using BD FACSAria III). Nuclei were pelleted for 3 minutes at 400 g and subsequently 5 minutes at 600 g (without stop).
Single-cell or single-nucleus libraries were generated using the Chromium Single Cell 3’ (V2 or V3) Reagent Kit according to the manufacturer’s protocol. Libraries were sequenced using an Illumina NovaSeq 6000 sequencing platform.

value: neuroblastoma

tag: subject id

value: Patient NB006

tag: tisse type

value: snap-frozen tissue


title: IL-2 + IL-15 + TGFb 001

description: Biological replicate 1

value: Spleen

value: CD8 T cell


title: Patient NB005 snRNA-seq, snap-frozen

description:
Patient NB005 snRNA-seq from snap-frozen tissue.
Bonine2023_nucleus_NBO004

value: Patient NB005


title: total VisCtx RNA, Dark condition, ZT13, biorep1

description:
Dark13_rep1
normalized_counts.xls, column 20


title: Patient NB004 snRNA-seq, snap-frozen

description:
Patient NB004 snRNA-seq from snap-frozen tissue.
Bonine2023_nucleus_NBO002

value: Patient NB004


title: IL-2 + IL-15 + RA 003

description: Biological replicate 3


title: total VisCtx RNA, Dark condition, ZT11.5, biorep3

description:
Dark11.5_rep3
normalized_counts.xls, column 18


title: M_D3_Inj_D45_RP2

description:
Male at D45
23123R-01-36


title: V_D3_Inj_D45_RP3

description:
Virgin female at D45
23123R-01-38


title: IL-2 + IL-15 003

description: Biological replicate 3


title: total VisCtx RNA, Dark condition, ZT11.5, biorep1

description:
Dark11.5_rep1
normalized_counts.xls, column 16


title: V_D3_Inj_D4_RP2

description:
Virgin female at D4
23123R-01-35


title: IL-2 + IL-15 + RA 001

description: Biological replicate 1


title: total VisCtx RNA, Dark condition, ZT11.5, biorep2

description:
Dark11.5_rep2
normalized_counts.xls, column 17


title: Patient NB003 snRNA-seq, biol repl 3, snap-frozen

description:
Patient NB003 snRNA-seq, biol rep 3 from snap-frozen tissue. CS214: technical replicate 1, CS215: technical replicate 2.
Bonine2023_nucleus_CS214-215

value: Patient NB003


title: V_D3_Inj_D45_RP2

description:
Virgin female at D45
23123R-01-34


title: Patient NB003 snRNA-seq, biol repl 4, snap-frozen

description:
Patient NB003 snRNA-seq, biol rep 4 from snap-frozen tissue. CS216: technical replicate 1, CS217: technical replicate 2.
Bonine2023_nucleus_CS216-217


title: IL-2 + IL-15 002

description: Biological replicate 2


title: total VisCtx RNA, Dark condition, ZT7.5, biorep4

description:
Dark7.5_rep4
normalized_counts.xls, column 15


title: Patient NB003 snRNA-seq, biol repl 2, snap-frozen

description:
Patient NB003 snRNA-seq, biol rep 2 from snap-frozen tissue. CS212: technical replicate 1, CS213: technical replicate 2.
Bonine2023_nucleus_CS212-213


title: IL-2 + IL-15 001

description: Biological replicate 1


title: total VisCtx RNA, Dark condition, ZT7.5, biorep3

description:
Dark7.5_rep3
normalized_counts.xls, column 14


title: CUT&RUN in EGR2 knock-out mouse alveolar macrophages, IgG (rep2)

description: CUT&RUN in EGR2 knock-out mouse alveolar macrophages (rep2)

data_processing:
alignment to mm10 reference genome and spike-in genome (Escherichia_coli_K_12_MG1655) with Bowtie2 (v2.4.2)
adapter and quality trimming with TrimGalore! (v0.6.6)
bam generation with SAMtools (v1.13) using default parameters
mark duplicated reads by using the MarkDuplicates tool of Picard (v2.25.7)
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
Assembly: mm10
Supplementary files format and content: bedgraph
Library strategy: CUT&RUN

value: alveolar macrophage

value: lung


title: Patient NB003 snRNA-seq, biol repl 1, snap-frozen

description:
Patient NB003 snRNA-seq, biol rep 1 from snap-frozen tissue. CS210: technical replicate 1, CS211: technical replicate 2.
Bonine2023_nucleus_CS210-211


title: total VisCtx RNA, Dark condition, ZT11.5, biorep4

description:
Dark11.5_rep4
normalized_counts.xls, column 19

value: WT


title: IL-2 + IL-15 + RA 002

description: Biological replicate 2


title: Patient NB004 snRNA-seq, viable-frozen

description:
Patient NB004 snRNA-seq from viably frozen tissue.
Bonine2023_nucleus_NBO001

value: viably frozen tissue


title: F_D3_Inj_D45_RP1

description:
Female at D45
23123R-01-37


title: V_sham_D45_RP3

description:
Virgin female at D45
23123R-01-31

value: CTRL (Sham)


title: Patient NB003 CITE-seq, biol rep 4, fresh

description:
Patient NB003 CITE-seq, biol rep 4 from fresh tissue. CS208: technical replicate 1, CS209: technical replicate 2. RNA and ADT (prefix ‘adt-‘) counts are aggregated.
Bonine2023_cell_CS208-209

data_processing:
library strategy: CITE-seq
The sequenced libraries were quantified with Cell Ranger software (version 6.1.2) with default parameters. For snRNA-seq, the option include-introns = T was added.
The reference genome GRCh38 (Ensembl v99) was used.
In addition, for CITE-seq, surface antibodies were quantified with the Cell Ranger count feature reference option.
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated values and matrix files.

value: fresh tissue


title: F_sham_D45_RP1

description:
Female at D45
23123R-01-30

value: brain


title: M_sham_D45_RP1

description:
Male at D45
23123R-01-29


title: total VisCtx RNA, Dark condition, ZT7.5, biorep1

description:
Dark7.5_rep1
normalized_counts.xls, column 12

value: visual cortex


title: CUT&RUN in EGR2 knock-out mouse alveolar macrophages, IgG (rep1)

description: CUT&RUN in EGR2 knock-out mouse alveolar macrophages (rep1)


title: V_sham_D4_RP3

description:
Virgin female at D4
23123R-01-28


title: total VisCtx RNA, Dark condition, ZT3, biorep3

description:
Dark3_rep3
normalized_counts.xls, column 10

value: Dark condition


title: SP_D3_Inj_D4_RP2

description:
Female mated with SP-null at D4
23123R-01-32


title: Patient NB003 CITE-seq, biol rep 2, fresh

description:
Patient NB003 CITE-seq, biol rep 2 from fresh tissue. CS204: technical replicate 1, CS205: technical replicate 2. RNA and ADT (prefix ‘adt-‘) counts are aggregated.
Bonine2023_cell_CS204-205

value: neuroblastoma


title: V_sham_D45_RP2

description:
Virgin female at D45
23123R-01-27


title: CUT&RUN in wild type mouse alveolar macrophages, IgG (rep1)

description: CUT&RUN in wild type mouse alveolar macrophages (rep1)


title: Patient NB002 scRNA-seq, viable-frozen

description:
Patient NB002 scRNA-seq from viably-frozen tissue.
Bonine2023_cell_KDP06

molecule: polyA RNA

value: Patient NB002

value: viably-frozen tissue


title: Patient NB003 CITE-seq, biol rep 1, fresh

description:
Patient NB003 CITE-seq, biol rep 1 from fresh tissue. CS202: technical replicate 1, CS203: technical replicate 2. RNA and ADT (prefix ‘adt-‘) counts are aggregated.
Bonine2023_cell_CS202-203


title: CUT&RUN in wild type mouse alveolar macrophages, IgG (rep2)

description: CUT&RUN in wild type mouse alveolar macrophages (rep2)


title: SP_D3_Inj_D4_RP1

description:
Female mated with SP-null at D4
23123R-01-25


title: CUT&RUN in EGR2 knock-out mouse alveolar macrophages, H3K4me3 (rep2)


title: total VisCtx RNA, Dark condition, ZT3, biorep2

description:
Dark3_rep2
normalized_counts.xls, column 9


title: total VisCtx RNA, Dark condition, ZT3, biorep1

description:
Dark3_rep1
normalized_counts.xls, column 8


title: total VisCtx RNA, Dark condition, ZT7.5, biorep2

description:
Dark7.5_rep2
normalized_counts.xls, column 13


title: Patient NB001 scRNA-seq, viable-frozen

description:
Patient NB001 scRNA-seq from viably-frozen tissue.
Bonine2023_cell_KDP02

value: Patient NB001


title: CUT&RUN in EGR2 knock-out mouse alveolar macrophages, H3K4me3 (rep1)


title: CUT&RUN in wild type mouse alveolar macrophages, H3K4me3 (rep2)


title: iPSCs dopa 24

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

data_processing:
STAR alignemnt, RSEM
Assembly: Human Build 38.99
Supplementary files format and content: raw read counts

extract_protocol:
Qiagen miRNeasy Mini Kit
Perkin Elmer Rapid Directional RNA-Seq kit 2.0 with NextFlex RNA-Seq Unique dual index barcodes

value: dopaminergic neurons


title: V_sham_D4_RP2

description:
Virgin female at D4
23123R-01-21


title: Patient NB003 CITE-seq, biol rep 3, fresh

description:
Patient NB003 CITE-seq, biol rep 3 from fresh tissue. CS206: technical replicate 1, CS207: technical replicate 2. RNA and ADT (prefix ‘adt-‘) counts are aggregated.
Bonine2023_cell_CS206-207


title: total VisCtx RNA, Dark condition, ZT1, biorep3

description:
Dark1_rep3
normalized_counts.xls, column 7


title: total VisCtx RNA, Dark condition, ZT3, biorep4

description:
Dark3_rep4
normalized_counts.xls, column 11


title: total VisCtx RNA, Dark condition, ZT1, biorep2

description:
Dark1_rep2
normalized_counts.xls, column 6


title: CUT&RUN in wild type mouse alveolar macrophages, H3K4me3 (rep1)


