title: DKO_Flcn-Tfe3_1

description:
DKO_2015_1
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep1
raw_counts_FLCN_TFE3_invivo.txt


title: KPK2_t0_rep1

status: Public on Mar 30 2023

type: SRA

city: New York

first: Dimitris

last: Karagiannis

state: NY

country: USA

institute: Columbia University

library_source: genomic

data_processing:
Computational analysis was done using MAGeCK. Briefly, the sequencing data were de-barcoded and the 20 bp sgRNA sequence was mapped to the reference sgRNA library without allowing for any mismatches.
The read counts were calculated for each individual sgRNA and normalized, and differential analysis was done between KP and KPK samples
Quality control, gene hit identification and graphs were generated using MAGeCKFlute.
Assembly: sgRNA library
Supplementary files format and content: sgRNA.raw.counts.txt: sgRNA raw counts for each sample
Supplementary files format and content: KP_KPK_mle_normalized3.sgrna_summary.txt; sgRNA - gene correspondence
Supplementary files format and content: KP_KPK_mle_normalized3.gene_summary.txt: Comparative analysis between KP and KPK cells in sgRNA enrichment for each gene

molecule: genomic DNA

organism: Mus musculus

growth_protocol: KP and KPK cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA from collected cell pellets were prepared with purelink mini kit (ThermoFisher) according to the manufacturer’s suggested protocol.
Libraries were generated by amplification from genomic DNA using a modified 2-step PCR   version of the protocol published by Doench et al. Briefly, we perform an initial “enrichment” PCR, whereby the integrated sgRNA cassettes are amplified from gDNA, followed by a second PCR to append Illumina sequencing adapters on the 5’- and 3’-ends of the amplicon, as well as a random nucleotide stagger and unique demultiplexing barcode on the 5’ end. Each “PCR1” reaction contains 25µL of Q5 High-Fidelity 2X Master Mix (NEB), 2.5µL of Nuc PCR#1 Fwd Primer (10µM), 2.5µL of Nuc PCR#1 Rev Primer (10µM), and 5µg of gDNA in 20µL of water (for a total volume of 50µL per reaction). The number of PCR1 reactions is scaled accordingly; therefore, we performed six PCR1 reactions per technical replicate, per time point (T0 or TF), and per condition. PCR1 amplicons were purified using the QIAquick PCR Purification Kit (Qiagen) and used as template for “PCR2” reactions. Each PCR2 reaction contains 25µL of Q5 High-Fidelity 2X Master Mix (NEB), 2.5µL of a unique Nuc PCR#2 Fwd Primer (10µM), 2.5µL of Nuc PCR#2 Rev Primer (10µM), and 300ng of PCR1 product in 20µL of water (for a total volume of 50µL per reaction). We performed two PCR2 reactions per PCR1 product.   PCR Program for PCR1 and PCR2: 1) 98°C x 30s; 2) 98°C x 10s; 3) 65°C x 30s; 4) 72°C x 30s; 5) Go to step 2 x 24 cycles; 6) 72°C x 2 min; 7) 4°C forever. Library amplicons were size-selected on a 2.5% agarose gel, purified using the QIAquick Gel Extraction Kit (Qiagen), and sequenced on an Illumina NextSeq500 instrument (75nt single end reads). Files resulting from 4 sequencing lanes were concatenated into a single file for each condition.

treatment_protocol: Derivatives of KP and KPK cells were generated by stable lentiviral transduction of Cas9 with blasticidin resistance (Addgene#52962). Cells were maintained with blasticidin selection throughout the experiment. Transduction of Cas9-expressing KP/KPK cells was performed at an MOI of approximately 0.2 by incubating cell suspension in lentiviral supernatant and centrifugation at 1500 rpm for 1.5 hours at room temperature before being returned to a humidified incubator. An initial population was infected to represent a 2500x representation of the epigenetic library; 36 hours post-transduction cells were resuspended and replated in 10 ug/mL puromycin and selected for another 48 hours. After complete puromycin selection cells were trypsinized, pooled, a cell sample representing time-0hr (t0) of the screen was reserved and stored at -20C. Each condition was performed in technical triplicate for the entire screen and maintained in 15 cm tissue culture dishes (Corning) with at least 2500x library representation maintained throughout all culture and library preparation steps. Population doublings for each cell line and condition were recorded and a sample was collected when a particular condition had reached 14 cumulative population doublings(t1) and stored at -20o C. At t1 cells were treated with DMSO as a control to other conditions that were not included in the final analysis. 3 biological replicates per condition are included.

tag: cell line

tag: cell type

value: Mouse LUAD

tag: genotype

tag: time

value: 0 doublings


title: IkBa clone A 330 repB

type: RNA

city: Manchester

first: Polly

last: Downton

address: Oxford Road

country: United Kingdom

institute: University of Manchester

scan_protocol: Samples were analysed using a custom codeset on the Nanostring nCounter analysis system (280fov).

data_processing: Data was processed in nSolver Analysis Software v4.0, with normalisation to five housekeeping genes and internal positive control probes.

molecule: total RNA

organism: Homo sapiens

source_name: IkBa clone A 330

growth_protocol: SK-N-AS neuroblastoma (Cat. No. 94092302) cells were obtained from the European Collection of Authenticated Cell Cultures (ECACC). Cells were cultured according to ECACC protocols.  Cells were cultured in Modified Eagle’s Medium supplemented with 10% foetal bovine serum (FBS) and 1% non-essential amino acids.

extract_protocol: Cells were seeded into 6-well plates (100000/well).  After treatments as described, cells were washed once with cold PBS then lysed.  Total RNA was isolated using the High Pure RNA isolation kit (Roche).  RNA concentration was determined using a Nanodrop ND-1000 spectrophotometer (Thermo).

treatment_protocol: Treatments used recombinant human TNF⍺ (10 ng/ml; Merck 654245) for indicated time.

value: SKNAS

value: IkBa clone A

tag: duration of tnfalpha treatment


title: IkBa clone A 430 repB

source_name: IkBa clone A 430


title: IkBa clone A 230 repB

source_name: IkBa clone A 230


title: DKO_Flcn-Tfe3_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
DKO_2015_4
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep4
raw_counts_FLCN_TFE3_invivo.txt

library_source: transcriptomic

data_processing:
Sequence reads were trimmed using Trim Galore software (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality end bases and then aligned on mm10 reference sequence using STAR.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts for each Sample.

source_name: mouse kidney sample

growth_protocol: All mice used were maintained in a C57BL/6 strain background.

extract_protocol:
RNA was quantified and mixed at 10ng/µl.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq 6000 (Illumina) with a read length of 100 bp.

treatment_protocol: RNA samples from mouse kidneys were extracted using RNeasy plus Mini kit (Qiagen) according to the manufacturer’s instructions.

tag: strain

tag: tissue

value: kidney

tag: age

value: postnatal day 2


title: DKO_Flcn-Tfe3_3

description:
DKO_2015_3
Transcriptome profile of mouse_DKO_Flcn-Tfe3_kidney, biological rep3
raw_counts_FLCN_TFE3_invivo.txt


title: Patient7_pre_BCG7 (ChIP-seq)

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for histone marks at p-value of 10-5. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac peaks were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files for visualization

source_name: Adult Human Peripheral Blood

growth_protocol: We performed a prospective cohort study (‘Tribute’) and isolated PBMCs collected before BCG therapy and at 8 time points during BCG therapy. Following PBMC isolation we further purified the monocytes using an isolation protocol with a ficoll gradient.

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated and 1ug of chromatin (~1 million cells) was incubated with 1µg of H3K27ac or H3K4me1 antibodies (Diagenode) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.

tag: individual

value: Monocyte

value: Exposed monocytes. Collected on the day of and before the 7th intravesical BCG instillation, approximately 6 weeks after 6th instillation (pre-BCG7).

tag: chip antibody

value: Rabbit anti-H3K4me3 Antibody (Cell Signaling Technology #9727)


title: Ctrl_Flcn-Tfe3_8

description:
CDM_CO5
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep8
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: KPK1_t1_rep3

value: 14 doublings


title: KPK1_t0_rep3


title: IkBa clone A 130 repB

source_name: IkBa clone A 130


title: Ctrl_Flcn-Tfe3_7

description:
CDM_CO4
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep7
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: Patient2_BCG9 (ChIP-seq)

value: Exposed monocytes. Collected on the day of the 9th intravesical BCG instillation (BCG9).


title: Ctrl_Flcn-Tfe3_5

description:
CDM_CO2
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep5
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: Ctrl_Flcn-Tfe3_6

description:
CDM_CO3
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep6
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: Patient2_pre_BCG10 (ChIP-seq)

value: Exposed monocytes. Collected on the day of and before the 10th intravesical BCG instillation, approximately 12 weeks after 9th instillation (pre-BCG10).


title: Ctrl_Flcn-Tfe3_4

description:
CDM_CO1
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep4
CDM_FLCN_TFE3_DKOp2_rawCounts.txt


title: Patient2_BCG6 (ChIP-seq)

value: Exposed monocytes. Collected on the day of the 6th intravesical BCG instillation (BCG6).


title: Patient2_pre_BCG7 (ChIP-seq)


title: KPK1_t0_rep2


title: KPK1_t1_rep2


title: KPK1_t1_rep1


title: IkBa clone A 430 repA


title: IkBa clone A 30 repB

source_name: IkBa clone A 30


title: IkBa clone A 0 repB

source_name: IkBa clone A 0


title: IkBa clone A 330 repA


title: Patient2_pre_BCG1 (ChIP-seq)

value: Baseline monocytes. Collected before the 1st intravesical BCG instillation (pre-BCG1).


title: IkBa clone A 230 repA


title: Patient1_pre_BCG10 (ChIP-seq)


title: KPK1_t0_rep1


title: KP2_t1_rep3


title: Ctrl_Flcn-Tfe3_2

description:
CO_2015_2
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep2
raw_counts_FLCN_TFE3_invivo.txt


title: Ctrl_Flcn-Tfe3_3

description:
CO_2015_3
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep3
raw_counts_FLCN_TFE3_invivo.txt


title: Patient1_BCG9 (ChIP-seq)


title: Ctrl_Flcn-Tfe3_1

description:
CO_2015_1
Transcriptome profile of control mouse_Ctrl_Flcn-Tfe3_kidney, biological rep1
raw_counts_FLCN_TFE3_invivo.txt


title: KP2_t0_rep3


title: KP2_t1_rep2


title: DKO_Flcn-Tfeb_4

description:
DKO_1921_4
Transcriptome profile of mouse DKO_Flcn-Tfeb_kidney, biological rep4


title: Patient1_pre_BCG7 (ChIP-seq)


title: Patient1_BCG6 (ChIP-seq)


title: DKO_Flcn-Tfeb_2

description:
DKO_1921_2
Transcriptome profile of mouse DKO_Flcn-Tfeb_kidney, biological rep2


title: KP2_t0_rep2


title: DKO_Flcn-Tfeb_1

description:
DKO_1921_1
Transcriptome profile of mouse DKO_Flcn-Tfeb_kidney, biological rep1


