title: Wild_Type_DMSO_Replicate_3

value: Wild-type

value: Adult

tag: treatment


title: Pou2f3.mTEC.rep#3

status: Public on Jun 16 2022

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description: CUT&Tag

library_source: genomic

data_processing:
Library strategy: CUT&Tag
Low quality reads were discared using Trimmomatic (v0.36)
Reads were mapped to the mouse reference genome (mm10) with bowtie2 (v2.29) using parameters --local --very-sensitive -no-mixed --no-discordant -I 10 -X 700
Bam files were generated and multimapping reads removed by samtools (v1.3.1), and duplicate reads were removed by picard (v2.8.0)
Bigwig files were generated using deeptools (v3.0.2) with counts-per-million normalization
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
mTECs were washed in wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), bound to concavalin A beads (Bangs Laboratories), permeabilized in wash buffer plus 0.05% digitonin, and incubated overnight with 1:50 primary antibody (anti-H3K27ac [Abcam], -Hnf4α [Abcam], -Grhl1 [Novus], -Pou2f3 [Sigma], or -IgG [Rockland]) at 4°C in wash buffer plus 0.05% digitonin, 2mM EDTA and 0.1% BSA. The next day, H3K27ac, Grhl1, IgG, and some Pou2f3 samples were lightly fixed with 0.1% paraformaldehyde at room temperature for 2 minutes before proceeding. (We and others have observed improved CUT&Tag signal-to-noise ratio for some TFs with light fixation.) Samples were incubated with secondary antibody (guinea pig anti-rabbit [Rockland] for H3K27ac, Grhl1, Pou2f3, and IgG; rabbit anti-mouse [Abcam] for Hnf4α) at 1:100 for 1 hour at room temperature in wash buffer plus 0.05% digitonin. Samples were washed and incubated with pA-Tn5 (Addgene #124601, gift from Steve Henikoff, purified in-house) at 1:200 for 1 hour at room temperature in 300mM NaCl wash buffer plus 0.01% digitonin. Samples were washed twice then tagmented for 1 hour at 37°C in 300mM NaCl wash buffer plus 0.01% digitonin and 10mM MgCl.
Tagmentation was halted with EDTA, sodium dodecyl sulfate and proteinase K for 1 hour at 55°C. Tagmented DNA was phenol-chloroform extracted and amplified by PCR with NEBNext 2X Master Mix (NEB) using the following program: 72°C for 2min, 98°C for 30s, 16 cycles of 98°C for 10s and 63°C for 10s, 72°C for 1min, hold. Amplified libraries were quantified by Qubit (Thermo) and Tapestation (Agilent).

treatment_protocol: mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, and flow sorting mTECs into DMEM/10%FCS.

tag: strain

tag: genotype

value: WT

tag: cell type

value: mTEC


title: WT.3D0

city: London,

first: Khaleda Afrin

last: Bari

state: ON

address: 1151 Richmond St

department: Anatomy and Cell Biology

country: Canada

institute: Western University

library_source: transcriptomic

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to S. cerevisiae whole genome using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Assembly: Saccharomyces cerevisiae S288C reference genome (assembly R64-2-1)
Supplementary files format and content: Raw gene counts table for every gene and every sample
Supplementary files format and content: Normalized counts text files for each gene for each sample

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Strains were grown to mid-log phase in synthetic complete media

extract_protocol:
RNA was extracted using the MasterPure Yeast RNA purification kit (Lucigen) according to the manufacturer’s instructions.
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1


title: Pou2f3.mTEC.rep#2

description: CUT&Tag


title: Wild_Type_DMSO_Replicate_2

city: Worcteser

first: SUSHILA

last: BHATTACHARYA

address: Albert Sherman Center, Room 5.1051 386 Plantation St.

department: Department of Systems Biology (DSB)

institute: UMass Chan Medical School

data_processing:
BGI internal software "SOAPnuke" was used to remove adaptors and low quality reads with parameters: -n 0.001 -l 20 -q 0.4 -A 0.25. Low quality reads are defined as having greater than 40% bases whose quality is less than 20.
Reads were aligned to the reference genome using Bowtie2 with default parameters.
RSEM was used for estimation of read counts with default parameters
The Deseq2 package in R 3.6.3 was used for differential expression analysis.
Assembly: c_elegans.PRJNA13758 (WormBase WS271)
Supplementary files format and content: tab dilimeted file containing TPM matrix for all samples and all genes

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were maintained on NGM-agar on an E. coli OP50 diet prior to experiment. They were synchronized by an 18 hour L1 arrest post-buffered bleach treatment.

extract_protocol:
A minumum of 1000 staged animals were collected and washed thrice in M9 bufferRNA was extracted from early adult stage animals and purified using Direct-zol RNA Miniprep Kit (Zymo Research) R2050)
BGI standard protocol

treatment_protocol: Synchronized L1 animals were grown on NGM-agar- 0.3µM Antimycin A in DMSO E. coli HT115 with DMSO E. coli HT115 as control

tag: Stage

value: grown on NGM + DMSO + E. coli HT115


title: WT.2D0


title: Human-Kidney-snATAC-seq Sample 2, snATAC-seq

city: Philadelphia

first: Hongbo

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: 10x single-cell ATAC-seq kit

data_processing:
After quality control, the library was sequenced on an Illumina NovaSeq 6000 paired-end kits. We integarated this new datasets (four samples) and our previous datasets (two samples, GSE172008) and obtaiend the open chromatin information of 61,440 high quality cells. Reads were aligned to human genome (hg19) with SnapATAC (v2.0). After quality control and peak calling, a cell-gene activity score matrix was built by integrating all fragments overlapping with gene transcripts (in GENCODE v19 annotations). Cluster annotation was performed using a published list of cell-type marker genes, and 13 main clusters were identified (Proximal tubule segment 1, Proximal tubule segment 2, Proximal tubule segment 3, Loop of Henle, Distal convoluted tubule, Collecting duct principal cell, Collecting duct intercalated cell, Podocyte, Endothelial, Stroma, Immune, Lymph cell and injured proximal tubule). The injured proximal tubule cells were not included in further analysis due to its potential disease status. For each of remained 12 clusters (57,229 cells), we identified cell type-specific differentially accessible regions (DARs) by one-sided Fisher’s exact test between a given cell type and each of the other cell types for each of 410,994 peaks. Peaks with FDR < 0.05 and fold change > 1 in at least half of pairwise comparisons were defined as cell type specific DARs, thus allowing inclusion of DARs shared by closely related cell types (the three segments of proximal tubules).
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: Kidney

growth_protocol: Human kidney samples were obtained from the non-tumor tissue of partial or radical nephrectomy patients from the Hospital of the University of Pennsylvania

extract_protocol:
Kidneys were minced and lysed in 2 mL lysis buffer for 15 min. Tissue lysis reaction was then blocked by adding 10 mL 1x PBS into each tube, and solution was passed through a 40 μm cell strainer. Cell debris and cytoplasmic contaminants were removed by Nuclei PURE Prep Nuclei Isolation Kit (Sigma, NUC-201) after centrifugation at 13,000 RPM for 45 min.  Libraries were prepared according to 10x Genomics's instructions (CG000209) accompanying the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1.  Single nuclei ATAC-seq
Single nucleus ATAC-seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit according to manufacturer’s manual.

tag: tissue

value: Kidney

tag: gender

value: Female

tag: age

value: 85 years old

tag: race

value: White


title: Pou2f3.mTEC.rep#7

description: CUT&Tag


title: WT.1D0


title: Wild_Type_DMSO_Replicate_1


title: Pou2f3.mTEC.rep#1

description: CUT&Tag


title: +Asn H3K4me3 rep2

city: Indianapolis

first: Ji

last: Zhang

state: IN

address: 1044 W Walnut Street, R4-170

department: Pediatrics

institute: Indiana University

data_processing:
Base calling and quality scoring were performed in Illumina NovaSeq 6000
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.4.4), PICARD (v2.18.26) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.2.7.1) were used to call peaks using Input as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Assembly: hg38
Supplementary files format and content: Bigwig file showing the normalized read signal, merged peak file

growth_protocol: RS4;11 cells were cultured in each condition for 24 hours. Around 10 million cells were used per collection.

extract_protocol:
For H3K4me3 ChIP-seq, we used the Covaris truChIP Chromatin Shearing Reagent Kit; for RNA-seq, we used Trizol for whole cell RNA extraction.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ferric Nitrate was added at 10 µM in the presence of 0.75 µM Hinokitiol

tag: cell line

value: complete medium

tag: chip antibody


title: Human-Kidney-snATAC-seq Sample 1, snATAC-seq

description: 10x single-cell ATAC-seq kit


title: PADP6+∆ldh1 iron unchelated, PALDH_RP52

status: Public on Jun 15 2022

city: Singapore

first: Casandra

last: Tan

address: 60 Nanyang Drive

country: Singapore

institute: SCELSE

description:
PADP6 + ∆ldh1 total RNA
PALDH_RP52
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt

data_processing:
Raw reads were quality and adapter trimmed using bbduk from BBMap tools (Version 39.79).
Trimmed reads were then mapped using bwa-mem of BWA (Version 0.7.17-r1188) with options “-T 20 -k 13” against E. faecalis OG1RF (NCBI accession: CP002621) or P. aeruginosa PAO1 (NCBI accession: NC_002516) reference genomes.
Reads mapped to predicted open reading frames were quantified using htseq-count of HTSeq (Version 0.12.4) with option “-m intersection-strict”.
Ribosomal sequences were filtered out from all data sets.
Differential gene expression analysis was performed in R using edgeR (Version 3.28.1).
Genome_build: E. faecalis OG1RF (NCBI accession: CP002621) and P. aeruginosa PAO1 (NCBI accession: NC_002516).
Supplementary_files_format_and_content: toOG1RF.txt, toPAO1.txt (Text files containing raw counts of sequencing reads for each sample mapped to E. faecalis OG1RF or P. aeruginosa PADP6.)
Supplementary_files_format_and_content: *VS*.txt (Normalized counts using edgeR for every comparison made. )
Supplementary_files_format_and_content: *conditions.txt (Sample metadata csv file used in DGE analysis in edgeR.)