title: M_D3_Inj_D45_RP1

description:
Male at D45
23123R-01-19


title: SP_sham_D4_RP3

description:
Female mated with SP-null at D4
23123R-01-18


title: 71-71-B8_S58: CBDL+DSS_Rep6

city: Ghent

first: Lindsey

last: Devisscher

address: Corneel Heymanslaan 10

data_processing:
Extract UMIs, UMI-tools 1.0.1, command: umi_tools extract -I <in.fastq.gz> -S <out.fastq.gz>  --extract-method=regex  --bc-pattern='(?P<umi_1>.{{6}})(?P<discard_1>.{{4}}).*'
Trimming reads, trimmomatic v 0.39, command: trimmomatic SE -threads 20 <in.fastq.gz> <out_trimmed.fastq.gz> ILLUMINACLIP:~/trimmomatic-0.39-1/adapters/TruSeq3-SE.fa:2:30:10 \ SLIDINGWINDOW:4:15 CROP:64 MINLEN:50
Mapping reads, STAR 2.7.5b, command: STAR --runThreadN 10 --genomeDir <index_star> --readFilesIn <in.fastq.gz> --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix <sample_> --quantMode TranscriptomeSAM
Process UMIs, UMI-tools 1.0.1, command: umi_tools dedup -I <in.bam> --output-stats=deduplicated -S <out.bam>
Quantify expression with RSEM, RSEM 1.3.1, rsem-calculate-expression -p 60 --strand-specific --no-bam-output --bam <in.bam> <rsem_index> <sample_name>
Genome_build: GRCm38.p6, release 100
Supplementary_files_format_and_content: normalized counts (DESeq2)

source_name: Monocyte

extract_protocol:
Total RNA was extracted using the RNAeasy Mini Kit by QIAGEN (Cat#74104) according to the manufacturer's guidelines.
Library construction was performed with the QuantSeq 3’ mRNA FWD kit (Lexogen) and UMI Second Strand Synthesis Module (Lexogen).

tag: disease state

value: advanced cholestatic liver injury + acute colitis

value: Monocyte


title: 69-69-A8_S57: CBDL+DSS_Rep6

source_name: Kupffer cell

value: Kupffer cell


title: iPSCs dopa 21


title: F_D3_Inj_D4_RP3

description:
Female at D4
23123R-01-14


title: iPSCs dopa 23


title: 68-68-H7_S56: CBDL+DSS_Rep4+5


title: total VisCtx RNA, Dark condition, ZT0, biorep3

description:
Dark0_rep3
normalized_counts.xls, column 3


title: total VisCtx RNA, Dark condition, ZT1, biorep1

description:
Dark1_rep1
normalized_counts.xls, column 5


title: total VisCtx RNA, Dark condition, ZT0, biorep4

description:
Dark0_rep4
normalized_counts.xls, column 4


title: 67-67-G7_S55: CBDL+DSS_Rep4+5

source_name: Monocytenocyte-derived Macrophage

value: Monocytenocyte-derived Macrophage


title: V_D3_Inj_D45_RP1

description:
Virgin female at D45
23123R-01-13


title: SP_sham_D4_RP2

description:
Female mated with SP-null at D4
23123R-01-11


title: total VisCtx RNA, Dark condition, ZT0, biorep2

description:
Dark0_rep2
normalized_counts.xls, column 2


title: V_D3_Inj_D4_RP1

description:
Virgin female at D4
23123R-01-10


title: iPSCs dopa 20


title: 66-66-E7_S53: CBDL+DSS_Rep4+5


title: iPSCs dopa 19


title: total VisCtx RNA, Dark condition, ZT0, biorep1

description:
Dark0_rep1
normalized_counts.xls, column 1


title: F_D3_Inj_D4_RP2

description:
Female at D4
23123R-01-09


title: 65-65-E6_S45: DSS_Rep5+6

value: acute colitis


title: M_D3_Inj_D4_RP1

description:
Male at D4
23123R-01-08

value: WT


title: LT_fasted_5

city: La Jolla

first: Terry

last: Lin

state: CA

address: 10010 N Torrey Pines Rd, RBIO-P

department: RBIO

institute: Salk Institute

data_processing:
Sequencing library read quality was assessed using FastQC v0.11.5 (Babraham Bioinformatics, Cambridge, UK)
Libraries were individually mapped to the mm10 genome using STAR v2.5.3a
Gene expression levels were quantified across exons using HOMERv4.10 and mm10 UCSC genome annotation
Data normalization and differential gene expression was carried out via edgeR v3.26.7
Assembly: mm10
Supplementary files format and content: matrix table containing annotated raw counts in csv format

extract_protocol:
Total RNA was extracted from 30mg frozen liver powder using TRIzol™ Reagent (ThermoFisher Scientific)
500ng of total RNA was used to prepare libraries using TruSeq Stranded mRNA kit (Illumina)

value: liver

value: LDLR-KO

value: TRF


title: iPSCs dopa 17


title: LT_fasted_6


title: iPSCs dopa 16


title: 54-54-D7_S52: CBDL+DSS_Rep2


title: iPSCs dopa 15


title: 53-53-C7_S51: CBDL+DSS_Rep2


title: LT_fasted_4


title: SP_sham_D4_RP1

description:
Female mated with SP-null at D4
23123R-01-04

value: brain

value: CTRL (Sham)


title: 52-52-B7_S50: CBDL+DSS_Rep2


title: V_sham_D4_RP1

description:
Virgin female at D4
23123R-01-03


title: iPSCs dopa 14


title: LT_fasted_2


title: LT_fasted_3


title: LT_fasted_1


title: iPSCs dopa 13


title: F_sham_D4_RP1

description:
Female at D4
23123R-01-02


title: 51-51-A7_S49: CBDL+DSS_Rep1


title: 50-50-H6_S48: CBDL+DSS_Rep1


title: iPSCs dopa 12


title: LT_fed_6


title: 56-56-F7_S54: CBDL+DSS_Rep3


title: 49-49-58-G6_S47: CBDL+DSS_Rep1+3


title: M_sham_D4_RP1

description:
Male at D4
23123R-01-01


title: iPSCs dopa 11


title: LT_fed_5


title: HEK293T, ASO U7 snRNA 3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

data_processing:
A quality check was performed with FastQC v0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read processing and quality control were performed with BBDUK2 v37.02 from the BBMAP package (sourceforge.net/projects/bbmap/).
Reads were mapped against the human genome version GRCh38 using STAR v2.5.3a_modified. The reads were required to map uniquely (--outFilterMultimapNmax 1 parameter was applied).
The resulting BAM files were then input to the featureCounts v1.5.0-p1 program from Subread software to calculate the raw expression values of the repeats.
Assembly: GRCh38
Supplementary files format and content: TSV files with repetitive sequence name and number of raw reads assigned to it; the repeats annotations were obtained from UCSC via TableBrowser

growth_protocol: HEK293T cells were grown in Dulbecco's modified Eagle’s medium with L-glutamine and 4.5 g/L glucose (DMEM; Lonza) supplemented with 10% fetal calf serum (Gibco) and antibiotics (100 U/ml penicillin, 100 μg/ml streptomycin, 0.25 μg/ml amphotericin B (Sigma)) at 37°C in a humid atmosphere containing 5% CO2

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Invitrogen). One microgram of RNA was first subjected to the rRNA depletion step using RiboCop rRNA Depletion Kit before the construction of sequencing libaraies.
Total RNA libraries were prepared using the Total RNA-Sense Library Preparation Kit (Lexogen) following the manufacturer’s instructions.

treatment_protocol: For U7 snRNA depletion, the chemically modified chimeric ASO was introduced to the cells at a 100 nM concentration using Lipofectamine 2000 according to the manufacturer’s protocol (GFP ASO was used as a control).

value: embryonic kidney cells

value: U7 snRNA knockdown


title: V_sham_D45_RP1

description:
Virgin female at D45
23123R-01-06


title: 48-48-F6_S46: DSS_Rep4


title: iPSCs dopa 10


title: LT_fed_4


title: 46-46-D6_S44: DSS_Rep4


title: HEK293T, ASO U7 snRNA 2


title: LT_fed_3


title: HEK293T, ASO U7 snRNA 1


title: LT_fed_2


title: iPSCs dopa 7


title: 44-44-B6_S42: DSS_Rep3


title: HEK293T, ASO control 3


title: LT_fed_1


title: LA_fasted_6

value: adlib


title: iPSCs dopa 6


title: iPSCs dopa 9


title: 43-43-A6_S41: DSS_Rep3


title: HEK293T, ASO control 1


title: 42-42-H5_S40: DSS_Rep2


title: iPSCs dopa 5


title: LA_fasted_5


title: 41-41-G5_S39: DSS_Rep2


title: iPSCs dopa 4


title: IL-2 + IL-15 + TGFb 003

description: Biological replicate 3

value: Spleen

value: CD8 T cell

value: IL-2 + IL-15 + TGFb


title: LA_fasted_4


title: iPSCs dopa 8

value: dopaminergic neurons


title: iPSCs dopa 3


title: LA_fasted_3


title: 45-45-C6_S43: DSS_Rep3

value: Monocyte


title: BJ cells, DMS CR4/5amplicon, rep1

city: Santa Cruz

first: Michael

last: Stone

address: 1156 High Street

institute: University of California Santa Cruz

data_processing:
Reads were quality filtered and size selected with TrimGalore. Command: --paired --nextera R1.fastq.gz R2.fastq.gz --length 120
Reads were mapped to the hTR sequence (451 nt) with bowtie2. Command: bowtie2 --local --no-unal --no-discordant --no-mixed --phred33
The Devonvolution of RNA Ensembles with Expectation Maximization (DREEM) program was run on BAM files of Pseudoknot and CR4/5 ampliconsusing start and end nucleotides 22-204 and 213-368, respectively.
Assembly: Assembly: Human Telomerase RNA (hTR)
Supplementary files format and content: Supplementary files format and content: Tab delimited text file containing normalized DMS reactivities for each nucleotide of hTR from the corresponding DREEM cluster. -999 corresponds to NaN.
Supplementary files format and content: Supplementary files format and content: Text file containing dot bracket secondary structures for the top predictions of DMS guided structure prediction from the corresponding DREEM cluster.

source_name: BJ cell culture

growth_protocol: HeLa and HEK293T/17 cells (ATCC CRL-11268, lot:70040949) were cultured in DMEM containing 10% fetal bovine serum, 100 units/mL of penicillin, 100 mg/m of streptomycin, and 1X Gibco GlutaMAX at 37°C, 5% CO2. Cells were seeded into 6-well plates at 0.3 x 106 cells per well and allowed to grow to 90% confluency prior to use.

