title: elav_rnai_4

type: RNA

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

country: USA

institute: Virginia Commonwealth Univ.

description: Gene expression data from whole fly heads tissue, rnai+ and elav+ knockdown strain

hyb_protocol: Following fragmentation, cRNA samples were hybridized to GeneChip Drosophila Gene 1.0 ST arrays by procedures outlined by Affymetrix.

scan_protocol: Affymetrix Genechip scanner 3000 7G was used scanning and AGCC software for analysis, per manufacturer protocols.

data_processing: Microarray CEL files were processed with the R package Oligo v1.44.0 for background subtraction and normalization, which implements the robust multi-array average (RMA) method.

label: biotin

organism: Drosophila melanogaster

source_name: RNA from fly heads, elav and rnai

label_protocol: Botinylated cRNA samples were prepared according to Affymetrix protocols.

extract_protocol: Total RNA was obtained from whole fly head homogenates as described previously (Jones et al. 2014).

treatment_protocol: Flies harboring the neuron-selective elav-Gal4 driver and/or Clic UAS-RNAi transgenev105975 were reared and crossed as previously described (Chan et al. 2014). Fly strains were raised and processed under identical conditions.

value: head


title: H3K9me3 ChIP-Seq V63

status: Public on Jul 01 2021

type: SRA

city: Barcelona

first: Anastasia

last: Pickford

state: Barcelona

address: Carrer Rosselló 153

country: Spain

institute: ISGlobal

library_source: genomic

data_processing:
Repetitive kmers removed from the reads using BBDuK (v36.99) with parameters ktrim=r k=22 mink=6.
Reads aligned using Bowtie (v1.2) with parameters --very-sensitive --local -5 4 -3 4 -I 50 -X 200.
For those samples that were resequenced (files with reseq suffix), alignments from different runs were merged at this level using samtools merge (v 1.7)
Peaks called using MACS2 “callpeak” (v2.2.7.1) with parameters -f BAMPE -g 2.41e7 --fe-cutoff 1.5 --nomodel --extsize 150
Differential peaks called using MACS2 “bdgdiff” (v2.2.7.1) with parameters -g 250 -l 300 --cutoff 5
Coverage per sample was calculated using DeepTools  “BamCompare” (v.3.5.0) with parameters --outFileFormat bedgraph --scaleFactorsMethod None --normalizeUsing RPKM -bs 100
For each sample, gene coverage for each gene was calculated as the average coverage of the region 1000bp upstream plus the first 500bp of its coding sequence with custom scripts (available on demand).
Genome_build: PlasmoDB-46_Pfalciparum3D7_Genome.fasta (P. falciparum 3D7 genome in PlasmoDB v.46)
genome annotation: PlasmoDB-46_Pfalciparum3D7_Genome.gff (P. falciparum 3D7 annotation in PlasmoDB v.46)
Supplementary_files_format_and_content: NF54_Macspeaks_peaks.narrowPeak/V63_Macspeaks_peaks.narrowPeak: Native MACS2 peaks format refer to documentation for description.
Supplementary_files_format_and_content: NF54IP_vs_V63IP_g250_l300_c5_c5.0_cond1.bed/NF54IP_vs_V63IP_g250_l300_c5_c5.0_cond2.bed: Differential peaks enriched in cond1 (NF54 over V63) or cond2 (V63 over NF54).  Standard BED format. Last column corrseponds to log10 likelihood ratio for the peak.
Supplementary_files_format_and_content: coverage_NF54_genewise.bed/coverage_V63_genewise.bed: Standard BED format. Last column corrsponds to average log2(IP/input) in RPKM coverage. For each sample, gene coverage for each gene was calculated as the average coverage of the region 1000bp upstream plus the first 500bp of its coding sequence with custom scripts (available on demand).

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: Cell culture

growth_protocol: Parasites were cultured in B+ erythrocytes at a 3 % haematocrit under standard culture conditions in RPMI-based supplemented with 10% human serum, in a 5% CO2, 3% O2, balance N2 atmosphere at 35ºC. Tight synchronization (5 h age window) was achieved by Percoll purification followed by sorbitol treatment 5 h later.

extract_protocol:
Chromatin was obtained from saponin-extracted parasites at the late trophozoite or schizont stage, crosslinked with formaldehyde and lysed following the MAGnifyTM Chromatin Immunoprecipitation System (Life Technologies). Samples were sonicated using an M220 sonicator (Covaris) at 10% duty factor, 200 cycles per burst, 140 W of peak incident power for 10 min. Immunoprecipitations were performed overnight at 4ºC with 4 µg of chromatin and 8 µg of antibodies against H3K9me3 (Diagenode pAb-193–050) coupled to protein A/G magnetic beads provided in the kit. Washing, de-crosslinking and elution were performed following the MAGnifyTM Chromatin Immunoprecipitation System recommendations, but avoiding high temperatures that may result in denaturation of extremely AT-rich intergenic regions: de-crosslinking, proteinase K treatment and elution were performed at 45ºC (for 2 h, over-night, and 1.5 h, respectively).
Libraries for Illumina sequencing were prepared from 5 ng of immunoprecipitated DNA using a protocol adapted to a genome with an extremely high AT-richness (Kensche et al., 2016. PMID: 26578577). In brief, after end-repair and addition of 3′ A-overhangs, NEBNext Multiplex Oligos for Illumina (NEB, E7335, E7500) were ligated. Purification steps were performed with Agencourt AMPure XP beads (Beckman Coulter, A63880). Libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KK2103) in KAPA HiFi Fidelity Buffer (5X) with the following conditions: 95°C for 3 min; 9 cycles at 98°C for 20 s and 62°C for 2 min 30 s; and 62 °C for 5 min. Amplified libraries were purified using 0.9X AMPure XP beads to remove adapter dimers. The library size was analyzed in a 4200 TapeStation System (Agilent Technologies).

treatment_protocol: No treatment performed on samples, just samples of different origin. The NF54 parental line was  an in vitro adapted strain always cultured in standard conditions and the V63 volunteer sample came from a previous controlled human malaria infection (CHMI) study in which volunteers were injected with NF54 sporozoites and blood samples were collected 11-14 days later (Gomez-Perez, G. P. et al., 2013. PMID: 26245196). We cultured the volunteer parasites in the same conditions as the NF54 parental line but for the minimum time possible so that their H3K9me3 distribution patterns wouldn’t be altered by in vitro growth conditions.

tag: strain

tag: culture method

value: mosquito and human passaged parasites

tag: chip antibody

value: H3K9me3 (Diagenode pAb-193-050)


title: H3K9me3 ChIP-Seq NF54

value: premosquito in vitro culture


title: elav_rnai_2

molecule: total RNA

tag: tissue


title: rnai_5

description: Gene expression data from whole fly heads tissue, rnai-only control strain

source_name: RNA from fly heads, rnai only

value: rnai


title: elav_4

description: Gene expression data from whole fly heads tissue, elav-only control strain

source_name: RNA from fly heads, elav only

value: elav


title: elav_rnai_5


title: rnai_2


title: Input of NF54


title: elav_2


title: rnai_1


title: elav_rnai_1


title: rnai_4


title: elav_3


title: elav_5


title: elav_rnai_3


title: rnai_3


title: Input of V63


title: UTSCC5_siOct4_rep1

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

country: Germany

institute: OncoRay

description: Gene expression in UTSCC5 transfected with siOct4

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C wit GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using scan protocol Agilent G3_GX_1_color for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612 to obtain background subtracted and spatially detrended Processed Signal intensities

organism: Homo sapiens

source_name: UTSCC5 transfected with siOct4, repeat 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: Standard tissue culture at 37 ºC in a humidified incubator with 5% CO2, in DMEM supplemented with 10% FBS, 10mM HEPES, and 1x Pen/Strep

extract_protocol: RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer's recommendations

treatment_protocol: Cells were seeded in 6-well plates at density 200000-300000 cells per well. Next day cells were transfected with 12ul Lipofectamine RNAiMax and 150 pmol of corresponding siRNA per well, and after 48h harvested for further analysis

tag: cell line

tag: treatment


title: UTSCC5_siOct4_rep2

source_name: UTSCC5 transfected with siOct4, repeat 2


title: UTSCC5_siOct4_rep3

source_name: UTSCC5 transfected with siOct4, repeat 3


title: UTSCC5_siScr_rep1

description: Gene expression in UTSCC5 transfected with siScr

source_name: UTSCC5 transfected with siScr, repeat 1

value: siScr


title: UTSCC5_siScr_rep2

source_name: UTSCC5 transfected with siScr, repeat 2


title: elav_1


title: Cal33_siOct4_rep3

description: Gene expression in Cal33 transfected with siOct4

source_name: Cal33 transfected with siOct4, repeat 3


title: UTSCC5_siScr_rep3

source_name: UTSCC5 transfected with siScr, repeat 3


title: Cal33_siOct4_rep2

source_name: Cal33 transfected with siOct4, repeat 2


title: DU145-RR_Gln+_rep3

description: Gene expression in DU145 radioresistant grown in complete medium

source_name: DU145 radioresistant, complete medium, repeat 3

growth_protocol: Standard tissue culture at 37 ºC in a humidified incubator with 5% CO2. DU145 - in DMEM supplemented with 10% dialyzed FBS, with or without 2 mM L-glutamine. LNCaP - in RPMI-1640 supplemented with 10% dialyzed FBS, with or without 2 mM L-glutamine.

treatment_protocol: Radioresistant sub-lines were generated from original (parental) DU145 and LNCaP cell lines by multiple X-ray irradiations, 4Gy/dose, 1 week recovery between doses.

value: DU145 radioresistant

tag: medium

value: complete


title: LNCaP-RR_Gln-_rep3

description: Gene expression in LNCaP radioresistant grown in glutamine deprived medium

source_name: LNCaP radioresistant, glutamine deprived medium, repeat 3

value: LNCaP radioresistant

value: glutamine deprived


title: DU145-RR_Gln-_rep3

description: Gene expression in DU145 radioresistant grown in glutamine deprived medium

source_name: DU145 radioresistant, glutamine deprived medium, repeat 3


title: FaDu_siOct4_rep3

description: Gene expression in FaDu transfected with siOct4

source_name: FaDu transfected with siOct4, repeat 3

value: FaDu


title: FaDu_siOct4_rep1

source_name: FaDu transfected with siOct4, repeat 1


title: Cal33_siScr_rep3

description: Gene expression in Cal33 transfected with siScr

source_name: Cal33 transfected with siScr, repeat 3


title: Cal33_siScr_rep1

source_name: Cal33 transfected with siScr, repeat 1


title: DU145_Gln-_rep1

description: Gene expression in DU145 parental grown in glutamine deprived medium

source_name: DU145 parental, glutamine deprived medium, repeat 1

value: DU145 parental


title: DU145-RR_Gln-_rep1

source_name: DU145 radioresistant, glutamine deprived medium, repeat 1


title: DU145_Gln-_rep3

source_name: DU145 parental, glutamine deprived medium, repeat 3


title: DU145_Gln+_rep3

description: Gene expression in DU145 parental grown in complete medium

source_name: DU145 parental, complete medium, repeat 3


title: DU145_Gln+_rep1

source_name: DU145 parental, complete medium, repeat 1


title: LNCaP-RR_Gln-_rep1

source_name: LNCaP radioresistant, glutamine deprived medium, repeat 1


title: FaDu_siScr_rep2

description: Gene expression in FaDu transfected with siScr

source_name: FaDu transfected with siScr, repeat 2


title: Cal33_siScr_rep2

source_name: Cal33 transfected with siScr, repeat 2


title: Cal33_siOct4_rep1

source_name: Cal33 transfected with siOct4, repeat 1


title: FaDu_siScr_rep3

source_name: FaDu transfected with siScr, repeat 3


title: FaDu_siOct4_rep2

source_name: FaDu transfected with siOct4, repeat 2


title: MTD_IR_DN1, H3K27-ac

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

description: InR-DN progeny

data_processing:
QC control: FASTQC report with basic sequencing quality statistics
mapping reads:Bowtie
Peak Calling: MACS2/HOMER
Genome_build: Drosophila release  6
Supplementary_files_format_and_content: bigWig