organism:
Pseudomonas aeruginosa
Enterococcus faecalis

source_name: P. aeruginosa PADP6 + E. faecalis ∆ldh1 macrocolonies on TSBG agar (mixed-species)

growth_protocol: Single-species (E. faecalis OG1RF, E. faecalis ∆ldh1 or P. aeruginosa PADP6) and mixed-species (PADP6+OG1RF or PADP6+∆ldh1) macrocolonies grown in TSBG agar (TSB supplemented with 10 mM glucose) at 37ᵒC for 48 hours.

extract_protocol:
Macrocolonies were first scraped into RNAprotect™ Bacteria Reagent and bacteria pellets were then subjected to total RNA extraction using RNeasy® mini kit with slight modifications. Briefly, cell pellets were resuspended in TE buffer containing 20 mg/mL lysozyme and further supplemented with 20 µL proteinase K. Followed by incubation at 37 °C for 1 h, and subsequent extraction steps was performed according to manufacturer’s protocol. Extracted RNA samples were treated with DNase (TURBO DNA-free™ kit, Invitrogen, USA) and purified using Monarch® RNA cleanup kit.
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.

treatment_protocol: Macrocolonies were grown in TSBG agar with or without 2 mM 2,2’ bipyridyl.

tag: genotype mapped

value: PADP6, OG1RF

tag: growth protocol

value: iron replete

tag: condition

value: mixed

tag: e. faecalis strain


title: PADP6+∆ldh1 iron chelated, PALDH_DP60

description:
PADP6 + ∆ldh1 total RNA
PALDH_DP60
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt

source_name: P. aeruginosa PADP6 + E. faecalis ∆ldh1 macrocolonies on iron chelated TSBG agar (mixed-species)

value: iron deplete


title: PADP6+∆ldh1 iron unchelated, PALDH_RP53

description:
PADP6 + ∆ldh1 total RNA
PALDH_RP53
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: PADP6+∆ldh1 iron chelated, PALDH_DP58

description:
PADP6 + ∆ldh1 total RNA
PALDH_DP58
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: PADP6+OG1RF iron unchelated, PAEF_RP39

description:
PADP6 + OG1RF total RNA
PAEF_RP39
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt

source_name: P. aeruginosa PADP6 + E. faecalis OG1RF macrocolonies on TSBG agar (mixed-species)


title: PADP6+∆ldh1 iron chelated, PALDH_DP55

description:
PADP6 + ∆ldh1 total RNA
PALDH_DP55
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: PADP6+OG1RF iron unchelated, PAEF_RP37

description:
PADP6 + OG1RF total RNA
PAEF_RP37
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: Molting dataset: Entire leg, from animal 58, collected 2 days relative to molting [M+2_58]

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 Av. Tony Garnier

country: France

institute: CNRS

data_processing:
Reads were mapped to custom made gene models built on the Phaw_5.0 genome assembly, using kallisto v. 0.42.5 (Bray et al. 2016).
We noticed that some genes were erroneously split in our gene annotation (genes described in the gtf file and referred by 'gene_ID' in the correspondance table). The split genes we identified were kept unmodified in the gtf file because the exact positions of the exon junctions were not known. Merging was done after read mapping by simply adding up the read counts or tpm of the split genes. The list of those modified gene models are referred to by 'RNAseq_gene_ID' in the correspondance table. Count and tpm levels are provided for those merged genes only.
Genome_build: Phaw_5.0 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001587735.2/)
Supplementary_files_format_and_content: Gene model annotation of the genome, on which the reads were mapped (gtf format)
Supplementary_files_format_and_content: Correspondance table between gene names from the annotation on which reads were mapped (column gene_ID) and gene names processed in the count and tpm matrices (column RNAseq_gene_ID)
Supplementary_files_format_and_content: Table of gene abundance measurements, in counts (1 value per gene per sample)
Supplementary_files_format_and_content: Table of gene abundance measurements, in tpm (1 value per gene per sample)

molecule: polyA RNA

organism: Parhyale hawaiensis

source_name: Entire adult T4 leg

growth_protocol:
To grow animals prior to collecting embryonic limbs, Parhyale females of the Chicago-F inbred line (Kao et al. 2016) were collected after fertilization, and their embryos removed about 3 days post fertilization. Each brood was kept separately, in a temperature-controlled incubator set to 27˚C, in sterile 6-well plates (Costar, #3516), in filtered artificial seawater (FASW; salinity at 30 PSU) containing antibiotics (Gibco #15240-062, at 1X final concentration).
To grow adults prior to collecting regeneration limbs, adult males of the Chicago-F line (Kao et al. 2016) and the DistalDsRed line (Kontarakis et al. 2011), measuring ~1 cm in length and with no damaged appendages, were selected and kept individually in homogeneous conditions – photoperiod (12:12 hours light:dark cycle), temperature (25-26˚C) and medium (individual containers separated by mesh, sharing artificial seawater at 30 PSU) – for three months prior to experiment. The same conditions were kept during the course of sampling. Sampling was performed between 8:00 and 10:00 am.

extract_protocol:
For the embryonic samples, embryos were dissected in the lid of a 5 ml Protein LoBind Tube (Eppendorf, #0030108302), in 1% BSA in FASW (80 ul). The eggshell was removed with fine forceps (Fine Science Tools, #11254-20), and legs were dissected with borosilicate needles (pulled capillaries; Sutter, #B100-50-15). Samples were transferred in 100 ul of ice-cold lysis solution (Agilent Absolutely RNA Nanoprep kit, #400753), homogenized though brief pipetting, and flash-frozen in liquid nitrogen. RNA extraction was performed with the Agilent Absolutely RNA Nanoprep kit (#400753), following manufacturer's instructions, and eluted in 10 ul of elution buffer. RNA extraction was performed in randomized batches, to avoid shared batch effects in biological replicates.
For the adult samples, leg fragments were transferred immediately after dissection in 1.5 ml LowBind tubes with 500 ul of ice-cold lysis buffer (Reliaprep RNA Tissue MiniPrep System - Promega, #Z6111), vortexed, then transferred to a sterile multiwell plate for manual disruption of cuticle with a clean surgical blade. The sample was then re-transferred to the tube, vortexed, and frozen in liquid nitrogen, for then being stored at -80°C until further processing. RNA extraction was randomized, avoiding to process at the same time related samples. RNA was extracted with the Reliaprep RNA Tissue MiniPrep System (Promega, #Z6111), and eluted in 15 ul of nuclease-free water (Invitrogen, #AM9937).
1ng of RNA was used for cDNA synthesis. For samples from embryonic legs, RNA concentration was too low to be directly quantified, 9ul of RNA solution was used for cDNA synthesis over 15 cycles of LD-PCR, using the SMART-Seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio, #634898) and the SeqAmp DNA Polymerase (Takara Bio, #638509); 1 ul of cDNA was then used for Qubit quantification (4.0 HS DNA), measuring in the range of 0.2- 0-7 ng/ul. Libraries were synthesized from 1 ng of cDNA, using the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096; with Dual indexing strategy, i7 and i5), and with a protocol that included an accelerated cooling step on ice after the 55°C step. Quantification and validation of libraries were done with both Qubit 4.0 (HS DNA kit, Thermofisher) and Tapestation D5000 equipment using the D5000 ScreenTape System (Agilent, #5067- 5588 and #5067- 5589).

tag: dissected part of the leg

value: full-limb

tag: collection time (hours post amputation)

tag: collection time (hours post fertilization)

tag: collection time (days relative to molting)

tag: animal id

tag: left or right leg


title: Molting dataset: Entire leg, from animal 8, collected 9 days relative to molting [M+9_8]


title: PADP6+OG1RF iron unchelated, PAEF_RP41

description:
PADP6 + OG1RF total RNA
PAEF_RP41
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: Molting dataset: Entire leg, from animal 59, collected -1 days relative to molting [M-1_59]


title: Molting dataset: Entire leg, from animal 61, collected 1 days relative to molting [M+1_61]


title: PADP6+OG1RF iron chelated, PAEF_DP44

description:
PADP6 + OG1RF total RNA
PAEF_DP44
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt

source_name: P. aeruginosa PADP6 + E. faecalis OG1RF macrocolonies on iron chelated TSBG agar (mixed-species)


title: Molting dataset: Entire leg, from animal 53, collected 9 days relative to molting [M+9_53]


title: Molting dataset: Entire leg, from animal 55, collected 10 days relative to molting [M+10_55]


title: Molting dataset: Entire leg, from animal 57, collected -3 days relative to molting [M-3_57]


title: PADP6+OG1RF iron chelated, PAEF_DP47

description:
PADP6 + OG1RF total RNA
PAEF_DP47
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: PADP6+∆ldh1 iron unchelated, PALDH_RP49

description:
PADP6 + ∆ldh1 total RNA
PALDH_RP49
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: Molting dataset: Entire leg, from animal 64, collected -5 days relative to molting [M-5_64]


title: Molting dataset: Entire leg, from animal 45, collected -5 days relative to molting [M-5_45]


title: siCTL 1

type: RNA

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: Keratinocytes transfected with siRNA control

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing: Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:  Array Type: Clariom_S_Human  Analysis Type: Expression (Gene)  Analysis Version: version 2  Summarization Method: Gene Level - SST-RMA  Pos vs Neg AUC Threshold: 0,7  Genome Version: hg38 (Homo sapiens)  Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv  Condition (Comparison): HOXC13-AS KD; ctr

label: biotin

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Adult Human Epidermal Keratinocytes (HEKa) were cultured in EpiLife medium (Gibco™) supplemented with 10% Human Keratinocyte Growth Supplement (HKGS, Gibco™) and 1% penicillin/streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (ThermoFisher Scientific).