title: KP2_t0_rep1


title: IkBa clone B 430 repB

description: Exogenous spike test - dsRedXP

source_name: IkBa clone B 430

value: IkBa clone B


title: IkBa clone A 0 repA


title: IkBa clone B 330 repB

description: Exogenous spike test - dsRedXP

source_name: IkBa clone B 330


title: IkBa clone A 30 repA


title: Ctrl2_3

description:
CO_1921_3
Transcriptome profile of control mouse_Flcn-Tfeb_kidney, biological rep3


title: IkBa clone B 230 repB

description: Exogenous spike test - dsRedXP

source_name: IkBa clone B 230


title: H9_DE_IMP1-KO#2_rep2

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

country: China

institute: WuHan university

description:
F35-3
IMP1-KO_TPM.csv

data_processing:
Illumina bcl2fastq v2.20software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim_glore version 0.6.6, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.0.
Raw RNAseq reads were performed with FeatureCounts (V2.0.1) using gencode v29 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2. RIPseq peaks were analyzed by Macs2 callpeak (V2.1.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM for RNAseq
Supplementary_files_format_and_content: peak bed for RIPseq

source_name: differentiated IMP1-KO endoderm cells

growth_protocol: hPSCs were treated with IMEM-F12 as basal medium, supplemented with 0.2% BSA, 1% Penicillin-Streptomycin and 100ng/mL Activin A  for the three days.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: definitive endoderm cells


title: KP1_t1_rep3


title: H9_DE_IMP1-KO#2_rep1

description:
F35-1
IMP1-KO_TPM.csv


title: IkBa clone A 130 repA


title: IkBa clone B 130 repB

description: Exogenous spike test - dsRedXP

source_name: IkBa clone B 130


title: Ctrl2_2

description:
CO_1921_2
Transcriptome profile of control mouse_Flcn-Tfeb_kidney, biological rep2


title: KP1_t0_rep3


title: H9_DE_IMP1-KO#1_rep2

description:
F142-3
IMP1-KO_TPM.csv


title: H9_DE_IMP1-KO#1_rep1

description:
F142-1
IMP1-KO_TPM.csv


title: DKO_Flcn-Tfeb_3

description:
DKO_1921_3
Transcriptome profile of mouse DKO_Flcn-Tfeb_kidney, biological rep3


title: IkBa clone B 30 repB

source_name: IkBa clone B 30


title: IkBa clone B 0 repB

source_name: IkBa clone B 0


title: Ctrl2_1

description:
CO_1921_1
Transcriptome profile of control mouse_Flcn-Tfeb_kidney, biological rep1


title: H9_DE_rep2

description:
WT-3
IMP1-KO_TPM.csv

source_name: differentiated endoderm cells

value: WT


title: Patient1_pre_BCG1 (ChIP-seq)


title: FLCN_KO_5

description:
KO_1380_5
Transcriptome profile of mouse Flcn-KO_kidney, biological rep5

value: Flcn-KO


title: KP1_t1_rep2

value: Mouse LUAD


title: KP1_t0_rep2

value: 0 doublings


title: KP2_t1_rep1


title: IkBa clone B 430 repA

description: Exogenous spike test - dsRedXP

value: SKNAS


title: H9_DE_rep1

description:
WT-1
IMP1-KO_TPM.csv


title: FLCN_KO_4

description:
KO_1380_4
Transcriptome profile of mouse Flcn-KO_kidney, biological rep4

value: kidney


title: KP1_t1_rep1


title: PGP1_DE_CTD-2501M5.1-KO_rep3

description:
1D6-3
CTD-2501M5.1-KO_TPM.csv

source_name: differentiated CTD-2501M5.1-KO endoderm cells


title: FLCN_KO_3

description:
KO_1380_3
Transcriptome profile of mouse Flcn-KO_kidney, biological rep3

value: postnatal day 2


title: FLCN_KO_2

description:
KO_1380_2
Transcriptome profile of mouse Flcn-KO_kidney, biological rep2


title: KP1_t0_rep1


title: PGP1_DE_CTD-2501M5.1-KO_rep1

description:
1D6-1
CTD-2501M5.1-KO_TPM.csv


title: 36B

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

data_processing:
6-bp long UMI tags followed with “TATA” spacer were extracted from reads using umi_tools v1.0.1 (Smith et al., 2017) command “extract” and pattern of sequence define as “^(?P<umi_1>.{6})(?P<discard_1>TATA){e<=1}”. Reads without spacer were removed.
Low quality reads and adaptors were removed using TrimmomaticSE v0.36 (Bolger et al., 2014) with parameters “ILLUMINACLIP:Lexogen_quantseq.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Ribosomal and mitochondrial reads were filtered out using sortmerna v2.1b (Kopylova et al., 2012).
BAM files with aligned reads were generated using STAR v2.7.3a (Dobin et al., 2013) with reference Mus musculus genome version GRCm38.
The reads in BAM file were indexed using samtools v1.7 (Li et al., 2009; Li et al., 2011) and deduplicated based on the UMI sequence using umi_tools dedup.
Final count tables were generated using python script htseq-count v0.11.4 (Anders et al., 2013) with annotation genecode.vM8.gtf and parameter “-m union”.
Differential expression analysis was performed using R package DEseq2 ver. 1.30.1 (Love et al., 2014). Counts were normalized using command DESeq using count matrix limited to data of compared samples.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and coma-delimited text file contain normalized number of reads for each Sample

source_name: brain cortex

growth_protocol: Mice were housed under standard conditions on a 12 h light/12 h dark cycle with food and water ad libitum.

extract_protocol:
Brains were divided into 1mm-thick slices using brain matrix and razor blades that were kept chilled with dry ice. Peri-infarct regions of primary motor and somatosensory cortex, homotopic regions in the contralesional cortex or corresponding uninjured cortex in naïve animals were dissected from the resulting slices using 1 mm ID tissue micropuncher (Reusable Rapid Punch kit, WPI, Hitchin, UK) in a setup that was continuously chilled with dry ice and kept at -80°C until use. Tissue micropunches were lysed with Qiazol reagent (Qiagen, Hilden, Germany) and homogenized by passing the lysate through microsyringe fitted with 23G needle 10 times followed by repeating the above procedure using a 27G needle. Total RNA was extracted with RNAeasy Mini Lipid kit (Qiagen), including on-column DNAase I digestion step, according to manufacturer’s recommendations.
The RNA-Seq libraries were prepared from 100 ng of Total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

treatment_protocol: Mice were breifly anesthetised with isolfurane and decapitated. Brians were quickly (within 2-3 min) isolated, flash frozen in isopentane cooled by dry ice and stored iat -80°C until dissection.

tag: treatment

tag: region

value: contralesional

tag: time post stroke

tag: biological replicate


title: FLCN_KO_1

description:
KO_1380_1
Transcriptome profile of mouse Flcn-KO_kidney, biological rep1


title: 35B


title: PGP1_DE_rep3

description:
PGP1-3
CTD-2501M5.1-KO_TPM.csv


title: Ctrl1_5

description:
CO_1380_5
Transcriptome profile of control mouse_Flcn_kidney, biological rep5


title: PGP1_DE_rep2

description:
PGP1-2
CTD-2501M5.1-KO_TPM.csv


title: 34B

value: PBS


title: Ctrl1_4

description:
CO_1380_4
Transcriptome profile of control mouse_Flcn_kidney, biological rep4


title: IkBa clone B 30 repA

description: Exogenous spike test - dsRedXP


title: PGP1_DE_rep1

description:
PGP1-1
CTD-2501M5.1-KO_TPM.csv


title: IkBa clone B 0 repA

description: Exogenous spike test - dsRedXP


title: Ctrl1_3

description:
CO_1380_3
Transcriptome profile of control mouse_Flcn_kidney, biological rep3


title: IkBa clone B 130 repA

description: Exogenous spike test - dsRedXP


title: IkBa clone B p65 430 repB

source_name: IkBa clone B p65 430

value: IkBa clone B p65


title: 32B


title: elfii_DSM9442_EXP_20MPa_batch02_repE1

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

data_processing:
In the preprocessing step, base-quality of raw and trimmed fastq files were analyzed with 'fastqc 0.11.5'.
Sequences were trimmed with 'TrimGalore 0.4.5' to remove low-quality bases (phred score <20) and eventual sequencing adapters before alignment to corresponding reference genome (p.elfii: GCF_000504085.1_ASM50408v1, p.lettingae: GCF_000017865.1_ASM1786v1) with 'STAR 2.5.3a' ('alignMatesGapMax'=10000, and disabling splicing alignment by setting 'alignSJoverhangMin'=999 and 'alignIntronMax'=1).
Post-alignment statistics were computed with 'RSeQC 2.6.4' 'preseq 2.0' and 'R 3.4.4' package 'dupradar'.
A summary of read counts for annotations categories was computed with the 'featurecount' from 'subread 1.6.0'.
Assembly: Pseudothermotoga lettingae:ASM1786v1(GCF_000017865.1), Pseudothermotoga elfii:ASM50408v1(GCF_000504085.1)
Supplementary files format and content: Text files (txt) contain gene counts computed by ‘featurecount’

molecule: polyA RNA

organism: Pseudothermotoga elfii DSM 9442 = NBRC 107921

source_name: Cultured bacteria

extract_protocol:
RNAs were prepared using the Maxwell 16 LEV samples kit (Promega) and ribosomal RNAs were depleted using the Illumina Ribo-zero Plus rRNA depletion kit (Illumina, San Diego, CA, USA)
The sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA). Sequencing libraries were validated using a DNA Chip on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA).
The sequencing libraries were multiplexed and clustered on six lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 2500 instrument according to manufacturer’s instructions. The multiplexed libraries were sequenced using paired-end 150 cycle chemistry for the HiSeq 2500 (Illumina). Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq 2500 instrument.

value: Cultured bacteria

tag: growth phase

value: exponential

tag: growth pressure


title: PGP1_DE_CTD-2501M5.1-KO_rep2

description:
1D6-2
CTD-2501M5.1-KO_TPM.csv


title: IkBa clone B 330 repA

description: Exogenous spike test - dsRedXP


title: Ctrl1_2

description:
CO_1380_2
Transcriptome profile of control mouse_Flcn_kidney, biological rep2

source_name: mouse kidney sample


title: IkBa clone B p65 330 repB

source_name: IkBa clone B p65 330


title: elfii_DSM9442_EXP_20MPa_batch02_repD1


title: IkBa clone B 230 repA

description: Exogenous spike test - dsRedXP


title: 25B


title: IkBa clone B p65 230 repB

source_name: IkBa clone B p65 230


title: 20B


title: IkBa clone B p65 130 repB

source_name: IkBa clone B p65 130


title: elfii_DSM9442_EXP_20MPa_batch02_repC1


title: 19B


title: elfii_DSM9442_EXP_20MPa_batch02_repB1


title: 33B


title: IkBa clone B p65 30 repB

source_name: IkBa clone B p65 30


title: 8B

value: no


title: IkBa clone B p65 0 repB

source_name: IkBa clone B p65 0


title: elfii_DSM9442_EXP_20MPa_batch02_repA1


title: Kidney, KO, 1

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were build index by hisat2, and masked for low-complexity or low-quality sequence
Mapped to mm9 whole genome using hisat2 and  exported StringTie readable format files
Expression values for all genes in each sample (FPKM) were calculated by StringTie
Differentially expressed gene between the paired groups were analyzed by using DEGseq
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from each tissue sample using Trizol method
RNA libraries were prepared for sequencing using standard illumina protocls

value: Kidney

value: 6-8 weeks

value: cisplatin (CP)

tag: disease state

value: CP-induced AKI model


title: 7B


title: Kidney, KO, 2


title: Kidney, KO, 4


title: elfii_DSM9442_EXP_0.1MPa_batch02_repE1


title: Kidney, WT, 3

value: WT


title: 6B


title: Kidney, WT, 2


title: Ctrl1_1

description:
CO_1380_1
Transcriptome profile of control mouse_Flcn_kidney, biological rep1


title: elfii_DSM9442_EXP_0.1MPa_batch02_repB1


title: elfii_DSM9442_EXP_0.1MPa_batch02_repD1


title: Kidney, WT, 1


title: IkBa clone B p65 430 repA

tag: cell line


title: elfii_DSM9442_EXP_0.1MPa_batch02_repA1

tag: cell type


title: IkBa clone B p65 330 repA

tag: genotype


title: 4B

value: intact

value: x


title: 5B


title: IkBa clone B p65 230 repA


title: IkBa clone B p65 30 repA


title: elfii_DSM9442_EXP_40MPa_batch01_rep5A


title: IkBa clone B p65 130 repA


title: 3B


title: 2B


title: IkBa clone B p65 0 repA


title: SVNI+GZ-161_020

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: Mouse: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain (perfused)

