title: D. virilis_stage5_replicate9

value: replicate 9


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_7_A

status: Public on Dec 04 2018

type: SRA

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

library_source: transcriptomic

data_processing:
Standard Illumina software used for basecalling and demultiplexing
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 using tophat
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation, normalization, and differential expression analysis were calculated using Cufflinks and cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements

molecule: total RNA

organism: Mus musculus

source_name: CASIN treated LT-HSC sorted from aged mouse (daughter cell)

growth_protocol: Cells were cultured in IMDM + 10% FBS + Cytokines mSCF,GCSF, and mTPO 50ng/ml at 37°C (5% CO2, 3% O2). Mother cells were collected 16hrs after culture. Daughter cells were cultured for 40 to 44 hrs, for first cell division.

extract_protocol:
For single cell transcriptome profiling, SMART-Seq v4 Ultra Low Input RNA kit from Clontech (Catalog # 634892) was used. The cDNA synthesis and amplification were performed as recommended by Clontech. The kit generates Illumina compatible cDNA library.
The amplified cDNA generated from single cells were used to make libraries using Illumina’s Nextera XT DNA Library Preparation kit (Catalog # FC-131-1096) as per Illumina’s instructions.

treatment_protocol: 5µM CASIN (CASIN treatment); 100 ng/ml Wnt5a directly added to the medium at the beginning of culture.

tag: treatment

value: CONTROL

tag: strain

value: B6.SJL mice

tag: tissue

value: Long-term Hematopoietic stem cells (LT-HSC)


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_6_A

value: CASIN


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_6_B


title: CONTROL_Aged_Mother TO4_CONTROL_M_O_1_O6_1_M

source_name: Untreated (Control) LT-HSC sorted from aged mouse (mother cell)


title: D. virilis_stage5_replicate7

city: Davis

first: Susan

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

country: USA

institute: University of California, Davis

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dvir-all-chromosome-r1.2.fa
annotation file used: dvir-all-r1.2.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

molecule: polyA RNA

organism: Drosophila virilis

source_name: single embryo

growth_protocol: All species were maintained on molasses food in uncrowded conditions

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Libraries were constructed using Illumina Tru-Seq kits and indices

treatment_protocol: Eggs were collected from vials, and imaged to determine stage

tag: embryonic stage

value: stage 5

tag: replicate number

value: replicate 7

tag: raw data mixed with d. melanogaster?

value: no


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_5_B


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_4_B


title: D. virilis_stage5_replicate8

value: replicate 8


title: D. virilis_stage2_replicate7

value: stage 2

value: yes


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_4_A


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_5_A


title: D. virilis_stage2_replicate6

value: replicate 6


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_3_B


title: D. virilis_stage2_replicate4

value: replicate 4


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_1_B


title: D. virilis_stage5_replicate12

value: replicate 12


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_7_B


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_3_A


title: D. virilis_stage2_replicate5

value: replicate 5


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_1_A


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_7_M


title: D. virilis_stage2_replicate3

value: replicate 3


title: D. virilis_stage2_replicate1

value: replicate 1


title: D. virilis_stage2_replicate2

value: replicate 2


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_6_M

value: CONTROL


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_4_M

value: B6.SJL mice


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_5_M

value: Long-term Hematopoietic stem cells (LT-HSC)


title: D. melanogaster_stage2_replicate5

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dmel-all-chromosome-r6.02.fa
annotation file used: dmel-all-filtered-r6.02.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila melanogaster


title: D. melanogaster_stage2_replicate6


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_6_B


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_1_M


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_7_B


title: D. melanogaster_stage2_replicate3


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_2_M


title: CONTROL_Aged_Mother TO2_CONTROL_M_O_1_O4_3_M


title: D. melanogaster_stage2_replicate4


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_7_A


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_5_B


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_6_A


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_5_A


title: D. melanogaster_stage2_replicate1


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_4_B


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_4_A


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_2_A


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_3_B


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_2_B


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_3_A


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_1_A


title: CONTROL_Aged_Daughter TO2_CONTROL_D_O_1_O4_1_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_9_B

value: CASIN


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_9_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_8_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_6_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_7_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_7_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_8_B


title: D. melanogaster_stage2_replicate2


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_5_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_6_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_5_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_4_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_2_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_4_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_3_A


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_3_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_1_B


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_2_A


title: CONTROL_Young_Mother B3_CONTROL_M_Y_1_Y3_1_M

source_name: Untreated (Control) LT-HSC sorted from young mouse (mother cell)


title: CASIN_Aged_Daughter TO2_CASIN_D_O_1_O4_1_A


title: CONTROL_Young_Mother B3_CONTROL_M_Y_0_Y3_5_M


title: CONTROL_Young_Mother B3_CONTROL_M_Y_0_Y3_2_M


title: pnt RNAi 4

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned to the Drosophila melanogaster.BDGP6.86 transcriptome using STAR (v. 2.5.3a).
The estimation of isoform and gene abundance was computed using RSEM (v. 1.2.31).
Genome_build: Drosophila melanogaster Ensembl release 86, BDGP6
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the RSEM software package.

source_name: antenna

growth_protocol: The flies (both control and pnt RNAi) were allowed to develop on standard cornmeal medium at 27ºC

extract_protocol:
The third antennal segments from 500-1000 flies were harvested via snap-freezing in a mini-sieve. Total RNA was extracted using a standard TRIzol/chloroform protocol.
From 100 ng total RNA, mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module. RNA-seq libraries were then prepared from the mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Massachusetts, USA).

treatment_protocol: The pnt RNAi flies expressed pnt RNA hairpin from a transgene specifically in the eye-atennal disc, whereas the control flies lacked the transgene in an otherwise identical genetic background.

tag: line

value: pnt RNAi ('constitutive' driver crossed to UAS-pnt RNAi-KK100473)

tag: sample pair

value: antenna


title: control 4

value: control ('constitutive' driver crossed to VDRC control 60100)


title: pnt RNAi 3


title: control 3


title: control 2


title: CONTROL_Aged_Mother B3_CONTROL_M_O_1_O3_6_M


title: CONTROL_Aged_Mother B3_CONTROL_M_O_1_O3_5_M


title: control 1


title: CONTROL_Aged_Mother B3_CONTROL_M_O_1_O3_2_M


title: pnt RNAi 1


title: CONTROL_Aged_Mother B3_CONTROL_M_O_1_O3_1_M


title: CONTROL_Young_Mother B3_CONTROL_M_Y_1_Y3_2_M


title: CONTROL_Aged_Mother B3_CONTROL_M_O_0_O3_5_M


title: CONTROL_Young_Mother B3_CONTROL_M_Y_0_Y3_6_M


title: CONTROL_Aged_Mother B3_CONTROL_M_O_0_O3_2_M


title: CONTROL_Aged_Mother B3_CONTROL_M_O_0_O3_4_M


title: 12_S32

city: Buffalo

first: Mira

last: Edgerton

state: NY

address: 310 Foster Hall, 3435 Main Street

institute: University at Buffalo

data_processing:
Base-calling was done using Illumina’s bcl2fastq version 2.17.1.14 using default parameters
Alignment was done using TopHat2 version 2.1.1 using default parameters
Filtering sequence quality assessment was done using FastQC version 0.11.5
Generation of normalized abundance measurements was done using Cufflinks version 2.2.1 using default parameters
Genome_build: C_albicans_SC5314_A22
Supplementary_files_format_and_content: tab-delimited diff files generated using CuffDiff

organism: Candida albicans

source_name: Deferasirox treated 2

extract_protocol: Candida plaques harvested from mice tongues were treated with 1% Triton X-100 for 10 min at room temperature to lyse murine cells. After incubation, candida cell pellet were re-suspended in 1 ml of TRIzol® Reagent (Life Technologies) for 5 min to further remove traces of  murine cells and centrifuged at 4000rpm for 5 min. The cell pellet was re-suspended in 1ml of TRIzol reagent and vortexed (4 cycles, 6m/s) with 0.45 µm glass beads using a FastPrepTM-24 instrument (MP Biomedicals). Lysed cells (1 ml) were collected and chloroform (200 µl) was added, then mixed vigorously for 15 sec and maintained for 2-3 min at room temperature. The cell lysate was centrifuged at 21000 x g for 10 min at 4°C to separate the RNA containing upper aqueous layer, which was collected and mixed with 0.5 volume of 100% ethanol to precipitate total RNA from C. albicans cells. The total RNA was further purified using RNAeasy minikit from Qiagen according to manufacturer?s instructions. The RNA samples were stored at -80 ºC for the next steps.Total RNA was quantified using Ribogreen Assay (Invitrogen) and the quality of RNA samples were checked using Fragment Analyzer Standard Sensitivity Assay (Advance Analyticals). Illumina TruSeq RNA sample preparation kit (Illumina) was used to prepare cDNA libraries from RNA samples as per manufacturer?s instructions. The cDNA libraries were quantified using Picogreen Assay (Invitrogen) and Library Quantification kit (Kappa Biosciences). Fragment Analyzer High Sensitivity NGS kit (Advance Analyticals) was used to confirm the quality and size of the cDNA libraries. The cDNA libraries were then normalized, multiplexed and sequenced using the Illumina HiSeq2500 following the manufacturer's instructions at the UB Genomics and Bioinformatics Core Facility (Buffalo, NY). Raw RNA-sequencing reads were generating using the illumina HiSeq 2500, using a 50-cycle single read flowcell.

tag: sample source

value: Tongue plaques

tag: agent

value: Deferasirox

tag: time point

value: 5 days Post infection


title: 2-S29

source_name: Control 2 mice

value: Control


title: 9_S31

source_name: Deferasirox treated 1


title: 2_Prime

source_name: Control 1 mice


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_7_A

source_name: Untreated (Control) LT-HSC sorted from young mouse (daughter cell)


title: CONTROL_Young_Mother B3_CONTROL_M_Y_0_Y3_1_M


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_5_B


title: pnt RNAi 2


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_4_B


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_4_A


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_5_A


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_2_B


title: PEO1_GeCKO_Day0_A [Ctrl_A]

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description:
Ctrl_A
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx

data_processing:
Hisat2 (version 2.1.0) used to map reads to human genome GRCh37
bedtools used to assemble transcripts
edgeR used to identify differenentially expressed genes
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized expression

organism: Homo sapiens

source_name: PEO1 GeCKO cells Day 0

extract_protocol:
RNeasy kit (Qiagen)/Quick DNA Mini-Prep protocol (Zymo Research)
RNAlibraries were prepared for sequencing using TruSEQ RNA Sample Prep v4 using standard Illumina protocols.

tag: cell line

tag: cell type

value: High grade serous ovarian cancer cell line

tag: tranduced with

value: GeCKO libraries (A and B), selected with puromycin

tag: culture condition

value: grown on tissue culture plastic. Day 0.


