title: VP64-Veh-4

data_processing:
Data was processed using nf-core/rnaseq (v3.10) of the nf-core collection of workflows. The pipeline was executed with Nextflow v22.10.4 with the following command:  nextflow run nf-core/rnaseq -r 3.10 --input samplesheet.csv --genome GRCh37 -profile singularity
Briefly, raw FASTQ files were aligned to the GRCh37 genome and quantified by salmon (v 1.9.0). Differential gene expression was obtained in R with DESeq2(1.28.0) package.
Assembly: GRCh37
Supplementary files format and content: tab-delimited TSV file contains gene TPM values for each sample

source_name: ectopic Activating MACC construct (VP64) expressed LNCaP cell line

growth_protocol: Parental LNCaP cells (ATCC Item # CRL-1740) were cultured on poly-L-lysine (Sigma-Aldrich; cat. P1274) coated plates in RPMI-1640 containing 10% Fetal Bovine Serum (FBS) and incubated at 37°C and 5% CO2. LNCaP MACC cells were selected and maintained in 3 μg/mL Blasticidin-containing medium.

extract_protocol:
Parental LNCaP cells and LNCaP MACC cells were stimulated with either vehicle (EtOH) or Tamoxifen (Sigma-Aldrich; cat. T176) and harvested for RNA-seq in biological replicates. Total RNA was extracted, and DNaseI treated by RNeasy Mini Kit (Qiagen; cat. 74104). Nanodrop quantified RNA was checked by Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies). Samples with RNA integrity number > 10 were used for library preparation (Illumina Stranded mRNA Prep kit) and sequenced on Illumina NovaSeq 6000 at the WCM Genomics Core.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit following manufacturer's protocols.

treatment_protocol: Parental LNCaP cells and LNCaP MACC cells were stimulated with 2.5uM Tamoxifen or vehicle 48 hours in biological replicates.

value: Ectopic expression of Activating MACC construct (VP64)

value: Vehicle


title: K9m2_Low-carbon_replicat1

status: Public on Sep 03 2024

type: SRA

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

country: China

institute: Hainan normal university

library_source: genomic

data_processing:
In brief, reads were trimmed using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), then aligned against the N. oceanica reference genome using BWA (Li, Durbin, 2009). The mapped reads were with duplication marked using Picard and analyzed by DeepTools (Ramirez, Dundar, Diehl, Gruning, Manke, 2014) and MACS2 (Liu, 2014; Zhang, Liu, Meyer, Eeckhoute, Johnson, Bernstein, Nusbaum, Myers, Brown, Li, Liu, 2008). The “--broad” flag was on for peak calling, with reads from the input samples used as controls. Besides, differential analysis was performed using diffReps (Shen, Shao, Liu, Maze, Feng, Nestler, 2013), the resulting differential peaks were annotated using ChIPpeakAnno package (Zhu, Gazin, Lawson, Pages, Lin, Lapointe, Green, 2010).
Genome_build: Nannochloropsis oceanica IMET1 genome
Supplementary_files_format_and_content: bedgraph were generated.
Supplementary_files_format_and_content: differential peak text files

molecule: genomic DNA

organism: Nannochloropsis oceanica

source_name: cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
N. oceanica cells (1-2 million cells · mL−1) from 400 mL culture were fixed under vacuum for 30 min with 1% formaldehyde (Sigma)at room temperature. After fixation, cells were incubated at room temperature for ten min under vacuum with 0.15 M glycine. Nuclei were isolated as described (Wei, Xu, 2018).
All subsequent end repairing, A-tailing, adaptor ligation, and library amplification steps were done following a standard protocol (Illumina). The final library was sequenced on an Illumina HiSeq 2500 instrument with 1×150-bp reads.

treatment_protocol: In total, six identical column reactors were employed. Each reactor contains 800 ml of fresh modified f/2 liquid medium, which was supplemented with 10 mM Tris-HCl buffer (pH=8.2) in order to accurately control the pH during the culture. Equal numbers of the seed cells were re-inoculated into each of the six column reactors to an OD750 of 1.5. The light intensity was maintained at 80±5 μmol m-2 s-1. The six algal cultures were first aerated with air enriched with 5% CO2 (“High CO2” conditions, or HC) for one hour. After the pre-adaption phase, three of the algal cultures proceeded under HC as the control condition, whereas the other three were switched to aeration with 0.04% CO2 (“Low CO2” conditions, or LC).After being transferred to the designated conditions, cell aliquots were taken at 24 h from each column by syringe for histone modification  profiling.

tag: strain

tag: chip antibody

tag: treatment

value: low carbon


title: XDP NPCs, B19, rep1

city: Padova

first: Giulia

last: Nicoletto

address: Via Gabelli 63

department: Molecular Medicine

country: Italy

institute: UNIPD

library_source: transcriptomic

data_processing:
Sequence reads were quality checked with FASTQC (v0.11.9) and align to hg38 or XDP custom genome with STAR (v2.7.10).
Alignments were sorted and indexed with samtools. Bigwig were generated with deeptools (v3.5.4) ( parameters - bamCoverage --normalizeUsing RPKM -bs 10)
RNA-seq raw count were generated with HT-seq (v0.11.2) (parameters --nonunique all -s no -a 10 -t exon -f bam -r name)
DE analyses was performed with DESeq2 R package.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Neuronal progenitor cells

growth_protocol: Cells were grown in standard conditions in NPM medium and geltrex coated wells.

extract_protocol:
RNA was harvested using Total RNA Purification Plus Micro Kit (Norgen Biotek, #NR48500).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep (Illumina) following manufacturer's protocols.

treatment_protocol: Cells were seeded at 70% confluence. The next day, cells were treated with B19 or Q. After 24 hours, RNA was harvested.

tag: cell type

value: Neuronal progenitor cells

tag: genotype

value: XDP

value: G4 ligand treatment B19


title: VP64-Veh-3

city: New York

first: Xuanrong

last: Chen

state: New York

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

tag: cell line

value: ectopic Activating MACC construct (VP64) expressed LNCaP cell line

value: human prostate cancer cell line


title: Control, replicate 3 [CTR3]

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Element Biosciences AVITI was used as the sequencing instrument

data_processing:
Raw read QC was done using FastQC (v0.11.9)
Adapter and quality trimming was done using cutadapt (v3.7)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.10a)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.4)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.3)
Assembly: Bos taurus ARS-UCD1.2 (Ensembl release 109)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

organism: Bos taurus

source_name: blastocyst

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy Micro kit (Qiagen) following the manufacturer protocol.
Modified Smart-seq3xpress for 5’-end mRNA sequencing

value: blastocyst

value: Untreated


title: K9m2_High-carbon_replicat2

value: High carbon


title: VP64-Veh-2


title: K9m2_High-carbon_replicat1


title: XDP NPCs, NT, rep1

value: NT


title: XDP NPCs, NT, rep3


title: XDP NPCs, Q, rep3

value: G4 ligand treatment Q


title: Mimic, replicate 4 [M4]

value: microRNA-34c mimic supplementation


title: Control, replicate 2 [CTR2]


title: XDP NPCs, NT, rep2


title: VP64-TAM-3

value: 2.5uM Tamoxifen


title: Control, replicate 1 [CTR1]


title: VP64-Veh-1


title: VP64-TAM-4


title: NMC hFib, NT, rep3

source_name: foreskin fibroblasts

value: foreskin fibroblasts


title: Ctrl hFib, Q, rep2

value: ctrl


title: VP64-TAM-1

value: Ectopic expression of Activating MACC construct (VP64)


title: Ctrl NPCs, B19, rep3


title: KRAB-Veh-4

source_name: ectopic Repressive MACC construct (KRAB) expressed LNCaP cell line

value: Ectopic expression of Repressive MACC construct (KRAB)

value: Vehicle


title: Ctrl NPCs, NT, rep3

value: Neuronal progenitor cells


title: VP64-TAM-2


title: Young, 6 week old kilifish, scRNAseq_2

city: Leuven

first: RAJAGOPAL

last: AYANA

state: Flemish brabant

address: Naamsestraat 59

department: Department of Biology

institute: KU Leuven

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Genome_build: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de/).
Supplementary files format and content: Tab-separated values files and matrix files

organism: Nothobranchius furzeri

source_name: brain

growth_protocol: All experiments were performed on adult 6 week-old African turquoise killifish (N. furzeri), from the inbred strain GRZ-AD. One male was housed with three females in a multilinking Tecniplast ZebTec aquarium system under standardized conditions; temperature 28°C, pH 7, conductivity 600 μs, 12h/12h light/dark cycle, and fed twice a day with Artemia salina (Ocean Nutrition) and mosquito larvae (Chironomidae).

extract_protocol:
Three fish for each sample were euthanized in 0.1% buffered tricain (MS-222, Sigma Aldrich). Blood was removed by intra-cardiac perfusion with cold, sterilized PBS 10,56. Next, telencephali were extracted and immediately placed in cold DMEM/F12 (Life Tech, Invitrogen). Telencephali were transferred into sterilized, freshly prepared papain solution (250 µL papain (Sigma Aldrich), 100 µL 1% DNase I (DN25, Sigma Aldrich®), 200 µL L-Cysteine (12 mg/ mL, Sigma Aldrich), in 5 mL DMEM/F12 (Life Tech, Invitrogen)) and digested for 10 min at 37°C. Hereafter telencephali were dissociated by gently triturating with a cut pipet tip and placed back for 10 min at 37 °C. This procedure was repeated until the brain tissue was completely dissociated into single cells. The suspension was then put through a polypropylene strainer (35 µm, Falcon) and 2 mL of ice-cold, sterilized, freshly prepared washing solution (650 µL D-(+)-glucose 45% (G8769, Sigma Aldrich®), 500 µL HEPES (1M, Thermo Fisher), 5 mL FBS (Life Tech, Invitrogen) in 1X DPBS (Life Tech, Invitrogen) was added. Cells were centrifuged for 10 min at 500 g on 4 °C and the supernatant was discarded. Next, debris was removed via the debris removal solution protocol (130-109-398, Miltenyi Biotec) to ensure a high viability of the suspension. Finally, cells were resuspended in cold sterilized 0.04% BSA in PBS.
The single-cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system. Library preparation was done using 10X Genomics droplet-based sequencing with the 10X Chromium Single Cell 3' (v3 Chemistry) reagents kit. The cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead, which was encapsulated with the cell. Following the guidelines of the 10x Genomics user manual, the droplets were directly subjected to reverse transcription, the emulsion was broken, and cDNA was purified using Silane beads. After the amplification of cDNA with 10 cycles, purification and quantification was performed. The 10X Genomics single-cell RNA-sequencing library preparation involving fragmentation, dA-tailing, adapter ligation, and 12-cycle indexing PCR was performed. After quantification, the libraries were sequenced on an Illumina NovaSeq machine using a HighOutput flowcell in paired-end mode (R1: 26 bp; I7: 8 bp; R2: 50 bp), thus generating 100 million fragments.

