title: Diabetic_0h_06

source_name: 2mm skin biopsy

value: Human skin grafted in diabetic mice

value: diabetic

value: 0 hours


title: cjnw5krpc00793h5vwvcp6dpp

status: Public on Feb 01 2021

type: SRA

city: South San Francisco

first: Adam

last: Freund

state: CA

address: 1170 Veterans Blvd

country: USA

institute: Calico Life Sciences LLC

library_source: transcriptomic

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5)
Transcript expression was then quantified using Salmon [1] (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing per-gene count estimates, using the Ensembl mm10 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each gene for each sample, in long-format

molecule: total RNA

organism: Mus musculus

source_name: Kidney

growth_protocol: Mice were maintained on a 12:12 hour light:dark cycle at 22℃ with environmental enrichment (e.g., nesting material and/or huts) with access to water and food ad libitum.

extract_protocol:
RNA was extracted from whole tissues using the Qiagen RNeasy 96 Universal Tissue Kit (Qiagen, 74881) and was digested with DNAseI before preparation for RNA-seq
Lib Prep method: TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat, Input Total Conc: 100ng in 10ul. PCR 12 cycles. Sequencing  - 3nM on Hiseq 4000

treatment_protocol: Mice were treated with control or anti-PAPP-A antibody for 17 weeks, then sacrificied and nine tissues were harvested and processed for RNA-seq:  lung, liver, kidney, heart, spleen, bone marrow, gonadal fat, subscapular (subcutaneous) fat, skin

tag: tissue

value: Kidney

tag: strain

tag: Sex

value: female

tag: treatment

value: aPAPPA


title: WT+AAV9-SMN Replicate 3

city: New York

first: Livio

last: Pellizzoni

state: NY

address: 630 W 168TH STREET, Physician & Surgeons Building Room 5-421, Mail Code #62, Physician & Surgeons Building Room 5-421

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
All RNA-Seq data were mapped to the reference mouse genome (mm10) and a database of exon junctions using OLego (v1.1.5)
The Quantas pipeline was used to quantify alternative splicing and perform differential splicing analysis, requiring read coverage ≥ 20 reads and false discovery rate (FDR) ≤ 0.05 (FDR was estimated by the Benjamini-Hochberg procedure).
The edgeR method included in the Quantas pipeline was used to perform differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: LM001_S17_L001_exp.txt, expression values for WT rep1. LM002_S18_L001_exp.txt, expression values for WT rep2. LM003_S19_L001_exp.txt, expression values for WT rep3. LM004_S20_L001_exp.txt, expression values for AAV-GFP rep1. LM005_S21_L001_exp.txt, expression values for AAV-GFP rep2. LM006_S22_L001_exp.txt, expression values for AAV-GFP rep3. LM007_S23_L001_exp.txt, expression values for AAV-SMN rep1. LM008_S24_L001_exp.txt, expression values for AAV-SMN rep2. LM009_S25_L001_exp.txt, expression values for AAV-SMN rep3.

source_name: DRG

extract_protocol:
Lumbar DRGs were isolated from uninjected and either AAV9-GFP or AAAV9-SMN injected wild type mice at P300 and flash frozen in dry ice. Total RNA was isolated using RNAqueous-Micro Kit (Ambion) including DNaseI treatment. RNA quality and quantity were assessed using the 2100 Bioanalyzer (Agilent).
We performed ribosomal depletion to remove rRNAs from total RNA samples, then proceeded with library construction using Illumina TruSeq chemistry. Libraries were sequenced using Illumina NovaSeq 6000.
Libraries were multiplexed and sequenced on Illumina NovaSeq 6000 to generate paired-end 100bp reads for each sample.

treatment_protocol: Wild type mice were injected intracerebroventricularly (ICV) at postnatal day 1 with 5x10E10 genome copies per gram of body weight of either AAV9-SMN or AAV9-GFP vectors.

value: DRG

tag: age

value: post natal day 300

value: injected with AAV9-SMN at P1


title: CLP 6h + 2h of DEX 2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 85 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecounts for all samples

source_name: liver

extract_protocol:
RNA was isolated using the Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: mice were either given a CLP or SHAM surgery. After 6h both groups were divided in 2 and one subgroup was injected with PBS, the other with 10 mg/kg DEX. 2H after injection liver was isolated for RNA extraction

value: CLP operation followed after 6h by injection of 10 mg/kg DEX (IP) with organ isolation 2h later


title: WT+AAV9-SMN Replicate 1


title: WT+AAV9-SMN Replicate 2


title: cjnw5krpc00783h5vovc6jn6l

source_name: Subscapular fat

value: Subscapular fat


title: CLP 6h + 2h of DEX 1


title: Diabetic_24h_02

type: RNA

city: Leganes

first: carlos

last: leon

state: Madrid

address: Avenida Universidad 30

department: Bioengineering

country: Spain

hyb_protocol: 16h of hybridization at 45ºC,

scan_protocol: arrays were washed, stained with streptavidin phycoerythrin, and were then scanned with the GeneArray Scanner (Affymetrix) to generate an image file.

data_processing: PCA on samples detected two outliers (C0_04 and C0_06). Raw data from microarrays excluding outliers was normalized using the rma algorithm from the affy package (Bioconductor)

label: Biotin

organism: Homo sapiens

source_name: 6mm skin biopsy around wound edge

label_protocol: generate double-stranded cDNA using the protocol for one-cycle cDNA synthesis. Biotin-labeled cRNA was fragmented and hybridized overnight to Affymetrix HU133 2.0 GeneChip

growth_protocol: Human skin biopsies of healthy donors, isolated by biomechanical and enzimatic digestion and expanded in vitro

extract_protocol: RNA isolation was performed using Trizol (Invitrogen) extraction based methods, followed by purification in columns (Qiagen).

treatment_protocol: Experimental diabetes was induced by intraperitoneal injections of STZ, administered on five consecutive days. Wound healing experiments were performed using a biopsy punch (Pfm Medical Ag.,Cologne, Germany) in the stable human skin engrafted on immunodeficient mice exposed to sustained hyperglycaemia for 6 weeks. Specifically, 2mm-circular excisional wounds were created and the excised tissue was harvested and used as a reference for gene expression analysis

tag: disease state

tag: time

value: 24 hours


title: cjnw5krpc00763h5vuhqmgzga

source_name: Skin

value: Skin


title: WT+AAV9-GFP Replicate 2

value: injected with AAV9-GFP at P1


title: cjnw5krpc00773h5vw7g6sldb

source_name: Gonadal fat

value: Gonadal fat


title: POLYA_scr_LPS_45min Replicate3

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
Strand specific paired end reads (76nt) were trimmed for removing the adapter sequence and discarding low quality bases using Trimmomatic v0.27 with PE option (PMID:24695404)
Read quality was then checked for each sample using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were then aligned with TopHat2 v2.1.0 (–very-sensitive --library-type fr-firststrand -r 200 --segment-length 35  --microexon-search --no-mixed --no-discordant -g 1 --coverage-search) (PMID:23618408). Indels due to sequencing errors were identifies using Bowtie2 v.2.6 (PMID: 19261174).
*.bigWig files were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)

source_name: Marcophages

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American origin, low endotoxin Foetal Bovine Serum,  1% L-Glutamax solution, 1% Penicillin/Streptomycin solution, and 30 % conditioned medium from L929 cells and allowed to differentiate for 7 days.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Mini Prep kit (Cat no. R1055) with on-column DNAse digestion.
After oligodT-based selection of polyadenylated transcripts from 3-5 ug total RNA, library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007).

treatment_protocol: Cells were treated for 45 min with LPS (10 ng/ml) before harvesting.

tag: cell type

value: Primary bone marrow derived macrophages

tag: genotype

value: wild type

value: FVB/Hsd

value: shScrambled_2, LPS 45 min


title: WT+AAV9-GFP Replicate 1


title: POLYA_shWDR82_LPS_45min Replicate3

source_name: Macrophages

value: shWdr82_1, LPS 45 min


title: Diabetic_0h_05

value: Human skin grafted in diabetic mice

value: diabetic

value: 0 hours


title: Diabetic_0h_03


title: WT Replicate 3

value: DRG

value: uninjected


title: Control_24h_04

value: Human skin grafted in mice

value: control


title: cjnw5krpc00753h5vzso0d9mt

source_name: Lung

value: Lung

value: female

value: aPAPPA


title: cjnw5krpc00743h5v7j27s912

source_name: Liver

value: Liver


title: Diabetic_0h_01


title: POLYA_shWDR82_LPS_45min Replicate2

description: polyA-RNAseq shWdr82_1, LPS 45 min, BMDMs, rep.2

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American FBS,  1% L-Glutamax solution, 1% Pen/Strep solution, and 30 % conditioned medium from L929 cells, 0,5% sodium pyruvate and 0,1% b-mercaptoethanol, to allow for differentiation into macrophages for 7 days. Cells under differentiation, from the day after plating, were infected two times pr day for two consecutive days with retrovirus produced in Phoenix-ECO cells, containing plasmids expressing either scrambled shRNA or shRNA specific for the mRNA to be depleted. At the end of the second day of infections, puromycin-selection (3,5 ug/ml) were started, and the cells were kept under selection until harvesting at day 7 after plating.

extract_protocol:
Total RNA was extracted using the Zymo kit with on-column DNAse digestion.
After oligodT-based selection of polyadenylated transcripts from 3-5 ug total RNA, library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007).


title: Diabetic_0h_02


title: Diabetic_0h_04


title: Control_0h_06

tag: time point


title: POLYA_scr_LPS_45min Replicate2

description: polyA-RNAseq shScrambled_2, LPS 45 min, BMDMs, rep.2


title: WT Replicate 2

value: post natal day 300


title: Control_24h_05

value: 24 hours


title: Control_24h_06


title: Control_24h_07


title: Control_24h_03


title: WT+AAV9-GFP Replicate 3

value: injected with AAV9-GFP at P1


title: cjnw5krpc00733h5vob8jps37

source_name: Heart

value: Heart


title: Control_24h_01


title: POLYA_shWDR82_LPS_45min Replicate1

description: polyA-RNAseq shWdr82_1, LPS 45 min, BMDMs_rep.1

value: Primary bone marrow derived macrophages

value: wild type

value: FVB/Hsd


title: cjnw5krpc00723h5vv3fcv7hi

source_name: Spleen

value: Spleen


title: Control_0h_04

value: 0 hours


title: POLYA_scr_LPS_45min Replicate1

description: polyA-RNAseq shScrambled_1, LPS 45 min, BMDMs_rep.1

value: shScrambled_2, LPS 45 min


title: WT Replicate 1

value: DRG

value: uninjected


title: Control_0h_07

value: Human skin grafted in mice

value: control


title: shxrn2_3_LPS_r1_SID100374

data_processing:
After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), strand specific single end reads (51 bp and 76 bp) were aligned to the mm9  reference genomes (Illumina iGenomes reference downloaded from UCSC, http://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat v2.1.0 1 (PMID:23618408), allowing up to two mismatches and using the option --b2-very- sensitive --library-type fr-firststrand.
Indels due to sequencing errors were identified using Bowtie2 v 2.2.6 (PMID: 19261174). Reads originating from the two strands were separated according to the XS:A:+/XS:A:-flag provided by TopHat2 (PMID:23618408).
SICER v2 (PMID: 24743992) was used to detect the extra-genic transcripts regulated in cells depleted of individual factors. The entire genome was partitioned into blocks of non-overlapping 500 bp windows with a gap size <1000 nt. An effective genome fraction of 1, a fragment size of 0 and a False Discovery Rate (FDR) cut-off <0.01 were used.
*.bigWig files were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: .bigWig strand specific tracks

source_name: 4sU-RNAseq, shXrn2_2, LPS 45 min, BMDMs

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American FBS,  1% L-Glutamax solution, 1% Pen/Strep solution, and 30 % conditioned medium from L929 cells, 0,5% sodium pyruvate and 0,1% b-mercaptoethanol, to allow for differentiation into macrophages for 7 days. Cells under differentiation, from the day after plating, were infected twice per day for two consecutive days with retrovirus produced in Phoenix-ECO cells, containing plasmids expressing either scrambled shRNA or shRNA specific for the mRNA to be depleted. At the end of the second day of infections, puromycin-selection (3,5 ug/ml) were started, and the cells were kept under selection until harvesting at day 7 after plating.