title: PEO1_GeCKO_Suspension_Day10_B [S10_B]

description:
S10_B
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx

source_name: PEO1 GeCKO cells suspension 10 days

value: grown in suspension for 10 days


title: PEO1_GeCKO_Day0_B [Ctrl_B]

description:
Ctrl_B
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: PEO1_GeCKO_Suspension_Day10_A [S10_A]

description:
S10_A
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: PEO1_GeCKO_Suspension_Day5_C [S5_C]

description:
S5_C
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx

source_name: PEO1 GeCKO cells suspension 5 days

value: grown in suspension for 5 days


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_2_A


title: PEO1_GeCKO_Suspension_Day5_B [S5_B]

description:
S5_B
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_1_B


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_1_A


title: PEO1_GeCKO_Day0_C [Ctrl_C]

description:
Ctrl_C
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: CONTROL_Young_Daughter B3_CONTROL_D_Y_1_Y3_7_B


title: PEO1_GeCKO_Adherent_Day10_B [A10_B]

description:
A10_B
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx

source_name: PEO1 GeCKO cells adherent 10 days

value: grown on tissue culture plastic for 10 days


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_7_B

value: CONTROL


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_7_A

value: B6.SJL mice


title: PEO1_GeCKO_Adherent_Day10_A [A10_A]

description:
A10_A
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: PEO1_GeCKO_Adherent_Day5_B [A5_B]

description:
A5_B
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx

source_name: PEO1 GeCKO cells adherent 5 days

value: grown on tissue culture plastic for 5 days


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_6_A

value: Long-term Hematopoietic stem cells (LT-HSC)


title: PEO1_GeCKO_Adherent_Day5_A [A5_A]

description:
A5_A
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_6_B


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_5_B


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_5_A


title: RNA_PEO1_Suspension_1 [SUS1]

description:
PEO1susp_USR17000474L_HJ35WBBXX_L6
processed data file: GEO_Submission_RNA_seq.xlsx

source_name: RNA-Seq Suspension PEO1 cells

value: cells grown in suspension for 7 days.


title: RNA_PEO1_Suspension_3 [SUS3]

description:
3_S3_L007
processed data file: GEO_Submission_RNA_seq.xlsx


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_3_A


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_3_B


title: PEO1_Adherent_2 [re-analysis]

description:
2_S2_L007
processed data file: GEO_Submission_RNA_seq.xlsx

source_name: parental PEO1 cells


title: PEO1_Adherent_1 [re-analysis]

description:
1_S1_L007
processed data file: GEO_Submission_RNA_seq.xlsx


title: PEO1_GeCKO_Suspension_Day5_A [S5_A]

description:
S5_A
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_2_B

source_name: CASIN treated LT-HSC sorted from aged mouse (daughter cell)


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_2_A


title: PEO1_GeCKO_Adherent_Day10_C [A10_C]

description:
A10_C
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_1_B


title: MYCT1-overexpressed Hep2 cells

city: Shenyang

first: Wei-Neng

last: Fu

state: Liaoning Province

address: No. 77 Puhe Road, Shenyang North New Area

department: Medidcal Genetics

country: China

institute: China Medical University

description:
Control-VS-MYCT1.GeneDiffExpFilter
lncRNA.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human reference genome build information
Genome_build: ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz
Genome_build: ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz
Genome_build: sRNA, Rfam and miRBase databases
Genome_build: mirdeep and mireap databases
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Supplementary_files_format_and_content: LncRNAs.xls
Supplementary_files_format_and_content: Control-VS-MYCT1.GeneDiffExpFilter.xls
Supplementary_files_format_and_content: miRNAs known.xls
Supplementary_files_format_and_content: miRNAs novel.xls

source_name: larngeal cancer cell

extract_protocol:
Hep2 cells were harvested, flash frozen on dry ice, and RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

value: laryngeal with stable transfection of MYCT1


title: MYCT1-non transfected Hep2 cells

value: laryngeal with non-transfect of MYCT1


title: MYCT1-overexpressed Hep2 cells [miRNA]

description: miRNA known, miRNA novel


title: CONTROL_Young_Mother B2_CONTROL_M_Y_1_Y2_5_M


title: CONTROL_Aged_Daughter B3_CONTROL_D_O_1_O3_1_A


title: PEO1_GeCKO_Adherent_Day5_C [A5_C]

description:
A5_C
processed data file: GEO_SUBMISSION_CRISPR_Counts2.xlsx


title: CONTROL_Young_Mother B2_CONTROL_M_Y_1_Y2_4_M


title: small RNA-seq on Dicer KD oocyte

city: Harbin

first: Xiaolei

last: Zhang

address: No.59 Mucai street

institute: Northeast Agricultural University

description: in vitro maturation of Dicer-KD GV oocytes for 42h

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to pig Sus_scrofa11.1 genome using bowtie2
The Rfam database 13.0 was used to identify rRNA, scRNA, snoRNA, snRNA, tRNA
Reads were searched against miRBase 22.0 to identify known miRNAs
Genome_build: Sus_scrofa11.1
Supplementary_files_format_and_content: length and counts of each small RNA with its sequences

organism: Sus scrofa

source_name: Dicer KD oocyte

extract_protocol:
Total RNAs from oocytes  were isolated using TRIzol® Reagent (Invitrogen) according to the instructions provided by the manufacturer.
RNA concentrations were quantified by measuring absorbance (A260/280ratio) on a NanoDrop Spectrophotometer ND-1000 (NanoDrop). RNA integrity number (RIN) was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Illumina protocols (available on the Illumina website at www.illumina.com/support) were followed to prepare the small RNA libraries from total RNA. Briefly, 3′ and 5′ adapters were ligated to small RNAs (< 200 nt) isolated from total RNAs from oocytes. After adapter ligation, an RT reaction was performed to cDNA synthesis. In order to avoid any bias, the cDNA was PCR amplified by using common primers that were designed against adapter sequences. After cDNA amplification, RCR products were isolated by gel purification and then sequenced by high-throughput deep sequencing using an Illumina® Hiseq2000 sequencer.

treatment_protocol: Dicer KD by siRNA in GV oocytes

value: MII oocyte

tag: genotype/variation

value: Dicer KD


title: MYCT1-non transfected Hep2 cells [miRNA]

description: miRNA known, miRNA novel


title: CONTROL_Young_Mother B2_CONTROL_M_Y_1_Y2_2_M

source_name: Untreated (Control) LT-HSC sorted from young mouse (mother cell)

tag: treatment


title: CONTROL_Young_Mother B2_CONTROL_M_Y_1_Y2_1_M

tag: strain


title: CONTROL_Young_Mother B2_CONTROL_M_Y_0_Y2_4_M

tag: tissue


title: CONTROL_Young_Mother B2_CONTROL_M_Y_0_Y2_3_M


title: CONTROL_Young_Mother B2_CONTROL_M_Y_0_Y2_2_M


title: HeLa-ADAR1KO, IFNA/D-treated (1,000 U/ml, 24 h)

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

description:
total RNA, rRNA depleted
Cuffnorm_gene_FPKM_tracking.tabular.gz

data_processing:
Base-calling was performed with RTA version 2.7.3 (Illumina).
Reads were aligned with Bowtie2 (v.2.2.6.2, sensitive end-to-end).
Single nucleotide variant calling was performed using the SAMtools (v. 1.3) and BCFtools (v. 1.3). Produced SNV list was passed to the GIREMI (v. 0.2.0), which splitted it into two groups: RNA editing positions and SNPs, dbSNP build 138 was used for the GIREMI statistical model evaluation.
A list of ADAR1-edited genes (A>G substitutions) was generated by comparing the number of editing sites in HeLa cells with the number in ADAR1-KO cells and ranked according to the highest differential. The following exclusion criteria were applied sequentially: (1) Genes were discarded, if the number of editing sites was smaller than 8 in HeLa cells; (2) genes were discarded, if the ratio of detected editing sites #ADAR1-KO/#HeLa was >0.5; (3) genes were discarded, if the number of editing sites per 100,000 bp gene length was <10; and (4) genes were discarded, if #HeLa/(#ADAR1-KO+1) was <1.75.
WIG files with base counts over ADAR1-edited regions were generated with IGVTools (count --bases -w 1).
Gene expression quantification was performed on all 12 samples using the Cufflinks suite (v. 2.2.1.0): Assembled transcripts were generated using Cufflinks and a final transcriptome assembly was generated from this using Cuffmerge. Mapped reads were quantified on this assembly using Cuffquant and normalized expression levels were calculated using Cuffnorm.
Genome_build: NCBI GRCh38.p7 (hg38): GCA_000001405.25
Supplementary_files_format_and_content: *.RES, GIREMI variant analysis output file (tab delimited); *.WIG, IGVTools base count file (tab delimited); *.tabular, FPKM quantification of gene expression levels, 12 samples matrix.

source_name: HeLa CRISPR/Cas9 clone E7

growth_protocol: Cells were cultivated in 6-well plates in 2 ml D-MEM +10% FBS and 1x Penicillin/Streptomycin

extract_protocol:
Trizol RNA extraction, isopropanol precipitation, rRNA depletion w/ Ribominus Kit (Life Technologies)
RNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, Cat# RS-122-2201).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced at 60-110 million reads per sample following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit (Illumina, Cat# PE-410-1001). The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit (Illumina, Cat# FC-410-1002 and FC-410-1001) and HCS v 3.3.52 collection software. Base-calling is performed using Illumina’s RTA version 2.7.3.

treatment_protocol: untreated, MeV-vac2(GFP)-infected (MOI=3, 24 h), MeV-CKO(GFP)-infected (MOI=3, 24 h), or IFNA/D-treated (1,000 U/ml) for 24 h prior to RNA extraction

value: HeLa CRISPR/Cas9 clone E7

value: CRISPR/Cas9 knock-out of ADAR1-p150 + ADAR1-p110


title: CONTROL_Aged_Mother B2_CONTROL_M_O_1_O2_5_M

source_name: Untreated (Control) LT-HSC sorted from aged mouse (mother cell)


title: CONTROL_Aged_Mother B2_CONTROL_M_O_1_O2_4_M


title: HeLa-ADAR1KO, MeV-CKO(GFP)-infected (MOI=3, 24 h)


title: CONTROL_Aged_Mother B2_CONTROL_M_O_1_O2_1_M


title: small RNA-seq on control oocyte

description: MII oocytes by in vitro maturation for 42h

source_name: MII oocyte

value: control


title: CONTROL_Aged_Mother B2_CONTROL_M_O_1_O2_2_M


title: HeLa-ADAR1KO, MeV-vac2(GFP)-infected (MOI=3, 24 h)


title: CONTROL_Aged_Mother B2_CONTROL_M_O_0_O2_6_M


title: CONTROL_Aged_Mother B2_CONTROL_M_O_0_O2_1_M


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_4_B


title: HeLa-p150KO, IFNA/D-treated (1,000 U/ml, 24 h)

source_name: HeLa CRISPR/Cas9 clone B13

value: HeLa CRISPR/Cas9 clone B13

value: CRISPR/Cas9 knock-out of ADAR1-p150


title: HeLa-p150KO, MeV-CKO(GFP)-infected (MOI=3, 24 h)