source_name: 16hr embryos

growth_protocol: flies were grown on standard bottle food supplemented with yeast paste

extract_protocol:
H3K27-ac (Cell signaling #8143-s)
DNA was isolated from 400 16hr embryos and subjected to H3K27-me3 immunoprecipatation
Ttakara hruPLEX® DNA-Seq Kit

tag: antibody

value: H3K27-ac ChIP sample


title: FaDu_siScr_rep1

source_name: FaDu transfected with siScr, repeat 1


title: MTD_IR_DN1

description:
InR-DN progeny
MTD_IR_DN1_S12

data_processing:
QC control: FASTQC report with basic sequencing quality statistics
mapping reads : Bowtie
Peak Calling : MACS2
Genome_build: Drosophila release  6
Supplementary_files_format_and_content: bigWig

extract_protocol:
DNA was isolated from 400 16hr embryos and subjected to H3K27-me3 immunoprecipatation
Ttakara hruPLEX® DNA-Seq Kit

tag: genotype/variation

value: progeny of  InR-DN expressing stage 14 oocytes

tag: developmental stage/tissue

value: 16hr embryos


title: MTD_IR_DN2

description:
InR-DN progeny
MTD_IR_DN2_S13


title: InR-DN 2 embryo

description:
polyA selected
InR-DN progeny

library_source: transcriptomic

data_processing:
baseliing using a HiSeq 2500
QC control: FASTQC report with basic sequencing quality statistics
mapping reads : Bowtie
tophat
differential analysis: Edge R
Genome_build: Drosophila release 6
Supplementary_files_format_and_content: igenomes_known_GENES_counts_con_embryos-VS-InR_embryos.glmLRT.txt

source_name: 16-20 hr embryos

extract_protocol:
rnA was collected from samples of 200 16-20hr embryos using tripure RNA isolation reagent
TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina

tag: genotype

value: InR-DN progeny


title: MTD_IR_DN2, H3K27-ac

description: InR-DN progeny


title: GFP control 2 embryo

description:
polyA selected
control

value: control


title: GFP control 3 oocyte

description:
polyA selected
control

data_processing:
baseliing using a HiSeq 2500
QC control: FASTQC report with basic sequencing quality statistics
mapping reads : Bowtie
tophat
differential analysis: Edge R
Genome_build: Drosophila release  6
Supplementary_files_format_and_content: igenomes_known_GENES_counts_con_embryos-VS-InR_embryos.glmLRT.txt

source_name: stage 14 oocytes

extract_protocol:
RNA was isolated from sample of 200 stage 14 oocytes using tripure RNA isolation reagent
TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina

value: GFP control


title: MTD_control1, H3K27-ac

description: control


title: InR-DN 1 oocyte

description:
polyA selected
InR-DN progeny

value: InR-DN


title: InR-DN 2 oocyte

description:
polyA selected
InR-DN progeny


title: InR-DN 3 embryo

description:
polyA selected
InR-DN progeny


title: InR-DN 1 embryo

description:
polyA selected
InR-DN progeny


title: GFP control 3 embryo

description:
polyA selected
control


title: GFP control 1 embryo

description:
polyA selected
control


title: MTD_control1

description:
control
MTD_control1_S10

value: progeny of  GFP expressing (control) stage 14 oocytes


title: MTD_control2

description:
control
MTD_control2_S11


title: InR-DN 3 oocyte

description:
polyA selected
InR-DN progeny


title: gas1_NAC_NA_Glucose_4

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

data_processing:
Align RNA-seq reads to reference genome (ws235) and transcriptome (WBcel235.79) using the STAR program (version 2.5.1b)
Reads uniquely mapped to known genes were counted to obtain a read count matrix
Genes were annotated by unique Entrez IDs
Genome_build: ws235
Supplementary_files_format_and_content: Tab-delimited text file inclduing an integer matrix of gene-level read counts. Row names are unique Entriez gene IDs. Data is not normalized.

organism: Caenorhabditis elegans

source_name: Whole worms

growth_protocol: Worms were grown at 20 C on NGM agar plates

extract_protocol:
Worm RNA was extracted using the Trizol method
cDNA library preparation was performed using the TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: Synchronized young adult gas-1(fc21) worms were treated for 24 h with water control, 2. 5 mM n-acetylcysteine, 1mM Nicotinic acid, 10mM Glucose and their respective double and triple combinations.  N2 wild-type were treated with water control.

tag: group

tag: nicotinic acid

value: Yes

tag: n-acetylcysteine

tag: glucose

tag: batch

tag: age at rna isolation

value: 24 hour old young adult

tag: dev_stage at treatment initiation

value: 1st day young adult

tag: Sex

value: Hermaphrodite

value: Erzsebet Polyak, PhD

tag: disease

value: mitochondrial disease

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

tag: phenotype

value: Complex I deficient

tag: drug-concentration

value: NAC(2.5mM) + Glu (10mM)+NA(1mM)


title: gas1_NAC_NA_Glucose_3

tag: strain


title: gas1_NAC_Glucose_4

value: No

value: NAC(2.5mM) + Glu (10mM)


title: GFP control 2 oocyte

description:
polyA selected
control


title: GFP control 1 oocyte

description:
polyA selected
control


title: gas1_NAC_NA_Glucose_2


title: gas1_NA_Glucose_2

value: NA(1mM)+Glu (10mM)


title: gas1_NA_Glucose_4


title: gas1_NA_Glucose_1


title: gas1_NAC_NA_Glucose_1


title: LNCaP-RR_Gln+_rep3

description: Gene expression in LNCaP radioresistant grown in complete medium

source_name: LNCaP radioresistant, complete medium, repeat 3

tag: cell line

value: LNCaP radioresistant

tag: medium

value: complete


title: DU145-RR_Gln+_rep1

source_name: DU145 radioresistant, complete medium, repeat 1

value: DU145 radioresistant


title: gas1_Glucose_1

value: Glucose (Glu) (10mM)


title: gas1_NAC_NA_1

value: NAC(2.5mM) + NA(1mM)


title: gas1_NA_1

value: Yes

value: Nicotinic acid (NA) (1mM)


title: gas1_NAC_Glucose_2

value: 24 hour old young adult

value: 1st day young adult


title: gas1_NAC_NA_2

value: Hermaphrodite

value: Erzsebet Polyak, PhD


title: gas1_NAC_4

value: mitochondrial disease

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

value: N-Acetylcysteine (NAC) (2.5mM)


title: gas1_NAC_Glucose_1

value: No

value: Complex I deficient


title: gas1_NAC_1


title: gas1_NAC_2


title: gas1_NAC_NA_4


title: gas1_NAC_NA_3


title: gas1_NA_2


title: LNCaP_Gln-_rep3

description: Gene expression in LNCaP parental grown in glutamine deprived medium

source_name: LNCaP parental, glutamine deprived medium, repeat 3

value: LNCaP parental

value: glutamine deprived


title: gas1_Glucose_4


title: gas1_Glucose_3


title: gas1_2


title: gas1_3


title: gas1_NA_Glucose_3

value: NA(1mM)+Glu (10mM)


title: gas1_1


title: N2_3

value: N2 Bristol

value: wild-type


title: gas1_Glucose_2

value: Glucose (Glu) (10mM)


title: REB088: MG1655 delta hsdSMR log rep 2

city: Singapore

first: Swaine

middle: L

last: Chen

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Medicine

country: Singapore

institute: National University of Singapore and Genome Institute of Singapore

data_processing:
Raw sequencing reads were mapped to their respective reference genomes: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073 using BWA-MEM (version 0.7.10) with default parameters, then the resulting bam files were sorted and deduplicated using PicardTools v.2.2.2
HTseq was used to quantify sequencing reads mapping to predicted open reading frames (ORFs)
Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences (based on the corresponding Genbank RefSeq annotation) were filtered out of the data set.
R (version 2.15.1) was used for differential expression analysis, using the edgeR package (samples were normalized by TMM (trimmed median of means), common and tagwise dispersion factors were estimated using a negative binomial model, and then fold change values were calculated from these normalized counts)
Genome_build: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression values, fold change, P-values, and FDR values.

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

source_name: MG1655 delta hsdSMR

growth_protocol: Stationary phase cells were obtained by propagating strains statically for two serial 24 hour passages at 37°C, with a 1:1000 dilution between passages (identical to the inoculum used for mouse infections). Log phase cells were obtained by diluting overnight cultures 1:100 in LB and growing to log phase (OD600 = 0.4 – 0.5) at 37°C with shaking.

extract_protocol:
RNA extraction with the Qiagen RNAEasy Mini Kit; ribosomal depletion with the Ribo Zero rRNA removal kit
RNA libraries were prepared using the ScriptSeq v2 RNA-seq library preparation kit

tag: growth condition

value: log phase

value: delta hsdSMR


title: gas1_NAC_Glucose_3

value: Yes

value: 24 hour old young adult

value: NAC(2.5mM) + Glu (10mM)


title: gas1_NA_4

value: 1st day young adult

value: Hermaphrodite

value: Erzsebet Polyak, PhD

value: Nicotinic acid (NA) (1mM)


title: REB078: MG1655 wt log rep 1

source_name: MG1655 wt

value: wt


title: gas1_NA_3

value: No

value: mitochondrial disease

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

value: Complex I deficient


title: LNCaP_Gln+_rep1

description: Gene expression in LNCaP parental grown in complete medium

source_name: LNCaP parental, complete medium, repeat 1

value: LNCaP parental

value: complete


title: gas1_NAC_3

value: N-Acetylcysteine (NAC) (2.5mM)


title: Pooled sera_50456

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900620215.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

organism: Staphylococcus aureus

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: Pooled sera

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: gas1_4

tag: group

tag: nicotinic acid

tag: n-acetylcysteine

tag: glucose

tag: batch

tag: age at rna isolation

tag: genotype


title: Pooled sera_50452

tag: strain


title: RPMI_50449

value: RPMI

value: 1 hr

value: Mid log phase


title: Pooled sera_50453


title: N2_4

value: N2 Bristol

value: 24 hour old young adult

tag: dev_stage at treatment initiation

value: 1st day young adult

tag: Sex

tag: disease

value: wild-type

tag: phenotype

tag: drug-concentration


title: RPMI_50448

tag: growth media

tag: growth time

tag: growth phase

tag: od600 reading


title: Pooled sera_50852

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900620225.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

tag: temperature

tag: bpa identifier

tag: serovar


title: N2_2

tag: group

tag: nicotinic acid

tag: n-acetylcysteine

tag: glucose

value: Hermaphrodite

value: Erzsebet Polyak, PhD


title: Pooled sera_50468

tag: strain


title: MTD_control2, H3K27-ac

description: control

tag: antibody

value: H3K27-ac ChIP sample


title: N2_1

value: No

tag: batch

tag: age at rna isolation

tag: dev_stage at treatment initiation

tag: Sex

tag: genotype


title: RPMI_50463

tag: growth media

tag: growth time


title: RPMI_50462

tag: growth phase

tag: od600 reading


title: RPMI_50461

tag: temperature

tag: bpa identifier


title: REB079: MG1655 delta hsdSMR log rep 1

tag: growth condition

value: log phase

value: delta hsdSMR


title: RPMI_50460

tag: serovar


title: RPMI_50459


title: REB087: MG1655 wt log rep 2

value: wt


title: Pooled sera_50457


title: LNCaP_Gln-_rep1

source_name: LNCaP parental, glutamine deprived medium, repeat 1

tag: cell line

value: LNCaP parental

tag: medium

value: glutamine deprived


title: RPMI_50458

tag: strain


title: Pooled sera_50455

value: Pooled sera

value: 2 hrs exposure to sera


title: RPMI_50450

value: RPMI

value: 1 hr


title: Pooled sera_50454


title: RPMI_50451

value: Mid log phase


title: LNCaP-RR_Gln+_rep1

source_name: LNCaP radioresistant, complete medium, repeat 1

value: LNCaP radioresistant

value: complete


title: RPMI_50447


title: LNCaP_Gln+_rep3

source_name: LNCaP parental, complete medium, repeat 3


title: RPMI_50446


title: Pooled sera_50469


title: Pooled sera_50467


title: Pooled sera_50465


title: RPMI_50473

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900620235.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: RPMI_50471