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer's protocol.
10 μg of HeLa cell derived total RNA was DNAse treated in 1X TURBO DNAse buffer with 1 μL TURBO DNAse enzyme (Thermo Fisher Scientific), followed by column-purification with DNA Clean and Concentrator-5 columns (Zymo Research) following the manufacturer protocol. 5 μg of DNAse-treated RNA was mixed with 5 pmol hTR targeting primer containing a 4-nucleotide unique molecular identifier (UMI) in a volume of 11 μL, heated to 75°C for 3 min and annealed at 35°C for 15 min. Next, 4 μL of 5X M-MLV buffer (Promega), 1 μL 0.1M DTT, 1 μL RNAsin Plus (Promega), and 1 μL TGIRT III (Ingex) were added and the mixture was incubated at room temperature for 30 min. Then, 2 μL of 10mM dNTPs were added, and the reaction was mixed and incubated at 60 °C for 2.5 h. After RT, 1 μL of 5M NaOH was added directly to the cDNA and incubated at 95°C, followed by 2.5 μL of 2M HCl and purification by DNA Clean and Concentrator-5 columns (Zymo Research) using an 8:1 ratio of DNA Binding Buffer to cDNA volume. The cDNA was mixed into a 50 μL second strand synthesis reaction containing 10 μL 5X GC Phusion Buffer (Thermo Fisher Scientific), 1 μL 10 mM dNTP, 25 pmol of a second hTR targeting primer containing a 4 nucleotide UMI, and 1 μL Phusion polymerase. The second strand synthesis reaction was incubated in a thermocycler with the following program: 98°C 2 min, 60°C 2 min, 72°C 10 min. Second strand product was cleaned up with Ampure XP beads (Beckman Coulter) at a 0.8:1 bead to sample volume ratio and eluted in 20 μL nuclease-free H2O. Illumina sequencing libraries of two partially overlapping hTR regions (Pseudoknot: nucleotides 1-286 and CR4/5: nucleotides 193-451) were generated by two successive 50 μL PCR reactions. For the first PCR, 4 μL second strand product was added to a 50 μL PCR reaction containing primers for either the pseudoknot or CR4/5 amplicon and run with the following program: 10 cycles at 66°C annealing temperature, followed by 10 cycles at a 60°C annealing temperature. Amplicons were bead cleaned with a 0.8:1 ratio and went into a second PCR of 10 cycles at an annealing temperature of 65°C to complete the sequencing adapters and multiplexing barcodes. Libraries were bead cleaned with a 0.8:1 ratio and quantified by Qubit (Thermo Fisher Scientific) and Tapestation (Agilent) for quality metrics before sequencing by 150 bp paired end reads on the iSeq100 (Illumina).

treatment_protocol: For DMS modification, plates of HeLa cells were divided into DMS and control groups (3 wells each). Media from the DMS group was aspirated and replaced with 2 mL of a 2% DMS (Sigma) solution in cell media (prepared by brief vortexing to incorporate DMS). Cells were incubated at 37°C for 4 min, media was aspirated from each well and replaced with 10 mL of ice cold DMS quench solution (30% beta-mercaptoethanol in phosphate-buffered saline). Plates were placed on ice and the cells were collected by scraping and brief trituration, then pelleted by centrifugation at 200 x g for 5 min. Cells were washed once with cold PBS.

value: BJ cell culture

value: BJ

value: Foreskin fibroblast

value: DMS


title: HEK293T, ASO control 2

value: WT


title: iPSCs dopa 2


title: BJ cells, DMS CR4/5 amplicon, rep2


title: LA_fasted_2

value: liver

value: LDLR-KO


title: 40-40-F5_S38: DSS_Rep2

value: acute colitis

value: Kupffer cell


title: iPSCs dopa 1


title: BJ cells, Untreated CR4/5 amplicon


title: 39-39-E5_S37: DSS_Rep1


title: LA_fasted_1


title: HeLa cells, DMS CR4/5 amplicon, hTERT transfection

source_name: HeLa cell culture

value: HeLa cell culture

value: HeLa

value: Cervical cancer


title: U2OS, 2, INPUT

city: Darlinghurst

first: Cristian

middle: David

last: Pena Martinez

state: NSW

address: 384 Victoria St, Garvan Institute of Medical Research Lvl 10 immunology

department: St Vincent’s Clinical School, Faculty of Medicine, Department of Immunology

institute: Garvan Institute of Medical research

data_processing:
Reads were trimmed using: trim_galore --paired (Cutadapt version: 3.5)
Reads were aligned to the hg19 reference genome using bowtie2 (Version: 2.4.5)
Samtools (Version: 1.10) was used to obtain and sort and fixmates when necessary in compressed binary files (.bam)
Duplicates were marked using picard MarkDuplicates (Version: 2.25.6)
A list of high signal regions was blacklisted using the Boyle Lab's hg19-blacklist.v2.bed file and a bedtools intersect command (Version: 2.30.0)
Files were indexed using Samtools (Version: 1.10) and bigWig files generated using bamCoverage (deeptools Version: 3.5.1) with the following parameters: -bs 10 -p 10 --normalizeUsing CPM
Regions were called using macs2 (Version: 2.2.7.1) using callpeak's default parameters and INPUT bam files as the controls for each experiment.
Intersecting regions were selected using bedops --intersect (Version:  2.4.39)
Assembly: hg19
Supplementary files format and content: bigWig, regions as narrowPeak (except for Input sample), merged regions by cell line and overall samples
Library strategy: Direct Immunoprecipitation sequencing

growth_protocol: Cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) + 10% v/v fetal bovine serum (FBS) and supplemented with antibiotics. Frozen cell line cultures were initiated from a single vial and split accordingly for biological replicates after the second passage.

extract_protocol:
Genomic DNA from cells was harvested using an AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Cat No: 80224). Purified DNA was concentrated using Amicon Ultra-0.5 Centrifugal Filter Unit (Millipore, UFC501096) and concentration adjusted. DNA was fragmented using AFA Fiber Pre-Slit Snap-Cap microtubes (Covaris, 520045) and a Covaris instrument (M220 Focused-ultrasonicator) at Peak power: 50, Duty factor: 20, Cycles/Burst: 200, Time: 700 s, Setpoint: 20 °C producing 100–200 bp fragments. DNA fragments were stored at -80 °C until a pull-down experiment. A 96-well MaxiSorp plate (Thermo Scientific, 442404) was coated by adding 60 µL per well of 50 µg mL-1 streptavidin diluted in PBS and incubated overnight at 4 °C. Fragmented DNA was thawed and diluted in DPBS (ThermoFisher, 14190144), pH adjusted to 7.4. For each experiment 140 µg DNA were diluted in 525 µL DPBS and heated at 90 °C for 10 min followed by cooling down at the rate of 1 °C per min to 21 °C and kept on ice until the pull-down experiment. A streptavidin-coated plate was washed once with PBS and blocked with 200 µL per well of SuperBlock (ThermoFisher, 37515) for 2 h at room temperature Biotinylated iMab-MycAviTag was diluted to 49 µg in 525 µL of DPBS pH 7.4 (7 wells, 75 µL each) for each experiment. Blocked wells were washed once with PBS and Biotinylated iMab-MycAviTag solution was added. After incubating for 1 h at room temperature while shaking at 200 rpm, wells were washed twice with DPBS pH 7.4. Then, 75 µL of DNA solution was added to each well and incubated 16–20 h at 4 °C, and additionally, in the case of the MCF7 cell line, two independent control experiments were also carried out at an incubation temperature of 16 ℃. The supernatant was aspirated, each well washed and tap-dried seven times with 200 µL of DPBS pH 7.4 supplemented with 0.1% v/v Tween 20 and twice with DPBS only at room temperature of 24 ℃. Elution was performed by adding 100 µL of 100 mM Tris/acetate pH 10 supplemented with 1% w/v SDS to each well and incubating for 1 h at 40 °C while the plate was shaking at 200 rpm. Eluted DNA was collected, combined, and concentrated using ssDNA/RNA Clean & Concentrator kit (Zymo, Cat No: D7011).
Libraries were constructed using a no-shearing IDT xGEN cfDNA & FFPE DNA library preparation kit following the manufacturer protocol

value: Human bone cancer osteosarcoma

tag: ip antibody


title: SeqScope_2nd colon

description:
2nd-Seq of Seq-Scope
Digital Expression Matrix

data_processing:
Sequencing by Illumina HiSeqX, HiSeq4000 and NovaSeq platforms .
Seq-Scope data were initially processed using the STtools package, utilizing STAR/STARsolo 2.7.5c, with a modification to use hexagonal array, instead of square array. The processed DGE matrix, pooled in non-overlapping hexagons with 12 μm sides, was analyzed in the Seurat V4 package.
First, we removed all genes starting with mt and Gm to remove mitochondrial genes and hypothetical gene models. After applying a cutoff, data were normalized using regularized negative binomial repression implemented in Seurat’s SCTransform function.
Clustering analysis was performed using the shared nearest neighbor modularity optimization implemented in Seurat’s FindClusters function. The clusters were visualized in the UMAP (uniform manifold approximation and projection) manifold or the histological space using ggplot functions. The markers for each cluster were identified through the FindAllMarkers function and used to annotate cell types.
Assembly: mm10
Supplementary files format and content: Digital expression matrix with barcode featuring spatial coordinates

