title: Cys100uM_4

city: Philadelphia

first: Zhe

last: Zhang

address: Translational Research Lab

institute: University of Pennsylvania

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

organism: Caenorhabditis elegans

source_name: Whole worms

growth_protocol:
Nematode Growth Media plates at 20C
Worms were grown at 20¡C on NGM agar plates

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

treatment_protocol: Synchronized young adult gas-1(fc21) worms were treated for 24 h with water control, 0.1 µM, 1 µM, 10 µM, or 100 µM cysteamine bitartrate, or 2. 5 mM n-acetylcysteine as a positive control.  N2 wild-type were treated with water control.

tag: group

tag: drug

value: Cysteamine

tag: dosage

tag: age at rna isolation

value: 24 hour old young adult

tag: dev_stage at treatment initiation

value: 1st day young adult

value: Hermaphrodite

value: Erzsebet Polyak, PhD

value: mitochondrial disease

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

tag: phenotype

value: Complex I deficient

tag: buffer

value: S. basal (water soluble)


title: Dermo1Cre/Mt1-mmp(fl/fl) mammary gland, biological replicate 1

status: Public on Mar 01 2019

type: RNA

city: Ann Arbor

first: Stephen

middle: J.

last: Weiss

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

country: USA

institute: University of Michigan

description: Gene expression data from intact mammary epithelium-containing inguinal mammary gland tissue harvested from 4-week mice

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 Arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Data was analyzed using the oligo and limma Bioconductor packages implemented in the R-statistical environment 3.1.1. RMA was used to normalize the data and fit log2 transformed expression values

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Intact inguinal mammary gland

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Intact mammary epithelium-containing inguinal mammary gland tissue was harvested from 4-week-old mice.

extract_protocol: Mammary tissue was flash frozen in liquid nitrogen and homogenized in 1mL TRIzol (Ambion, Life Technologies). Total RNA was extracted with chloroform according to standard protocols and purified with QIAGEN Rneasy Mini-kit columns.

tag: genotype/variation

tag: strain

tag: age

value: 4 weeks


title: 25_35-H4

type: SRA

city: Cambridge

first: Hojun

last: Li

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_22

library_source: transcriptomic

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 74.
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

molecule: polyA RNA

source_name: intermediate stages of erythroid development cell with 25-35% expression of CD71/CD24

extract_protocol:
Erythroid progenitor cell isolation: Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).   Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in 0.2% Triton X-100 (Sigma), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

tag: cell type


title: 25_35-G5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_20


title: C6LP_NZn17_113 (RNA-seq)

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Data Filtering: 1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read,  we define the low quality base to be the base whose sequencing quality is no more than 5).
Reads Mapping: Bowtie2 [4] to map clean reads to reference gene and use HISAT [3] to reference  genome;  [4] Langmead B, et al. (2009). Ultrafast and memory-efficient alignment of short DNA sequences  to the human genome. Genome Biology, 10(3): 25-34.;  [3] Kim D, Langmead B and Salzberg SL.(2015). HISAT: a fast spliced aligner with low memory  requirements. Nature Methods,12(4):357-60. doi: 10.1038/nmeth.3317
Gene Quantification: use of RSEM [5] to calculate FPKM values;    [5] Li B and Dewey C N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with  or without a reference genome. BMC bioinformatics, 12(1): 323.
DEG definition:  use of the NOISeq method [16];   [16] Sonia Tarazona, et al. (2011). Differential expression in RNA-seq: A matter of depth.  Genome Research, 21:2213–2223.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-35/fasta/brassica_oleracea/dna/
Supplementary_files_format_and_content: files include FPKM values for each Sample

organism: Brassica oleracea

source_name: Plant root

growth_protocol: Hydroponic experiments were performed as follows: Seeds were germinated on the surface of filter paper moistened with deionized water in Petri dishes placed at 16°C in the dark for five days. Six five-day-old seedlings per accession were transferred to a five-litre bucket holding a solution containing 2 mM Ca(NO3)2, 2 mM NH4NO3, 0.75 mM MgSO4, 0.5 mM KOH, 0.1 mM FeNaEDTA, 30 µM H3BO3, 25 µM CaCl2, 10 µM MnSO4,3µM CuSO4 and 0.5 µM Na2MoO4, and either 0.25 mM KH2PO4 (High P treatment) or 0.025 mM KH2PO4 plus 0.225 mM KCl (Low P treatment). Either 1 µM ZnSO4 (High Zn) or no ZnSO4 (Low Zn) was added to each P treatment. Plants were, therefore, subjected to four treatments (Low P & Low Zn, Low P & High Zn, High P & Low Zn and High P & High Zn). The pH was adjusted to 6 in all treatments by addition of H2SO4. Experiments were performed in a glasshouse at the James Hutton Institute (Invergowrie, Scotland, UK, latitude 56°27'22.7" N, longitude 03°04'09.9" W) and lasted two weeks, with one change of the nutrient solution, which was continuously aerated. Buckets were set in a complete randomized design on a single bench. Daytime and night time temperatures were maintained at 24 °C and 18 °C, respectively. Daily irradiance (> 200 W m-2 for 16 h) was obtained by artificial illumination (MASTER SON-T PIA Green Power lamps, Philips, Guildford, UK).

extract_protocol:
Frozen root samples were ground to powder using a pre-cooled pestle and mortar, after which the powdered material was transferred to a 2 ml Eppendorf tube. One mL of Trizol® was added to each sample, shaken thoroughly and incubated at room temperature for 5 min. Subsequently 200µl chloroform were added to each sample after which they were again shaken and incubated for 5 min at room temperature. The samples were centrifuged at 12000×g for 15 min at 4°C and 600µl supernatant was transferred to a new 2 ml Eppendorf tube to which 600µl of isopropanol was added. The Eppendorf tubes were inverted for mixing after which samples were centrifuged at 12000 × g for 15 min at 4 °C. The supernatant was removed and the pellet was rinsed in 700µl 70 % ethanol and dried at room temperature for 10 min before being resuspended in 100 µl of MiliQ water. The RNA was further purified using the ENZO kit (Zymo Research, Irvine, California, USA) following the manufacturer’s instructions. An “On column DNAse treatment” was included and DNA was eluted twice with 100µl of pre-warmed MilliQ water.
Library preparation, SE50 sequencing, data filtering and cleaning, alignments with the reference database (ftp://ftp.ensemblgenomes.org/pub/plants/release-35/fasta/brassica_oleracea/dna/) and gene expression quantification as well as detection of differential gene expression was performed by BGI (https://www.bgi.com/global/) according to their standard analysis pipeline (Fig. S1).

tag: tissue

value: Plant root

tag: developmental stage

value: post germination 2weeks

tag: genotype

value: wild type

tag: accession

tag: treatment

value: LP_NZ (Low P & High Zn)


title: C6LP_NZn17_16 (RNA-seq)


title: Cys100uM_3

state: PA

tag: Sex

tag: disease


title: Cys100uM_2

tag: group

tag: drug


title: 25_35-G4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_19


title: C6LP_LZn2_129 (RNA-seq)

value: LP_LZ (Low P & Low Zn)


title: C6LP_NZn17_5 (RNA-seq)


title: Cys100uM_1

tag: dosage

tag: age at rna isolation


title: Mt1-mmp(+/+) mammary gland, biological replicate 1


title: C6LP_LZn2_39 (RNA-seq)


title: 25_35-F6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_18


title: C6LP_LZn2_2 (RNA-seq)


title: C6NP_NZn29_6 (RNA-seq)

value: NP_NZ (High P & High Zn)


title: Cys10uM_4

tag: dev_stage at treatment initiation

tag: phenotype


title: C6NP_LZn6_97 (RNA-seq)

value: NP_LZ (High P & Low Zn)


title: 25_35-F5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_17


title: Fertile female [1448]

type: genomic

city: Pittsburgh

first: Svetlana

middle: A

last: Yatsenko

address: 300 Halket St

institute: University of Pittsburgh

description: copy number

hyb_protocol: According to Agilent protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
normalized log2 ratio (Cy5/Cy3) representing test/reference

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: According to Agilent protocol

growth_protocol: uncultured

extract_protocol: Genomic DNA extracted using Puregene Kit following manufacturer's instructions

tag: gender

value: Female

value: peripheral blood

source_name: Promega

tag: reference dna gender

tag: reference dna cell line

value: pooled


title: Fertile female [908]

description: copy number


title: Fertile female [860]

description: copy number


title: Fertile female [532]

description: copy number


title: 25_35-F4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_16

tag: strain

tag: cell type


title: Cys10uM_2

value: Cysteamine

value: 24 hour old young adult

value: 1st day young adult

value: Hermaphrodite

tag: buffer


title: Cys10uM_3

tag: genotype

value: Erzsebet Polyak, PhD

value: mitochondrial disease

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

value: Complex I deficient


title: 25_35-E6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_15


title: 25_35-E5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_14


title: Cys10uM_1

value: S. basal (water soluble)


title: Fertile female [1116]

description: copy number

tag: tissue


title: Fertile female [1110]

description: copy number


title: Fertile female [1112]

description: copy number


title: Cys1uM_3


title: BFUE_Day1_25

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 39
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

source_name: burst forming unit-erythroid

extract_protocol:
cell extraction protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).  For quantification of erythroid differentiation markers, cultured BFU-E cells were stained with PE anti-CD71 (clone R127217, E-Biosciences) and APC anti-Ter119 (E-Biosciences).  Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
cell culture protocol: BFU-E cell culture. FACS-isolated BFU-E enriched cells were cultured for the denoted number of days in progenitor culture media (PCM) consisting of serum free expansion media (SFEM2, Stem Cell Technologies) supplemented with 100 ng/mL murine SCF (Peprotech), 40 ng/mL murine insulin-like growth factor 1 (Peprotech), 2 U/mL human erythropoietin (Amgen), 1% penicillin/streptomycin (Gibco), and for indicated cultures 100 nM Dexamethasone (Sigma).
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