treatment_protocol: Third passage HEKa cells were seeded in 24-well plates. At 60-70% confluence, cells were transfected with 20nM siRNA against HOXC13-AS or a non-targeting siRNA control (GE Healthcare Dharmacon) using Lipofectamine 2000 (ThermoFisher Scientific). After 24 hours, cells were induced for differentiation for 3 days by 1.5 mM calcium.

value: Skin

tag: cell type

value: Keratinocytes

tag: genotype

value: Control


title: Molting dataset: Entire leg, from animal 47, collected -3 days relative to molting [M-3_47]


title: siCTL 2

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

source_name: Keratinocytes transfected with siRNA control

tag: tissue


title: siHOXC13-AS 1

description: Keratinocytes transfected with siRNA targeting HOXC13-AS

value: si-HOXC13-AS knockdown


title: siCTL 3


title: Molting dataset: Entire leg, from animal 41, collected -2 days relative to molting [M-2_41]


title: Molting dataset: Entire leg, from animal 43, collected -1 days relative to molting [M-1_43]


title: siHOXC13-AS 3

source_name: Keratinocytes transfected with siRNA targeting HOXC13-AS


title: Molting dataset: Entire leg, from animal 38, collected 1 days relative to molting [M+1_38]


title: Molting dataset: Entire leg, from animal 30, collected -4 days relative to molting [M-4_30]


title: PADP6+OG1RF iron chelated, PAEF_DP45

description:
PADP6 + OG1RF total RNA
PAEF_DP45
PAnorm_PAEFdepVSPALDH1dep.txt, PAnorm_PAEF_repVSdep.txt, PAnorm_PALDH1_repVSdep.txt, Panorm_PA_repVSdep.txt, toPAO1conditions.txt, toOG1RF.txt, Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, toOG1RF.txt


title: Molting dataset: Entire leg, from animal 22, collected 9 days relative to molting [M+9_22]


title: Molting dataset: Entire leg, from animal 3, collected -5 days relative to molting [M-5_3]


title: Molting dataset: Entire leg, from animal 17, collected -1 days relative to molting [M-1_17]


title: Molting dataset: Entire leg, from animal 19, collected -1 days relative to molting [M-1_19]


title: Molting dataset: Entire leg, from animal 10, collected -5 days relative to molting [M-5_10]


title: Molting dataset: Entire leg, from animal 13, collected 1 days relative to molting [M+1_13]


title: Entire leg, from animal 82. R side, [full_limb_Pre_molt_full_R_82]

description: Entire leg, from animal 82. R side.

value: R


title: (Ef and Ed): leg, collected 192h after fertilization, from animal 90_1, distal part [Ed_192_90_1]

description: Development dataset (Ef and Ed): leg, collected 192h after fertilization, from animal 90_1, distal part of the leg.

source_name: Distal part of the developing T4 leg: carpus, propodus and dactylus

value: distal


title: Entire leg, from animal 82. L side, [full_limb_Pre_molt_full_L_82]

description: Entire leg, from animal 82. L side.

value: L


title: (Ef and Ed): leg, collected 180h after fertilization, from animal 91_1, distal part [Ed_180_91_1]

description: Development dataset (Ef and Ed): leg, collected 180h after fertilization, from animal 91_1, distal part of the leg.


title: (Ef and Ed): leg, collected 186h after fertilization, from animal 70_3, distal part [Ed_186_70_3]

description: Development dataset (Ef and Ed): leg, collected 186h after fertilization, from animal 70_3, distal part of the leg.


title: (Ef and Ed): leg, collected 180h after fertilization, from animal 81_3, distal part [Ed_180_81_3]

description: Development dataset (Ef and Ed): leg, collected 180h after fertilization, from animal 81_3, distal part of the leg.


title: (Ef and Ed): leg, collected 186h after fertilization, from animal 74_3, distal part [Ed_186_74_3]

description: Development dataset (Ef and Ed): leg, collected 186h after fertilization, from animal 74_3, distal part of the leg.


title: (Ef and Ed): leg, collected 180h after fertilization, from animal 79_5, distal part [Ed_180_79_5]

description: Development dataset (Ef and Ed): leg, collected 180h after fertilization, from animal 79_5, distal part of the leg.


title: (Ef and Ed): leg, collected 174h after fertilization, from animal 122_1, distal part [Ed_174_122_1]

description: Development dataset (Ef and Ed): leg, collected 174h after fertilization, from animal 122_1, distal part of the leg.


title: (Ef and Ed): leg, collected 174h after fertilization, from animal 102_2, distal part [Ed_174_102_2]

description: Development dataset (Ef and Ed): leg, collected 174h after fertilization, from animal 102_2, distal part of the leg.


title: (Ef and Ed): leg, collected 174h after fertilization, from animal 102_3, distal part [Ed_174_102_3]

description: Development dataset (Ef and Ed): leg, collected 174h after fertilization, from animal 102_3, distal part of the leg.


title: (Ef and Ed): leg, collected 168h after fertilization, from animal 69_2, distal part [Ed_168_69_2]

description: Development dataset (Ef and Ed): leg, collected 168h after fertilization, from animal 69_2, distal part of the leg.


title: (Ef and Ed): leg, collected 162h after fertilization, from animal 82_4, distal part [Ed_162_82_4]

description: Development dataset (Ef and Ed): leg, collected 162h after fertilization, from animal 82_4, distal part of the leg.


title: (Ef and Ed): leg, collected 162h after fertilization, from animal 123B_1, distal part [Ed_162_123B_1]

description: Development dataset (Ef and Ed): leg, collected 162h after fertilization, from animal 123B_1, distal part of the leg.


title: (Ef and Ed): leg, collected 168h after fertilization, from animal 101_2, distal part [Ed_168_101_2]

description: Development dataset (Ef and Ed): leg, collected 168h after fertilization, from animal 101_2, distal part of the leg.


title: siHOXC13-AS 2


title: (Ef and Ed): leg, collected 156h after fertilization, from animal 86_2, distal part [Ed_156_86_2]

description: Development dataset (Ef and Ed): leg, collected 156h after fertilization, from animal 86_2, distal part of the leg.


title: (Ef and Ed): leg, collected 150h after fertilization, from animal 102_1, distal part [Ed_150_102_1]

description: Development dataset (Ef and Ed): leg, collected 150h after fertilization, from animal 102_1, distal part of the leg.


title: (Ef and Ed): leg, collected 150h after fertilization, from animal 81_1, distal part [Ed_150_81_1]

description: Development dataset (Ef and Ed): leg, collected 150h after fertilization, from animal 81_1, distal part of the leg.


title: (Ef and Ed): leg, collected 144h after fertilization, from animal 87_2, distal part [Ed_144_87_2]

description: Development dataset (Ef and Ed): leg, collected 144h after fertilization, from animal 87_2, distal part of the leg.


title: (Ef and Ed): leg, collected 144h after fertilization, from animal 73_1, distal part [Ed_144_73_1]

description: Development dataset (Ef and Ed): leg, collected 144h after fertilization, from animal 73_1, distal part of the leg.


title: (Ef and Ed): leg, collected 192h after fertilization, from animal 123B_2, distal part [Ed_192_123B_2]

description: Development dataset (Ef and Ed): leg, collected 192h after fertilization, from animal 123B_2, distal part of the leg.


title: (Ef and Ed): leg, collected 132h after fertilization, from animal 80_3, distal part [Ed_132_80_3]

description: Development dataset (Ef and Ed): leg, collected 132h after fertilization, from animal 80_3, distal part of the leg.

source_name: Distal part of the developing T4 leg: prospective merus, carpus, propodus and dactylus


title: (Ef and Ed): leg, collected 144h after fertilization, from animal 101_1, distal part [Ed_144_101_1]

description: Development dataset (Ef and Ed): leg, collected 144h after fertilization, from animal 101_1, distal part of the leg.


title: (Ef and Ed): leg, collected 138h after fertilization, from animal 87_1, distal part [Ed_138_87_1]

description: Development dataset (Ef and Ed): leg, collected 138h after fertilization, from animal 87_1, distal part of the leg.


title: (Ef and Ed): leg, collected 132h after fertilization, from animal 77_1, distal part [Ed_132_77_1]

description: Development dataset (Ef and Ed): leg, collected 132h after fertilization, from animal 77_1, distal part of the leg.


title: (Ef and Ed): leg, collected 138h after fertilization, from animal 74_1, distal part [Ed_138_74_1]

description: Development dataset (Ef and Ed): leg, collected 138h after fertilization, from animal 74_1, distal part of the leg.


title: (Ef and Ed): leg, collected 120h after fertilization, from animal 83_1, distal part [Ed_120_83_1]

description: Development dataset (Ef and Ed): leg, collected 120h after fertilization, from animal 83_1, distal part of the leg.


title: (Ef and Ed): leg, collected 126h after fertilization, from animal 126_2, distal part [Ed_126_126_2]

description: Development dataset (Ef and Ed): leg, collected 126h after fertilization, from animal 126_2, distal part of the leg.


title: (Ef and Ed): leg, collected 120h after fertilization, from animal 69_1, distal part [Ed_120_69_1]

description: Development dataset (Ef and Ed): leg, collected 120h after fertilization, from animal 69_1, distal part of the leg.


title: (Ef and Ed): leg, collected 192h after fertilization, from animal 90_1, full-limb part [Ef_192_90_1]

description: Development dataset (Ef and Ed): leg, collected 192h after fertilization, from animal 90_1, full-limb part of the leg.

source_name: Entire developing T4 leg: primordia of the basis, the ischium, the merus, the carpus, the propodus, the dactylus, and of the coxal plates and the gills


title: (Ef and Ed): leg, collected 192h after fertilization, from animal 123B_2, full-limb part [Ef_192_123B_2]

description: Development dataset (Ef and Ed): leg, collected 192h after fertilization, from animal 123B_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 156h after fertilization, from animal 71_1, distal part [Ed_156_71_1]

description: Development dataset (Ef and Ed): leg, collected 156h after fertilization, from animal 71_1, distal part of the leg.