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_4_A


title: 11_GCas9-3

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Reads were aligned to an assembly of Mus musculus (house mouse) (Genome Reference Consortium Mouse Build 38 patch release 3 (GRCm38.p3)) using STAR software (v2.5.2b).
Transcripts were annotated with GENCODE M3 release
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: striatal tissue

growth_protocol: 3-month old wild type mice

extract_protocol:
Total RNA was purified using RNAeasy Mini Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
Libraries were prepared on cDNA generated using Clontech SmartER kits. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.

treatment_protocol: Injected with adeno-associated virus into the striatum.

value: striatal tissue

tag: treatment (viral injection)

tag: age

value: 3 weeks-old


title: 9_GCas9-1


title: 10_GCas9-2


title: 12_GCas9-4


title: HeLa-p150KO, MeV-vac2(GFP)-infected (MOI=3, 24 h)


title: HeLa-p150KO, mock treated


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_3_A

source_name: Untreated (Control) LT-HSC sorted from young mouse (daughter cell)


title: 8_Cas9-4


title: 7_Cas9-3


title: HeLa, IFNA/D treated (1,000 U/ml, 24 h)

source_name: HeLa cell line

value: HeLa cell line

value: parental HeLa


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_2_B

value: CONTROL

value: B6.SJL mice


title: 6_Cas9-2


title: human_neutrophil_real_39

type: genomic

city: Toronto

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

country: Canada

institute: Centre for Addiction and Mental Health

description:
N21_ZT73
technical_replicate_1

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting.

data_processing:
Values were extracted from the IDAT files using minfi package for R. The raw data was processed using “functional” normalization.
The file 450K_Matrix_signal_intensities.txt includes the raw unmethylated and methylated signal.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Neutrophils

label_protocol: Standard Infinium HD Methylation Assay protocol.

extract_protocol: DNA was extracted  with NucleoSpin® Blood XL (Macherey-Nagel) using the standard protocol.

value: Neutrophils

value: 52 years

tag: Sex

value: Male


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_2_A

value: Long-term Hematopoietic stem cells (LT-HSC)


title: HeLa, MeV-CKO(GFP)-infected (MOI=3, 24 h)


title: human_neutrophil_real_40

description:
N21_ZT73_R1
technical_replicate_2


title: HeLa, MeV-vac2(GFP)-infected (MOI=3, 24 h)


title: 5_Cas9-1


title: human_neutrophil_real_38

description:
N20_ZT70_R1
technical_replicate_2


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_1_B


title: human_neutrophil_real_43

description:
N23_ZT79
technical_replicate_1


title: 4_GFP-4

value: GFP


title: human_neutrophil_real_37

description:
N20_ZT70
technical_replicate_1


title: human_neutrophil_real_41

description:
N22_ZT76
technical_replicate_1


title: human_neutrophil_real_44

description:
N23_ZT79_R1
technical_replicate_2


title: human_neutrophil_real_46

description:
N24_ZT82_R1
technical_replicate_2


title: 3_GFP-3


title: human_neutrophil_real_45

description:
N24_ZT82
technical_replicate_1


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_3_B


title: human_neutrophil_real_32

description:
N17_ZT61_R1
technical_replicate_2


title: human_neutrophil_real_36

description:
N19_ZT67_R1
technical_replicate_2


title: human_neutrophil_real_42

description:
N22_ZT76_R1
technical_replicate_2


title: 2_GFP-2


title: human_neutrophil_real_47

description:
N25_ZT85
technical_replicate_1


title: human_neutrophil_real_31

description:
N17_ZT61
technical_replicate_1


title: human_neutrophil_real_29

description:
N16_ZT58
technical_replicate_1


title: human_neutrophil_real_35

description:
N19_ZT67
technical_replicate_1


title: human_neutrophil_real_48

description:
N25_ZT85_R1
technical_replicate_2


title: CONTROL_Young_Daughter B2_CONTROL_D_Y_1_Y2_1_A


title: 8_GCas9-2


title: human_neutrophil_real_33

description:
N18_ZT64
technical_replicate_1


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_7_A


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_6_B


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_5_B


title: 9_GCas9-3


title: human_neutrophil_real_28

description:
N15_ZT55_R1
technical_replicate_2


title: human_neutrophil_real_30

description:
N16_ZT58_R1
technical_replicate_2


title: human_neutrophil_real_26

description:
N13_ZT49_R1
technical_replicate_2


title: 7_GCas9-1


title: 6_Cas9-3


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_5_A


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_7_B


title: human_neutrophil_real_27

description:
N15_ZT55
technical_replicate_1


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_4_B


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_6_A


title: 5_Cas9-2


title: 4_Cas9-1


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_4_A


title: 3_WT-3

value: WT


title: human_neutrophil_real_34

description:
N18_ZT64_R1
technical_replicate_2


title: 1_GFP-1


title: KNKO rep1

city: La Jolla

first: Yongxin

last: Mu

address: 9500 Gilman Drive

department: medicine

institute: University of California SD

description: knockout

data_processing:
We used Illumia basespace online Tophat App (version 1.0.0), witch runs Bowtie2, TopHat2, the Isaac Variant Caller, and Cufflinks2 to map and align reads to mouse reference genome mm10, and calculated the FPKM for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: heart

extract_protocol:
whole hearts were dissected from 10.5 embryos and snap frozen in liquid nitrogen and stored at -80oC until use. Trizol was used to isolated total RNA. Then about 1ug total RNA was used for library construction using Illumina True seq kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Comparison between control and knockout embryo hearts

value: 129sv/black swiss

tag: developmenal stag

value: embryonic day 10.5

value: heart


title: KNKO rep2

description: knockout


title: KNWT rep3

description: control


title: KNKO rep3

description: knockout


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_3_A


title: 2_WT-2


title: 1_WT-1


title: KNWT rep1

description: control


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_3_B


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_2_B


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_2_A


title: human_neutrophil_real_25

description:
N13_ZT49
technical_replicate_1


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_1_B


title: Young_Daughter 5y6A

library_source: genomic

data_processing:
Standard Illumina software used for basecalling and demultiplexing
Adaptor trimming was performed using cutadapt 1.9.1
Sequences were aligned to the UCSC mouse reference genome mm10 using Bowtie 2
Peak calling was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bed format

source_name: LT-HSC sorted from young mouse (daughter cell)

extract_protocol:
cells were separated by pipetting and singularly subjected to fragmentation of open chromatin-regions using Tn5 transposase (Illumina), followed by a pre-amplification step, library preparation and subsequent paired-end sequencing.
For the pre-amplification step, NEBNext Ultra II Q5 Master Mix was used with Primer 1: 5’GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG3’ and Primer 2: 5’TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG3’. For dual-indexing, 10 μL of the pre-amplified ATAC reaction was used as input for Nextera index kit (Illumina). The generated libraries were quantified using agilent bio-analyzer and qPCR kit (New England Biolabs).


title: human_neutrophil_real_24

description:
N12_ZT46_R1
technical_replicate_2


title: Young_Daughter 5y6B


title: KNWT rep2

description: control


title: Young_Daughter 5y5B


title: G2_m_2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

description: processed data file: sox2_raw_counts.tsv.gz, sox2_tpm.tsv.gz

data_processing:
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & ATAC-seq:  Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4.
RNA-seq: Stranded Reads pairs were aligned to the mm9 genome using RSEM-STAR pipeline with options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 –paired-end”.
MNase/ATAC-seq Meta Plot Library: Mid-points of MNase-fragments (140-200 bp), cut sites of ATAC-seq fragments (0-100 bp), counted at base pair resolution and normalised per million reads, in +/- 1000bp of TSS, EP300 summits, Esrrb Bookmarked Sites, Esrrb Lost Sites and Oct4/Sox2 sites. Mid-point/cutsite data smoothed by sparse Gaussian process regression using Gpy.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BigWig files, MNase-seq/ATAC-seq: Library of meta-plots in tab-separated format; RNA-seq: Raw and normalised read-counts tab-separated format.

growth_protocol: ES cells were cultured on 0.1% gelatine in DMEM + GlutaMax-I (Gibco, Cat# 31966-021) 10% FCS, 100 μM 2-mercaptoethanol, 1× MEM non-essential amino acids, and 10 ng×ml−1 recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895). When required medium was supplemented with 1 µM PD0325901 and 3 µM CHIR99021 (Axon Medchem Bv).