value: BFUE

value: erythroid progenitor media

tag: time in culture

value: 24 hrs

tag: treatment

value: No


title: Fertile female [1106]

description: copy number


title: 25_35-E4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_13


title: Fertile female [1096]

description: copy number


title: 25_35-D6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_12


title: Fertile female [1090]

description: copy number


title: Fertile female [1086]

description: copy number


title: 25_35-D5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_11


title: Cys1uM_2

tag: Sex

tag: disease


title: Cys1uM_1

tag: group

tag: drug


title: Fertile female [1115]

description: copy number


title: Fertile female [1122]

description: copy number


title: Fertile female [1075]

description: copy number


title: Fertile female [1074]

description: copy number


title: Dermo1Cre/Mt1-mmp(fl/fl) mammary gland, biological replicate 3

tag: genotype/variation

tag: age

value: 4 weeks


title: Fertile female [1117]

description: copy number

value: Female


title: Cys100nM_4

tag: dosage

tag: age at rna isolation

tag: dev_stage at treatment initiation

tag: phenotype


title: 25_35-D4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_10

tag: strain


title: Fertile female [1068]

description: copy number

tag: gender

value: peripheral blood

tag: reference dna gender

tag: reference dna cell line


title: Cys1uM_4

tag: genotype

tag: buffer


title: Fertile female [1042]

description: copy number

tag: tissue

value: pooled


title: Fertile female [1041]

description: copy number


title: 25_35-C5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_8

tag: cell type


title: Fertile female [1018]

description: copy number


title: 25_35-C6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_9


title: Fertile female [1229]

description: copy number


title: 25_35-C4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_7


title: Cys100nM_2

value: Cysteamine

tag: Sex

tag: disease


title: Fertile female [1228]

description: copy number


title: 25_35-B6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_6


title: Fertile female [1476]

description: copy number


title: Nac_4

tag: group

value: Nac

tag: drug

value: Nacetylcysteine

value: 24 hour old young adult


title: Cys100nM_1

value: 1st day young adult

value: Hermaphrodite

value: Erzsebet Polyak, PhD


title: Fertile female [1474]

description: copy number


title: Fertile female [1464]

description: copy number


title: 25_35-B5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_5


title: Nac_3

value: mitochondrial disease

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

value: Complex I deficient


title: Fertile female [1461]

description: copy number


title: Fertile female [1452]

description: copy number


title: Nac_2

value: S. basal (water soluble)


title: 25_35-B4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_4


title: Cys100nM_3


title: Fertile female [1458]

description: copy number


title: Nac_1


title: Fertile female [1445]

description: copy number


title: Fertile female [1444]

description: copy number


title: 25_35-A5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_2


title: Gas1_3_3


title: 25_35-A4

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_1


title: 25_35-A6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_3


title: Gas1_3_4


title: Fertile female [1443]

description: copy number


title: Fertile female [1446]

description: copy number


title: Fertile female [1432]

description: copy number


title: CFUE-H11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_23

source_name: colony forming unit-erythroid

value: CFUE


title: Fertile female [1421]

description: copy number


title: Fertile female [1419]

description: copy number


title: Gas1_3_1


title: CFUE-H10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_22


title: Fertile female [1460]

description: copy number


title: Fertile female [1418]

description: copy number


title: N2_3_4

value: N2 Bristol

value: wild-type


title: Fertile female [1417]

description: copy number

value: Female


title: N2_3_3


title: Fertile female [1416]

description: copy number

value: peripheral blood


title: Fertile female [1415]

description: copy number

value: pooled


title: CFUE-G12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_21


title: Fertile female [1413]

description: copy number


title: CFUE-G11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_20


title: Fertile female [1468]

description: copy number


title: CFUE-H12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_24


title: N2_3_2


title: Fertile female [1411]

description: copy number


title: Fertile female [1425]

description: copy number


title: Fertile female [1401]

description: copy number


title: CFUE-G10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_19


title: Gas1_3_2


title: Fertile female [1405]

description: copy number


title: N2_3_1


title: Fertile female [1433]

description: copy number


title: 28373-DAF-16(MU86);DAF-2(E1370)

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

description:
Sample_28373
Sample_ID:
e1370-mu86_4

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC (version 0.10.1) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).  We trimmed reads based on quality scores using CutAdapt with default parameters.
Aligment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads to the reference transcriptome using TopHat (version 2.0.9) and Bowtie (version 2.1.0.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” and "--no-coverage-search".
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis, using UCSC ce10.fa as the reference genome sequence and UCSC ce10.gtf for the reverence transcriptome. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Genome_build: ce10
Supplementary_files_format_and_content: .txt table of mapped raw read counts for each gene for each sample produced by Cufflinks. Partial reads are allocated in the case of multimapping.

source_name: whole organism

growth_protocol: Wild-type and daf-2animals from a synchronized four hour egg lay were grown at 15C until early L4 then moved to 20C for an additional 20-24 hour day until they reached young adulthood.  Egg lay of daf-2(e1370) was performed 6 hours earlier than control strains to adjust for slower growth.  glp-1(e2141)animals were raised at 25C for 48 hours to ablate the germline

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and purified using an RNeasy kit (QIAGEN Inc., Valencia, CA) according to manufacturers’ instructions.
mRNA was isolated from 0.1-3 ug of total RNA by polyA+ purification, fragmented, and copied into first strand cDNA using reverse transcriptase and random primers. 3’ cDNA ends were then adenylated and adapters ligated. One of the adapters contained a 6-nucleotide barcode to enable multiplexing of samples. Products were purified and enriched by PCR to create the final cDNA library. Libraries were checked for quality and quantity by Agilent TapeStation and qPCR using a library quantification kit for Illumina sequencing platforms (catalog #KK4835, Kapa Biosystems, Wilmington, MA).  Clonal clusters were generated using cBot (Illumina, Inc., San Diego, CA). Quadriplexed samples were sequenced using the HiSeq 2000 system (Illumina) with a 100-cycle paired-end run in high output mode using Version 3 reagents according to manufacturer’s protocols.

tag: developmental stage

value: YOUNG ADULT

value: LONGEVITY SUPPRESSED

value: whole animal


title: Fertile female [1400]

description: copy number


title: CFUE-F11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_17


title: Fertile female [1399]

description: copy number


title: Fertile female [1395]

description: copy number


title: 28371-DAF-2(E1370)

description:
Sample_28371
Sample_ID:
e1370_4

value: LONG LIVED


title: CFUE-F10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_16


title: Fertile female [1393]

description: copy number


title: Fertile female [1392]

description: copy number


title: CFUE-E12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_15


title: CFUE-F12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_18


title: CFUE-E11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_14


title: Fertile female [1387]

description: copy number


title: Fertile female [1385]

description: copy number


title: Fertile female [1391]

description: copy number


title: Fertile female [1384]

description: copy number


title: Fertile female [1382]

description: copy number


title: CFUE-E10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_13


title: 28370-DAF-16(MU86);DAF-2(E1368)

description:
Sample_28370
Sample_ID:
e1368-mu86_4


title: 28367-WT

description:
Sample_28367
Sample_ID:
WT_4

value: WT


title: 28369-DAF-16(MG54);DAF-2(E1368)

description:
Sample_28369
Sample_ID:
e1368-mg54_4


title: Fertile female [1377]

description: copy number


title: 28368-DAF-2(E1368)

description:
Sample_28368
Sample_ID:
e1368_4


title: CFUE-D11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_11


title: CFUE-D12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_12


title: Fertile female [1379]

description: copy number


title: Fertile female [1396]

description: copy number


title: 28366-DAF-16(MU86);DAF-2(E1370)

description:
Sample_28366
Sample_ID:
e1370-mu86_3


title: 28372-DAF-16(MG54);DAF-2(E1370)

description:
Sample_28372
Sample_ID:
e1370-mg54_4


title: Fertile female [1375]

description: copy number


title: Fertile female [1374]

description: copy number


title: Fertile female [1376]

description: copy number


title: 28365-DAF-16(MG54);DAF-2(E1370)

description:
Sample_28365
Sample_ID:
e1370-mg54_3


title: CFUE-D10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_10


title: Fertile female [1372]

description: copy number


title: CFUE-C12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_9


title: Fertile female [1406]

description: copy number


title: 28364-DAF-2(E1370)

description:
Sample_28364
Sample_ID:
e1370_3


title: Fertile female [1373]

description: copy number


title: Fertile female [1370]

description: copy number


title: CFUE-C11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_8


title: Fertile female [1364]

description: copy number


title: Fertile female [1363]

description: copy number


title: CFUE-C10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_7


title: 28362-DAF-16(MG54);DAF-2(E1368)

description:
Sample_28362
Sample_ID:
e1368-mg54_3


title: Fertile female [1365]

description: copy number


title: Fertile female [1357]

description: copy number


title: Fertile female [1352]

description: copy number


title: Fertile female [1353]

description: copy number


title: Fertile female [1351]

description: copy number


title: 28360-WT

description:
Sample_28360
Sample_ID:
WT_3


title: 28361-DAF-2(E1368)

description:
Sample_28361
Sample_ID:
e1368_3


title: CFUE-B12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_6


title: CFUE-B10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_4


title: 28363-DAF-16(MU86);DAF-2(E1368)