title: (Ef and Ed): leg, collected 186h after fertilization, from animal 70_3, full-limb part [Ef_186_70_3]

description: Development dataset (Ef and Ed): leg, collected 186h after fertilization, from animal 70_3, full-limb part of the leg.


title: (Ef and Ed): leg, collected 186h after fertilization, from animal 74_3, full-limb part [Ef_186_74_3]

description: Development dataset (Ef and Ed): leg, collected 186h after fertilization, from animal 74_3, full-limb part of the leg.


title: (Ef and Ed): leg, collected 180h after fertilization, from animal 81_3, full-limb part [Ef_180_81_3]

description: Development dataset (Ef and Ed): leg, collected 180h after fertilization, from animal 81_3, full-limb part of the leg.


title: (Ef and Ed): leg, collected 180h after fertilization, from animal 91_1, full-limb part [Ef_180_91_1]

description: Development dataset (Ef and Ed): leg, collected 180h after fertilization, from animal 91_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 174h after fertilization, from animal 122_1, full-limb part [Ef_174_122_1]

description: Development dataset (Ef and Ed): leg, collected 174h after fertilization, from animal 122_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 180h after fertilization, from animal 79_5, full-limb part [Ef_180_79_5]

description: Development dataset (Ef and Ed): leg, collected 180h after fertilization, from animal 79_5, full-limb part of the leg.


title: (Ef and Ed): leg, collected 174h after fertilization, from animal 102_3, full-limb part [Ef_174_102_3]

description: Development dataset (Ef and Ed): leg, collected 174h after fertilization, from animal 102_3, full-limb part of the leg.


title: (Ef and Ed): leg, collected 120h after fertilization, from animal 75_3, distal part [Ed_120_75_3]

description: Development dataset (Ef and Ed): leg, collected 120h after fertilization, from animal 75_3, distal part of the leg.


title: (Ef and Ed): leg, collected 174h after fertilization, from animal 102_2, full-limb part [Ef_174_102_2]

description: Development dataset (Ef and Ed): leg, collected 174h after fertilization, from animal 102_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 162h after fertilization, from animal 123B_1, full-limb part [Ef_162_123B_1]

description: Development dataset (Ef and Ed): leg, collected 162h after fertilization, from animal 123B_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 168h after fertilization, from animal 101_2, full-limb part [Ef_168_101_2]

description: Development dataset (Ef and Ed): leg, collected 168h after fertilization, from animal 101_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 162h after fertilization, from animal 82_4, full-limb part [Ef_162_82_4]

description: Development dataset (Ef and Ed): leg, collected 162h after fertilization, from animal 82_4, full-limb part of the leg.


title: (Ef and Ed): leg, collected 126h after fertilization, from animal 128_1, distal part [Ed_126_128_1]

description: Development dataset (Ef and Ed): leg, collected 126h after fertilization, from animal 128_1, distal part of the leg.


title: (Ef and Ed): leg, collected 168h after fertilization, from animal 69_2, full-limb part [Ef_168_69_2]

description: Development dataset (Ef and Ed): leg, collected 168h after fertilization, from animal 69_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 150h after fertilization, from animal 81_1, full-limb part [Ef_150_81_1]

description: Development dataset (Ef and Ed): leg, collected 150h after fertilization, from animal 81_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 144h after fertilization, from animal 87_2, full-limb part [Ef_144_87_2]

description: Development dataset (Ef and Ed): leg, collected 144h after fertilization, from animal 87_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 144h after fertilization, from animal 101_1, full-limb part [Ef_144_101_1]

description: Development dataset (Ef and Ed): leg, collected 144h after fertilization, from animal 101_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 156h after fertilization, from animal 100_1, full-limb part [Ef_156_100_1]

description: Development dataset (Ef and Ed): leg, collected 156h after fertilization, from animal 100_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 138h after fertilization, from animal 87_1, full-limb part [Ef_138_87_1]

description: Development dataset (Ef and Ed): leg, collected 138h after fertilization, from animal 87_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 150h after fertilization, from animal 102_1, full-limb part [Ef_150_102_1]

description: Development dataset (Ef and Ed): leg, collected 150h after fertilization, from animal 102_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 132h after fertilization, from animal 80_3, full-limb part [Ef_132_80_3]

description: Development dataset (Ef and Ed): leg, collected 132h after fertilization, from animal 80_3, full-limb part of the leg.


title: (Ef and Ed): leg, collected 132h after fertilization, from animal 77_1, full-limb part [Ef_132_77_1]

description: Development dataset (Ef and Ed): leg, collected 132h after fertilization, from animal 77_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 126h after fertilization, from animal 128_1, full-limb part [Ef_126_128_1]

description: Development dataset (Ef and Ed): leg, collected 126h after fertilization, from animal 128_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 126h after fertilization, from animal 126_2, full-limb part [Ef_126_126_2]

description: Development dataset (Ef and Ed): leg, collected 126h after fertilization, from animal 126_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 120h after fertilization, from animal 75_3, full-limb part [Ef_120_75_3]

description: Development dataset (Ef and Ed): leg, collected 120h after fertilization, from animal 75_3, full-limb part of the leg.


title: (Ef and Ed): leg, collected 120h after fertilization, from animal 83_1, full-limb part [Ef_120_83_1]

description: Development dataset (Ef and Ed): leg, collected 120h after fertilization, from animal 83_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 114h after fertilization, from animal 78_5, full-limb part [Ef_114_78_5]

description: Development dataset (Ef and Ed): leg, collected 114h after fertilization, from animal 78_5, full-limb part of the leg.


title: (Ef and Ed): leg, collected 114h after fertilization, from animal 80_2, full-limb part [Ef_114_80_2]

description: Development dataset (Ef and Ed): leg, collected 114h after fertilization, from animal 80_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 108h after fertilization, from animal 82_1, full-limb part [Ef_108_82_1]

description: Development dataset (Ef and Ed): leg, collected 108h after fertilization, from animal 82_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 156h after fertilization, from animal 86_2, full-limb part [Ef_156_86_2]

description: Development dataset (Ef and Ed): leg, collected 156h after fertilization, from animal 86_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 108h after fertilization, from animal 80_1, full-limb part [Ef_108_80_1]

description: Development dataset (Ef and Ed): leg, collected 108h after fertilization, from animal 80_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 102h after fertilization, from animal 86_1, full-limb part [Ef_102_86_1]

description: Development dataset (Ef and Ed): leg, collected 102h after fertilization, from animal 86_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 102h after fertilization, from animal 78_2, full-limb part [Ef_102_78_2]

description: Development dataset (Ef and Ed): leg, collected 102h after fertilization, from animal 78_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 96h after fertilization, from animal 78_1, full-limb part [Ef_96_78_1]

description: Development dataset (Ef and Ed): leg, collected 96h after fertilization, from animal 78_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 102h after fertilization, from animal 118_1, full-limb part [Ef_102_118_1]

description: Development dataset (Ef and Ed): leg, collected 102h after fertilization, from animal 118_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 102h after fertilization, from animal 75_2, full-limb part [Ef_102_75_2]

description: Development dataset (Ef and Ed): leg, collected 102h after fertilization, from animal 75_2, full-limb part of the leg.


title: (Ef and Ed): leg, collected 96h after fertilization, from animal 75_1, full-limb part [Ef_96_75_1]

description: Development dataset (Ef and Ed): leg, collected 96h after fertilization, from animal 75_1, full-limb part of the leg.


title: (Ef and Ed): leg, collected 96h after fertilization, from animal 121_1, full-limb part [Ef_96_121_1]

description: Development dataset (Ef and Ed): leg, collected 96h after fertilization, from animal 121_1, full-limb part of the leg.


title: (Rp): Control to regenerating leg, collected Distal_posh after amputation, adult animal 9, R, proximal [Rp_Distal_R_9]

description: Regeneration dataset (Rp): Control to regenerating leg, collected Distal_posh after amputation, from adult animal 9, R side. proximal part of the leg.

source_name: Part of the adult T4 leg proximal to the amputation plain: merus

value: proximal


title: (Rp): Control to regenerating leg, collected Distal_posh after amputation, adult animal 11, R, proximal [Rp_Distal_R_11]

description: Regeneration dataset (Rp): Control to regenerating leg, collected Distal_posh after amputation, from adult animal 11, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected Post-molth after amputation, animal 56, L, proximal [Rp_Post_molt_L_56]

description: Regeneration dataset (Rp): Control to regenerating leg, collected Post-molth after amputation, from adult animal 56, L side. proximal part of the leg.

value: Post-molt


title: (Rp): Control to regenerating leg, collected Post-molth after amputation, animal 54, L, proximal [Rp_Post_molt_L_54]

description: Regeneration dataset (Rp): Control to regenerating leg, collected Post-molth after amputation, from adult animal 54, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 120h after amputation, adult animal 53, R side, proximal part [Rp_120_R_53]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 120h after amputation, from adult animal 53, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 120h after amputation, adult animal 53, L side, proximal part [Rp_120_L_53]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 120h after amputation, from adult animal 53, L side. proximal part of the leg.


title: (Ef and Ed): leg, collected 138h after fertilization, from animal 77_2, full-limb part [Ef_138_77_2]

description: Development dataset (Ef and Ed): leg, collected 138h after fertilization, from animal 77_2, full-limb part of the leg.