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

tag: infection

value: SVNI (15pfu/mice, ip)

value: brain


title: 1B


title: elfii_DSM9442_EXP_40MPa_batch01_rep4A


title: elfii_DSM9442_EXP_40MPa_batch01_rep3A


title: SVNI+GZ-161_019


title: elfii_DSM9442_EXP_40MPa_batch01_rep2A


title: 36A

value: ipsilesional


title: WT 330 repB

value: SKNAS

tag: duration of tnfalpha treatment


title: WT 230 repB


title: SVNI_017

tag: strain

value: untreated


title: SVNI_016

tag: tissue


title: 35A


title: elfii_DSM9442_EXP_40MPa_batch01_rep1A


title: 34A

value: PBS


title: elfii_DSM9442_EXP_30MPa_batch01_rep5AB


title: elfii_DSM9442_EXP_30MPa_batch01_rep4AB


title: SVNI_015


title: SVNI+GZ-161_028


title: WT 130 repB


title: WT 30 repB

source_name: WT 30


title: 33A


title: SVNI+GZ-161_021


title: elfii_DSM9442_EXP_30MPa_batch01_rep3AB


title: SVNI_011


title: 32A


title: SVNI_010


title: WT 0 repB

source_name: WT 0


title: WT 430 repB


title: 25A


title: GZ-161_008

value: uninfected


title: 20A


title: elfii_DSM9442_EXP_30MPa_batch01_rep1AB

value: Cultured bacteria


title: WT 330 repA


title: WT 430 repA


title: elfii_DSM9442_EXP_0.1MPa_batch01_rep4B

value: exponential


title: 19A


title: GZ-161_006


title: 8A

value: no


title: elfii_DSM9442_EXP_0.1MPa_batch01_rep3A


title: Control_003


title: 6A


title: Control_002


title: 7A


title: elfii_DSM9442_EXP_0.1MPa_batch01_rep1A


title: elfii_DSM9442_EXP_0.1MPa_batch01_rep2B


title: WT 130 repA


title: WT 0 repA


title: 5A


title: elfii_DSM9442_EXP_30MPa_batch01_rep2AB


title: GZ-161_007


title: EV, replicate 1, scRNAseq

city: Guangzhou

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

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 (v3.1.0) (http://support.10xgenomics.com/single-cell/software/overview/welcome) provided by 10X Genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Electrophorus voltai

source_name: main electric organ

extract_protocol:
The muscle samples from the main EO were prepared to single-cell suspensions (living cell rate > 90%) with the mixture of collagenase and Dispase II. Cell viability and concentration were evaluated using trypan blue dye (Invitrogen) with a Countess® II Automated Cell Counter. Cell concentration was adjusted to 1000-2000 cells per µL.
Single cells were captured in droplet emulsions using a 10X Genomics GemCode Single-Cell Instrument, and the scRNA-seq library was constructed as the 10X Genomics protocol using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1.

value: muscle cells

value: main electric organ


title: WT 230 repA


title: Klrg1neg_MTRhigh:Klrg1neg_MTRhigh_1

status: Public on Mar 29 2023

city: San Diego

first: Thomas

last: Riffelmacher

state: California

address: Athena Circle drive

institute: La Jolla Institute for Immunology

data_processing:
The single-end were then aligned to the mouse reference genome using TopHat (v 1.4.1). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and read counts to each genomic feature were obtained with the Ht-Seq-count program (v 0.6.0) and imported to R/Bioconductor package DESeq2. P-values for differential expression were calculated using binomial test adjusted for multiple test correction with threshold adjusted P-value <0.1 and the fold change >1.5.
Assembly: mouse reference genome using TopHat (v 1.4.1).
Supplementary files format and content: The DE seq analysis including all raw data values for all samples is included in the .xlsx excel file labelled: Day40 bullk-seq-MAIT-subset-DESeqandRaw.xlsx

source_name: mouse lung infected BRD509 day 40 MAIT

extract_protocol:
Bulk MAIT cells were sorted by flow cytometry into 500 μL of Trizol LS (Thermo Fisher). RNA extraction, reverse transcription, cDNA amplification, fragmentation, additional PCR amplification, final library purification, and quality control were performed as previously described in Riffelmacher et al, Mucosal Immunology, 2018. Sequencing was performed using the HiSeq2500 sequencer (Illumina).
final library purification, and quality control were performed as previously described in Riffelmacher et al, Mucosal Immunology, 2018

treatment_protocol: BRD509 1x10e6 retropharyngeal

value: lung

value: MAIT

value: BRD509 infection


title: Klrg1neg_MTRhigh:Klrg1neg_MTRhigh_3

value: WT


title: Klrg1neg_MTRhigh:Klrg1neg_MTRhigh_2


title: Klrg1neg_MTRlow:Klrg1neg_MTRlow_3


title: Klrg1pos_MTRlow:Klrg1pos_MTRlow_1


title: Klrg1pos_MTRlow:Klrg1pos_MTRlow_2


title: Klrg1neg_MTRlow:Klrg1neg_MTRlow_1


title: unifected_MAIT:Uninfected_MAIT

source_name: mouse lung uninfected MAIT


title: Jurkat GFP-luc Donor 63

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD7
21ID00923_RNA1047

data_processing:
Trimmomatic was used to eliminate the remnants from the adaptors and discard those low quality sequences
Reads were mapped (STAR) and quantified on the transcriptome using RSEM
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include RSEM expected counts for each sample and gene

source_name: Peripheral blood

growth_protocol: RPMI 10%FBS

extract_protocol:
Sorted Jurkat-GFP cells that remained after overnight exposition to NKG2D-CAR T cells were washed in PBS and pelleted in RLT lysis buffer supplemented with 1:1000 β-mercaptoethanol. RNA isolation and sequencing was carried out as our group previously reported (Fernández A et al. Cancers, 2021).
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina ́s recommendations. Poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base to the 3’ end and then ligation of the adapters. Finally, the products are purified and enriched with PCR to create the indexed final double stranded cDNA library.

treatment_protocol: Jurkat GFP-luc cells were  co-cultured with NKG2D-CAR T cells or left untreated for 16h, sorted and used to perform transcriptome analysis

value: Peripheral blood

value: Jurkat

value: T lymphoblasts

tag: karyotype

value: pseudodiploid

value: Treated with NKG2D CAR T cells


title: Jurkat GFP-luc Donor 60

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD6
21ID00922_RNA1046


title: Jurkat GFP-luc biol rep 2

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD4
21ID00920_RNA1044B

value: Untreated


title: Jurkat GFP-luc Donor 51

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD5
21ID00921_RNA1045


title: Klrg1neg_MTRlow:Klrg1neg_MTRlow_2


title: Jurkat GFP-luc biol rep 1

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD3
21ID00919_RNA1044A


title: Control_001

value: untreated

value: brain


title: WT 30 repA

value: SKNAS


title: NEMO_NS

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
RNA-sequencing was performed on the Illumina NovaSeq platform, with a read length of 100 bp and a read depth of 40 million reads.
Quality trimming is performed to remove adapter sequences and polyA tails.  Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Read count extraction and normalization were performed using edger
Assembly: hg38
Supplementary files format and content: tab-delimited text files include cpm values for each Sample

source_name: mesenchymal stem Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblastcells

extract_protocol:
RNA was extracted from primary fibroblasts with the Quick-RNA MicroPre Kit (#R1051, Zymo Research).
RNA-Seq libraries were prepared with the Illumina RiboZero TruSeq Stranded Total RNA Library Prep Kit (Illumina)

value: NEMO

value: NS


title: NEMO_HSV

value: mesenchymal stem Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblast  Fibroblastcells

value: HSV


title: RIPK3_NS


title: RIPK3_HSV


title: TLR3_HSV


title: IFNAR1_NS


title: C288_NS


title: C288_HSV


title: C286_NS


title: C286_HSV


title: IFNAR1_HSV


title: Control1_HSV


title: Control1_NS


title: TLR3_NS


title: CONV-RT_10Gy_Hypoxia_0.5%O2_Rep3

city: Stanford

first: Richard

middle: L

last: Frock

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg38 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg38
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Supplementary files format and content: The processed data files are the data files used for analysis.
Library strategy: JoinT-seq

growth_protocol: HEK293T cells were cultured at 37°C, 5% CO2 using DMEM supplemented with glutamine, 10% FCS and 0.5% penicillin/streptomycin

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina Miseq or Novaseq sequencing

treatment_protocol: HEK293T cells were cultured in Normoxia/Air (21% O2), Physioxia (4%O2), Physiological hypoxia (2% O2), or Pathological hypoxia (0.5% O2) and optionally exposed to electron beam ionizing radiation at CONV (0.06-0.21 Gy/sec) or FLASH (100-1,000Gy/sec) dose rates.

tag: nuclease delivery

tag: transfection protocol

value: PEI; 48 hour culture post transfection

tag: oxygen tension (o2)

value: 0.5% O2; Hypoxia

tag: radiation treatment (rt) type

value: CONV-RT

tag: dose

tag: radiation facility

value: LINAC; Stanford

tag: treatment protocol

value: Trypsinize cells 24 hour post transfection at 0.5% O2, radiation exposure, replate cells for another 24 hours and then collect gDNA

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract_protocol (dna fragmentation)

value: Sonication

tag: illumina sequencing

value: Illumina NovaSeq 6000 System; 150PE

tag: figure displaying results for this library

value: Fig 4; Sup. Fig. 3-5

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

value: JoinT-seq


title: FLASH-RT_10Gy_Hypoxia_0.5%O2_Rep2

tag: cell line

tag: genotype

value: WT

value: FLASH-RT


title: FLASH-RT_10Gy_Hypoxia_0.5%O2_Rep1


title: FLASH-RT_10Gy_Hypoxia_0.5%O2_Rep3


title: HA LifeAct Dendra2 2

city: Boulder

first: Alexandra

last: Whiteley

state: CO

address: 596 UCB

institute: University of Colorado, Boulder

data_processing:
.fastq files from Illumina sequencing were mapped to human genome using STAR 2.7.3.
.bam files were indexed and sorted using Samtools 1.8 and counts generated with featureCounts software.
Assembly: GRCh38.p13
Supplementary files format and content: .tsv file including matrix of featureCounts for all samples

extract_protocol:
RNA was extracted using RNEasy kit with on-column DNA digestion.
RNA libraries for RNA-Seq were prepared using Tecan Universal Plus mRNA-Seq library preparation kit according to manufacturer's instructions.