source_name: colon

value: colon

value: biopsy-induced injury


title: U2OS, 1, INPUT


title: 37-37-C5_S35: DSS_Rep1


title: LA_fed_6

value: adlib


title: HeLa cells, DMS CR4/5 amplicon, rep 4


title: LA_fed_5


title: HEK293T, 2, INPUT

value: Human embryonic kidney


title: HeLa cells, DMS CR4/5 amplicon, rep 3


title: LA_fed_4


title: HEK293T, 1, INPUT


title: HeLa cells, DMS PK amplicon, rep 4


title: LA_fed_3


title: 34-34-H4_S32: CBDL2w_Rep4

value: onset cholestatic liver injury


title: HeLa cells, DMS PK amplicon, rep 3


title: 33-33-G4_S31: CBDL2w_Rep3

value: Monocyte


title: LA_fed_2


title: 38-38-D5_S36: DSS_Rep1

value: Monocytenocyte-derived Macrophage


title: MCF7, 2, 16C, INPUT

value: Human breast cancer adenocarcinoma


title: MCF7, 1, 16C, INPUT


title: LA_fed_1


title: HeLa cells, DMS PK amplicon, rep 2

value: WT

value: DMS


title: 32-32-F4_S30: CBDL2w_Rep3


title: MCF7, 2, INPUT


title: Telomerase RNP, 2% DMS

source_name: HEK293T cell culture

value: HEK293T cell culture

value: Embryonic kidney cells


title: 36-36-B5_S34: CBDL2w_Rep4


title: Telomerase RNP, 0% DMS


title: 31-31-E4_S29: CBDL2w_Rep3

value: Kupffer cell


title: MCF7, 1, INPUT


title: 35-35-A5_S33: CBDL2w_Rep4


title: Telomerase RNP, 1% DMS


title: U2OS, 2, iMab, DIP

description:
U2OS_2_MACS_peaks.narrowPeak
U2OS_1_2_intersect_peaks.bed
iMab_MCF7_HEK293T_U2OS_intersect_peaks.bed

value: iMab (Biotin, scFv)


title: iPSCs dopa 22

value: dopaminergic neurons


title: 29-29-C4_S27: CBDL2w_Rep2


title: 30-30-D4_S28: CBDL2w_Rep2


title: U2OS, 1, iMab, DIP

description:
U2OS_1_MACS_peaks.narrowPeak
U2OS_1_2_intersect_peaks.bed
iMab_MCF7_HEK293T_U2OS_intersect_peaks.bed


title: HEK293T, 2, iMab, DIP

description:
HEK293T_2_MACS_peaks.narrowPeak
HEK293T_1_2_intersect_peaks.bed
iMab_MCF7_HEK293T_U2OS_intersect_peaks.bed


title: Liver tissue from male 6 Eu-MYC mice housed in chronic jet lag lighting conditions

first: Rebecca

last: Mello

state: California

address: 10550 North Torrey Pines Road

institute: Scripps Research

data_processing:
STAR alignment with SeqMan NGen 17
Counts table with ArrayStar 17
DESeq2 using GenePattern online tool
Assembly: mm10
Supplementary files format and content: text file "EuMYC_RNAseq_RAW_counts.txt" contain the raw count output from ArrayStar17
Supplementary files format and content: cvs file "1212vCJL_DESeq2_report.csv" DESeq2 report output from GenePattern
Supplementary files format and content: text file "EuMYC_RNAseq_.CJL.vs.1212.normalized_counts.txt" normalized counts output from GenePattern DESeq2

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
DNBSEQ stranded mRNA library by BGI

value: liver


title: 28-28-B4_S26: CBDL2w_Rep2


title: Liver tissue from male 7 Eu-MYC mice housed in chronic jet lag lighting conditions


title: MCF7, 2, 16C, iMab, DIP

description:
MCF7_2_16C_MACS_peaks.narrowPeak
MCF7_1_2_16C_intersect_peaks.bed


title: 25-25-G3_S23: CBDL2w_Rep1


title: MCF7, 1, 16C, iMab, DIP

description:
MCF7_1_16C_MACS_peaks.narrowPeak
MCF7_1_2_16C_intersect_peaks.bed


title: Liver tissue from male 6 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: Liver tissue from male 8 Eu-MYC mice housed in chronic jet lag lighting conditions


title: 24-24-F3_S22: Sham6w_Rep4

value: controls


title: iPSCs dopa 18


title: Liver tissue from male 5 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: 23-23-63-E3_S21: Sham6w_Rep4+6


title: Liver tissue from male 4 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: MCF7, 2, iMab, DIP

description:
MCF7_2_MACS_peaks.narrowPeak
MCF7_1_2_intersect_peaks.bed
iMab_MCF7_HEK293T_U2OS_intersect_peaks.bed


title: Melanoma tumors, RNA _IFNAR1 3

type: RNA

city: Gainesville

first: Sadeem

last: Qdaisat

address: 1333 Center Dr.

institute: University of Florida

hyb_protocol: Nanostring NS_CancerImmune_V1.1 kit protocol nCounter

scan_protocol: nCounter FLEX High sensitivity scan

data_processing: Rosalind

label: biotin

source_name: Melanoma tumors in C57B6

label_protocol: Nanostring NS_CancerImmune_V1.1 kit on a BIO-RAD T100 Thermal Cycler

growth_protocol: In vivo

extract_protocol: TriZol followed by RNA purification

value: Melanoma tumors

value: ML uRNA + IFNAR1


title: MCF7, 1, iMab, DIP

description:
MCF7_1_MACS_peaks.narrowPeak
MCF7_1_2_intersect_peaks.bed
iMab_MCF7_HEK293T_U2OS_intersect_peaks.bed


title: HEK293T, 1, iMab, DIP

description:
HEK293T_1_MACS_peaks.narrowPeak
HEK293T_1_2_intersect_peaks.bed
iMab_MCF7_HEK293T_U2OS_intersect_peaks.bed


title: 26-26-H3_S24: CBDL2w_Rep1


title: 22-22-D3_S20: Sham6w_Rep4


title: Melanoma tumors, RNA _IFNAR1 2


title: Melanoma tumors, RNA _IFNAR1 1


title: Liver tissue from male 5 Eu-MYC mice housed in chronic jet lag lighting conditions


title: Pitx3-GFP/AK vs. Pitx3-GFP/wt-3

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan) * Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C

scan_protocol: scanning of slides using Agilent G256BA Features were extracted using Imagene software from Biodiscovery.

data_processing: genes, no bg corr - Normalization was done using LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol: FJ004-cust_lab: Pre-amplification of the RNA was performed using the standard solutions from the QuickAmp labeling kit, no dye from Agilent following a procedure supplied by Agilent on request. For the generation of cDNA, 1.2 ul of T7 promoter primer solution was added to the 10 ul of RNA (1ng/ul), incubated at 65oC for 10 minutes and put on ice. The following was added to the reaction mix: 4 ul of 5x First Strand Buffer, 2ul of 0.1M DTT, 1ul of 10mM dNTP mix, 1ul of MMLV RT Polymerase and 0.5  ul of Rnase Out to a total volume of 20ul. Samples were incubated for 2 hours at 40oC and inactivation was carried out at 65oC for 15 minutes. For in vitro transcription the following was added to the reaction mix: 12.1ul mQ, 20ul of 4x Transcription Buffer, 6ul of 0.1M DTT, 8ul of dNTP mix, 5.6ul of CTP, 6.4ul of 50% PEG, 0.5 ul of Rnase out, 0.6ul of Inorganic Phosphate and 0.8ul of T7 RNA Polymerase to a total volume of 80ul. Reaction mixture was incubated in a waterbath at 40oC for 4 hours. Samples were purified on a Qiagen Rneasy Micro Spin column according to the supplied protocol, and cRNA was eluted in 10.5ul of water. Random hexamer primers were added to the cRNA to a final concentration of 20mM in a final volume of 11.5ul, incubated at  65oC for 10 minutes and stored on ice, after which cDNA was performed as described above. The second round of in vitro transcription, labeling and hybridizations was performed as described by Roepman et al.

extract_protocol: FACS-RNA: RNA was isolated from FACS-purified Pitx3(gfp/+) mdDA neurons derived from 3 pooled samples of dissected E14.5 embryonic brain (69.000-83.000 cells per sample, each sample contained multiple embryos). FACS-purified neurons were immediately collected in Trizol LS and RNA was isolated according to the manufacturer's protocol with small adaptations to increase purity. RNA for microarray was column purified using the Arcturus Picopure Kit with DNAse treatment on column. In short, a 1:1 mixture of RNA and Extraction Buffer (XB) was combined with an equal volume of 70% EtOH and loaded on column and spun down. Flowthrough was discarded, columns were washed and 40 ul of DNAse mix (35 ul RDD buffer + 5ul DNAseI stock solution (Qiagen RNAse-free DNAse set #79254)) was applied. After 15' incubation at Room Temperature, columns were washed and RNA was eluted according to the manufacturer's protocol.

tag: strainorline

tag: celltype

value: E14.5 embryonic brain


title: Pitx3-GFP/AK vs. Pitx3-GFP/wt-2


title: Pitx3-GFP/wt-3 vs. Pitx3-GFP/AK


title: Pitx3-GFP/wt-1 vs. Pitx3-GFP/AK


title: Pitx3-GFP/wt-2 vs. Pitx3-GFP/AK


title: 21-21-64-C3_S19: Sham6w_Rep3+6


title: MCF7 cells, WT 3

data_processing:
Raw sequences were trimmed of adapters using trim_galore
Sequences were mapped using Hisat2 to the hg19 reference genome
Read count was performed using FeatureCounts and using the NCBI RefSeq gtf for hg19
Assembly: hg19
Supplementary files format and content: featureCounts

source_name: cell line

growth_protocol: Cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) + 10% v/v fetal bovine serum (FBS) and supplemented with antibiotics (Penicillin and Streptomycin). Frozen cell line cultures were initiated from a single vial and split accordingly for biological replicates after the second passage.