tag: tissue

value: brain

value: brain cells

value: GRZ-AD-Leuven

tag: age

value: young adult (6 week old)

tag: Sex

value: female


title: Ctrl hFib, Q, rep1


title: KRAB-Veh-2

value: ectopic Repressive MACC construct (KRAB) expressed LNCaP cell line

value: human prostate cancer cell line


title: Young, 6 week old kilifish, scRNAseq

description: 10X Genomics

extract_protocol:
Three fish were euthanized in 0.1% buffered tricain (MS-222, Sigma Aldrich). Blood was removed by intra-cardiac perfusion with cold, sterilized PBS 10,56. Next, telencephali were extracted and immediately placed in cold DMEM/F12 (Life Tech, Invitrogen). Telencephali were transferred into sterilized, freshly prepared papain solution (250 µL papain (Sigma Aldrich), 100 µL 1% DNase I (DN25, Sigma Aldrich®), 200 µL L-Cysteine (12 mg/ mL, Sigma Aldrich), in 5 mL DMEM/F12 (Life Tech, Invitrogen)) and digested for 10 min at 37°C. Hereafter telencephali were dissociated by gently triturating with a cut pipet tip and placed back for 10 min at 37 °C. This procedure was repeated until the brain tissue was completely dissociated into single cells. The suspension was then put through a polypropylene strainer (35 µm, Falcon) and 2 mL of ice-cold, sterilized, freshly prepared washing solution (650 µL D-(+)-glucose 45% (G8769, Sigma Aldrich®), 500 µL HEPES (1M, Thermo Fisher), 5 mL FBS (Life Tech, Invitrogen) in 1X DPBS (Life Tech, Invitrogen) was added. Cells were centrifuged for 10 min at 500 g on 4 °C and the supernatant was discarded. Next, debris was removed via the debris removal solution protocol (130-109-398, Miltenyi Biotec) to ensure a high viability of the suspension. Finally, cells were resuspended in cold sterilized 0.04% BSA in PBS.
The single-cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system. Library preparation was done using 10X Genomics droplet-based sequencing with the 10X Chromium Single Cell 3' (v3 Chemistry) reagents kit. The cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead, which was encapsulated with the cell. Following the guidelines of the 10x Genomics user manual, the droplets were directly subjected to reverse transcription, the emulsion was broken, and cDNA was purified using Silane beads. After the amplification of cDNA with 10 cycles, purification and quantification was performed. The 10X Genomics single-cell RNA-sequencing library preparation involving fragmentation, dA-tailing, adapter ligation, and 12-cycle indexing PCR was performed. After quantification, the libraries were sequenced on an Illumina NovaSeq machine using a HighOutput flowcell in paired-end mode (R1: 26 bp; I7: 8 bp; R2: 50 bp), thus generating 100 million fragments.


title: KRAB-Veh-3


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep2 (miRNA-seq)

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
Clean reads of mature small RNAs comprised between 20 to 24 nucleotides were extracted
20-24nt clean reads mapped on the reference mature miRNA database available in miRBase (release 22, Kozomara et al 2019) using bowtie (Langmead et al. 2009)
Mapped reads were quantified using samtools (Li et al. 2009)
Assembly: reference mature miRNA database available in miRBase (release 22) available at https://www.mirbase.org/ftp.shtml
Supplementary files format and content: Pocessed data files are count files

organism: Phaseolus vulgaris

source_name: Seed developmental stages

growth_protocol: Experiments were performed with a variety of common bean (Phaseolus vulgaris L. cv. Flavert) susceptible to common bacterial blight. Seeds were sown in pots containing one liter of soil substrate (Tray substrat, NF U 44–551, Klasmann- Deilmann GmbL, Rippert France). Plants were grown in a controlled growth chamber with 16 h of light at 23 °C and 8 h of darkness at 20 °C and a relative humidity (RH) of 70%. Plants were watered twice a week during the first three weeks and then with a nutrient solution (N/P/K=15/10/30).

extract_protocol:
we extracted small RNA using the NucleoSpin® miRNA Kit (Macherey‐Nagel, Düren, Germany), according to the manufacturer’s instructions. Small RNA enrichment was validated using the Bioanalyzer small RNA analysis using a Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified using the  NanoDrop ND‐1000 (NanoDrop Technologies, Wilmington, DE, USA).
Small RNA were, then, sent to the BGI for small RNA sequencing including library construction and single‐end sequencing using DNBseq sequencing technology (SE50 40M).

treatment_protocol: Plants were spray-inoculated with water or bacterial suspension(106 CFU/ml) at the flower bud stage (R5 stage, Michael 1994). The day prior to inoculation, temperature (day 25°C/night 23°C) and relative humidity (RH, 95%) were increased. Inoculation was performed in a two-step protocol. First, small green flower buds were sprayed. Three days later, flower buds at the pollination stage were tagged. Then, a second inoculation was performed at one DAP (day after pollination) when tagged organs became open flowers. RH was reduced to 70% the day after to limit symptom development and seed abortion. Three independent replicates of 15 plants per treatment were inoculated. Tagged pods of five plants per repeat were harvested at 24 and 42 DAP. Seeds were collected aseptically from pods to avoid contamination by contact with external bacterial populations on pods (Darsonval et al., 2008).

tag: cultivar

value: Flavert

value: Seed developmental stages

value: Xcf CFBP7767R

tag: developmental stage

value: Phaseolus vulgaris Flavert

value: Inoculated with Xcf 10power6 CFU ml-1 by spray-inoculation


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep3 (miRNA-seq)


title: Ctrl hFib, NT, rep2

value: foreskin fibroblasts

value: ctrl

value: NT


title: Ctrl hFib, B19, rep1

value: G4 ligand treatment B19


title: KRAB-Veh-1

value: Ectopic expression of Repressive MACC construct (KRAB)

value: Vehicle


title: Ctrl hFib, B19, rep2


title: Ctrl hFib, NT, rep1


title: Ruxolitinib-treated ELC52 cells

type: RNA

city: Kasugai

first: Yukiya

last: Yamamoto

state: Aichi

address: 1200 Matsumoto-cho,  Biomedical Sciences, 11F, Building#51

country: Japan

institute: Chubu University

description: Gene expression data from Ruxolitinib-treated ELC54 cells.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA

label: biotin

source_name: Ruxolitinib treated

label_protocol: Affymetrix protocol

extract_protocol: Resuspend cells in serum-free medium. (2.8 x 10e6 cells). Add desired reagents. Incubate cells for 2 hours @ 37 degrees Celsius. C.f.g cells for 2 min @ 400 x g. Extract total RNA with a kit. Analyze RNA concentration. Send to facility.

tag: reagent

value: Ruxolitinib


title: 24 DAP seed inoculated by Xcf (Xanthomonas) rep3 (miRNA-seq)


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep1 (miRNA-seq)


title: IFNa-treated ELC52 cells

description: Gene expression data from IFNa-treated ELC55 cells.

source_name: IFNa treated

value: Interferon alpha2b


title: DMSO-treated ELC52 cells

description: Gene expression data from DMSO-treated ELC52 cells.

source_name: DMSO treated

value: DMSO


title: frontal_cortex_pd_16

city: Barcelona

first: Eulalia

last: Marti

address: Passeig de la Vall d’Hebron, 171

department: Institute of Neurosciences

country: Spain

institute: University of Barcelona

description: Parkinson Disease, Braak Stage 4

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to the array (Agilent AMADID 047718) in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at room temperature in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: data were read and pre-processed with the R/Bioconductor package “limma”. The “normexp” background correction was applied, with an offset of 50, followed by the “quantile” normalization.

source_name: Frontal Cortex, post-mortem sample, Parkinson Disease

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit version 6.5 – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All samples were obtained from the Institute of Neuropathology Brain Bank (IDIBELL), in accordance with the standards of the local ethics committee.

extract_protocol: RNA isolation was performed with the miRNeasy kit (QIAGEN) following manufacturer’s instructions. RNA was reverse transcribed using Transcriptor First Strand cDNA Synthesis Kit (Roche).

treatment_protocol: Brain samples were frozen at -80ºC.

value: Frontal Cortex

tag: diagnosis

value: Parkinson Disease

tag: braak stage


title: 24 DAP seed inoculated by Xcf (Xanthomonas) rep2 (miRNA-seq)


title: frontal_cortex_pd_13

description: Parkinson Disease, Braak Stage 4


title: 24 DAP seed inoculated by Xcf (Xanthomonas) rep1 (miRNA-seq)


title: frontal_cortex_pd_17

description: Parkinson Disease, Braak Stage 4


title: KRAB-TAM-2

value: ectopic Repressive MACC construct (KRAB) expressed LNCaP cell line

value: human prostate cancer cell line

value: 2.5uM Tamoxifen


title: XDP hFib, Q, rep2

value: XDP

value: G4 ligand treatment Q


title: frontal_cortex_pd_15

description: Parkinson Disease, Braak Stage 5


title: frontal_cortex_pd_18

description: Parkinson Disease, Braak Stage 4


title: KRAB-TAM-4


title: TPO-treated ELC52 cells

description: Gene expression data from TPO-treated ELC53 cells.

source_name: TPO treated

value: TPO


title: frontal_cortex_control_16

description: Individual without neuropathological lesions or neurological signs

source_name: Frontal Cortex, post-mortem sample, Control

value: Control


title: XDP hFib, B19, rep2

value: foreskin fibroblasts


title: KRAB-TAM-1


title: frontal_cortex_pd_12

description: Parkinson Disease, Braak Stage 4


title: frontal_cortex_control_18


title: frontal_cortex_pd_14

description: Parkinson Disease, Braak Stage 4


title: 42 DAP seed inoculated by water rep3 (miRNA-seq)

value: Flavert

value: Seed developmental stages

value: no strain

value: Phaseolus vulgaris Flavert

value: Inoculated by water


title: frontal_cortex_control_15


title: frontal_cortex_control_17


title: 3x-Veh-4

source_name: ectopic Neutral MACC construct (3X) expressed LNCaP cell line

value: Ectopic expression of the neutral MACC construct (3X)

value: Vehicle


title: 42 DAP seed inoculated by water rep2 (miRNA-seq)


title: KRAB-TAM-3

value: Ectopic expression of Repressive MACC construct (KRAB)


title: XDP hFib, NT, rep2

value: NT


title: frontal_cortex_control_14

value: Frontal Cortex


title: 3X-Veh-3

value: ectopic Neutral MACC construct (3X) expressed LNCaP cell line

value: human prostate cancer cell line


title: 42 DAP seed inoculated by water rep1 (miRNA-seq)


title: XDP hFib, NT, rep1

value: XDP


title: frontal_cortex_control_13


title: XDP hFib, Q, rep1

value: G4 ligand treatment Q


title: 24 DAP seed inoculated by water rep3 (miRNA-seq)


title: XDP hFib, B19, rep1

value: G4 ligand treatment B19


title: NMC hFib, Q, rep2


title: 3X-Veh-1


title: 24 DAP seed inoculated by water rep2 (miRNA-seq)


title: NMC hFib, Q, rep1


title: frontal_cortex_control_12

value: Control


title: 3X-TAM-4

value: 2.5uM Tamoxifen


title: frontal_cortex_control_11


title: 24 DAP seed inoculated by water rep1 (miRNA-seq)

value: Flavert


title: NMC hFib, B19, rep2

value: foreskin fibroblasts


title: 3X-TAM-3


title: frontal_cortex_pd_11

description: Parkinson Disease, Braak Stage 5

value: Parkinson Disease


title: E3KO-Male.4

city: Boston

first: Camron

middle: Davis

last: Bryant

state: MA

address: 140 The Fenway, X138

institute: Northeastern Universitty

data_processing:
Raw files were processed to get normalized read counts using GALAXY.
Reads were trimmed for quality using Trimmomatic. Reads under 30bp were removed as where reads <15 QC averaged across 4 bases.
Trimmed sequences were aligned to the mm10 reference genome using STAR alignment.
Raw counts for each gene were performed using featureCounts.
TMM normalized values for each gene were calculated using edgeR. Genes without at least 10 reads per million in at least 3 samples were excluded from normalization and differential gene expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM normalized counts for each sample

organism: Mus musculus

source_name: Whole brain hemisphere

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated for RNA-Seq using a NovaSeq Special Oligo-dT mRNA directional based protocol.