extract_protocol:
ATAC-Seq: 5x104 cells pellets were resuspended in 25 µl TD buffer (Nextera kit; Illumina, Cat# FC-121-1030). After the addition of 2.5 µl of transposase TDE1 and 22.5 µl nuclease free water, reactions were mixed and incubated for 30min at 37oC. Reactions were stopped by adding the appropriate volume of Binding Buffer and the DNA was purified using the Qiagen MinElute PCR Kit according to manufacturer’s protocol. The purified DNA was either stored at -20oC or used directly for library preparation.
ATAC-seq: Reactions were prepared mixing 10 µl transposed DNA, 2.5 µl 25 µM primer Ad1.noMX, 2.5 µl 25 µM primer Ad2 from (Buenrostro et al. 2013), 9 µl Nuclease Free Water, 1 µl of a 1:8 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496) and 25µl of KAPA HiFi HotStart 2× Master Mix (Kapa Bioscience Cat# KK2502). Amplification was carried out under the following conditions: Pre-amplification: 1 cycle: 5’ at 72°C; 30” at 98°C; 5 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C; Amplification: 1 cycle: 30” at 98°C; 11/12 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C. After amplification libraries were purified with SPRI beads, using a sample to bead ratio of 1: 1.4.
Cell-cycle RNA-seq: ES cells were sorted on the basis of Hoechst and GFP levels in three populations (early G1, late G1 and G2) as previously described (Festuccia et al. 2016). RNA was extracted with TRIzol (ThermoFisher, Cat# 15596026). Samples were DNAse I treated (Qiagen, Cat# 79254), phenol/chloroform extracted and ethanol precipitated.
ChIP-seq and MNase-seq: Precipitated DNA was resuspended in 37.5µl of water and mixed with 2µl of 10mM dNTPs, 5µl of NEB T4 ligase buffer, 2.5µl of NEB T4 polymerase (Cat# M0203L), 0.5µl of NEB Klenow polymerase (Cat# M0210L) and 2.5µl of NEB T4 PNK (Cat# M0201L). Samples were incubated 30min at 20oC. DNA was purified with 90µl of SPRI beads and 50µl isopropanol and eluted in 21µl of water. DNA was mixed with 2.5µl of NEB Buffer #2, 1µl of 5mM dATP, 1.5µl of NEB Klenow 3'-5' exo minus (Cat# M0212L), and incubated at 37oC for 30min. DNA was purified with SPRI beads as before, but using a volume of 45µl of beads and 25µl isopropanol. DNA was elute in 20µl of water and mixed with 2.5µl of NEB T4 ligase buffer, 1.25µl of a 0.2µM solution of annealed adapters (See below), and 2.5µl of NEB concentrated T4 ligase (Cat# M0202M) and incubated overnight at 16oC. DNA was purified with SPRI beads as before, but using a volume of 35µl of beads and no isopropanol, eluting in 20 µl of water. Sample were mixed with 1µl of a 1:10 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496), 25µl of KAPA HiFi HotStart 2× master Mix (Kapa Bioscience Cat# KK2502), 1µl of 10µM PCR 1.0 and 1µl of PCR 2.0 Illumina primers. The amplification mix was distributed in two wells of a LightCycler 384 plate (Roche, Cat# 4729749001) and on a LightCycler 480 II instrument (Roche, Cat# 05015243001) using the following program: 1’ at 98°C; N cycles: 10” at 98°C; 20” at 64°C; 45” at 72°C. The number of cycles N was determined on real time by monitoring the fluorescence such that the amplification was stopped during the exponential phase. Samples were removed from the plate and purified with SPRI beads using 70µl beads, no isopropanol, and eluting in water. Barcoded adaptor: 5’P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-IIIIII-NNNNNNNN-ATCTCGTATGCCGTCTTCTGCTTG. 5’P indicates the presence of a 5’phosphate group. IIIIII represent the six base index nucleotides, and NNNNNNNN a stretch of 8 random nucleotides used for single molecule barcoding. Universal adapter: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T. * indicates the presence of a phosphorothioate bond between the last C and T.
ChIP-seq/Mnase-seq Chromatin preparation: Interphase cells were resuspended in 2 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) and 0.5% IGEPAL. After 30 min on ice, the suspension was passed 40 times in a dounce homogenizer. Both mitotic and interphase cells were resuspended in 300 μl of TSE150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1× PIC. Samples were sonicated in 1.5 ml tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power. After centrifugation (30 min, full speed, 4 °C), the supernatant was either used immediately for immunoprecipitation or stored at −80 °C until use.
ChIP-seq: Chromatin was pre-cleared for 3 hours rotating on-wheel at 4 °C in 300 μl of TSE150 containing 50 μl of protein G Sepharose beads 50% slurry, previously blocked with BSA and yeast tRNA. Immunoprecipitations with anti-ESRRB mouse monoclonal (1µg per 2x106cells, 5 μg per 107 cells; Perseus Proteomics, Cat# H6-705-00), anti-NANOG rabbit polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Cosmobio, Cat#  REC-RCAB001P); anti-POU5F1 goat polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Santa Cruz Biotechnology, Cat # sc-5279); anti-SOX2 goat polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Santa Cruz Biotechnology, Cat # sc- 17320), were performed overnight rotating on-wheel at 4 °C in 500 μl of TSE150. Twenty-five microliters of blocked protein G beads 50% slurry was added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 5 min rotating on-wheel at room temperature with 1 ml of buffer in the following order: 3 × TSE150, 1 × TSE500 (as TSE150 but 500 mM NaCl), 1× washing buffer (10 mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA), and 2 × TE (10 mM Tris-HCl pH8, 1 mM EDTA). Elution was performed in 100 μl of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) for 15 min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150 μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
Chip-seq: Fixation DSG+FA.  ES cells were crosslinked in PBS-DSG 2 mM at pH 7.0 (Sigma, Cat# 80424-5 mg) for 50 min at room temperature with occasional shaking and incubated for 10 min in 2 ml PBS 1% formaldehyde after washing in PBS. Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. Fixation FA: ES cells crosslinked in 3 ml of pre-warmed DMEM/FCS/LIF for 10 min at room temperature adding 1% formaldehyde (Thermo, Cat# 28908). Crosslinking was stopped with 0.125 M glycine for 5 min at room temperature.
H3 ChIP-seq:  ChIP was performed as described using 5 µg of anti-Histone H3 rabbit polyclonal (Abcam, Cat# ab1791).
MNase-seq: Cells fixed in formaldehyde as for ChIP were pre-incubated for 10 min at 37°C and ½ U, 16 U or 128 U of MNase (Expressed in KUntiz, 1 Kunitz is equivalent to 10 gel units, NEB Cat# M0247S) added to the reaction. Cells were incubated for further 10 min at 37°C, inverting the tubes occasionally. The reaction was stopped on ice by adding 500ul of 2 × STOP buffer (2% Triton X-100, 0.2% SDS, 300mM NaCl, 10mM EDTA). Tubes were left rotating overnight on a wheel to allow diffusion of the digested fragments. The cell suspension was spun down and the supernatant stored at -80°C. Samples were then incubated over night at 65°C in TE 1% SDS to revert the crosslinking, and treated with Proteinase K. DNA was phenol/chloroform extracted, ethanol precipitated, and RNase treated. 50 µl of DNA was purified with 90µl of SPRI beads and 50 µl isopropanol.
RNA-seq:Ribo-depleted, stranded and paired-end RNA-seq libraries were prepared and sequenced by Novogene Co Ltd.

treatment_protocol:
ChIP-seq and MNase-seq: E14tg2a cells grown in T150 flasks were treated for 4-5 h with 50 ng×ml−1 nocodazole. Shake-off was performed and the cell suspension was filtered through a 10µm filter (pluriSelect, Cat# 43-50010-03). For interphase samples, untreated cells were trypsinised and collected in parallel.
Cell-cycle RNA-seq: GFP Sox2-AID ES cells were cultured in the presence of 0.5mM of auxin (Sigma, Cat# I5148) for 3 hours. During the last 20 minutes 20μM Hoechst-33342 was added.

value: embryonic stem cells

tag: cellcycle

tag: barcode

tag: auxin

value: minus Auxin

tag: molecule subtype

value: Ribo Depleted total RNA


title: G2_m_3

tag: cell line


title: CONTROL_Aged_Daughter B2_CONTROL_D_O_1_O2_1_A


title: human_neutrophil_real_22

description:
N11_ZT43_R1
technical_replicate_2


title: CONTROL_Young_Mother B1_CONTROL_M_Y_1_Y1_5_M


title: G2_m_1

tag: cell type


title: Young_Daughter 5y5A


title: G2_p_3

value: plus Auxin


title: human_neutrophil_real_21

description:
N11_ZT43
technical_replicate_1


title: Young_Daughter 4y5B


title: Young_Daughter 4y5A


title: CONTROL_Young_Mother B1_CONTROL_M_Y_1_Y1_1_M


title: Young_Daughter 4y3B


title: G2_p_2


title: G2_p_1


title: CONTROL_Young_Mother B1_CONTROL_M_Y_1_Y1_4_M


title: LG1_m_3


title: CONTROL_Young_Mother B1_CONTROL_M_Y_0_Y1_4_M


title: human_neutrophil_real_23

description:
N12_ZT46
technical_replicate_1


title: LG1_m_2


title: LG1_m_1


title: CONTROL_Young_Mother B1_CONTROL_M_Y_1_Y1_2_M


title: CONTROL_Young_Mother B1_CONTROL_M_Y_0_Y1_2_M


title: human_neutrophil_real_17

description:
N9_ZT37
technical_replicate_1


title: human_neutrophil_real_16

description:
N8_ZT34_R1
technical_replicate_2


title: CONTROL_Young_Mother B1_CONTROL_M_Y_0_Y1_3_M


title: human_neutrophil_real_20

description:
N10_ZT40_R1
technical_replicate_2


title: CONTROL_Aged_Mother B1_CONTROL_M_O_1_O1_5_M


title: human_neutrophil_real_14

description:
N7_ZT31_R1
technical_replicate_2


title: human_neutrophil_real_13

description:
N7_ZT31
technical_replicate_1


title: Young_Daughter 4y1B


title: LG1_p_2


title: Young_Daughter 4y1A


title: MYCOE_56h_3

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

data_processing:
adaptor trimming using Cutadapt
filtering using Xenome
alignment using STAR - hg38 Ensembl 79
quantification using STAR - hg38 Ensembl 79
Genome_build: hg38 / Ensembl 79
Supplementary_files_format_and_content: RSEM quantification of human reads

source_name: HPAF-II xenograft - mouse pancreas

growth_protocol: HPAF-II cells injected into the mouse pancreas. Tumors were allowed to develop for 28 days before start of treatment

extract_protocol:
RNAeasy kit (Qiagen)
Illumina TruSeq Stranded polyA enrichment

treatment_protocol: Treatment with ETC-159 bid

tag: host

value: mouse

tag: timepoint

tag: celltype

value: HPAF-II MYC OE

tag: condition


title: LG1_p_1


title: CONTROL_Aged_Mother B1_CONTROL_M_O_1_O1_4_M

tag: treatment

value: CONTROL


title: MYCOE_8h_3


title: human_neutrophil_real_15

description:
N8_ZT34
technical_replicate_1


title: Young_Daughter 4y2B

tag: strain

value: B6.SJL mice


title: human_neutrophil_real_19

description:
N10_ZT40
technical_replicate_1

tag: tissue

value: Neutrophils


title: CONTROL_Aged_Mother B1_CONTROL_M_O_1_O1_3_M


title: Young_Daughter 4y3A


title: Aged_Daughter 4a12B

source_name: LT-HSC sorted from aged mouse (daughter cell)


title: Young_Daughter 4y2A


title: human_neutrophil_real_11

description:
N6_ZT28
technical_replicate_1

value: 52 years


title: EG1_m_3


title: MYCOE_0h_3

value: Veh


title: human_neutrophil_real_12

description:
N6_ZT28_R1
technical_replicate_2

value: Male


title: human_neutrophil_real_8

description:
N4_ZT22_R1
technical_replicate_2


title: Aged_Daughter 4a12A

value: Long-term Hematopoietic stem cells (LT-HSC)