extract_protocol:
RNA was extracted using Rneasy Plus mini plus kit (Qiagen).
RNA quality was calculated using an Agilent TapeStation system and samples undergo library preparation using KAPA mRNA HyperPrep Kit (Roche) following the manufacturer's protocol.

tag: tissue

value: cell line


title: 20-20-B3_S18: Sham6w_Rep3


title: Liver tissue from male 1 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark

source_name: liver


title: Liver tissue from female 8 Eu-MYC mice housed in chronic jet lag lighting conditions


title: Melanoma tumors, RNA 2

value: ML uRNA


title: MCF7 cells, WT 2


title: MCF7 cells, WT 1


title: Liver tissue from male 3 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: Liver tissue from female 7 Eu-MYC mice housed in chronic jet lag lighting conditions


title: 19-19-A3_S17: Sham6w_Rep3


title: Melanoma tumors, RNA 3


title: LM9_circPETH_KO_rep2

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome using Hisat2.
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM value.
Genes differential expression analysis was performed by DESeq2 software between two different groups. The genes with the parameter of false discovery rate (FDR) below0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cells were cultured at 37°C in a humidified incubator with 5% CO2 in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA of HCC cells was extracted  and purified using Trizol reagent. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit.
RNA libraries were prepared for sequencing using Illumina Novaseq TM 6000 sequence platform protocols

treatment_protocol: Hep3B cells were transfected with circPETH overexpression plasmid and circPETH knockout was performed in HCCLM9 cells using CRISPR-Cas9 techniques.

value: HCC cells

value: circPETH KO


title: 15-15-18-62-G2_S15: Sham6w_Rep1+2+5

value: Monocyte


title: Melanoma tumors, RNA 1


title: Liver tissue from male 2 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: Liver tissue from female 6 Eu-MYC mice housed in chronic jet lag lighting conditions


title: LM9_circPETH_KO_rep1


title: 14-14-17-61-F2_S14: Sham6w_Rep1+2+5

value: Monocytenocyte-derived Macrophage


title: 13-13-E2_S13: Sham6w_Rep1


title: Liver tissue from female 5 Eu-MYC mice housed in chronic jet lag lighting conditions


title: LM9_circPETH_KO_rep3


title: Liver tissue from female 4 Eu-MYC mice housed in chronic jet lag lighting conditions


title: 16-16-H2_S16: Sham6w_Rep2


title: 12-12-D2_S12: CBDL6w_Rep4

value: advanced cholestatic liver injury


title: LM9_NTC_rep2

value: NTC


title: Liver tissue from female 3 Eu-MYC mice housed in chronic jet lag lighting conditions


title: LM9_NTC_rep1


title: Liver tissue from female 2 Eu-MYC mice housed in chronic jet lag lighting conditions


title: Hep3B_OE_circPETH_rep3

value: circPETH overexpresion


title: 10-10-B2_S10: CBDL6w_Rep4

value: Kupffer cell


title: 11-11-C2_S11: CBDL6w_Rep4


title: Liver tissue from female 1 Eu-MYC mice housed in chronic jet lag lighting conditions


title: Pitx3-GFP/AK vs. Pitx3-GFP/wt-1


title: Hep3B_OE_circPETH_rep2


title: 9-9-A2_S9: CBDL6w_Rep3


title: Hep3B_OE_circPETH_rep1


title: IgG_ChIP_rep2

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: IgG ChIP, replicate 2

data_processing:
Sample demultiplexing was performed using Illumina's bcl2fastq Conversion Software v.2.19.1.403 and read quality was checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads were aligned to the Xenopus tropicalis genome assembly version 7.1 (https://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1) using weighted multi-mapping strategy employing bowtie2 v.2.2.7 (http://bowtie-bio.sourceforge.net/bowtie2) with default parameters.
Normalized bigWig coverage tracks were generated from the mapped paired-end reads extended to fragment size using deepTools bamCoverage v.2.5.1 (https://deeptools.readthedocs.io/) with parameters “--normalizeUsing RPKM --extendReads”.
Assembly: Xenopus tropicalis v.7.1 (JGI7.1)
Supplementary files format and content: bigWig coverage tracks with RPKM normalization

organism: Xenopus tropicalis

source_name: blastula stage 9 embryos

extract_protocol:
Around 1,000 stage 9 Xenopus tropicalis embryos were cross-linked in 1% methanol-free formaldehyde for 30 min at RT. Cross-linking was quenched with 125 mM glycine for 30 min at RT and the embryos were washed twice with 0.3x Modified Barth’s Saline (88 mM NaCl, 1 mM CaCl2, 1 mM MgSO4, 5 mM HEPES pH 7.8, 2.5 mM NaHCO3). Embryos were homogenized in 200 µl sonication buffer (20 mM Tris–HCl pH 8, 70 mM KCl, 1 mM EDTA, 10% glycerol, 5 mM DTT, 0.125% Nonidet P40 and cOmplete EDTA-free Protease Inhibitor Cocktail (Roche). Chromatin was sheared to around 500 bp using a Biorupter Plus (Diagenode) and centrifuged for 5 min at 16,000 g to remove yolk and pigment. 10% chromatin was kept aside as input control and 100 µl of chromatin was added to 100 µl incubation buffer (50 mM Tris–HCl pH 8, 100 mM NaCl, 2 mM EDTA, 1 mM DTT, 1% Nonidet P40 and cOmplete EDTA-free Protease Inhibitor Cocktail). 5 µg of POLR3F (ab151495, Abcam) or IgG (ab171870, Abcam) antibody was added and incubated overnight at 4°C with overhead shaking. 50 µl Dynabeads Protein G (10004D, Thermo Scientific) per reaction were blocked with incubation buffer + 0.1% BSA for 10 min at 4°C with overhead shaking. Beads were washed twice in incubation buffer for 5 min at 4°C, chromatin was added and the samples were incubated overnight at 4°C with overhead shaking. Beads were washed sequentially with wash buffer 1 (50 mM Tris–HCl pH 8, 100 mM NaCl, 2 mM EDTA, 1 mM DTT, 1% Nonidet P40, 0.1% deoxycholate, and cOmplete EDTA-free Protease Inhibitor Cocktail), wash buffer 2 (wash buffer 1 + 400 mM NaCl), wash buffer 3 (wash buffer 1 + 250 mM LiCl), wash buffer 1, and finally 10 mM Tris + 1 mM EDTA buffer. 200 µl elution buffer (100 mM NaHCO3 pH 8.8, 1% SDS) was added to the beads and incubated for 15 min at RT with overhead shaking. Elution was repeated with additional 200 μl elution buffer. 16 µl 5 M NaCl was added to each elution and input control, and cross-links were reversed by incubating at 65°C overnight with shaking.
ChIP-seq library preparation was performed using NuGEN´s Ovation Ultralow System V2 1-16 (2014). Libraries were prepared with a starting amount of 1 ng of DNA and were amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). All samples were pooled in equimolar ratio and sequenced on a NextSeq 500 Highoutput Flowcell, PE mode for 2x 42 cycles plus 7 cycles for the index read.

value: blastula stage 9 embryos

tag: chip antibody

value: IgG (ab171870, Abcam)


title: LM9_NTC_rep3


title: Hep3B_Vector_rep3

value: control vector


title: 8-8-H1_S8: CBDL6w_Rep3


title: F_D3_Inj_D4_RP1

description:
Female at D4
23123R-01-07

data_processing:
Galaxy web platform: usegalaxy.org
Quality control on the data was performed using FastQC
214 using FastQC
data was subsequently mapped using RNA STAR 35 and the Ensembl gene annotation for Drosophila genome (dm6)
Gene count was done using FeatureCount software
Assembly: Drosophila melanogaster DM6
Supplementary files format and content: raw counts

extract_protocol:
Injured and sham flies were injured at 3 days post-eclosion. At 1 day and 6 weeks post-injury, brains from males, wildtype-mated females, virgin females, and SP0-mated females were collected, resulting in 16 conditions, each condition containing three independent cohorts of n=40 flies. RNA from brain tissue was extracted by TRIzol®/Chloroform extraction (ThermoFisher, 15596026) and further clean-up with the Zymo DNA Clean & Concentrator-5 kit (D4004) with on column DNase treatment (ThermoFisher, AM1907). Once obtained, RNA samples were transferred on dry ice to Admera Health for library preparation and sequencing. Total RNA integrity was checked by BioAnalyzer. QIAseq FastSelect rRNA Fly + NEB Ultra II Directional kit was used to deplete rRNA and prepare stranded cDNA libraries. Samples were sequenced on NextSeq High Output Flow Cell (Illumina) for 150 cycles to generate a total of 60M paired-ended, 101 base-pair reads.
Once obtained, RNA samples were transferred on dry ice to Admera Health for library preparation and sequencing. Total RNA integrity was checked by BioAnalyzer. QIAseq FastSelect rRNA Fly + NEB Ultra II Directional kit was used to deplete rRNA and prepare stranded cDNA libraries.