value: Whole brain hemisphere

value: Male

value: Zhx2 Exon3 knockout


title: 3X-Veh-2

value: Ectopic expression of the neutral MACC construct (3X)

value: Vehicle


title: E3KO-Female.4

value: Female


title: NMC hFib, B19, rep1


title: 3X-TAM-1


title: NMC hFib, NT, rep1

value: NT


title: 3X-TAM-2

value: ectopic Neutral MACC construct (3X) expressed LNCaP cell line


title: NMC hFib, NT, rep2


title: Ctrl NPCs, Q, rep2

value: Neuronal progenitor cells

value: ctrl


title: E3KO-Male.3


title: frontal_cortex_pd_10

description: Parkinson Disease, Braak Stage 5

value: Frontal Cortex


title: frontal_cortex_pd_8

description: Parkinson Disease, Braak Stage 5


title: frontal_cortex_pd_9

description: Parkinson Disease, Braak Stage 5


title: E3KO-Male.2


title: Ctrl-Veh-4

source_name: LNCaP cell line

value: LNCaP cell line

value: human prostate cancer cell line

value: Parental control


title: Ctrl-Veh-3


title: WT-Female.4

value: Wildtype


title: Ctrl NPCs, Q, rep1

value: G4 ligand treatment Q


title: frontal_cortex_pd_7

description: Parkinson Disease, Braak Stage 4

value: Parkinson Disease


title: Ctrl-TAM-4

value: 2.5uM Tamoxifen


title: Ctrl-Veh-2


title: E3KO-Female.2

value: Whole brain hemisphere


title: Ctrl NPCs, B19, rep2

value: G4 ligand treatment B19


title: frontal_cortex_pd_6

description: Parkinson Disease, Braak Stage 4


title: frontal_cortex_pd_4

description: Parkinson Disease, Braak Stage 4


title: WT-Female.3


title: Ctrl-Veh-1


title: WT-Female.2


title: frontal_cortex_pd_5

description: Parkinson Disease, Braak Stage 4


title: Ctrl NPCs, NT, rep1


title: frontal_cortex_pd_3

description: Parkinson Disease, Braak Stage 4


title: WT-Male.4

value: Male


title: A20 KO MLL-AF9 rep 3

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file, raw gene-count matrix

source_name: hematopoietic cell

growth_protocol: Cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS), 1X Penicillin-Streptomycin, 10ng/mL human IL-6, 10ng/mL mouse IL-3, and 10ng/mL mouse SCF at 37C with 5% CO2.

extract_protocol:
Total RNA was extracted using a Qiagen RNAeasy II kit. 15ug of RNA was used for sequencing.
TruSeq Stranded mRNA library prep, follwing manufacturer protocol (Illumina)

treatment_protocol: Cells were treated with 1uM 4-hydroxytamoxifen for 48 hours.

value: hematopoietic cell

tag: cell subset

value: lineage negative

value: A20 f/f

value: 48hr 1uM 4-hydroxy-tamoxifen


title: WT-Male.3


title: Ctrl NPCs, Q, rep3

value: Neuronal progenitor cells


title: Ctrl NPCs, B19, rep1

value: ctrl


title: DU145, EPZ015666

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

data_processing:
Sequencing data were processed by Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) according to instructions (https://sourceforge.net/p/mageck/wiki/demo/#the-second-demo-starting-from-raw-fastq-files).
Assembly: hg38
Supplementary files format and content: txt, count for sgRNA

extract_protocol:
For the pooled screening, 1.1x10^8 DU145 cells were infected with the pooled lentiviral GeCKO v2 library at a multiplicity of infection of 0.3. After 5 days of puromycin (1 μg/ml) selection, 3x10^7 of the surviving cells were collected as day 0 control (baseline) sample, and the rest cells were equally divided into two groups and maintained in medium containing either DMSO or EPZ015666 (1μM) for 21 days. Medium was refreshed every 3 days and the cell density was kept at 1x106 cells/ml and cell number at a minimum of 300-fold coverage of the library (a representation of 300 cells per sgRNA) during each passaging. Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen 69504). The general procedure regarding amplification and sequencing of sgRNA library was described previously [PMID: 25075903]. Here, we amplified the sgRNA sequences from 3 μg genomic DNA isolated from each group using the following PCR primers: ATCACGCTTGTGGAAAGGACGAAACA (F-Screening-Control), TGACCACTTGTGGAAAGGACGAAACA (F-Screening-DMSO), TTAGGCCTTGTGGAAAGGACGAAACA (F-Screening-EPZ) and GCCAATTCCCACTCCTTTCA (R-Screening). Library preparation and subsequent sequencing on a Novaseq-PE510 (Illumina) were performed by Novogene BioTechnology. Each library was sequenced at an average of 69.59 million reads to achieve >50 average coverage over the CRISPR library and data were analyzed by MAGeCK [PMID: 25476604].
We constructed GeCKO v2 library according to GeCKO instructions.
GeCKO v2 library

value: Human prostate cancer


title: Ctrl-TAM-3

value: LNCaP cell line


title: WT-Female.1

value: Female


title: frontal_cortex_control_10

value: Frontal Cortex

value: Control


title: frontal_cortex_pd_2

description: Parkinson Disease, Braak Stage 4


title: A20 WT MLL-AF9 rep 3


title: frontal_cortex_pd_1

description: Parkinson Disease, Braak Stage 4


title: Ctrl-TAM-2

value: human prostate cancer cell line

value: Parental control


title: E3KO-Female.3

value: Zhx2 Exon3 knockout


title: Ctrl-TAM-1

value: 2.5uM Tamoxifen


title: A20 KO MLL-AF9 rep 2


title: DU145, control

value: control


title: E3KO-Male.1

value: Whole brain hemisphere

value: Male


title: A20 WT MLL-AF9 rep 2

value: hematopoietic cell

value: lineage negative


title: A20 KO MLL-AF9 rep 1

value: A20 f/f

value: 48hr 1uM 4-hydroxy-tamoxifen


title: Ctrl NPCs, NT, rep2

value: Neuronal progenitor cells

value: ctrl

value: NT


title: DU145, DMSO

value: Human prostate cancer

value: DMSO


title: frontal_cortex_control_9

value: Frontal Cortex

value: Control


title: E3KO-Female.1

value: Female


title: PC3_IgG

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the Ensembl hg38 genome using Bowtie version 1.1.1 with default settings.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=1e-5.
Peaks were annotated by R package ChIPseeker.
Assembly: hg38
Supplementary files format and content: bedGraph, narrowPeak (except for Input samples)
Library strategy: CUT&Tag

growth_protocol: RPMI-1640, 8% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
100,000 cells and the HyperactiveTM In-Site ChIP Library Prep Kit (Vazyme Biotech, TD902) were used according to manufacturer’s instructions.
ChIP-seq libraries were prepared using the HyperactiveTM In-Site ChIP Library Prep Kit (Vazyme Biotech, TD902). Cells suspended in 100μL Wash Buffer were incubated with 10μL pre-washed ConA beads for 10 min at room temperature (RT). Primary antibody was added and incubated for 2h at RT. After washing with Dig-wash buffer, secondary antibody was diluted in Dig-wash buffer (1:100) and incubated with cells for 60min. After washing three times with Dig-wash buffer, cells were re-suspended in 100μL Dig-300 buffer containing 0.58μL hyperactive pG-Tn5, and were incubated at RT for 1h. After washing twice with Dig-300 buffer, 300μL Tagmentation buffer was added and incubated at 37 °C for 1h. The reaction was stopped with 10μL 0.5M EDTA, 3μL 10% SDS and 2.5μL 20 mg/mL Proteinase K for 1h at 50 °C. After DNA extraction with phenol-chloroform and ethanol precipitation, PCR was performed with TruePrep Index Kit V2 for Illumina (Vazyme Biotech, TD202) to amplify the libraries using 16 cycles. All libraries were sequenced by Illumina NovaSeq 6000.

value: 2nd Ab


title: frontal_cortex_control_8


title: A20 WT MLL-AF9 rep 1


title: frontal_cortex_control_6


title: frontal_cortex_control_5


title: WT-Male.1

value: Wildtype


title: PC3_METTL3Abcam


title: frontal_cortex_control_7


title: PC3_PRMT5AM

value: PRMT5 (Active Motif, #61001)


title: No_ImmSyst_003 [HP043]

first: Leonardo

middle: V.

last: Riella

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

hyb_protocol: See manufacturer's website (www.nanostring.com).

data_processing: We normalized raw gene expression counts and performed background correction, quality control and analyses with the nSolver Analysis Software (Version 4.0.70)

source_name: kidney tissue

extract_protocol: Total RNA extraxted from six consecutive 10 um sections from formalin-fixed paraffin-embedded kidney tissues using the RNeasy FFPE Kit (Qiagen).

value: kidney tissue

value: No ImmSyst


title: frontal_cortex_control_3


title: WT-Male.2

value: Whole brain hemisphere

value: Male


title: LNCaP_IgG

source_name: LNCaP

value: LNCaP


title: frontal_cortex_control_2


title: frontal_cortex_control_4


title: LNCaP_METTL3Abcam


title: frontal_cortex_control_1


title: LNCaP_PRMT5AM


title: PBMC Virus challenge group at T9, biological rep2

city: Shanghai

first: Yingji

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

description: Gene expression data from peripheral blood mononuclear cells Virus challenge group at day 9

hyb_protocol: The biotin-tagged cRNA was hybridized to the Affymetrix GeneChip® Porcine Genome Array, containing 23,937 oligonucleotide transcript probe sets representing 20,201 genes. The hybridization was performed for 16 hours at 45°C in an Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: After hybridization, the GeneChip arrays were washed and stained with streptavidin-phycoerythrin using an Affymetrix Fluidics Station 450. The stained arrays were then scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Hybridization data were analyzed using GeneChip Operating Software, which assigned a 'present' or 'absent' call to genes represented by each probe set. Genes scored as 'absent' were filtered out, and the remaining genes were subjected to further analysis. Significance Analysis of Microarrays (SAM) was employed to identify differentially expressed genes in CSFV-infected samples compared to negative controls. SAM uses a set of gene-specific t-tests and estimates the false discovery rate (FDR). Genes with an FDR below 5% and a fold change of ≥2 or ≤−2 were considered significant. Fold-change analysis was conducted to calculate the ratios of geometric means of expression intensities between CSFV-infected samples and controls, reporting the results as up- or down-fold changes.

organism: Sus scrofa domesticus

label_protocol: One microgram of total RNA was used for cDNA synthesis. The cDNA was then used to produce biotin-tagged complementary RNA (cRNA) using the GeneChip IVT Labeling kit (Affymetrix).

extract_protocol: Total RNA were extracted from PBMC using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions, and then digested with DNase I at 37 ◦C for 15 min to remove contaminating DNA. RNA quantities and qualities were determined by spectrophometer and electrophoresis.

value: lymphocyte


title: No_ImmSyst_002 [HP041]

scan_protocol: See manufacturer's website (www.nanostring.com).


title: ctrl_E2_G4ChIPseq_rep02

data_processing:
Reads were quality checked with FASTQC (v) and align to hg38 with bowtie2 (parameters --end-to-end --very-sensitive -X 600 -I 20)
Alignments were sorted, indexed, removed of duplicates and converted to BAMs using Samtools.
Bigwig were generated with deeptools (v3.5.4) (pamaters bamCoverage --normalizeUsing RPKM -p 32 --binSize 1)
Assembly: hg38
Supplementary files format and content: bigWig

source_name: foreskin derived fibroblasts

growth_protocol: hFib cell line was cultured in DMEM supplemented with 15% FBS, 1x Penicillin-Streptomycin, 1x NEAA. Cells were grown under standard conditions (5 % CO2, 95 % humidity, 37 °C).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and isolation of nuclei, chromatin was sonicated using an E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the ThruPLEX DNA-Seq Kit with dual indexes. Libraries were validated using the Agilent High Sensitivity DNA kit.

value: foreskin derived fibroblasts

value: BG4 (Merck, #MABE917)


title: pleD_2

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

description: processed data file: rpg_table2.csv

data_processing:
RiboSeq
clipping using cutadapt (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie -m 1
RNASeq
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie --trim3 1 -m 1
RNASeq_repetition
cutadapt --nextseq-trim=20 -g 'TTTTT;min_overlap=1' -G 'GGGGGGG;min_overlap=3' -m 36
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie2 --very-sensitive-local -I 100 -X 1200
Supplementary_files_format_and_content: raw count data

organism: Pseudomonas aeruginosa PAO1

source_name: RNA-seq of planktonic culture of Pseudomonas aeruginosa PA01  treated with 0.2% arabinose from 45 min after inoculation (OD of 0.05) to OD 1.5

growth_protocol: Bacterial cultures were grown in liquid LB supplemented with 400 µg/ml carbenicillin at 37 °C and 180 rpm. Cultures were inoculated with OD600 of 0.05.