title: CONTROL_Aged_Mother B1_CONTROL_M_O_0_O1_5_M


title: EG1_m_1


title: human_neutrophil_real_7

description:
N4_ZT22
technical_replicate_1


title: MYCOE_0h_2


title: CONTROL_Aged_Mother B1_CONTROL_M_O_0_O1_4_M


title: EG1_p_3


title: WT_8h_2

value: HPAF-II WT


title: human_neutrophil_real_18

description:
N9_ZT37_R1
technical_replicate_2


title: human_neutrophil_real_10

description:
N5_ZT25_R1
technical_replicate_2


title: Aged_Daughter 4a10B


title: EG1_p_2


title: human_neutrophil_real_5

description:
N3_ZT19
technical_replicate_1


title: Aged_Daughter 4a11A


title: CONTROL_Aged_Mother B1_CONTROL_M_O_0_O1_3_M


title: human_neutrophil_real_9

description:
N5_ZT25
technical_replicate_1


title: WT_56h_2


title: human_neutrophil_real_6

description:
N3_ZT19_R1
technical_replicate_2


title: human_neutrophil_real_3

description:
N2_ZT16
technical_replicate_1


title: CONTROL_Aged_Mother B1_CONTROL_M_O_0_O1_2_M


title: human_neutrophil_real_4

description:
N2_ZT16_R1
technical_replicate_2


title: EG1_p_1


title: WT_0h_2


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_7_B


title: Aged_Daughter 4a10A


title: Aged_Daughter 4a8B


title: human_neutrophil_real_2

description:
N1_ZT13_R1
technical_replicate_2


title: WT_56h_1


title: ATACM_2

description: processed data file: mnase_atac_meta_plot_library.tsv.gz

value: M


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_7_A


title: human_neutrophil_real_1

description:
N1_ZT13
technical_replicate_1


title: ATACM_1


title: WT_0h_1


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_6_B


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_6_A


title: MYCT58A_8h_3

value: HPAF-II MYC T58A


title: ATACA_1

value: I


title: Aged_Daughter 4a6B


title: ATACA_2

value: embryonic stem cells


title: Aged_Daughter 4a6A


title: MYCT58A_8h_2


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_5_B


title: MYCT58A_0h_3


title: Young_Daughter 3y8A


title: MNaseH3_M_128_2

tag: fixative

value: FA

tag: mnase concentration

tag: chip antibody

value: MNase-ChIP-seq


title: Young_Daughter 3y8B


title: MNaseH3_M_16_2


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_2_B


title: Young_Daughter 3y7B


title: MNaseH3_M_0.5_2


title: MYCT58A_56h_3


title: Aged_Daughter 4a8A


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_2_A


title: Young_Daughter 3y7A


title: MNaseH3_A_128_2


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_6_B


title: MYCOE_8h_2


title: EG1_m_2

value: minus Auxin

value: Ribo Depleted total RNA


title: MYCT58A_8h_1

value: mouse


title: MNaseH3_A_16_2


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_6_A

value: CONTROL


title: CONTROL_Young_Daughter B1_CONTROL_D_Y_1_Y1_5_A

value: B6.SJL mice


title: MNaseH3_A_0.5_2


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_5_B


title: MYCT58A_0h_2


title: Young_Daughter 3y5B


title: MNaseH3_M_128_1


title: MYCT58A_56h_1


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_5_A


title: Aged_Daughter 4a11B


title: MNaseH3_M_16_1


title: WT_8h_1


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_4_B


title: Young_Daughter 3y4B


title: MYCOE_56h_2

value: HPAF-II MYC OE


title: MYCT58A_56h_2


title: MNaseH3_M_0.5_1


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_4_A


title: Young_Daughter 3y4A


title: LG1_p_3

value: plus Auxin


title: Young_Daughter 3y6B


title: MNaseH3_A_128_1


title: MYCT58A_0h_1

value: Veh


title: MYCOE_56h_1


title: Young_Daughter 3y6A


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_2_B


title: MYCOE_8h_1


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_2_A


title: Young_Daughter 3y3B


title: MYCOE_0h_1


title: Young_Daughter 3y3A


title: MNaseH3_A_0.5_1


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_1_B


title: Young_Daughter 3y2B


title: CONTROL_Aged_Mother B1_CONTROL_M_O_1_O1_2_M


title: Young_Daughter 3y5A


title: 48h Veh Replicate 2

data_processing:
adaptor trimming using Cutadapt
alignment using STAR - hg38 Ensembl 79
quantification using STAR - hg38 Ensembl 79
Genome_build: hg38 / Ensembl 79
Supplementary_files_format_and_content: RSEM quantification of human reads

source_name: HPAF-II

growth_protocol: HPAF-II cells grow in vitro

treatment_protocol: Treatment with ETC-159

value: HPAF-II


title: CONTROL_Aged_Daughter B1_CONTROL_D_O_1_O1_1_A

source_name: CASIN treated LT-HSC sorted from aged mouse (daughter cell)

value: Long-term Hematopoietic stem cells (LT-HSC)


title: 12406X8 3716-dnR2b

city: Salt Lake City

first: Suzanne

middle: L.

last: Mansour

state: UT

address: 15 North 2030 East

department: Human Genetics

institute: University of Utah

data_processing:
Sequencing reads were aligned to mm10 + splice junctions (Ensembl build 74) using Novoalign (v2.08.03).
Spliced alignments were converted back to genomic space, sorted and indexed using USeq (v8.8.8) SamTranscriptomeParser.
Normalized coverage tracks (coverage per million mapped reads) were generated using USeq Sam2USeq and USeq2UCSCExe.
Read counts and differential expression were analyzed using USeq DefinedRegionDifferentialSeq (DRDS).
Genome_build: mm10
Supplementary_files_format_and_content: raw count tables from DRDS

source_name: otocyst epithelium

extract_protocol:
Otocyst epithelia were dissected from each embryo and pooled into control (con) and experimental (R2b) samples for each of 4 pregnant females. RNA was extracted from each pool using a Micro RNAeasy kit (Qiagen)
TruSeq Stranded mRNA Sample Prep kit (Illumina) with oligo(dT) selection

treatment_protocol: Pregnant females received an ip injection of 0.1 ml/10 g body weight of 0.15 mg/ml [1.5mg/kg body weight] doxycycline hyclate (Sigma-Aldrich) prepared in PBS at the indicated stage, followed by provision of 200 mg/kg DOX chow ad libitum for the indicated duration

tag: genotype

tag: dox exposure


title: Young_Daughter 3y1B


title: Young_Daughter 3y1A


title: 48h Veh Replicate 1


title: 24h Veh Replicate 3


title: 12406X6 329-dnR2b


title: 48h Veh Replicate 3


title: 12406X7 3716-con


title: Aged_Daughter 3a5B


title: 24h Veh Replicate 2


title: 12406X5 329-con


title: Aged_Daughter 3a5A


title: MNaseH3_A_16_1

tag: cellcycle

tag: barcode


title: 24h Veh Replicate 1


title: 12406X4 315-dnR2b


title: Aged_Daughter 3a4B


title: 12406X3 315-con


title: Aged_Daughter 3a4A


title: 48h ETC-159 Replicate 3


title: 12406X2 310-dnR2b


title: 48h ETC-159 Replicate 2


title: Aged_Daughter 3a3B


title: Young_Daughter 3y2A


title: 12406X1 310-con


title: Aged_Daughter 3a3A


title: Ng2 3112

city: New York

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Alignment was performed using STAR with default settings
The reference genome was mm10.
The gene counts were performed by STAR using HTSeq-counter

source_name: glioma primary tissue

extract_protocol:
Qiagen Rneasy Extraction kit
Libraries were prepared according to Illumina's instructions

value: mixed background

value: Glioblastoma tumor

tag: model


title: Ng2 3349


title: 24h ETC-159 Replicate 3


title: 11734X8 070915-cont


title: Ng2 2898


title: 24h ETC-159 Replicate 2


title: 24h ETC-159 Replicate 1


title: Nst 4619


title: Aged_Daughter 3a2A


title: 11734X6 070715-cont


title: 11734X7 070915-R2b


title: Nst 3605


title: Aged_Daughter 3a1B


title: Veh Replicate 4

source_name: HPAF-II xenograft - mouse flank

extract_protocol:
RNAeasy kit (Qiagen)
Illumina TruSeq Stranded riboZero depletion


title: Aged_Daughter 3a1A


title: 11734X4 061215-cont


title: Veh Replicate 5


title: Nst 3153


title: 11734X5 070715-R2b


title: Syn 301

value: Synapsin-cre


title: Veh Replicate 3


title: Syn 300


title: 48h ETC-159 Replicate 1


title: 11734X3 061215-R2b


title: 11734X2 061115-R2b


title: Syn 90


title: Veh Replicate 2


title: 11734X1 061115-con


title: 56 h ETC-159 Replicate 1


title: 11639X9 052215B-R2b


title: 11639X10 052215B-con


title: Aged_Daughter 3a2B


title: 56 h ETC-159 Replicate 4


title: 56 h ETC-159 Replicate 5


title: 11639X8 052715B-con


title: 11639X7 052715B-R2b


title: 56 h ETC-159 Replicate 3


title: D. erecta_stage5_replicate2

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dere-all-chromosome-r1.3.fasta
annotation file used: dere-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila erecta

source_name: single embryo

tag: embryonic stage

value: stage 5

tag: replicate number

value: replicate 2

tag: raw data mixed with d. melanogaster?

value: no


title: 56 h ETC-159 Replicate 2

tag: host

tag: timepoint


title: 11639X6 052015-con


title: D. erecta_stage5_replicate1

value: replicate 1


title: D. erecta_stage2_replicate3

value: stage 2

value: replicate 3


title: 7d Replicate 5

description: Human graft / mouse host

source_name: 7d, HPAF-II xenograft - mouse pancreas

value: mouse

tag: rin

tag: cell type

value: ETC-159 (PORCN inhbitor)


title: 11639X5 052015-R2b


title: 7d Replicate 6

description: Human graft / mouse host

tag: treatment


title: 11639X1 052815-R2b


title: D. erecta_stage2_replicate1


title: 11639X2 052815-con


title: D. erecta_stage2_replicate2


title: 7d Replicate 4

description: Human graft / mouse host


title: 7d Replicate 2

description: Human graft / mouse host


title: mir_latest5_M_3 [reanalyzed]

data_processing:
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Genome_build: See sample for information
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila miranda

source_name: embryo

tag: tissue

value: embryo

tag: maternal genotype

tag: paternal genotype

tag: Sex

value: M

tag: illumina index


title: 7d Replicate 3

description: Human graft / mouse host


title: mir_latest5_M_2 [reanalyzed]


title: Veh Replicate 1

tag: celltype

tag: condition


title: 7d Replicate 1

description: Human graft / mouse host


title: D. erecta_stage5_replicate3


title: mir_latest5_M_1 [reanalyzed]


title: 56h Replicate 6

description: Human graft / mouse host

source_name: 56h, HPAF-II xenograft - mouse pancreas


title: WT5

city: Los Angeles

first: James

last: Joly

state: California

address: 923 Bloom Walk

department: Chemical Engineering

institute: University of Southern California

data_processing:
Base Quality and Phred score relationship with the Illumina CASAVA v1.8 software
Raw reads were filtered to discard reads with adaptor contamination, discard reads when uncertain nucleotides constitute more than 10% of either read, and discard reads when low quality nucleotides constitute more than 50 percent of the read
TopHat2 was run for tumor genomes.  The mismatch parameter were set to two, and other parameters were set to default. Only filtered reads are used to analyze the mapping status of RNA-seq data to the reference genome.
Gene expression level was measured by transcript abundance to generate FPKM counts, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount & FPKM values for each sample

source_name: Squamous carcinoma cells

extract_protocol:
Total RNA was isolated from fresh tumor samples.  Fresh tumor samples were placed in Trizol LS reagent and homogenized by vortexing, microgrinding and mechanical dissociation through a syringe. Total RNA isolation was subsequently performed using a RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol with chloroform, isopropanol and ethanol washes.
mRNA from tumor samples was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

tag: genotype

value: Wild type

value: Squamous carcinoma cells


title: WT4


title: mir_latest5_F_3 [reanalyzed]