tag: treatment

value: LifeAct-Dendra2 transfection


title: NC PEG10 1

value: PEG10 NC transfection


title: RF1 3

value: PEG10 gag transfection


title: RF1 2


title: NC PEG10 3


title: HA LifeAct Dendra2 3


title: FL PEG10 1

value: PEG10 gag-pol transfection


title: HA LifeAct Dendra2 1


title: NC PEG10 2


title: RF1 1


title: FL PEG10 2


title: FL PEG10 3


title: FLASH-RT_5Gy_Hypoxia_0.5%O2_Rep3


title: CONV-RT_5Gy_Hypoxia_0.5%O2_Rep1


title: Control_NoRT_Hypoxia_0.5%O2_Rep6

value: NoRT

value: Trypsinize cells 24 hour post transfection at 0.5% O2, NO radiation exposure, replate cells for another 24 hours and then collect gDNA


title: FLASH-RT_10Gy_Normoxia_21%O2_Rep3

value: PEI; 48 hour culture post transfection

value: 21% O2; Normoxia

value: Trypsinize cells 24 hour post transfection, radiation exposure, replate cells for another 24 hours and then collect gDNA


title: Control_NoRT_Hypoxia_0.5%O2_Rep4

value: 0.5% O2; Hypoxia


title: FLASH-RT_10Gy_Normoxia_21%O2_Rep2

value: LINAC; Stanford

value: RAG1 (saCas9:RAG1.1 gRNA)


title: CONV-RT_10Gy_Hypoxia_0.5%O2_Rep2

value: CONV-RT

value: Trypsinize cells 24 hour post transfection at 0.5% O2, radiation exposure, replate cells for another 24 hours and then collect gDNA

value: Sonication

value: Illumina NovaSeq 6000 System; 150PE


title: CONV-RT_10Gy_Hypoxia_0.5%O2_Rep1

value: WT

value: Fig 4; Sup. Fig. 3-5

value: JoinT-seq


title: FLASH-RT_5Gy_Hypoxia_0.5%O2_Rep2

value: FLASH-RT


title: CONV-RT_5Gy_Hypoxia_0.5%O2_Rep2


title: Control_NoRT_Hypoxia_0.5%O2_Rep5


title: FLASH-RT_10Gy_Normoxia_21%O2_Rep1


title: CONV-RT_5Gy_Hypoxia_0.5%O2_Rep3


title: CONV-RT_10Gy_Normoxia_21%O2_Rep2 (PGB197_RLF_N009)


title: FLASH-RT_5Gy_Normoxia_21%O2_Rep3


title: FLASH-RT_5Gy_Hypoxia_0.5%O2_Rep1


title: CONV-RT_10Gy_Normoxia_21%O2_Rep3 (PGB217_RLF_N009)


title: CONV-RT_10Gy_Normoxia_21%O2_Rep1 (PGB166_RLF_N007)


title: FLASH-RT_5Gy_Normoxia_21%O2_Rep1


title: CONV-RT_5Gy_Normoxia_21%O2_Rep1


title: CONV-RT_5Gy_Normoxia_21%O2_Rep3


title: CONV-RT_20Gy_Hypoxia_0.5%O2_Rep1


title: FLASH-RT_20Gy_Hypoxia_0.5%O2_Rep3


title: CONV-RT_20Gy_Hypoxia_0.5%O2_Rep2


title: Control_NoRT_Normoxia_21%O2_Rep6

value: Trypsinize cells 24 hour post transfection, NO radiation exposure, replate cells for another 24 hours and then collect gDNA


title: Control_NoRT_Normoxia_21%O2_Rep4

value: NoRT


title: FLASH-RT_20Gy_Hypoxia_0.5%O2_Rep1


title: FLASH-RT_2Gy_Hypoxia_0.5%O2_Rep3


title: CONV-RT_5Gy_Normoxia_21%O2_Rep2


title: FLASH-RT_2Gy_Hypoxia_0.5%O2_Rep2


title: FLASH-RT_2Gy_Hypoxia_0.5%O2_Rep1


title: FLASH-RT_20Gy_Hypoxia_0.5%O2_Rep2


title: CONV-RT_2Gy_Hypoxia_0.5%O2_Rep3


title: CONV-RT_2Gy_Hypoxia_0.5%O2_Rep2


title: CONV-RT_2Gy_Hypoxia_0.5%O2_Rep1


title: Control_NoRT_Hypoxia_0.5%O2_Rep2

value: Trypsinize cells 24 hour post transfection at 0.5% O2, NO radiation exposure, replate cells for another 24 hours and then collect gDNA


title: Control_NoRT_Hypoxia_0.5%O2_Rep3

value: PEI; 48 hour culture post transfection


title: Control_NoRT_Hypoxia_0.5%O2_Rep1


title: FLASH-RT_20Gy_Normoxia_21%O2_Rep3

value: 21% O2; Normoxia


title: FLASH-RT_5Gy_Normoxia_21%O2_Rep2

value: Trypsinize cells 24 hour post transfection, radiation exposure, replate cells for another 24 hours and then collect gDNA


title: CONV-RT_20Gy_Hypoxia_0.5%O2_Rep3

value: 0.5% O2; Hypoxia


title: Control_NoRT_Normoxia_21%O2_Rep5


title: FLASH-RT_20Gy_Normoxia_21%O2_Rep1

value: LINAC; Stanford


title: CONV-RT_20Gy_Normoxia_21%O2_Rep3

value: RAG1 (saCas9:RAG1.1 gRNA)


title: FLASH-RT_2Gy_Normoxia_21%O2_Rep3


title: CONV-RT_20Gy_Normoxia_21%O2_Rep1

value: CONV-RT


title: FLASH-RT_2Gy_Normoxia_21%O2_Rep2


title: CONV-RT_20Gy_Normoxia_21%O2_Rep2


title: CONV-RT_2Gy_Normoxia_21%O2_Rep3


title: FLASH-RT_2Gy_Normoxia_21%O2_Rep1


title: CONV-RT_2Gy_Normoxia_21%O2_Rep1


title: Hypoxia_2%O2_NoRT_Rep1

value: 2% O2; Hypoxia

value: 48 hours Hypoxia and then collect gDNA

value: Fig 2; Sup. Fig. 2


title: Hypoxia_2%O2_NoRT_Rep2

value: WT

value: Sonication

value: Illumina NovaSeq 6000 System; 150PE


title: Control_NoRT_Normoxia_21%O2_Rep3 (PGB224_RLF_N009)

value: Fig 4; Sup. Fig. 3-5

value: JoinT-seq


title: Hypoxia_0.5%O2_NoRT_Rep3

value: NoRT


title: Hypoxia_0.5%O2_NoRT_Rep1


title: Control_Nomoxia_21%O2_NoRT_Rep2

value: 48 hours Normoxia and then collect gDNA


title: Control_NoRT_Normoxia_21%O2_Rep2 (PGB204_RLF_N009)

value: PEI; 48 hour culture post transfection

value: Trypsinize cells 24 hour post transfection, NO radiation exposure, replate cells for another 24 hours and then collect gDNA


title: Hypoxia_2%O2_NoRT_Rep3


title: Hypoxia_0.5%O2_NoRT_Rep2


title: Control_Nomoxia_21%O2_NoRT_Rep3

value: 21% O2; Normoxia


title: CONV-RT_10Gy_Normoxia_21%O2_Rep1 (PGB258_RLF_N010)

value: Trypsinize cells 24 hour post transfection, radiation exposure, replate cells for another 24 hours and then collect gDNA

value: Fig 1; Sup. Fig. 1


title: FLASH-RT_20Gy_Normoxia_21%O2_Rep2

value: FLASH-RT

value: LINAC; Stanford

value: RAG1 (saCas9:RAG1.1 gRNA)


title: CONV-RT_10Gy_Normoxia_21%O2_Rep3 (PGB262_RLF_N010)

value: CONV-RT


title: Control_NoRT_Normoxia_21%O2_Rep1 (PGB175_RLF_N008)


title: CONV-RT_10Gy_Normoxia_21%O2_Rep2 (PGB260_RLF_N010)


title: Control_NoRT_Normoxia_21%O2_Rep1 (PGB257_RLF_N010)


title: Control_NoRT_Normoxia_21%O2_Rep2 (PGB259_RLF_N010)


title: Control_Nomoxia_21%O2_NoRT_Rep1

value: Fig 2; Sup. Fig. 2


title: Prom_Input, CTCF, BioRep1

first: Liang-Fu

last: Chen

state: CA

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

department: Chemical and Systems Biology

data_processing:
Raw reads were aligned to the human genome (hg19) using the bowtie2 (version 2.4.1). bigWig files for visualization were generated using deeptools v3.5.0 with the normalization setting : -- normalizeUsing RPGC.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: H9 hESC

growth_protocol: hESCs were differentiated to human cranial neural crest cells (CNCCs) as described previously (Long et al., 2020; Prescott et al., 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, which were disaggregated using collagenase IV and gentle pipetting. Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm Petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, cranial neural crest cells (CNCCs) emerged from neural spheres that had attached to the Petri dish. After 11 days, CNCCs were passaged onto fibronectin-coated 6-well plates using accutase and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini, 700-104P). After 2-3 days, CNCCs were split 1:3 and the following day cells were fed with neural crest long-term media. Long term media: neural crest maintenance media plus 50pg/ml BMP2 (PeproTech, 120-02) and 3uM CHIR-99021 (Selleck Chemicals, S2924). CNCCs were then passaged twice to passage 4 and processed for various assays.

extract_protocol:
5-15 million cells were cross-linked per ChIP experiment in 2mL PBS per 6-well with 1% methanol-free formaldehyde for 5-10 min and quenched with a final concentration of 0.125M glycine for 5 min with nutation. Cross-linked cells were washed with PBS, scraped and pelleted by centrifugation, flash-frozen in liquid nitrogen and stored at -80°C. Samples were defrosted on ice and resuspended in 5mL LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, with 1X cOmplete Protease Inhibitor Cocktail and 1 mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 5mL LB2 (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with 1X cOmplete Protease Inhibitor Cocktail and 1mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 1mL LB3 per 10 million cells (up to 1 mL per ChIP). Samples were sonicated in 1mL AFA tubes for 5 min on E220 evolution Covaris with settings Peak power = 140, Duty Factor = 10, Cycles per burst = 200 to achieve chromatin sized approximately 500-2000bp. Following sonication, samples were re-combined (if aliquoted for sonication), Triton X-100 was added to the fragmented chromatin to a final concentration of 1%, and the chromatin divided for input (1%–2%) and ChIP samples.
Samples were quantified by Qubit dsDNA HS assay kit, and 30 ng of ChIP DNA was used for library preparation with end repair, A-tailing, and adaptor ligation (NEB). Following USER enzyme treatment, libraries were cleaned up with one round of single-side AMPure XP bead clean-up. Libraries were then amplified to add indices using NEBNext HiFi 2X PCR mix and NEBNext Multiplex Oligos for Illumina kit (NEB, E7335S) with 9 cycles (as determined by qPCR. ChIP libraries were purified by two rounds of double-sided AMPure XP bead clean-up to deplete adaptors. Library concentration and quality within ChIP or input groups was assessed by Qubit dsDNA HS assay kit and used to pool within ChIP or input groups.

value: H9 hESC

tag: cell type

value: hESC-derived P4 CNCC

value: SSEProm CTCF site deletion

tag: chip antibody


title: Prom_Input, CTCF, BioRep2


title: Control_NoRT_Normoxia_21%O2_Rep3 (PGB261_RLF_N010)

value: WT

tag: nuclease delivery

tag: transfection protocol

value: Sonication

value: Illumina NovaSeq 6000 System; 150PE


title: CONV-RT_2Gy_Normoxia_21%O2_Rep2

tag: oxygen tension (o2)

tag: radiation treatment (rt) type

value: Fig 4; Sup. Fig. 3-5

value: JoinT-seq


title: E135_Input, CTCF, BioRep1

value: SSE1.35 CTCF site deletion


title: Control, Input, BioRep1

value: Wildtype


title: Control, Input, BioRep2

value: non-targeting gRNA


title: E135_RAD21, CTCF, BioRep2

value: RAD21 (Abcam, #ab992)


title: Prom_RAD21, CTCF, BioRep1


title: Prom_RAD21, CTCF, BioRep2


title: E135_RAD21, CTCF, BioRep1


title: Control, RAD21, BioRep2


title: Prom_CTCFdel, CTCF, BioRep1

value: CTCF (Cell Signalling, # 2899)


title: Prom_CTCFdel, CTCF, BioRep2


title: E135_CTCFdel, CTCF, BioRep1


title: OVCAR3_THZ531_rep_2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: OVCAR3 cells treated with THZ531 200nM for 6hr replicate 2

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: hg38
Supplementary files format and content: Deseq2_normalized_gene_expression_with_annotations.txt
Supplementary files format and content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2021_3 were also provide

growth_protocol: OVCAR3 cells were cultured in RPMI 1640 (Euroclone) supplemented with 10% fetal bovine serum (FBS) (Gibco), 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted and DNAse treated using RNeasy Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology)  according to the manufacturer's instructions.

treatment_protocol: OVCAR3 cells were treated with DMSO or THZ1 (200nM) for 6hr.

value: human high-grade serous ovarian adenocarcinoma cell line

tag: tumor


title: OVCAR3_THZ531_rep_3

description: OVCAR3 cells treated with THZ531 200nM for 6hr replicate 3

value: high-grade serous ovarian adenocarcinoma


title: OVCAR3_DMSO_rep_3

description: OVCAR3 cells  treated with DMSO for 6hr replicate 3

value: OVCAR3 cells  treated with DMSO for 6hr


title: E135_Input, CTCF, BioRep2


title: OVCAR3_DMSO_rep_2

description: OVCAR3 cells  treated with DMSO for 6hr replicate 2


title: Control, CTCF, BioRep1


title: OVCAR3_THZ531_rep_1

description: OVCAR3 cells treated with THZ531 200nM for 6hr replicate 1


title: PBMC_perf_10X

first: Stuart

last: EDELSTEIN

state: Île-de-France

address: 29 rue du Faubourg Saint Jacques, Pépinière Paris Santé Cochin

institute: Scipio bioscience

description: Scipio bioscience. All provided R1 and R2 FASTQ files are already demultiplexed by sample index.

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools based on the first 100 millions input raw reads of the R1 FASTQ file of the sample.
Raw read downsampling was perfomed for each sample by randomly subsampling raw reads from the FASTQ files such that the mean number of raw reads belonging to cell-associated barcodes was 20,000.
The provided processed data is composed of one count matrix per sample, computed after raw read downsampling, such that for each sample the same sequencing depth is simulated at 20,000 mean number of raw reads per cell.
Data post-processing (filtering, normalization, HVG, PCA, 2D embedding, clustering, DGE) was performed using Seurat and automated cell annotation was performed using SingleR algorithm and the reference dataset MonacoImmuneData.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38).  Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A;  Species: Homo_sapiens;  Genome Source: ensembl;  Genome Version: GRCh38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/;  Annotation Source: ensembl;  Annotation Version: 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: Blood

extract_protocol:
scRNA was extracted from 10,000 human PBMCs. A frozen stock of PBMC (isolated from whole blood with Histopaque and stored in FBS with 10% DMSO at -80°C) was thawed, washed twice with RPMI1640 complete media then kep in CO2 incubator for 4 hours. After this short incubation, cells were washed twice with DPBS with 0.1% BSA. Cell concentration was adjusted to 10,000 input cells to 10x Genomics Chromium system. Single cell sample preparation was done according to instruction of 10x Genomics 3' kit version 3.1.
Library preparation was made accoding to instruction of 10x Genomcis's 3' kit version 3.1.

value: Peripheral Blood Mononuclear Cells

tag: tissue

value: Blood

tag: age

value: anonymous blood donor


title: Cardiomyocyte, subsample 1

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools based on the first 100 millions input raw reads of the R1 FASTQ file of the sample.
Raw read downsampling was perfomed for each sample by randomly subsampling raw reads from the FASTQ files such that the mean number of raw reads belonging to cell-associated barcodes was 50,000.
The provided processed data is composed of one count matrix per sample, computed after raw read downsampling, such that for each sample the same sequencing depth is simulated at 50,000 mean number of raw reads per cell.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38).  Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A;  Species: Homo_sapiens;  Genome Source: ensembl;  Genome Version: GRCh38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/;  Annotation Source: ensembl;  Annotation Version: 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: cardiomyocyte derived from ES cell

extract_protocol:
Sample preparation was started from 10,000 cardiomyocyte cell line (Takara Bio Y10060) according to the RevGel-Seq protocol instructions. Briefly, barcode beads and cells are attached via a bifunctional chemical linker. These tandems are dispersed in an hydrogel in the liquid state and immobilized upon gelation. Following cell lysis, polyA+ RNA molecules are captured on the barcoded beads via polyA-polyT interactions. Barcoded beads (and associated RNA molecules) are recovered following degelation, and reverse transcriptionand subsequent second strand synthesis with random primer are performed. Each sample is then split in 8 subfractions and PCR-amplified to obtain cell barocded cDNA. Two subfractions were used as subsample 1 and subsample 2, respectively, for library preparation, sequencing and data analysis separately.
Each of barcoded cDNA subftractions was purified with SPRIselect to remove short fragments. Sequencing libraries were prepared with illumina's Nextera XT kit for each of 8 purified barcoded cDNA according to manufacturer's instructions with the following adaptations: 600pg of the cDNA was subjected to tagmentation reaction. The tagmented DNA was amplified by 12 cycles PCR. During this PCR, DNA fragments with cell barcode sequence at one end are selectively amplified by using a primer pair of custom P5-read1 primer to the original barcode end and Nextera N7xx P7 index primer to the tagmented end. Paired end sequencing was done.

value: cardiomyocyte derived from ES cell

tag: strain

value: Takara Bio, ref. Y10060


title: PBMC_perf_Scipio

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
For each sample, the R1 (resp. R2) FASTQ files of the 8 sample subfractions were concatenated into one R1 (resp. R2) FASTQ file.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools based on 100 millions input raw reads randomly sampled from the concatenated R1 FASTQ file of the sample.
Raw read downsampling was perfomed for each sample by randomly subsampling raw reads from the concatenated FASTQ files such that the mean number of raw reads belonging to cell-associated barcodes was 20,000.
The provided processed data is composed of one count matrix per sample, computed after raw read downsampling, such that for each sample the same sequencing depth is simulated at 20,000 mean number of raw reads per cell.
Data post-processing (filtering, normalization, HVG, PCA, 2D embedding, clustering, DGE) was performed using Seurat and automated cell annotation was performed using SingleR algorithm and the reference dataset MonacoImmuneData.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38).  Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A;  Species: Homo_sapiens;  Genome Source: ensembl;  Genome Version: GRCh38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/;  Annotation Source: ensembl;  Annotation Version: 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

extract_protocol:
scRNA was extracted from 10,000 human PBMCs, according to the RevGel-Seq protocol instructions. Briefly, barcode beads and cells are attached via a bifunctional chemical linker. These tandems are dispersed in an hydrogel in the liquid state and immobilized upon gelation. Following cell lysis, polyA+ RNA molecules are captured on the barcoded beads via polyA-polyT interactions. Barcoded beads (and associated RNA molecules) are recovered following degelation, and reverse transcription and subsequent second strand synthesis with random primer are performed. Each sample is then split in 8 subfractions and PCR-amplified.
Each of the 8 fractions of barcoded cDNA was purified with SPRIselect to remove short fragments. Sequencing libraries were prepared with illumina's Nextera XT kit for each of 8 purified barcoded cDNA  according to manufacturer's instructions with the following adaptations: 600pg of the cDNA was subjected to tagmentation reaction.The tagmented DNA was amplified by 12 cycles PCR. During this PCR, DNA fragments with cell barcode sequence at one end are selectively amplified by using a primer pair of custom P5-read1 primer to the original barcode end and Nextera N7xx P7 index primer to the tagmented end.Paired end sequencing was done.


title: OVCAR3_DMSO_rep_1

description: OVCAR3 cells  treated with DMSO for 6hr replicate 1


title: Control, CTCF, BioRep2

value: H9 hESC

value: hESC-derived P4 CNCC


title: Control, RAD21, BioRep1


title: E135_CTCFdel, CTCF, BioRep2


title: serum_longRNA_PH181_w0pre

city: Birmingham

first: Kaleen

middle: M

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

institute: University of Alabama at Birmingham

description:
long RNA from serum extracellular vesicles
serumEV_long_counts.txt
serumEV_circRNA_counts.txt

data_processing:
Long reads were aligned using STAR to GRCh38 and LNCpedia; separately, long reads were used to identify circular RNA using CIRI2; small reads were aligned using exceRpt
Long RNA count data were generated using featureCounts
Assembly: GRCh38
Supplementary files format and content: txt file containing read counts for genes and samples

source_name: serum EV

extract_protocol:
Skeletal muscle RNA was extracted using Qiagen miRNeasy kit (Cat. No. 217004); serum EV RNA was extracted using Qiagen exoRNeasy kits (Cat. No. 77144).
Long RNA libraries for both skeletal muscle and serum EVs were constructed using Takara Bio SMARTer Stranded Total RNA-Seq kit v2 Pico Input Mammalian (Cat. No. 634418) and SMARTer RNA Unique Dual Index Kit (Cat. No. 634452). Small RNA libraries for both skeletal muscle and serum EVs were prepared using NEXTflex Small RNA Library Prep Kit v3 (Ca. No. # NOVA-5132-23, Perkin Elmer

value: serum EV

tag: timepoint

tag: cohort

value: TRAD

tag: Sex

value: F


title: serum_longRNA_PH181_w0h24


title: serum_longRNA_PH177_w0pre

value: HITT

value: M


title: serum_longRNA_PH183_w0h0


title: serum_longRNA_PH183_w0h24


title: serum_longRNA_PH183_w0pre


title: serum_longRNA_PH181_w0h0


title: serum_longRNA_PH181_w0h3


title: serum_longRNA_PH177_w0h3


title: serum_longRNA_PH183_w0h3


title: serum_longRNA_PH177_w0h0


title: serum_longRNA_PH175_w0h3


title: serum_longRNA_PH175_w0pre


title: Cardiomyocyte, subsample 2


title: serum_longRNA_PH175_w0h24


title: serum_longRNA_PH174_w0h24


title: serum_longRNA_PH174_w0h3


title: serum_longRNA_PH174_w0pre


title: serum_longRNA_PH175_w0h0


title: serum_longRNA_PH170_w0pre


title: serum_longRNA_PH174_w0h0


title: serum_longRNA_PH170_w0h3


title: serum_longRNA_PH170_w0h24


title: serum_longRNA_PH166_w0pre


title: serum_longRNA_PH170_w0h0


title: serum_longRNA_PH166_w0h0


title: serum_longRNA_PH177_w0h24


title: serum_longRNA_PH165_w0h3


title: serum_longRNA_PH165_w0pre


title: serum_longRNA_PH165_w0h24


title: serum_longRNA_PH150_w0h24


title: serum_longRNA_PH165_w0h0


title: serum_longRNA_PH150_w0pre


title: serum_longRNA_PH150_w0h3


title: serum_longRNA_PH149_w0h0


title: serum_longRNA_PH150_w0h0


title: serum_longRNA_PH149_w0pre


title: serum_longRNA_PH149_w0h3


title: serum_longRNA_PH149_w0h24


title: serum_longRNA_PH135_w0h24


title: serum_longRNA_PH134_w0h3


title: serum_longRNA_PH135_w0pre


title: serum_longRNA_PH134_w0h0


title: serum_longRNA_PH128_w0h3


title: serum_longRNA_PH134_w0pre


title: serum_longRNA_PH134_w0h24


title: serum_longRNA_PH128_w0pre


title: serum_longRNA_PH128_w0h0


title: serum_longRNA_PH128_w0h24


title: serum_longRNA_PH126_w0h3


title: serum_longRNA_PH126_w0h0


title: serum_longRNA_PH126_w0h24


title: serum_longRNA_PH125_w0pre


title: serum_longRNA_PH124_w0pre


title: serum_longRNA_PH124_w0h3


title: serum_longRNA_PH124_w0h24


title: serum_longRNA_PH135_w0h3


title: serum_longRNA_PH124_w0h0


title: serum_longRNA_PH135_w0h0


title: serum_longRNA_PH120_w0pre


title: serum_longRNA_PH120_w0h3


title: serum_longRNA_PH120_w0h0


title: serum_longRNA_PH116_w0h3


title: serum_longRNA_PH116_w0pre


title: serum_longRNA_PH109_w0pre


title: serum_longRNA_PH109_w0h3


title: serum_longRNA_PH107_w0pre


title: serum_longRNA_PH109_w0h0


title: serum_longRNA_PH107_w0h24


title: serum_longRNA_PH101_w0pre


title: serum_longRNA_PH101_w0h24


title: serum_longRNA_PH107_w0h3


title: serum_longRNA_PH125_w0h0


title: serum_longRNA_PH107_w0h0


title: serum_longRNA_PH098_w0pre


title: serum_longRNA_PH100_w0h0


title: serum_longRNA_PH101_w0h3


title: serum_longRNA_PH098_w0h3


title: serum_longRNA_PH101_w0h0


title: serum_longRNA_PH098_w0h24


title: serum_longRNA_PH090_w0h3


title: serum_longRNA_PH098_w0h0


title: serum_longRNA_PH090_w0pre


title: serum_longRNA_PH100_w0h24


title: serum_longRNA_PH120_w0h24


title: serum_longRNA_PH116_w0h24


title: serum_longRNA_PH116_w0h0


title: serum_longRNA_PH090_w0h24


title: serum_longRNA_PH109_w0h24


title: serum_longRNA_PH090_w0h0


title: Heart, Nkx2.5-RIP140KO, TAC/MI, rep3

city: Philadelphia

first: Daniel

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Expression of transcripts of the GRCm38 (mm10) genome was quantified using Salmon 1.3.0
The transcripts expression was then summarized at the gene level, and differentially expressed genes were found using DESeq2 1.36.0 with ashr adaptive shrinkage estimator
Genes with FDR < 0.05, when comparing conditions of interest, were selected as differentially expressed. Furthermore, we only consider those genes which change at least 1.2-fold, in any direction.
Assembly: mm10
Supplementary files format and content: Tab-separated files contain gene name, log2 fold change, and FDR values for each differentially expressed gene in a comparison between two conditions

source_name: Cardiac-specific RIP140 KO - KO - TAC/MI

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. cDNAs were synthesized using the Affinity Script cDNA Synthesis Kit (Agilent) with 0.5 μg of total RNA.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a single (two lanes in 30-209309547) lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Transverse aortic constriction combined with small apical myocardial infarction (TAC/MI) surgeries were performed on 8 week-old male mice. Mice were anesthetized with ketamine [90mg/kg] / xylazine [10mg/kg] / Acepromazine [2mg/kg], intubated and ventilated (Harvard Apparatus). TAC was performed on anesthetized mice by first freeing the aortic arch by blunt dissection. A 7-0 silk suture was passed under the aorta. The suture was then tied around a blunt needle (25 to 28 gauge depending on size of animal) lying on the artery, and the blunt needle was removed to induce constriction. Second, to generate a small myocardial infarction (MI), the chest wall was retracted through the 4th intercostal space to clearly visualize the left ventricle and the left anterior descending artery. The left anterior descending branch (LAD) of the left coronary artery was ligated with a 8-0 nylon suture. Prior to analysis of all TAC/MI samples, the infarcted apical region was removed from the hearts (and the corresponding cardiac tissue region was removed from sham operated controls). Post-weaning aortic banding (PWAB) surgeries were performed on 21- to 28-day-old mice, weighing 7–13 g, received ascending aortic constrictions as described above (26 gauge).

value: Heart

value: Nrip1 f/f Cre+

value: TAC/MI surgery


title: Heart, Nkx2.5-RIP140KO, TAC/MI, rep2


title: serum_longRNA_PH086_w0h3


title: serum_longRNA_PH086_w0h24


title: Heart, Nkx2.5-RIP140KO, TAC/MI, rep4


title: serum_longRNA_PH100_w0h3


title: Heart, Nkx2.5-RIP140KO, Sham, rep4

source_name: Cardiac-specific RIP140 KO - KO - Sham

value: Sham surgery


title: Heart, Nkx2.5-RIP140KO, Sham, rep3


title: Heart, Nkx2.5-RIP140KO, Sham, rep1


title: serum_longRNA_PH086_w0h0


title: Heart, Control, TAC/MI, rep4

source_name: Cardiac-specific RIP140 KO - Control - TAC/MI

value: Nrip1 f/f Cre-


title: serum_longRNA_PH085_w0pre


title: serum_longRNA_PH085_w0h24


title: serum_longRNA_PH085_w0h3


title: Heart, Control, TAC/MI, rep3


title: Heart, Control, TAC/MI, rep2


title: serum_longRNA_PH085_w0h0


title: serum_longRNA_PH082_w0pre


title: Heart, Control, Sham, rep3

source_name: Cardiac-specific RIP140 KO - Control - Sham


title: Heart, Control, Sham, rep2


title: Heart, Control, Sham, rep4


title: serum_longRNA_PH082_w0h24


title: serum_longRNA_PH082_w0h0


title: serum_longRNA_PH082_w0h3


title: serum_longRNA_PH086_w0pre


title: serum_longRNA_PH077_w0h3


title: Heart, Control, Sham, rep1


title: Heart, Nkx2.5-RIP140KO, TAC/MI, rep1


title: serum_longRNA_PH077_w0h0


title: 223 054-XXXX

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

institute: INSERM

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Star 2.5.3 with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Aligned reads were quantified to annotation model hg19 - GENCODE Genes - release 19, with Partek E/M. Normalization and differential analysis  were performed using DEARSEQ R package
Assembly: hg19
Supplementary files format and content: Normalized_counts of 75 samples.txt

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the Illumina TruSeq® Stranded mRNA kit. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomic Platform

tag: status

value: COVID-19 convalescents

tag: patient

tag: time point

value: 6 months hospital discharge


title: 224 101-XXXX


title: 222 095-XXXX


title: serum_longRNA_PH076_w0h3


title: serum_longRNA_PH076_w0pre


title: serum_longRNA_PH076_w0h24


title: 221 094-XXXX


title: 219 097-XXXX


title: 211 065-XXXX


title: serum_longRNA_PH071_w0pre


title: 209 066-XXXX


title: 208 058-XXXX


title: 205 048-SENS


title: 204 046-MOBE


title: serum_longRNA_PH071_w0h24


title: serum_longRNA_PH071_w0h0


title: serum_longRNA_PH070_w0h3


title: 195 146-XXXX


title: 201 052-PALE


title: 196 042-BIBO


title: serum_longRNA_PH070_w0pre


title: serum_longRNA_PH070_w0h24


title: 188 036-BRMA


title: 187 016-SATA


title: serum_longRNA_PH061_w0pre


title: 184 041-NABO


title: 186 142-XXXX


title: 185 069-XXXX


title: serum_longRNA_PH070_w0h0


title: serum_longRNA_PH061_w0h24


title: 217 108-XXXX

value: 3 months hospital discharge


title: serum_longRNA_PH076_w0h0


title: serum_longRNA_PH059_w0pre


title: 215 135-XXXX


title: serum_longRNA_PH061_w0h0


title: serum_longRNA_PH059_w0h3


title: serum_longRNA_PH071_w0h3


title: serum_longRNA_PH059_w0h24


title: serum_longRNA_PH059_w0h0


title: serum_longRNA_PH046_w0pre


title: 206 122-XXXX


title: 203 126-XXXX


title: 191 094-XXXX


title: 200 093-XXXX


title: serum_longRNA_PH046_w0h0


title: serum_longRNA_PH046_w0h24


title: 199 113-XXXX


title: serum_longRNA_PH061_w0h3


title: serum_longRNA_PH029_w0h3


title: 194 097-XXXX


title: serum_longRNA_PH029_w0pre


title: 182 096-XXXX


title: 177 053-XXXX


title: 178 052-PALE


title: serum_longRNA_PH029_w0h0


title: 175 025-CHDO


title: serum_longRNA_PH029_w0h24


title: 213 118-XXXX


title: serum_longRNA_PH024_w0h3


title: serum_longRNA_PH024_w0h24


title: 173 031-YAAT


title: 210 123-XXXX


title: serum_longRNA_PH018_w0pre


title: 172 046-MOBE


title: serum_longRNA_PH024_w0h0


title: 171 092-XXXX


title: 174 102-XXXX


title: serum_longRNA_PH046_w0h3


title: serum_longRNA_PH018_w0h3


title: 170 056-JODO


title: serum_longRNA_PH018_w0h24


title: 169 089-XXXX


title: serum_longRNA_PH018_w0h0


title: 166 029-FIDI


title: 165 007-BETP


title: serum_longRNA_PH011_w0h3


title: serum_longRNA_PH011_w0h24


title: 164 016-SATA


title: 161 008-RAFE


title: serum_longRNA_PH011_w0h0


title: serum_longRNA_PH024_w0pre


title: serum_longRNA_PH010_w0pre


title: 115 083-XXXX


title: 193 126-XXXX

value: 1 month hospital discharge


title: serum_longRNA_PH010_w0h24


title: serum_longRNA_PH010_w0h3


title: serum_longRNA_PH010_w0h0


title: 192 122-XXXX


title: 190 118-XXXX


title: 183 094-XXXX


title: 197 135-XXXX


title: muscle_longRNA_PH183_w0pre

description:
long RNA from skeletal muscle
muscle_longRNA_long_counts.txt
muscle_longRNA_circRNA_counts.txt