extract_protocol: Total RNA was extracted by mixing bacterial cells 1:1 with RNAprotect Bacteria Reagent (Qiagen) and by using the RNeasy® Mini Kit (Qiagen) in combination with QIAshredderTM (Qiagen) according to the manufacturer’s instructions. Genomic DNA was removed by DNase treatment (DNA-free™ Kit DNase Treatment & Removal, ambion). Tag-seq was used for library preparation including rRNA removal by treatment with RiboZero (Illumina).

treatment_protocol: Expression of pHERD20T based plasmids was induced with 0.2 % arabinose after 45 min of growth. Cells were harvested at indicated OD.


title: ImmSyst_RAPA_003 [HP040]

label_protocol: See manufacturer's website (www.nanostring.com).

value: ImmSyst + RAPA


title: pleD_1

description: processed data file: rpg_table2.csv


title: PBMC Virus challenge group at T9, biological rep1

source_name: peripheral blood mononuclear cells Virus challenge group at day 9


title: pHERD_2

description: processed data file: rpg_table2.csv


title: XDP_B2_G4ChIPseq_rep02

value: XDP


title: PBMC Virus challenge group at T3, biological rep2

description: Gene expression data from peripheral blood mononuclear cells Virus challenge group at day 3


title: ImmSyst_004 [HP039]

value: ImmSyst


title: PBMC Virus challenge group at T6, biological rep2

description: Gene expression data from peripheral blood mononuclear cells Virus challenge group at day 6


title: pHERD_1

description: processed data file: rpg_table2.csv


title: PBMC Virus challenge group at T6, biological rep1

source_name: peripheral blood mononuclear cells Virus challenge group at day 6


title: NMC_A2_G4ChIPseq_rep02

value: NMC


title: ImmSyst_003 [HP038]


title: ctrl_E2_G4ChIPseq_rep01

value: ctrl


title: PBMC Virus challenge group at T3, biological rep1

source_name: peripheral blood mononuclear cells Virus challenge group at day 3


title: RiboSeq_PleD2

description: ribosome protected RNA

data_processing:
Library strategy: Ribo-Seq
RiboSeq
clipping using cutadapt (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
bowtie -m 1
RNASeq
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie --trim3 1 -m 1
RNASeq_repetition
cutadapt --nextseq-trim=20 -g 'TTTTT;min_overlap=1' -G 'GGGGGGG;min_overlap=3' -m 36
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie2 --very-sensitive-local -I 100 -X 1200
Genome_build: Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
Supplementary_files_format_and_content: contains RiboSeq_EV[1-2], RiboSeq_PleD[1-2], RNASeq_EV[1-2], and RNASeq_PleD[1-2] data
Supplementary_files_format_and_content: contains RNASeq repetition samples
Supplementary_files_format_and_content: raw count data

source_name: Ribo-seq of planktonic culture of Pseudomonas aeruginosa PA01  treated with 0.2% arabinose from 45 min after inoculation (OD of 0.05) to OD 0.5-0.7

extract_protocol: For the isolation of ribosome protected RNA, bacterial cells were harvested by fast filtration and flash frozen in liquid nitrogen. Cell lysates were subjected to MNase digestion and subsequently separated into their different components by rate zonal centrifugation on a sucrose gradient. The fraction containing 70S ribosomes was collected and ribosome protected RNA was isolated with the Direct-zol™ Kit (Zymo Research). RNA fragments between 26 – 34 nt were extracted from denaturing 15% polyacrylamide gels and subjected to cDNA library preparation using the NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs) following manufacturer´s instructions.

treatment_protocol: Expression of pHERD20T based plasmids was induced with 0.2 % arabinose after 45 min of growth. Cells were harvested between OD600 of 0.5 - 0.7.


title: PBMC Virus challenge group at T1, biological rep2

description: Gene expression data from peripheral blood mononuclear cells Virus challenge group at day 1


title: RiboSeq_PleD1

description: ribosome protected RNA


title: XDP_B2_G4ChIPseq_rep01


title: ImmSyst_RAPA_002 [HP036]


title: RiboSeq_EV2

description: ribosome protected RNA


title: ImmSyst_002 [HP037]


title: RiboSeq_EV1

description: ribosome protected RNA


title: Vibrio anguillarum strain 90-11-287 ΔvanO LCD rep3

status: Public on Sep 02 2024

city: Helsingør

first: Mathias

last: Middelboe

address: Strandpromenaden 5

country: Denmark

institute: University of Copenhagen

description:
raw_counts_output_90-11-287.txt
counts_gg_notrRNA_90-11-287_no_C5.txt
Spike-in_counts_90-11-287_no_C5.txt
vanO.LCD_vs_WT.LCD - 90-11-287 - TMM normalized.txt
vanO.LCD_vs_vanO.HCD - 90-11-287 - Spike-in normalized.txt
variancePartition_90-11-287_Spike-in_normalized.txt

data_processing:
Trimmed reads were mapped to a concatenated reference genome including the spike-in plasmid pEVS143 using Rsubread v.2.4.0 allowing multi-mapping reads, disallowing ambiguous reads (Liao et al., 2013). Mapped fragments (read pairs) were counted using featureCounts counting multi-mapping fragments fractionally (Liao et al., 2014).
To identify replicated genes in the bacterial genomes, all gene sequences were extracted and aligned against their native reference genome using blastn. To handle the replicated genes, ‘gene groups’ were defined as genes having a relative length of >80 % and a complete nucleotide identity for >150 consecutive bp. The fragment counts of all genes within a gene group were summed and analyzed as a gene group.
To analyze cross-strain transcript abundance differences, shared genes across the two strains were identified using a best-hit all vs all blastn analysis (E-value < 1E-6, relative length > 80 %). As some genes across the strains were of different length, the counts of the longest gene were scaled according to their relative gene length between the strains. For example, if gene X had a length of 792 bp in strain PF430-3, but a length of 720 bp in strain 90-11-287, the fragments counts in strain PF430-3 would be divided by 1.1 (the gene length in PF430-3 relative to 90-11-287).
Ribosomal RNA and tRNA genes were removed from analysis and lowly expressed genes were filtered using the filterByExpr function in R package edgeR v. 3.30.3 (Robinson et al., 2010). Distribution plots of library-size-normalized gene expression revealed that one replicate of each of strain PF430-3 ΔvanT at LCD and strain 90-11-287 ΔvanT at LCD were outliers and therefore excluded from further analysis (Supplementary fig. 1). Fragment counts were normalized using the sum of spike-in counts as the library size or using the trimmed mean of M-values (TMM) (Robinson & Oshlack, 2010). To account for heteroscedasticity, precision weights were estimated using the function voomWithDreamWeights (Hoffman & Roussos, 2020; Law et al., 2014).
For each strain, linear mixed models were used to decompose the total variance of each gene into variance associated with cell density, genotype (i.e. WT, ΔvanT, ΔvanO), biological replicate and residual variation using R package variancePartition v. 1.18.3 modeling parameters as categorical (Hoffman & Schadt, 2016).
For differential expression analysis, dream (Hoffman & Roussos, 2020), a limma-based method (Ritchie et al., 2015), was used to fit the counts to linear mixed models for each comparison, modeling genotype and cell density as a combined fixed effect and biological replicate as a random effect. Hypothesis testing was performed using the topTable function and p-values were adjusted for multiple testing using the Benjamini-Hochberg approach. Genes with an adjusted p-value < 0.05 were considered differentially expressed. Volcano plots were visualized using R package EnhancedVolcano v. 1.6.0 (Blighe et al., 2019). Heatmaps were constructed using R package pheatmap v. 1.0.12 (Kolde, 2015).
Genes were assigned Biological Process Gene Ontology terms using PANNZER (Törönen et al., 2018) and gene set enrichment analysis (GSEA) was performed using R package topGO v. 2.40.0 with adjusted p-values from the differential expression analysis as the ranking metric with weight01 algorithm and Kolmogorov-Smirnov statistics (Alexa & Rahnenfuhrer, 2020).
To compare the transcriptome between LCD and HCD samples, we applied whole-cell spike-in normalization, allowing normalization of the sequencing read pair (fragment) counts to the number of cells (OD units) and thereby not assuming equal total mRNA content per cell (Gummesson et al., 2020). This was done by adding to each experimental culture an aliquot of spike-in culture corresponding to 1 % of the experimental cells, as measured in units of OD. The spike-in counts will therefore represent a larger fraction of the total fragment counts if added to an experimental culture with a low content of RNA per cell, than if added to an experimental culture with a high content of RNA per cell. In this experiment, fragments unique to the plasmid harbored by the spike-in cells represented a significantly larger fraction of the total fragment counts when cells were sampled at HCD compared to LCD (Supplementary fig. 2), and the HCD population showed a lower median expression than the LCD population. These observations are in accordance with the expectation that the total mRNA pool is reduced as populations reach high cell density and transition from the exponential to the early stationary growth phase. Without the spike-in normalization for differential mRNA content between samples, RNA-seq counts will underestimate the expression levels of many genes in LCD populations compared to HCD populations (Supplementary fig. 2). This ultimately leads to misinterpretation of downstream differential expression analysis (Supplementary fig. 3). Analyzing data without spike-in normalization results in an overestimation of the number of genes that are underexpressed at LCD relative to HCD, and an underestimation of the number of genes that are overexpressed at LCD with cells at HCD (Supplementary fig. 3). Therefore, we analyzed spike-in normalized counts for analyses that included both LCD and HCD populations, while TMM normalization was sufficient for analyses that compared strains harvested at the same cell density.
Genome_build: Concatenated genomes and gene positions in folder "Input files for mapping and counting"
Supplementary_files_format_and_content: Read mapping and feature counting stats overview in file "Read mapping and feature counting stats.xlsx"
Supplementary_files_format_and_content: Count matrices in folder "featureCounts output and count matrices"
Supplementary_files_format_and_content: Differential expression analysis output in folder "dream output"
Supplementary_files_format_and_content: variancePartition analysis output in folder "variancePartition output"

organism: Vibrio anguillarum

source_name: Vibrio anguillarum

growth_protocol: Cells were grown in 50 ml marine broth in 300 ml Erlenmeyer flasks at 30 C agitating

extract_protocol:
Total RNA was extracted with a hot acidic phenol RNA purification method.
rRNA was removed with Illumina Ribo-Zero rRNA removal kit. Strand-specific libraries were prepared with the TruSeq stranded mRNA Library prep kit

treatment_protocol: Samples were stopped with stop solution and prior RNA extracting, all samples were spiked-in with 1 % 90-11-287 carrying plasmid pEVS143 with IPTG-inducible gfp and cmr

value: strain 90-11-287 {delta}vanO

tag: cell density

value: LCD

tag: replicate


title: ImmSyst_RAPA_001 [HP035]


title: Vibrio anguillarum strain 90-11-287 ΔvanO HCD rep3

description:
raw_counts_output_90-11-287.txt
counts_gg_notrRNA_90-11-287_no_C5.txt
Spike-in_counts_90-11-287_no_C5.txt
vanO.LCD_vs_vanO.HCD - 90-11-287 - Spike-in normalized.txt
vanO.HCD_vs_WT.HCD - 90-11-287 - TMM normalized.txt
variancePartition_90-11-287_Spike-in_normalized.txt

tag: strain

value: HCD


title: Vibrio anguillarum strain 90-11-287 ΔvanO HCD rep2


title: NMC_A2_G4ChIPseq_rep01


title: PBMC Virus challenge group at T1, biological rep1

source_name: peripheral blood mononuclear cells Virus challenge group at day 1


title: Vibrio anguillarum strain 90-11-287 ΔvanO HCD rep1


title: ImmSyst_001 [HP025]