title: (Rp): Control to regenerating leg, collected 120h after amputation, adult animal 51, R side, proximal part [Rp_120_R_51]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 120h after amputation, from adult animal 51, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 120h after amputation, adult animal 51, L side, proximal part [Rp_120_L_51]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 120h after amputation, from adult animal 51, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 108h after amputation, adult animal 23, R side, proximal part [Rp_108_R_23]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 108h after amputation, from adult animal 23, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 108h after amputation, adult animal 23, L side, proximal part [Rp_108_L_23]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 108h after amputation, from adult animal 23, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 108h after amputation, adult animal 22, R side, proximal part [Rp_108_R_22]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 108h after amputation, from adult animal 22, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 96h after amputation, adult animal 45, R side, proximal part [Rp_96_R_45]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 96h after amputation, from adult animal 45, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 96h after amputation, adult animal 45, L side, proximal part [Rp_96_L_45]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 96h after amputation, from adult animal 45, L side. proximal part of the leg.


title: (Ef and Ed): leg, collected 96h after fertilization, from animal 124_1, full-limb part [Ef_96_124_1]

description: Development dataset (Ef and Ed): leg, collected 96h after fertilization, from animal 124_1, full-limb part of the leg.


title: (Rp): Control to regenerating leg, collected 96h after amputation, adult animal 44, R side, proximal part [Rp_96_R_44]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 96h after amputation, from adult animal 44, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 84h after amputation, adult animal 19, L side, proximal part [Rp_84_L_19]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 84h after amputation, from adult animal 19, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 96h after amputation, adult animal 44, L side, proximal part [Rp_96_L_44]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 96h after amputation, from adult animal 44, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 84h after amputation, adult animal 20, L side, proximal part [Rp_84_L_20]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 84h after amputation, from adult animal 20, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 84h after amputation, adult animal 20, R side, proximal part [Rp_84_R_20]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 84h after amputation, from adult animal 20, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 84h after amputation, adult animal 19, R side, proximal part [Rp_84_R_19]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 84h after amputation, from adult animal 19, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 84h after amputation, adult animal 21, R side, proximal part [Rp_84_R_21]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 84h after amputation, from adult animal 21, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 72h after amputation, adult animal 41, L side, proximal part [Rp_72_L_41]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 72h after amputation, from adult animal 41, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 72h after amputation, adult animal 38, R side, proximal part [Rp_72_R_38]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 72h after amputation, from adult animal 38, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 72h after amputation, adult animal 39, R side, proximal part [Rp_72_R_39]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 72h after amputation, from adult animal 39, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 72h after amputation, adult animal 39, L side, proximal part [Rp_72_L_39]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 72h after amputation, from adult animal 39, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 72h after amputation, adult animal 41, R side, proximal part [Rp_72_R_41]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 72h after amputation, from adult animal 41, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 60h after amputation, adult animal 15, L side, proximal part [Rp_60_L_15]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 60h after amputation, from adult animal 15, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 60h after amputation, adult animal 17, L side, proximal part [Rp_60_L_17]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 60h after amputation, from adult animal 17, L side. proximal part of the leg.


title: nhr-45(tm1307)_DMSO_Replicate_2

tag: strain

value: Mutant

tag: Stage

value: Adult

tag: treatment

value: grown on NGM + DMSO + E. coli HT115


title: (Rp): Control to regenerating leg, collected 60h after amputation, adult animal 15, R side, proximal part [Rp_60_R_15]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 60h after amputation, from adult animal 15, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 108h after amputation, adult animal 24, L side, proximal part [Rp_108_L_24]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 108h after amputation, from adult animal 24, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 96h after amputation, adult animal 46, L side, proximal part [Rp_96_L_46]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 96h after amputation, from adult animal 46, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 60h after amputation, adult animal 14, R side, proximal part [Rp_60_R_14]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 60h after amputation, from adult animal 14, R side. proximal part of the leg.


title: nhr-45(tm1307)_DMSO_Replicate_1


title: (Rp): Control to regenerating leg, collected 108h after amputation, adult animal 22, L side, proximal part [Rp_108_L_22]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 108h after amputation, from adult animal 22, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 120h after amputation, adult animal 50, L side, proximal part [Rp_120_L_50]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 120h after amputation, from adult animal 50, L side. proximal part of the leg.


title: -Asn H3K4me3 rep1

tag: cell line

value: asparagine-free medium

tag: chip antibody


title: (Rp): Control to regenerating leg, collected 48h after amputation, adult animal 67, R side, proximal part [Rp_48_R_67]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 48h after amputation, from adult animal 67, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 48h after amputation, adult animal 69, L side, proximal part [Rp_48_L_69]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 48h after amputation, from adult animal 69, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 48h after amputation, adult animal 67, L side, proximal part [Rp_48_L_67]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 48h after amputation, from adult animal 67, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 36h after amputation, adult animal 92, R side, proximal part [Rp_36_R_92]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 36h after amputation, from adult animal 92, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 36h after amputation, adult animal 92, L side, proximal part [Rp_36_L_92]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 36h after amputation, from adult animal 92, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 36h after amputation, adult animal 91, R side, proximal part [Rp_36_R_91]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 36h after amputation, from adult animal 91, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 60h after amputation, adult animal 14, L side, proximal part [Rp_60_L_14]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 60h after amputation, from adult animal 14, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 36h after amputation, adult animal 89, R side, proximal part [Rp_36_R_89]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 36h after amputation, from adult animal 89, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 36h after amputation, adult animal 91, L side, proximal part [Rp_36_L_91]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 36h after amputation, from adult animal 91, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 24h after amputation, adult animal 63, R side, proximal part [Rp_24_R_63]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 24h after amputation, from adult animal 63, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 24h after amputation, adult animal 62, R side, proximal part [Rp_24_R_62]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 24h after amputation, from adult animal 62, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 48h after amputation, adult animal 66, L side, proximal part [Rp_48_L_66]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 48h after amputation, from adult animal 66, L side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 24h after amputation, adult animal 61, R side, proximal part [Rp_24_R_61]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 24h after amputation, from adult animal 61, R side. proximal part of the leg.


title: (Rp): Control to regenerating leg, collected 48h after amputation, adult animal 66, R side, proximal part [Rp_48_R_66]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 48h after amputation, from adult animal 66, R side. proximal part of the leg.


title: PLC, ATAD2, biological rep3

city: balcova

first: umut

last: ekin

state: izmir

address: mithatpasa st.

country: Turkey

institute: Izmir Biomedicine and Genome Center

hyb_protocol: These are described in manufacturer’s protocol.

data_processing: R packages affy and Limma.

source_name: PLC, ATAD2

label_protocol: We labeled samples according to ATAD2 siRNA treatment and non-targeting controls.

growth_protocol: Each cell line was growth in RPMI.

extract_protocol: Total RNAs of cells were extracted with NucloSpin RNA II Kit (MN Macherey-Nagel, Duren, Germany)

treatment_protocol: siRNAs transfected with Lipofectamine RNAiMax (Thermo Fisher)

value: HCC cell line PLC

value: Knockout


title: PLC, control, biological rep3

scan_protocol: These are described in manufacturer’s protocol.

source_name: PLC, control


title: PLC, ATAD2, biological rep1


title: (Rp): Control to regenerating leg, collected 24h after amputation, adult animal 61, L side, proximal part [Rp_24_L_61]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 24h after amputation, from adult animal 61, L side. proximal part of the leg.


title: SNU449, ATAD2, biological rep2

source_name: SNU449, ATAD2

value: HCC cell line SNU449


title: PLC, control, biological rep1


title: Hep3B, ATAD2, biological rep3

source_name: Hep3B, ATAD2

value: HCC cell line Hep3B


title: SNU449, control, biological rep2

source_name: SNU449, control


title: SNU449, ATAD2, biological rep3


title: Hep3B, ATAD2, biological rep1


title: SNU449, ATAD2, biological rep1


title: Hep3B, control, biological rep2

source_name: Hep3B, control


title: Hep3B, ATAD2, biological rep2


title: (Rp): Control to regenerating leg, collected 24h after amputation, adult animal 63, L side, proximal part [Rp_24_L_63]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 24h after amputation, from adult animal 63, L side. proximal part of the leg.


title: PLC, ATAD2, biological rep2


title: SNU449, control, biological rep3


title: PLC, control, biological rep2


title: (Rp): Control to regenerating leg, collected 12h after amputation, adult animal 87, L side, proximal part [Rp_12_L_87]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 12h after amputation, from adult animal 87, L side. proximal part of the leg.


title: Hep3B, control, biological rep3


title: SNU449, control, biological rep1


title: (Rp): Control to regenerating leg, collected 12h after amputation, adult animal 87, R side, proximal part [Rp_12_R_87]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 12h after amputation, from adult animal 87, R side. proximal part of the leg.


title: Animal_Vehicle6

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description:
RNAseq_Animal_Fulv
Aligned_human_rnaseq_featurecounts.txt

data_processing:
Reads from the HiSeq 2000 were processed and analyzed through a series of steps. Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2.
For RNAseq, STAR (version 2.7.6a) was employed to map RNA-Seq reads to either version mm39 of the Mus musculus reference genome, GRCm39, from NCBI Genome Reference Consortium Mouse Build 39 or version GRCh38.p13 of the human reference genome from NCBI Genome Reference Consortium Human Build 38 patch release 13. For ChIPseq, Bowtie2 was employed to obtain BAM files.
For RNAseq, gene expression values (raw read counts) from BAM files were calculated using FeatureCounts function from the Subread module (version 2.0.0). For ChIPseq, gene expression values (raw read counts) from BAM files were calculated using BigWig and outputed as BW files.
DESeq normalization algorithm with DESeq2 module in R using default values was used.  Differentially expressed genes were then determined by fold-change and p-value for each gene for each treatment relative to the vehicle control.
Genome_build: mm39 for mouse, GRCh38.p13 for human

organism:
Homo sapiens
Mus musculus

source_name: Liver/ liver tumor (MCF7-ESR1Y537S)

growth_protocol: MCF7 (ATCC HTB-22) (RRID:CVCL_0031) and T47D (ATCC HTB-133) (RRID:CVCL_0553) parental cells were cultured in RPMI-1640 medium with NEAA salts (Sigma, St Louis, MO, USA), 5% fetal bovine serum (FBS)  (HyClone, Logan, UT), 100 μg/mL penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA) and 50 mg/mL Gentamicin (Gibco, Gaithersburg, MD). MCF7/ESR1D537S and - ESR1Y537S cells (RRID:CVCL_0031-citation needed) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with NEAA salts, 10% FBS, 100 μg/mL penicillin/streptomycin, and 50 mg/mL gentamicin. T47D ESR1D537S and T47D ESR1Y537S cells (RRID: CVCL_0553-citation needed) were cultured in Modified Eagle Medium (MEM) with NEAA salts, 10% FBS, 100 μg/mL penicillin/streptomycin, and 50 mg/mL gentamicin. Cell line authentication was performed by checking activity and expression of ERα, proliferative responses to ER agonists and antagonists for all cell lines, and sequencing of MCF7/ESR1Y537S and MCF7/ESR1D537G as described.