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Libraries were constructed using Illumina Tru-Seq kits and indices

value: F


title: 56h Replicate 5

description: Human graft / mouse host

value: HPAF-II


title: WT1


title: KO5

value: LDHA-/-


title: mir_latest5_F_1 [reanalyzed]


title: 56h Replicate 3

description: Human graft / mouse host


title: 56h Replicate 4

description: Human graft / mouse host


title: KO4


title: 56h Replicate 2

description: Human graft / mouse host


title: KO3


title: mir_st2_6 [reanalyzed]


title: 56h Replicate 1

description: Human graft / mouse host


title: KO2


title: mir_st2_4 [reanalyzed]


title: 32h Replicate 6

description: Human graft / mouse host

source_name: 32h, HPAF-II xenograft - mouse pancreas


title: KO1


title: mir_st2_5 [reanalyzed]


title: mir_st2_3 [reanalyzed]


title: WT3


title: 32h Replicate 5

description: Human graft / mouse host


title: mir_st2_2 [reanalyzed]


title: 32h Replicate 4

description: Human graft / mouse host


title: 32h Replicate 3

description: Human graft / mouse host


title: D. willistoni_stage5_replicate6

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dwil-all-chromosome-r1.3.fa
annotation file used: dwil-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila willistoni

value: replicate 6


title: Group H, Cow 6, post

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
H6post
processed data file:
PreVPost_gene_exp.diff: p7_2
4groups_gene_exp.diff: Hp7_2
genes.read_group_tracking: Hp7_2

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.1.1 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the Bos taurus UMD3.1 reference genome+transcriptome (Ensembl).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the Bos taurus UMD3.1 reference genome+transcriptome (Ensembl).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the Bos taurus UMD3.1 reference genome+transcriptome (Ensembl).
Genome_build: Bos taurus UMD3.1 (Ensembl)
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The '*gene_exp.diff' files contain average FPKM values for each set of replicates as well as results for statistical testing for differential expression (PreVPost = all prepartum vs all postpartum samples; 4groups = H1-3pre vs H1-3post vs L1-3pre vs L1-3post). The 'genes.read_group_tracking' file contains raw mapped read counts and FPKM values for individual samples.

organism: Bos taurus

source_name: Group H_post_venous blood PBMC

growth_protocol: standard dairy cow housing

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were separated from veinous blood by Ficoll density gradient. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Diretional RNA-seq libraries were prepared from 500ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

tag: breed

value: dairy cows

tag: sample group

value: Group H with increased metabolic stress

tag: age

value: Adult

tag: lactation stage

value: 7 days postpartum


title: mir_st2_1 [reanalyzed]


title: D. willistoni_stage5_replicate5

tag: embryonic stage

value: stage 5

tag: replicate number

value: replicate 5

tag: raw data mixed with d. melanogaster?

value: no


title: mir_latest5_F_2 [reanalyzed]


title: Group H, Cow 4, post

description:
H4post
processed data file:
PreVPost_gene_exp.diff: p7_0
4groups_gene_exp.diff: Hp7_0
genes.read_group_tracking: Hp7_0

tag: cell type

value: Peripheral blood mononuclear cells (PBMC)


title: WT2


title: 32h Replicate 1

description: Human graft / mouse host

tag: host

value: mouse

tag: rin

tag: timepoint

tag: treatment

value: ETC-159 (PORCN inhbitor)


title: 32h Replicate 2

description: Human graft / mouse host


title: 16h Replicate 6

description: Human graft / mouse host

source_name: 16h, HPAF-II xenograft - mouse pancreas


title: D. willistoni_stage5_replicate3

value: replicate 3


title: Group L, Cow 3, post

description:
L3post
processed data file:
PreVPost_gene_exp.diff: p7_5
4groups_gene_exp.diff: Lp7_2
genes.read_group_tracking: Lp7_2

source_name: Group L_post_venous blood PBMC

value: Group L


title: D. willistoni_stage5_replicate4

value: replicate 4


title: Group L, Cow 2, post

description:
L2post
processed data file:
PreVPost_gene_exp.diff: p7_4
4groups_gene_exp.diff: Lp7_1
genes.read_group_tracking: Lp7_1


title: Group L, Cow 1, post

description:
L1post
processed data file:
PreVPost_gene_exp.diff: p7_3
4groups_gene_exp.diff: Lp7_0
genes.read_group_tracking: Lp7_0


title: D. willistoni_stage5_replicate2

value: replicate 2


title: 16h Replicate 4

description: Human graft / mouse host

value: HPAF-II


title: D. willistoni_stage2_replicate6

value: stage 2


title: 16h Replicate 5

description: Human graft / mouse host


title: Group H, Cow 5, pre

description:
H5pre
processed data file:
PreVPost_gene_exp.diff: m21_1
4groups_gene_exp.diff: Hm21_1
genes.read_group_tracking: Hm21_1

source_name: Group H_pre_venous blood PBMC

value: 21 days prepartum


title: 16h Replicate 3

description: Human graft / mouse host


title: D. willistoni_stage5_replicate1

value: replicate 1


title: D. willistoni_stage2_replicate5


title: Group H, Cow 4, pre

description:
H4pre
processed data file:
PreVPost_gene_exp.diff: m21_0
4groups_gene_exp.diff: Hm21_0
genes.read_group_tracking: Hm21_0

value: dairy cows

value: Group H with increased metabolic stress


title: Group H, Cow 5, post

description:
H5post
processed data file:
PreVPost_gene_exp.diff: p7_1
4groups_gene_exp.diff: Hp7_1
genes.read_group_tracking: Hp7_1

value: Adult

value: 7 days postpartum


title: D. willistoni_stage2_replicate4


title: Group L, Cow 2, pre

description:
L2pre
processed data file:
PreVPost_gene_exp.diff: m21_4
4groups_gene_exp.diff: Lm21_1
genes.read_group_tracking: Lm21_1

source_name: Group L_pre_venous blood PBMC


title: Group L, Cow 3, pre

description:
L3pre
processed data file:
PreVPost_gene_exp.diff: m21_5
4groups_gene_exp.diff: Lm21_2
genes.read_group_tracking: Lm21_2


title: 8h Replicate 6

description: Human graft / mouse host

source_name: 8h, HPAF-II xenograft - mouse pancreas


title: D. willistoni_stage2_replicate3


title: Group L, Cow 1, pre

description:
L1pre
processed data file:
PreVPost_gene_exp.diff: m21_3
4groups_gene_exp.diff: Lm21_0
genes.read_group_tracking: Lm21_0


title: D. willistoni_stage2_replicate2


title: 8h Replicate 4

description: Human graft / mouse host


title: D. willistoni_stage2_replicate1


title: 8h Replicate 3

description: Human graft / mouse host


title: Group H, Cow 6, pre

description:
H6pre
processed data file:
PreVPost_gene_exp.diff: m21_2
4groups_gene_exp.diff: Hm21_2
genes.read_group_tracking: Hm21_2


title: CKO(GFP) genomes from ADAR1KO cells

description:
total viral genomic RNA
derived from CsCl density gradient purification

data_processing:
Base-calling was performed using Illumina’s RTA version 1.18.54.
Raw BAM files were converted to FASTQ files (SAM-to-FASTQ v. 1.56.1), generating two FASTQ files for each data set (split by read group)
Adapter sequences were clipped (FASTX Toolkit), using Illumina adapter recognition sequences GATCGGAAGA GCACACGTCT GAACT (read 1 files) or AGATCGGAAG AGCGTCGTGT AGGGA (read 2 files), quality-trimmed (3’ ends, sliding window 1, step size 1, quality score ≥20) and quality-filtered (35-301 nt length; discard reads with N;  >95% of nucleotides with quality scores >30).
The resulting FASTQ files were aligned against a custom built genome containing sequences of hg38, hsa-45S-pre-rRNA and MeV-vac2(GFP)H using Bowtie2 (v. 2.2.6; sensitive end-to-end)
Aligned BAM files were filtered for number of mutations per read (NM>5; NM>8; NM>11) using BAMtools filter (v. 2.4.1)
Count tables of BAM alignments (WIG) were generated using IGVTools (count --bases -w 1)
Genome_build: custom-built genome consisting of hg38 (GCA_000001405.25), 45S-pre-rRNA (Genbank: NR_046235) and MeV-vac2(GFP)H (Genbank: MH144178)
Supplementary_files_format_and_content: *.WIG, IGVTools base count file (tab delimited)

source_name: HeLa CRISPR/Cas9 clone E7

growth_protocol: Cells were cultivated in 10x 150 mm dishes per sample in D-MEM +10% FBS + 1% Penicillin/Streptomycin

extract_protocol:
Viral ribonucleocapsids were purified from cellular RNA through CsCl density gradient centrifugation. Viral genomic RNA was extracted from ribonucleocapsids with Trizol and isopropanol-precipitated.
5 μl ribonucleocapsid RNA were fragmented for 7.5 min using the Ambion Fragmentation Reagent according to the manual. The samples were then diluted with nuclease-free H2O to a final volume of 100 μl, mixed with an equal volume of phenol/chloroform/isoamyl alcohol and phase-separated by centrifugation (12,000g, 4°C, 10 min). RNA was precipitated from the aqueous phase using sodium acetate / ethanol overnight at −20°C followed by centrifugation (20,000g, 4°C, 30 min). Pellets were washed with 70% (w/v) ethanol, dried and resuspended in 11 μl nuclease-free H2O. RNA libraries were prepared using 220-500 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced at 8-14 million reads per sample following Illumina’s standard protocol. The flow cells were sequenced as 300 × 2 paired end reads on an Illumina MiSeq using MiSeq v2 sequencing kit and MCS v2.6.2.1collection software.