extract_protocol:
Total RNA was extracted using Trizol whereafter nascent 4sU-labelled RNA was extracted as described in Austenaa et al. 2015 .
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 100-300 ng of nascent 4sU-labelled RNA, without ribosomal depletion.

treatment_protocol: Cells were untreated or treated for 45 min with LPS (10 ng/ml) before harvesting. 4-thio-uridine was added to the medium to a final concentration of 150 uM for 45 min before harvesting to allow for incorporation into newly synthesized RNA.


title: Input for GST-fused AP2 domain of AP2-G

city: Tsu

first: Tsubasa

last: Nishi

state: Mie

address: Edobashi

country: Japan

institute: Mie university

library_source: genomic

data_processing:
PlasmoDB, version 3
Genome_build: Mapping data, bedgraph; Peak-calling, text.

molecule: genomic DNA

organism: Plasmodium berghei ANKA

source_name: input

extract_protocol: Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Recombinant GST-fused AP2 domain of AP2-G and genomic DNA fragments were incubated at RT for 30 min in 100 μL of binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol). The mixture was then incubated with 50 μL glutathione sepharose resin at RT with rotation. Resin was washed three times with 150 μL of binding/washing buffer, and bound protein was eluted with 10 mM glutathione solution. Recovered DNA (5 ng) was sequenced using the same procedures as in ChIP-seq. Input genomic DNA fragments were also sequenced as a control.

value: input


title: cjnw5krpc00713h5vnuqrnbgs

value: Kidney

value: female

value: aPAPPA


title: cjnw5krpc00703h5v8dxhnfu6

value: Subscapular fat


title: shxrn2_1_LPS_r1_SID100373

source_name: 4sU-RNAseq, shXrn2_1, LPS 45 min, BMDMs


title: GST-fused AP2 domain of AP2-G

source_name: IP

value: GST-fused AP2 domain of AP2-G


title: cjnw5krpc006z3h5ve5facesb

value: Gonadal fat


title: Control_24h_02

value: 24 hours


title: shxrn2_3_UT_r1_SID100372

source_name: 4sU-RNAseq, shXrn2_2, untreated BMDMs

value: Primary bone marrow derived macrophages

value: wild type


title: shxrn2_1_UT_r1_SID100371

source_name: 4sU-RNAseq, shXrn2_1, untreated BMDMs

value: FVB/Hsd


title: cjnw5krpc006x3h5vquz6mggf

value: Lung


title: R848 3

city: Saint Louis

first: Daniel

middle: C

last: Link

state: MO

address: 660 S. Euclid Avenue

department: Department of Medicine, Division of Oncology

institute: Washington University School of Medicine

data_processing:
Partek® Flow® software, version 7.0 (Partek)
Low-quality bases (below PHRED score of 20) and adapter sequences are trimmed using TrimGalore
Contaminant rDNA, mtrDNA, and tRNA reads are removed
Reads are aligned to the mm10 genome using STAR v2.5.3a
Aligned reads are quantified to mm10 using Ensembl transcripts release 95
Features are filtered to reduce noise based on quartile 3 values
Genome_build: mm10
Supplementary_files_format_and_content: Excel file providing RPKM values for all samples

growth_protocol: Not relevant

extract_protocol:
RNA was purified from sorted dendritic cells using the Qiagen RNeasy Micro Kit (74004, Qiagen)
KAPA RNA HyperPrep Kit

treatment_protocol: C57Bl/6J mice were treated with a single dose of R848 (100 ug) and, 24 hours later, bone marrow dendritic cells flow sorted as MHCIIhigh CD11chigh CX3CR1-GFPhigh Gr-1- B220- cells

value: BM dendritic cells

tag: agent

value: R848 treated

value: Wildtype


title: R848 2


title: scr_2_LPS_r1_SID100370

source_name: 4sU-RNAseq, shScrambled_2, LPS 45 min, BMDMs


title: AP2-G ChIP-seq experiment-1 INPUT

data_processing:
Reads were mapped on the P. berghei genome with allowing one mismatch within 32 bp sequence using Bowtie 2.0. Bedgraph files were created from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using approximately 2.75 × 10e6  in the experiment-1 and 3.39 × 10e6 in the experiment-2. Numbers of INPUT reads used for normalization were 1.35× 10e7 in the experiment-1 and 1.19 × 10e7 in the experiment-2. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: P. berghei (PlasmoDB, version 3)
Supplementary_files_format_and_content: Mapping data, bedgraph; Peak-calling, text.

source_name: Gametocyte

growth_protocol: Balb/c mice were synchronously infected with P. berghei expressing GFP-fused AP2-G, and blood was harvested at 18 hpi.

extract_protocol:
Blood was filtered with Plasmodipur to remove lymphocytes and fixed with 1% formaldehyde for 60 min at 30C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were subjected to ChIP-seq. Cells were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power in the cell lysis solution containing 1% sodium dodecyl sulfate. The supernatant was subjected to immunoprecipitation with anti-GFP antibodies using Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - Illumina NextSeq 500).

value: whole body

tag: developmental stage

value: gametocyte

value: GFP-fused AP2-G expressing

tag: chip antibody


title: AP2-G ChIP-seq experiment-2 IP

value: anti-GFP


title: AP2-G ChIP-seq experiment-2 INPUT


title: Control_0h_05

source_name: 2mm skin biopsy

value: Human skin grafted in mice

value: control

value: 0 hours


title: Control_0h_03


title: AP2-G ChIP-seq experiment-1 IP


title: R848 1


title: scr_1_LPS_r1_SID100369

source_name: 4sU-RNAseq, shScrambled_1, LPS 45 min, BMDMs


title: cjnw5krpb006v3h5v2di2lg77

value: Heart

value: female

value: aPAPPA


title: cjnw5krpc006w3h5vs4dh73b4

value: Liver


title: Control_0h_01


title: scr_2_UT_r1_SID100368

source_name: 4sU-RNAseq, shScrambled_2, untreated BMDMs

value: Primary bone marrow derived macrophages

value: wild type


title: cjnw5krpb006u3h5vfj0zmehb

value: Spleen


title: Control 4

source_name: Control 4

value: BM dendritic cells

value: vehicle-alone treated


title: Control 3

source_name: Control 3

value: Wildtype


title: RalA-IR_Ecc15_4

city: Glasgow

first: Mate

last: Naszai

address: Wolfson Wohl Cancer Research Centre

country: United Kingdom

institute: University of Glasgow

data_processing:
Quality checks were done using fastqc version 0.11.7 and fastqc_screen version 0.12.0
Reads were aligned using HiSat2 version 2.1.0
Differential gene expression analysis was based on the negative binomial distribution using DESeq2 package version 1.18.1
Genome_build: dm6 / BDGP 6
Supplementary_files_format_and_content: xlsx, expression levels and differential gene expression between different conditions

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole adult midgut

extract_protocol:
Extracted midguts were frozen on dry ice then RNA was extracted using the QIAGEN RNAeasy kit with on column DNase digestion.
RNA libraries were prepared for sequencing using Illumina TrueSeq RNA Library Preparation Kit v2 following standard Illumina protocols

value: midgut

value: UAS-Dcr2 / +; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / P{KK108989}VIE-260B; tub-Gal80ts / +

value: Ecc15 in 5% sucrose

value: 10-14 days after eclosion


title: cjnw5krpc006y3h5vapo3ygzh

source_name: Skin

value: Skin


title: Control_0h_02

value: Human skin grafted in mice

value: control


title: Gametocyte transcriptome

description: cDNA

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” set to 1000.
Raw counts of reads mapped on each gene were measured using featureCounts. All parameters were set to default.
Genome_build: P. berghei (PlasmoDB, version 3)
Supplementary_files_format_and_content: Gametocyte_RNA-seq_counts.txt: Tab-delimited text file includes raw counts.

growth_protocol: Balb/c mice were infected with P. berghei ANKA strain. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Parasites were harvested after drug treatment for 2 days.

extract_protocol:
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s protocols.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - Illumina NextSeq 500).

value: whole body

value: gametocyte


title: cjnw5krpb006t3h5v7jlinsb6

source_name: Kidney

value: Kidney

value: female

value: aPAPPA


title: scr_1_UT_r1_SID100367

source_name: 4sU-RNAseq, shScrambled_1, untreated BMDMs

value: Primary bone marrow derived macrophages

value: wild type

value: FVB/Hsd


title: Input_BMDM_SID100750

description: Genomic DNA, no IP performed

data_processing:
Pol II raw data were downloaded from GEO (GSM1634808) and re-analysed
Reads were mapped using Bowtie2 v 2.2.6 (PMID: 19261174). We used default parameters with the options --very-sensitive, --no-unal and with the pre-built bowtie2 index. Only uniquely mapping reads were retained.
Peak calling was performed using SICER v2 (PMID: 24743992). We identified significantly enriched clusters using a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp  and a False Discovery Rate (FDR) cut-off <0.01 were used. Fragment size was set to 150nt and the effective genome fraction to 0.80. The ChIP was compared to input DNA from primary bone marrow-derived macrophages. Regions that overlapped with the blacklists of the ENCODE and modENCODE consortia (http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-blacklist.bed.gz) were filtered out.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: Tracks (*.bigWig files)

source_name: Macrophages

growth_protocol: Primary bone marrow cells were cultured in DMEM containing 10% North American FBS,  1% L-Glutamax solution, 1% Pen/Strep solution, and 30 % conditioned medium from L929 cells to allow for differentiation into macrophages for 7 days before the experiments were performed.

extract_protocol:
Ca. 100-150 mill. cells were fixed with 1% formaldehyde for 10 min. Nuclear lysates were prepared, sonicated to reach an average fragment length of 300 bp, whereafter protein-DNA complexes were immunoprecipitated with specific antibodies.
DNA libraries of immunoprecipiated DNA were prepared for sequencing on the Illumina NextSeq as previously described (Ostuni, 2013).