title: RPMI_50470


title: RPMI_50487

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900620245.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: Pooled sera_50489


title: RPMI_50486


title: Pooled sera_50851


title: Pooled sera_50481


title: RPMI_50483


title: Pooled sera_50480


title: Pooled sera_50478


title: RPMI_50482


title: Pooled sera_50504

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900620255.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: Pooled sera_50490


title: Pooled sera_50477


title: Pooled sera_50476


title: RPMI_50475


title: RPMI_50474


title: RPMI_50498


title: RPMI_50495


title: RPMI_50494


title: Pooled sera_50502


title: Pooled sera_50627


title: Pooled sera_50492


title: Pooled sera_50491


title: Pooled sera_50493


title: CompGrowth_Thirty_Kin_MinusATc_Rep2

city: Heidelberg

first: Cosimo

last: Jann

address: Meyerhofstr. 1

department: Genome Biology

institute: EMBL Heidelberg

description: PCR-amplified DNA barcodes

data_processing:
Library strategy: CRISPR screen
Sequencing data was demultiplexed with Jemultiplexer with standard parameters and base call quality controlled with FastQC. Reads were trimmed and aligned to the FASTA of DNA barcode sequences (FASTA available on series record) with the Burrows-Wheeler algorithm to compute read counts.
Fold changes for gRNA barcodes and for genes were computed in R code using the edgeR package, although other read-count based packages can be used alternatively, such as limma or DeSeq2. Read counts were normalized by library size. Fitness fold changes were calculated as contrasts between +ATc and -ATc condition (+ATc/-ATc) of populations that both underwent competitive growth selection (fitness effect). Fold changes of the thermotolerance screen are ratios between +ATc samples after heat shock versus before heat shock (thermotolerance effect). Fold changes of the HSR screen denote ratios between +ATc samples sorted for high cellular GFP reporter intensity versus low cellular GFP reporter intensity (Heat shock response effect, based on activity of the Hsp70 Ssa1 chaperone promoter). Gene log2FCs were computed as mean log2FC of all gRNAs per gene. Alternatively, these can be computed without prior calculation of gRNA log2FCs by starting the edgeR analysis from the geometric mean of readcounts per gene. We further calculate rank-based gene score measures based on a subset of gRNAs with extreme effects and the median log2FC of gRNAs.
Supplementary_files_format_and_content: raw read counts and Log2 fold changes of gRNAs and genes

organism: synthetic construct

source_name: Saccharomyces cerevisiae transformed with Plasmid-encoded DNA barcodes

growth_protocol:
design protocol: Guide RNA oligonucleotides were designed to target 161 TFs (retrieved from yetfasco.ccbr.utoronto.ca on 16/04/2014 with DNA-binding=1 and dubious=false; De Boer and Hughes, 2012) and 129 PKs (retrieved from yeastkinome.org on 16/04/2014; Breitkreutz et al., 2010), consisting of 885 and 668 gRNAs, respectively. Each gene was covered by up to six different gRNAs. Guide RNA oligonucleotides were integrated into the NotI site of the pRS416 dCas9-Mxi1 plasmid via Gibson Assembly, amplified in E. coli, and transformed into the S. cerevisiae BY4743 SSA1pr-GFP reporter strain.
Transformed yeast populations were constantly grown in sythetic complete uracil dropout medium (URA3 selection gene on CRISPRi plasmids).

extract_protocol:
Before and after selection procedures, plasmid DNA was extracted using FastPrep and glass beads to destroy the yeast cell wall in combination with standard extraction methods. The gRNA barcodes amplified from the one-copy-per-cell CEN-plasmids. Illumina sequencing was performed in paired-end and 75-100 base pairs read length on NextSeq500 machines with 15% PhiX spike-in.
DNA barcode libraries were generated by introducing standard Illumina P5 and P7 adapters and inline sample barcodes by PCR. Library preparation is otherwise performed according to standard Illumina protocols

treatment_protocol: Bulk yeast populations were treated with 250ng/µl anhydrotetracycline (ATc) to induce gRNA expression and CRISPR interference and without ATc as reference in 2-4 replicates. Yeast populations were grown in exponential phase. For competitive growth assays, populations were diluted to OD600=0.005 and grown over 1.5-2 days at temperatures 23, 30 and 38°C. For thermotolerance assays, populations were diluted to OD600=0.3, exposed to a lethal heat shock (150 min at 50°C) and recovered without maintaining CRISPRi induction. For HSR activity screens, populations were diluted to OD600=0.3, exposed to 42°C for 5h to induce HSR, and sorted based on their cellular Hsp70 GFP reporter intensity. At least 250.000 cells in both the top and bottom 5% of populations were collected and recovered.

tag: yeast strain

tag: treatment

value: Competitive growth selection at 30 degrees C

value: Protein kinase gRNA library

value: No Atc

tag: sequenced molecule

value: plasmid DNA


title: CompGrowth_Thirty_Kin_PlusATc_Rep2

description: PCR-amplified DNA barcodes

value: With Atc


title: CompGrowth_Thirty_Kin_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_Thirty_TF_MinusATc_Rep1

description: PCR-amplified DNA barcodes

value: Transcription factor gRNA library


title: RPMI_50484


title: RPMI_50472


title: RPMI_50496


title: FACS_TF_PlusATC_high_Rep3

description: PCR-amplified DNA barcodes

value: Sorted by FACS for SSA1pr-GFP expression. Cellular GFP intensity:high


title: Pooled sera_50505


title: FACS_TF_MinusATC_low_Rep3

description: PCR-amplified DNA barcodes

value: Sorted by FACS for SSA1pr-GFP expression. Cellular GFP intensity:low


title: FACS_TF_MinusATC_high_Rep3

description: PCR-amplified DNA barcodes


title: CompGrowth_Thirty_TF_MinusATc_Rep2

description: PCR-amplified DNA barcodes


title: Pooled sera_50503


title: FACS_Kin_PlusATC_high_Rep3

description: PCR-amplified DNA barcodes


title: FACS_Kin_MinusATC_low_Rep3

description: PCR-amplified DNA barcodes


title: Pooled sera_50501


title: FACS_Kin_MinusATC_high_Rep3

description: PCR-amplified DNA barcodes


title: FACS_TF_MinusATC_low_Rep2

description: PCR-amplified DNA barcodes


title: Pooled sera_50628


title: FACS_Kin_PlusATC_low_Rep2

description: PCR-amplified DNA barcodes


title: FACS_Kin_PlusATC_high_Rep2

description: PCR-amplified DNA barcodes


title: RPMI_50499


title: RPMI_50485


title: FACS_Kin_MinusATC_low_Rep2

description: PCR-amplified DNA barcodes


title: FACS_TF_PlusATC_low_Rep1

description: PCR-amplified DNA barcodes


title: RPMI_50497


title: FACS_TF_MinusATC_low_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_Thirty_TF_PlusATc_Rep2

description: PCR-amplified DNA barcodes


title: CompGrowth_Thirty_TF_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: FACS_Kin_MinusATC_low_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_TF_PlusATc_Rep2

description: PCR-amplified DNA barcodes

value: Competitive growth selection at 23 degrees C


title: CompGrowth_TwentyThree_TF_MinusATc_Rep2

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_Kin_MinusATc_Rep2

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_Kin_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_Kin_PlusATc_Rep2

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_Kin_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: FACS_TF_PlusATC_low_Rep2

description: PCR-amplified DNA barcodes


title: FACS_TF_PlusATC_low_Rep3

description: PCR-amplified DNA barcodes


title: FACS_TF_PlusATC_high_Rep2

description: PCR-amplified DNA barcodes


title: FACS_TF_MinusATC_high_Rep2

description: PCR-amplified DNA barcodes


title: CompGrowth_Thirty_Kin_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_ThirtyEight_TF_MinusATc_Rep2

description: PCR-amplified DNA barcodes

value: Competitive growth selection at 38 degrees C


title: CompGrowth_ThirtyEight_TF_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_ThirtyEight_Kin_PlusATc_Rep2

description: PCR-amplified DNA barcodes


title: FACS_Kin_PlusATC_low_Rep3

description: PCR-amplified DNA barcodes


title: CompGrowth_ThirtyEight_Kin_MinusATc_Rep2

description: PCR-amplified DNA barcodes


title: CompGrowth_ThirtyEight_Kin_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: beforeFACS_TF_PlusATc_Rep3

description: PCR-amplified DNA barcodes

value: Before FACS


title: CompGrowth_ThirtyEight_TF_PlusATc_Rep2

description: PCR-amplified DNA barcodes


title: FACS_Kin_MinusATC_high_Rep2

description: PCR-amplified DNA barcodes


title: FACS_TF_PlusATC_high_Rep1

description: PCR-amplified DNA barcodes


title: beforeFACS_TF_MinusATc_Rep3

description: PCR-amplified DNA barcodes


title: beforeFACS_TF_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: beforeHS_TF_MinusATC_Rep1

description: PCR-amplified DNA barcodes

value: Before heat shock treatment


title: beforeHS_TF_PlusATC_Rep2

description: PCR-amplified DNA barcodes


title: beforeFACS_Kin_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: beforeHS_TF_MinusATC_Rep2

description: PCR-amplified DNA barcodes


title: FACS_TF_MinusATC_high_Rep1

description: PCR-amplified DNA barcodes


title: beforeHS_Kin_PlusATC_Rep4

description: PCR-amplified DNA barcodes


title: beforeHS_Kin_PlusATC_Rep3

description: PCR-amplified DNA barcodes


title: FACS_Kin_PlusATC_low_Rep1

description: PCR-amplified DNA barcodes


title: FACS_Kin_PlusATC_high_Rep1

description: PCR-amplified DNA barcodes


title: FACS_Kin_MinusATC_high_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_TF_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: beforeHS_Kin_MinusATC_Rep4

description: PCR-amplified DNA barcodes


title: beforeHS_Kin_MinusATC_Rep3

description: PCR-amplified DNA barcodes


title: CompGrowth_TwentyThree_TF_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_ThirtyEight_TF_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: CompGrowth_ThirtyEight_Kin_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: afterHS_Kin_PlusATC_Rep2

description: PCR-amplified DNA barcodes

value: After heat shock treatment


title: afterHS_Kin_MinusATC_Rep4

description: PCR-amplified DNA barcodes


title: beforeFACS_Kin_PlusATc_Rep3

description: PCR-amplified DNA barcodes


title: afterHS_Kin_MinusATC_Rep3

description: PCR-amplified DNA barcodes


title: beforeFACS_Kin_MinusATc_Rep3

description: PCR-amplified DNA barcodes


title: afterHS_Kin_MinusATC_Rep1

description: PCR-amplified DNA barcodes


title: afterHS_Kin_MinusATC_Rep2

description: PCR-amplified DNA barcodes


title: Input

city: Nanjing

first: Pengyue

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

country: China

institute: NanJing Argriculture University

data_processing:
Raw G4-ChIP-seq data were cleaned through trimming adapter contamination and removing low-quality reads using Trim Galore! (version 0.4.4). All cleaned reads were aligned to the MSU v7.0 reference genome using BWA (Burrows-Wheeler Aligner) (mem algorithm, version 0.7.17) with default parameters. Any PCR duplicates were removed using Picard. Reads with mapping quality below ten were excluded using SAMtools (version 1.5, option -q). Only reads with alignment length greater than 50 were used for G4 peak calling and further analyses.
G4 Peak calling was performed using MACS (version 2.1.1) with the following command and parameters: macs2 callpeak -g 3.8e+8 -f BAM --extsize 200 -p 1e-5 –nomodel, and the input library was used as control.