treatment_protocol: Cells were infected with MeV-vac2(GFP) or MeV-CKO(GFP) at MOI=0.1 and harvested 72 h post infection.

tag: cell line

value: HeLa CRISPR/Cas9 clone E7

tag: genotype/variation

value: CRISPR/Cas9 knock-out of ADAR1-p150 + ADAR1-p110


title: 16h Replicate 2

description: Human graft / mouse host


title: 8h Replicate 2

description: Human graft / mouse host


title: vac2(GFP) genomes from ADAR1KO cells


title: 8h Replicate 1

description: Human graft / mouse host


title: 16h Replicate 1

description: Human graft / mouse host


title: CKO(GFP) genomes from p150KO cells

source_name: HeLa CRISPR/Cas9 clone B13

value: HeLa CRISPR/Cas9 clone B13

value: CRISPR/Cas9 knock-out of ADAR1-p150


title: 3h Replicate 5

description: Human graft / mouse host

source_name: 3h, HPAF-II xenograft - mouse pancreas

value: mouse

value: ETC-159 (PORCN inhbitor)


title: FA_3h_D_rep4

type: RNA

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description: SAMPLE 110

data_processing:
Data were analyzed in excel using Ct values for each sample, normalized to he average Ct of four mRNA housekeeping controls (Actb, B2m, Gapdh, Hsp90ab1)
For fold change calculations, ΔΔCt based fold-change values were obtained using sample 31 as control (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])).
Matrix non-normalized are raw Ct values. Matrix normalized are normalized to the average of housekeeping mRNAs (H3, H4, H5, H6, H8). Fold changes are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

label: SYBR Green

source_name: female mouse exposed to filtered air

label_protocol: RNAs were retro-transcribed from 400 ng of total RNA using the RT² First Strand kit (Qiagen). The expression of 84 mouse mRNAs predicted to regulate inflammatory genes was assayed with the Mouse Inflammatory Response and Autoimmunity PCR Array (PAMM-077Z, Qiagen)

extract_protocol: Lung tissue was homogenized in Trizol. Total RNA was extracted with the Direct-zol (Zymo Research)

treatment_protocol: Female C57BL/6 mice of 8 weeks of age were exposed to 2ppm ozone (O3) or filtered air (FA) for 3 hours at different stages of the estrous cycle: Metestrus (M), Diestrus (D), Proestrus (P), Estrus (E). Total RNA was extracted from whole lung homogenates and PCR arrays were used to determine the expression of 84 mRNAs associated with inflammation and immunity (3-6 animals per condition).

value: exposed to filtered air

tag: tissue

value: lung tissue homogenate

tag: strain

tag: exposure time

value: 3 hours

tag: Sex

value: female

tag: estrous cycle stage

value: diestrus


title: D27PrTzF_StPDPNp

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description:
PDPN+ Stroma from normal human prostate tissue
D27_FACS_filtered_matrix.mtx
D27_FACS_filtered_barcodes.tsv
D27_FACS_filtered_genes.tsv

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 2.1.1 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 2.1.1 was used to generate mapped bam files using default settings
10x Genomics’ cellranger aggr version 2.1.1 was used to aggregate samples from the same patient to generate filtered gene-by-cell matrices using default settings
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix market file with cell barcode and gene name tab-delimited text files

source_name: Viable human prostate PDPN positive stroma

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced R1=26cycles R2=58cycles, i7=8cycles

treatment_protocol: Populations of single-cells dissociated from health prostates from organ donors were isolated by FACS

tag: phenotype

value: StPDPNp

tag: facs ab profile


title: O3_3h_M_rep3

description: SAMPLE 109

source_name: female mouse exposed to 2ppm ozone

value: exposed to 2ppm ozone

value: metestrus


title: CKO(GFP) genomes from HeLa cells

source_name: HeLa cell line

value: HeLa cell line

value: parental HeLa


title: 8h Replicate 5

description: Human graft / mouse host

value: HPAF-II


title: 3h Replicate 6

description: Human graft / mouse host


title: FA_3h_M_rep4

description: SAMPLE 107


title: FA_3h_P_rep6

description: SAMPLE 102

value: proestrus


title: D27PrTzF_StPDPNn

description:
PDPN- Stroma from normal human prostate tissue
D27_FACS_filtered_matrix.mtx
D27_FACS_filtered_barcodes.tsv
D27_FACS_filtered_genes.tsv

source_name: Viable human prostate PDPN negative stroma

value: StPDPNn


title: D27PrTzF_Edn

description:
"Double negative" Epithelia from normal human prostate tissue
D27_FACS_filtered_matrix.mtx
D27_FACS_filtered_barcodes.tsv
D27_FACS_filtered_genes.tsv

source_name: Viable human prostate “double negative” epithelia

value: Edn


title: vac2(GFP) genomes from HeLa cells


title: 3h Replicate 4

description: Human graft / mouse host


title: D27PrTzF_OE

description:
"Other" Epithelia from normal human prostate tissue
D27_FACS_filtered_matrix.mtx
D27_FACS_filtered_barcodes.tsv
D27_FACS_filtered_genes.tsv

source_name: Viable human prostate "other" epithelia

value: OE


title: D. yakuba_stage5_replicate3

city: Davis

first: Susan

last: Lott

institute: University of California, Davis

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dyak-all-chromosome-r1.3.fa
annotation file used: dyak-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila yakuba

source_name: single embryo

tag: embryonic stage

value: stage 5

value: replicate 3

value: no


title: 3h Replicate 3

description: Human graft / mouse host

value: mouse

value: ETC-159 (PORCN inhbitor)


title: O3_3h_P_rep5

description: SAMPLE 101

value: lung tissue homogenate

value: 3 hours

value: female


title: FA_3h_E_rep6

description: SAMPLE 100

value: exposed to filtered air

value: estrus


title: D27PrTzF_LE

description:
Luminal Epithelia from normal human prostate tissue
D27_FACS_filtered_matrix.mtx
D27_FACS_filtered_barcodes.tsv
D27_FACS_filtered_genes.tsv

source_name: Viable human prostate luminal epithelia

value: LE


title: O3_3h_D_rep3

description: SAMPLE 112

value: exposed to 2ppm ozone

value: diestrus


title: vac2(GFP) genomes from p150KO cells

value: HeLa CRISPR/Cas9 clone B13

value: CRISPR/Cas9 knock-out of ADAR1-p150


title: O3_3h_P_rep4

description: SAMPLE 99

value: proestrus


title: D27PrTzF_BE

description:
Basal Epithelia from normal human prostate tissue
D27_FACS_filtered_matrix.mtx
D27_FACS_filtered_barcodes.tsv
D27_FACS_filtered_genes.tsv

source_name: Viable human prostate basal epithelia

value: BE


title: D. yakuba_stage2_replicate3

value: stage 2

tag: replicate number


title: FA_3h_E_rep5

description: SAMPLE 98


title: D. yakuba_stage2_replicate2

value: replicate 2

tag: raw data mixed with d. melanogaster?


title: FA_3h_E_rep4

description: SAMPLE 97


title: 0h Replicate 5

description: Human graft / mouse host

source_name: 0h, HPAF-II xenograft - mouse pancreas

tag: cell type

value: HPAF-II

value: Veh


title: 0h Replicate 6

description: Human graft / mouse host

tag: host

value: mouse


title: 0h Replicate 7

description: Human graft / mouse host

tag: rin


title: D. yakuba_stage2_replicate1

value: replicate 1

value: no


title: FA_3h_M_rep2

description: SAMPLE 94

value: lung tissue homogenate

value: 3 hours

value: female

value: metestrus


title: D17PrPzF_FMSt

description:
Fibromuscular Stroma from normal human prostate tissue
D17_FACS_filtered_matrix.mtx
D17_FACS_filtered_barcodes.tsv
D17_FACS_filtered_genes.tsv

source_name: Viable human prostate fibromuscular stroma

value: FMSt


title: D17PrPzF_OE

description:
"Other" Epithelia from normal human prostate tissue
D17_FACS_filtered_matrix.mtx
D17_FACS_filtered_barcodes.tsv
D17_FACS_filtered_genes.tsv

value: OE


title: FA_3h_P_rep5

description: SAMPLE 96

value: exposed to filtered air


title: D17PrPzF_LE

description:
Luminal Epithelia from normal human prostate tissue
D17_FACS_filtered_matrix.mtx
D17_FACS_filtered_barcodes.tsv
D17_FACS_filtered_genes.tsv

value: LE


title: 0h Replicate 4

description: Human graft / mouse host

tag: timepoint


title: FA_3h_M_rep3

description: SAMPLE 95

tag: treatment


title: 3h Replicate 2

description: Human graft / mouse host

value: ETC-159 (PORCN inhbitor)


title: 0h Replicate 3

description: Human graft / mouse host


title: D. yakuba_stage5_replicate2

value: stage 5


title: 0h Replicate 2

description: Human graft / mouse host


title: 3h Replicate 1

description: Human graft / mouse host


title: D. yakuba_stage5_replicate1


title: GR+/- female AECSq-22

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

country: Israel

institute: Ariel University

description: pool of 4 individual placentas

data_processing:
FastQC assessed sequencing scores and other quality metrics. Trimmomatic was used to remove  low scoring sequencing results and/or adapter contents.
Sequences were aligned to the mm9 mouse reference genome using Bsmap v2.89. Output data were strand-sorted, filtered, and  deduplicated with Picard tools.
Methylation levels and coverage levels were extracted with  methratio.py command in Bsmap.
Differential methylation cytosines were analyzed with  methylKit R package with FDR threshold of 0.2.
Differentially methylated positions were  annotated with HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: data files are in txt format and contain DNA methylation level for each sample

source_name: fetal part of placenta

extract_protocol:
During a caesarean section protocol, the placenta was removed, flash frozen on dry ice, the marked fetal part was cut in slices in the cryostat at -20 degrees and ?? Kit was used to harvest the DNA.
DNA libraries were prepared for sequencing using standard Illumina protocols
capture sequencing

tag: genotype


title: GR+/- female AECSq-24

description: pool of 3 individual placentas


title: GR+/- female AECSq-23

description: pool of 3 individual placentas


title: FA_3h_M_rep1

description: SAMPLE 93


title: D17PrPzF_BE

description:
Basal Epithelia from normal human prostate tissue
D17_FACS_filtered_matrix.mtx
D17_FACS_filtered_barcodes.tsv
D17_FACS_filtered_genes.tsv

value: BE


title: D7PrF_FMSt

description: Fibromuscular Stroma from normal human prostate tissue

data_processing:
Illumina's RTA version 2 was used for basecalling followed by bcl2fastq version 2.20 to generate fastq files.
Reads were mapped to GRCh38 using HISAT2.
Duplicates were removed using SAMtools.
Mapped reads were counted using FeatureCount using annotations from Gencode V20.
Genes identified as Goblins, rRNAs, and pseudogenes were removed.
Counts were normalized to FPKM with edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: Human prostate fibromuscular stroma

extract_protocol:
Total RNA from 500K FACS-purified cells was extracted using RNEasy micro columns (Qiagen). RNA quality and quantity were measured by a TapeStation and NanoDrop.
Total RNA was subjected to enrichment of polyA+ RNA using the NEBNext Poly(A) kit (NEB). Strand-specific polyA+ RNA-Seq was performed using the LM-Seq method, as described previously. Briefly, PolyA+ RNA was fragmented at 85°C in SmartScribe first-strand buffer (CloneTech) supplemented with a 3' sequencing adapter containing a random hexamer sequence. The fragmented RNA were subjected to first strand cDNA synthesis, followed by RNase A/H treatment. The remaining single-stranded DNA were ligated to a 5' sequencing adapter. The libraries were then amplified by PCR using Illumina TruSeq-compatible primers and purified using SPRI purification beads.