value: Bone marrow derived macrophages


title: RalA-IR_Ecc15_2


title: Control 2

source_name: Control 2

value: BM dendritic cells

value: vehicle-alone treated

value: Wildtype


title: cjnw5krpb006s3h5vav6gun6w

source_name: Subscapular fat

value: Subscapular fat


title: mm10_INPUT_RAW_SID100742

description: Genomic DNA, no IP performed

data_processing:
Single end reads (76bp) were trimmed and clipped for quality control with Trimmomatic v0.27 (PMID:24695404). Read quality was then checked for each sample using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were mapped using Bowtie2 v 2.2.6 (PMID: 19261174). We used default parameters with the options --very-sensitive, --no-unal and with the pre-built bowtie2 index. Only uniquely mapping reads were retained.
Peak calling was performed using SICER v2 (PMID: 24743992). We identified significantly enriched clusters using a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp  and a False Discovery Rate (FDR) cut-off <0.01 were used. Fragment size was set to 150nt and the effective genome fraction to 0.80. The ChIP was compared to input DNA derived from RAW264.7 mouse macrophages. Regions that overlapped with the blacklists of the ENCODE and modENCODE consortia (http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-blacklist.bed.gz) were filtered out.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: bigWig

growth_protocol: RAW 264.7 mouse macrophage cell line was purchased from the American Type Culture Collection (ATCC). Cells were grown in DMEM containing 10% South American FBS, 1% L-Glutamax solution and 1% Pen/Strep solution.

extract_protocol:
Ca. 200 mill. cells were pelleted and resuspended in PBS and fixed first with disuccinimidyl glutarate at 2mM final concentration for for 45 min at room temperature, followed by 1% formaldehyde fixation for 10 min. Nuclear lysates were prepared, sonicated to reach an average fragment length of 300 bp, whereafter protein-DNA complexes were immunoprecipitated with specific antibodies.
DNA libraries were prepared for sequencing on the NextSeq as previously described (Ostuni, 2013).

treatment_protocol: Cells were treated for 45 minutes with LPS (10 ng/ml) before harvesting.

value: RAW 264.7 Macrophages

value: BALB/c


title: Control 1

source_name: Control 1


title: RalA-IR_Ecc15_1

value: midgut

value: UAS-Dcr2 / +; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / P{KK108989}VIE-260B; tub-Gal80ts / +

value: Ecc15 in 5% sucrose

value: 10-14 days after eclosion


title: RalA-IR_Mock_4

value: Mock treated (5% sucrose)


title: cjnw5krpb006q3h5vt6ccj01a

value: Skin

value: female

value: control


title: ZC3H4-ChIPseq_LPS_45min_rep2

description: Chromatin IP against ZC3H4

data_processing:
Single end reads (76bp) were trimmed and clipped for quality control with Trimmomatic v0.27 (PMID:24695404). Read quality was then checked for each sample using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were mapped using Bowtie2 v 2.2.6 (PMID: 19261174). We used default parameters with the options --very-sensitive, --no-unal and with the pre-built bowtie2 index. Only uniquely mapping reads were retained.
Peak calling was performed using SICER v2 (PMID: 24743992). We identified significantly enriched clusters using a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp  and a False Discovery Rate (FDR) cut-off <0.01 were used. and a False Discovery Rate (FDR) cut-off <0.01 were used Fragment size was set to 150nt and the effective genome fraction to 0.80. The ChIP was compared to input DNA derived from RAW264.7 mouse macrophages. Regions that overlapped with the blacklists of the ENCODE and modENCODE consortia (http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-blacklist.bed.gz) were filtered out.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975)
Genome_build: mm10 (GENCODE) https://www.gencodegenes.org/mouse/release_M24.html
Supplementary_files_format_and_content: bigWig

value: wild type

value: anti-ZC3H4 (Sigma, cat.no. HPA040934)


title: CLP 24h + 2h of PBS 3

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 95 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: count matrix containg the counts output from featurecounts for all samples

source_name: CLP 24h + 2h of PBS

treatment_protocol: mice were either given a CLP or SHAM surgery. After 24h both groups were divided in 2 and one subgroup was injected with PBS, the other with 10 mg/kg DEX. 2H after injection liver was isolated for RNA extraction

value: CLP operation followed after 24h by injection of PBS (IP) with organ isolation 2h later

value: liver


title: RalA-IR_Mock_3


title: ZC3H4-ChIPseq_LPS_45min_rep1

description: Chromatin IP against ZC3H4


title: cjnw5krpb006p3h5v4nz1og7m

source_name: Lung

value: Lung


title: noCadmium_231_Input

city: Aurora

first: Joshua

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

data_processing:
ChIP-seq experiments were aligned to a custom genome combining human hg38 and drosophila dr3 genomes using Bowtie2 (2.3.4.1).
Sam files were transformed into bam files, sorted and indexed using samtools (version 1.8).
Total reads for each chromosome were calculated using samtools (version 1.8) idxstats and ChIP-seq alignment bigwig files were created with deeptools bamCoverage (version 3.1.3) using CPM with 50 bp binning and were normalized between IP type (H3 or H3K27me3) by calculating a scaling factor for each sample based on total read number of all Drosophila chromosomes
Biological replicates were averaged using WiggleTools (version 1.2) using the mean operation and the resulting wig file was converted to bigwig using wigToBigWig command.
Genome_build: HG38 and DR3
Supplementary_files_format_and_content: bigwig

growth_protocol: MDA-MB-231 female breast cancer cell line were maintained at 37°C in Dulbecco’s Modified Essential Medium (DMEM) with 10% FB essence (VWR), 1% penicillin/streptomycin, and L-glutamine.

extract_protocol:
Cells were crosslinked by adding 1% formaldehyde to media for 10 minutes at 37°C. Crosslinking was stopped by addition of Glycine to 0.125M and incubating for 5 minutes at room temperature. Cells were washed with PBS and collected and centrifuged. Cells were resuspended in cellular lysis buffer (5mM PIPES pH 8, 85 mM KCl, 0.5% NP40), incubated on ice for 5 minutes and centrifuged. Samples were resuspended in nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 1% SDS) and sonicated for 45 minutes using 30 second on/off cycle repeats at 70% intensity (using a Qsonica Q800R). 10 ug crosslinked DNA and 2 ug crosslinked Drosophila control spike-in chromatin was used per immunoprecipitation. Chromatin was pulled down overnight using Invitrogen Protein A Dynabeads with antibodies for H3 (Cell Signaling Technology), H3K27m33 (Abcam) or IgG (Cell Signaling Technology). Beads were washed twice with IP buffer (16.7 mM Tris pH 8, 1.2 mM EDTA pH 8, 167 mM NaCl, 0.1% SDS, 1.84% Triton X100), once with TSE buffer (20 mM Tris pH 8, 2 mM EDTA pH 8, 500 mM NaCl, 1% Triton X100, 0.1% SDS) and LiCl buffer (100mM Tris pH 8, 500 mM LiCl, 1% deoxycholic acid, 1% NP40), and twice with TE (10mM Tris pH 8, 1 mM EDTA pH 8). DNA was eluted from beads with proteinase K and purified with Promega Wizard SV PCR clean up kit. DNA was analyzed with qPCR and compared to 10% input collected prior to pulldown.
ChIP-seq libraries were prepared using the Illumina NEBNext Ultra II ChIP-Seq sample kit, according to the manufacturer’s protocol. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer. Samples were sequenced on a llumina NovaSEQ6000 paired end

treatment_protocol: Cadmium-resistant cell (MDA-MB-231cadR) cell lines were selected by passage in medium containing CdSO4. The CdSO4 concentration was increased by increments of 5 μM after 10 passages at the current concentration and when cell count increased at least 1.8 times average daily over at least four passages consistently. Cells used in this study were adapted to CdSO4 containing medium for 7 months at 10uM.

tag: cell line

value: Breast cancer cell line

value: No treatment control

value: none; input


title: noCadmium_231_k27me3


title: 10umCadmium_231_k27me3

value: 10um Cadmium


title: WDR82-ChIPseq_LPS_45min_rep2

description: Chromatin IP against  WDR82

value: RAW 264.7 Macrophages

value: BALB/c

value: anti-WDR82 (Cell Signaling Technologies, cat.no. 99751, clone D2I3B)


title: cjnw5krpb006o3h5v7aalhmcm

source_name: Liver

value: Liver


title: RalA-IR_Ecc15_3

value: midgut

value: UAS-Dcr2 / +; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / P{KK108989}VIE-260B; tub-Gal80ts / +

value: Ecc15 in 5% sucrose

value: 10-14 days after eclosion


title: cjnw5krpb006n3h5vd67ivaoq

source_name: Heart

value: Heart

value: female

value: control


title: ChIP-seq_HA-HA-JICD

city: Seoul

first: Eun-Jung

last: Kim

address: Anamro 5ga

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: mm10
Supplementary_files_format_and_content: 1) Transcription factor name, 2) DNA binding consensus, 3) P-value, 4) log P-pvalue, 5) q-value(Benjamini), 6) #Target sequences with motif, 7)% of Targets sequences with motif, 8) #Background sequences with motif, 9) % of Background sequences with motif

source_name: Ink4a-/- murine astrocyte

growth_protocol: Ink4a-/- astrocytes were cultured in DMEM with high glucose supplemented with 10% fetal bovine serum, 1% penicilin/streptomycin, 2mM L-glutamine and 50ug/mL gentamicin.

extract_protocol:
Chromatin DNA was immunoprecipitated with anti-HA or anti-H3K9Ac and Protein A/G beads
DNA enrichment was performed using EpiMark® Methylated DNA Enrichment Kit (New England Biolabs, UK).
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

value: Astrocyte

value: Brain

tag: antibody

value: HA (Cell Signaling, 3724s)

tag: transfected with

value: pcDNA HA-JICD puro


title: 10umCadmium_231_input

value: Breast cancer cell line

value: none; input


title: WDR82-ChIPseq_LPS_45min_rep1

description: Chromatin IP against  WDR82

value: RAW 264.7 Macrophages

value: wild type


title: cjnw5krpa006m3h5vi7nec9h6

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5)
Transcript expression was then quantified using Salmon [1] (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing per-gene count estimates, using the Ensembl mm10 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each gene for each sample, in long-format

source_name: Spleen

value: Spleen


title: WT_Ecc15_4

value: UAS-Dcr2 / w1118; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / +; tub-Gal80ts / +


title: 3-D Elf1 cells_rep2

city: Rochester

first: G Rasul

last: Chaudhry

state: MI

address: 118 Library Dr

department: Biological Sciences

institute: Oakland University

data_processing:
Sequencing performed by GENEWIZ, Inc. via Illumina NovaSeq/HiSeq 2x150 bp
Sequenced reads were trimmed for adaptor sequence using Trim Galore! v0.6.3, and HiSat2 v2.1.0 was used to map the raw reads to the reference genome hg38
Expression for each gene were evaluated using featureCounts v1.6.4 based on annotation from GENCODE release 30
The raw counts were then normalized and differential gene expression was determined using DESeq2 v2.11.40.6
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include featurecounts values for each sample
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample

source_name: 3-D Elf1 cells

growth_protocol: ESCs were maintained in ESC expansion medium as outlined in Ware et al., 2014

extract_protocol:
Samples were flash frozen on dry ice, and RNA was harvested using the GeneJET RNA purification kit (Cat#K0732) was used to isolate total RNA for the construction of sequencing libraries
cDNA libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems, Wilmington, MA) according to the manufacturer’s protocol

treatment_protocol: For 2-D culture, ESCs were grown adherent on Matrigel coated plastic plates. For 3-D culture, ESCs were dissociated into single cells and 5x10^6 cells were encpasulated in PEG-8-SH/PEG-8-Acr scaffolds at the time of self-assembly and maintained in ESC expansion medium for 21 days.