The PQS loci file were generate using fastaRegexFinder.py through the rice7 MSU genome
G2 pattern were identified using regular expression ([gG]{2}\w{1,12}){3,}[gG]{2}
G3 pattern were identified using regular expression ([gG]{3}\w{1,12}){3,}[gG]{3}

Genome_build: Rice MSU v7.0
Supplementary_files_format_and_content: wig files were generated using bamCoverage and bigWigToWig, bed files were generated using macs2
Supplementary_files_format_and_content: xlsx files with PQS loci for each chromosome

organism: Oryza sativa

source_name: Seedlling

growth_protocol: Rice (Oryza. sativa L. spp. japonica) seeds were immerged in tap water at RT in the lab for three days. Uniformly germinated seeds were sowed in the nutrient soil and grown in a greenhouse at a temperature at 28-30 ℃ and a 14 h/10 h light-dark cycle. Two-week-old rice seedlings were collected and cross-linked using 1% of formaldehyde for 10 min under vacuum. The cross-linked seedlings were ground into a fine powder in liquid nitrogen, and stored in -80 ℃ or immediately used for preparation of genomic DNA.

extract_protocol: The purified nuclei were fragmented into sizes ranging from 100-500 bp in sonication buffer (50 mM Tris-HCl + 10 mM EDTA + 1% SDS) using the water-based Biorupter (Diagnode) followed by reverse cross-linking at 65 ℃ overnight，which 5M NaCl was added to a final concentration 0.2M. The reverse cross-linked DNA was purified by phenol:chloroform extraction and ethanol precipitation.Total 5 μg fragmented genomic DNA was diluted in G4 stabilization buffer (GSB) (150 mM KCl + 40% PEG200 + 10 mM Tris-HCl, pH=7.5), and denatured at 95 ℃ for 5 min followed by reassociation with the temperature slowly dropped down to RT. The reassociated DNA was diluted with G4-ChIP incubation buffer (GCB) (50 mM HEPES + 150 mM KCl+ 1 mM MgCl2+ 130 nM CaCl2+1 % BSA+ 40% PEG200 + Complete mini, pH 7.5). 3 μg purified BG4-FLAG recombinant protein was added and incubated at 4 ℃ for 4 h with constant rotation. 3 μg anti-FLAG antibody (D110005, BBI) was then added and incubated at 4 ℃ for additional 4 h. 30 μl protein G Dynalbeads (10004D, Invitrogen) was washed with incubation buffer for three times, and added to the reaction for incubation at 4℃ for another 4 h. After protein G beads incubation, the beads were collected and washed with washing buffer (10 mM Tris-HCl + 150 mM KCl + 1% Tween20) for three times. The BG4-bound DNA was eluted with 200 μl elution buffer (0.1 M NaHCO3 + 1% SDS) at 65 ℃ for two times with 15 min each. ChIPed and corresponding input DNA was recovered and dissolved in 20 EB (10 mM Tris-HCl, pH=8.0). For BG4-ChIP-seq assay, the BG4-ChIPed DNA was used for library preparation for Illumina sequencing followed by data analysis.

tag: cultivar

value: Nipponbare

tag: tissue

value: Seedling

tag: age

value: two weeks

tag: antibody


title: beforeFACS_TF_MinusATc_Rep2

description: PCR-amplified DNA barcodes


title: afterHS_TF_PlusATC_Rep2

description: PCR-amplified DNA barcodes


title: G4-ChIP-seq_K++PEG_rep1

value: anti-FLAG antibody (D110005, BBI)


title: beforeFACS_TF_PlusATc_Rep2

description: PCR-amplified DNA barcodes


title: beforeFACS_Kin_MinusATc_Rep2

description: PCR-amplified DNA barcodes


title: afterHS_TF_MinusATC_Rep1

description: PCR-amplified DNA barcodes


title: beforeFACS_TF_PlusATc_Rep1

description: PCR-amplified DNA barcodes


title: beforeFACS_Kin_PlusATc_Rep2

description: PCR-amplified DNA barcodes


title: beforeFACS_Kin_MinusATc_Rep1

description: PCR-amplified DNA barcodes


title: beforeHS_TF_PlusATC_Rep1

description: PCR-amplified DNA barcodes


title: Root Slice 16a

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

data_processing:
Sequenced reads were trimmed for adaptor sequences using trimmomatic and trancript abundances were map to Zea mays ssp mays B73 v4 Reference Genome and quatified using Kallisto version 0.43 in single end mode .
DeSeq2 was used for count normalization using median of ratios method.
Genome_build: Zea mays ssp mays B73 v4
Supplementary_files_format_and_content: Matrix table with raw counts for every sample (column) and gene (rows)

organism: Zea mays

source_name: Root longitudinal cut

growth_protocol: Growth chamber: 26 oC, 12h light/12 h dark. Plantlets were grown on germination paper to avoid the presence of substrate when cutting.

extract_protocol:
Longitudinal cuts were applied from the tip to the back of the root until 16 slices where obtained. Two roots were aligned and pinned together to obtain two replicates of comparable longitudinal cuts. Root tissue slices were immediately stored in Qiagen RTL buffer and flash frozen in liquid nitrogen. RNA was extracted using Qiagen RNeasy Micro Kit (Cat No./ID: 74004).
Libraries were prepared using Ovation® RNA-Seq System V2

tag: genotype

value: wild type

value: 7 DAG

value: root A, sixteenth slice, hand section


title: Root Slice 15b

value: root B, fifteenth slice, hand section


title: Root Slice 14a

value: root A, fourteenth slice, hand section


title: beforeHS_Kin_PlusATC_Rep2

description: PCR-amplified DNA barcodes

value: Protein kinase gRNA library

value: With Atc

value: plasmid DNA


title: Root Slice 13a

value: root A, thirteenth slice, hand section


title: Root Slice 12a

value: root A, twelfth slice, hand section


title: Root Slice 12b

value: root B, twelfth slice, hand section


title: beforeHS_Kin_PlusATC_Rep1

description: PCR-amplified DNA barcodes

value: Before heat shock treatment


title: Root Slice 10b

value: root B, tenth slice, hand section


title: Root Slice 9b

value: root B, ninth slice, hand section


title: Root Slice 11a

value: root A, eleventh slice, hand section


title: beforeHS_Kin_MinusATC_Rep2

description: PCR-amplified DNA barcodes

value: No Atc


title: afterHS_TF_MinusATC_Rep2

description: PCR-amplified DNA barcodes

value: After heat shock treatment

value: Transcription factor gRNA library


title: Root Slice 8b

value: wild type

value: 7 DAG

value: root B, eighth slice, hand section


title: afterHS_Kin_PlusATC_Rep4

description: PCR-amplified DNA barcodes


title: Root Slice 7a

value: root A, seventh slice, hand section


title: Root Slice 6b

value: root B, sixth slice, hand section


title: afterHS_Kin_PlusATC_Rep3

description: PCR-amplified DNA barcodes

value: Protein kinase gRNA library

value: With Atc


title: Root Slice 6a

value: root A, sixth slice, hand section


title: afterHS_Kin_PlusATC_Rep1

description: PCR-amplified DNA barcodes

value: plasmid DNA


title: Root Slice 5a

value: root A, fifth slice, hand section


title: Root Slice 2b

value: root B, second slice, hand section


title: Root Slice 2a

value: root A, second slice, hand section


title: G4-ChIP-seq_K++PEG_rep2

value: Nipponbare

value: Seedling

value: two weeks

value: anti-FLAG antibody (D110005, BBI)


title: Zmroot_sc_read1/2_rep3

description:
HY5VMBGX9_*_S2
barcode read single cell run3 (4 primers combined)
transcript read single cell run3 (4 primers combined)

data_processing:
Raw base calls were demultiplexed using Illumina's bcl2fastq.
Alignment, barcode and UMI quantification were performed with Chromium 10x Cell Ranger software package. Samples were normalized, and cell clusters determined using Seurat.
Differential gene expression analyses between cell clusters was perfomed using the ROC algorithm from Seurat.
Genome_build: Zea mays ssp mays B73 v4
Supplementary_files_format_and_content: Matrix table with raw counts for every cell (column) and gene (rows). The three replicates were combined.

source_name: Maize root meristem

growth_protocol: Growth chamber: 26 oC, 12h light/12 h dark. Plantlets were grown on germination paper to avoid the presence of substrate.

extract_protocol:
Root tips from maize seminal and principal roots were cut and collected (3-4 mm lenght). Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts. Protoplasts were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' V2 pipeline.
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2

value: Maize root meristem


title: afterHS_TF_PlusATC_Rep1

description: PCR-amplified DNA barcodes

value: After heat shock treatment

value: Transcription factor gRNA library


title: Zmroot_sc_read1/2_rep2

description:
HY5VMBGX9_*_S1
barcode read single cell run2 (4 primers combined)
transcript read single cell run2 (4 primers combined)

value: wild type

value: 7 DAG


title: beforeHS_Kin_MinusATC_Rep1

description: PCR-amplified DNA barcodes

value: Before heat shock treatment

value: No Atc


title: Root Slice 15a

value: root A, fifteenth slice, hand section


title: CD_I_LI_M_15

city: Oxford

first: Fiona

last: Powrie

address: Roosevelt Drive

department: Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences

country: United Kingdom

institute: University of Oxford

data_processing:
Sequence reads were aligned to the human genome with Hisat2 (version 2.1.0) [1] using a “genome” index built from the GRCh38 release of the human genome and known splice sites extracted from Ensembl version 91 annotations (using the hisat2_extract_splice_sites.py tool). A two-pass mapping strategy was used to discover novel splice sites (with the additional parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.6.3; Ensembl version 91 annotations; default parameters).
TPMs were estimated with salmon (version 0.9.1); using a quasi-index (built with Ensembl version 91 annotations and k=31) and gc bias correction (parameter “--gcBias”)
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) "featurecounts_counts.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "salmon.genes.tpms.txt" is a tab-delimited text file containing the table of gene-by-sample raw TPMs computed with salmon.

source_name: CD_I_LI_M_whole intestinal tissue

extract_protocol:
surgical resection tissue was stored in RNAlater (Qiagen) upon collection until further processing. Tissue was homogenised using the soft tissue homogenizing CK14 kit (Precellys, Stretton Scientific 03961) in 300µl of RLT lysis buffer (Qiagen) and 20µM DTT (Sigma). RNA was isolated using the Qiagen Mini kit with a DNA digestion step (Qiagen).
Sequencing libraries were prepared using either the QuantSeq 3’ mRNA-Seq FWD Library Prep Kit (Lexogen) for whole tissue samples or the Smart-seq2 protocol (Picelli et al., 2013) for bulk and cultured cell populations (with in-house indexing primers)
RNA-sequencing, Libraries were sequenced using an Illumina HiSeq4000 with 75bp paired-end sequencing (Lamble et al., 2013).

tag: disease

value: CD

value: inflamed

tag: gender

value: male

tag: disease_duration (y)

tag: qc

value: include


title: Root Slice 16b

value: root B, sixteenth slice, hand section


title: UC_U_SI_F_17

source_name: UC_U_SI_F_whole intestinal tissue

value: UC

value: uninflamed

value: female


title: Root Slice 14b

value: root B, fourteenth slice, hand section


title: CRC_N_LI_M_13

source_name: CRC_N_LI_M_whole intestinal tissue

value: Control


title: Root Slice 11b

value: root B, eleventh slice, hand section


title: CD_U_LI_M_12

source_name: CD_U_LI_M_whole intestinal tissue


title: Root Slice 13b

value: root B, thirteenth slice, hand section


title: Root Slice 10a

value: wild type

value: root A, tenth slice, hand section


title: Root Slice 9a

value: 7 DAG

value: root A, ninth slice, hand section


title: CD_I_SI_M_10

source_name: CD_I_SI_M_whole intestinal tissue


title: Root Slice 7b

value: root B, seventh slice, hand section


title: Root Slice 8a

value: root A, eighth slice, hand section


title: Root Slice 5b

value: root B, fifth slice, hand section


title: UC_I_LI_F_8

source_name: UC_I_LI_F_whole intestinal tissue

value: inflamed


title: Root Slice 4b

value: root B, fourth slice, hand section


title: CD_U_LI_M_6

value: CD

value: male

value: include


title: Root Slice 3b

value: root B, third slice, hand section


title: Root Slice 4a

value: root A, fourth slice, hand section


title: Root Slice 3a

value: root A, third slice, hand section


title: Root Slice 1a

value: root A, first slice, hand section


title: Root Slice 1b

value: root B, first slice, hand section


title: CD_I_SI_F_20

source_name: CD_I_SI_F_whole intestinal tissue

value: female


title: UC_I_LI_F_19

value: UC


title: 8_E

extract_protocol:
Cell populations from tissue or blood were FACS-sorted directly into 300µl of RLT lysis buffer (Qiagen) and 20µM DTT (Sigma). RNA was isolated using the Qiagen Mini kit with a DNA digestion step (Qiagen).
Sequencing libraries were prepared using the the Smart-seq2 protocol (Picelli et al., 2013)  (using in-house indexing primers)
RNA-sequencing, Libraries were sequenced using an Illumina HiSeq4000 with 75bp paired-end sequencing (Lamble et al., 2013).

value: E

value: EXCLUDE


title: UC_I_LI_F_16


title: CD_U_LI_M_14

value: uninflamed


title: CD_I_SI_M_4


title: 7_M

value: M


title: 6_M


title: 6_E


title: 4_N

value: N

value: healthy


title: 7_N

value: inflamed


title: CRC_N_LI_M_11

value: Control


title: UC_M_LI_F_18

source_name: UC_M_whole intestinal tissue


title: 3_N


title: 3_M


title: 26_S

value: S

value: male

value: CD


title: 26_N


title: 26_M

value: include


title: CD_I_SI_F_3


title: 25_E


title: 24_M


title: 23_S


title: 9_M


title: 9_N


title: 9_E


title: 23_N


title: UC_I_LI_M_9

source_name: UC_I_LI_M_whole intestinal tissue


title: 8_M


title: 8_N


title: 23_E


title: CD_I_LI_M_5


title: CD_U_SI_F_7

source_name: CD_U_SI_F_whole intestinal tissue


title: 22_S


title: 22_E


title: 7_E


title: 6_N


title: UC_NA_LI_F_2

source_name: UC_NA_LI_F_whole intestinal tissue


title: 5_N


title: 21_S


title: UC_I_LI_M_1


title: 5_M


title: 5_E


title: 20_M


title: 4_M


title: 4_E


title: 2_E


title: 19_S


title: 3_E


title: 26_E


title: 19_E


title: 25_S


title: 25_N


title: 18_S


title: 25_M


title: 24_E


title: 24_S


title: 24_N


title: 19_M


title: 16_M


title: 18_N


title: 23_M


title: 16_E


title: 22_N


title: 22_M


title: 15_M


title: 17_E


title: 14_N


title: 21_M


title: 21_N


title: 14_M


title: 14_E


title: 21_E


title: 20_S


title: 20_N


title: 2_M


title: 20_E


title: 12_N


title: 19_N


title: 12_M


title: 18_E


title: 2_N


title: 18_M


title: 12_E


title: 11_N


title: 17_N


title: 17_S


title: 17_M


title: 11_E


title: 10_S


title: 16_S


title: 16_N


title: 10_M


title: 15_N


title: 15_S


title: 15_E


title: 1_N


title: 13_S


title: 13_N


title: 13_M


title: CD90-CD49f+ HSC  514

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

institute: DKFZ

data_processing:
Sequencing was set for 3 million 100 bp paar-end reads per cell under Illumina’s kit instructions.
Raw sequencing reads were mapped with STAR
Expression counts estimates and transcripts per million (TPM) were generated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts (TPM) in txt matrix from

molecule: polyA RNA

source_name: CD90-CD49f+ HSC

extract_protocol:
0.2% TrixonX-100 supplemented with 1 U/ul of RNAse inhibitor
Multiplexed Nextera XT; each single cell was barcoded then pooled per plate.
scRNA-seq

value: cord blood

tag: cell type

value: CD90-CD49f+ HSC


title: CD90-CD49f+ HSC  513


title: 12_S


title: CD90-CD49f+ HSC  512


title: CD90-CD49f+ HSC  509


title: 11_M


title: 11_S


title: CD90-CD49f+ HSC  507


title: 1_M


title: 13_E


title: 10_N


title: 10_E


title: CD90-CD49f+ HSC  502


title: 1_E


title: CD90-CD49f+ HSC  500


title: CD90-CD49f+ HSC  497


title: hESC_Primed_SOX2_ChIP_rep2

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: SOX2 ChIP in primed hESCs

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the human genome hg38 using the bowtie2 (v2.3.4) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings. Board peaks were called from ChIP of BAF subunits, and narrow peaks were call from transcription factors.
Genome_build: hg38
Supplementary_files_format_and_content: Bed file of MACS called peaks.

source_name: Embryonic stem cells

growth_protocol: Conventional (primed) human ESCs were maintained on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers and passaged using Collagenase (1 mg/mL) or manual methods. Primed human ESCs were cultured in human ESC medium (hESM) [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (Gibco HI FBS, 10082-147), 5% KnockOut Serum Replacement (Invitrogen), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Naive human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium [DMEM (Invitrogen) supplemented with 10% FBS (Gibco HI FBS, 10082-147), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza) and 0.1 mM β-mercaptoethanol (Sigma)]. For conversion of pre-existing primed human ESC lines, we seeded 2 x 105 trypsinized single cells on a MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (Stemgent, 10 μM). 2 days later medium was switched to 5i/L/A or 4i/L/A (no IM12)-containing naive human ESC medium. Following an initial wave of cell death, naive colonies appeared within 10 days and were expanded polyclonally using Accutase (Gibco) on a MEF feeder layer. Naive human pluripotent cells were derived and maintained in serum-free N2B27-based media supplemented with inhibitors and cytokines. 500 mL of medium was generated by including: 240 mL DMEM/F12 (Invitrogen; 11320), 240 mL Neurobasal (Invitrogen; 21103), 5 mL N2 supplement (Invitrogen; 17502048), 10 mL B27 supplement (Invitrogen; 17504044), 10 μg recombinant human LIF (made in-house), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Lonza), 50 µg/ml BSA (Gibco Fraction V, 15260), and the following small molecules and cytokines: PD0325901 (Stemgent, 1 μM), IM-12 (Enzo, 1 μM or 0 µM), SB590885 (R&D systems, 0.5 μM), WH4-023 (A Chemtek or Selleckchem, 1 μM), Y-27632 (Stemgent, 10 μM) and Activin A (Peprotech, 10 ng/mL). All naïve hESC experiments were conducted in 5% O2, 5% CO2.

extract_protocol:
ChIP was performed following the standard protocol of Millipore (#17-371).
For ChIP of KLF4, SOX2, and SNF2L, about 5 million hESCs were used for each ChIP experiment. Sonication was performed on a Bioruptor system, with 30s ON, 30s OFF, 30 cycles, high amplitude. ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained. For BRG1, BRM, and BAF155, about 20 million hESCs were used for each ChIP experiment. Library prep and sequencing was performed on Illumina NextSeq 500 in the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute. Data with 75-bp single-end reads were obtained.

value: Embryonic stem cells

tag: culture condition

value: Primed (conventional)

tag: chip antibody

value: SOX2 (R&D Systems, AF2018)


title: CD90-CD49f+ HSC  496


title: CD90-CD49f+ HSC  506


title: CD90-CD49f+ HSC  505


title: hESC_Primed_BRM_ChIP

description: BRM ChIP in primed hESCs

tag: cell line

value: BRM (Cell Signaling, #11966)


title: hESC_Naive_SOX2_ChIP_rep2

description: SOX2 ChIP in naive hESCs

value: Naive (5i/L/A)


title: CD90-CD49f+ HSC  516


title: CD90-CD49f+ HSC  493


title: CD90-CD49f+ HSC  491


title: 14_S

value: female

value: UC


title: CD90-CD49f+ HSC  508


title: CD90-CD49f+ HSC  511


title: CD90-CD49f+ HSC  510


title: CD90-CD49f+ HSC  495


title: CD90-CD49f+ HSC  486


title: CD90-CD49f+ HSC  503


title: CD90-CD49f+ HSC  481


title: CD90-CD49f+ HSC  482


title: CD90-CD49f+ HSC  488


title: CD90-CD49f+ HSC  501


title: CD90-CD49f+ HSC  515


title: CD90-CD49f+ HSC  499


title: CD90-CD49f+ HSC  498


title: CD90-CD49f+ HSC  473


title: CD90-CD49f+ HSC  471


title: CD90-CD49f+ HSC  494


title: CD90-CD49f+ HSC  469


title: CD90-CD49f+ HSC  504


title: CD90-CD49f+ HSC  470


title: CD90-CD49f+ HSC  468


title: CD90-CD49f+ HSC  476


title: CD90-CD49f+ HSC  489


title: CD90-CD49f+ HSC  490


title: CD90-CD49f+ HSC  467


title: CD90-CD49f+ HSC  487


title: CD90-CD49f+ HSC  492


title: CD90-CD49f+ HSC  463


title: CD90-CD49f+ HSC  485


title: CD90-CD49f+ HSC  480


title: CD90-CD49f+ HSC  461


title: CD90-CD49f+ HSC  478


title: CD90-CD49f+ HSC  479


title: CD90-CD49f+ HSC  458


title: CD90-CD49f+ HSC  453


title: CD90-CD49f+ HSC  452


title: CD90-CD49f+ HSC  446


title: CD90-CD49f+ HSC  455


title: CD90-CD49f+ HSC  447


title: CD90-CD49f+ HSC  477


title: CD90-CD49f+ HSC  472


title: CD90-CD49f+ HSC  475


title: CD90-CD49f+ HSC  439


title: CD90-CD49f+ HSC  474


title: CD90-CD49f+ HSC  436


title: CD90-CD49f+ HSC  465


title: CD90-CD49f+ HSC  466


title: CD90-CD49f+ HSC  454


title: CD90-CD49f+ HSC  462


title: CD90-CD49f+ HSC  459


title: CD90-CD49f+ HSC  484


title: CD90-CD49f+ HSC  451


title: CD90-CD49f+ HSC  464


title: CD90-CD49f+ HSC  450


title: CD90-CD49f+ HSC  460


title: CD90-CD49f+ HSC  448


title: CD90-CD49f+ HSC  449


title: CD90-CD49f+ HSC  457


title: CD90-CD49f+ HSC  483


title: CD90-CD49f+ HSC  445


title: CD90-CD49f+ HSC  438


title: CD90-CD49f+ HSC  456


title: CD90-CD49f+ HSC  443


title: CD90+CD49f+ HSC  429

source_name: CD90+CD49f+ HSC

value: CD90+CD49f+ HSC


title: CD90-CD49f+ HSC  442


title: CD90-CD49f+ HSC  435


title: CD90-CD49f+ HSC  441


title: CD90+CD49f+ HSC  422


title: CD90-CD49f+ HSC  437


title: CD90+CD49f+ HSC  424


title: CD90-CD49f+ HSC  434


title: CD90-CD49f+ HSC  440


title: CD90+CD49f+ HSC  430


title: CD90+CD49f+ HSC  420


title: CD90-CD49f+ HSC  444


title: CD90+CD49f+ HSC  418


title: CD90+CD49f+ HSC  417


title: CD90-CD49f+ HSC  432


title: CD90+CD49f+ HSC  423


title: CD90+CD49f+ HSC  425


title: CD90+CD49f+ HSC  427


title: CD90+CD49f+ HSC  426


title: CD90-CD49f+ HSC  431


title: CD90+CD49f+ HSC  421


title: CD90+CD49f+ HSC  413


title: CD90+CD49f+ HSC  412


title: CD90+CD49f+ HSC  410


title: CD90+CD49f+ HSC  409


title: CD90-CD49f+ HSC  433


title: CD90+CD49f+ HSC  419


title: CD90+CD49f+ HSC  415


title: CD90+CD49f+ HSC  407


title: CD90+CD49f+ HSC  405


title: CD90+CD49f+ HSC  411


title: CD90+CD49f+ HSC  416


title: CD90+CD49f+ HSC  428


title: CD90+CD49f+ HSC  396


title: CD90+CD49f+ HSC  395


title: CD90+CD49f+ HSC  402


title: CD90+CD49f+ HSC  401


title: CD90+CD49f+ HSC  414


title: CD90+CD49f+ HSC  404


title: CD90+CD49f+ HSC  403


title: CD90+CD49f+ HSC  406


title: CD90+CD49f+ HSC  392


title: CD90+CD49f+ HSC  390


title: CD90+CD49f+ HSC  391


title: CD90+CD49f+ HSC  398


title: CD90+CD49f+ HSC  399


title: CD90+CD49f+ HSC  408


title: CD90+CD49f+ HSC  393


title: CD90+CD49f+ HSC  394


title: CD90+CD49f+ HSC  397


title: CD90+CD49f+ HSC  386


title: CD90+CD49f+ HSC  381


title: CD90+CD49f+ HSC  380


title: CD90+CD49f+ HSC  388


title: CD90+CD49f+ HSC  400


title: CD90+CD49f+ HSC  389


title: CD90+CD49f+ HSC  385


title: CD90+CD49f+ HSC  375


title: CD90+CD49f+ HSC  370


title: CD90+CD49f+ HSC  372


title: CD90+CD49f+ HSC  383


title: CD90+CD49f+ HSC  376


title: CD90+CD49f+ HSC  387


title: CD90+CD49f+ HSC  366


title: CD90+CD49f+ HSC  368


title: CD90+CD49f+ HSC  382


title: CD90+CD49f+ HSC  365


title: CD90+CD49f+ HSC  379


title: CD90+CD49f+ HSC  378


title: CD90+CD49f+ HSC  360


title: CD90+CD49f+ HSC  384


title: CD90+CD49f+ HSC  361


title: CD90+CD49f+ HSC  369


title: CD90+CD49f+ HSC  374


title: CD90+CD49f+ HSC  359


title: CD90+CD49f+ HSC  373


title: CD90+CD49f+ HSC  367


title: CD90+CD49f+ HSC  353


title: CD90+CD49f+ HSC  362


title: CD90+CD49f+ HSC  354


title: CD90+CD49f+ HSC  352


title: CD90+CD49f+ HSC  357


title: CD90+CD49f+ HSC  377


title: CD90+CD49f+ HSC  358


title: CD90+CD49f+ HSC  364


title: CD90+CD49f+ HSC  346


title: CD90+CD49f+ HSC  348


title: CD90+CD49f+ HSC  350


title: CD90+CD49f+ HSC  349


title: CD90+CD49f+ HSC  351


title: CD90-CD49f+ HSC  342


title: CD90+CD49f+ HSC  355


title: CD90+CD49f+ HSC  356


title: CD90+CD49f+ HSC  345


title: CD90+CD49f+ HSC  363


title: CD90+CD49f+ HSC  347


title: CD90-CD49f+ HSC  343


title: CD90-CD49f+ HSC  340


title: CD90-CD49f+ HSC  333


title: CD90-CD49f+ HSC  334


title: CD90-CD49f+ HSC  338


title: CD90-CD49f+ HSC  337


title: CD90-CD49f+ HSC  330


title: CD90-CD49f+ HSC  332


title: CD90-CD49f+ HSC  341


title: CD90-CD49f+ HSC  335


title: CD90-CD49f+ HSC  339


title: CD90-CD49f+ HSC  324


title: CD90-CD49f+ HSC  344


title: CD90-CD49f+ HSC  326


title: CD90-CD49f+ HSC  327


title: CD90-CD49f+ HSC  329


title: CD90-CD49f+ HSC  328


title: CD90-CD49f+ HSC  317


title: CD90-CD49f+ HSC  318


title: CD90-CD49f+ HSC  331


title: CD90-CD49f+ HSC  316


title: CD90-CD49f+ HSC  322


title: CD90-CD49f+ HSC  336


title: CD90-CD49f+ HSC  313


title: CD90-CD49f+ HSC  321


title: CD90-CD49f+ HSC  311


title: CD90-CD49f+ HSC  323


title: CD90-CD49f+ HSC  319


title: CD90-CD49f+ HSC  315


title: CD90-CD49f+ HSC  325


title: CD90-CD49f+ HSC  314


title: CD90-CD49f+ HSC  307


title: CD90-CD49f+ HSC  312


title: CD90-CD49f+ HSC  304


title: CD90-CD49f+ HSC  310


title: CD90-CD49f+ HSC  309


title: CD90-CD49f+ HSC  305


title: CD90-CD49f+ HSC  303


title: CD90-CD49f+ HSC  302


title: CD90-CD49f+ HSC  301


title: CD90-CD49f+ HSC  320


title: CD90-CD49f+ HSC  299


title: CD90-CD49f+ HSC  298


title: CD90-CD49f+ HSC  300


title: CD90-CD49f+ HSC  297


title: CD90-CD49f+ HSC  295


title: CD90-CD49f+ HSC  293


title: CD90-CD49f+ HSC  290


title: CD90-CD49f+ HSC  291


title: CD90-CD49f+ HSC  284


title: CD90-CD49f+ HSC  286


title: CD90-CD49f+ HSC  283


title: CD90-CD49f+ HSC  287


title: CD90-CD49f+ HSC  285


title: CD90-CD49f+ HSC  282


title: CD90-CD49f+ HSC  281


title: CD90-CD49f+ HSC  288


title: CD90-CD49f+ HSC  306


title: CD90-CD49f+ HSC  308


title: CD90-CD49f+ HSC  280


title: CD90-CD49f+ HSC  277


title: CD90-CD49f+ HSC  279


title: CD90-CD49f+ HSC  289


title: CD90-CD49f+ HSC  275


title: CD90-CD49f+ HSC  276


title: CD90-CD49f+ HSC  296


title: CD90-CD49f+ HSC  294


title: CD90-CD49f+ HSC  272


title: CD90-CD49f+ HSC  292


title: CD90-CD49f+ HSC  270


title: CD90-CD49f+ HSC  269


title: CD90-CD49f+ HSC  267


title: CD90-CD49f+ HSC  265


title: CD90-CD49f+ HSC  278


title: CD90-CD49f+ HSC  266


title: CD90-CD49f+ HSC  264


title: CD90-CD49f+ HSC  263


title: CD90-CD49f+ HSC  262


title: CD90-CD49f+ HSC  268


title: CD90+CD49f+ HSC  258


title: CD90+CD49f+ HSC  257


title: CD90+CD49f+ HSC  254


title: CD90-CD49f+ HSC  274


title: CD90-CD49f+ HSC  260


title: CD90-CD49f+ HSC  259


title: CD90+CD49f+ HSC  256


title: CD90+CD49f+ HSC  255


title: CD90+CD49f+ HSC  253


title: CD90+CD49f+ HSC  251


title: CD90-CD49f+ HSC  273


title: CD90+CD49f+ HSC  252


title: CD90-CD49f+ HSC  271


title: CD90+CD49f+ HSC  247


title: CD90+CD49f+ HSC  248


title: CD90+CD49f+ HSC  249


title: CD90+CD49f+ HSC  250


title: CD90+CD49f+ HSC  245


title: CD90+CD49f+ HSC  243


title: CD90+CD49f+ HSC  239


title: CD90+CD49f+ HSC  240


title: CD90+CD49f+ HSC  244


title: CD90+CD49f+ HSC  238


title: CD90+CD49f+ HSC  237


title: CD90+CD49f+ HSC  242


title: CD90-CD49f+ HSC  261


title: CD90+CD49f+ HSC  241


title: CD90+CD49f+ HSC  236


title: CD90+CD49f+ HSC  235


title: CD90+CD49f+ HSC  232


title: CD90+CD49f+ HSC  234


title: CD90+CD49f+ HSC  230


title: CD90+CD49f+ HSC  229


title: CD90+CD49f+ HSC  246


title: CD90+CD49f+ HSC  231


title: CD90+CD49f+ HSC  233


title: CD90+CD49f+ HSC  228


title: CD90+CD49f+ HSC  226


title: CD90+CD49f+ HSC  225


title: CD90+CD49f+ HSC  227


title: CD90+CD49f+ HSC  224


title: CD90+CD49f+ HSC  222


title: CD90+CD49f+ HSC  221


title: CD90+CD49f+ HSC  220


title: CD90+CD49f+ HSC  223


title: CD90+CD49f+ HSC  219


title: CD90+CD49f+ HSC  213


title: CD90+CD49f+ HSC  371


title: CD90+CD49f+ HSC  216


title: CD90+CD49f+ HSC  204


title: CD90+CD49f+ HSC  211


title: CD90+CD49f+ HSC  218


title: CD90+CD49f+ HSC  208


title: CD90+CD49f+ HSC  207


title: CD90+CD49f+ HSC  206


title: CD90+CD49f+ HSC  212


title: CD90+CD49f+ HSC  200


title: CD90+CD49f+ HSC  201


title: CD90+CD49f+ HSC  210


title: CD90+CD49f+ HSC  203


title: CD90+CD49f+ HSC  199


title: CD90+CD49f+ HSC  205


title: CD90+CD49f+ HSC  196


title: CD90+CD49f+ HSC  198


title: CD90+CD49f+ HSC  197


title: CD90+CD49f+ HSC  214


title: CD90+CD49f+ HSC  195


title: CD90+CD49f+ HSC  215


title: CD90+CD49f+ HSC  217


title: CD90+CD49f+ HSC  191


title: CD90+CD49f+ HSC  194


title: CD90+CD49f+ HSC  193


title: CD90+CD49f+ HSC  192


title: CD90+CD49f+ HSC  189


title: CD90+CD49f+ HSC  190


title: CD90+CD49f+ HSC  209


title: CD90+CD49f+ HSC  188


title: CD90+CD49f+ HSC  202


title: CD90+CD49f+ HSC  186


title: CD90+CD49f+ HSC  185


title: CD90+CD49f+ HSC  177


title: CD90+CD49f+ HSC  184


title: CD90+CD49f+ HSC  175


title: CD90+CD49f+ HSC  183


title: CD90+CD49f+ HSC  180


title: CD90+CD49f+ HSC  173


title: CD90+CD49f+ HSC  181


title: CD90+CD49f+ HSC  176


title: CD90+CD49f+ HSC  179


title: CD90-CD49f+ HSC  172


title: CD90+CD49f+ HSC  174


title: CD90-CD49f+ HSC  171


title: CD90-CD49f+ HSC  170


title: CD90-CD49f+ HSC  169


title: CD90-CD49f+ HSC  168


title: CD90-CD49f+ HSC  167


title: CD90-CD49f+ HSC  165


title: CD90-CD49f+ HSC  166


title: CD90-CD49f+ HSC  164


title: CD90+CD49f+ HSC  187


title: CD90-CD49f+ HSC  163


title: CD90+CD49f+ HSC  178


title: CD90+CD49f+ HSC  182


title: CD90-CD49f+ HSC  159


title: CD90-CD49f+ HSC  161


title: CD90-CD49f+ HSC  158


title: CD90-CD49f+ HSC  154


title: CD90-CD49f+ HSC  155


title: CD90-CD49f+ HSC  153


title: CD90-CD49f+ HSC  156


title: CD90-CD49f+ HSC  146


title: CD90-CD49f+ HSC  148


title: CD90-CD49f+ HSC  152


title: CD90-CD49f+ HSC  157


title: CD90-CD49f+ HSC  162


title: CD90-CD49f+ HSC  145


title: CD90-CD49f+ HSC  149


title: CD90-CD49f+ HSC  147


title: CD90-CD49f+ HSC  136


title: CD90-CD49f+ HSC  139


title: CD90-CD49f+ HSC  160


title: CD90-CD49f+ HSC  143


title: CD90-CD49f+ HSC  138


title: CD90-CD49f+ HSC  132


title: CD90-CD49f+ HSC  151


title: CD90-CD49f+ HSC  133


title: CD90-CD49f+ HSC  150


title: CD90-CD49f+ HSC  144


title: CD90-CD49f+ HSC  135


title: CD90-CD49f+ HSC  142


title: CD90-CD49f+ HSC  125


title: CD90-CD49f+ HSC  127


title: CD90-CD49f+ HSC  126


title: CD90-CD49f+ HSC  137


title: CD90-CD49f+ HSC  140


title: CD90-CD49f+ HSC  120


title: CD90-CD49f+ HSC  131


title: CD90-CD49f+ HSC  134


title: CD90-CD49f+ HSC  141


title: CD90-CD49f+ HSC  123


title: CD90-CD49f+ HSC  124


title: CD90-CD49f+ HSC  116


title: CD90-CD49f+ HSC  121


title: CD90-CD49f+ HSC  110


title: CD90-CD49f+ HSC  119


title: CD90-CD49f+ HSC  111


title: CD90-CD49f+ HSC  115


title: CD90-CD49f+ HSC  114


title: CD90-CD49f+ HSC  113


title: CD90-CD49f+ HSC  129


title: CD90-CD49f+ HSC  109


title: CD90-CD49f+ HSC  128


title: CD90-CD49f+ HSC  130


title: CD90-CD49f+ HSC  117


title: CD90-CD49f+ HSC  118


title: CD90-CD49f+ HSC  112


title: CD90-CD49f+ HSC  102


title: CD90-CD49f+ HSC  100


title: CD90-CD49f+ HSC  122


title: CD90-CD49f+ HSC  107


title: CD90-CD49f+ HSC  96


title: CD90-CD49f+ HSC  108


title: CD90-CD49f+ HSC  97


title: CD90-CD49f+ HSC  104


title: CD90-CD49f+ HSC  103


title: CD90-CD49f+ HSC  101


title: CD90-CD49f+ HSC  89


title: CD90-CD49f+ HSC  91


title: CD90-CD49f+ HSC  93


title: CD90-CD49f+ HSC  90


title: CD90-CD49f+ HSC  87


title: CD90-CD49f+ HSC  95


title: CD90-CD49f+ HSC  105


title: CD90+CD49f+ HSC  83


title: CD90-CD49f+ HSC  99


title: CD90+CD49f+ HSC  81


title: CD90+CD49f+ HSC  86


title: CD90-CD49f+ HSC  106


title: CD90+CD49f+ HSC  78


title: CD90+CD49f+ HSC  75


title: CD90-CD49f+ HSC  98


title: CD90+CD49f+ HSC  77


title: CD90+CD49f+ HSC  76


title: CD90+CD49f+ HSC  85


title: CD90-CD49f+ HSC  92


title: CD90+CD49f+ HSC  73


title: CD90+CD49f+ HSC  72


title: CD90+CD49f+ HSC  69


title: CD90+CD49f+ HSC  70


title: CD90+CD49f+ HSC  84


title: CD90+CD49f+ HSC  68


title: CD90+CD49f+ HSC  66


title: CD90-CD49f+ HSC  88


title: CD90-CD49f+ HSC  94


title: CD90+CD49f+ HSC  64


title: CD90+CD49f+ HSC  79


title: CD90+CD49f+ HSC  63


title: CD90+CD49f+ HSC  62


title: CD90+CD49f+ HSC  67


title: CD90+CD49f+ HSC  59


title: CD90+CD49f+ HSC  61


title: CD90+CD49f+ HSC  58


title: CD90+CD49f+ HSC  74


title: CD90+CD49f+ HSC  71


title: CD90+CD49f+ HSC  82


title: CD90+CD49f+ HSC  54


title: CD90+CD49f+ HSC  53


title: CD90+CD49f+ HSC  55


title: CD90+CD49f+ HSC  80


title: CD90+CD49f+ HSC  51


title: CD90+CD49f+ HSC  57


title: CD90+CD49f+ HSC  65


title: CD90+CD49f+ HSC  48


title: CD90+CD49f+ HSC  47


title: CD90+CD49f+ HSC  43


title: CD90+CD49f+ HSC  56


title: CD90+CD49f+ HSC  42


title: CD90+CD49f+ HSC  41


title: CD90+CD49f+ HSC  60


title: CD90+CD49f+ HSC  45


title: CD90+CD49f+ HSC  37


title: CD90+CD49f+ HSC  44


title: CD90+CD49f+ HSC  52


title: CD90+CD49f+ HSC  49


title: CD90+CD49f+ HSC  34


title: CD90+CD49f+ HSC  29


title: CD90+CD49f+ HSC  46


title: CD90+CD49f+ HSC  50


title: CD90+CD49f+ HSC  26


title: CD90+CD49f+ HSC  27


title: CD90+CD49f+ HSC  35


title: CD90+CD49f+ HSC  39


title: CD90+CD49f+ HSC  38


title: CD90+CD49f+ HSC  33


title: CD90+CD49f+ HSC  18


title: CD90+CD49f+ HSC  23


title: CD90+CD49f+ HSC  36


title: CD90+CD49f+ HSC  32


title: CD90+CD49f+ HSC  31


title: CD90+CD49f+ HSC  30


title: CD90+CD49f+ HSC  19


title: CD90+CD49f+ HSC  40


title: CD90+CD49f+ HSC  24


title: CD90+CD49f+ HSC  25


title: CD90+CD49f+ HSC  16


title: CD90+CD49f+ HSC  15


title: CD90+CD49f+ HSC  28


title: CD90+CD49f+ HSC  10


title: CD90+CD49f+ HSC  8


title: CD90+CD49f+ HSC  9


title: CD90+CD49f+ HSC  21


title: CD90+CD49f+ HSC  22


title: CD90+CD49f+ HSC  20


title: CD90+CD49f+ HSC  13


title: CD90+CD49f+ HSC  6


title: CD90+CD49f+ HSC  3


title: EPCR+ HSC  4 [AFO296A30]

description:
AFO296A30_S29
AFO296A30_S38

data_processing:
Raw sequencing reads were mapped with STAR
Expression counts estimates and transcripts per million (TPM) were generated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: EPCR+ HSC

extract_protocol:
total RNA using RNeasy Plus Micro Kit (Qiagen) and quality was verified in an Agilent 2100 Bioanalyzer (Agilent).
KAPA Stranded with RiboErase RNA-seq kit (Kapa Biosystems)
RNA-seq 30 million single-end 100 bp reads/sample

value: post-natal

value: primitive human stem (CD34+CD38-CD45RA-EPCR+) cells


title: EPCR+ HSC  1 [AFO296A18]

description:
AFO296A18_S19
AFO296A18_S28


title: CD90+CD49f+ HSC  17


title: CD90+CD49f+ HSC  11


title: WT_Input_3

city: Gothenburg

first: Ayman

last: Osman

address: Medicinaregatan 1F

department: Laboratory medicine

country: Sweden

institute: Gothenburg University

data_processing:
Fastq files were aligned to hg38 reference genome using BWA.
Mapped bam files were used for peak calling by MACS2. Minimum FDR (q-value) cutoff for peak detection was set to 0.01
To visualize the peaks, ChIP signals (bigwig) were generated by bamcompare tool from deepTools using signal extraction scaling (SES) method, and the background signal were subtracted from ChIP signal.
Differential binding analysis was performed using DiffBind R/Bioconductor package. Motifs analysis were performed using (findMotifsGenome.pl) program from HOMER. Search for known motifs followed by de novo motif discovery were performed.
The DDIT3 microarray expression data was combined with DDIT3 ChIP-seq data using binding and expression target analysis (BETA) software to examine the effect of DDIT3 on regulation of gene. BETA basic was used with the following parameters: --da 500 -d 150000 -c 0.5 -g hg19.
Genome_build: hg38
Supplementary_files_format_and_content: BED

source_name: HT1080 cell line

growth_protocol: Human parental fibrosarcoma cell line HT1080 and transfected clones were cultured at 37oC and 5% CO2 in RPMI 1640 medium supplemented with 2 mM L-glutamine, 50 U/ml penicillin, 50 g/ml streptomycin and 8% FCS (all Invitrogen). G418 (200 g/ml, Invitrogen) was added to the transfected cell clones to ensure stable expression of EGFP constructs in the cell population.

extract_protocol:
For chromatin immunoprecipitation, we used the iDeal ChIP-seq kit for Transcription Factors (Diagenode, cat No: C01010170). For cross-linking proteins with DNA, formaldehyde (37%) was mixed with Fixation Buffer (Diagenode), to a final concentration of 11% and added to the cultured cells medium in a proportion of 1:10, and incubated with gentle shaking at room temperature for 15 minutes. The reaction was stopped by adding glycine (1:10) for 5 minutes with gentle shaking at room temperature. The cells were collected by scraping and lysed with lysis buffers from Diagenode. chromatin was sheared by sonication using Bioruptor Pico sonication device (Diagenode, Belgium) (7 cycles, 30 seconds ON, 30 seconds OFF).
Chip-seq grade antibodies (H3K27ac #C15410196, H3K27me3 #C15410195, CTCF #C15410210, Diagenode), (DDIT3 #2895, Cell Signaling Technology) mixed with magnetic beads (Diagenode) were added to 250 µl of sheared chromatin and incubated under constant rotation at 4 ⁰C overnight. A volume of 2.5 µl was treated in the same but without antibody and used as input. The beads were washed with washing buffers from (Diagenode) and elution buffer was added and samples were incubated overnight at 65 ⁰C. for DNA purification  IPure beads v2 (Diagenode) were used. The beads were washed with washing buffers from (Diagenode), then resuspended with buffer C (Diagenode) and kept for further analysis.
Library preparation was performed by (Diagenode, Belgium). ChIP’d DNA was quantified using QuBit HS ds DNA kit. Libraries were prepared using IP-Star® Compact Automated System (Diagenode Cat# B03000002) from input and ChIP’d DNA using MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Optimal library amplification was assessed by qPCR using KAPA SYBR® FAST (Sigma-Aldrich) on LightCycler® 96 System (Roche) and by using High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent). Libraries were then purified (double-size selected) using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analised by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Agilent).
Libraries were pooled and sequenced with Illumina technology with single-end reads of 50bp length. Sequencing was performed by (Diagenode, Belgium).

value: fibrosarcoma cell line

tag: oncogene transfection

value: WT

value: Input


title: WT_Input_2


title: WT_Input_1


title: EWS-FLI1_Input_1


title: CD90+CD49f+ HSC  7


title: FUS-DDIT3_Input_3


title: CD90+CD49f+ HSC  5


title: CD90+EPCR- HSC  9 [AFO296A39]

description:
AFO296A39_S36
AFO296A39_S45

source_name: CD90+EPCR- HSC


title: CD90+CD49f+ HSC  2


title: CD90+EPCR- HSC  6 [AFO296A15]

description:
AFO296A15_S16
AFO296A15_S25


title: EPCR+ HSC  2 [AFO296A22]

description:
AFO296A22_S22
AFO296A22_S31


title: CD90+CD49f+ HSC  14


title: CD90+CD49f+ HSC  1


title: DDIT3_Input_3


title: DDIT3_Input_2


title: CD90+EPCR- HSC  7 [AFO296A27]

description:
AFO296A27_S26
AFO296A27_S35


title: WT_DDIT3_2


title: WT_CTCF_1

value: CTCF


title: EWS-FLI1_H3K27me3_2


title: FUS-DDIT3_H3K27ac_1


title: EPCR+ HSC  5 [AFO296A38]

description:
AFO296A38_S35
AFO296A38_S44


title: CD90+CD49f+ HSC  12


title: WT_H3K27ac_1


title: EWS-FLI1_H3K27me3_1


title: CD90+CD49f+ HSC  4


title: EWS-FLI1_H3K27ac_2


title: EWS-FLI1_CTCF_2


title: CD90+EPCR- HSC  8 [AFO296A31]

description:
AFO296A31_S30
AFO296A31_S39


title: EWS-FLI1_Input_2


title: EWS-FLI1_H3K27ac_1


title: FUS-DDIT3_DDIT3_2


title: FUS-DDIT3_Input_1


title: FUS-DDIT3_H3K27me3_1


title: DDIT3_Input_1


title: FUS-DDIT3_CTCF_1


title: AMP10

city: Helsinki

first: Mridul

last: Johari

state: Uusimaa

address: Haartmaninkatu 8, Biomedicum

country: Finland

institute: Folkhälsan Research Center

data_processing:
Illumina RTA2 for HiSeq 4000
Adapter sequences and low quality bases removed using fastp 0.19.5
STAR 2.7.0d two pass method based on ENCODE guidelines for long RNA
featureCounts v1.6.3,  DESeq2 v1.26.0, Rstudio v1.2.5019 based on R v3.6.1
Genome_build: Gencode.v29 based on ENSEMBL GRCh38.p12
Supplementary_files_format_and_content: raw counts from featureCounts on primary comprehensive gene annotation Gencode.v29
Supplementary_files_format_and_content: normalized abundance measurement using DESeq2

source_name: Skeletal muscle (Vastus Lateralis)

extract_protocol:
RNA was extracted from snap formzen skeletal muscle biopsies using Qiagen Rneasy Plus Universal Mini Kit (Cat No./ID: 73404)
tissue homogenization steps were performed using SpeedMill PLUS (Analytik Jena AG, Germany)
Extracted RNA was treated with Invitrogen TURBO Dnase (Catalog number:  AM2238)
PolyA+ RNA selection using NEBNext Ultra II Directional RNA library Prep kit (E7760) for Illumina for the preparation of strand specific RNA-seq libraries

value: Skeletal muscle (Vastus Lateralis)

tag: group

value: Amputee

tag: age at biopsy (in years)

tag: age of onset (in years)

value: Male


title: DDIT3_DDIT3_1


title: DDIT3_CTCF_1


title: EPCR+ HSC  3 [AFO296A26]

description:
AFO296A26_S25
AFO296A26_S34

value: cord blood


title: FUS-DDIT3_Input_2


title: FUS-DDIT3_Input_4


title: test-d8-2

city: Shanghai

first: Sun

middle: Jia

last: Ming

address: No. 639, Zhi Zao Ju Road,

department: Department of Plastic & Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: adipose tissue-derived stromal cells (ADSCs)

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.

tag: treatment

value: Sal-B-treated

tag: day


title: FUS-DDIT3_H3K27me3_2


title: con-d4-3

value: adipose tissue-derived stromal cells (ADSCs)

value: control


title: Exp1 96h UL87HF Flavo 2h dTAG Pro-seq

city: Iowa City

first: Jeffery

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 or KF297339.1 (Towne and TB40, respectively), and, for samples that included moth spike-in cells, JQCY02.1 (spodoptera) genome assemblies.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and Data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils.
Custom UCSC track hubs were set up for Towne and TB40/E data.
For analysis of host transcription effects upon depletion of UL87LTF or UL79LTF and annotation of gene 5' ends based on PRO-Seq data, we applied a new truQuant algorithm that utilizes our previously published tsrfinder tool. Our application of these tools is described in the manuscript. Source code is avaliable on GitHub at https://github.com/meierjl/truQuant.
Genome_build: hg38 (human), FJ616285.1 (HCMV Towne), KF297339.1 (HCMV TB40/E), JQCY02.1 (Spodoptera).
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, bigwigs for ChIP-Seq samples

source_name: HCMV-infected primary human foreskin fibroblast

growth_protocol: HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Nuclei isolation was carried out as described in Parida et. al. (2019, PMID: 30755505) and Li et. al. (2020, PMID: 32251483) .
PRO-Seq library preparation to extract and sequence nascent RNAs and ChIP-seq library preparation to extract and sequence is carefully detailed in the manuscript and was carried out as previously described by  Li et. al. (2020, PMID: 32251483), with noted modifications.

treatment_protocol:
Cells were treated with the indicated drugs (dTAG 2h and Flavo 1h ) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

tag: infection

value: HCMV strain Towne BAC

tag: infection duration

value: 96 hours

tag: ltf depletion

value: dTAG 2h and Flavo 1h

tag: fraction

value: nascent RNA


title: Exp1 96h UL87HF Flavo 2h dTAG 6h PFA Pro-seq

treatment_protocol:
Cells were treated with the indicated drugs (dTAG 2h, Flavo 1h, and PFA 6h) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: dTAG 2h, Flavo 1h, and PFA 6h


title: WT_DDIT3_1

value: fibrosarcoma cell line

tag: antibody


title: FUS-DDIT3_DDIT3_1


title: DDIT3_H3K27ac_2


title: FUS-DDIT3_H3K27ac_2


title: DDIT3_H3K27me3_2


title: WT_H3K27me3_1

value: WT


title: DDIT3_CTCF_2


title: TNF-6

data_processing:
Sequence reads were aligned to the human genome with Hisat2 (version 2.1.0) [1] using a “genome” index built from the GRCh38 release of the mouse genome and known splice sites extracted from Ensembl version 91 annotations (using the hisat2_extract_splice_sites.py tool). A two-pass mapping strategy was used to discover novel splice sites (with the additional parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.6.3; Ensembl version 91 annotations; default parameters).
TPMs were estimated with salmon (version 0.9.1); using a quasi-index (built with Ensembl version 91 annotations and k=31) and gc bias correction (parameter “--gcBias”)
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) "featurecounts_counts.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "salmon.genes.tpms.txt" is a tab-delimited text file containing the table of gene-by-sample raw TPMs computed with salmon.

source_name: cultured Ccd18-Co intestinal fibroblasts_TNF

growth_protocol: Ccd18-Co intestinal fibroblasts were grown in MEMalpha (+PenStrep+HEPES) with 20% FCS before cytokine stimulation

extract_protocol:
cultured cells were directly lysed in RNA lysis buffer, followed by RNA isolation using the Qiagen Mini kit with a DNA digestion step (Qiagen)
Sequencing libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) (with in-house indexing primers)
RNA-sequencing, Libraries were sequenced using an Illumina HiSeq4000 with 75bp paired-end sequencing (Lamble et al., 2013).

treatment_protocol: cells were starved for 72h in serum-free medium, followed by 3 hour mock stimulation (0.1%BSA/PBS) or 3 hour stimulation with 100ng/ml TNF-alpha or 0.01ng/ml IL-1beta

value: Ccd18-Co intestinal fibroblasts

tag: stimulation

value: TNF

tag: replicate

value: EXCLUDE


title: Exp1 96h UL87HF Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1 h and DMSO 6h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: cell type

value: Flavo 1h and DMSO 6h


title: DDIT3_H3K27me3_1


title: con-d8-3


title: test-d8-1


title: TNF-1

tag: qc

value: include


title: IL1betaTNF-6

source_name: cultured Ccd18-Co intestinal fibroblasts_IL1betaTNF


title: AMP9

source_name: Skeletal muscle (Tibialis Anterior)

tag: tissue

value: Skeletal muscle (Tibialis Anterior)

value: Amputee

tag: gender

value: Male


title: TNF-3


title: con-d8-2

value: adipose tissue-derived stromal cells (ADSCs)

value: control


title: EWS-FLI1_CTCF_1

tag: oncogene transfection

value: CTCF


title: Exp1 96h UL87HF Flavo 6h PFA Pro-seq

treatment_protocol:
Cells were treated with the indicated drugs (PFA 6h and Flavo 1h ) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

value: HCMV strain Towne BAC

value: 96 hours

value: PFA 6h and Flavo 1h


title: IL1betaTNF-5


title: test-d4-1

value: Sal-B-treated


title: DDIT3_DDIT3_2

value: fibrosarcoma cell line


title: test-d4-2


title: con-d4-1


title: Unstimulated-6

source_name: cultured Ccd18-Co intestinal fibroblasts_Unstimulated

value: Ccd18-Co intestinal fibroblasts

value: Unstimulated


title: Unstimulated-5


title: IL1betaTNF-2


title: IL1betaTNF-1


title: IL1beta-5

source_name: cultured Ccd18-Co intestinal fibroblasts_IL1beta


title: Unstimulated-4


title: Exp1 96h UL87HF Flavo 6h dTAG Pro-seq

treatment_protocol:
Cells were treated with the indicated drugs (dTAG 6h and Flavo 1h) during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: dTAG 6h and Flavo 1h

value: nascent RNA


title: IL1beta-4

value: include


title: CRC_N_LI_F_96

source_name: CRC_N_LI_F_whole intestinal tissue

tag: disease

value: Control

value: uninflamed

value: female

tag: disease_duration (y)


title: IL1beta-1


title: TNF-5

value: TNF


title: Unstimulated-2


title: TNF-4


title: Unstimulated-1


title: CRC_N_LI_M_93

source_name: CRC_N_LI_M_whole intestinal tissue

value: male


title: CRC_N_LI_M_89


title: IL1betaTNF-3


title: CRC_N_LI_M_94


title: IL1beta-6

value: EXCLUDE


title: CRC_N_LI_F_92


title: CRC_N_LI_M_84


title: TNF-2


title: CRC_N_LI_F_90


title: CRC_N_LI_F_85


title: CRC_N_LI_M_95


title: IL1betaTNF-4


title: CRC_N_LI_F_88


title: CRC_N_LI_F_86


title: IL1beta-2


title: Unstimulated-3


title: CRC_N_LI_M_87


title: CRC_N_LI_M_83


title: OTHER_N_LI_M_79

source_name: OTHER_N_LI_M_whole intestinal tissue

value: OTHER


title: CRC_N_LI_M_91


title: CRC_N_LI_F_78


title: IL1beta-3


title: CRC_N_LI_M_80


title: CRC_N_LI_M_76


title: CRC_N_LI_M_77


title: CD_U_SI_M_75

source_name: CD_U_SI_M_whole intestinal tissue

value: CD


title: CRC_N_LI_F_73


title: CRC_N_LI_M_74


title: CRC_N_LI_F_71


title: CRC_N_LI_M_69


title: CRC_N_LI_M_68


title: CRC_N_LI_M_70


title: CRC_N_LI_M_82


title: CRC_N_LI_M_67


title: CRC_N_LI_F_72


title: CRC_N_LI_F_64


title: OTHER_N_NA_NA_63


title: CRC_N_LI_F_60


title: CRC_N_LI_F_65


title: CRC_N_LI_M_62


title: CRC_N_LI_F_66


title: CRC_N_LI_M_59


title: CRC_N_LI_F_58


title: OTHER_U_SI_F_54

source_name: OTHER_U_SI_F_whole intestinal tissue


title: OTHER_I_LI_F_53

source_name: OTHER_I_LI_F_whole intestinal tissue

value: inflamed


title: CRC_N_LI_M_56


title: CD_U_SI_F_51

source_name: CD_U_SI_F_whole intestinal tissue


title: CD_I_SI_F_52

source_name: CD_I_SI_F_whole intestinal tissue


title: CD_I_SI_M_46

source_name: CD_I_SI_M_whole intestinal tissue


title: CD_I_LI_M_49

source_name: CD_I_LI_M_whole intestinal tissue


title: CD_U_LI_F_48

source_name: CD_U_LI_F_whole intestinal tissue


title: CRC_N_LI_M_61


title: CRC_N_LI_F_57


title: IBDU_I_LI_F_47

source_name: IBDU_I_LI_F_whole intestinal tissue

value: IBDu


title: CRC_N_LI_F_55


title: UC_I_LI_F_45

source_name: UC_I_LI_F_whole intestinal tissue

value: UC


title: UC_I_LI_F_41


title: CD_I_SI_M_43


title: CD_U_SI_M_42


title: OTHER_I_LI_M_44

source_name: OTHER_I_LI_M_whole intestinal tissue


title: CD_I_SI_F_38


title: CD_U_LI_F_32


title: CD_I_LI_M_36


title: UC_I_LI_M_34

source_name: UC_I_LI_M_whole intestinal tissue


title: CD_U_LI_F_37


title: CD_U_LI_M_50

source_name: CD_U_LI_M_whole intestinal tissue


title: CD_I_SI_F_31


title: UC_U_LI_F_40

source_name: UC_U_LI_F_whole intestinal tissue


title: CD_U_LI_M_35


title: CRC_N_LI_F_26

source_name: CRC_N_LI_F_whole intestinal tissue


title: CD_M_LI_F_28

source_name: CD_M_whole intestinal tissue


title: CD_I_LI_F_29

source_name: CD_I_LI_F_whole intestinal tissue


title: CD_U_SI_F_30


title: CD_U_SI_F_21


title: CD_I_LI_F_22