treatment_protocol: Bulk RNA-Sequencing of cell types isolated by FACS: CD326+/CD271+/CD26- basal epithelia, CD326+/CD271-/CD26+ luminal epithelia, CD326+/CD271-/CD26- "other" epithelia, and CD326-/CD45-/CD31- fibromuscular stroma.

tag: cell subtype


title: 0h Replicate 1

description: Human graft / mouse host


title: O3_3h_D_rep2

description: SAMPLE 92

value: exposed to 2ppm ozone

tag: tissue

value: diestrus


title: FA_3h_P_rep4

description: SAMPLE 90

tag: strain

value: proestrus


title: A673_Input_DNA

city: Guangzhou

first: Lehang

last: Lin

address: 107, West Yanjiang Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.1.2 with parameters -m 2 -k 2 --best --strata
Using Picard to mark and remove duplicate reads
using macs2 to peaks calling with parameters -q 0.01 --extsize 200 --nomodel
Genome_build: hg19

source_name: Ewing sarcoma cells

growth_protocol: A673 Ewing sarcoma cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and kept at 37℃ with 5% CO2.

extract_protocol: Cell lysates were clarified from sonicated nuclei and MEIS1-DNA complexes were isolated with antibody.

tag: cell line

value: Ewing sarcoma

tag: chip antibody

tag: cell number


title: D7PrF_OE

description: "Other" Epithelia from normal human prostate tissue

source_name: Human prostate "other" epithelia

tag: phenotype


title: WT female AECSq-21

description: pool of 5 individual placentas

tag: Sex

value: wild type


title: WT female AECSq-20

description: pool of 4 individual placentas


title: FA_3h_E_rep3

description: SAMPLE 89

tag: exposure time

tag: estrous cycle stage

value: estrus


title: D7PrF_LE

description: Luminal Epithelia from normal human prostate tissue

source_name: Human prostate luminal epithelia


title: O3_3h_E_rep3

description: SAMPLE 87

value: lung tissue homogenate


title: A673_MEIS1_ChIP-seq

value: MEIS1 (Abcam, ab19867)


title: D4PrF_FMSt


title: WT female AECSq-19

description: pool of 4 individual placentas

value: female


title: GR+/- male AECSq-5

description: pool of 3 individual placentas

value: male


title: GR+/- male AECSq-4

description: pool of 4 individual placentas


title: O3_3h_D_rep1

description: SAMPLE 86

value: 3 hours


title: D4PrF_OE

value: OE


title: O3_3h_M_rep2

description: SAMPLE 84

value: metestrus


title: O3_3h_P_rep3

description: SAMPLE 81


title: WT male AECSq-3

description: pool of 5 individual placentas


title: D4PrF_LE

value: LE


title: D3PrF_FMSt

value: FMSt


title: D4PrF_BE

description: Basal Epithelia from normal human prostate tissue

source_name: Human prostate basal epithelia


title: FA_3h_E_rep2

description: SAMPLE 80

source_name: female mouse exposed to filtered air

value: exposed to filtered air


title: WT male AECSq-2

description: pool of 5 individual placentas


title: WT male AECSq-1

description: pool of 5 individual placentas


title: D3PrF_OE


title: FA_3h_D_rep3

description: SAMPLE 79


title: FA_3h_P_rep3

description: SAMPLE 78


title: O3_3h_P_rep2

description: SAMPLE 77

source_name: female mouse exposed to 2ppm ozone


title: D3PrF_LE


title: GR+/- male AECSq-6

description: pool of 3 individual placentas


title: D7PrF_BE

value: BE


title: D2PrF_FMSt


title: D3PrF_BE


title: O3_3h_E_rep2

description: SAMPLE 76

value: exposed to 2ppm ozone


title: FA_3h_E_rep1

description: SAMPLE 75


title: D2PrF_OE


title: O3_3h_M_rep1

description: SAMPLE 73


title: D2PrF_LE


title: FA_3h_P_rep2

description: SAMPLE 71


title: D2PrF_BE


title: C32_OrgPod_3_S15

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
Transcript level counts were estimated using Salmon v0.8.2, using the ENSEMBL GRCh38 version of the human transcriptome.
Transcript level counts were converted to gene level counts using the Bioconductor R package tximport v1.3.13.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files with ensemble gene id and the averaged gene length across all 9 samples (salmon-counts-timecourse.txt) and 6 samples (salmon-counts.txt) in the first two columns, followed by 9 columns (salmon-counts-timecourse.txt) and 6 columns (salmon-counts.txt) containing counts for each sample

source_name: organoid-derived podocytes grown out for 3 days from day 25 kidney organoid derived glomeruli

extract_protocol:
RNA were extracted using QIAGEN RNeasy micro kit.
TruSeq stranded total RNA with RiboZero rRNA depletion

tag: clone

value: human iPSC line CRL1502 (clone C32)

value: WT


title: C32_OrgPod_2_S14

tag: cell type

value: organoid-derived podocytes grown out for 3 days from day 25 kidney organoid derived glomeruli


title: FA_3h_D_rep2

description: SAMPLE 33

value: diestrus


title: O3_3h_P_rep1

description: SAMPLE 70

value: proestrus


title: C32_OrgPod_1_S13


title: C32_OrgGlom_3_S12

source_name: Day 25 kidney organoid derived glomeruli


title: FA_3h_P_rep1

description: SAMPLE 32

value: lung tissue homogenate


title: FA_3h_D_rep1

description: SAMPLE 31


title: O3_3h_E_rep1

description: SAMPLE 34

value: estrus


title: C32_OrgGlom_2_S11

value: Day 25 kidney organoid derived glomeruli


title: THLE5B_Ginkgo_3

city: Mainz

first: Jens

last: Marquardt

address: Langenbeckstraße 1

department: Department of Medicine I

institute: Johannes Gutenberg University Mainz

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array normalization was performed with Illumina Genome Studio Gene Expression module xxx using quantile normalisation.

label: biotin

label_protocol: Standard Illumina scanning protocol

growth_protocol: Human hepatoma cell lines WRL68, Huh7, immortalized human hepatocyte cell line THLE5B and primary human HCC cells, Pitts1, have been cultured in DMEM, supplemented with 2mM L-glutamine, 1unit/ml penicillin/streptomycin, and 10% FCS at 37°C and 5% CO2.

extract_protocol: Total RNAs was extracted using Qiagen RNEasy mini Kit (Qiagen GmBH, Hilden, Germany) following the manufacturer’s protocol. RNA quantity and purity were estimated using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and integrity was assessed by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Cells were treated for 72hours with Ginkgo biloba extract (EGb761) at various concentration in dose-finding experiments (50 to 1000μg/ml) and with the inhibitory concentration 50 for each of the hepatoma cell lines (IC50Huh7=252,7μg/ml; IC50WRL68=156,0μg/ml; IC50Pitts1=191,6μg/ml) and THLE5B were treated with median IC50 (200 μg/ml) of all hepatoma cells for functional analyses.


title: THLE5B_untreated_3


title: THLE5B_Ginkgo_2


title: THLE5B_untreated_2


title: Huh7_1_Ginkgo_1


title: THLE5B_untreated_1


title: MNase_M_128_3

description: processed data file: mnase_atac_meta_plot_library.tsv.gz

data_processing:
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & ATAC-seq:  Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4.
RNA-seq: Stranded Reads pairs were aligned to the mm9 genome using RSEM-STAR pipeline with options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 –paired-end”.
MNase/ATAC-seq Meta Plot Library: Mid-points of MNase-fragments (140-200 bp), cut sites of ATAC-seq fragments (0-100 bp), counted at base pair resolution and normalised per million reads, in +/- 1000bp of TSS, EP300 summits, Esrrb Bookmarked Sites, Esrrb Lost Sites and Oct4/Sox2 sites. Mid-point/cutsite data smoothed by sparse Gaussian process regression using Gpy.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BigWig files, MNase-seq/ATAC-seq: Library of meta-plots in tab-separated format; RNA-seq: Raw and normalised read-counts tab-separated format.

value: embryonic stem cells

tag: mnase concentration

tag: cellcycle

value: M

tag: barcode


title: MNase_M_128_2


title: MNase_M_128_1


title: HET.19.2_Glomeruli_S8

source_name: Day 26 kidney organoid derived glomeruli, MAFB-BFP heterozygous

value: human iPSC line CRL 2436

value: MAFB +/-


title: HET.19.3_Glomeruli_S9

value: Day 26 kidney organoid derived glomeruli, MAFB-BFP heterozygous

value: human iPSC line CRL 2437


title: HET.19.1_Glomeruli_S7

value: human iPSC line CRL 2435


title: THLE5B_Ginkgo_1

tag: treatment


title: HET.14.3_Glomeruli_S6

source_name: Day 21 kidney organoid derived glomeruli, MAFB-BFP heterozygous

value: human iPSC line CRL 2434

tag: genotype


title: C32_OrgGlom_1_S10


title: MNase_M_16_3


title: MNase_M_16_2


title: HET.14.2_Glomeruli_S5

value: Day 21 kidney organoid derived glomeruli, MAFB-BFP heterozygous

value: human iPSC line CRL 2433


title: Huh7_1_untreated_2


title: MNase_M_16_1


title: Huh7_1_Ginkgo_2


title: Huh7_1_untreated_3


title: WRL68_1_Ginkgo_3


title: WRL68_1_Ginkgo_2


title: Huh7_1_Ginkgo_3


title: Huh7_1_untreated_1