value: Human embryonic stem cells

value: Grown in 3-D culture conditions


title: RalA-IR_Mock_1

value: midgut

value: UAS-Dcr2 / +; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / P{KK108989}VIE-260B; tub-Gal80ts / +

value: Mock treated (5% sucrose)


title: ChIP-seq_HA-Con

value: pcDNA puro (control)


title: 3-D Elf1 cells_rep1


title: WT_Ecc15_3

value: Ecc15 in 5% sucrose

value: 10-14 days after eclosion


title: cjnw5krpb006r3h5vrajy78gf

source_name: Gonadal fat

extract_protocol:
RNA was extracted from whole tissues using the Qiagen RNeasy 96 Universal Tissue Kit (Qiagen, 74881) and was digested with DNAseI before preparation for RNA-seq
Lib Prep method: TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat, Input Total Conc: 100ng in 10ul. PCR 12 cycles. Sequencing  - 3nM on Hiseq 4000

value: Gonadal fat

value: female

value: control


title: ChIP-seq_H3K9Ac-HA-JICD

value: Astrocyte

value: Brain

value: H3K9Ac (Millipore, 07-352)

value: pcDNA HA-JICD puro


title: 2-D Elf1 cells_rep2

source_name: 2-D Elf1 cells

value: Grown in 2-D culture conditions


title: WT_Ecc15_2

source_name: whole adult midgut

value: UAS-Dcr2 / w1118; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / +; tub-Gal80ts / +


title: cjnw5krpa006k3h5v1sbdj696

value: Subscapular fat


title: WT_Ecc15_1


title: cjnw5krpa006j3h5vyhzjcbvd


title: ChIP-seq_H3K9Ac-Con


title: 2-D Elf1 cells_rep1

value: Human embryonic stem cells


title: RalA-IR_Mock_2

value: midgut


title: HeLa_4sU_CTermZC3H4_rep3

data_processing:
After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), strand specific paired end reads (51 bp) were aligned using TopHat v2.1.0 1 (PMID:23618408), allowing up to two mismatches and using the option --b2-very- sensitive --library-type fr-firststrand --no-discordant. Indels due to sequencing errors were identified using Bowtie2 v 2.2.6 (PMID: 19261174). Reads originating from the two strands were separated according to the XS:A:+/XS:A:-flag provided by TopHat2 (PMID:23618408).
SICER v2 (PMID: 24743992) was used to detect the extra-genic transcripts regulated in cells depleted of individual factors. The entire genome was partitioned into blocks of non-overlapping 500 bp windows with a gap size <1000 nt. An effective genome fraction of 1, a fragment size of 0 and a False Discovery Rate (FDR) cut-off <0.01 were used.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM containing 10% Foetal Bovine Serum, 1% L-Glutamax solution and 1% Penicillin/Streptomycin solution. Cells were transfected with 2.5 mg of the empty vector or with 2.5 mg of the ZC3H4 C-TERMINAL fragment expression vector.

extract_protocol:
Total RNA was extracted using Trizol (Thermofisher cat. 15596026); 4sU-labelled RNA was extracted as described (Austenaa et al. 2015, PMID 26593720)
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 80-200 ng of nascent 4sU-labelled RNA, without ribosomal depletion.

treatment_protocol: 4-thio-uridine (4sU) was added to the medium at a final concentration of 300 mM for 45 min before harvesting the cells.

value: HeLa, human cervix, epitheloid carcinoma


title: HeLa_4sU_CTermZC3H4_rep2


title: cjnw5krpa006h3h5vq3vv6ndg

value: Lung


title: WT_Mock_4

description: MNR22170301_S8_R1_001_MN08_WT_S08_R1_001_MN08_WT_SUC4

value: Mock treated (5% sucrose)


title: cjnw5krpa006g3h5v2zcnhuvm

value: Liver


title: HeLa_4sU_CTermZC3H4_rep1


title: HeLa_4sU_empty_rep3

value: empty vector


title: WT_Mock_2

description: MNR22170301_S6_R1_001_MN06_WT_S06_R1_001_MN06_WT_SUC2

value: 10-14 days after eclosion


title: WT_Mock_1

description: MNR22170301_S5_R1_001_MN05_WT_S05_R1_001_MN05_WT_SUC1


title: cjnw5krpa006l3h5v6t20dkcy

source_name: Kidney

value: Kidney

value: female


title: cjnw5krpa006f3h5vbtepitbo

value: Heart

value: control


title: HeLa_4sU_empty_rep2


title: HeLa_4sU_empty_rep1


title: DNAMe_SID4X_TIS_Rep2

city: Lewiston

first: Andrew

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

data_processing:
Reads were QC’d by FastQC (v0.11.5)
filtered by quality (average quality score < 20), Illumina adapters removed, and sequencing primers trimmed using Trim_Galore! (v0.4.5)
The filtered and trimmed reads were then mapped to the mouse genome (mm10), deduplicated, and CpG methylation levels extracted using Bismark (v0.19.0)
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts text file for all genes tested with featureCounts
Supplementary_files_format_and_content: One tab-delimited text file includes percent CpG methylation values for each 25 CpG window

source_name: Cultured Hippocampal Neurons

extract_protocol:
gDNA was bisulfite converted (Accel-NGS Methyl-Seq DNA Library, Swift) and sequenced (Hudson Alpha GSL) on the Illumina platform (HiSeq_X10, paired end, 150 bp, 400-600 million reads per sample).
An AllPrep DNA/RNA Mini Kit was used for experiments requiring genomic DNA and total RNA from the sample.

value: Cultured Hippocampal Neurons

tag: isoform


title: cjnw5krpa006e3h5vl7zfdckv

tag: tissue

value: Spleen


title: cjnw5krpa006d3h5voro09k76

tag: strain


title: DNAMe_VP64_TIS_Rep2

data_processing:
Reads were QC’d by FastQC (v0.11.5)
filtered by quality (average quality score < 20), Illumina adapters removed, and sequencing primers trimmed using Trim_Galore! (v0.4.5)
The filtered and trimmed reads were then mapped to the mouse genome (mm10), deduplicated, and CpG methylation levels extracted using Bismark (v0.19.0)
Altered CpG methylation was determined by dividing the mouse genome into 870,336 windows, each containing 25 CpG sites. Differentially methylated regions (DMRs) were determined using the EdgeR (for/rev) algorithm available in the Seqmonk (v1.44.0) software package, where a significant difference for any manipulation (VP64, SID4X, and NFD) was determined by a FDR < 0.3 independently against both other groups
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts text file for all genes tested with featureCounts
Supplementary_files_format_and_content: One tab-delimited text file includes percent CpG methylation values for each 25 CpG window


title: cjnw5krpa006i3h5vyws64moz

source_name: Skin

value: Skin

tag: Sex


title: cjnw5krpa006c3h5v7mb3su51

tag: treatment


title: HeLa_polyA_siWdr82_rep3

description: polyA-RNAseq HeLa siWdr82 rep 3

data_processing:
Strand specific paired end reads (76nt) were trimmed for removing the adapter sequence and discarding low quality bases using Trimmomatic v0.27 with PE option (PMID:24695404)
Read quality was then checked for each sample using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were then aligned with TopHat2 v2.1.0 (–very-sensitive --library-type fr-firststrand -r 200 --segment-length 35  --microexon-search --no-mixed --no-discordant -g 1 --coverage-search) (PMID:23618408). Indels due to sequencing errors were identifies using Bowtie2 v.2.6 (PMID: 19261174).
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)

growth_protocol: HeLa cells were cultured in DMEM containing 10% South American origin Foetal Bovine Serum, 1% L-Glutamax solution and 1% PenicillinStreptomycin solution.

treatment_protocol: Cells were left untreated.

value: HeLa

value: human cervix, epitheloid carcinoma


title: WT_Mock_3

description: MNR22170301_S7_R1_001_MN07_WT_S07_R1_001_MN07_WT_SUC3

value: UAS-Dcr2 / w1118; esg-Gal4NP5130, UAS-GFP, UAS-GFPnLacZ / +; tub-Gal80ts / +

tag: age


title: LUC_2

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: MDA-MB-231 control cells

hyb_protocol: Hybridization was carried out with GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations.

scan_protocol: Gene-Chip Scanner 3000 7G system (Affymetrix).

data_processing:
CEL-files were jointly processed in Transcriptome Analysis Console 4.0.0.25 (Thermo Fisher Scientific, USA) with summation method Gene + Exon - SST-RMA (Analysis Version 1) and empirical Bayes method.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

label: biotin

source_name: LUC

label_protocol: Labelling was carried out with GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations using 500 ng total RNA as starting material.

growth_protocol: MDA-MB-231 breast cancer cell line was cultured in complete cell culture medium consisting of DMEM high glucose (Gibco) supplemented with 10% vol. fetal bovine serum (Gibco), 2 mM L-glutamine (PanEco), 1% vol. pencillin-streptomycin solution (Gibco). The cells were incubated in cell culture incubator (37 °C, 5% CO2).

extract_protocol: RNA was extracted from frozen tumor samples using the miRNeasy Micro Kit (Qiagen) as recommended by the manufacturer.

treatment_protocol: not applicable

tag: origin

value: Cell line

tag: knockdown elovl5

value: no

tag: knockdown igfbp6


title: LUC_3

description: MDA-MB-231 control cells


title: LUC_1

description: MDA-MB-231 control cells


title: IGFBP6_2

description: MDA-MB-231 cells with knockdown of IGFBP6 gene

value: yes


title: HeLa_polyA_siCtl_rep3

description: polyA-RNAseq HeLa siCtl rep 3

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Mini Prep kit (Cat no. R1055) with on-column DNAse digestion.
After oligodT-based selection of polyadenylated transcripts from 3-5 ug total RNA, library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007).

tag: cell type

value: siCtl


title: IGFBP6_3


title: DNAMe_NFD_TIS_Rep2


title: ZAP-g3 knockout HFF, 1h 4sU, CMV infected 72hpi, replicate B [zap-g3.72hpi.B]

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
4sU_RNAseq_12_KO2_72h_S30
processed data file:
4sU_RNAseq_counts.tsv