description:
Sample_28363
Sample_ID:
e1368-mu86_3


title: Fertile female [1360]

description: copy number


title: Fertile female [1346]

description: copy number


title: 28358-DAF-16(MG54);DAF-2(E1370)

description:
Sample_28358
Sample_ID:
e1370-mg54_2


title: Fertile female [1348]

description: copy number


title: Fertile female [1345]

description: copy number


title: CFUE-A12

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_3


title: CFUE-A11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_2


title: Fertile female [1341]

description: copy number


title: Fertile female [1344]

description: copy number


title: 28357-DAF-2(E1370)

description:
Sample_28357
Sample_ID:
e1370_2


title: Fertile female [1361]

description: copy number


title: Fertile female [1335]

description: copy number


title: 28356-DAF-16(MU86);DAF-2(E1368)

description:
Sample_28356
Sample_ID:
e1368-mu86_2


title: BFUE-H3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_24

value: BFUE


title: Fertile female [1334]

description: copy number


title: Fertile female [1332]

description: copy number


title: Fertile female [1323]

description: copy number


title: CFUE-A10

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_1


title: CFUE-B11

description:
BFUE_CFUE_andInterm.counts.txt
CFUE_5


title: 28355-DAF-16(MG54);DAF-2(E1368)

description:
Sample_28355
Sample_ID:
e1368-mg54_2


title: BFUE-H2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_23


title: BFUE-H1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_22


title: 28354-DAF-2(E1368)

description:
Sample_28354
Sample_ID:
e1368_2


title: Fertile female [1317]

description: copy number


title: 28353-WT

description:
Sample_28353
Sample_ID:
WT_2


title: Fertile female [1310]

description: copy number


title: BFUE-G3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_21


title: Fertile female [1316]

description: copy number


title: POR_i1_CD_05

city: Leuven

first: Sare

last: Verstockt

address: O&N4 Herestraat 49 box 610

country: Belgium

institute: KU Leuven

description: Biopsy from ileal mucosa of a post-operative recurrent CD patient (Rutgeerts score i1)

hyb_protocol: Hybridization to GeneChip Human Gene 1.0ST arrays (Affymetrix) was performed at 45°C for 17 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).

data_processing: Quality assessment and outlier detection was performed before and after normalization using the Bioconductor package arrayQualityMetrics. Data were analyzed using the RMA algorithm with the aroma.affymetrix package (R version 3.2.2)

label_protocol: Total RNA (150 ng) was reverse-transcribed into cDNA, followed by the generation of cRNA and ss DNA using the GeneChip WT Synthesis and Amplification kit (Ambion). Fragmented DNA is labeled with biotin (GeneChip WT terminal Labeling kit).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. RNA quality and quantity were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit.

value: Crohn's disease

value: ileum


title: Fertile female [1314]

description: copy number


title: 28359-DAF-16(MU86);DAF-2(E1370)

description:
Sample_28359
Sample_ID:
e1370-mu86_2


title: Fertile female [1305]

description: copy number


title: Fertile female [1307]

description: copy number


title: BFUE-G2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_20


title: Fertile female [1302]

description: copy number


title: BFUE-G1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_19


title: 28350-DAF-2(E1370)

description:
Sample_28350
Sample_ID:
e1370_1


title: Fertile female [1299]

description: copy number


title: Fertile female [1301]

description: copy number


title: BFUE-F3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_18


title: 28349-DAF-16(MU86);DAF-2(E1368)

description:
Sample_28349
Sample_ID:
e1368-mu86_1


title: Fertile female [1308]

description: copy number


title: Fertile female [1298]

description: copy number


title: BFUE-F2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_17


title: 28348-DAF-16(MG54);DAF-2(E1368)

description:
Sample_28348
Sample_ID:
e1368-mg54_1


title: Fertile female [1291]

description: copy number


title: Fertile female [1294]

description: copy number


title: BFUE-F1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_16


title: 28347-DAF-2(E1368)

description:
Sample_28347
Sample_ID:
e1368_1


title: Fertile female [1279]

description: copy number


title: Fertile female [1286]

description: copy number


title: 28352-DAF-16(MU86);DAF-2(E1370)

description:
Sample_28352
Sample_ID:
e1370-mu86_1


title: 28346-WT

description:
Sample_28346
Sample_ID:
WT_1


title: Fertile female [1278]

description: copy number


title: Fertile female [1285]

description: copy number


title: Fertile female [1277]

description: copy number


title: BFUE-E3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_15


title: 28345-DAF-16(MU86);DAF-2(E1370)

description:
Sample_28345
Sample_ID:
e1370-mu86_0


title: BFUE-E2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_14


title: 28351-DAF-16(MG54);DAF-2(E1370)

description:
Sample_28351
Sample_ID:
e1370-mg54_1


title: Fertile female [1274]

description: copy number


title: Fertile female [1276]

description: copy number


title: 28344-DAF-16(MG54);DAF-2(E1370)

description:
Sample_28344
Sample_ID:
e1370-mg54_0


title: Fertile female [1272]

description: copy number


title: Fertile female [1269]

description: copy number


title: BFUE-D3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_12


title: 28343-DAF-2(E1370)

description:
Sample_28343
Sample_ID:
e1370_0


title: Fertile female [1295]

description: copy number


title: Fertile female [1257]

description: copy number


title: 28342-DAF-16(MU86);DAF-2(E1368)

description:
Sample_28342
Sample_ID:
e1368-mu86_0


title: 28341-DAF-16(MG54);DAF-2(E1368)

description:
Sample_28341
Sample_ID:
e1368-mg54_0


title: Fertile female [1249]

description: copy number


title: BFUE-D1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_10


title: Fertile female [1248]

description: copy number


title: Fertile female [1245]

description: copy number


title: BFUE-C3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_9


title: BFUE-C2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_8


title: BFUE-E1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_13


title: Fertile female [1239]

description: copy number


title: Fertile female [1243]

description: copy number


title: 28340-DAF-2(E1368)

description:
Sample_28340
Sample_ID:
e1368_0


title: 22951-DAF-16(MG54);GLP-1(E2141)

description:
Sample_22951
Sample_ID:
e2141-mg54_4


title: Fertile female [1227]

description: copy number


title: Fertile female [1230]

description: copy number


title: BFUE-C1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_7


title: BFUE-B3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_6


title: Fertile female [1225]

description: copy number


title: 22950-DAF-16(MU86);GLP-1(E2141)

description:
Sample_22950
Sample_ID:
e2141-mu86_4


title: BFUE-B2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_5


title: Fertile female [1260]

description: copy number


title: Fertile female [1218]

description: copy number


title: Fertile female [1224]

description: copy number


title: 22949-GLP-1(E2141)

description:
Sample_22949
Sample_ID:
e2141_4


title: Fertile female [1217]

description: copy number


title: BFUE-D2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_11


title: Fertile female [1215]

description: copy number


title: BFUE-B1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_4


title: 28339-WT

description:
Sample_28339
Sample_ID:
WT_0


title: Fertile female [1211]

description: copy number


title: 22944-DAF-16(MG54);GLP-1(E2141)

description:
Sample_22944
Sample_ID:
e2141-mg54_3


title: Fertile female [1208]

description: copy number


title: 22943--DAF-16(MU86);GLP-1(E2141)

description:
Sample_22943
Sample_ID:
e2141-mu86_3


title: Fertile female [1203]

description: copy number


title: Fertile female [1233]

description: copy number


title: Fertile female [1200]

description: copy number


title: Fertile female [1195]

description: copy number


title: BFUE-A1

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_1


title: BFUE-A2

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_2


title: 22942-GLP-1(E2141)

description:
Sample_22942
Sample_ID:
e2141_3


title: Fertile female [1197]

description: copy number


title: Fertile female [1190]

description: copy number


title: Fertile female [1185]

description: copy number


title: 22937-DAF-16(MG54);GLP-1(E2141)

description:
Sample_22937
Sample_ID:
e2141-mg54_2


title: 22936--DAF-16(MU86);GLP-1(E2141)

description:
Sample_22936
Sample_ID:
e2141-mu86_2


title: Fertile female [1189]

description: copy number


title: Fertile female [1181]

description: copy number


title: CFUE_96

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TCTTAC-s_3

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 100
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

growth_protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).

extract_protocol:
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).   Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).


title: 22935-GLP-1(E2141)

description:
Sample_22935
Sample_ID:
e2141_2


title: 22930-DAF-16(MG54);GLP-1(E2141)

description:
Sample_22930
Sample_ID:
e2141-mg54_1


title: CFUE_94

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TATGCA-s_3


title: BFUE-A3

description:
BFUE_CFUE_andInterm.counts.txt
BFUE_3


title: Fertile female [1167]

description: copy number


title: Fertile female [1166]

description: copy number


title: CFUE_93

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TACTCC-s_3


title: Fertile female [1164]

description: copy number


title: 22929--DAF-16(MU86);GLP-1(E2141)

description:
Sample_22929
Sample_ID:
e2141-mu86_1


title: 22928-GLP-1(E2141)

description:
Sample_22928
Sample_ID:
e2141_1


title: CFUE_91

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-ATAGAG-s_3


title: Fertile female [1161]

description: copy number


title: Fertile female [1162]

description: copy number


title: Fertile female [1156]

description: copy number


title: 22923-DAF-16(MG54);GLP-1(E2141)

description:
Sample_22923
Sample_ID:
e2141-mg54_0


title: Fertile female [1157]

description: copy number


title: CFUE_90

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-AGGCTT-s_3


title: Fertile female [1163]

description: copy number


title: CFUE_95

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TCTACT-s_3


title: Fertile female [1153]

description: copy number


title: 22922-DAF-16(MU86);GLP-1(E2141)

description:
Sample_22922
Sample_ID:
e2141-mu86_0


title: CFUE_89

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-AGAGGA-s_3


title: Fertile female [1144]

description: copy number


title: Fertile female [1148]

description: copy number


title: Fertile female [1169]

description: copy number


title: 22921-GLP-1(E2141)

description:
Sample_22921
Sample_ID:
e2141_0


title: Fertile female [1139]

description: copy number


title: Fertile female [1135]

description: copy number


title: Fertile female [1142]

description: copy number


title: CFUE_92

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-CTCCTT-s_3


title: CFUE_87

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TCTACT-s_3


title: Fertile female [1136]

description: copy number


title: Fertile female [1125]

description: copy number


title: ItprCtrl3

city: Bangalore

first: Gaiti

last: Hasan

address: GKVK Campus,

country: India

institute: NCBS, TIFR

description: third instar

data_processing:
Illumina Casava software used for basecalling
Good quality sequencing reads after adapter trimming were mapped to Drosophila genome using Tophat v 2.0.11 with parameters -m 1 -F 0 -p 6 -g 1 --microexon-search --no-coverage-search
Mapped reads of both conditions at each individual timepoint were used for differential expression analysis by cuffdiff v2.2.0 using default options
Gene counts for both conditions at each time point were independantly generated using BioConductor packages GenomicRanges and IRanges which were then used to call differentially expressed genes using the Bioconductor packages EdgeR and DESeq
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files with expression levels, fold change and p-values for all genes from Cuffdiff, DESeq and edgeR

organism: Drosophila melanogaster

source_name: Central Nervous Sytem

growth_protocol: Flies were reared on corn meal medium at 25°C

extract_protocol:
Larval nervous systems were dissected in Heamolymph like saline (HL3), immediately transferred to ice and about 15 CNS were pooled together per sample to isolate RNA using Trizol
Libraries were made with 500ng total RNA using Illumina v2 protocol with 1/3rd the kit recommended volumes. Purification and size selection using Ampure beads.

value: 84h after egg laying larvae

value: Central Nervous Sytem

value: control

value: UAS-dsitpr/+; UAS-dicer/+


title: ItprCtrl2

description: third instar


title: Fertile female [1134]

description: copy number


title: Fertile female [1094]

description: copy number


title: CFUE_85

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TACTCC-s_3

value: CFUE


title: ItprKD2

description: third instar

value: IP3R knockdown


title: Fertile female [1089]

description: copy number

value: Female


title: Fertile female [1097]

description: copy number

value: peripheral blood


title: Fertile female [1015]

description: copy number

value: pooled


title: Fertile female [1147]

description: copy number


title: ItprCtrl1

description: third instar


title: CFUE_88

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TCTTAC-s_3


title: Fertile female [1084]

description: copy number


title: CFUE_82

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-AGGCTT-s_3


title: CFUE_84

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-CTCCTT-s_3


title: CFUE_86

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TATGCA-s_3


title: Fertile female [1081]

description: copy number


title: CFUE_83

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-ATAGAG-s_3


title: Fertile female [1080]

description: copy number


title: CFUE_80

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TCTTAC-s_3


title: Fertile female [1065]

description: copy number


title: Fertile female [1083]

description: copy number


title: S. clavuligerus::pimM_96h_rep2

type: mixed

city: León

first: Paloma

middle: Liras

last: Padín

state: Spain

address: Vegazana Campus

department: Molecular Biology

country: Spain

institute: University of León

description: Biological replicate 2 of 2. pimM_96h-rep2

hyb_protocol: Cy3-cDNA (300 ng) and Cy5-labeled gDNA (4 pmol) were mixed, resuspended in 32 μl of hybridization solution (Agilent) and applied on the microarray surface. Hybridizations were carried out at 55°C and extended to 60 h to improve the quality of the results.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2565BA. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Microarrays data were processed with the Bioconductor package limma (Smyth and Speed 2003; Smyth 2004). Background corrected signals (the median background signal was substracted from the mean foreground signal) were log2-transformed and normalized with the global median procedure (within arrays), and with the cyclic loess procedure (between arrays). The Mg value is the normalized log2 of Cy3/Cy5 intensities, which is proportional to the abundance of the transcript for a particular gene.

organism: Streptomyces clavuligerus

source_name: pimM_96h _totalRNA

label_protocol: Labelling reactions were performed according to the recommendations described by BioPrime® Array CGH Genomic Labeling Systems (Life Technologies). Total RNA was labelled with Cy3-dCTP (Amersham) using random primers and SuperScript™ II reverse transcriptase (Invitrogen). gDNA was labelled with Cy5-dCTP (Amersham) from random primers extended with the Klenow fragment of DNA polymerase (Roche). The final products were purified with MinElute columns (Qiagen) and labelling efficiencies were quantified spectrophotometrically.

growth_protocol: Culture conditions were optimized using MEY medium (Hopwood et al., 1985) and the samples to extract RNA were collected at 84 h, 90 h and 96 h of the cultures.

extract_protocol: lisozime 30 mg/ml in TE was added to stabilized culture samples. After 10 min, 600 µl RLT-β-mercaptoethanol was added to samples, mixed with vortex and, samples within microtubes containing silica beads were processed in FastPrep equipment with the following program: 30 s 6.5 m/s, 1 min at 0 °C, 30 s 6.5 m/s, 1 min at 0 °C. The preparation was extracted with one volume of phenol/chloroform-isoamilic alcohol and the aqueous-phase was applied to RNeasy Mini Kit Columns (Qiagen) according to the manufacturer’s instructions. RNA preparations were incubated with DNaseI (Qiagen) to eliminate DNA contamination. Sample quantification was done with a NanoDrop ND-1000 UV-Vis Spectrophotometer and the integrity of the RNA was determined in a Bioanalyzer 2100 (Agilent Technologies). Only RNAs with an RNA integrity value above 7.0 were used.

treatment_protocol: Samples from the Streptomyces cultures were stabilized with two volumes of RNA Protect Bacteria Reagent (Qiagen) for 5 min

value: pimM

tag: time

source_name: ATCC 27064_ Stationary growth phase _genomicDNA [reference]

extract_protocol: Genomic DNA from a stationary phase culture was purified by the salting out procedure (Pospiech, and Neumann, 1995).

tag: growth phase

value: Stationary


title: Fertile female [1063]

description: copy number


title: CFUE_79

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TCTACT-s_3


title: Fertile female [1057]

description: copy number


title: CFUE_78

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TATGCA-s_3


title: Fertile female [1044]

description: copy number


title: Fertile female [1049]

description: copy number


title: Fertile female [1040]

description: copy number


title: Fertile female [1043]

description: copy number


title: S. clavuligerus::pimM_84h_rep2

description: Biological replicate 2 of 2. pimM_84h-rep2

source_name: pimM_84h _totalRNA


title: CFUE_77

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TACTCC-s_3


title: Fertile female [1054]

description: copy number


title: CFUE_76

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-CTCCTT-s_3


title: Fertile female [1038]

description: copy number


title: CFUE_81

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-AGAGGA-s_3


title: Fertile female [1034]

description: copy number


title: S. clavuligerus::pimM_96h_rep1

description: Biological replicate 1 of 2. pimM_96h-rep1


title: Fertile female [1031]

description: copy number


title: S. clavuligerus::pimM_90h_rep1

description: Biological replicate 1 of 2. pimM_90h-rep1

source_name: pimM_90h _totalRNA


title: Fertile female [1032]

description: copy number


title: S. clavuligerus::pIB139_96h_rep2

description: Biological replicate 2 of 2. Control strain. pIB139_96h-rep2

source_name: pIB139_96h _totalRNA


title: S. clavuligerus::pimM_84h_rep1

description: Biological replicate 1 of 2. pimM_84h-rep1


title: CFUE_75

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-ATAGAG-s_3


title: S. clavuligerus::pimM_90h_rep2

description: Biological replicate 2 of 2. pimM_90h-rep2


title: Fertile female [1061]

description: copy number


title: CFUE_74

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-AGGCTT-s_3


title: Fertile female [1028]

description: copy number


title: Fertile female [1025]

description: copy number


title: Fertile female [1027]

description: copy number


title: CFUE_73

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-AGAGGA-s_3


title: S. clavuligerus::pIB139_84h_rep2

description: Biological replicate 2 of 2. Control strain. pIB139_84h-rep2

source_name: pIB139_84h _totalRNA


title: Fertile female [1008]

description: copy number


title: Fertile female [1007]

description: copy number


title: CFUE_71

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TCTACT-s_3


title: CFUE_72

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TCTTAC-s_3


title: Fertile female [1001]

description: copy number


title: Fertile female [1021]

description: copy number


title: S. clavuligerus::pIB139_90h_rep2

description: Biological replicate 2 of 2. Control strain. pIB139_90h-rep2

source_name: pIB139_90h _totalRNA


title: S27-D3-6hr

city: DAVIS

first: Danielle

middle: G

last: Lemay

state: CA

address: 430 West Health Sciences Dr.

institute: USDA ARS WHNRC

description:
S27-D3-6hr_S31
combinedCounts.txt
fixed_combinedCounts.txt

data_processing:
Fastq files were demultiplexed to assign reads to the originating sample.
Read pairs were processed using the expHTS tool which trims low quality 3'-ends of read pairs using a modified version of Sickle, then merges overlapping read pairs using a modified version of FLASH, that trims off Illumina adapters as a by-product of read merging.
Both sets of single-ended reads (merged by FLASH2) and paired-end reads (unmerged) were aligned to UCSC annotations from the hg19 iGenomes database for Homo sapiens using STAR with the default parameters.
Gene counts from single- and paired-reads were summed within each sample.
Genome_build: hg19
Supplementary_files_format_and_content: combinedCounts.txt; raw count matrix
Supplementary_files_format_and_content: fixed_combinedCounts.txt;  this is the count matrix with one duplicate entry removed (TTTY17B.0.0) and non-gene features removed (N_unmapped, N_multimapping, N_noFeature, N_ambiguous)

source_name: Whole blood

growth_protocol: Subject inclusion criteria included: 1) age between 18 and 60 y and 2) a normal BMI (in kg/m2, 18–24.9). Exclusion criteria included: 1) total blood cholesterol >240 mg/dL, 2) TGs >300 mg/dL, 3) hemoglobin <11.5 mg/dL, 4) blood pressure > 140/90 mmHg, 5) abnormal results in clinical chemistry and hematology panels, 6) inflammatory or metabolic diseases, 7) use of nonsteroidal anti-inflammatory drugs including asthma and allergy medications, 8) unwillingness to discontinue use of dietary supplements before and during the study period, and 9) vegetarianism. 62 subjects (36 female and 26 male) completed the parent study. For the present study, 5 subjects were randomly selected for the RNA-Seq study. This included 3 male and 2 female subjects.

extract_protocol:
Three mL of venous whole blood was drawn into a Tempus Blood RNA tube (Life Technologies, Foster City, CA), shaken vigorously, and then frozen at -80 °C until use. Total RNA was purified with the Tempus Spin RNA Isolation Kit (Life Technologies) with minor modifications to the manufacturer’s protocol.  To remove residual genomic  modifications to the manufacturer’s protocol.  To remove residual genomic DNA, RNA samples were treated on-column with RNase-Free DNase (Qiagen, Hilden, Germany) per manufacturer’s instructions. RNA quantity, quality, and integrity were assessed with NanoDrop 1000 (NanoDrop, Wilmington, DE) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All isolated RNA had A260/A280 ratios greater than 2 and RNA integrity numbers higher than 7.3.
RNA-Seq libraries were constructed at the DNA Technologies and Expression Core (University of California, Davis) using the Ovation Human Blood RNA-Seq Library System which utilizes “Insert Dependent Adaptor Cleavage” technology to enrich for non-rRNA and non-globin sequences (NuGEN Technologies, San Carlos, CA). Sequencing was performed in a 2x100bp format with 45 samples multiplexed on 3 lanes on an Illumina HiSeq 4000.

treatment_protocol: This investigation was a double blinded, placebo-controlled and randomized crossover study. Subjects were fed a test breakfast on the three test days in a random order with at least four weeks washout period between each test day. Subjects and study coordinators were blinded with respect to the treatments received with the test breakfast. Researchers handling samples and data did not know what treatments subjects received on all test days. The study diets were calculated by a registered dietitian using the Nutrition Data System for Research 2014 (Nutrition Coordinating Center, University of Minnesota) and produced using ProNutra (Viocare, Inc.) software programs. The registered dietitian coded the different test breakfasts, obtained a randomized list from a statistician, and assigned subjects sequentially as subject numbers were assigned. Subjects were instructed by a registered dietitian or study coordinator to follow a low polyphenol and low omega-3 FA diet and limit consumption of fruits; vegetables; soy; fatty fish (e.g., salmon); non-fatty fish, crustaceans, and mollusks (e.g., cod, lobster, clams, respectively); whole grains; flaxseed, walnut, canola, and other vegetable oils; nuts and seeds; coffee; tea; alcohol-based beverages; herbs, spices, and condiments; and chocolate starting 3 days before each test day. Participants were also allowed to take one study team-approved multivitamin per day that did not contain any added antioxidants (e.g., green tea extract). Between 6:00 p.m. and 8:00 p.m. on the night before each test day, subjects were instructed to eat a standardized dinner provided by the metabolic kitchen that included a sandwich (bagel, butter, egg patty, beef sausage, cheddar cheese), vanilla wafer cookies, chocolate-hazelnut spread, yogurt (yogurt, heavy cream, raspberry-flavored syrup), and lemonade. Subjects were instructed to refrain from eating or drinking anything after 8:00 p.m., except plain water; they were instructed to document the time they ate the meal and to document any deviations on the meal checklists provided with the meal. On each test day, subjects arrived at the WHNRC after a 12-h overnight fast. Subjects had their body temperature, blood pressure, and weight measured and had fasting blood withdrawn by venipuncture. Subjects were then fed a breakfast meal with a test smoothie supplemented with either placebo powder or blueberry powder and either placebo control oil or DHA oil. The breakfast meal included a sandwich (bagel, butter, egg patty, beef sausage, cheddar cheese) and vanilla wafer cookies. The test smoothie base used on all treatments contained nonfat milk, water, blackberry-flavored Italian soda syrup, heavy whipping cream, and xanthan gum. The test smoothie was supplemented with either placebo control powder (sucrose, wheat dextrin, artificial blueberry flavor, whey protein, high-oleic sunflower oil, maltodextrin, artificial red and blue food coloring, dextrose, ascorbic acid, citric acid, and silicon dioxide), placebo control oil (high-oleic sunflower oil), blueberry powder (freeze-dried 50/50 blend of Tifblue/Rubel (Vaccinium  virgatum (ashei)/Vaccinium corymbosum) blueberries), or DHA oil (algal vegetable oil from Schizochytrium sp.). The total energy of the meal and smoothie was 849 +/- 2.6 kcal with approx. 36.2% kcal from fat by calculation. This test meal is referred to as a high-fat  meal in this study. More specifically, it is a moderately high-fat, high-saturated-fat meal. The meals with the placebo, blueberry powder, or DHA smoothies contained 15.4 g, 15.4 g, or 14.9 g of saturated fat, respectively, primarily as palmitic acid and stearic acid. Subjects were given 20 min to consume the entire breakfast, after which they were provided water ad libitum and remained in the Metabolic Unit in the WHNRC until they completed the test day. Postprandial blood draws were conducted at 1, 3 and 6 h after consumption of the test meal.

tag: study subject id #

value: Male

tag: test day

tag: time of blood draw

value: 6 hr postprandial

tag: coded/blinded study arm

value: S

tag: unblinded study arm


title: CFUE_70

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TATGCA-s_3

tag: strain


title: Fertile female [980]

description: copy number

tag: gender

tag: reference dna gender

tag: reference dna cell line


title: Fertile female [952]

description: copy number

tag: tissue


title: CFUE_69

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TACTCC-s_3

tag: cell type


title: S. clavuligerus::pIB139_96h_rep1

description: Biological replicate 1 of 2. Control strain. pIB139_96h-rep1


title: S. clavuligerus::pIB139_84h_rep1

description: Biological replicate 1 of 2. Control strain. pIB139_84h-rep1


title: S27-D3-Fast

description:
S27-D3-Fast_S29
combinedCounts.txt
fixed_combinedCounts.txt

tag: Sex

value: fasting


title: Fertile female [942]

description: copy number


title: S. clavuligerus::pIB139_90h_rep1

description: Biological replicate 1 of 2. Control strain. pIB139_90h-rep1


title: S27-D3-3hr

description:
S27-D3-3hr_S30
combinedCounts.txt
fixed_combinedCounts.txt

value: 3 hr postprandial


title: S27-D2-6hr

description:
S27-D2-6hr_S28
combinedCounts.txt
fixed_combinedCounts.txt

value: T


title: Fertile female [979]

description: copy number


title: CFUE_68

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-CTCCTT-s_3


title: Fertile female [938]

description: copy number


title: Fertile female [1011]

description: copy number


title: CFUE_67

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-ATAGAG-s_3


title: Fertile female [940]

description: copy number


title: Fertile female [937]

description: copy number


title: Fertile female [935]

description: copy number


title: CFUE_66

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-AGGCTT-s_3


title: Fertile female [932]

description: copy number


title: Fertile female [936]

description: copy number


title: Fertile female [1247]

description: copy number


title: CFUE_65

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-AGAGGA-s_3


title: S27-D2-Fast

description:
S27-D2-Fast_S26
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [931]

description: copy number


title: Fertile female [927]

description: copy number


title: CFUE_64

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TCTTAC-s_3


title: S27-D1-6hr

description:
S27-D1-6hr_S25
combinedCounts.txt
fixed_combinedCounts.txt

value: R


title: S27-D1-3hr

description:
S27-D1-3hr_S24
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_63

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TCTACT-s_3


title: S27-D1-Fast

description:
S27-D1-Fast_S23
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [905]

description: copy number


title: Fertile female [924]

description: copy number


title: CFUE_61

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TACTCC-s_3


title: Fertile female [911]

description: copy number


title: S21-D3-6hr

description:
S21-D3-6hr_S22
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [904]

description: copy number


title: Fertile female [901]

description: copy number


title: S21-D3-3hr

description:
S21-D3-3hr_S21
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_62

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TATGCA-s_3


title: Fertile female [900]

description: copy number


title: S21-D3-Fast

description:
S21-D3-Fast_S20
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_60

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-CTCCTT-s_3


title: Fertile female [888]

description: copy number


title: Fertile female [890]

description: copy number


title: CFUE_59

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-ATAGAG-s_3


title: ItprKD1

description: third instar

value: 84h after egg laying larvae

value: Central Nervous Sytem

tag: phenotype

tag: genotype


title: Fertile female [886]

description: copy number


title: S21-D2-6hr

description:
S21-D2-6hr_S19
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [925]

description: copy number


title: Fertile female [926]

description: copy number


title: S21-D2-3hr

description:
S21-D2-3hr_S18
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_57

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-AGAGGA-s_3


title: Fertile female [920]

description: copy number


title: Fertile female [789]

description: copy number


title: Fertile female [741]

description: copy number


title: Fertile female [743]

description: copy number


title: S21-D2-Fast

description:
S21-D2-Fast_S17
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_56

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TCTTAC-s_3


title: CFUE_58

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-AGGCTT-s_3


title: S27-D2-3hr

description:
S27-D2-3hr_S27
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [735]

description: copy number


title: S21-D1-6hr

description:
S21-D1-6hr_S16
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_55

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TCTACT-s_3


title: Fertile female [739]

description: copy number


title: S21-D1-3hr

description:
S21-D1-3hr_S15
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [732]

description: copy number


title: CFUE_54

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TATGCA-s_3


title: S21-D1-Fast

description:
S21-D1-Fast_S14
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [728]

description: copy number


title: CFUE_53

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TACTCC-s_3


title: Fertile female [717]

description: copy number


title: Fertile female [716]

description: copy number


title: Fertile female [715]

description: copy number


title: CFUE_52

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-CTCCTT-s_3


title: Fertile female [712]

description: copy number


title: S17-D3-3hr

description:
S17-D3-3hr_S12
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_51

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-ATAGAG-s_3


title: Fertile female [711]

description: copy number


title: Fertile female [709]

description: copy number


title: S17-D3-Fast

description:
S17-D3-Fast_S11
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [751]

description: copy number


title: CFUE_50

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-AGGCTT-s_3


title: Fertile female [707]

description: copy number


title: Fertile female [699]

description: copy number


title: Fertile female [703]

description: copy number


title: Fertile female [702]

description: copy number


title: CFUE_49

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-AGAGGA-s_3


title: S17-D2-3hr

description:
S17-D2-3hr_S9
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_48

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TCTTAC-s_3


title: Fertile female [698]

description: copy number


title: S17-D2-Fast

description:
S17-D2-Fast_S8
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [697]

description: copy number


title: Fertile female [690]

description: copy number


title: S17-D3-6hr

description:
S17-D3-6hr_S13
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [821]

description: copy number


title: Fertile female [688]

description: copy number


title: S17-D1-6hr

description:
S17-D1-6hr_S7
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_46

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TATGCA-s_3


title: Fertile female [618]

description: copy number


title: Fertile female [621]

description: copy number


title: Fertile female [617]

description: copy number


title: S17-D1-Fast

description:
S17-D1-Fast_S5
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [610]

description: copy number


title: Fertile female [608]

description: copy number


title: CFUE_44

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-CTCCTT-s_3


title: S17-D2-6hr

description:
S17-D2-6hr_S10
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_45

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TACTCC-s_3


title: S9-D3-6hr

description:
S9-D3-6hr_S4
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_43

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-ATAGAG-s_3


title: Fertile female [606]

description: copy number


title: S9-D3-3hr

description:
S9-D3-3hr_S3
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [692]

description: copy number


title: Fertile female [603]

description: copy number


title: Fertile female [607]

description: copy number


title: CFUE_47

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TCTACT-s_3


title: Fertile female [604]

description: copy number


title: CFUE_42

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-AGGCTT-s_3


title: Fertile female [1113]

description: copy number


title: S17-D1-3hr

description:
S17-D1-3hr_S6
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [593]

description: copy number


title: CFUE_40

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TCTTAC-s_3


title: S9-D3-Fast

description:
S9-D3-Fast_S2
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [594]

description: copy number


title: CFUE_41

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-AGAGGA-s_3


title: S9-D2-6hr

description:
S9-D2-6hr_S76
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [589]

description: copy number


title: CFUE_39

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TCTACT-s_3


title: S9-D2-3hr

description:
S9-D2-3hr_S75
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [581]

description: copy number


title: Fertile female [580]

description: copy number


title: CFUE_38

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TATGCA-s_3


title: Fertile female [574]

description: copy number


title: Fertile female [565]

description: copy number


title: S9-D2-Fast

description:
S9-D2-Fast_S74
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [559]

description: copy number


title: CFUE_37

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TACTCC-s_3


title: CFUE_36

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-CTCCTT-s_3


title: Fertile female [556]

description: copy number


title: S9-D1-6hr

description:
S9-D1-6hr_S73
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_35

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-ATAGAG-s_3


title: Fertile female [551]

description: copy number


title: Fertile female [584]

description: copy number


title: S9-D1-Fast

description:
S9-D1-Fast_S71
combinedCounts.txt
fixed_combinedCounts.txt


title: S9-D1-3hr

description:
S9-D1-3hr_S72
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_34

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-AGGCTT-s_3


title: Fertile female [540]

description: copy number


title: Fertile female [548]

description: copy number


title: Fertile female [534]

description: copy number


title: Fertile female [530]

description: copy number


title: S2-D3-3hr

description:
S2-D3-3hr_S69
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [515]

description: copy number


title: CFUE_33

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-AGAGGA-s_3


title: CFUE_32

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TCTTAC-s_3


title: Fertile female [518]

description: copy number


title: S2-D3-Fast

description:
S2-D3-Fast_S68
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [494]

description: copy number


title: Fertile female [555]

description: copy number


title: Fertile female [510]

description: copy number


title: Fertile female [558]

description: copy number


title: Fertile female [493]

description: copy number


title: Fertile female [490]

description: copy number


title: CFUE_30

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TATGCA-s_3


title: Fertile female [550]

description: copy number


title: S2-D3-6hr

description:
S2-D3-6hr_S70
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_31

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TCTACT-s_3


title: S2-D2-3hr

description:
S2-D2-3hr_S66
combinedCounts.txt
fixed_combinedCounts.txt


title: S2-D2-Fast

description:
S2-D2-Fast_S65
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_29

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TACTCC-s_3


title: Fertile female [483]

description: copy number


title: CFUE_28

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-CTCCTT-s_3


title: Fertile female [489]

description: copy number


title: S2-D1-6hr

description:
S2-D1-6hr_S64
combinedCounts.txt
fixed_combinedCounts.txt


title: Fertile female [477]

description: copy number


title: S2-D1-Fast

description:
S2-D1-Fast_S62
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_27

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-ATAGAG-s_3


title: POI female [PPOF-045]

description: copy number


title: S2-D1-3hr

description:
S2-D1-3hr_S63
combinedCounts.txt
fixed_combinedCounts.txt


title: CFUE_26

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-AGGCTT-s_3


title: POI female [PPOF-039]

description: copy number


title: POI female [PPOF-095]

description: copy number


title: POI female [PPOF-042]

description: copy number


title: S2-D2-6hr

description:
S2-D2-6hr_S67
combinedCounts.txt
fixed_combinedCounts.txt


title: IPF 4 TGFβ treated [IPFC4TGF]

city: La Jolla

first: Paul

last: Insel

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

data_processing:
FASTQC for verifying quality of sequencing
Transcript expression was quantified using Kallisto v0.43.1 with mean fragment length = 190 and standard deviation of fragment length = 20, using the human Ensembl release 79 reference transcriptome
Gene-level quantifications of estimated counts were obtained using tximport
Genome_build: hg38, with ensembl v79 annotations
Supplementary_files_format_and_content: excel files with gene expression in TPM and counts

source_name: IPF TGFβ treated

growth_protocol: RPMI + 10% FBS + Antibiotics, at 37 deg C, and 5% CO2

extract_protocol:
Fibroblasts were taken down using Qiagen's RLT lysis buffer, followed by RNA extraction using RNeasy mini kits, with on-column DNase digestion.
Truseq stranded mRNA (Illumina)

treatment_protocol: Treated with TGFβ at 1nM for ~16 hrs, as indicated per sample

value: lung

value: human lung fibroblasts (HPFs)

tag: sample group

value: IPF (Idiopathic Pulmonary Fibrosis) HPFs

tag: treatment

value: Treated with TGFβ at 1nM for ~16 hrs


title: IPF 4 Untreated [IPFC4UT]

source_name: IPF Untreated

value: Untreated


title: POI female [PPOF-037]

description: copy number

value: Female

value: peripheral blood

value: pooled


title: CFUE_25

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-AGAGGA-s_3

value: CFUE


title: IPF 2 TGFβ treated [IPFC2TGF]


title: POI female [PPOF-031]

description: copy number


title: POI female [PPOF-036]

description: copy number


title: CFUE_24

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TCTTAC-s_3


title: POI female [PPOF-034]

description: copy number


title: Fertile female [465]

description: copy number


title: CFUE_23

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TCTACT-s_3


title: POI female [PPOF-017]

description: copy number


title: POI female [PPOF-029]

description: copy number


title: POI female [PPOF-028]

description: copy number


title: IPF 1 TGFβ treated [IPFC1TGF]


title: IPF 2 Untreated [IPFC2UT]


title: CFUE_22

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TATGCA-s_3


title: POI female [PPOF-016]

description: copy number


title: CFUE_21

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TACTCC-s_3


title: POI female [PPOF-014]

description: copy number


title: IPF 1 Untreated [IPFC1UT]


title: CFUE_20

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-CTCCTT-s_3


title: CFUE_19

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-ATAGAG-s_3


title: Control 3 Untreated [CtrC3UT]

source_name: Control Untreated

value: Normal HPFs


title: POI female [PPOF-009]

description: copy number

source_name: peripheral blood


title: P7_2_rep1

city: Bethesda

first: Daniel

middle: L

last: Kastner

state: MD

address: 9000 Rockville Pike

department: NHGRI

institute: NIH

data_processing:
RNA-seq reads were mapped against GRCh38 using hisat 2.2.1.0. Mapped reads were quantified using HTSeq. All the count data were normalized by total mapped reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read-count text file

source_name: patient_blood RNA

extract_protocol:
Total RNA was isolated from whole blood collected in PAXgene Blood RNA Tubes using PAXgene Blood RNA Kit (PreAnalytiX) per manufacturer’s instructions
Total RNA was used for cDNA library preparation using the TruSeq Stranded mRNA Library Preparation kit for NeoPrep (Illumina). Sequencing was performed on an Illumina HiSeq 3000 System in a 1 x 50 bp single read mode

tag: subject status

value: patient with heterozygous mutation in RIPK1 cleavage site (p.D324Y)

value: whole blood


title: P7_1_rep2


title: POI female [PPOF-007]

description: copy number

source_name: Promega


title: P7_1_rep1


title: C2_rep2

source_name: control_blood RNA

value: control


title: CFUE_16

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TCTTAC-s_3

source_name: colony forming unit-erythroid


title: POI female [IPOF-047]

description: copy number


title: Control 1 TGFβ treated [CtrC1TGF]

source_name: Control TGFβ treated


title: Fertile female [464]

description: copy number


title: CFUE_17

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-AGAGGA-s_3


title: C2_rep1


title: CFUE_18

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-AGGCTT-s_3


title: Control 2 Untreated [CtrC2UT]


title: Control 2 TGFβ treated [CtrC2TGF]


title: C1_rep2


title: POI female [PPOF-001]

description: copy number


title: CFUE_14

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TATGCA-s_3


title: P7_2_rep2


title: POI female [IPOF-046]

description: copy number


title: CFUE_15

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TCTACT-s_3


title: CFUE_13

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TACTCC-s_3


title: POI female [IPOF-043]

description: copy number


title: POI female [PPOF-010]

description: copy number


title: POI female [IPOF-042]

description: copy number


title: CFUE_11

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-ATAGAG-s_3


title: POI female [IPOF-045]

description: copy number


title: ChIP_HySp5_dDBD

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: Cells were transfected with the HySp5 promoter

library_source: genomic

data_processing:
Adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation). Then reads were mapped using bowtie2  (ref Langmead et al. 2012 version 2.2.4 default parameters).
The peaks and the coverage were obtained as the output of MACS2 (ref Zhang et al 2008 version 2.1.1.20160309 command line: macs2 callpeak -t input.bam --call-summits -B).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph of the ChIPseq read coverage, divided by the number of millions of mapped reads in each sample.

source_name: Immunoprecipitated Chromatin from Hek cells transfected with HySp5_dDBD expression plasmid

growth_protocol: HEK293T cells, a kind gift from the laboratory of Ariel Ruiz i Altaba (University of Geneva Medical School), were maintained in DMEM High Glucose + 1mM Na pyruvate + 6mM L-glutamine + 10% fetal bovine serum.

extract_protocol:
24 hours after transfection, cells were collected by scraping, washed twice in pre-warmed culture medium and fixed in 1% FA solution (Sigma) for 15 minutes. The fixative was quenched by adding Glycine (125 mM) and incubation for 3 minutes. The cells were washed once in ice-cold PBS and re-suspended in 5 mL chromatin prep buffer (Active Motif), containing 0.1mM PMSF and 0.1% protease inhibitor cocktail (PIC). To release the nuclei the sample was transferred into a pre-cooled 15 mL glas Douncer and dounced with 30 strokes. After 10 minutes incubation on ice and centrifugation at 1250 g for 5 minutes at 4°C, the nuclei were re-suspended in 500 uL sonication buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1 mM PMSF, 1% PIC). Following another 10 minutes incubation on ice, the chromatin was sonicated with a Bioblock Scientific VibraCell 75042 sonicator (Amplitude: 25%, Time: 12 minutes, 30 seconds on, 30 seconds off, 24 cycles). Note: The sonication conditions were optimized to have a fragmentation size of around 250 bp. Then 100 uL of the sonicated chromatin was added to 900 uL ChIP dilution buffer (0.1% NP-40, 0.02 M HEPES pH 7.3, 1 mM EDTA pH 8.0, 0.15 M NaCl, 1 mM PMSF, 1% PIC) and incubated with 4 ug anti-HA antibody (NB600-363, Novus Biologicals) over night at 4°C on a rotator. Next, the sample was loaded on a ChIP-IT ProteinG Agarose Column (Active Motif) and incubated for 3 hours at 4°C on a rotator. The column was washed 6 times with 1 mL buffer AM1 (Active Motif) and the DNA eluted with 180 uL of pre-warmed buffer AM4 (Active Motif). The sample was decrosslinked by adding 30 uL 10x TE buffer, 18 uL 5 M NaCl, 57 uL H2O and incubated for 5 hours at 65°C. 5 uL of RNAse A (10 ug/uL) was added and the sample incubated at 37°C for 30 minutes before adding 10 uL of Proteinase K (10 ug/uL), and further incubation for 2 hours at 55°C. The DNA was purified with the MiniElute PCR purification kit (Qiagen). For preparing the Input DNA, 5 uL sonicated chromatin was added to 5 uL 5M NaCL in 40 uL H2O, and incubated for 15 minutes at 95°C. Next the sample was incubated at 37°C for 5 minutes with 2.5 uL of RNAse A (10 ug/ul), 2.5 uL PK (10 ug/uL) was then added, and the incubation continued at 55°C for 30 minutes. 10 uL were taken for purification (MiniElute PCR purification kit from Qiagen).
5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

treatment_protocol: HEK293T cells were seeded into a 10 cm dish (920 000 cells) and transfected  18-19 hours later with X-tremeGENETM HP DNA transfection reagent (Roche).  Plasmids used were: HySp5-420, ZfSp5-377, HySp5-ΔDBD-337, ZfSp5-ΔDBD-289, 3666 ng

tag: cell line

tag: transfected with

tag: age post-transfection

tag: antibody

value: anti-HA (Novus biologicals NB600-363)


title: C1_rep1


title: POI female [IPOF-041]

description: copy number


title: POI female [IPOF-036]

description: copy number


title: ChIP_ZfSp5_dDBD

description: Cells were transfected with the ZfWnt3 promoter

source_name: Immunoprecipitated Chromatin from Hek cells transfected with ZfSp5_dDBD expression plasmid


title: TIC_ZfSp5

source_name: Total input Chromatin from Hek cells transfected with zFSp5 expression plasmid


title: POI female [IPOF-044]

description: copy number


title: POI female [IPOF-039]

description: copy number


title: RJ-S1

city: Shanghai

first: Xue

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

country: China

institute: SJTU CHINA

data_processing:
9918 barcodes that contain more than 5039 unique molecular identifiers (UMIs) were identify as cells by the Cell Ranger Single Cell Software.
Poor-quality cells with less than 1000 genes detected or more than 5% UMI mapped to mitochondria genes were further removed. This lead to 9833 high-quality single cell RNA-seq data with an average gene detected to be around 2400.
10x Genomics workflow and Cell Ranger Single Cell Software was used to process raw sequencing data and to align reads to the mm10 mouse reference genome.
Normalized gene expression values were calculated by dividing UMI of each gene by a size factor that was computed using Cell Ranger pipeline (version no. 2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: Data1.Epi.Clusters.DGEs.Markers.xlsx

source_name: FACS prostate basal cells

growth_protocol: Tempreture is 25℃ and the humidity is 50%, 14h lights on/ 10h lights off.

extract_protocol:
P14 mouse prostate tissues were got and digested with collagenase and trypsin/EDTA. Single cell suspension was obtained from passing through a 40µm cell strainer and then counted manually before processing to single cell RNA-seq library preparation. 1x 104 cells  were used for the construction of sequencing libraries.
Libraries were constructed following the instruction of the Chromium single cell 3’ solution (10x Genomics). The libraries were sequenced on Illumina Hiseq X Ten platform.

treatment_protocol: Normal growth condtion

value: prostate tissue cells

tag: developmental stage

value: postnatal 14


title: CFUE_12

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-CTCCTT-s_3

tag: strain


title: POI female [IPOF-035]

description: copy number

tag: gender


title: CFUE_10

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-AGGCTT-s_3


title: Control 1 Untreated [CtrC1UT]


title: POI female [IPOF-040]

description: copy number

tag: reference dna gender


title: ChIP_ HySp5

source_name: Immunoprecipitated Chromatin from Hek cells transfected with HySp5 expression plasmid


title: CFUE_5

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TACTCC-s_3


title: TIC_HySp5_dDBD

source_name: Total input Chromatin from Hek cells transfected with HySp5_dDBD expression plasmid


title: POI female [IPOF-033]

description: copy number

tag: reference dna cell line


title: TIC_HySp5

source_name: Total input Chromatin from Hek cells transfected with HySp5 expression plasmid


title: POI female [IPOF-030]

description: copy number

tag: tissue


title: Control 3 TGFβ treated [CtrC3TGF]

tag: cell type


title: CFUE_8

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TCTTAC-s_3


title: CFUE_9

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-AGAGGA-s_3


title: TIC_ZfSp5_dDBD

source_name: Total input Chromatin from Hek cells transfected with ZfSp5_dDBD expression plasmid


title: CFUE_6

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TATGCA-s_3


title: CFUE_4

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-CTCCTT-s_3


title: CFUE_7

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TCTACT-s_3


title: POI female [IPOF-027]

description: copy number


title: day 14 IRI group #3

city: Miyazaki

first: Masahiro

last: Ikeda

state: Miyazaki

address: 1-1 Gakuenkibanadai-Nishi

department: Faculty of Agriculture

country: Japan

institute: University of Miyazaki, Miyazaki

hyb_protocol: biotin labeled miRNA was hybridized to Affymetrix GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with  with median polish summarization and quantile normalization by Affymetrix® Transcriptome Analysis Console Software, and obtained normalized intensity values.