source_name: skeletal muscle

value: skeletal muscle


title: muscle_longRNA_PH183_w0h3


title: 181 101-XXXX


title: muscle_longRNA_PH183_w0h24


title: muscle_longRNA_PH181_w0pre


title: 176 097-XXXX


title: serum_longRNA_PH011_w0pre


title: muscle_longRNA_PH181_w0h3


title: 162 084-XXXX


title: 198 144-XXXX


title: 113 053-XXXX


title: 110 042-BIBO


title: 93 063-XXXX


title: 86 056-JODO


title: 68 041-NABO


title: muscle_longRNA_PH181_w0h24


title: muscle_longRNA_PH180_w0pre


title: 111 078-XXXX


title: muscle_longRNA_PH180_w0h3


title: muscle_longRNA_PH180_w0h24


title: muscle_longRNA_PH177_w0h24


title: muscle_longRNA_PH177_w0h3


title: muscle_longRNA_PH177_w0pre


title: muscle_longRNA_PH175_w0pre


title: 55 032-MAFI


title: 61 036-BRMA


title: 54 029-FIDI


title: muscle_longRNA_PH175_w0h3


title: 48 015-ODBI


title: muscle_longRNA_PH174_w0pre


title: muscle_longRNA_PH175_w0h24


title: 47 008-RAFE


title: muscle_longRNA_PH174_w0h3


title: muscle_longRNA_PH170_w0pre


title: muscle_longRNA_PH174_w0h24


title: 46 006-JEHU


title: 3538-V

value: Healthy


title: 3136-V


title: muscle_longRNA_PH170_w0h24


title: muscle_longRNA_PH166_w0pre


title: 2064-V


title: 3054-V


title: muscle_longRNA_PH166_w0h3


title: 1951-V


title: 1995-V


title: muscle_longRNA_PH165_w0pre


title: 1918-V


title: 1406-V


title: muscle_longRNA_PH165_w0h24


title: muscle_longRNA_PH165_w0h3


title: 49 022-ANIE


title: 507-V


title: muscle_longRNA_PH150_w0h24


title: muscle_longRNA_PH149_w0pre


title: muscle_longRNA_PH149_w0h24


title: muscle_longRNA_PH135_w0pre


title: muscle_longRNA_PH150_w0h3


title: muscle_longRNA_PH135_w0h24


title: muscle_longRNA_PH134_w0h3


title: muscle_longRNA_PH150_w0pre


title: muscle_longRNA_PH134_w0pre


title: muscle_longRNA_PH128_w0pre


title: muscle_longRNA_PH134_w0h24


title: muscle_longRNA_PH166_w0h24


title: muscle_longRNA_PH128_w0h3


title: muscle_longRNA_PH128_w0h24


title: CHL-1, CREM KD, rep 3

city: Turku

first: Heidi

last: Kaprio

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description:
CREM3
melanoma (skin)

data_processing:
Read alignment
Tool(s): R(v.3.6.1) [7]/Bioconductor(v.3.9) [3]::Rsubread(v.2.0.0) [4]::align
(source: https://support.illumina.com/sequencing/sequencing software/igenome.html (UCSC))
Gene models (annot.inbuilt): RefSeq gene annotation in-built in Rsubread package.
Assembly: hg38
Supplementary files format and content: Excel file: Contains the results of each sample normalized counts as cpm (counts per million) values, according to GAPDH expression.
Supplementary files format and content: Excel file: Results are normalized according to GAPDH expression and mean gene expression levels are reported as RPKM values.

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells (500 x10^3) were plated on twelve-well plates, treated with Control or CREM siRNA and, after 48 h, RNA samples were collected and purified using the NucleoSpin RNA/Protein Kit (Macherey-Nagel; Allentown, PA, USA) according to the manufacturer's protocol.
Illumina Stranded mRNA Prep.

treatment_protocol: Transfection with 50 nM of CREM siRNA or control using Darmafect 4.

tag: cell line

value: melanoma cells

tag: genotype

value: CREM knockdown

tag: treatment

value: CREM siRNA


title: CHL-1, CREM KD, rep 2

description:
CREM2
melanoma (skin)

tag: cell type


title: CHL-1, control, rep 3

description:
Control3
melanoma (skin)

value: WT

value: Control siRNA


title: muscle_longRNA_PH126_w0pre

value: TRAD

value: M


title: muscle_longRNA_PH126_w0h3


title: CHL-1, control, rep 2

description:
Control2
melanoma (skin)


title: muscle_longRNA_PH125_w0pre

value: HITT


title: CHL-1, CREM KD, rep 1

description:
CREM1
melanoma (skin)


title: CHL-1, control, rep 1

description:
Control1
melanoma (skin)


title: muscle_longRNA_PH125_w0h3


title: 1189-V


title: muscle_longRNA_PH124_w0pre


title: muscle_longRNA_PH126_w0h24


title: serum_shortRNA_PH183_w0h24

description:
small RNA from serum extracellular vesicles
serumEV_small_counts.txt