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome using standard parameter, using the Refseq gtf file downloaded from the UCSC genome browser.
Reads were then quantified using quasR (Gaidatzis et al, 2015) and the above mentioned gtf file, or the HCMV TB40/E annotation (accession number MF871618).
Differential expression and corresponding p-values were calculated using edgeR (McCarthy et al, 2012).
For 4sU sequencing, reads were mapped to a combined index of the human genome (Hg38 / Ensembl v90) and the HCMV genome (accession number KF297339.1) using STAR (v2.5.3a) with parameters --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH.
We used GRAND-SLAM (v2.0.5d) (Jurges et al., 2018) to estimate the new-to-total RNA ratios.
We only used the parts of the reads that were sequenced by both mates in a read pair (parameter -double) for the estimation.
New RNA was computed by multiplying total RNA with the maximum a posteriori estimate of the new-to-total RNA ratio.
For further analyses, we removed all cellular genes that had less than 10 transcripts per million transcripts (TPM) in more than 6 (cellular genes) or 2 (viral genes) samples.
To remove artefacts due to imprecise quantification, we furthermore removed all viral genes with less than 100 new reads. Log2 fold changes were estimated using PsiLFC (Erhard, 2018) with uninformative prior (corresponding to no pseudocounts).
Normalization factors were computed from total RNA such that the median log2 foldchange was 0 and applied to both total and new RNA.
Genome_build: hg19 and HCMV MF871618 (bulk RNA-seq); hg38 and HCMV KF297339.1 (4sU seq)
Supplementary_files_format_and_content: tab-separated values

growth_protocol:
Primary human foreskin fibroblasts (HFF-1) cells (ATCC SCRC-1041) were maintained in DMEM (high glucose) supplemented with 15% FCS, 1% P/S and 1% non‐essential amino acids (NEAA). Cells were cultured at 37°C and 7.5% CO2.
Knockouts of ZAP (ZC3HAV1) were done using CRISPR/Cas9, with components transduced by lentiviruses

extract_protocol:
NEBNext Single Cell/Low Input RNA Library Prep
adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
adapter sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs)

treatment_protocol: Cells were subjected to CMV infection and 4sU treatment as indicated

value: Primary human foreskin fibroblasts (HFF) cells

tag: genotype/variation

value: ZAP-g3 knockout

value: 1h 4sU, CMV infected 72hpi

tag: grna sequence forward

value: CACCGGCCGGGATCACCCGATCGG

tag: grna sequence reverse

value: AAACCCGATCGGGTGATCCCGGCC

tag: grna name

tag: 4su treatment

value: 1h before harvesting

tag: cmv infection

tag: harvesting timepoint


title: cjnw5krpa006a3h5vkp6fgoie

growth_protocol: Mice were maintained on a 12:12 hour light:dark cycle at 22℃ with environmental enrichment (e.g., nesting material and/or huts) with access to water and food ad libitum.

value: female

value: control


title: DNAMe_SID4X_TIS_Rep1

value: Cultured Hippocampal Neurons

tag: isoform


title: DNAMe_NFD_TIS_Rep1

tag: tissue


title: cjnw5krpa00693h5v00qoo5y6

value: Lung

tag: strain


title: cjnw5krpa006b3h5vd190k9tr

value: Gonadal fat

tag: Sex


title: cjnw5krpa00683h5vipl504x6

value: Liver

tag: treatment


title: ZAP-g3 knockout HFF, 1h 4sU, CMV infected 72hpi, replicate A [zap-g3.72hpi.A]

description:
4sU_RNAseq_11_KO1_72h_S29
processed data file:
4sU_RNAseq_counts.tsv


title: IGFBP6_1

tag: cell line


title: ELOVL5_2

description: MDA-MB-231 cells with knockdown of ELOVL5 gene

tag: origin


title: ELOVL5_3

tag: knockdown elovl5


title: HeLa_polyA_siZc3h4_rep3

description: polyA-RNAseq HeLa siZc3h4 rep 3

value: HeLa

value: human cervix, epitheloid carcinoma


title: parental wild type HFF, 1h 4sU, CMV infected 72hpi, replicate B [wt.72hpi.B]

description:
4sU_RNAseq_10_WT2_72h_S28
processed data file:
4sU_RNAseq_counts.tsv

value: parental wild type


title: DNAMe_SID4X_TIL_Rep2

tag: age


title: DNAMe_VP64_TIS_Rep1


title: parental wild type HFF, 1h 4sU, CMV infected 72hpi, replicate A [wt.72hpi.A]

description:
4sU_RNAseq_9_WT1_72h_S27
processed data file:
4sU_RNAseq_counts.tsv

tag: cell type

value: yes


title: cjnw5krpa00673h5v08w2jq34

value: Heart


title: Sample_S4_sRNA

city: Vasant Kunj

first: Neeti

last: Sanan-Mishra

state: Delhi

address: Aruna Asaf Ali Marg

department: Plant RNAi Biology

country: India

institute: ICGEB

data_processing:
Quality filtering  and adapter trimming was done by NGStool kit
Abundance was calculated for unique reads

organism: Oryza sativa

source_name: Root

growth_protocol: Rice seeds were grown under green house conditions at temperature (28±2°C), relative air humidity (70%), and 16/8‐h light/dark cycle.

extract_protocol:
Total RNA was isolated using Trizol reagent and enriched with 50% PEG and 0.1% NaCl for small RNA isolation. The RNA bands of corresponding size ranging between 15-30 nucleotides were gel purified
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For salt treatment, seedlings were transferred to plastic containers containing 200 mM NaCl for definite time.

tag: stress

value: Salt Stress

tag: cultivar

value: Pokkali

tag: physiological character

value: Naturally Salt Tolerant


title: Sample_Index4_sRNA

data_processing:
Quality filtereing  and adapter trimming was done by NGStool kit
Abundance was calculated for unique reads

source_name: Panicle

growth_protocol: The seeds were grown under controlled temperature (28 ± 2 °C), relative air humidity (70%) and 16/8-h light/dark cycle conditions.

treatment_protocol: Heat stress was given at 42°C for 6 hours.

value: Heat Stress

value: Pusa basmati

value: Susceptible


title: cjnw5krpa00663h5vavzcqf9f

treatment_protocol: Mice were treated with control or anti-PAPP-A antibody for 17 weeks, then sacrificied and nine tissues were harvested and processed for RNA-seq:  lung, liver, kidney, heart, spleen, bone marrow, gonadal fat, subscapular (subcutaneous) fat, skin

value: Spleen

value: female


title: ZAP-g3 knockout HFF, 1h 4sU, CMV infected 18hpi, replicate B [zap-g3.18hpi.B]

description:
4sU_RNAseq_8_KO2_18h_S26
processed data file:
4sU_RNAseq_counts.tsv

value: Primary human foreskin fibroblasts (HFF) cells

tag: genotype/variation

value: ZAP-g3 knockout

value: 1h 4sU, CMV infected 18hpi

tag: grna sequence forward

value: CACCGGCCGGGATCACCCGATCGG

tag: grna sequence reverse

value: AAACCCGATCGGGTGATCCCGGCC

tag: grna name

value: 1h before harvesting


title: Sample_Index2_sRNA

value: Normal (control for stress)


title: cjnw5krpa00653h5vbos8tmlw

value: Kidney

value: control


title: ZAP-g3 knockout HFF, 1h 4sU, CMV infected 18hpi, replicate A [zap-g3.18hpi.A]

description:
4sU_RNAseq_7_KO1_18h_S25
processed data file:
4sU_RNAseq_counts.tsv

tag: 4su treatment

tag: cmv infection

value: yes

tag: harvesting timepoint


title: DNAMe_NFD_TIL_Rep2

tag: strain

tag: tissue

value: Cultured Hippocampal Neurons

tag: isoform


title: DNAMe_VP64_TIL_Rep2


title: cjnw5krpa00643h5vh9r50eaw

source_name: Subscapular fat

value: Subscapular fat

tag: Sex

tag: treatment


title: DNAMe_NFD_TIL_Rep1

tag: age


title: parental wild type HFF, 1h 4sU, CMV infected 18hpi, replicate B [wt.18hpi.B]

description:
4sU_RNAseq_6_WT2_18h_S24
processed data file:
4sU_RNAseq_counts.tsv

tag: cell type

value: parental wild type


title: PfAP2-G2::KO gametocytes TP15

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP15

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinßs, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213û219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: PfAP2-G2::KO gametocytes stage IV

growth_protocol: Both strains of Plasmodium falciparum parasites were cultured at 37 deg C under standard conditions in the presence of 5% CO2 and 6% O2 in RPMI 1640 media. The media was supplemented with HEPES, NaHCO3, hypoxanthine, 2.5% (w/v) Albumax II, and gentamycin (50 ug/ml).

extract_protocol: Total RNA was extracted from induced PfAP2-G2::KO and WT parasites every 12 hours for 7.5 days using TRIzol. Timepoint 6 was excluded due to collection error.

treatment_protocol: The early gametocyte rings were treated with media containing heparin (20 U/ml) for four days to prevent the reinvasion of asexual parasites.

tag: genotype

tag: hours post invasion

value: Day 8 gametocytes

tag: Stage

value: stage IV

source_name: 3D7 Asexual and Sexual Mixed Stage Reference Pool + cDNA from Gametocyte Samples

value: Asexual and Sexual Mixed Stage


title: parental wild type HFF, 1h 4sU, CMV infected 18hpi, replicate A [wt.18hpi.A]

description:
4sU_RNAseq_5_WT1_18h_S23
processed data file:
4sU_RNAseq_counts.tsv

tag: genotype/variation


title: ELOVL5_1

tag: origin

value: Cell line

tag: knockdown elovl5

tag: knockdown igfbp6

value: no

tag: cell line


title: DNAMe_SID4X_TIL_Rep1


title: RNA-seq WT exp rep 2

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

data_processing:
Sequencing reads were filtered and trimmed with Trimmomatic (v 0.36, Phred score of 6 consecutive bases below 15, minimum read length of 36nt) and mapped to the human genome (GENCODE’s GRCh38 primary assembly, annotation v24) with STAR (v 2.5.2b).
Read to gene assignment was done with featureCounts (1) (v1.5.2, reverse stranded).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (tsv file).

source_name: Myoblast

growth_protocol: Myoblast SOP Eurobiobank http://www.eurobiobank.org/biobanking-sops/

extract_protocol:
600,000 cells from human myoblast cell lines CMD, LGMD2i and control were harvested and RNA extracted using RNAeasy Micro kit (QIAGEN, Cat 74004). RNA concentrations were measured using Quibit RNA HS Assay Kit (Life Technologies, Cat Q32855) on a Denovix Fluorometer. Samples were processed with 200ng of total RNA. PolyA RNA seq libraries were generated using IIlumina TruSeq Stranded mRNA Sample prep, protocol 15031047 RevE Oct 2013.
Libraries were prepared according to the Illumina standard RNA protocol. Each library was single-end with a 76 nt read length.