value: brain

value: WT


title: Liver tissue from female 8 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark

value: liver


title: IgG_ChIP_rep1

description: IgG ChIP, replicate 1


title: Liver tissue from female 6 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: 7-7-G1_S7: CBDL6w_Rep3


title: Hep3B_Vector_rep2


title: 6-6-F1_S6: CBDL6w_Rep2


title: Liver tissue from female 5 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: Input_ChIP_rep3

description: Input chromatin, replicate 3


title: Hep3B_Vector_rep1


title: Input_ChIP_rep2

description: Input chromatin, replicate 2


title: 5-5-E1_S5: CBDL6w_Rep2


title: H9 ESCs, wild type (WT), biol rep 4

city: Heidelberg

first: Rachel

middle: B

last: Gilmore

state: BW

address: Im Neuenheimer Feld 366

department: Institute for Human Genetics

institute: Heidelberg University

data_processing:
For hESC-derived neurons, .fastq.gz files from flow cell lanes were concatenated using pigz v2.2.3.
Quality of reads were checked using fastqc v0.11.7 and then MultiQC v1.10.1; equal distribution of reads across the gene body was verified using geneBody_coverage.py v3.0.1 from RSeQC on indexed BAM files (.bai) generated from sorted BAM files using samtools v1.9
Reads were aligned to the genome using HISAT2 v2.2.1 (using options --fr --no-discordant --avoid-pseudogene --no-mixed) and STAR v2.7.1a (using options --readFilesCommand zcat, --outFilterType BySJout, --outFilterMultimapNmax 1, --alignSJoverhangMin 8, --alignSJDBoverhangMin 2, --outFilterMismatchNoverReadLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMtype BAM SortedByCoordinate, --outWigType bedGraph)
For samples aligned using HISAT2, resulting SAM files were converted to sorted BAM files using samtools v1.9
Sorted BAM files were used to extract read counts using featureCounts from subread v2.0 (with options -s 2)
Assembly: hg38, gencodev25
Supplementary files format and content: Resultant read counts from featureCounts for STAR aligned reads as a text file (.txt) in tab-delimited format for ESCs and hESC-derived inducible neurons.
Supplementary files format and content: Resultant read counts from featureCounts for STAR aligned reads as a text file (.txt) in tab-delimited format for hESC-derived inducible neurons for both smDEL and lgDEL analyses.
Supplementary files format and content: Resultant read counts from featureCounts for HISAT2 aligned reads as a text file (.txt) in tab-delimited format for hESC-derived inducible neurons for both smDEL and lgDEl analyses.

growth_protocol: Human embryonic stem cells were maintained in mTeSR™ Plus (STEMCELL Technologies, Catalog #100-0276) on Matrigel™ hESC-Qualified Matrix (Corning™, Catalog #354277) coated 6-well plates in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For hESCs, RNA was harvested using the miRNeasy® Mini Kit (QIAGEN, Catalog #1038703) following manufacturer's protocol with minor modifications, including homogenization with QIAshredder (QIAGEN, Catalog #1011711), addtional chloroform extration step, and on-column DNase treatment using RNase-Free DNase Set (QIAGEN, Catalog #79254). For hESC-derived neurons, RNA was harvested using the Direct-zol RNA Miniprep kit (Zymo Research, Cat No. R2050) following manufacturer's protocols. For both hESCs and hESC-derived neurons, 1 ug of RNA was used for the construction of sequencing libraries.
For hESCs, RNA libraries for RNA-seq were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, Catalog #E7760L) following manufacturer's protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). For hESC-derived neurons, RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat No. 20020594 ) following manufacturer's protocols.

treatment_protocol: hESCs were differentiated into iNeurons following the published protocol by Fernandopulle et al (2020) with minor modifications. In brief, when hESCs reached 70-80% confluency, they were singularized using Accuatse (Millipore, SCR005), collected in mTeSR™ Plus media, transferred to a Falcon tube, and pelleted at 1.2X1000 rpm for 3 min. The cell pellet was resuspended, cells were counted using a hemocytometer, and cells were plated for differentiation in modified Induction Media (IM) supplemented with freshly added Doxycycline Hydrochloride (Fisher Scientific, BP2653-5) and ROCK inhibitor Y-27632 (Tocris, 1254) at final concentrations of 2uM and 10uM respectively (day 0 of differentiation). Media was changed using IM plus freshly added supplements for 3 more days before singularizing and replating for terminal differentiation with modified Cortical Neuron Media (CM) on day 4. Cells were plated at 1 million cells per PDL/laminin-coated well in a 6-well plate or 7 million cells per PDL/laminin-coated 10cm dish. CM was supplemented with 10uM ROCK inhibitor. Complete media change with CM was performed on day 5. Neurons were collected for RNA extraction on day 11.

value: hESCs

tag: Sex

value: F


title: Liver tissue from female 4 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: 4-4-D1_S4: CBDL6w_Rep2


title: 3-3-C1_S3: CBDL6w_Rep1


title: Liver tissue from female 7 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: H9 ESCs, wild type (WT), biol rep 3

tag: treatment


title: Pol_III_ChIP_rep3

description: Pol III ChIP, replicate 3

value: POLR3F (ab151495, Abcam)


title: Liver tissue from female 2 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: H9 ESCs, wild type (WT), biol rep 2


title: H9 ESCs, wild type (WT), biol rep 1


title: Liver tissue from female 3 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark


title: 2-2-B1_S2: CBDL6w_Rep1


title: Pol_III_ChIP_rep2

description: Pol III ChIP, replicate 2


title: heartfailure_2

status: Public on Aug 28 2024

first: Florian

last: Leuschner

address: INF 669

institute: Uni Heidelberg

description:
10x Genomics Single Cell 3' v3, aligned with cellranger-6.0.1 to mm10-2020-A
integrated_seurat_obj.rds
cell_ranger_outs.tar.gz

data_processing:
The resulting single-cell RNA-seq outputs were processed using CellRanger provided by 10x genomics. Count data was processed samplewise with the following filters: >300 Feature numbers, <25% mitochondrial genes, <1% ribosomal genes and >500 RNA counts. Doublet scores were calculated with the R-package scDblFinder [60] and only predicted singlets were kept. We further calculated a dissociation score by estimating expression of dissociation associated gene expression [67] with Seurat’s [40] AddModuleScore function and we removed cells above the 99% quantile. Data was log-normalized. Samples were clustered individually by selecting the 3,000 highest variable genes with the FindVariableFeatures function from the Seurat package. From the overlap of these lists, the top 3,000 genes were selected to calculate principal components (PCs). Top 30 PC embeddings were adjusted with harmony R-package, with samples as covariates. In the resulting integrated feature space the nearest neighbor approach and graph based louvain algorithm implemented in Seurat was used to cluster cells and stepwise test optimal cluster resolution (from 0.1 to 1.6 in 0.1 steps) and computing silhouette widths. Celltype markers were calculated with the FindMarkers function with default parameters (wilcoxon test) in Seurat and cell types were manually annotated based on known canonical markers.
We removed four distinct small clusters that were inconclusive for different reasons, i.e. high expression of mitochondrial genes, expression of multiple cell type markers, consistently low RNA and Feature counts. After removal the integration process was repeated and a final atlas was created.
Assembly: GRCm38 (mm10)
Supplementary files format and content: integrated_seurat_obj.rds  contains processed gene expression matrices (raw counts, log-normalized expression), and metadata with cell annotation as a seurat object
Supplementary files format and content: cell_ranger_outs.tar.gz contains cell ranger output files for each sample

source_name: ventricular cardiac tissue

extract_protocol:
Sample preparation and sequencing of murine cardiac interstitial cells was performed according to the detailed protocol published previously with only minor modifications[30]. In brief, rapidly after sacrificing the animals by cervical dislocation, the still beating heart was directly placed in ice-cold HBSS where atria and large vessels were dissected. After chopping the heart into small pieces, enzymatic digestion was initiated in two rounds of 15min duration at 37°C using collagenase type II ( Worthington Biochemical Corporation,  # LS004177). The single-cell suspension was subsequently passed through a 40 µm cell strainer, washed and red blood cell lysis performed. Dead cells were removed by Dead Cell Removal MicroBeads   (Miltenyi Biotec, 130-090-101) binding to MACS  LS columns (Miltenyi Biotec, 130-042-401). Prior to loading the 10x platform, live nucleated cells (DRAQ5+, propidium iodine-) were sorted using a FACSAriaTM IIu (BD) cell sorter.
Following washing and resuspending in PBS, cells were counted manually using trypan blue and a Neubauer chamber. We aimed to load about 5,000 cells per lane on a Chromium Next GEM Chip (10x Genomics, 1000127), that was placed into a 10X Chromium Controller (10X Genomics). The cDNA output was amplified and library construction was performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000269) and Dual Index Kit TT Set A (10x Genomics, 1000215). Respective library quantification and quality controls were performed using an Agilent 2100 Bioanalyzer and in addition a Qubit HS Assay. Indexed libraries were equimolarly pooled resulting in two sequencing runs (control1+HFpEF1; control2+HFpEF2) using a High Output kit v2.5 (Illumina, 20024907) and a NextSeq® 550 (Illumina) sequencer.

value: ventricular cardiac tissue

value: male


title: Pol_III_ChIP_rep1

description: Pol III ChIP, replicate 1


title: 27-27-A4_S25: CBDL2w_Rep1

value: onset cholestatic liver injury

value: Monocyte


title: heartfailure_1

source_name: ventricular cardiac tissue 1/2 heart

value: ventricular cardiac tissue 1/2 heart


title: Input_ChIP_rep1

description: Input chromatin, replicate 1


title: control_1


title: control_2


title: Melanoma tumors, UT 1

value: Melanoma tumors

value: Untreated


title: Melanoma tumors, UT 3


title: Melanoma tumors, UT 2


title: EN Organoid, IgG, Cut&Tag, R2

city: New York City

first: Kristjan

middle: H.

last: Gretarsson

state: New York

institute: Columbia University

data_processing:
CUT&TAG reads were mapped to the mouse genome assembly GRCm39 using bowtie2 (parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700)
Coverage tracks (bigwig) were generated by the bamCoverage function of deepTools with bin size as 50bp and normalizing to 1x depth (reads per genome coverage, RPGC)
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

source_name: EN Organoid

growth_protocol: See Methods (Organoid Culture Isolation and propagation)

extract_protocol:
See Cut&Tag in methods for detailed protocol. In short, cells were collected, washed, and immobilized to concavalin beads, permeabilized with digitonin and incubated with antibody overnight. Next the cells were incubated with Tn5 protein which was activated to digest and tag around the protein bound DNA. The Tn5 tagged DNA-protein complexes diffuse out of the cells and the DNA was purified using PCR purification kit.
The Tn5 tagged DNA was PCR amplified and purified with Ampure XP beads.