title: Vibrio anguillarum strain 90-11-287 ΔvanO LCD rep1


title: Vibrio anguillarum strain 90-11-287 ΔvanT HCD rep3

description:
raw_counts_output_90-11-287.txt
counts_gg_notrRNA_90-11-287_no_C5.txt
Spike-in_counts_90-11-287_no_C5.txt
vanT.LCD_vs_vanT.HCD - 90-11-287 - Spike-in normalized.txt
vanT.HCD_vs_WT.HCD - 90-11-287 - TMM normalized.txt
variancePartition_90-11-287_Spike-in_normalized.txt

value: strain 90-11-287 {delta}vanT


title: Vibrio anguillarum strain 90-11-287 ΔvanT HCD rep2


title: No_ImmSyst_001 [HP010]

value: kidney tissue


title: Vibrio anguillarum strain 90-11-287 ΔvanT LCD rep3

description:
raw_counts_output_90-11-287.txt
counts_gg_notrRNA_90-11-287_no_C5.txt
Spike-in_counts_90-11-287_no_C5.txt
vanT.LCD_vs_WT.LCD - 90-11-287 - TMM normalized.txt
vanT.LCD_vs_vanT.HCD - 90-11-287 - Spike-in normalized.txt
variancePartition_90-11-287_Spike-in_normalized.txt


title: Vibrio anguillarum strain 90-11-287 ΔvanT HCD rep1


title: Vibrio anguillarum strain 90-11-287 ΔvanT LCD rep1


title: Vibrio anguillarum strain 90-11-287 WT HCD rep2

description:
raw_counts_output_90-11-287.txt
counts_gg_notrRNA_90-11-287_no_C5.txt
counts_gg_notrRNA_SharedGenes_only_WTs_uneven_sized_genes_normalized.txt
Spike-in_counts_90-11-287_no_C5.txt
WT.LCD_vs_WT.HCD - 90-11-287 - TMM normalized.txt
WT.LCD_vs_WT.HCD - 90-11-287 - Spike-in normalized.txt
vanT.HCD_vs_WT.HCD - 90-11-287 - TMM normalized.txt
vanO.HCD_vs_WT.HCD - 90-11-287 - TMM normalized.txt
90-11-287.WT.LCD_vs_90-11-287.WT.HCD - SharedGenes - Spike-in normalized.txt
90-11-287.WT.HCD_vs_PF430-3.WT.HCD - SharedGenes - TMM normalized.txt
variancePartition_90-11-287_Spike-in_normalized.txt
variancePartition_SharesGenes_Spike-in_normalized_only_WTs.txt


title: PBMC Mock group, biological rep2

description: Gene expression data from peripheral blood mononuclear cells Mock group


title: PBMC Mock group, biological rep1

source_name: peripheral blood mononuclear cells Mock group


title: Vibrio anguillarum strain 90-11-287 WT LCD rep2

description:
raw_counts_output_90-11-287.txt
counts_gg_notrRNA_90-11-287_no_C5.txt
counts_gg_notrRNA_SharedGenes_only_WTs_uneven_sized_genes_normalized.txt
Spike-in_counts_90-11-287_no_C5.txt
WT.LCD_vs_WT.HCD - 90-11-287 - TMM normalized.txt
WT.LCD_vs_WT.HCD - 90-11-287 - Spike-in normalized.txt
vanT.LCD_vs_WT.LCD - 90-11-287 - TMM normalized.txt
vanO.LCD_vs_WT.LCD - 90-11-287 - TMM normalized.txt
90-11-287.WT.LCD_vs_90-11-287.WT.HCD - SharedGenes - Spike-in normalized.txt
90-11-287.WT.LCD_vs_PF430-3.WT.LCD - SharedGenes - TMM normalized.txt
variancePartition_90-11-287_Spike-in_normalized.txt
variancePartition_SharesGenes_Spike-in_normalized_only_WTs.txt


title: Vibrio anguillarum strain 90-11-287 WT LCD rep3


title: Vibrio anguillarum strain 90-11-287 WT HCD rep3


title: Vibrio anguillarum strain 90-11-287 WT LCD rep1


title: Vibrio anguillarum strain 90-11-287 ΔvanO LCD rep2


title: Vibrio anguillarum strain PF430-3 ΔvanO HCD rep3

description:
raw_counts_output_PF430-3.txt
counts_gg_notrRNA_PF430-3_no_A2.txt
Spike-in_counts_PF430-3_no_A2.txt
vanO.LCD_vs_vanO.HCD - PF430-3 - Spike-in normalized.txt
vanO.HCD_vs_WT.HCD - PF430-3 - TMM normalized.txt
variancePartition_PF430-3_Spike-in_normalized.txt

value: strain PF430-3 {delta}vanO


title: Vibrio anguillarum strain PF430-3 ΔvanO LCD rep3

description:
raw_counts_output_PF430-3.txt
counts_gg_notrRNA_PF430-3_no_A2.txt
Spike-in_counts_PF430-3_no_A2.txt
vanO.LCD_vs_WT.LCD - PF430-3 - TMM normalized.txt
vanO.LCD_vs_vanO.HCD - PF430-3 - Spike-in normalized.txt
variancePartition_PF430-3_Spike-in_normalized.txt


title: Vibrio anguillarum strain PF430-3 ΔvanO HCD rep2


title: Vibrio anguillarum strain PF430-3 ΔvanO LCD rep2


title: Vibrio anguillarum strain 90-11-287 ΔvanT LCD rep2


title: Vibrio anguillarum strain PF430-3 ΔvanT HCD rep3

description:
raw_counts_output_PF430-3.txt
counts_gg_notrRNA_PF430-3_no_A2.txt
Spike-in_counts_PF430-3_no_A2.txt
vanT.LCD_vs_vanT.HCD - PF430-3 - Spike-in normalized.txt
vanT.HCD_vs_WT.HCD - PF430-3 - TMM normalized.txt
variancePartition_PF430-3_Spike-in_normalized.txt

value: strain PF430-3 {delta}vanT


title: Vibrio anguillarum strain PF430-3 ΔvanO HCD rep1


title: Vibrio anguillarum strain PF430-3 ΔvanO LCD rep1


title: Vibrio anguillarum strain PF430-3 ΔvanT HCD rep2


title: Vibrio anguillarum strain PF430-3 ΔvanT HCD rep1


title: Vibrio anguillarum strain PF430-3 ΔvanT LCD rep1


title: Vibrio anguillarum strain PF430-3 ΔvanT LCD rep2

description:
raw_counts_output_PF430-3.txt
counts_gg_notrRNA_PF430-3_no_A2.txt
Spike-in_counts_PF430-3_no_A2.txt
vanT.LCD_vs_WT.LCD - PF430-3 - TMM normalized.txt
vanT.LCD_vs_vanT.HCD - PF430-3 - Spike-in normalized.txt
variancePartition_PF430-3_Spike-in_normalized.txt


title: Vibrio anguillarum strain PF430-3 WT HCD rep3

description:
raw_counts_output_PF430-3.txt
counts_gg_notrRNA_PF430-3_no_A2.txt
counts_gg_notrRNA_SharedGenes_only_WTs_uneven_sized_genes_normalized.txt
Spike-in_counts_PF430-3_no_A2.txt
WT.LCD_vs_WT.HCD - PF430-3 - TMM normalized.txt
WT.LCD_vs_WT.HCD - PF430-3 - Spike-in normalized.txt
vanT.HCD_vs_WT.HCD - PF430-3 - TMM normalized.txt
vanO.HCD_vs_WT.HCD - PF430-3 - TMM normalized.txt
PF430-3.WT.LCD_vs_PF430-3.WT.HCD - SharedGenes - Spike-in normalized.txt
90-11-287.WT.HCD_vs_PF430-3.WT.HCD - SharedGenes - TMM normalized.txt
variancePartition_PF430-3_Spike-in_normalized.txt
variancePartition_SharesGenes_Spike-in_normalized_only_WTs.txt

value: strain PF430-3 WT


title: Vibrio anguillarum strain PF430-3 WT HCD rep2


title: Vibrio anguillarum strain PF430-3 WT LCD rep2

description:
raw_counts_output_PF430-3.txt
counts_gg_notrRNA_PF430-3_no_A2.txt
counts_gg_notrRNA_SharedGenes_only_WTs_uneven_sized_genes_normalized.txt
Spike-in_counts_PF430-3_no_A2.txt
WT.LCD_vs_WT.HCD - PF430-3 - TMM normalized.txt
WT.LCD_vs_WT.HCD - PF430-3 - Spike-in normalized.txt
vanT.LCD_vs_WT.LCD - PF430-3 - TMM normalized.txt
vanO.LCD_vs_WT.LCD - PF430-3 - TMM normalized.txt
PF430-3.WT.LCD_vs_PF430-3.WT.HCD - SharedGenes - Spike-in normalized.txt
90-11-287.WT.LCD_vs_PF430-3.WT.LCD - SharedGenes - TMM normalized.txt
variancePartition_PF430-3_Spike-in_normalized.txt
variancePartition_SharesGenes_Spike-in_normalized_only_WTs.txt


title: Vibrio anguillarum strain PF430-3 WT HCD rep1


title: Vibrio anguillarum strain PF430-3 WT LCD rep1


title: Vibrio anguillarum strain 90-11-287 WT HCD rep1


title: Vibrio anguillarum strain PF430-3 WT LCD rep3


title: HeLa HP1 knockdown biol + HP1αI165E overexpression biological rep 1

city: Melbourne

first: Elizabeth

last: Hinde

address: Grattan street

department: School of Physics

country: Australia

institute: University of Melbourne

description: Sample name in processed data matrix = KDOE1

data_processing:
Generate aligned BAM files using bwa (0.7.13)
Generate HiC matices for each sample using HiCExplorer v3.7.2. File type = mcool, Function = buildmatrix, Resolution = 100 kb.
Check reulting QC files from previous step before proceeding
Nomalise and correct using HiCExplorer functions hicNormalise (method = src) and hicCorrect (method = KR).
Use Genova (v1.01) to analyse resulting mcool files. For the manuscript (Figure 2), the rcp function (relative contact probability) was used.
Assembly: hg38
Supplementary files format and content: comma delimited csv containing all the data points underpinning the rcp plot in the main manuscript (Fig 2d)
Supplementary files format and content: region, distance, P, samplename, colour
Supplementary files format and content: mcool

source_name: HeLa

growth_protocol: Cell lines were grown in DMEM (Lonza) supplemented with 10% bovine growth serum (Gibco), 1 x Pen-Strep (Lonza) and 2 μg/ml puromycin at 37°C in 5% CO2.

extract_protocol:
Genomic DNA was extracted from 500,000 cells
Crosslinking was carried out with 1% formaldehyde for 10min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI. After reversal of crosslinks, ligated DNA was size selected between 200-1000 bp and subsequently prepped for Illumina sequencing.

value: HeLa

value: Cervical Cancer

value: HP1 knockdown + HP1alphaI165E overexpression

tag: hic digestion_enzyme

value: MboI


title: HeLa HP1 knockdown biological rep 2

description: Sample name in processed data matrix = HPKD2

value: HP1 knockdown


title: HeLa HP1 knockdown biological rep 1

description: Sample name in processed data matrix = HPKD1


title: HeLa biological rep 2

description: Sample name in processed data matrix = Hela2

value: wild type


title: 11-786O-C19orf6kd5-RNAseq, rep1

city: Cold Spring Harbor

first: Katherine

middle: Ann

last: Alexander

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
C19orf6kd5_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_FIBP_TMEM259[c19orf6].txt

data_processing:
RNA-seq data was aligned to the reference human genome assembly, GRC37/hg19, using the splice-aware STAR alignment
PCR duplicates were removed using Picard
Reads for each gene with RefSeq annotations were counted using htseq-counts
Normalized counts and significant differences were calculated using Deseq2
Assembly: hg19
Supplementary files format and content: Processed data files are ouput text files from Deseq2, with SON TSA-seq signal added (from GSE248710; files linked to GSE248711)

molecule: polyA RNA

growth_protocol: 786-O cells were grown in RPMI media with 10% FBS under atmoshperic oxygen and 5% carbon dioxide

extract_protocol:
Cells were lysed in TRIzol (15596018, Thermo Fisher Scientific) and snap frozen. RNA was then isolated using chloroform extraction, followed by QIAGEN Rneasy Mini Kit isolation (#74106), including DNA digestion with Dnase. Poly(A) + RNA was then isolated using double selection with poly-dT bead (E7490, NEB)
RNA-seq libraries were prepared using a NEB-Next Ultra II Directional Lybrary Prep Kit for Illumina (E7760, NEB). Library sizes were determined on a Bioanalyzer, and concentrations determined using NEBNext Lib Quant Kit (E7630, NEB). Libraries were sequenced on an Illumina NextSeq 550, using paired-end sequencing of 42 bases per read.