value: serum EV

value: F


title: muscle_longRNA_PH120_w0pre


title: serum_shortRNA_PH183_w0pre


title: muscle_longRNA_PH120_w0h3


title: serum_shortRNA_PH181_w0h24


title: serum_shortRNA_PH181_w0h0


title: muscle_longRNA_PH116_w0h3


title: muscle_longRNA_PH109_w0h3


title: muscle_longRNA_PH109_w0h24


title: muscle_longRNA_PH135_w0h3


title: serum_shortRNA_PH177_w0h0


title: serum_shortRNA_PH183_w0h3


title: serum_shortRNA_PH177_w0h3


title: muscle_longRNA_PH124_w0h3


title: serum_shortRNA_PH175_w0h3


title: muscle_longRNA_PH107_w0h3


title: serum_shortRNA_PH183_w0h0


title: muscle_longRNA_PH120_w0h24


title: serum_shortRNA_PH181_w0pre


title: serum_shortRNA_PH174_w0h3


title: serum_shortRNA_PH181_w0h3


title: muscle_longRNA_PH101_w0pre


title: muscle_longRNA_PH116_w0h24


title: muscle_longRNA_PH116_w0pre


title: serum_shortRNA_PH174_w0h24


title: serum_shortRNA_PH177_w0pre


title: serum_shortRNA_PH177_w0h24


title: muscle_longRNA_PH125_w0h24


title: muscle_longRNA_PH109_w0pre


title: serum_shortRNA_PH175_w0pre


title: serum_shortRNA_PH170_w0h0


title: muscle_longRNA_PH098_w0pre


title: muscle_longRNA_PH098_w0h3


title: muscle_longRNA_PH124_w0h24


title: muscle_longRNA_PH107_w0pre


title: serum_shortRNA_PH174_w0pre


title: serum_shortRNA_PH166_w0h3


title: muscle_longRNA_PH101_w0h3


title: serum_shortRNA_PH175_w0h0


title: serum_shortRNA_PH166_w0h0


title: serum_shortRNA_PH170_w0pre


title: serum_shortRNA_PH174_w0h0


title: muscle_longRNA_PH101_w0h24


title: serum_shortRNA_PH170_w0h3


title: muscle_longRNA_PH100_w0h3


title: serum_shortRNA_PH170_w0h24


title: muscle_longRNA_PH107_w0h24


title: muscle_longRNA_PH100_w0h24


title: muscle_longRNA_PH098_w0h24


title: serum_shortRNA_PH165_w0h0


title: muscle_longRNA_PH085_w0h3


title: serum_shortRNA_PH150_w0pre


title: muscle_longRNA_PH085_w0pre


title: muscle_longRNA_PH090_w0pre


title: serum_shortRNA_PH166_w0h24


title: muscle_longRNA_PH085_w0h24


title: serum_shortRNA_PH165_w0pre


title: muscle_longRNA_PH090_w0h3


title: muscle_longRNA_PH090_w0h24


title: muscle_longRNA_PH082_w0pre


title: serum_shortRNA_PH165_w0h3


title: muscle_longRNA_PH100_w0pre


title: serum_shortRNA_PH166_w0pre


title: muscle_longRNA_PH086_w0pre


title: muscle_longRNA_PH086_w0h3


title: serum_shortRNA_PH165_w0h24


title: serum_shortRNA_PH149_w0h3


title: serum_shortRNA_PH150_w0h24


title: serum_shortRNA_PH150_w0h3


title: muscle_longRNA_PH086_w0h24


title: serum_shortRNA_PH149_w0pre


title: muscle_longRNA_PH077_w0h24


title: serum_shortRNA_PH135_w0h24


title: serum_shortRNA_PH135_w0h3


title: muscle_longRNA_PH076_w0pre


title: muscle_longRNA_PH082_w0h3


title: muscle_longRNA_PH076_w0h3


title: muscle_longRNA_PH082_w0h24


title: serum_shortRNA_PH150_w0h0


title: muscle_longRNA_PH077_w0pre


title: serum_shortRNA_PH149_w0h0


title: muscle_longRNA_PH077_w0h3


title: serum_shortRNA_PH149_w0h24


title: serum_shortRNA_PH135_w0pre


title: serum_shortRNA_PH135_w0h0


title: muscle_longRNA_PH071_w0pre


title: serum_shortRNA_PH134_w0pre


title: serum_shortRNA_PH134_w0h3


title: serum_shortRNA_PH134_w0h24


title: muscle_longRNA_PH071_w0h3


title: serum_shortRNA_PH128_w0pre


title: serum_shortRNA_PH134_w0h0


title: muscle_longRNA_PH071_w0h24


title: muscle_longRNA_PH070_w0pre


title: muscle_longRNA_PH070_w0h24


title: serum_shortRNA_PH128_w0h3


title: muscle_longRNA_PH170_w0h3


title: serum_shortRNA_PH128_w0h24


title: serum_shortRNA_PH128_w0h0


title: muscle_longRNA_PH149_w0h3


title: serum_shortRNA_PH126_w0h3


title: serum_shortRNA_PH126_w0h24


title: muscle_longRNA_PH061_w0h24


title: muscle_longRNA_PH076_w0h24


title: muscle_longRNA_PH061_w0h3


title: serum_shortRNA_PH125_w0pre


title: muscle_longRNA_PH059_w0h24


title: serum_shortRNA_PH126_w0h0


title: muscle_longRNA_PH059_w0h3


title: muscle_longRNA_PH046_w0pre


title: serum_shortRNA_PH125_w0h24


title: serum_shortRNA_PH125_w0h0


title: serum_shortRNA_PH124_w0pre


title: muscle_longRNA_PH046_w0h3


title: muscle_longRNA_PH029_w0h3


title: muscle_longRNA_PH029_w0pre


title: muscle_longRNA_PH070_w0h3


title: serum_shortRNA_PH124_w0h24


title: muscle_longRNA_PH024_w0pre


title: serum_shortRNA_PH124_w0h0


title: serum_shortRNA_PH126_w0pre


title: muscle_longRNA_PH059_w0pre


title: serum_shortRNA_PH120_w0pre


title: muscle_longRNA_PH029_w0h24


title: serum_shortRNA_PH124_w0h3


title: serum_shortRNA_PH120_w0h3


title: muscle_longRNA_PH024_w0h24


title: muscle_longRNA_PH061_w0pre


title: muscle_longRNA_PH018_w0pre


title: muscle_longRNA_PH018_w0h3


title: serum_shortRNA_PH116_w0pre


title: muscle_longRNA_PH018_w0h24


title: muscle_longRNA_PH011_w0pre


title: muscle_longRNA_PH024_w0h3


title: serum_shortRNA_PH116_w0h3


title: serum_shortRNA_PH116_w0h24


title: muscle_longRNA_PH046_w0h24


title: muscle_longRNA_PH011_w0h24


title: serum_shortRNA_PH109_w0pre


title: muscle_longRNA_PH010_w0h3


title: muscle_longRNA_PH010_w0pre


title: serum_shortRNA_PH109_w0h3


title: serum_shortRNA_PH109_w0h24


title: muscle_longRNA_PH010_w0h24


title: serum_shortRNA_PH109_w0h0


title: serum_shortRNA_PH107_w0pre


title: serum_shortRNA_PH120_w0h24


title: serum_shortRNA_PH120_w0h0


title: PT85C I liLL

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Sequencing reads in fastq format were adapter-trimmed using BBDuk (38.80)
Sequence quality was checked using FastQC (0.11.9)
Reads were mapped to the human reference genome (GRCh38/hg38) with STAR aligner  (2.7.1a).
Read counts for NCBI Gene/Refseq annotation were calculated using featureCounts (2.0.0).
Differentially expressed genes were calculated and read count normalization were performed using the R package DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited matrix text file include raw counts for each sample and each gene
Supplementary files format and content: tab-delimited matrix text file include normalized counts for each sample and each gene

source_name: liver

extract_protocol:
Tissue homogenization using Tissue Ruptor (Qiagen), sample lysis and RNA isolation using miRNeasy Mini Kit (Qiagen)
Lexogen QuantSeq 3' FWD kit (polyA mRNA-seq)

value: liver

tag: sample type


title: serum_shortRNA_PH107_w0h24


title: serum_shortRNA_PH107_w0h3


title: PT 85 2 re


title: serum_shortRNA_PH107_w0h0


title: PT85C I reLL


title: PT85 2 li


title: serum_shortRNA_PH101_w0pre


title: PT62 III reLL


title: PT85 1 re

value: PRE


title: serum_shortRNA_PH101_w0h3


title: PT62 III liLL


title: PT62 II reLL


title: serum_shortRNA_PH116_w0h0


title: serum_shortRNA_PH101_w0h0


title: muscle_longRNA_PH011_w0h3


title: serum_shortRNA_PH101_w0h24


title: serum_shortRNA_PH100_w0pre


title: PT62 II liLL


title: PT62 I reLL


title: PT2 A re


title: serum_shortRNA_PH100_w0h3


title: PT2 A li


title: serum_shortRNA_PH100_w0h24


title: serum_shortRNA_PH100_w0h0


title: PT2 II re


title: serum_shortRNA_PH098_w0pre


title: PT2 II li


title: serum_shortRNA_PH098_w0h3


title: PT2 I


title: serum_shortRNA_PH098_w0h0


title: PT 84 II li LL

value: POST


title: serum_shortRNA_PH098_w0h24


title: PT 84 I li LL


title: serum_shortRNA_PH090_w0pre


title: PT68 II li


title: serum_shortRNA_PH090_w0h24


title: serum_shortRNA_PH090_w0h3


title: PT 68 I


title: ZC3H41-depleted, replicate 1

city: Armilla

first: Antonio

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

institute: CSIC

description:
trasfected with pGR309 (RNAi plasmid)
RNAi induced
RNAi A

data_processing:
TruSeq RNA Single Indexes (set A&B)
The resulting 75-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using the ‘align’ program of the Subread package with options nTrim5=4, nTrim3=1, unique=TRUE
Reads assignment to mRNAs and counting were carried out using the ‘featureCounts’ program of the Subread package (options -p -B -C -ignoreDup -Q 20)
Replicates were compared using the edgeR package with control trypanosomes (parental 449 cell line, three biological replicates available in GSE186563 series, samples GSM5655679, GSM5655680 and GSM56556781)
Assembly: TREU927, version 5.7
Supplementary files format and content: featureCounts output, tab-delimited text file

organism: Trypanosoma brucei brucei

source_name: Cultured trypanosomes

growth_protocol: Grown in SDM-79 medium at 28ºC

extract_protocol:
Cells were centrifuged and RNA was extracted using the RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA® Illumina

treatment_protocol: ± 1 µg/ml tetracycline for RNAi induction

value: Procyclic forms, 449 strain expressing a TAP-tagged version of ZC3H41


title: ZC3H41-depleted, replicate 3

description:
trasfected with pGR309 (RNAi plasmid)
RNAi induced
RNAi C


title: PT 61 II re


title: ZC3H41-depleted, replicate 2

description:
trasfected with pGR309 (RNAi plasmid)
RNAi induced
RNAi B


title: serum_shortRNA_PH086_w0pre


title: PT 61 I li


title: serum_shortRNA_PH086_w0h3


title: PT 59 II li


title: TAP, replicate 2

description: TAP affinity purified RNA

data_processing:
Truseq RNA Single Indexes (set A&B)
The resulting 76-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using the ‘align’ program of the Subread package with options nTrim5=4, nTrim3=1, unique=TRUE
BAM files were analyzed with the module 'callpeak' of MACS2 with options -q 0.005 -g 3.5e7 --nomodel -f BAMPE
BAM files corresponding to input RNA were used as controls for the peak calling
The resulting 'narrowPeak' files obtained from both biological duplicates were intersected using the 'intersect' module of bedtools with options -f 0.9 -r
The final peak list was further intersected with a BED file containing the coordinates of all genes (open-reading frames plus untranslated regions) present in the T. brucei 11 megabase chromosomes using option -f 0.5.
Assembly: TREU927, version 5.7
Supplementary files format and content: MACS2 scores, tab-delimited text file

extract_protocol:
Input RNA was isolated using peqGOLD Tri-fast. Affinity purified RNA was isolated after TEV cleavage, phenol:chloroform extraction and ethanol precipitation
TruSeq Stranded mRNA® Illumina

value: Procyclic forms, 449 strain expressing a TAP-tagged version of Z41AP (Tb927.7.7460)


title: serum_shortRNA_PH085_w0h3


title: TAP, replicate 1

description: TAP affinity purified RNA


title: serum_shortRNA_PH085_w0h24


title: PT 59 I


title: serum_shortRNA_PH085_w0h0


title: input, replicate 2

description: total RNA


title: serum_shortRNA_PH082_w0h3


title: PT 51 II li


title: serum_shortRNA_PH090_w0h0


title: serum_shortRNA_PH082_w0h24


title: PT 51 I


title: input, replicate 1

description: total RNA


title: serum_shortRNA_PH082_w0pre


title: serum_shortRNA_PH077_w0pre


title: serum_shortRNA_PH086_w0h0


title: serum_shortRNA_PH077_w0h3


title: serum_shortRNA_PH082_w0h0


title: serum_shortRNA_PH077_w0h24


title: serum_shortRNA_PH086_w0h24


title: PT 50 II li


title: serum_shortRNA_PH077_w0h0


title: serum_shortRNA_PH076_w0pre


title: PT 50 I R


title: PT 49 II li


title: serum_shortRNA_PH085_w0pre


title: serum_shortRNA_PH076_w0h3


title: serum_shortRNA_PH076_w0h0


title: PT 49 I re


title: serum_shortRNA_PH076_w0h24


title: PT 40 II li LL


title: serum_shortRNA_PH071_w0h3


title: serum_shortRNA_PH071_w0h24


title: PT 40 I re LL


title: PT 37 II reLL


title: serum_shortRNA_PH070_w0pre


title: serum_shortRNA_PH070_w0h3


title: serum_shortRNA_PH070_w0h24


title: serum_shortRNA_PH070_w0h0


title: PT37 II liLL


title: LP-LP_C11

type: genomic

city: Yayoi, Bunkyo-ku

first: Chika

last: Ando

state: Tokyo

country: Japan

institute: University of Tokyo

hyb_protocol: 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation. Microarrays were hybridize d at 42°C during 16 to 20h with Cy 3 5 labelled DNA in Nimble Gen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit ( NimbleGen Systems, Inc., Madison, WI, USA). For array hybridization, ArrayStar Rat RefSeq Promoter Array was used, which is a single array designs that includes 23 ,148 gene promoter regions (from about 1300bp to +500bp of the TSSs) totally covered by ~180,000 probes with approxim ately 210 bp spacing, dependent on the sequence composition of the region

scan_protocol: Scanning was performed by using Agilent Scanner G2505C

data_processing:
Raw data was extracted as txt files by Agilent Feature Extraction softwar e (version 11.0.1.1) 11.0.1.1). We perform Median centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2 ratio data (*_ratio.gff file) was created for each sample. From the nor malized log2 ratio data, a sliding window peak finding algorithm provided by NimbleScan v2.5 (Roche NimbleGen) was applied to find the enriched peaks with specified parameter s (sliding window width: 1 5 0 0bp; mini probes per peak: 2; P value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500bp). After getting the *_peaks.gff files, the identified peaks were mapped
NimbleScan detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged. PeakMvalue is the median log2-ratio from probes within the peak.

label: Cy3 and Cy5

organism: Rattus norvegicus

source_name: Kidney of rat

label_protocol: For DNA labelling, the NimbleGen Dual Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP chip protocol NimbleGen Syst ems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5 9mer primer (IP sample) or Cy3 9mer primer (Input sample) sample). Then, 100 pmol of deoxynucleoside

extract_protocol: DNA from the kidney was extracted using DNAiso Reagent (Takara Bio, Tokyo, Japan).  The samples were checked for quality via electrophoresis (100 V, 20 min) using a 1.2% agarose gel and the DNA concentrations were measured using a NanoDrop instrument (ND-1000, NanoDrop Technologies)and a Qubit instrument (Thermo Fisher Scientific, Waltham, MA, USA).

value: Kidney

tag: maternal diet

value: LP

tag: offspring diet


title: serum_shortRNA_PH061_w0h24


title: serum_shortRNA_PH071_w0pre


title: serum_shortRNA_PH061_w0h3


title: PT 37 I liLL


title: serum_shortRNA_PH059_w0pre


title: serum_shortRNA_PH061_w0h0


title: LP-LP_C12


title: serum_shortRNA_PH061_w0pre


title: PT 37 I reLL


title: PT 32 II li LL


title: serum_shortRNA_PH071_w0h0


title: LP-LP_C10


title: serum_shortRNA_PH059_w0h3


title: serum_shortRNA_PH059_w0h24


title: LP-HP_C9

value: HP


title: LP-HP_C8


title: LP-HP_C7


title: PT 32 I re LL


title: serum_shortRNA_PH059_w0h0


title: LP-CN_C6

value: CN


title: LP-CN_C5


title: serum_shortRNA_PH046_w0pre


title: PT 31 II li LL


title: serum_shortRNA_PH046_w0h24


title: serum_shortRNA_PH046_w0h3


title: serum_shortRNA_PH029_w0pre


title: PT 31 I re LL