treatment_protocol: Not applicable

tag: line type

value: Primary Myoblast Line

value: Muscle

value: Wild Type

value: Unknown


title: cjnw5krpa00633h5veqb0dzdl

city: South San Francisco

first: Adam

last: Freund

address: 1170 Veterans Blvd

value: Gonadal fat

value: female


title: Sample_S3_sRNA

tag: stress

value: Normal (control for stress)

tag: cultivar

value: Pokkali

tag: physiological character

value: Naturally Salt Tolerant


title: ZAP-g3 knockout HFF, 1h 4sU, untreated, replicate B [zap-g3.0hpi.B]

description:
4sU_RNAseq_4_KO2_S22
processed data file:
4sU_RNAseq_counts.tsv

source_name: ZAP-g3 knockout HFF, 1h 4sU, untreated

value: Primary human foreskin fibroblasts (HFF) cells

value: ZAP-g3 knockout

value: 1h 4sU, untreated

tag: grna sequence forward

value: CACCGGCCGGGATCACCCGATCGG

tag: grna sequence reverse

value: AAACCCGATCGGGTGATCCCGGCC

tag: grna name

tag: 4su treatment

value: 1h before harvesting

tag: cmv infection

tag: harvesting timepoint


title: RNA-seq WT exp rep 1

tag: tissue

tag: genotype

tag: age


title: cjnw5krpa00613h5vel3rd3hu

source_name: Lung

value: Lung

tag: strain

tag: Sex

tag: treatment

value: control


title: ZAP-g3 knockout HFF, 1h 4sU, untreated, replicate A [zap-g3.0hpi.A]

description:
4sU_RNAseq_3_KO1_S21
processed data file:
4sU_RNAseq_counts.tsv

tag: cell type

tag: genotype/variation

value: no


title: cjnw5krpa00603h5va0az2nn1

source_name: Liver

value: Liver


title: RNA-seq LGM exp rep 1

tag: line type

value: Primary Myoblast Line

value: Muscle

value: c.826C>A,  p.Leu276Ile

value: 4.5 years


title: PfAP2-G2::KO gametocytes TP12

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP12

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinßs, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213û219 (2013).

tag: hours post invasion

value: Day 6 gametocytes

tag: Stage

value: stage IV

value: Asexual and Sexual Mixed Stage


title: parental wild type HFF, 1h 4sU, untreated, replicate A [wt.0hpi.A]

description:
4sU_RNAseq_1_WT1_S19
processed data file:
4sU_RNAseq_counts.tsv

value: Primary human foreskin fibroblasts (HFF) cells

value: parental wild type

tag: grna sequence forward


title: PfAP2-G2::KO gametocytes TP13

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP13

value: Day 7 gametocytes


title: cjnw5krpa005z3h5v5tkvg1n2

source_name: Heart

value: Heart

value: female


title: RNA-seq CMD exp rep 2

value: c.693G>C,  p.Ile478Thr

value: 15 Months


title: PfAP2-G2::KO gametocytes TP14

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP14


title: PfAP2-G2::KO gametocytes TP9

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP9

source_name: PfAP2-G2::KO gametocytes stage III

value: Day 5 gametocytes

value: stage III


title: PfAP2-G2::KO gametocytes TP11

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP11


title: cjnw5krpa005y3h5v7io4somw

source_name: Spleen

value: Spleen

value: control


title: cjnw5krpa00623h5vv13nrsjb

value: Skin


title: RNA-seq CMD exp rep 1

value: Primary Myoblast Line

value: Muscle


title: ascc3_ko_with_shield-3

city: St. Louis

first: Nima

last: Mosammaparast

address: 660 S Euclid Ave

department: Pathology & Immunology

institute: Washington University in St. Louis

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 18

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma.
Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.
The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05. For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term. Heatmaps were generated using the Heatmapper online tool (heatmapper.ca).
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: tsv and xls files contain the gene and transcript expression data and differential expression data

source_name: U-2 OS [ATCC HTB-96]

growth_protocol: Cells were grown in DMEM +10%FBS + Pen/Strep

extract_protocol:
RNA was purified using the Qiagen RNeasy mini kit.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina Hi-Seq 3000 or NovaSeq 6000

treatment_protocol: Untreated or treated with 500 mM MMS or 300nM Shield1 as indicated

tag: cell line

value: U-2 OS

tag: cell line origin

value: human osteosarcoma

value: ASCC3-/- CRISPR/Cas9

value: treated with 300 nM Shield1


title: ascc3_ko_with_shield-2

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 17


title: cjnw5krpa005x3h5vilqowzia

institute: Calico Life Sciences LLC

source_name: Kidney

value: Kidney


title: cjnw5krpa005w3h5vbk4vbk0g

value: Subscapular fat

value: aPAPPA


title: ascc3_ko_with_shield-1

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 16


title: RNA-seq LGM exp rep 2

value: c.826C>A,  p.Leu276Ile

value: 4.5 years


title: parental wild type HFF, 1h 4sU, untreated, replicate B [wt.0hpi.B]

description:
4sU_RNAseq_2_WT2_S20
processed data file:
4sU_RNAseq_counts.tsv

value: Primary human foreskin fibroblasts (HFF) cells

value: parental wild type

value: 1h 4sU, untreated

tag: grna sequence reverse

tag: grna name

tag: 4su treatment

value: 1h before harvesting

value: no


title: PfAP2-G2::KO gametocytes TP8

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP8

value: Day 4 gametocytes

value: stage III

value: Asexual and Sexual Mixed Stage


title: ASCC3_KO.pos_MMS-2

description:
Processed data are in all ascc2Exp_*.txt files
Sample 35

value: U-2 OS

value: treated with 500 microM MMS


title: cjnw5krpa005v3h5vwu6f6h7h

source_name: Gonadal fat

tag: tissue

value: Gonadal fat

value: female


title: PfAP2-G2::KO gametocytes TP5

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP5

source_name: PfAP2-G2::KO gametocytes stage II

tag: genotype

value: Day 3 gametocytes

value: stage II


title: PfAP2-G2::KO gametocytes TP7

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP7


title: ascc3_ko_with_mms-3

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 15

value: human osteosarcoma

value: ASCC3-/- CRISPR/Cas9


title: ASCC3_KO.pos_MMS-1

description:
Processed data are in all ascc2Exp_*.txt files
Sample 34


title: PfAP2-G2::KO gametocytes TP4

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP4

source_name: PfAP2-G2::KO gametocytes stage I

value: Day 2 gametocytes

value: stage I


title: cjnw5krpa005u3h5v3kbgoelp

source_name: Skin

value: Skin

value: aPAPPA


title: ascc3_ko_with_mms-2

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 14


title: PfAP2-G2::KO gametocytes TP10

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP10

value: Day 5 gametocytes


title: cjnw5krpa005t3h5vd0ybxe5u

value: Lung


title: ASCC2_KO.pos_MMS-3

description:
Processed data are in all ascc2Exp_*.txt files
Sample 33

value: ASCC2-/- CRISPR/Cas9


title: ascc3_ko_with_mms-1

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 13


title: ASCC2_KO.pos_MMS-2

description:
Processed data are in all ascc2Exp_*.txt files
Sample 32


title: cjnw5krpa005s3h5vwaoh5lpv

value: Liver


title: ascc3_ko_control-3

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 12

value: untreated


title: ASCC3_KO.pos_MMS-3

description:
Processed data are in all ascc2Exp_*.txt files
Sample 36

value: U-2 OS


title: ASCC2_KO.pos_MMS-1

description:
Processed data are in all ascc2Exp_*.txt files
Sample 31

value: treated with 500 microM MMS


title: cjnw5krpa005r3h5vazltkv86

value: Heart


title: ascc3_ko_control-2

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 11


title: cjnw5krpa005q3h5vsyrvp8oi

value: Spleen

value: female


title: PfAP2-G2::KO gametocytes TP2

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP2

value: Day 1 gametocytes

value: Asexual and Sexual Mixed Stage


title: WT.pos_MMS-3

description:
Processed data are in all ascc2Exp_*.txt files
Sample 30

value: human osteosarcoma

value: wild-type


title: WT.pos_MMS-2

description:
Processed data are in all ascc2Exp_*.txt files
Sample 29


title: wt_with_shield-3

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 9

value: treated with 300 nM Shield1


title: ascc3_ko_control-1

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 10

value: ASCC3-/- CRISPR/Cas9


title: WT.pos_MMS-1

description:
Processed data are in all ascc2Exp_*.txt files
Sample 28


title: cjnw5krpa005p3h5vhny13jcc

value: Kidney

value: aPAPPA


title: WT E5 gametocytes TP14

description:
WT E5 strain gametocytes
WT GC TP14

source_name: WT gametocytes stage IV

value: WT

value: Day 7 gametocytes

value: stage IV


title: PfAP2-G2::KO gametocytes TP3

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP3

value: Day 2 gametocytes

value: stage I


title: WT E5 gametocytes TP15

description:
WT E5 strain gametocytes
WT GC TP15

value: Day 8 gametocytes


title: cjnw5krpa005o3h5vfapjd00t

source_name: Subscapular fat

value: Subscapular fat


title: cjnw5krp9005n3h5v2o35ya3p

value: Gonadal fat


title: wt_with_shield-2

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 8

value: U-2 OS


title: wt_with_shield-1

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 7


title: cjnw5krp9005m3h5vubjkv3yd

value: Skin

value: female


title: wt_with_mms-3

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 6

value: human osteosarcoma

value: treated with 500 microM MMS


title: ASCC3_KO.neg_MMS-2

description:
Processed data are in all ascc2Exp_*.txt files
Sample 26

value: ASCC2-/- CRISPR/Cas9

value: untreated


title: WT E5 gametocytes TP13

description:
WT E5 strain gametocytes
WT GC TP13

value: Asexual and Sexual Mixed Stage


title: ASCC3_KO.neg_MMS-1

description:
Processed data are in all ascc2Exp_*.txt files
Sample 25


title: PfAP2-G2::KO gametocytes TP1

description:
E5 strain gametocytes with disrupted ap2-g2 gene
AP2-G2::KO GC TP1

value: Day 1 gametocytes


title: ASCC3_KO.neg_MMS-3

description:
Processed data are in all ascc2Exp_*.txt files
Sample 27


title: wt_with_mms-2

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 5

value: wild-type


title: cjnw5krp9005l3h5v3er5zuhy

value: Lung

value: aPAPPA


title: WT E5 gametocytes TP11

description:
WT E5 strain gametocytes
WT GC TP11

source_name: WT gametocytes stage III

value: WT

value: Day 6 gametocytes

value: stage III


title: WT E5 gametocytes TP12

description:
WT E5 strain gametocytes
WT GC TP12

value: stage IV

source_name: 3D7 Asexual and Sexual Mixed Stage Reference Pool + cDNA from Gametocyte Samples