treatment_protocol: Speckle protein genes were knocked down in 786-O cells using FlexiTub siRNAs (Qiagen) and compared to a non-targeting siRNA control (Qiagen Allstars Neg Ctrl). 786-O cells were split one day prior to transfection and plated 50-60% confluency. siRNAs were transfected into cells using the DharmaFECT 1 Transfection Reagent (Horizon T-2001-03) according to the instructions of the manufacturer. siRNA-treated 786-O cells were split into fresh media 24 hours after transfection and harvested 48 hours after transfection.

tag: treatment

value: TMEM259 siRNA5


title: 12-786O-C19orf6kd5-RNAseq, rep2


title: Vibrio anguillarum strain PF430-3 ΔvanT LCD rep3


title: 10-786O-FIBPkd7-RNAseq, rep2

description:
FIBPkd7_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_FIBP_TMEM259[c19orf6].txt

value: FIBP siRNA7


title: 9-786O-FIBPkd7-RNAseq, rep1


title: 1-786O-NEGsiRNA-RNAseq, rep1

description:
FIBPkd6_withSONcounts.txt (linked to SuperSeries GSE248711)
FIBPkd7_withSONcounts.txt (linked to SuperSeries GSE248711)
C19orf6kd5_withSONcounts.txt (linked to SuperSeries GSE248711)
C19orf6kd6_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_FIBP_TMEM259[c19orf6].txt

value: non-targeting siRNA


title: 19-786O-DDX39Akd4, rep2

description:
DDX39Akd4_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_DDX39A_SARNP.txt

value: DDX39A siRNA4


title: 2-786O-NEGsiRNA-RNAseq, rep2


title: 16-786O-DDX39Akd1, rep2

description:
DDX39Akd1_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_DDX39A_SARNP.txt

value: DDX39A siRNA1


title: 7-786O-FIBPkd6-RNAseq, rep1

description:
FIBPkd6_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_FIBP_TMEM259[c19orf6].txt

value: FIBP siRNA6


title: 18-786O-DDX39Akd4, rep1


title: 8-786O-FIPBkd6-RNAseq, rep2


title: 8-786O-SARNPkd3, rep2

description:
SARNPkd3_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_DDX39A_SARNP.txt

value: SARNP siRNA3


title: 15-786O-DDX39Akd1, rep1


title: 10-786O-SARNPkd9, rep2

description:
SARNPkd9_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_DDX39A_SARNP.txt

value: SARPN siRNA9


title: HeLa HP1 knockdown biol + HP1αI165E overexpression biological rep 2

tag: cell type


title: HeLa biological rep 1

description: Sample name in processed data matrix = Hela1

tag: genotype


title: 2-786O-NTC, rep2

description:
SARNPkd3_withSONcounts.txt (linked to SuperSeries GSE248711)
SARNPkd9_withSONcounts.txt (linked to SuperSeries GSE248711)
DDX39Akd1_withSONcounts.txt (linked to SuperSeries GSE248711)
DDX39Akd4_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_DDX39A_SARNP.txt

tag: cell line


title: 16-786O-SART1-4siRNA-RNAseq, rep2

description:
SART1kd4_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_SART1.txt

value: SART1 siRNA4


title: 15-786O-SART1-4siRNA-RNAseq, rep1


title: 1-786O-NTC, rep1


title: 15-786O-PT2399-3h-PD-rep2

data_processing:
SON TSA-seq reads were aligned to the human reference genome assembly GRC37/hg19 using Bowtie2 allowing for a maximum fragment size of 1000 base pairs
PCR duplicates were removed using Picard
SON signal was quantified over sliding windows of 50 or 100kb slid by 1/10th of the window size using DiffBind with input (TSA-seq) or IgG (Cut&Run) subtraction
Differential 50kb and 100kb windows identified from DiffBind were merged using BEDTools, with input samples as background
Genes within differential domains were then extracted using Python. Genes within decreasing domains that had an adjusted p-value of less than 0.01 in either SON TSA-seq or SON Cut&Run were considered to have speckle association regulated by HIF-2a
Assembly: hg19
Supplementary files format and content: DiffBindResults files, called "DiffBindResults_*" are the DiffBind output for sliding windows of 50kb or 100kb.
Supplementary files format and content: Bed files called "significant_3hdown*" are the significantly decreased SON windows with the annotated adjusted p-value cutoff < 0.01, and sliding window size (50kb or 100kb)
Supplementary files format and content: Text files labelled "*_genes_*" are the genes within significantly decreasing SON signal windows for the annotated adjusted p-values (0.01) and window size (50kb or 100kb)

extract_protocol:
Cells were treated with 2µM of PT2399 or equivalent volume of DMSO vehicle control for 3 hours.
TSA-seq was performed using an antibody against SON (ab121759). SON TSA-seq was carried out using the protocol for SON TSA-seq 2.0 on attached cells with Condition E as described (labeling with 50% sucrose, 1:300 tyramide-biotin, and 0.0015% hydrogen peroxide for 30 minutes), with the following minor modifications: DNA was fragmented to an average size of 250bp using a Covaris S220
Libraries from DNA fragments were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Library sizes were determined on a Bioanalyzer, and concentration determined using NEBNext Lib Quant Kit (E7630, NEB).

treatment_protocol: 786-O cells were grown in RPMI media with 10% FBS under atmospheric oxygen and 5% carbon dioxide.

tag: antibody

value: SON (abcam ab121759)


title: 14-786O-PT2399-3h-PD-rep1


title: 14-786O-NEGsiRNA-RNAseq, rep2

description:
SART1kd4_withSONcounts.txt (linked to SuperSeries GSE248711)
SART1kd6_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_SART1.txt


title: 18-786O-SART1-6siRNA-RNAseq, rep1

description:
SART1kd6_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_SART1.txt

value: SART1 siRNA6


title: 19-786O-SART1-6siRNA-RNAseq, rep2


title: 23-786O-PT2399-3h-input-rep2

value: DMSO


title: 13-786O-DMSO-PD-rep2

value: input


title: 9-786O-SARNPkd9, rep1


title: 35-786O-PT2399-12h-rep2

data_processing:
RNA-seq data was aligned to the reference human genome assembly, GRC37/hg19, using the splice-aware STAR alignment
PCR duplicates were removed using Picard
Reads for each gene with RefSeq annotations were counted using htseq-counts
Normalized counts and significant differences were calculated using Deseq2
Assembly: hg19
Supplementary files format and content: Processed data files, "*vsDMSO.txt" are the Deseq2 output of differential expression between PT2399 treated groups of the four timepoints (3h, 6h, 9h, 12h) versus the DMSO control condition. "normalizedCounts.txt" is the normalized counts files from Deseq2 of all conditions.

extract_protocol:
786-O cells were treated with DMSO for 12 hours or with 2µM of PT2399 for 3, 6, 9, or 12 hours.
Cells were lysed in TRIzol (15596018, Thermo Fisher Scientific) and snap frozen. RNA was then isolated using chloroform extraction, followed by QIAGEN RNeasy Mini Kit isolation (#74106), including DNA digestion with DNase. Poly(A) + RNA was then isolated using double selection with poly-dT bead (E7490, NEB)
RNA-seq libraries were prepared using a NEB-Next Ultra II Directional Library Prep Kit for Illumina (E7760, NEB). Library sizes were determined on a Bioanalyzer, and concentrations determined using NEBNext Lib Quant Kit (E7630, NEB). Libraries were sequenced on an Illumina NextSeq 550, using paired-end sequencing of 42 bases per read.

treatment_protocol: 786-O cells were grown in RPMI media with 10% FBS under atmospheric oxygen and 5% carbon dioxide


title: 21-786O-DMSO-input-rep2


title: 13-786O-NEGsiRNA-RNAseq, rep1


title: 34-786O-PT2399-9h-rep2


title: 28-786O-PT2399-9h-rep1


title: 7-786O-SARNPkd3, rep1


title: 24-786O-PT2399-3h-rep1


title: 22-786O-PT2399-3h-input-rep1


title: 12-786O-DMSO-PD-rep1


title: 17-786O-DMSO-rep1


title: 20-786O-DMSO-input-rep1


title: 43-MCF7-DELstms10

data_processing:
RNA-seq data was aligned to the reference human genome assembly, GRC37/hg19, using the splice-aware STAR alignment
PCR duplicates were removed using Picard
Reads for each gene with RefSeq annotations were counted using htseq-counts
Normalized counts and significant differences were calculated using Deseq2
Assembly: hg19
Supplementary files format and content: Processed data files, "noHIF2AvsWTstms.txt" and "noHIF2AvsDELstms.txt" are the Deseq2 output of differential expression between negative control with no HIF-2a induction and induction with HIF-2a with wild type (WT) or STM deleted (DELstms). Data file "WTvsDELstms.txt" is the Deseq2 output file comparing HIF-2a with wild type (WT) and deleted (DELstms) STMs.

extract_protocol:
To generate MCF7 cells with dox-inducible HIF-2a, we packaged the reverse tetracycline controlled transactivator plasmid (Lenti CMV rtTA3 Blast [w756-1]) into viruses, infected MCF7 cells, and performed selection for cells with stably-integrated rtTA using blasticidin. MCF7-rtTA cells were then infected with viruses containing stabilized HIF-2a with wild type STMs or with deleted STMs under the control of a TRE3G promoter (pRetroX-TRE3G HIF-2a) and selected for stable integration using puromycin. After puromycin selection, single cell cloning was performed by diluting cells, plating in a 96 well plate and selecting wells with single clones. Individual clones were screened for HIF-2a levels by Western blotting. For virus generation, HEK293T cells were transfected with pPAX2, pVSV-G, and the lentiviral vector (rtTA or pRetroX-TRE3G) using Lipofectamine2000 and infected MCF7 cells with a 1:1 ratio of virus-containing media and MCF7 growth media. To induce HIF-2a expression, doxycycline was dissolved in water to a 30mM stock solution and added to MCF7 cells at a final concentration of 3µM.
Cells were lysed in TRIzol (15596018, Thermo Fisher Scientific) and snap frozen. RNA was then isolated using chloroform extraction, followed by QIAGEN RNeasy Mini Kit isolation (#74106), including DNA digestion with DNase. Poly(A) + RNA was then isolated using double selection with poly-dT bead (E7490, NEB)
RNA-seq libraries were prepared using a NEB-Next Ultra II Directional Library Prep Kit for Illumina (E7760, NEB). Library sizes were determined on a Bioanalyzer, and concentrations determined using NEBNext Lib Quant Kit (E7630, NEB). Libraries were sequenced on an Illumina NextSeq 550, using paired-end sequencing of 42 bases per read.

treatment_protocol: MCF7 cells were grown in DMEM media with 10% FBS under atmospheric oxygen and 5% carbon dioxide

value: HIF2As-dSTM clone 10

value: doxycycline


title: 33-786O-PT2399-6h-rep2


title: 29-786O-PT2399-12h-rep1


title: 26-786O-PT2399-6h-rep1


title: 38-MCF7-WTstm4

value: HIF2As-wtSTM clone 4


title: 5-786O-ALYkd8-rep1

data_processing:
RNA-seq data was aligned to the reference human genome assembly, GRC37/hg19, using the splice-aware STAR alignment
PCR duplicates were removed using Picard
Reads for each gene with RefSeq annotations were counted using htseq-counts
Normalized counts and significant differences were calculated using Deseq2
Assembly: hg19
Supplementary files format and content: Processed data files, "ALYkd5.txt" and "ALYkd8.txt" are the Deseq2 output of differential expression between ALYREF knockdown 5 or 8 respectively, and the non-targeting control.

extract_protocol:
ALYREF was knocked down in 786-O cells using FlexiTube siRNAs (Qiagen) and compared to a non-targeting siRNA control (Qiagen Allstars Neg Ctrl). 786-O cells were split one day prior to transfection and plated at 50-60% confluency. siRNAs were transfected into cells using the DharmaFECT 1 Transfection Reagent (Horizon T-2001-03) according to the instructions of the manufacturer. siRNA-treated 786-O cells were split into fresh media 24 hours after transfection and harvested 48 hours after transfection.
Cells were lysed in TRIzol (15596018, Thermo Fisher Scientific) and snap frozen. RNA was then isolated using chloroform extraction, followed by QIAGEN RNeasy Mini Kit isolation (#74106), including DNA digestion with DNase. Poly(A) + RNA was then isolated using double selection with poly-dT bead (E7490, NEB)
RNA-seq libraries were prepared using a NEB-Next Ultra II Directional Library Prep Kit for Illumina (E7760, NEB). Library sizes were determined on a Bioanalyzer, and concentrations determined using NEBNext Lib Quant Kit (E7630, NEB). Libraries were sequenced on an Illumina NextSeq 550, using paired-end sequencing of 42 bases per read.

value: ALYREF siRNA8


title: 6-786O-ALYkd8-rep2


title: 13-786O-C19orf6kd6-RNAseq, rep1

description:
C19orf6kd6_withSONcounts.txt (linked to SuperSeries GSE248711)
normalizedCounts_FIBP_TMEM259[c19orf6].txt

value: TMEM259 siRNA6


title: 2-786O-NTC-rep2


title: 1-786O-NTC-rep1


title: 32-786O-PT2399-3h-rep2


title: 31-786O-DMSO-rep2


title: 6-786O-CnR-DMSO-SON-rep2

data_processing:
SON TSA-seq or SON Cut&Run reads were aligned to the human reference genome assembly GRC37/hg19 using Bowtie2 allowing for a maximum fragment size of 1000 base pairs
PCR duplicates were removed using Picard
SON signal was quantified over sliding windows of 50 or 100kb slid by 1/10th of the window size using DiffBind with input (TSA-seq) or IgG (Cut&Run) subtraction
Differential 50kb and 100kb windows identified from DiffBind were merged using BEDTools, with IgG samples as background
Genes within differential domains were then extracted using Python. Genes within decreasing domains that had an adjusted p-value of less than 0.01 in either SON TSA-seq or SON Cut&Run were considered to have speckle association regulated by HIF-2a
Assembly: hg19
Supplementary files format and content: DiffBindResults files, called "DiffBindResults_*" are the DiffBind output for sliding windows of 50kb or 100kb.
Supplementary files format and content: Bed files called "significant_3hdown*" are the merged significantly decreased SON windows with the annotated adjusted p-value cutoff (0.01 or 0.05) and sliding window size (50kb or 100kb)
Supplementary files format and content: Text files labelled "*_genes_*" are the genes within significantly decreasing SON signal windows for the annotated adjusted p-values (0.01 or 0.05) and window size (50kb or 100kb)

extract_protocol:
Cells were treated with 2µM of PT2399 or equivalent volume of DMSO vehicle control for 3 hours.
For each condition, nuclei from ~600k cells was isolated using nuclear isolation buffer [10mM HEPES-KOH (pH 7.9), 10mM KCl, 0.1% NP40, 0.5mM spermidine, 1x Halt protease inhibitor cocktail] and bound to concanavalin A lectin beads which had been washed in binding buffer [BioMag Plus; binding buffer: 20mM HEPES-KOH (pH 7.9), 10mM KCl, 1mM CaCl2, 1mMnCl2], as described. After bead binding, samples were split into two tubes, one for each antibody, where binding buffer was replaced with 1:100 antibody diluted in blocking buffer [20mM HEPES-KOH (pH 7.5), 150mM NaCl, 0.1% BSA, 0.5mM spermidine, 1x Halt protease inhibitor cocktail, 2mM EDTA](IgG antibody: Millipore 06-371; SON antibody: abcam ab121759) and incubated overnight at 4°C. Samples were washed in washing buffer [20mM HEPES-KOH (pH 7.5), 150mM NaCl, 0.1% BSA, 0.5mM spermidine, 1x Halt protease inhibitor cocktail], and treated with pA-MNase and CaCl2 for 30 minutes on an ice-cold pre-chilled metal block on ice. The reaction was stopped by addition of STOP buffer [200mM NaCl, 20mM EDTA, 4mM EGTA, 50µg/mL RNase A, 40µg/mL glycogen] while gently vortexing, and DNA fragments were released by incubation at 37°C for 10 minutes. The DNA fragments were collected from bead supernatants, treated with Proteinase K for 10 minutes at 70°C, then subjected to PCI-choroform purification.
Libraries from DNA fragments were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Library sizes were determined on a Bioanalyzer, and concentration determined using NEBNext Lib Quant Kit (E7630, NEB).


title: 5-786O-CnR-DMSO-SON-rep1


title: 48-MCF7-DELstms12

value: HIF2As-dSTM clone 12


title: 25-MCF7-DELstms4

value: HIF2As-dSTM clone 4


title: 41-MCF7-WTstm7

value: HIF2As-wtSTM clone 7


title: 3-MCF7-WTstm1

value: HIF2As-wtSTM clone 1


title: 2-786O-CnR-DMSO-IgG-rep2

value: IgG (Millipore 06-371)


title: 1-786O-CnR-DMSO-IgG-rep1


title: 3-786O-CnR-PT2399-IgG-rep1


title: 37-MCF7-noHIF2A-rep2

value: no exogenous HIF-2alpha


title: 30-MCF7-noHIF2A-rep1


title: 39-786O-PT2399-3h-input-rep2

data_processing:
Reads were mapped to the reference human genome assembly GRCh37/hg19 using Bowtie2 (maximum fragment size set to 2000 bp).
PCR duplicates were removed using Picard
Properly aligned, nonduplicated pairs were retained for peak calling using MACS2
Assembly: hg19
Supplementary files format and content: Processed data files include BED files of called peaks for each DMSO condition, merged DMSO-called peaks, and input subtracted bigwig genome browser track files of each treatment and replicate.

extract_protocol:
786-O cells were treated with 2µM of PT2399 or equivalent volume of DMSO vehicle control for 3 hours.
Cells were crosslinked in formaldehyde (1% final concentration) for 10 minutes. Crosslinked cells were quenched with glycine (125mM final) for 5 minutes, followed by two washes in ice-cold PBS. Nuclei were isolated from approximately 20 million cells as previously described, and chromatin was sheared using a Covaris S220. Immunoprecipitation was performed using 500µg of sheared chromatin lysate and 5µg of HIF-2alpha antibody (Novus NB100-122) pre-conjugated to protein G beads (Invitrogen). Lysate and antibody-beads were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50mM HEPES-HCl(pH 8), 100mM NaCl, 1mM EDTA, 0,5mM EGTA, 0.1% sodium deoxycholate, and 0.5% N-laurylsarcosine], followed by one wash in ChIP final wash buffer [1x tris-EDTA (TE) Buffer and 50mM NaCl]. Immunoprecipitated DNA was eluted from washed beads, reverse cross-linked overnight and purified.
DNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Library sizes were determined on a Bioanalyzer, and concentration determined using NEBNext Lib Quant Kit (E7630, NEB). Input and pulldown libraries were sequenced with an Illumina NextSeq550 with 42bp per read using the NextSeq 500/550 High Output 75-cycle v2.5 kit.

tag: chip antibody


title: 38-786O-PT2399-3h-input


title: 17-786O-DMSO-HIF2a-rep1

value: HIF-2alpha (Novus NB100-122)


title: 4-786O-ALYkd5-rep2

value: ALYREF siRNA5


title: 8-786O-CnR-PT2399-SON-rep2

value: SON (abcam ab121759)


title: 3-786O-ALYkd5-rep1


title: 7-786O-CnR-PT2399-SON-rep1


title: 4-786O-CnR-PT2399-IgG-rep2


title: AND00446-4_PBS_1.5HR

city: Billerica

first: Nicholas

last: Geraci

address: 45 Middlesex Turnpike 01821

department: Neuroscience & Immunology

institute: EMD Serono

description: 10X Genomics Chromium Next GEM Single Cell 3ʹ Kit v3.1

data_processing:
FASTQ files were used as input to the scRNA-seq workflow of the Python-based snakePipes pipeline (v2.6.1). STARsolo methods were used for read mapping and quantification. The GENCODE Mouse Release M19 (GRCm38.p6 assembly) was used as a reference. The Single Cell 3' v3 whitelist (10x Genomics) was provided for barcode identification.
Read counts were used as input to the Seurat 4.3 package in R (version 4.2.1) to perform quality control and quantitative analyses. Cells were filtered out when the number of unique features (genes) were <200 or >5000. Additionally, cells were also excluded if >10% of their identified genes were mitochondrial. Any cells expressing erythrocyte marker genes (i.e., Hbb-bs, Hba-a1, Alas2, and Bpgm) were removed to provide clarity of cellular clustering of cells of interest. Raw gene count matrices of filtered cells from three separate experiments of identical design were merged in R.
Using Seurat, the combined data were successively log normalized, variable gene features identified, scaled, and underwent linear dimensional reduction by principal component analysis. The data were then batch corrected by experiment using the Harmony method. Finally, the combined data were clustered in Seurat using a resolution of 0.3 and projected using uniform manifold approximation and projection (UMAP).
Cellular identification was performed using the SingleR (version 1.10.0) in R, with reference datasets of mouse muscle tissue derived from PanglaoDB (SRA653146,SRA851241). Differential expression and sub-clustering analyses were also performed using Seurat.
Assembly: GRCm38.p6
Supplementary files format and content: A R readable Seurat5 class object file (.h5Seurat) with all processed data and metadata annotations, ms.muscle.scrnaseq.combo_harmonyfinal_pc15_res0.3_v6.h5Seurat
Supplementary files format and content: A AnnData class object file (.h5ad) with all processed data and metadata annotations, ms.muscle.scrnaseq.combo_harmonyfinal_pc15_res0.3_v6.h5ad

source_name: Skeletal muscle

extract_protocol:
Mice were euthanized 1.5 hours after injection by CO2 inhalation and tibialis anterior muscle was collected in 6-well plates containing Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY) with 10% FBS. The skeletal muscle tissue was cut into 2–4 mm pieces and transferred into gentleMACS C tubes for homogenization using an Octo Dissociator with Heaters (Miltenyi, Gaithersburg, MD). A single-cell suspension was prepared using the Miltenyi Skeletal Muscle Dissociation Kit according to the manufacturer’s instructions. The cells were resuspended in DMEM and filtered through a MACS SmartStrainer (70 µm). The cell suspension was centrifuged at 300 g for 20 minutes and the supernatant was completely aspirated. Cells were resuspended in 1 mL DMEM with 10% FBS, counted, and changes in gene expression were evaluated.
Single-cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics platform (California, USA). Chromium Next GEM Single Cell 3ʹ Kit v3.1 was used for sample processing and library construction. The cells were loaded into the Chromium Controller with a target of 10,000 cells collected per sample and were captured and processed according to the manufacturer’s instructions. Library QC was performed using the Agilent Bioanalzyer and High Sensitivity DNA kit (California, USA) and DNA concentrations were measured using a Qubit fluorometer (ThermoFisher Scientific). Sequencing was performed using the Illumina NextSeq 2000 (California, USA). Libraries were loaded at a concentration of 650 pM and were sequenced using a P3 200 cycle sequencing kit. Sample AND00433-6 was removed from all downstream analyses due to a technical error with sequencing equipment resulting in sample contamination.

treatment_protocol: Healthy C57BL/6 female mice, 8–12 weeks of age, were purchased from Charles River Laboratories (Wilmington, MA). Mice were prepared for intramuscular injection by shaving the hind right thigh and anesthetized using isoflurane. The injection site was sterilized using isopropyl alcohol pads. R848 was injected directly into the tibialis anterior muscle in the right hind limb at a dose of 25 μg/animal in a volume of 50 μL. Control mice were injected with sterile PBS.

tag: tissue

value: Skeletal muscle

value: Whole tissue

value: PBS

tag: dosage

tag: collection timepoint

tag: Sex

value: Female


title: AND00446-7_R848_1.5HR


title: AND00446-5_R848_1.5HR


title: 24-786O-DMSO-HIF2a-rep2

value: DMSO


title: AND00446-3_PBS_1.5HR


title: 28-786O-PT2399-3h-HIF2a-rep2


title: 37-786O-DMSO-input-rep2

value: input


title: AND00441-5_R848_1.5HR


title: AND00441-6_R848_1.5HR


title: AND00446-6_R848_1.5HR


title: AND00441-3_PBS_1.5HR


title: AND00441-8_R848_1.5HR


title: AND00433-7_R848_1.5HR


title: AND00446-2_PBS_1.5HR


title: AND00446-1_PBS_1.5HR


title: 26-786O-PT2399-3h-HIF2a-rep1


title: 30-786O-DMSO-input-rep1


title: AND00441-1_PBS_1.5HR


title: AND00441-4_PBS_1.5HR


title: AND00441-7_R848_1.5HR


title: AND00433-2_Untreated_1.5HR

value: Untreated

value: No Injection


title: AND00441-2_PBS_1.5HR


title: AND00446-8_R848_1.5HR


title: AND00433-4_PBS_1.5HR


title: AND00433-8_R848_1.5HR


title: AND00433-3_PBS_1.5HR


title: AND00433-5_R848_1.5HR


title: AND00433-1_Untreated_1.5HR


title: 14-786O-C19orf6kd6-RNAseq, rep2

value: TMEM259 siRNA6


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse liver, biological replicate 1

city: Cleveland

first: Ming

last: Hu

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

data_processing:
To facilitate comparison across different samples, only R1 reads was used and was trimed to 50bp for downstream analysis.
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeaks (except for input samples)

source_name: liver

extract_protocol:
~30 mg fixed tissues were thawed on ice and the nuclei preparation was performed using truChIP® Chromatin Shearing Kit (Covaris) following the manufacturer’s instruction. The lysed nuclei were sheared using Covaris M220 with following setting: Setting: power, 75 W; duty factor, 8%; cycle per burst, 200; time, 12 min; temp, 7 °C. The sheared chromatins were cleared by centrifugation at 15,000×g for 12 min. The supernatant was collected and incubated with M-280 sheep anti-rabbit magnetic beads (Thermo Fisher, 11203D) for 3 hours at 4°C with slow rotation for preclearing. ~5% of precleared cell lysate was saved as input control after the incubation was done. The rest of precleared lysate was mixed M-280 sheep anti-rabbit magnetic beads that coupled with 0.9 μg of CTCF antibody (3418, Cell Signaling) and rotate at 4°C for 16 hours. On the next day, the beads were collected using magnetic stand and the supernatant was discarded. The beads are then washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. Washed beads were treated with 10 μg Rnase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 hours at 37°C, followed by reverse crosslinking in the presence of proteinase K (20 μg) overnight at 65°C. After reverse crosslinking the DNA was purified and quantified. The input control DNA was reverse crosslinked and purified in the same way as ChIPed DNA as described above.
Library preparation was performed using QIAseq Ultralow Input Library Kit (Qiagen) starting from 10–100 ng ChIPed DNA or input DNA. After PCR the amplified libraries were purified with SPRI Beads to extract fragments between 200-600bp for sequencing.

value: liver

tag: developmental stage

value: embryonic 12.5 day


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse limb, biological replicate 2

source_name: limb

value: limb


title: Wfdc15aRST_KO2

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

data_processing:
Raw RNA-seq reads were quality-checked with FastQC (version 0.11.8, Babraham Bioinformatics), trimmed using Trim Galore! (version 0.6.6, Babraham Bioinformatics).
Reads were mapped with Hisat2 (version 2.1.0) on the mm10 mouse genome using default parameters.
Read count was performed with SeqMonk (version 1.48.1, Babraham Bioinformatics).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including log2-transformed RPM values for each sample

source_name: Testis

extract_protocol:
FACS-sorted round spermatids were lysed in 2.5 μl of RLT plus buffer (Qiagen) supplemented with 0.06 μl SUPERase-In RNase inhibitor (Thermo Fisher).
The samples were directly processed according to the Smart-seq2 protocol with 15 cycles of PCR. The amplified cDNA (200 pg) was used for Tagmentation reaction using Nextera XT DNA Sample Preparation Kit (Illumina) with dual index primers from Nextera XT Index Kit v2 (Illumina) according to manufacturer’s instructions.

value: Testis

value: Germ cells

value: Round spermatid

tag: strain background

value: ICR


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse liver, biological replicate 2


title: Wfdc15aRST_Het2


title: CTCF ChIP-seq on embryonic 13.5 day mouse forebrain, biological replicate 1

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
bigwig file represents the signal track for fold change over control from each replicate. Peak files are in narrowPeak format. Replicated peaks are the set of peak calls from the pooled replicates that are either observed in both biological/technical replicates, or are observed in two pseudoreplicates (https://www.encodeproject.org/chip-seq/histone/).
Assembly: mm10

source_name: forebrain

value: forebrain

value: embryonic 13.5 day

value: CTCF (Cell Signaling, 3418, lot 3&4)


title: Blood_Recovery_late_Patient-a9

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

description: Gene expression data from blood of patient a9 (Recovery outcome) collected at day 21 (latetimepoint)

hyb_protocol: Transcriptomic data generation was performed by Gene Tech (Shanghai) using a Affymetrix GeneChip Human Gene 2.0 ST Array according to manufacturer instructions.

data_processing: All analyses used the R statistical programming environment (v3.03). Raw CEL intensity files underwent ‘Perfect Match’ probe set-level normalization including background correction using robust multiarray averaging (RMA), quantile normalization and summarization of gene expression using the median published algorithm (Irizarry et al., 2003). Probe set intensity distributions between arrays (before and after normalization) and MA plots of the log intensity ratio versus the average log intensity were assessed for excessive technical variability. The early phase sample from patient a20 was excluded from analysis as the interquartile range of the expression deviation was substantially outside that exhibited by all other samples. Unexpressed probe sets, exhibiting less fluorescence than background probes and w a PSDABG P value > 0.05 were removed from subsequent analyses.

source_name: Blood

extract_protocol: Peripheral blood (2 ml) was collected from each patient, preserved in PAXgene Blood RNA Tubes (QIAGEN) and stored at -80°C until use. Total RNA was extracted using a PAXgene Blood RNA Kit (QIAGEN).

value: Blood

tag: outcome

value: Recovery

tag: day

value: late


title: Blood_Death_late_Patient-a22

description: Gene expression data from blood of patient a22 (Death outcome) collected at day 22 (latetimepoint)

scan_protocol: Transcriptomic data generation was performed by Gene Tech (Shanghai) using a Affymetrix GeneChip Human Gene 2.0 ST Array according to manufacturer instructions.

value: Death


title: Blood_Death_early_Patient-a131

description: Gene expression data from blood of patient a131 (Death outcome) collected at day 12 (earlytimepoint)

label_protocol: Transcriptomic data generation was performed by Gene Tech (Shanghai) using a Affymetrix GeneChip Human Gene 2.0 ST Array according to manufacturer instructions.

value: early


title: Blood_Recovery_late_Patient-a20

description: Gene expression data from blood of patient a20 (Recovery outcome) collected at day 22 (latetimepoint)


title: Blood_Death_early_Patient-a33

description: Gene expression data from blood of patient a33 (Death outcome) collected at day 12 (earlytimepoint)


title: Blood_Recovery_early_Patient-a9

description: Gene expression data from blood of patient a9 (Recovery outcome) collected at day 14 (earlytimepoint)


title: Blood_Recovery_late_Patient-a134

description: Gene expression data from blood of patient a134 (Recovery outcome) collected at day 22 (latetimepoint)


title: CTCF ChIP-seq on embryonic 12.5 day mouse neural tube, biological replicate 2

source_name: neural tube

value: neural tube


title: CTCF ChIP-seq on embryonic 14.5 day mouse forebrain, technical replicate 1

value: embryonic 14.5 day


title: Blood_Death_late_Patient-a131

description: Gene expression data from blood of patient a131 (Death outcome) collected at day 22 (latetimepoint)


title: CTCF ChIP-seq on embryonic 12.5 day mouse neural tube, biological replicate 1


title: Blood_Recovery_early_Patient-a134

description: Gene expression data from blood of patient a134 (Recovery outcome) collected at day 10 (earlytimepoint)


title: Blood_Death_early_Patient-a118

description: Gene expression data from blood of patient a118 (Death outcome) collected at day 9 (earlytimepoint)


title: Blood_Death_early_Patient-a22

description: Gene expression data from blood of patient a22 (Death outcome) collected at day 17 (earlytimepoint)


title: Blood_Recovery_late_Patient-a73

description: Gene expression data from blood of patient a73 (Recovery outcome) collected at day 11 (latetimepoint)


title: Blood_Recovery_early_Patient-a73

description: Gene expression data from blood of patient a73 (Recovery outcome) collected at day 6 (earlytimepoint)


title: Wfdc15aRST_Het1


title: CTCF ChIP-seq on embryonic 12.5 day mouse limb, biological replicate 2


title: Blood_Death_late_Patient-a33

description: Gene expression data from blood of patient a33 (Death outcome) collected at day 21 (latetimepoint)


title: CTCF ChIP-seq on embryonic 13.5 day mouse forebrain, biological replicate 2


title: Wfdc15aRST_KO1


title: CTCF ChIP-seq on embryonic 12.5 day mouse forebrain, biological replicate 1


title: CTCF ChIP-seq on embryonic 12.5 day mouse craniofacial prominence, biological replicate 1

source_name: craniofacial prominence

value: craniofacial prominence


title: CTCF ChIP-seq on embryonic 12.5 day mouse midbrain, biological replicate 1

source_name: midbrain

value: midbrain

value: embryonic 12.5 day


title: Control ChIP-seq (input DNA) on embryonic 15.5 day mouse forebrain, biological replicate 2

description: The library was sequenced twice on different machines with both single and paired-end reads.

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Assembly: mm10

value: embryonic 15.5 day


title: CTCF ChIP-seq on embryonic 12.5 day mouse forebrain, biological replicate 2


title: CTCF ChIP-seq on embryonic 12.5 day mouse liver, technical replicate 2

value: liver


title: CTCF ChIP-seq on embryonic 12.5 day mouse midbrain, biological replicate 2


title: CTCF ChIP-seq on embryonic 12.5 day mouse liver, technical replicate 1


title: CTCF ChIP-seq on embryonic 15.5 day mouse forebrain, biological replicate 2


title: CTCF ChIP-seq on embryonic 15.5 day mouse forebrain, biological replicate 1


title: CTCF ChIP-seq on embryonic 12.5 day mouse limb, biological replicate 1

value: limb


title: CTCF ChIP-seq on embryonic 12.5 day mouse craniofacial prominence, biological replicate 2


title: Blood_Death_late_Patient-a118

description: Gene expression data from blood of patient a118 (Death outcome) collected at day 19 (latetimepoint)