value: EN Organoid

value: Esophogus Organoid

tag: antibody

value: IgG (#2729, Cell Signaling)


title: EN Organoid, H3K4me3, Cut&Tag, R2

value: H3K4me3(#PA5-27029, Invitrogen)


title: EN Organoid, H3K27me3, Cut&Tag, R2

value: H3K27m3 (#9733, Cell Signaling)


title: EN Organoid, H2AK119Ub, Cut&Tag, R2

value: H2AK119Ub (#8240, Cell Signaling)


title: RPMA in vitro replicate 1 (bulk RNAseq)

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
mRNAseq sequencing
MA4-plus-Cre2D

data_processing:
For snRNA-seq data, Cell Ranger (v7.0.0) was used to demultiplex and align reads to the reference genome (mm10). Further analysis, including clustering, dimensionality reduction and differential gene expression analysis, was performed using the Seurat (V4.2.0) in R. Cells with less than 200 genes and genes expressed in less than 3 cells were removed. Cells with percentage of mitochondrial gene expression greater than 20%  were removed. Samples were integrated for clustering and cell type identification. Cell clusters were identified for the integrated data using the top 30 dimensions from the principal component analysis (PCA). Cell types were annotated manually using cell type specific marker genes. Cluster marker genes were identified using “FindAllMarkers” function in Seurat. Differential gene expression analysis between ASCL1 Mut and ASCL1 WT was done using "FindMarkers" function in Seurat with the pseudobulk method. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
For bulk RNA-seq data, adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the mouse genome (mm10) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package. Low-expressed genes (genes with the expression value of 0 in more than 30% of samples) were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were then identified using the same package. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
Assembly: mm10
Supplementary files format and content: tab delimited text files

source_name: Prostate

growth_protocol: Organoids were grown in culture in full organoid medium for 2 weeks in 3D, grown in 2D for a week and  infected with lentiviral Cre to induce Cre-recombination, and selected 48hrs after infection with puromycin/Nutlin for 2 weeks. Cells were grown in 3D for another week and grown in 2D for a week before harvesting cells for bulk RNA-sequencing and injecting subcutaneously into mice to generate tumor allografts for snRNAseq.

extract_protocol:
For bulk RNA sequencing, cells were harvested by centrifugation and resuspended in Trizol. RNA was isolated with Arcturus Picopure RNA isolation kit or Direct-zol RNA Microprep. For snRNAseq, tumors were harvested and either snapfrozen or embedded in OCT for cryosectioning. For snap-frozen tumors, nuclei were isolated with manual homogenization with Dounce homogenizer. For cryo-sectioned tumors, nuclei of cryosectioned scrolls were isolated with the Singulator.
For RNA-seq, library was constructed with NextSeq 500/550 High Output kit v2.5 (75 cycles) (Illumina #20024906)
For snRNA-seq, library was constructed according to manufacturer's instructions (10x Genomics 3' Gene Expression) with a barcode plate Dual Index Kit TT Set A

value: Prostate

value: RPMA

value: organoid

value: Lentiviral Cre infection


title: RPM in vitro replicate 5 (bulk RNAseq)

description:
mRNAseq sequencing
RPMATdRGFP19-plus-Cre

value: RPM


title: RPM in vitro replicate 3 (bulk RNAseq)

description:
mRNAseq sequencing
RPMTd1-plus-Cre


title: RPM in vitro replicate 4 (bulk RNAseq)

description:
mRNAseq sequencing
RPMTd2-plus-Cre


title: RPMA in vitro replicate 2 (bulk RNAseq)

description:
mRNAseq sequencing
RPMA5-plus-Cre


title: 1-1-A1_S1: CBDL6w_Rep1

data_processing:
Extract UMIs, UMI-tools 1.0.1, command: umi_tools extract -I <in.fastq.gz> -S <out.fastq.gz>  --extract-method=regex  --bc-pattern='(?P<umi_1>.{{6}})(?P<discard_1>.{{4}}).*'
Trimming reads, trimmomatic v 0.39, command: trimmomatic SE -threads 20 <in.fastq.gz> <out_trimmed.fastq.gz> ILLUMINACLIP:~/trimmomatic-0.39-1/adapters/TruSeq3-SE.fa:2:30:10 \ SLIDINGWINDOW:4:15 CROP:64 MINLEN:50
Mapping reads, STAR 2.7.5b, command: STAR --runThreadN 10 --genomeDir <index_star> --readFilesIn <in.fastq.gz> --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix <sample_> --quantMode TranscriptomeSAM
Process UMIs, UMI-tools 1.0.1, command: umi_tools dedup -I <in.bam> --output-stats=deduplicated -S <out.bam>
Quantify expression with RSEM, RSEM 1.3.1, rsem-calculate-expression -p 60 --strand-specific --no-bam-output --bam <in.bam> <rsem_index> <sample_name>
Genome_build: GRCm38.p6, release 100
Supplementary_files_format_and_content: normalized counts (DESeq2)

value: advanced cholestatic liver injury

value: Kupffer cell


title: Liver tissue from female 1 Eu-MYC mice housed in repeated exposure of 12 hourse of light followed by 12 hours of dark

value: liver


title: EN Organoid, H3K4me3, Cut&Tag, R1


title: EN Organoid, IgG, Cut&Tag, R1


title: EN Organoid, H2AK119Ub, Cut&Tag, R1


title: ESCC Organoid, IgG, Cut&Tag

source_name: ESCC Organoid

value: ESCC Organoid

value: Esophogus SCC Organoid


title: ESCC Organoid, H3K4me3, Cut&Tag, R3


title: ESCC Organoid, H2AK119Ub, Cut&Tag, R3


title: EN Organoid, H3K27me3, Cut&Tag, R1


title: ESCC Organoid, H2AK119Ub, Cut&Tag, R2


title: ESCC Organoid, H3K27me3, Cut&Tag, R3


title: ESCC Organoid, H3K4me3, Cut&Tag, R1


title: ESCC Organoid, H3K4me3, Cut&Tag, R2


title: ESCC Organoid, H3K27me3, Cut&Tag, R2


title: RPM in vitro replicate 2 (bulk RNAseq)

description:
mRNAseq sequencing
RPM5-plus-Cre


title: QKO, DNMT3A WT, Input ChIP R1

data_processing:
ChIP-seq reads were aligned to mouse genome (GRCm38) using bowtie2
Coverage tracks (bigwig) were generated by the bamCoverage function of deepTools, normalizing to 1x depth (reads per genome coverage, RPGC) with bin size as 50bp and read extension as 200bp
Assembly: GRCm38
Supplementary files format and content: bigwig

source_name: mESC QKO

growth_protocol: mESC were cultured in Serum/LIF media: DMEM-KO, 15% FBS, 1000U/ml murine recombinant LIF, 1× nonessential amino acids, 1× GlutaMax and 0.1 mM 2-mercaptoethanol

extract_protocol:
2 × 107 cells were cross-linked directly on a plate after media removal and one wash with PBS, using 1% paraformaldehyde for 10 min at room temperature. Lysed chromatin extracts were sonicated for 20 min using a Covaris M220 focused ultrasonicator. After antibody incubation overnight at 4C the antibody bound chromatin was washed and purified using PCR purificaiton spin column (Qiagen)
ChIP–seq, library preparation was carried out using NEBNext Ultra II Library Prep Kit reagents

value: mESC QKO

value: Mouse Embryonic Stem cell

value: DNMT1, DNMT3A/B/L KO + DNMT3A-WT


title: QKO, DNMT3A UBmutant, DNMT3A ChIP R1

value: DNMT1, DNMT3A/B/L KO + DNMT3A-Ubmutant

value: DNMT3A (#3598, Cell Signaling)


title: QKO, DNMT3A R181E, DNMT3A ChIP R1

value: DNMT1, DNMT3A/B/L KO + DNMT3A-R181E


title: QKO, DNMT3A UBmutant, DNMT3A ChIP R2


title: ESCC Organoid, H2AK119Ub, Cut&Tag, R1

value: H2AK119Ub (#8240, Cell Signaling)


title: QKO, DNMT3A WT, Input ChIP R2


title: QKO, DNMT3A W330R, DNMT3A ChIP R1

value: DNMT1, DNMT3A/B/L KO + DNMT3A-W330R


title: QKO, DNMT3A W330R, DNMT3A ChIP R2


title: QKO, DNMT3A R181E, DNMT3A ChIP R2


title: 10T1/2 cells, DNMT3A W330R-R181E, day6, rep2

data_processing:
RNAseq reads were pseudoaligned to the mouse genome (GRCm39) using kallisto(v, quant).
Transcript-level abundances were read with tximport (v.1.28.0) to get gene-level abundances.
Raw counts per gene were used with DEseq2(v.1.40) to find significantly differently expressed genes between samples
Assembly: GRCm39
Supplementary files format and content: tab delimited file includes raw gene counts for each sample

growth_protocol: Mouse mesenchymal stem cells, C3H10T1/2 cells (ATCC), were cultured in Dulbecco’s modified Eagle’s medium (DMEM,Invitrogen) with 10% fetal bovine serum (FBS,Gemini) and antibiotics at 37C and 5% CO2

extract_protocol:
Total RNA was isolated using TriZol and precipitated with isopropanol
RNA-seq library generated using NEBNext Ultra II Library Prep Kit (NEB, #E7770)

treatment_protocol: adipocyte differentiation induced by adipocyte media: DMEM + 10% FBS containing 0.5 mM isobutylmethylxanthine, 1 μM dexamethasone, 5 μg/mL insulin and 5 μM troglitazone. After two days in adipocyte media the media was changed to DMEM + 10% FBS + 5 μg/mL Insulin and changed every 2 days.