organism: Rattus norvegicus

source_name: sample 14 days after IRI surgery individual#3

label_protocol: 130ng of total RNAs were labeled  using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

extract_protocol: Total RNAs including miRNAs were isolated and purified from cells using miRNeasy Mini Kit  (Qiagen)　according to the manufacturer's instructions.

value: whole kidney

value: male

tag: age

value: 7 weeks old at surgery


title: CFUE_3

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-ATAGAG-s_3


title: POI female [IPOF-029]

description: copy number


title: CFUE_2

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-AGGCTT-s_3


title: CFUE_1

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-AGAGGA-s_3


title: POI female [IPOF-028]

description: copy number


title: day 14 sham group #3

source_name: sample 14 days after sham surgery individual#3


title: day 14 sham group #2

source_name: sample 14 days after sham surgery individual#2


title: POI female [IPOF-026]

description: copy number

source_name: peripheral blood


title: BFUE_96

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TCTTAC-s_2

source_name: burst forming unit-erythroid

value: BFUE


title: BFUE_95

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TCTACT-s_2


title: POI female [IPOF-023]

description: copy number

source_name: Promega


title: day 14 sham group #1

source_name: sample 14 days after sham surgery individual#1


title: POI female [IPOF-025]

description: copy number


title: day 14 IRI group #2

source_name: sample 14 days after IRI surgery individual#2


title: day 3 IRI group #3

source_name: sample 3 days after IRI surgery individual#3


title: BFUE_93

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TACTCC-s_2


title: POI female [IPOF-022]

description: copy number


title: day 3 IRI group #2

source_name: sample 3 days after IRI surgery individual#2


title: day 14 IRI group #1

source_name: sample 14 days after IRI surgery individual#1


title: BFUE_92

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-CTCCTT-s_2


title: day 3 IRI group #1

source_name: sample 3 days after IRI surgery individual#1


title: BFUE_91

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-ATAGAG-s_2


title: POI female [IPOF-021]

description: copy number


title: POI female [IPOF-020]

description: copy number


title: BFUE_90

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-AGGCTT-s_2


title: day 3 sham group #3

source_name: sample 3 days after sham surgery individual#3


title: POI female [IPOF-017]

description: copy number


title: day 1.5 IRI group #6

source_name: sample 1.5 days after IRI surgery individual#3


title: POI female [IPOF-013]

description: copy number


title: BFUE_89

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-AGAGGA-s_2


title: POI female [IPOF-018]

description: copy number


title: day 1.5 IRI group #5

source_name: sample 1.5 days after IRI surgery individual#2


title: BFUE_94

description:
BFUE_CFUE.counts.txt.gz
TCCTGAG-TATGCA-s_2


title: BFUE_88

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TCTTAC-s_2


title: POI female [IPOF-009]

description: copy number


title: day 3 sham group #1

source_name: sample 3 days after sham surgery individual#1


title: day 1.5 IRI group #4

source_name: sample 1.5 days after IRI surgery individual#1


title: BFUE_86

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TATGCA-s_2


title: day 1.5 sham group #3

source_name: sample 1.5 days after sham surgery individual#3


title: POI female [IPOF-007]

description: copy number


title: POI female [IPOF-006]

description: copy number


title: POI female [IPOF-008]

description: copy number


title: POI female [IPOF-003]

description: copy number


title: BFUE_85

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TACTCC-s_2


title: day 3 sham group #2

source_name: sample 3 days after sham surgery individual#2


title: Macrophage LDM rep2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequenced reads were aligned to the mm9 mouse (for RAW 264-7) or hg19 human genome (for T-cell) assembly using STAR
Uniquely aligned reads were quantified at exons of annotated genes and normalized to sequence depth and gene length using HOMER. The number of reads per kilobase per million mapped (RPKM) for all RefSeq annotated genes were calculated
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all annotated genes for each sample

source_name: Macrophage

growth_protocol: Cells were resuspended in a mix of rat tail collagen type I (Corning), 0.02N acetic acid, 10x DMEM with Phenol Red (Sigma Aldrich) and 10x reconstitution buffer (0.2M Hepes (Gibco) and 0.262M NaHCO3). To neutralize the pH, 2N NaOH was added to the reconstitution buffer before use. For all cell lines, low density (LD) and high density (HD) gels contained 1 mg/ml and 4 mg/ml collagen type I respectively. First, 300 to 400 μl of the collagen solution was plated per well of a non-tissue culture treated 24-wells plate (Corning) and allowed to polymerize at 37ºC for at least 30 min. Afterwards a second layer of collagen solution containing the cells was seeded on top of the first gel and allowed to polymerize for 1-2 h at 37ºC, after which 600 μl of culture media was added. For culturing cells in 2D conditions (no matrix), the same number of cells were seeded in the wells of a tissue culture treated 24-well plate.

extract_protocol:
Cells were treated with 3 mg/ml collagenase solution for 45-60 min to extract them from the gels and subsequently RNA was isolated using RNeasy Mini purification kit (Qiagen)
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA (1000 ng) was prepared for sequencing using polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina. Library quality was assessed using the Fragment Analyzer (AATI) followed by library quantification (Illumina library quantification kit). Sequencing was carried out on a HiSeq1500 platform (Illumina) with a read length of 50 bp.

treatment_protocol: Cells were cultured in high or low density type I collagen matrix. Control cells (no matrix) were cultured on rgular tissue culture treated plastic without type I collagen matrix.

value: 1mg/ml Type I collagen

tag: culture

value: low density matrix


title: BFUE_82

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-AGGCTT-s_2


title: BFUE_84

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-CTCCTT-s_2


title: day 1.5 sham group #1

source_name: sample 1.5 days after sham surgery individual#1


title: day 1.5 sham group #2

source_name: sample 1.5 days after sham surgery individual#2


title: Macrophage LDM rep3


title: BFUE_81

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-AGAGGA-s_2

source_name: burst forming unit-erythroid


title: BFUE_83

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-ATAGAG-s_2


title: Macrophage LDM rep1


title: Macrophage noM rep2

value: plastic

value: no matrix


title: POI female [IPOF-005]

description: copy number

source_name: peripheral blood

value: Female

value: peripheral blood

source_name: Promega

value: pooled


title: BFUE_87

description:
BFUE_CFUE.counts.txt.gz
TAGGCAT-TCTACT-s_2


title: POI female [BPOF-123]

description: copy number


title: POI female [IPOF-002]

description: copy number


title: BFUE_79

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TCTACT-s_2


title: BFUE_78

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TATGCA-s_2


title: Macrophage HDM rep3

value: 4mg/ml Type I collagen

value: high density matrix


title: BFUE_80

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TCTTAC-s_2


title: Macrophage noM rep3


title: POI female [BPOF-124]

description: copy number


title: Macrophage noM rep1


title: POI female [BPOF-122]

description: copy number


title: BFUE_76

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-CTCCTT-s_2


title: Macrophage HDM rep2


title: BFUE_74

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-AGGCTT-s_2


title: BFUE_75

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-ATAGAG-s_2


title: POI female [BPOF-120]

description: copy number


title: POI female [BPOF-115]

description: copy number


title: BFUE_73

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-AGAGGA-s_2


title: Macrophage HDM rep1


title: POI female [BPOF-109]

description: copy number


title: BFUE_72

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TCTTAC-s_2


title: 019_10d_ecto_hiGFP_D

first: Yvan

last: Wenger

state: Geneva

address: 30 Quai Ernest-Ansermet

description: 10 days starvation, high GFP selection

data_processing:
Adapter and removal of known trans-spliced leader: Cutadapt 1.11 (--trim-n -m 50 -q 5)
Generation of pseudo counts: Salmon 0.7.2 (--libType SR --seqBias --gcBias)
Normalization using DESeq2
Reference transcriptome (Fasta): Hv_AEP_transcriptome.fasta.gz
Genome_build: Hv_AEP_transcriptome.fasta.gz
Supplementary_files_format_and_content: counts2017_stem.csv.gz: Raw abundance measurements (estimated counts)
Supplementary_files_format_and_content: normacounts_stem2017.csv.gz: Normalized abundance measurements (estimated counts)

organism: Hydra vulgaris

source_name: Central body column (no apical/basal regions), FACS

growth_protocol: 3 feedings per weeks

extract_protocol:
Qiagen RNeasy, followed by polyA enrichment
Illumina TruSeq, directional

treatment_protocol: No treatment

value: AEP

tag: transgenics

tag: egfp expression

value: eESC (epidermal epithelial stem cells)

tag: time point

value: 10 days starvation, high GFP selection


title: 022_10d_endo_hiGFP_C

description: 10 days starvation, high GFP selection

value: gESC (gastrodermal epithelial stem cells)


title: 018_10d_ecto_hiGFP_C

description: 10 days starvation, high GFP selection


title: 020_10d_endo_hiGFP_A

description: 10 days starvation, high GFP selection


title: 021_10d_endo_hiGFP_B

description: 10 days starvation, high GFP selection


title: POI female [BPOF-107]

description: copy number


title: POI female [BPOF-125]

description: copy number


title: BFUE_71

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TCTACT-s_2


title: POI female [BPOF-106]

description: copy number


title: BFUE_69

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TACTCC-s_2


title: 017_10d_ecto_hiGFP_B

description: 10 days starvation, high GFP selection


title: 016_10d_ecto_hiGFP_A

description: 10 days starvation, high GFP selection


title: POI female [BPOF-108]

description: copy number