title: ASCC2_KO.neg_MMS-3

description:
Processed data are in all ascc2Exp_*.txt files
Sample 24


title: wt_with_mms-1

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 4


title: cjnw5krp9005j3h5v63zn289q

value: Heart


title: ASCC2_KO.neg_MMS-2

description:
Processed data are in all ascc2Exp_*.txt files
Sample 23

value: U-2 OS


title: WT E5 gametocytes TP9

description:
WT E5 strain gametocytes
WT GC TP9

value: Day 5 gametocytes


title: wt_control-3

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 3


title: cjnw5krp9005i3h5vbu19be6x

value: Spleen

value: female


title: ASCC2_KO.neg_MMS-1

description:
Processed data are in all ascc2Exp_*.txt files
Sample 22

value: human osteosarcoma


title: cjnw5krp9005h3h5vru7d8kg6

value: Kidney


title: WT.neg_MMS-3

description:
Processed data are in all ascc2Exp_*.txt files
Sample 21

value: untreated


title: WT E5 gametocytes TP8

description:
WT E5 strain gametocytes
WT GC TP8

value: Day 4 gametocytes

value: Asexual and Sexual Mixed Stage


title: wt_control-1

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 1

value: wild-type


title: WT.neg_MMS-2

description:
Processed data are in all ascc2Exp_*.txt files
Sample 20


title: WT E5 gametocytes TP10

description:
WT E5 strain gametocytes
WT GC TP10


title: cjnw5krp9005g3h5vrbzrnxag

value: Subscapular fat

value: control


title: WT.neg_MMS-1

description:
Processed data are in all ascc2Exp_*.txt files
Sample 19


title: WT E5 gametocytes TP7

description:
WT E5 strain gametocytes
WT GC TP7

source_name: WT gametocytes stage II

value: WT

value: stage II


title: WT E5 gametocytes TP5

description:
WT E5 strain gametocytes
WT GC TP5

value: Day 3 gametocytes


title: WT E5 gametocytes TP3

description:
WT E5 strain gametocytes
WT GC TP3

source_name: WT gametocytes stage I

value: Day 2 gametocytes

value: stage I


title: SUIT-2_Reverse_Adapted_Exome_clone6

city: Boston

first: Nada

middle: Y

last: Kalaany

state: MA

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

data_processing:
Library strategy: Exome-seq
RNA-seq: Data was aligned to the hg19 genome using STAR. Read counts were obtained using Salmon and analyzed using the tximport and DESeq2 packages in R.
ATAC-seq: Data was aligned to the hg19 genome using Bowtie2. Bigwigs were obtained using bamCoverage from the deeptools tool suite, normalized to 1X coverage
WES: Data was processed with bcbio-nextgen; reads were aligned with bwa mem, variants called with GATK Haplotype caller and annotated with snpEff.
Genome_build: ATAC-seq and RNA-seq: hg19; WES: hg38.
Supplementary_files_format_and_content: ATAC-seq: bigwig files; RNA-seq: raw gene counts file; WES: Variant Call Format (vcf) file.

source_name: SUIT-2 cells

growth_protocol: Grown in RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM). Then regrown in RPMI medium with high glucose (11 mM) and high glutamine (2 mM).

extract_protocol:
DNA was isolated and purified using Genomic DNA Mini Kit (Invitrogen, K1820-01).
DNA libraries were prepared using the Agilent SureSelect Human All Exon V6 kit.

treatment_protocol: Cells were seeded overnight at 700,000 per 10 cm plate. The cells were then washed once with PBS and incubated in L-L medium for 24 h. L-L medium refers to customized RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM).


title: SUIT-2_Reverse_Adapted_Exome_clone5


title: cjnw5krp9005f3h5vvbi04l2o

value: Gonadal fat


title: cjnw5krp9005k3h5vvwlcq9q8

source_name: Liver

value: Liver

value: aPAPPA


title: cjnw5krp9005e3h5vn06eo275

value: Skin

value: female


title: SUIT-2_Reverse_Adapted_Exome_clone4


title: WT E5 gametocytes TP2

description:
WT E5 strain gametocytes
WT GC TP2

value: Day 1 gametocytes


title: SUIT-2_Adapted_Exome_clone6

growth_protocol: Grown in RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM).


title: wt_control-2

description:
Processed data are in all ascc3Exp_*.tsv files
Sample 2

value: U-2 OS

value: human osteosarcoma

value: untreated


title: cjnw5krp9005d3h5vsox6ka3b

source_name: Lung

value: Lung


title: WT E5 gametocytes TP1

description:
WT E5 strain gametocytes
WT GC TP1

value: Asexual and Sexual Mixed Stage


title: cjnw5krp9005c3h5vp2v4s8me

value: control


title: SUIT-2_Adapted_Exome_clone5


title: SUIT-2_Adapted_Exome_clone4


title: cjnw5krp9005a3h5vokbx1nxo

value: Spleen


title: WT E5 gametocytes TP4

description:
WT E5 strain gametocytes
WT GC TP4

value: WT


title: SUIT-2_Non-Adapted_Exome_clone3

growth_protocol: Grown in RPMI medium with high glucose (11 mM) and high glutamine (2 mM).


title: PfAP2-G2::KO 39 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP7

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

source_name: E5 PfAP2-G2::KO

extract_protocol: Total RNA was extracted from tightly synchronized PfAP2-G2::KO and WT asexual parasites every 6 hours for 48 hours using TRIzol.

source_name: 3D7 Asexual Mixed Stage Reference Pool


title: SUIT-2_Non-Adapted_Exome_clone2


title: PfAP2-G2::KO 45 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP8

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: PfAP2-G2::KO 33 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP6


title: cjnw5krp900583h5vs57r6v5e

value: Subscapular fat


title: SUIT-2_Non-Adapted_Exome_clone1


title: PfAP2-G2::KO 27 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP5


title: 03_MigA9+/-DB818 24H

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Two-colors Mouse Whole Genome Agilent 44K 60-mer oligonucleotide Microarrays  were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

source_name: Murine Hoxa9-transformed MigA9 cell line treated with 2.5 µM of DB818

label_protocol: manufacturer's instructions

growth_protocol: RPMI-1640, 10% FCS, 1% of GM-CSF-conditioned media, 1% Pen/Strep, 37°C, 5% CO2

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Murine Hoxa9-transformed MigA9 cell line were treated or not with 2.5 µM of DB818  for 6, 12 or 24H

value: Hoxa9-transformed MigA9 cell line

tag: treatment time

source_name: Hoxa9-transformed MigA9 cell line, untreated

tag: exposure time

value: not exposed


title: 01_MigA9+/-DB818 6H


title: 02_MigA9+/-DB818 12H


title: cjnw5krp900573h5vrov77sjf

source_name: Gonadal fat

value: Gonadal fat

tag: strain

tag: Sex


title: cjnw5krp9005b3h5v09lqwb9z

source_name: Heart

value: Heart

tag: treatment


title: PfAP2-G2::KO 15 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP3


title: PfAP2-G2::KO 21 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP4


title: cjnw5krp900563h5v82vzqftn


title: cjnw5krp900593h5vluz7ee1v

source_name: Kidney

value: Kidney


title: cjnw5krp900553h5vmc2shi88


title: cjnw5krp900543h5vz70cd5yc

value: Liver


title: cjnw5krp900533h5vqu74itb9

value: female


title: cjnw5krp800513h5v72ggza50


title: WT E5 45 hours post invasion

description:
WT E5 strain
WT TP8

source_name: E5 WT


title: PfAP2-G2::KO 3 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP1


title: cjnw5krp900523h5vgjndrtp7

source_name: Spleen


title: WT E5 33 hours post invasion

description:
WT E5 strain
WT TP6


title: cjnw5krpg009w3h5v8h9cb3t1

source_name: Subscapular fat

value: male


title: DNAMe_VP64_TIL_Rep1

source_name: Cultured Hippocampal Neurons

value: Cultured Hippocampal Neurons

tag: age

tag: isoform


title: WT E5 27 hours post invasion

description:
WT E5 strain
WT TP5

tag: hours post invasion


title: PfAP2-G2::KO 9 hours post invasion

description:
E5 strain with disrupted ap2-g2 gene
AP2-G2::KO TP2


title: WT E5 39 hours post invasion

description:
WT E5 strain
WT TP7


title: cjnw5krpg009v3h5vlz4voj3f


title: WT E5 15 hours post invasion

description:
WT E5 strain
WT TP3


title: cjnw5krpg009u3h5v05gg924d

source_name: Skin

value: Skin


title: WT E5 9 hours post invasion

description:
WT E5 strain
WT TP2


title: WT E5 3 hours post invasion

description:
WT E5 strain
WT TP1


title: cjnw5krpg009t3h5vihrdx32r


title: cjnw5krpg009s3h5v9yncxacz


title: WT E5 21 hours post invasion

description:
WT E5 strain
WT TP4


title: Pituitary, control, sample 27

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

description: 27 H

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent). A t-test with a Benjamini-Hochberg correction (P < 0.05) was used as the criteria for defining genes differentially expressed between the control and stressed groups for each organ.

organism: Oncorhynchus mykiss

source_name: Pituitary, control

label_protocol: Pituitary and head kidney RNA from the fish sampled on day 21 (8 control (C) and 7-8 stressed (S) fish) were labelled and hybridized following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol.  Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Rainbow trout stress trials were performed at the facilities of PEIMA (INRA fish farming in Brittany, France) using fish hatched and reared in an open flow system. Immature rainbow trout (~ 118 g) were distributed into 6 tanks and acclimatized to a 50 kg/cm3 density (84-86 fishes/tank with 200 litres of water) for 2 weeks with 3 water renewals/h. During the 3-week experiment (deteriorated water quality stress), the photoperiod was maintained at 12:12 (Light: Dark) and the mean water temperature increased from 10.5 to 12.25°C. The fish were fed ad libitum 3 times per day.

extract_protocol: Total RNA from pituitary gland, and head kidney was extracted using TRIzol reagent according to the manufacturer's instruction (Promega). RNA was quantified by measuring the optical density at 260 nm. RNA integrity was checked using the Bioanalyzer 2100 Agilent and RNA 6000 LabChip® kits (Agilent Technologies, Waldbroon, Germany) according to the manufacturer’s instructions.

treatment_protocol: To obtain deteriorated water quality stress for 3 weeks, water renewal was modified to decrease the oxygen level to 3-4 mg/l (30-40% O2 saturation) during the day in 3 tanks for 3 weeks (Stress group = S) while the oxygen level was adjusted to 8-12 mg/l (70-110% O2 saturation) in the remaining 3 tanks (Control group = C). After 21 days under such deteriorated water quality conditions, the HPI axis response in the C and S groups was measured. The fish were not fed the day before sampling. For microarray, 8 fish of the C and S groups were caught, euthanized rapidly with a lethal dose of phenoxy-ethanol and weighed. The pituitary gland and interrenal were frozen in nitrogen liquid and stored at -80°C until use.