extract_protocol:
RNA extraction: For gene expression analysis, total RNA was extracted from at least 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN.                           ChIP-seq analysis was performed as described previously using MCF7-ESR1Y537S cells. ChIP: ERα–DNA or IgG–DNA complexes were immunoprecipitated using ERα- specific F10 and HC20 antibodies (Santa Cruz Biotech, 3:100 dilution).
Once the sample quality and replicate reproducibility was verified at least 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina). Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.                                                                                ChIP DNA was obtained from three pooled biological replicates. Libraries were prepared according to Illumina Solexa ChIP-Seq sample processing (San Diego, CA), and single-read sequencing was performed using the Illumina HiSeq 2000. Sequences generated were mapped uniquely onto the human genome (hg18) by Bowtie2 (RRID:SCR_016368). The MACS (model-based analysis of ChIP-seq) algorithm was used to identify enriched peak regions (default settings) with a P value cutoff of 6.0e−7 and FDR of 0.01, as we have described.

treatment_protocol: In vivo study: four-week-old, ovariectomized, NOD SCID gamma (NSG) immunodeficient female mice were obtained from The Jackson Laboratory (Bar Harbor, ME).After one week of acclimatization to the housing facility, we injected 1×106 MCF7-ESR1Y537S cells resuspended in 1% PBS via tail vein and randomized animals to indicated treatment groups.We randomized N=8 mice to one of the two treatments Vehicle (Veh) or Fulv in each diet group. Fulv (Sigma) was dissolved in 10% DMSO and 90% corn oil and administrated via intramuscular injection (100 mg/kg) twice a week (Monday, Friday) for four weeks. In vitro study, IN SITE Metastasis Kit (Xylyx Bio, Inc., NY) containing TissueSpec Bone (MTSBN101), Liver (MTSLV101), and Lung (MTSLG101) ECM Hydrogels, were used to model tumor microenvironments according to the manufacturer’s protocol. Briefly, 2×103 cells were encapsulated in corresponding extracellular matrix (ECM) hydrogels by mixing them with tissue culture matrix. A mixture volume of 100 uL/well was placed in 96-well plates in triplicate. Plates were incubated at 37°C in a humidified environment with 5% CO2 for at least 45 minutes to achieve gelation. Cells were treated with media containing Veh or 1μM Fulv every Monday and Friday for three weeks.

tag: Sex

value: female

value: Vehicle

value: Liver/ liver tumor

value: NOD SCID gamma (NSG)/ ATCC HTB-22 (RRID:CVCL_0031)


title: Animal_Vehicle4


title: Animal_Vehicle5


title: (Rp): Control to regenerating leg, collected 12h after amputation, adult animal 86, L side, proximal part [Rp_12_L_86]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 12h after amputation, from adult animal 86, L side. proximal part of the leg.


title: Animal_Vehicle3


title: (Rp): Control to regenerating leg, collected 12h after amputation, adult animal 85, R side, proximal part [Rp_12_R_85]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 12h after amputation, from adult animal 85, R side. proximal part of the leg.

value: R


title: (Rp): Control to regenerating leg, collected 12h after amputation, adult animal 86, R side, proximal part [Rp_12_R_86]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 12h after amputation, from adult animal 86, R side. proximal part of the leg.


title: Hep3B, control, biological rep1

value: Control


title: (Rp): Control to regenerating leg, collected 24h after amputation, adult animal 62, L side, proximal part [Rp_24_L_62]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 24h after amputation, from adult animal 62, L side. proximal part of the leg.

value: L


title: (Rp): Control to regenerating leg, collected 0h after amputation, adult animal 81, R side, proximal part [Rp_0_R_81]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 0h after amputation, from adult animal 81, R side. proximal part of the leg.

value: proximal


title: Animal_Vehicle2


title: Animal_Vehicle1


title: (Rp): Control to regenerating leg, collected 0h after amputation, adult animal 80, R side, proximal part [Rp_0_R_80]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 0h after amputation, from adult animal 80, R side. proximal part of the leg.


title: Animal_Fulv11

value: Fulvestrant


title: (Rp): Control to regenerating leg, collected 0h after amputation, adult animal 80, L side, proximal part [Rp_0_L_80]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 0h after amputation, from adult animal 80, L side. proximal part of the leg.


title: Animal_Fulv12


title: Animal_Fulv10


title: (Rp): Control to regenerating leg, collected 0h after amputation, adult animal 77, L side, proximal part [Rp_0_L_77]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 0h after amputation, from adult animal 77, L side. proximal part of the leg.


title: (Rd): leg, collected Distal_posh after amputation, adult animal 11, R side, distal part [Rd_Distal_R_11]

description: Regeneration dataset (Rd): leg, collected Distal_posh after amputation, from adult animal 11, R side. distal part of the leg.

source_name: Part of the adult T4 leg distal to the amputation plain: carpus

value: distal


title: (Rd): leg, collected Distal_posh after amputation, adult animal 9, R side, distal part [Rd_Distal_R_9]

description: Regeneration dataset (Rd): leg, collected Distal_posh after amputation, from adult animal 9, R side. distal part of the leg.


title: (Rd): leg, collected Post-molth after amputation, adult animal 56, L side, distal part [Rd_Post_molt_L_56]

description: Regeneration dataset (Rd): leg, collected Post-molth after amputation, from adult animal 56, L side. distal part of the leg.

value: Post-molt


title: (Rd): leg, collected Post-molth after amputation, adult animal 54, L side, distal part [Rd_Post_molt_L_54]

description: Regeneration dataset (Rd): leg, collected Post-molth after amputation, from adult animal 54, L side. distal part of the leg.


title: 60min_rep1_dsRNase_minusP

first: Mengge

last: Shan

address: 433 South University Avenue

department: Biology

institute: University of Pennylsvania

description: P. patens protonema with 60 minutes ABA, dsRNase treated, without proteinase K

data_processing:
PIP-seq reads were trimmed using cutadapt to remove 3’ sequencing adapters (cutadapt version 1.2.1 with parameters –e 0.006 –O 6 –m 14). Resulting trimmed reads were then collapsed into unique reads and aligned to the mm10 mouse genome sequence using TopHat (version 2.0.10 with parameters – library-type fr-secondstrand –read-mismatches 2 –read-edit-dist 2 –max-multihits 10 –b2-very-sensitive –transcriptome-max-hits 10 –no-coverage-search –no-novel juncs). Any PCR duplicates were collapsed to single reads for all downstream analysis.
PPSs were identified using a modified version of the R package CSAR (Muino et al., 2011). Read coverage values were calculated for each base in the genome and a Poisson test was used to determine an enrichment score for footprint as compared to structure only libraries. PPSs were then called with a false discovery rate of 5% as previously described (Silverman et al., 2014).
Structure scores for each transcript are based on the coverage for dsRNA-seq and ssRNA-seq coverages for each base in detectable transcripts from structure-only samples in each replicate. The structure score for each base was calculated as previously described (Gosai et al., 2015; Silverman et al., 2014).
Genome_build: mm10

organism: Physcomitrium patens

source_name: P. patens protonema

growth_protocol: Physcomitrella patens was grown on PpNH4 media plates for 7-10 days and then propagated following instructions provided by the Benzanilla lab. Specifically, samples are homogenized until no big clumps remain visible. Each new plate is layered with a sterile cellophane and 0.5 mL of the tissue mixture is placed on the cellophane. The plate is then gently swirled to evenly distribute the tissue and sealed with micropore plate. Then the plates are placed in Percival chambers at 25C with 16 hours/8 hours light/dark cycles.

extract_protocol:
Homogenized samples were divided into 2 subsamples one for interrogation of protein binding, the other for interrogation of secondary structure. For protein binding samples, each subsample were then was further divided and half was incubated in either 100 U/ml of a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI, USA)) with 200 μg/ml BSA in 1X RNaseONE buffer for 1 hour at room temperature (RT), or 2.5 U/ml of a double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX, USA)) 1X RNA structure buffer for 1 hour at 37°C as previously described (Anderson et al., 2016). Following RNAse treatment, proteins were denatured and digested by treatment with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) for 15 minutes at RT. Finally, RNAse crosslinks were reversed by incubation at 65°C for 2 hours. For structure only samples, we performed the identical treat-ments as described for protein bound samples, except that the cross-linked homogenate was treated with 1% SDS and 0.1 mg/ml Proteinase K (Roche;Basel,Switzerland)and ethanol precipitated before treatment with the structure specific RNAses. Post digestion, RNA was then isolated using Qiagen miRNeasy RNA isolation kit as described in the manual.
Strand specific libraries were constructed as previously described (Silverman et al, 2014).
PIP-seq

treatment_protocol: 10 -day old P. patens protonema tissue was sonicated and then transferred to 250 mL liquid PpNH4 media. After 3 days of growth on a plate shaker at ~100 rpm, ABA was added to the liquid culture for a final concentration of 10 mM and the same volume of methanol was added to the control samples. Samples were placed back on the shaking incubator for 30 or 60 minutes before being collected and flash frozen with liquid nitrogen.

tag: differentiation stage

value: 60 min ABA


title: Animal_Fulv9


title: 60min_rep2_dsRNase_minusP


title: Animal_Fulv8


title: 60min_rep2_ssRNase_plusP

description: P. patens protonema with 60 minutes ABA, ssRNase treated, protein kinase treated


title: (Rd): leg, collected 120h after amputation, adult animal 51, L side, distal part [Rd_120_L_51]

description: Regeneration dataset (Rd): leg, collected 120h after amputation, from adult animal 51, L side. distal part of the leg.


title: (Rd): leg, collected 120h after amputation, adult animal 53, L side, distal part [Rd_120_L_53]

description: Regeneration dataset (Rd): leg, collected 120h after amputation, from adult animal 53, L side. distal part of the leg.


title: (Rd): leg, collected 120h after amputation, adult animal 51, R side, distal part [Rd_120_R_51]

description: Regeneration dataset (Rd): leg, collected 120h after amputation, from adult animal 51, R side. distal part of the leg.


title: (Rd): leg, collected 120h after amputation, adult animal 53, R side, distal part [Rd_120_R_53]

description: Regeneration dataset (Rd): leg, collected 120h after amputation, from adult animal 53, R side. distal part of the leg.


title: (Rp): Control to regenerating leg, collected 0h after amputation, adult animal 81, L side, proximal part [Rp_0_L_81]

description: Regeneration dataset (Rp): Control to regenerating leg, collected 0h after amputation, from adult animal 81, L side. proximal part of the leg.


title: 60min_rep2_dsRNase_plusP

description: P. patens protonema with 60 minutes ABA, dsRNAse treated, proteinase K treated


title: 60min_rep2_ssRNase_minusP

description: P. patens protonema with 60 minutes ABA, ssRNase treated, without proteinase K


title: (Rd): leg, collected 108h after amputation, adult animal 24, L side, distal part [Rd_108_L_24]

description: Regeneration dataset (Rd): leg, collected 108h after amputation, from adult animal 24, L side. distal part of the leg.


title: 60min_rep1_dsRNase_plusP


title: 60min_rep1_ssRNase_plusP


title: (Rd): leg, collected 120h after amputation, adult animal 50, L side, distal part [Rd_120_L_50]

description: Regeneration dataset (Rd): leg, collected 120h after amputation, from adult animal 50, L side. distal part of the leg.


title: (Rd): leg, collected 108h after amputation, adult animal 23, R side, distal part [Rd_108_R_23]

description: Regeneration dataset (Rd): leg, collected 108h after amputation, from adult animal 23, R side. distal part of the leg.


title: 30min_rep2_dsRNase_minusP

description: P. patens protonema with 30 minutes ABA, dsRNase treated, without proteinase K

value: 30 min ABA


title: (Rd): leg, collected 108h after amputation, adult animal 22, L side, distal part [Rd_108_L_22]

description: Regeneration dataset (Rd): leg, collected 108h after amputation, from adult animal 22, L side. distal part of the leg.


title: (Rd): leg, collected 108h after amputation, adult animal 22, R side, distal part [Rd_108_R_22]

description: Regeneration dataset (Rd): leg, collected 108h after amputation, from adult animal 22, R side. distal part of the leg.


title: 60min_rep1_ssRNase_minusP


title: Animal_Fulv7

description:
RNAseq_Animal_Fulv
Aligned_human_rnaseq_featurecounts.txt

source_name: Liver/ liver tumor (MCF7-ESR1Y537S )


title: 30min_rep2_ssRNase_minusP

description: P. patens protonema with 30 minutes ABA, ssRNase treated, without proteinase K


title: 30min_rep1_ssRNase_minusP


title: (Rd): leg, collected 108h after amputation, adult animal 23, L side, distal part [Rd_108_L_23]

description: Regeneration dataset (Rd): leg, collected 108h after amputation, from adult animal 23, L side. distal part of the leg.


title: 30min_rep1_dsRNase_minusP


title: 30min_rep2_dsRNase_plusP

description: P. patens protonema with 30 minutes ABA, dsRNAse treated, proteinase K treated


title: (Rd): leg, collected 96h after amputation, adult animal 44, R side, distal part [Rd_96_R_44]

description: Regeneration dataset (Rd): leg, collected 96h after amputation, from adult animal 44, R side. distal part of the leg.


title: (Rd): leg, collected 96h after amputation, adult animal 45, L side, distal part [Rd_96_L_45]

description: Regeneration dataset (Rd): leg, collected 96h after amputation, from adult animal 45, L side. distal part of the leg.


title: 30min_rep1_dsRNase_plusP


title: (Rd): leg, collected 96h after amputation, adult animal 45, R side, distal part [Rd_96_R_45]

description: Regeneration dataset (Rd): leg, collected 96h after amputation, from adult animal 45, R side. distal part of the leg.


title: 00min_rep2_dsRNase_minusP

description: P. patens protonema with 00 minutes ABA,dsRNase treated, without proteinase K

value: 00 min ABA


title: (Rd): leg, collected 84h after amputation, adult animal 21, R side, distal part [Rd_84_R_21]

description: Regeneration dataset (Rd): leg, collected 84h after amputation, from adult animal 21, R side. distal part of the leg.


title: 30min_rep2_ssRNase_plusP

description: P. patens protonema with 30 minutes ABA, ssRNase treated, protein kinase treated


title: 00min_rep1_dsRNase_minusP

description: P. patens protonema with 00 minutes ABA, dsRNase treated, without proteinase K


title: 30min_rep1_ssRNase_plusP


title: (Rd): leg, collected 84h after amputation, adult animal 20, L side, distal part [Rd_84_L_20]

description: Regeneration dataset (Rd): leg, collected 84h after amputation, from adult animal 20, L side. distal part of the leg.


title: 00min_rep2_ssRNase_minusP

description: P. patens protonema with 00 minutes ABA, ssRNase treated, without proteinase K


title: (Rd): leg, collected 84h after amputation, adult animal 19, R side, distal part [Rd_84_R_19]

description: Regeneration dataset (Rd): leg, collected 84h after amputation, from adult animal 19, R side. distal part of the leg.


title: 00min_rep2_dsRNase_plusP

description: P. patens protonema with 00 minutes ABA, dsRNAse treated, proteinase K treated


title: (Rd): leg, collected 84h after amputation, adult animal 19, L side, distal part [Rd_84_L_19]

description: Regeneration dataset (Rd): leg, collected 84h after amputation, from adult animal 19, L side. distal part of the leg.


title: (Rd): leg, collected 72h after amputation, adult animal 41, L side, distal part [Rd_72_L_41]

description: Regeneration dataset (Rd): leg, collected 72h after amputation, from adult animal 41, L side. distal part of the leg.


title: (Rd): leg, collected 96h after amputation, adult animal 46, L side, distal part [Rd_96_L_46]

description: Regeneration dataset (Rd): leg, collected 96h after amputation, from adult animal 46, L side. distal part of the leg.


title: (Rd): leg, collected 72h after amputation, adult animal 41, R side, distal part [Rd_72_R_41]

description: Regeneration dataset (Rd): leg, collected 72h after amputation, from adult animal 41, R side. distal part of the leg.


title: 00min_rep2_ssRNase_plusP

description: P. patens protonema with 00 minutes ABA, ssRNase treated, protein kinase treated


title: (Rd): leg, collected 72h after amputation, adult animal 39, R side, distal part [Rd_72_R_39]

description: Regeneration dataset (Rd): leg, collected 72h after amputation, from adult animal 39, R side. distal part of the leg.


title: 00min_rep1_dsRNase_plusP


title: 00min_rep1_ssRNase_plusP


title: (Rd): leg, collected 72h after amputation, adult animal 39, L side, distal part [Rd_72_L_39]

description: Regeneration dataset (Rd): leg, collected 72h after amputation, from adult animal 39, L side. distal part of the leg.


title: 00min_rep1_ssRNase_minusP


title: Pp_60min_ABA_rep2

data_processing:
Adapters were trimmed with cutadapt -f fastq -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG-e 0.06 -O 6 -m 14
Reads were mapped with tophat --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive  --no-coverage-search  -p 4 -o
HTSeq was used to create read counts from the aligned BAM files
Genome_build: P.pates_318
Supplementary_files_format_and_content: Read counts are presented in tab-delimited format (*mRNA_read_counts.txt) with transcript ID in the first column and the number of reads in the second column; variance stabilize transformed values are calculated by DESeq2 and found in allDays_VSTvalues.txt

extract_protocol:
Total RNA extracted using¬†Trizol¬†Reagent per the manufacturer's protocol
TruSeq Stranded mRNA-seq

value: 60 minutes ABA


title: Pp_60min_ABA_rep1


title: (Rd): leg, collected 72h after amputation, adult animal 38, R side, distal part [Rd_72_R_38]

description: Regeneration dataset (Rd): leg, collected 72h after amputation, from adult animal 38, R side. distal part of the leg.


title: Pp_30min_ABA_rep2

value: 30 minutes ABA


title: (Rd): leg, collected 60h after amputation, adult animal 15, L side, distal part [Rd_60_L_15]

description: Regeneration dataset (Rd): leg, collected 60h after amputation, from adult animal 15, L side. distal part of the leg.


title: Pp_00min_ABA_rep2

value: 00 minutes ABA


title: (Rd): leg, collected 60h after amputation, adult animal 17, L side, distal part [Rd_60_L_17]

description: Regeneration dataset (Rd): leg, collected 60h after amputation, from adult animal 17, L side. distal part of the leg.


title: (Rd): leg, collected 84h after amputation, adult animal 20, R side, distal part [Rd_84_R_20]

description: Regeneration dataset (Rd): leg, collected 84h after amputation, from adult animal 20, R side. distal part of the leg.


title: (Rd): leg, collected 60h after amputation, adult animal 15, R side, distal part [Rd_60_R_15]

description: Regeneration dataset (Rd): leg, collected 60h after amputation, from adult animal 15, R side. distal part of the leg.


title: (Rd): leg, collected 60h after amputation, adult animal 14, R side, distal part [Rd_60_R_14]

description: Regeneration dataset (Rd): leg, collected 60h after amputation, from adult animal 14, R side. distal part of the leg.


title: Pp_30min_ABA_rep1


title: Pp_00min_ABA_rep1


title: (Rd): leg, collected 60h after amputation, adult animal 14, L side, distal part [Rd_60_L_14]

description: Regeneration dataset (Rd): leg, collected 60h after amputation, from adult animal 14, L side. distal part of the leg.


title: (Rd): leg, collected 48h after amputation, adult animal 69, L side, distal part [Rd_48_L_69]

description: Regeneration dataset (Rd): leg, collected 48h after amputation, from adult animal 69, L side. distal part of the leg.


title: (Rd): leg, collected 96h after amputation, adult animal 44, L side, distal part [Rd_96_L_44]

description: Regeneration dataset (Rd): leg, collected 96h after amputation, from adult animal 44, L side. distal part of the leg.


title: (Rd): leg, collected 48h after amputation, adult animal 66, R side, distal part [Rd_48_R_66]

description: Regeneration dataset (Rd): leg, collected 48h after amputation, from adult animal 66, R side. distal part of the leg.


title: (Rd): leg, collected 36h after amputation, adult animal 92, R side, distal part [Rd_36_R_92]

description: Regeneration dataset (Rd): leg, collected 36h after amputation, from adult animal 92, R side. distal part of the leg.


title: (Rd): leg, collected 48h after amputation, adult animal 67, R side, distal part [Rd_48_R_67]

description: Regeneration dataset (Rd): leg, collected 48h after amputation, from adult animal 67, R side. distal part of the leg.


title: (Rd): leg, collected 48h after amputation, adult animal 67, L side, distal part [Rd_48_L_67]

description: Regeneration dataset (Rd): leg, collected 48h after amputation, from adult animal 67, L side. distal part of the leg.


title: (Rd): leg, collected 48h after amputation, adult animal 66, L side, distal part [Rd_48_L_66]

description: Regeneration dataset (Rd): leg, collected 48h after amputation, from adult animal 66, L side. distal part of the leg.


title: Pediatric AD patient 1 plasmal exosome

city: Beijing

first: Teng

last: Zhu

address: 56 South Lishi Road

department: Dermatology

country: China

institute: Beijing Children's Hospital

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 22.0
Supplementary files format and content: Excel, expression profiles (raw, norm)

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from plasma exosomes with TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: peripheral blood

tag: disease state

value: Pediatric AD

tag: sample type

value: plasma exosome


title: (Rd): leg, collected 36h after amputation, adult animal 91, L side, distal part [Rd_36_L_91]

description: Regeneration dataset (Rd): leg, collected 36h after amputation, from adult animal 91, L side. distal part of the leg.

tag: dissected part of the leg

tag: collection time (hours post amputation)


title: Healthy control 3 plasmal exosome

value: control


title: Pediatric AD patient 5 plasmal exosome


title: Healthy control 5 plasmal exosome


title: Healthy control 2 plasmal exosome


title: Healthy control 4 plasmal exosome


title: Pediatric AD patient 4 plasmal exosome


title: Pediatric AD patient 2 plasmal exosome


title: Healthy control 1 plasmal exosome


title: Pediatric AD patient 3 plasmal exosome


title: (Rd): leg, collected 36h after amputation, adult animal 91, R side, distal part [Rd_36_R_91]

description: Regeneration dataset (Rd): leg, collected 36h after amputation, from adult animal 91, R side. distal part of the leg.

tag: collection time (hours post fertilization)

tag: collection time (days relative to molting)

value: R


title: (Rd): leg, collected 36h after amputation, adult animal 89, R side, distal part [Rd_36_R_89]

description: Regeneration dataset (Rd): leg, collected 36h after amputation, from adult animal 89, R side. distal part of the leg.

tag: animal id

tag: left or right leg


title: (Rd): leg, collected 24h after amputation, adult animal 63, R side, distal part [Rd_24_R_63]

description: Regeneration dataset (Rd): leg, collected 24h after amputation, from adult animal 63, R side. distal part of the leg.


title: (Rd): leg, collected 24h after amputation, adult animal 62, R side, distal part [Rd_24_R_62]

description: Regeneration dataset (Rd): leg, collected 24h after amputation, from adult animal 62, R side. distal part of the leg.


title: (Rd): leg, collected 24h after amputation, adult animal 63, L side, distal part [Rd_24_L_63]

description: Regeneration dataset (Rd): leg, collected 24h after amputation, from adult animal 63, L side. distal part of the leg.


title: (Rd): leg, collected 24h after amputation, adult animal 62, L side, distal part [Rd_24_L_62]

description: Regeneration dataset (Rd): leg, collected 24h after amputation, from adult animal 62, L side. distal part of the leg.


title: EMFF_4

city: Shanghai

first: Yangshuo

last: Li

address: 168 Changhai Road

institute: Navy Medical University

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2.
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM value for each Sample

source_name: follicular fluid

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) > 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

value: follicular fluid

value: EMFF


title: EMFF_3


title: EMFF_2


title: (Rd): leg, collected 36h after amputation, adult animal 92, L side, distal part [Rd_36_L_92]

description: Regeneration dataset (Rd): leg, collected 36h after amputation, from adult animal 92, L side. distal part of the leg.

value: L


title: EMFF_5


title: EMFF_6


title: EMFF_1


title: COFF_6


title: (Rd): leg, collected 24h after amputation, adult animal 61, R side, distal part [Rd_24_R_61]

description: Regeneration dataset (Rd): leg, collected 24h after amputation, from adult animal 61, R side. distal part of the leg.


title: COFF_4


title: (Rd): leg, collected 12h after amputation, adult animal 87, L side, distal part [Rd_12_L_87]

description: Regeneration dataset (Rd): leg, collected 12h after amputation, from adult animal 87, L side. distal part of the leg.


title: (Rd): leg, collected 24h after amputation, adult animal 61, L side, distal part [Rd_24_L_61]

description: Regeneration dataset (Rd): leg, collected 24h after amputation, from adult animal 61, L side. distal part of the leg.


title: COFF_3


title: (Rd): leg, collected 12h after amputation, adult animal 87, R side, distal part [Rd_12_R_87]

description: Regeneration dataset (Rd): leg, collected 12h after amputation, from adult animal 87, R side. distal part of the leg.


title: (Rd): leg, collected 12h after amputation, adult animal 86, R side, distal part [Rd_12_R_86]

description: Regeneration dataset (Rd): leg, collected 12h after amputation, from adult animal 86, R side. distal part of the leg.


title: COFF_5


title: 081715 11P4M podo low ecadh high NL

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA sequencing analysis was performed by BioWardrobe
Adapter sequences were trimmed from unaligned reads using TrimGalore.
Alignment of trimmed raw sequencing data to Homo sapiens (GRCh37/hg19) reference genome is done by STAR allowing maximum 5 mismatches and reporting only uniquelly mapped reads.
Mapped reads are then being sorted and indexed by Samtools sort and index utilities. Sorted reads are used for RPKM calculation.
Assembly: hg19
Supplementary files format and content: Excel file containing read counts per gene including RefSeq ID, gene symbol, raw read count, and RPKM-normalized read count

source_name: esophageal biopsy

growth_protocol: Three biopsies collected from the distal esophagus typically yielded ~2,500–10,000 epithelial cells in each subpopulation, which were subsequently collected into RPMI-1640 media supplemented with 10% FBS and pelleted/centrifuged for immediate RNA isolation procedures

extract_protocol:
RNeasy Micro Kit (Qiagen).
Total RNA was amplified using the Ovation RNA-Seq System v2 assay (Tecan Genomics) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies).

value: esophageal biopsy

tag: cell type

value: suprabasal epithelium

value: Healthy controls


title: COFF_2

tag: tissue


title: 011316 11MGC podo low ecadh high NL


title: COFF_1


title: 112415 11PT1 podo low ecadh high NL


title: 112415 11PT1 podo high ecadh high NL

value: basal epithelium


title: (Rd): leg, collected 0h after amputation, adult animal 77, L side, distal part [Rd_0_L_77]

description: Regeneration dataset (Rd): leg, collected 0h after amputation, from adult animal 77, L side. distal part of the leg.

value: distal


title: (Rd): leg, collected 0h after amputation, adult animal 81, R side, distal part [Rd_0_R_81]

description: Regeneration dataset (Rd): leg, collected 0h after amputation, from adult animal 81, R side. distal part of the leg.


title: (Rd): leg, collected 12h after amputation, adult animal 86, L side, distal part [Rd_12_L_86]

description: Regeneration dataset (Rd): leg, collected 12h after amputation, from adult animal 86, L side. distal part of the leg.


title: (Rd): leg, collected 0h after amputation, adult animal 80, L side, distal part [Rd_0_L_80]

description: Regeneration dataset (Rd): leg, collected 0h after amputation, from adult animal 80, L side. distal part of the leg.


title: (Rd): leg, collected 12h after amputation, adult animal 85, R side, distal part [Rd_12_R_85]

description: Regeneration dataset (Rd): leg, collected 12h after amputation, from adult animal 85, R side. distal part of the leg.


title: 011316 11MGC podo high ecadh high NL


title: 081715 11P4M podo high ecadh high NL


title: (Rd): leg, collected 0h after amputation, adult animal 81, L side, distal part [Rd_0_L_81]

description: Regeneration dataset (Rd): leg, collected 0h after amputation, from adult animal 81, L side. distal part of the leg.


title: 011116 11RAP podo low ecadh high NL