value: mesenchymal stem cell

value: adipocyte differentiation

tag: time


title: QKO, DNMT3A WT, DNMT3A ChIP R1

tag: genotype


title: 10T1/2 cells, DNMT3AW330R-R181E, day2, rep1

tag: cell line


title: 10T1/2 cells, DNMT3A W330R-R181E, day4, rep2

tag: cell type


title: 10T1/2 cells, DNMT3A W330R, day6, rep2


title: 10T1/2 cells, DNMT3A W330R-R181E, day2, rep2


title: 10T1/2 cells, DNMT3A W330R-R181E, day4, rep1


title: 10T1/2 cells, DNMT3A W330R, day4, rep1


title: 10T1/2 cells, DNMT3A W330R, day2, rep2


title: QKO, DNMT3A WT, DNMT3A ChIP R2


title: 10T1/2 cells, DNMT3A W330R, day6, rep1


title: 10T1/2 cells, DNMT3A WT, day6, rep1


title: 10T1/2 cells, DNMT3A W330R, day2, rep1


title: 10T1/2 cells, DNMT3A W330R, day4, rep2


title: ESCC Organoid, H3K27me3, Cut&Tag,R1

value: H3K27m3 (#9733, Cell Signaling)


title: 10T1/2 cells, DNMT3A WT, day4, rep2


title: 10T1/2 cells, DNMT3A WT, day4, rep1


title: 10T1/2 cells, DNMT3A WT, day2, rep1


title: 10T1/2 cells, DNMT3A WT, day2, rep2


title: 10T1/2 cells, DNMT3A W330R-R181E, day6, rep1


title: 10T1/2 cells, DNMT3A W330R, undiff, rep2


title: 10T1/2 cells, DNMT3A WT, undiff, rep1


title: 10T1/2 cells, DNMT3A W330R, undiff, rep1


title: 10T1/2 cells, DNMT3A WT, undiff, rep2


title: pair35case-P-FU [PC_360]

city: Memphis

first: Hyo Young

last: Choi

state: TN

address: 66 N. Pauline Street

department: Preventive Medicine

institute: University of Tennessee Health Science Center

data_processing:
RNA reads were aligned to the hg19 genome assembly using TopHat followed by quantification of gene-level raw reads counts using the HTseq. In the present study, we only considered protein-coding genes from the ENSEMBL database available on the biomaRt R package, which reduced the gene set to 19217 genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was extracted from frozen TZ biopsies at baseline and follow-up. Prior to extraction, excess OCT from each biopsy sample was physically removed on an aluminum block surrounded by dry ice to ensure the tissue does not thaw. Frozen tissue was sectioned to 20 µM slices QIAzol ensuring that the sample is submerged in the liquid and stored at -80C. RNA extraction used the miRNAeasy kit from QIAgen (Item # 69989) following manufacturer instructions
RNA samples were sequenced at Novagene in a blinded manner by Illumina HiSeq 2500

value: Prostate

tag: race

value: CAU

tag: side

value: LTZ

tag: baseline age

tag: baseline auass

tag: baseline tzvol

value: Placebo


title: pair46cont-C-FU [PC_365]

value: Hispanic

value: RTZ

value: Combination


title: pair34cont-F-FU [PC_367]

value: Finasteride


title: pair34cont-F-BL [PC_373]


title: pair38cont-F-FU [PC_362]


title: pair33case-F-FU [PC_359]


title: pair46case-P-FU [PC_364]


title: pair46cont-C-BL [PC_356]


title: 10T1/2 cells, DNMT3A WT, day6, rep2


title: pair39cont-C-FU [PC_372]


title: pair38case-D-FU [PC_354]

value: Doxazosin


title: pair40cont-C-BL [PC_371]


title: pair34case-F-BL [PC_361]


title: pair36cont-D-FU [PC_369]


title: pair38cont-F-BL [PC_352]


title: pair35cont-P-BL [PC_350]


title: pair36cont-D-BL [PC_351]


title: pair40cont-C-FU [PC_348]


title: pair39cont-C-BL [PC_347]


title: pair34case-F-FU [PC_346]


title: pair35cont-P-FU [PC_343]


title: pair46case-P-BL [PC_357]


title: pair35case-P-BL [PC_344]


title: pair69cont-C-FU [PC_340]


title: pair56case-D-FU [PC_339]


title: pair64case-P-BL [PC_337]


title: pair45case-F-FU [PC_334]

value: AA


title: pair38case-D-BL [PC_358]


title: pair69cont-C-BL [PC_333]


title: pair37case-P-FU [PC_313]


title: pair32cont-C-BL [PC_307]


title: pair45case-F-BL [PC_321]


title: pair32cont-C-FU [PC_302]


title: pair25case-D-BL [PC_308]


title: pair64case-P-FU [PC_316]


title: pair24case-F-BL [PC_301]


title: pair37cont1-P-BL [PC_315]


title: pair31case-P-BL [PC_309]


title: pair23case-F-BL [PC_298]


title: pair28cont-P-FU [PC_300]


title: pair32case-D-BL [PC_306]


title: pair22cont-C-FU [PC_304]


title: pair25case-D-FU [PC_299]


title: pair37case-P-BL [PC_328]


title: pair28case-P-FU [PC_297]


title: pair28case-P-BL [PC_292]


title: pair32case-D-FU [PC_303]


title: pair28cont-P-BL [PC_296]


title: pair22case-D-FU [PC_295]


title: pair33case-F-BL [PC_342]


title: pair24case-F-FU [PC_294]


title: pair23cont-P-BL [PC_291]


title: pair23cont-P-FU [PC_283]


title: pair22case-D-BL [PC_285]


title: pair26case-D-FU [PC_282]


title: pair37cont1-P-FU [PC_327]


title: pair24cont-C-FU [PC_287]


title: pair25cont-F-BL [PC_281]


title: pair24cont-C-BL [PC_279]


title: pair26case-D-BL [PC_277]


title: pair71case-P-BL [PC_264]


title: pair70case-D-FU [PC_262]


title: pair70case-D-BL [PC_272]


title: pair67case-C-FU [PC_258]


title: pair56case-D-BL [PC_329]


title: pair59case-D-BL [PC_273]


title: pair63case-P-BL [PC_260]


title: pair61cont-C-FU [PC_254]


title: pair70cont-P-FU [PC_269]


title: pair44case-C-BL [PC_244]


title: pair67cont-C-FU [PC_248]


title: pair60cont-F-BL [PC_245]


title: pair13case-P-BL [PC_239]


title: pair71case-P-FU [PC_276]


title: pair13case-P-FU [PC_232]


title: pair13cont-F-BL [PC_233]

value: L/R


title: pair21case-F-BL [PC_241]


title: pair71cont-D-FU [PC_266]


title: pair44cont-P-FU [PC_242]


title: pair27cont-D-BL [PC_288]


title: pair09case-P-BL [PC_231]


title: pair09cont-P-FU [PC_230]


title: pair29case-F-BL [PC_228]

value: Asian


title: pair03cont2-P-FU [PC_226]


title: pair09cont-P-BL [PC_229]


title: pair29case-F-FU [PC_227]


title: pair29cont-F-FU [PC_220]


title: pair21case-F-FU [PC_225]


title: pair08case-P-FU [PC_217]


title: pair08case-P-BL [PC_223]


title: pair03cont1-F-BL [PC_215]


title: pair81cont-F-FU [PC_211]


title: pair08cont-P-BL [PC_222]


title: pair03case-P-BL [PC_214]


title: pair80cont-F-BL [PC_204]


title: pair03case-P-FU [PC_216]


title: pair74case-P-FU [PC_206]


title: pair81cont-F-BL [PC_205]


title: pair74cont-P-FU [PC_208]


title: pair76case-D-BL [PC_200]


title: pair73cont-C-FU [PC_190]


title: pair77case-F-FU [PC_194]


title: pair77cont-F-BL [PC_188]


title: pair77case-F-BL [PC_187]


title: pair74cont-P-BL [PC_199]


title: pair77cont-F-FU [PC_186]


title: pair76case-D-FU [PC_198]


title: pair79cont-D-BL [PC_195]


title: pair75case-D-BL [PC_192]


title: pair79cont-D-FU [PC_189]


title: pair73case-D-FU [PC_185]


title: pair73cont-C-BL [PC_184]


title: pair08cont-P-FU [PC_224]


title: pair75case-D-FU [PC_183]


title: pair91cont-P-FU [PC_180]


title: pair50cont-P-FU [PC_171]


title: pair86case-F-FU [PC_168]


title: pair91cont-P-BL [PC_178]


title: pair85cont-D-FU [PC_175]


title: pair86case-F-BL [PC_165]


title: pair91case-P-BL [PC_169]


title: pair65cont1-P-FU [PC_155]


title: pair47cont1-D-BL [PC_149]


title: pair82case-F-FU [PC_151]


title: pair82cont-C-FU [PC_150]


title: pair74case-P-BL [PC_201]


title: pair47cont2-F-FU [PC_147]


title: pair85cont-D-BL [PC_167]


title: pair80cont-F-FU [PC_203]


title: pair47cont2-F-BL [PC_144]


title: pair43case-D-FU [PC_142]


title: pair47cont1-D-FU [PC_146]


title: pair43cont1-P-BL [PC_143]


title: pair49case-C-FU [PC_141]


title: pair49cont-C-BL [PC_140]


title: pair65cont1-P-BL [PC_181]


title: pair88cont2-P-FU [PC_162]


title: pair82cont-C-BL [PC_160]


title: pair73case-D-BL [PC_182]


title: pair88cont1-F-BL [PC_154]


title: pair43cont3-D-BL [PC_134]


title: pair49case-C-BL [PC_139]


title: pair49cont-C-FU [PC_138]


title: pair43cont2-P-BL [PC_135]


title: pair48cont1-F-FU [PC_130]