tag: stress

value: Control Sample

value: Pituitary


title: Pituitary, control, sample 53

description: 53 H


title: Pituitary, control, sample 51

description: 51 H


title: cjnw5krpg009q3h5v6qjruxa3


title: Pituitary, control, sample 50

description: 50 H


title: 75umCadmium.ReRep.Rep2

data_processing:
Library strategy: Rerep-seq
Fastq files were aligned to HG38 using BWA-mem
Sam files were transformed into bam files and blacklisted using samtools (v1.2, RRID:SCR_002105). Blacklists were the same as previously used for Rerep-seq analysis (Menzel et al., 2020). Bedtools (v2.26.0, RRID:SCR_006646) was used to generate bedGraphs
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
Replicates were then averaged
Genome_build: HG38
Supplementary_files_format_and_content: bedgraph

growth_protocol: MDA-MB-231 female breast cancer cell line and hTERT-RPE-1 female retinal pigment epithelial cell line (called RPE throughout) were maintained at 37°C in Dulbecco’s Modified Essential Medium (DMEM) with 10% FB essence (VWR), 1% penicillin/streptomycin, and L-glutamine.

extract_protocol:
Rerep-seq was performed as described in . Briefly, In an 8 strip PCR tube 1 – 5 ug high molecular weight genomic DNA was mixed with 2.5uL 10X Hoechst 33258 (0.1mg/ml) and 2.5uL 10X NEB 4 (50 mM Potassium Acetate, 20 mM Tris-acetate , 10 mM Magnesium Acetate, 1 mM DTT pH 7.9@25°C) to a final volume of 24uL; open tubes placed upright in PCR tube rack, covered with a glass plate (3" x 3" glass plate from VWR Vertical Gel Electrophoresis Systems), exposed to 7.5 minutes of glass plate filtered (UVA only) from Stratalinker followed by addition of 0.5uL UDG (5 units of Uracil-DNA Glycosylase), 0.5uL APE1 (10 units of human apurinic/apyrimidinic endonuclease 1) for 2 hours at 37°C. The digested DNA was repaired with NEB’s FFPE DNA Repair Mix for 30 minutes; mixed with 10X loading dye then run on 0.8% agarose gel for 15 minutes. The fragmented DNA ranging from 0.1Kb to 3Kb was gel extracted with Wizard® SV Gel and PCR Clean-Up System with the purified DNA eluted in 50uL nuclease free water.
Sequencing libraries were constructed using the Illumina Nextera DNA Flex Library Prep Kit (catalog number 20018704) following the manufacturers’ protocol and using 14 cycles of amplification for final library construction. Libraries were constructed using dual index barcodes from the Nextera DNA CD Indexes (catalog number 20018707).

treatment_protocol: Cadmium-resistant cell (MDA-MB-231cadR) cell lines were selected by passage in medium containing CdSO4. The CdSO4 concentration was increased by increments of 5-25 μM after 10 passages at the current concentration and when cell count increased at least 1.8 times average daily over at least four passages consistently. Cells used in this study were adapted to CdSO4 containing medium for 7 months up to 75 μM CdSO4.

value: 75uM cadmium resistance

tag: input or rerep

value: rerep


title: Pituitary, control, sample 54

description: 54 H


title: Pituitary, control, sample 48

description: 48 H


title: Pituitary, control, sample 49

description: 49 H


title: Pituitary, control, sample 47

description: 47 H


title: Pituitary, stressed, sample 46

description: 46 H

source_name: Pituitary, stressed

value: Stressed sample


title: cjnw5krpg009p3h5vbxcs0aqz

data_processing:
Sequencing quality control was performed using FastQC (v0.11.5)
Transcript expression was then quantified using Salmon [1] (v0.9.1) in pseudo-alignment mode, without adapter trimming, producing per-gene count estimates, using the Ensembl mm10 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each gene for each sample, in long-format

value: control


title: Pituitary, stressed, sample 45

description: 45 H


title: 75umCadmium.ReRep.Rep1

tag: cell line


title: cjnw5krpg009o3h5vus45dofh

value: Subscapular fat

value: aPAPPA


title: cjnw5krpg009r3h5vsythyb4j


title: cjnw5krpg009n3h5vtem4u60k


title: cjnw5krpg009m3h5vm4b7rwv7


title: LNCaP_RNA

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

description: deep seqiemcomg for high coverage

data_processing:
Deep paired-end RNA-sequencing was performed on 1 sample of LNCaP (prostate cancer cell line) cells.Reads were filtered to remove Illumina adapter sequences and trimmed for quality using Trimmomatic v0.35.
Trimmed reads were decontaminated by aligning them to human ribosomal RNA, mitochondrial sequence, poly-A or poly-C sequences, or phi-X sequence.  After decontamination, 317,808,783 read pairs remained for further analysis.
RNA-seq reads were aligned to the human genome build GRCh38 (hg38) using the HISAT2 alignment software (v 2.0.4). The reference genome was annotated with SNP and transcript (splice site) information to improve matching of read pairs to appropriate locations in the genome.
Sample transcriptome within specific loci of intrest was reconstructed with StringTie (v.1.2.3).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id, annotations, coverage, FPKM. TPM for each isoform

source_name: LNCaP cells

extract_protocol:
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate; derived from metastatic site:left supraclavicular lymph node


title: LNCaP_TDHT3

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to hg19 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id  and raw counts for each gene, in each sample

tag: shRNA

tag: growth condition

value: DHT


title: cjnw5krpg009k3h5vmb6tphh3

source_name: Liver


title: LNCaP_TDHT2


title: cjnw5krpf009j3h5vasl2wkfr

value: Heart


title: LNCaP_TDHT1


title: cjnw5krpf009i3h5vepoa0jze

value: Spleen


title: Pituitary, stressed, sample 37

description: 37 H


title: Head Kidney, control, sample 54

description: 54 I

source_name: Head Kidney, control

value: Head Kidney


title: Head Kidney, control, sample 53

description: 53 I


title: LNCaP_T_DHT3

value: vehicle


title: Pituitary, stressed, sample 42

description: 42 H


title: Pituitary, stressed, sample 43

description: 43 H


title: Head Kidney, control, sample 50

description: 50 I


title: Pituitary, stressed, sample 44

description: 44 H


title: Head Kidney, control, sample 27

description: 27 I


title: Pituitary, stressed, sample 40

description: 40 H


title: Pituitary, stressed, sample 38

description: 38 H


title: cjnw5krpf009h3h5va41o9mlo

value: Kidney

value: male


title: cjnw5krpg009l3h5v1mutjx0o

source_name: Lung

value: Lung


title: NCI-H3122

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy3, Cy5

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cells were growth in RPMI plus 1% of sodium pyruvate and 10% of FBS

extract_protocol: Total DNA was isolated by standard procedures

treatment_protocol: Cells were treated with TAE684 and crizotinib with an IC90 dose for two months to obtained the resitant clones.


title: NCI-H3122-TR1

description: resistant clone


title: LNCaP_T_DHT1


title: Head Kidney, control, sample 49

description: 49 I

value: Control Sample


title: Head Kidney, control, sample 51

description: 51 I


title: cjnw5krpf009f3h5vzuy27k7r

extract_protocol:
RNA was extracted from whole tissues using the Qiagen RNeasy 96 Universal Tissue Kit (Qiagen, 74881) and was digested with DNAseI before preparation for RNA-seq
Lib Prep method: TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat, Input Total Conc: 100ng in 10ul. PCR 12 cycles. Sequencing  - 3nM on Hiseq 4000

value: Gonadal fat


title: NCI-H3122-TR7

description: resistant clone


title: LNCaP_SDHT3

value: shScramble


title: cjnw5krpf009g3h5v1y8fz5kk


title: cjnw5krpf009e3h5v8swev51r

value: Skin


title: LNCaP_SDHT2


title: NCI-H3122-TR9

description: resistant clone


title: Head Kidney, control, sample 47

description: 47 I


title: LNCaP_SDHT1


title: Head Kidney, control, sample 48

description: 48 I


title: cjnw5krpf009c3h5vaa0jqhaz

value: Liver


title: cjnw5krpf009d3h5vadhylxra

value: control


title: cjnw5krpf009b3h5vmlnc0gve


title: LNCaP_S_DHT3


title: LNCaP_S_DHT2


title: LNCaP_S_DHT1


title: cjnw5krpf009a3h5v3a4u9rki


title: cjnw5krpf00993h5vyeovw34n


title: noCopper_rep2

data_processing:
Library strategy: Rerep-seq
Fastq files were aligned to SacCer3 using BWA-mem
Sam files were transformed into bam files and blacklisted using samtools (v1.2, RRID:SCR_002105). Blacklists were the same as previously used for Rerep-seq analysis (Menzel et al., 2020). Bedtools (v2.26.0, RRID:SCR_006646) was used to generate bedGraphs
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
Replicates were then averaged
The CUP1 gene is exactly duplicated in the yeast genome, so we replaced the CUP1.1 gene copy with ambiguous nucleotides “N” to force alignment to CUP1.2 rather than allow for random alignment between the two copies.
Genome_build: SacCer3, with cup 1.1 removed
Supplementary_files_format_and_content: bedgraph

organism: Saccharomyces cerevisiae

source_name: noCopper

growth_protocol: Yeast strains and plasmids used in this study are listed in Table 1 and were grown according to standard procedures in YPD (yeast extract, peptone, and 2% dextrose) at 30°C for all experiments unless otherwise stated. To accommodate S. cerevisiae’s lack of the thymidine salvage pathway, yeast strains in this paper are all stably transformed with NheI linearized p403–BrdU–Inc HIS3, a reconstituted thymidine salvage pathway cassette, consisting of Herpes simplex virus thymidine kinase (HSV–TK) and human equilibrative nucleoside transporter (hENT1), that enables efficient cellular uptake and incorporation of the thymidine analogue BrdU into DNA . Inserts were confirmed by spot assays for sensitivity to 75 µg/ml FUDR and susceptibility to BrdU uptake and genomic fragmentation via Rerep-seq.

treatment_protocol: We developed a copper-resistant yeast strain by culturing cells in the presence of 6 mM copper for approximately 30 generations. Controls were cultured under normal conditions.

value: untreated

value: ReRep-Seq


title: Head Kidney, stressed, sample 44

description: 44 I

source_name: Head Kidney, stressed

value: Stressed sample


title: noCopper_rep1


title: cjnw5krpf00973h5v1gojgvj5

value: aPAPPA


title: cjnw5krpf00963h5v8fjrl3t7


title: Head Kidney, stressed, sample 45

description: 45 I


title: cjnw5krpf00953h5vwrot36vq


title: Head Kidney, stressed, sample 43

description: 43 I


title: RECQ1 siRNA_rep 3_mRNA seq

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

institute: NIH

data_processing:
none provided by the submitter
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Breast cancer cell line MCF7

growth_protocol: MCF7 cells were purchsed from ATCC and grown in complete medium as per the instructions from ATCC.

extract_protocol:
For RNA-seq, ~10 million MCF7 cells transfected with CTL siRNA, ESR1 siRNAs (smartpool) or RECQ1 siRNAs (smartpool) for 48 hr were harvested and total RNA was isolated with the use of the RNeasy plus micro kit (Qiagen). The mRNA-seq samples were pooled and sequenced on HiSeq using Illumina TruSeq mRNA Prep Kit RS-122-2101 and paired-end sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols