title: 739 F 136


title: pair 1, diagnosis Schiz, replicate 2

status: Public on Jul 01 2018

type: RNA

city: Pittsburgh

first: David

last: Lewis

state: PA

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

country: USA

institute: University of Pittsburgh

hyb_protocol: CDNA was synthesized and amplified using the Ovation Pico WTA System.

scan_protocol: Loaded on an Affymetrix GeneChip® U219.

data_processing: Expression intensities were extracted from Affymetrix Expression Console and normalized using Robust Multi-array Average Express.

label: Encore Biotin module (Nugen)

molecule: total RNA

organism: Homo sapiens

source_name: pair 1_diagnosis Schiz

label_protocol: Labeled using the Encore Biotin module (Nugen).

growth_protocol: Brain specimens were obtained during autopsies conducted at the Allegheny County Office of the Medical Examiner (Pittsburgh, PA) after consent was obtained from the next-of-kin.

extract_protocol: For each sample, RNA was extracted using the QIAGEN® RNeasy Plus Micro kit (QIAGEN, Valencia).

treatment_protocol: An independent committee of experienced research clinicians made consensus DSM-IV diagnoses for each subject using information obtained from medical records and structured diagnostic interviews conducted with the decedent’s family members.

tag: pair id

value: pair 1

tag: dsm-iv diagnoses

value: Chronic undifferentiated schizophrenia

tag: subject group

value: schizophrenia

tag: tissue

value: dorsolateral prefrontal cortex (DLPFC)

tag: cell type

value: parvalbumin (PV) neurons


title: pair 27, diagnosis Control, replicate 2

source_name: pair 27_diagnosis Control

value: pair 27

value: Unaffected Comparison

value: Control


title: breast cancer with BSC_LR014 [nanostring]

city: Lund

first: Martin

last: Sjöström

address: Scheelevägen 2

country: Sweden

institute: Lund University

hyb_protocol: Hybridization Protocol for nCounter XT CodeSet Gene Expression assays (version: APRIL 2016 MAN-10023-09)

scan_protocol: Nanostring Digital Analyzer with RLF file: Sjostrom_1_C4440. FOV: 555

data_processing:
Summarization of RCC files with nSolver, no further processing for the raw data (included in the sample data table)
The 'final_nano_data (SUPPLEMENTAL FILE).csv' contains the final filtered, processed data as described below;
Quality filtering of the probes was applied based on negative control probes. Probes expressed above the negative controls (geometric mean) in less than 80% the samples were removed from further analysis. This affected 7/248 probes (AKNA, KCNMB2, OR8G2, hcg2023290, GCSH, PRAME and MYOG1). Samples were then normalized based on the positive control probes and a normalization factor calculated as the average geometric mean of positive controls divided by the sample specific geometric mean of positive controls. As a quality filter for technical problems, samples with positive normalization factors <0.3 or >3 were removed, excluding four samples (three from the discovery set and one from the validation set). The data was further normalized based on housekeeping genes and the seven most stable housekeeping genes from analysis with the NormqPCR package were used (MRPL19, PUM1, SF3A1, PSMC4, HPRT1, ACTB, PGK1). A normalization factor was calculated as the average geometric mean of the seven housekeeping genes divided with the geometric mean of the seven housekeeping genes of each sample. As a quality filter for sample problems, samples with normalization factors <0.1 or >10 were excluded (25 samples were excluded, one from the discovery cohort and 24 from the validation cohort). Finally, log2 transformation was performed. For the final analysis, 168 samples were used from the discovery cohort and 139 from the validation cohort.

source_name: breast cancer operated with breast conserving surgery (BSC)

extract_protocol: Qiagen AllPrep kit with Qiacube automatization

tag: cohort

value: training

tag: biobank center

tag: er (estrogen receptor status)

value: pos

tag: rt (radiotherapy)

tag: lr (local recurrence)

tag: ibtr (ipsilateral breast tumor recurrence)

tag: follow-up time (years)


title: pair 27, diagnosis Control, replicate 1


title: 5156 M 130

city: Bar Harbor

first: Jason

middle: A

last: Bubier

state: ME

address: 600 Main St

institute: The Jackson Laboratory

hyb_protocol: The resulting cRNA was column purified, quantitated, and diluted to 150 ng/µl in RNase free water. The sample was then applied to a BeadChip (Illumina MouseWG-6 v2 BeadChip) and hybridized overnight at 58ºC to allow the cRNA to anneal to the oligonucleotides corresponding to their specific gene. The BeadChips were then washed, blocked with E1, and fluorescently labeled with streptavidin-Cy3

scan_protocol: BeadChips were dried by spinning 300 rpm for 4 min in a benchtop centrifuge and imaged using the Illumina BeadArray Reader

data_processing: Image data obtained from the BeadArray Reader was analyzed using BeadStudio version 3.0.19 with Gene Expression module 3.0.14. Rank invariant normalization was used with no background subtraction. We filtered the probes that targeted polymorphic sequence due to the bias introduced by microarray probe-target variation in genetic studies and the high density of mouse polymorphisms in the CC. The probes on the Ilumina Mouse WG-6v2.0 Bead Chip were tested by comparing the sequenced genomes from Sanger Wellcome Trust (https://www.sanger.ac.uk/) 78 to determine if they contained a SNP between the strains. 8,972 probes were removed due to SNPs in one of the eight strains and 36,308 probes remained for subsequent QTL mapping and genetic correlation analysis.

organism: Mus musculus

source_name: cecal tissue

label_protocol: All assay methods conformed to the exact protocol listed in the Whole-Genome Gene Expression Assay Manual. Diluted RNA (11 µl, ~500ng) was converted to biotinylated cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). First, single-stranded cDNA was synthesized from the total RNA using the T7 Oligo(dT) primer, then converted to double-stranded cDNA using the combination of DNA polymerase and RNase H. Second, the cDNA was transcribed to biotinylated cRNA using the T7 enzyme and biotin-labled NTP’s.

extract_protocol: Each dissected cecum was filled with a solution of 1.5mM KCL/96 mM NaCl/27mM NaCitrate/8mM KH2PO4/5.6 mM Na2HPO4, pH7.3. were incubated at 37°C after which the intestines were rinsed and filled with Phosphate-buffered saline/1.5 mM EDTA/0.5 mM dithiothreitol. They were incubated at 37°C in a conical centrifuge tube. After an incubation time of 15 minutes, the tube was centrifuged at 900 x g. The resulting pellet was rinsed 3x in Phosphate-buffered saline (centrifuged at 900 x g for 5 minutes after each rinse). The resulting cell pellet was suspended in Trizol (Invitrogen) and RNA was purified by column chromatography as specified by the manufacturer’s protocol. Purified total RNA was fluorescently labeled with riboGreen (Invitrogen) and quantitated using a Spectamax Gemini XPS spectrofluorometer (Molecular Devices). RNA was then prepared for assay by diluting to 50 ng/µl in RNase free water and transferring to a clean 1.5 ml assay tube.

tag: gender

value: M

tag: animal id


title: breast cancer with BSC_LR012 [nanostring]

value: neg


title: breast cancer with BSC_LR016 [nanostring]


title: breast cancer with BSC_LR011 [nanostring]


title: breast cancer with BSC_LR010 [nanostring]


title: breast cancer with BSC_LR009 [nanostring]


title: pair 26, diagnosis Control, replicate 2

source_name: pair 26_diagnosis Control

value: pair 26


title: pair 26, diagnosis Control, replicate 1


title: 157 M41


title: 1635 F 140

value: F


title: 232 F 144


title: breast cancer with BSC_LR007 [nanostring]


title: pair 25, diagnosis Control, replicate 1

source_name: pair 25_diagnosis Control

value: pair 25


title: pair 25, diagnosis Control, replicate 2


title: pair 24, diagnosis Control, replicate 1

source_name: pair 24_diagnosis Control

value: pair 24


title: 1288 M 142


title: pair 24, diagnosis Control, replicate 2


title: 896 F 53


title: pair 23, diagnosis Control, replicate 2

source_name: pair 23_diagnosis Control

value: pair 23


title: 3571 M 55


title: breast cancer with BSC_LR003 [nanostring]


title: breast cancer with BSC_LR005 [nanostring]


title: 1519 M 140


title: breast cancer with BSC_LR001 [nanostring]


title: pair 23, diagnosis Control, replicate 1


title: pair 22, diagnosis Control, replicate 2

source_name: pair 22_diagnosis Control

value: pair 22


title: pair 22, diagnosis Control, replicate 1


title: 5549 M 130


title: 3168 F 67


title: 1519 F 137


title: breast cancer with BSC_LR002 [nanostring]


title: pair 36, diagnosis Control, replicate 2

source_name: pair 36_diagnosis Control

value: pair 36


title: 1119 F 135


title: 99_S48_R1_001

type: SRA

city: Columbia

first: Matthew

last: Lucy

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri

library_source: transcriptomic

data_processing:
The raw sequences (fastq) were subjected to adapter removal and quality trimming using fqtrim (https://ccb.jhu.edu/software/fqtrim/).
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/) .
To produce a global gene annotation file (GTF) for comprehensive quantification of gene expressions across the samples, the sorted binary alignment maps of sequence reads from each sample were assembled to generate transcriptomes those were then merged, along with the gene annotations from reference genome assembly.
The transcript assembly step was accomplished using the software ‘Stringtie’ (https://ccb.jhu.edu/software/stringtie/) .
The merged global transcriptome was then used in Stringtie to quantify transcript abundance of each sample. Differential expression analysis between sample groups were performed by robustly fitting the expression data to a weighted generalized linear model using edgeR robust.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.

organism: Bos taurus

source_name: endometrium

extract_protocol:
Total RNA was extracted from endometrium using a Trizol-based method
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

tag: week after calving

tag: cyclicity status

value: not cycling at week five after calving


title: 792 F 51


title: 3087 F 44


title: pair 21, diagnosis Control, replicate 1

source_name: pair 21_diagnosis Control

value: pair 21

value: dorsolateral prefrontal cortex (DLPFC)


title: 5181 M 144


title: 2650 F 44


title: 205 M 44


title: 70 F 55


title: pair 36, diagnosis Control, replicate 1

value: parvalbumin (PV) neurons


title: 5118 M 126


title: 2595 F 46


title: pair 33, diagnosis Control, replicate 1

source_name: pair 33_diagnosis Control

value: pair 33

value: Unaffected Comparison


title: pair 34, diagnosis Control, replicate 1

source_name: pair 34_diagnosis Control

value: pair 34

value: Control


title: 98_S47_R1_001

value: cycling progesterone at week five after calving


title: 97_S46_R1_001


title: 1009 M 140

value: M


title: pair 35, diagnosis Control, replicate 1

source_name: pair 35_diagnosis Control

value: pair 35


title: pair 32, diagnosis Control, replicate 1


title: pair 33, diagnosis Control, replicate 2


title: pair 31, diagnosis Control, replicate 2

source_name: pair 31_diagnosis Control

value: pair 31


title: 96_S45_R1_001


title: pair 32, diagnosis Control, replicate 2

source_name: pair 32_diagnosis Control

value: pair 32


title: pair 31, diagnosis Control, replicate 1


title: 95_S44_R1_001


title: 1141 M 138


title: 94_S43_R1_001

value: cycling no progesterone at week five after calving


title: 93_S42_R1_001


title: 92_S41_R1_001


title: 754 M 49


title: 91_S40_R1_001


title: breast cancer with BSC_LR054 [nanostring]

value: training

value: pos


title: 5118 F 124

value: F


title: 3549 F 60


title: pair 30, diagnosis Control, replicate 2

source_name: pair 30_diagnosis Control

value: pair 30


title: 749 N 59

value: N


title: pair 29, diagnosis Control, replicate 1

source_name: pair 29_diagnosis Control

value: pair 29

value: dorsolateral prefrontal cortex (DLPFC)


title: 87_S36_R1_001


title: 690 M 45


title: 667 M 59


title: 692 M 156


title: pair 8, diagnosis Control, replicate 2

source_name: pair 8_diagnosis Control

value: pair 8

value: parvalbumin (PV) neurons


title: pair 30, diagnosis Control, replicate 1

value: Unaffected Comparison


title: pair 35, diagnosis Control, replicate 2

value: Control


title: pair 29, diagnosis Control, replicate 2


title: pair 20, diagnosis Control, replicate 1

source_name: pair 20_diagnosis Control

value: pair 20


title: 652 M 143

source_name: cecal tissue

value: M


title: 810 F 52


title: 3154 M 60


title: 90_S39_R1_001

value: not cycling at week five after calving


title: 691 F 48


title: pair 9, diagnosis Control, replicate 2

source_name: pair 9_diagnosis Control

value: pair 9


title: pair 20, diagnosis Control, replicate 2


title: 3232 M 53


title: pair 9, diagnosis Control, replicate 1


title: 3118 M 50


title: pair 8, diagnosis Control, replicate 1


title: 88_S37_R1_001


title: pair 21, diagnosis Control, replicate 2

value: pair 21


title: 83_S35_R1_001

value: cycling progesterone at week five after calving


title: 82_S34_R1_001


title: 89_S38_R1_001


title: 79_S31_R1_001

value: cycling no progesterone at week five after calving


title: 80_S32_R1_001


title: 363 F 46


title: pair 6, diagnosis Control, replicate 1

source_name: pair 6_diagnosis Control

value: pair 6


title: pair 7, diagnosis Control, replicate 2

source_name: pair 7_diagnosis Control

value: pair 7


title: 75_S29_R1_001


title: 2650 M 47


title: 76_S30_R1_001


title: 74_S28_R1_001


title: 70_S26_R1_001


title: 72_S27_R1_001


title: 81_S33_R1_001


title: 69_S25_R1_001


title: pair 7, diagnosis Control, replicate 1


title: pair 5, diagnosis Control, replicate 2

source_name: pair 5_diagnosis Control

value: pair 5


title: KO_Alkb_and_NaBH4_Treated_TRAC-Seq.fastq.gz

city: Boston

first: Shuibin

last: Lin

address: 1 Blackfan Circle

institute: Boston Childrens Hospital

description:
small RNA-TRAC-Seq
m7G_TRAC-Seq_score.txt

data_processing:
Library strategy: TRAC-Seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to mouse reference genome (mm10) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to mouse rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For m7G-MeRIP-Seq and TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file showing the normalized reads

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells R1/E  were cultured in LIF/serum medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockout was mediated by CRISPR/cas9.

tag: genotype/variation

value: Mettl1 knockout

tag: differentiation

value: undifferentiated


title: 5370 M 141


title: pair 5, diagnosis Control, replicate 1

tag: pair id

tag: dsm-iv diagnoses

value: dorsolateral prefrontal cortex (DLPFC)


title: 3154 F 57

value: F


title: 2417 F 49


title: 70 M 56


title: WT_Alkb_and_NaBH4_Treated_TRAC-Seq.fastq.gz

value: wild type


title: pair 4, diagnosis Control, replicate 1

source_name: pair 4_diagnosis Control

value: pair 4

value: Unaffected Comparison

tag: subject group

tag: tissue

value: parvalbumin (PV) neurons


title: pair 6, diagnosis Control, replicate 2

value: Control

tag: cell type


title: pair 3, diagnosis Control, replicate 2

source_name: pair 3_diagnosis Control

value: pair 3


title: 3011 M 56

value: M


title: pair 4, diagnosis Control, replicate 2


title: pair 3, diagnosis Control, replicate 1


title: 2227 F 41


title: 68_S24_R1_001

source_name: endometrium

value: not cycling at week five after calving


title: 67_S23_R1_001

value: cycling progesterone at week five after calving


title: KO_Alkb_Treated_Input_for_TRAC-Seq

description:
small RNA-Seq
m7G_TRAC-Seq_score.txt


title: 821 M 46


title: pair 2, diagnosis Control, replicate 1

source_name: pair 2_diagnosis Control

value: pair 2


title: WT_Alkb_Treated_Input_for_TRAC-Seq

description:
small RNA-Seq
m7G_TRAC-Seq_score.txt


title: 66_S22_R1_001


title: KO_Alkb_Treated_smRNA_m7G_MeRIP-Seq_repeat2

description:
small RNA-MeRIP-Seq
m7G_MeRIP-Seq_reads.txt

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to mouse reference genome (mm10) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to mouse rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For m7G-MeRIP-Seq and TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file showing the normalized reads


title: 65_S21_R1_001


title: 64_S20_R1_001

value: cycling no progesterone at week five after calving


title: WT_Alkb_Treated_smRNA_m7G_MeRIP-Seq_repeat2


title: 63_S19_R1_001


title: KO_Alkb_Treated_smRNA_m7G_MeRIP-Seq_repeat1


title: 61_S18_R1_001


title: 5515 M 135


title: KO_Alkb_Treated_smRNA_Input_repeat2

description:
small RNA-Seq
m7G_MeRIP-Seq_reads.txt


title: pair 19, diagnosis Control, replicate 2

source_name: pair 19_diagnosis Control

value: pair 19


title: WT_Alkb_Treated_smRNA_m7G_MeRIP-Seq_repeat1


title: pair 19, diagnosis Control, replicate 1


title: 5140 F 126


title: 5140 M 129


title: 59_S17_R1_001


title: 5389 M 146


title: pair 2, diagnosis Control, replicate 2


title: KO_Alkb_Treated_smRNA_Input_repeat1

description:
small RNA-Seq
m7G_MeRIP-Seq_reads.txt


title: 3548 F 56


title: pair 18, diagnosis Control, replicate 1

source_name: pair 18_diagnosis Control

value: pair 18


title: pair 18, diagnosis Control, replicate 2


title: 58_S16_R1_001


title: WT_Alkb_Treated_smRNA_Input_repeat2

description:
small RNA-Seq
m7G_MeRIP-Seq_reads.txt


title: pair 17, diagnosis Control, replicate 1

source_name: pair 17_diagnosis Control

value: pair 17


title: 863 M 52


title: pair 17, diagnosis Control, replicate 2


title: 863 F 53


title: 57_S15_R1_001


title: 780 F 50


title: part2_Fir1i_rep2

city: Shanghai

first: Qing

last: Jing

state: Shanghai

address: 320 Yue Yang Road

department: Institute of Health Sciences

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

description: Total RNA was hybridized on a custom-designed 8*67K microarray.

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: The raw data was normalized with Quantile embedded in GeneSpring Software GX 12.6.1 (Agilent technologies, Santa Clara, CA, US).

organism: Schmidtea mediterranea

source_name: planarian tissues far from the wound

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

growth_protocol: All planarians for microarray were maintained in clean 1 X Montjuic salts at 21℃ in the dark.

extract_protocol: ‘part1’ and ‘part2’ RNA was harvested with Trizol (Invitrogen).

treatment_protocol: planarians were fed 2 times Fir1 dsRNA, and amputated post-pharynx at Day 8. The tail pieces were left for regenerating 2 days, and part1 and part2 region  were separated immediately prior to RNA extration.

value: planarian tissues far from the wound


title: WT_Alkb_Treated_smRNA_Input_repeat1

description:
small RNA-Seq
m7G_MeRIP-Seq_reads.txt

value: undifferentiated


title: WT_No-Alkb_smRNA_Input_repeat2

description:
small RNA-Seq
m7G_MeRIP-Seq_reads.txt


title: 56_S14_R1_001


title: pair 16, diagnosis Control, replicate 2

source_name: pair 16_diagnosis Control

value: pair 16

value: dorsolateral prefrontal cortex (DLPFC)


title: part2_controli_rep2

description: Total RNA was hybridized on a custom-designed 8*66K microarray.


title: 54_S12_R1_001


title: WT_No-Alkb_smRNA_Input_repeat1

description:
small RNA-Seq
m7G_MeRIP-Seq_reads.txt

value: wild type


title: KO_RiboSeq

description:
RiboSeq
RiboSeq_reads.txt

data_processing:
Library strategy: Ribo-Seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to mouse reference genome (mm10) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to mouse rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For m7G-MeRIP-Seq and TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file showing the normalized reads

value: Mettl1 knockout


title: KO_Input_for_RiboSeq

description:
RiboSeq
RiboSeq_reads.txt


title: pair 15, diagnosis Control, replicate 1

source_name: pair 15_diagnosis Control

value: pair 15

value: Unaffected Comparison

value: parvalbumin (PV) neurons


title: part2_controli_rep1

description: Total RNA was hybridized on a custom-designed 8*64K microarray.


title: 52_S10_R1_001


title: WT_RiboSeq

description:
RiboSeq
RiboSeq_reads.txt


title: 51_S9_R1_001


title: WT_Input_for_RiboSeq

description:
RiboSeq
RiboSeq_reads.txt


title: 55_S13_R1_001


title: pair 16, diagnosis Control, replicate 1

value: Control


title: 49_S8_R1_001

value: not cycling at week five after calving


title: pair 14, diagnosis Control, replicate 1

source_name: pair 14_diagnosis Control

value: pair 14


title: 48_S7_R1_001


title: part1_Fir1i_rep2

description: Total RNA was hybridized on a custom-designed 8*63K microarray.

source_name: planarian tissues near the wound

value: planarian tissues near the wound


title: part2_Fir1i_rep1

description: Total RNA was hybridized on a custom-designed 8*65K microarray.


title: pair 13, diagnosis Control, replicate 2

source_name: pair 13_diagnosis Control

value: pair 13


title: pair 14, diagnosis Control, replicate 2


title: pair 13, diagnosis Control, replicate 1


title: part1_controli_rep2

description: Total RNA was hybridized on a custom-designed 8*62K microarray.


title: part1_Fir1i_rep1

description: Total RNA was hybridized on a custom-designed 8*61K microarray.


title: pair 15, diagnosis Control, replicate 2


title: mESC_Mettl1_KO2_Day6

description:
RNA-Seq
mRNA_expression.txt

value: differentiation for 6 days


title: 53_S11_R1_001


title: part1_controli_rep1

description: Total RNA was hybridized on a custom-designed 8*60K microarray.


title: mESC_Mettl1_KO1_Day6

description:
RNA-Seq
mRNA_expression.txt


title: pair 12, diagnosis Control, replicate 2

source_name: pair 12_diagnosis Control

value: pair 12


title: mESC_WT_Day6

description:
RNA-Seq
mRNA_expression.txt


title: 45_S5_R1_001

value: cycling progesterone at week five after calving


title: mESC_Ctr_Day6

description:
RNA-Seq
mRNA_expression.txt


title: pair 11, diagnosis Control, replicate 2

source_name: pair 11_diagnosis Control

value: pair 11


title: 44_S4_R1_001


title: mESC_Mettl1_KO2_Day0

description:
RNA-Seq
mRNA_expression.txt

value: undifferentiated


title: 14_S3_R1_001


title: mESC_Mettl1_KO1_Day0

description:
RNA-Seq
mRNA_expression.txt


title: pair 11, diagnosis Control, replicate 1


title: pair 10, diagnosis Control, replicate 2

source_name: pair 10_diagnosis Control

value: pair 10


title: 47_S6_R1_001


title: mESC_WT_Day0

description:
RNA-Seq
mRNA_expression.txt

source_name: embryonic stem cells


title: pair 12, diagnosis Control, replicate 1

value: dorsolateral prefrontal cortex (DLPFC)


title: 12_S1_R1_001


title: pair 10, diagnosis Control, replicate 1


title: mESC_Ctr_Day0

description:
RNA-Seq
mRNA_expression.txt

value: wild type


title: 101_S50_R1_001


title: 100_S49_R1_001


title: sox32 amplicon 2 dpf, Embryo 4

city: San Francisco

first: Roland

middle: S

last: Wu

state: CA

address: 555 Mission Bay Blvd South MC3122

department: CVRI

institute: UCSF

description:
Whole embryo PCR amplicon
sox32 amplicon from 2 dpf embryo injected with multi-guide Cas9 RNP targeting sox32

library_source: genomic

data_processing:
Circular Consensus Sequences were generated using SMRT Link tools using the -bystrand option
Reads were filtered by minimum phred score
Reads were filtered by presence of adapter and sox32 sequence
Pooled samples were demultiplexed
Reads were revised based on reference sox32 sequence to decrease false-positive mutation calls
Genome_build: GRCz10
Supplementary_files_format_and_content: fasta files with each unique sox32 genomic sequence. sox32 amplicon counts are noted in the sequence name field.

molecule: genomic DNA

organism: Danio rerio

growth_protocol: Embryos were generated

extract_protocol:
Genomic DNA was extracted using Qiagen Dneasy Blood and Tissue DNA extraction kit
Amplicons generated using barcoded, gene-specific primers. Library generated using SMRTbell template prep
Amplicon Sequencing

treatment_protocol: 1-cell stage embryos were cell-injected with Cas9 RNP programmed with a pool of 4 guides directed at the sox32 coding sequence

tag: strain

value: EKW

tag: age

value: 2 dpf

tag: developmental stage

value: embryo


title: Lithospermum_officinale_Root

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
In this study we used three popular assemblers, Trinity program ver 2.6.5 and CLC Genomics Workbench 8.0.3 with their default paarmeters, and SOAPdenovo-Trans with kmer-size 41 and de novo assembly was generated by merging the assemblies obtained from each assemblers using clean reads from all the samples and was further processed by CD-HIT-EST program (Li and Godzik 2006) to remove sequence redundancies from the final assembly. This resulted in the final de novo transcriptome assembly of L. officinale, which consists of 77,047 unigenes with an impressive N50 value as 1524 bps.
We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 and RSEM respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were aligned on Lithospermum officinale de novo transcriptome assembly, and abundace were measured using RSEM. Content of each file contains Unigene_id , length, effective_length, expected_count, TPM and FPKM for each tissues. FPKM values for each tissues were used for furthur analysis.
Supplementary_files_format_and_content: Comma seperated value files includes Unigene_id, Unigene_length and FPKM values for each tissues. FPKM values were calculated using RSEM program. Results files for all tissues were used to extract FPKM values for each tissues, and were combined/aligned against Unigene_id
Supplementary_files_format_and_content: fasta file contain the de novo transcriptome assembly generated by merging individual assembly obtained by Trinity, CLC Genomics Workbench and SOAPdenovo-Trans

organism: Lithospermum officinale

growth_protocol: All three tissues, namely leaf, stem and root of L. officinale growing in the natural environment of Chiba University, Japan (located at 35°36′17.7″ N; 140°08′06.9″ E), and were harvested on May 2014.

extract_protocol:
Frozen samples of L. officinale were powdered using a Multi Beads Shocker (Yasui Kikai, Japan) for subsequent RNA extraction. Total RNA for each of the three tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.

treatment_protocol: Not applicable

value: Root


title: TruSeq_Universal miRNA Reference Kit_1 ug

city: Santa Cruz

first: Sergio

last: Barberan-Soler

address: 2161 Delaware Avenue

institute: Somagenics Inc

description: Processed data file: Raw_counts_Universal_miRNA.csv

data_processing:
Basecalling performed by Illumina RTA 1.18.54
Reads demultiplexed by NextSeq instrument
Reads trimmed of adapter with cutadapt with the following specifications: For TruSeq and RealSeq libraries: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 15; For NEXTFlex libraries: cutadapt -u 4 -a NNNNTGGAATTCTCGGGTGCCAAGG -m 15;  For QIASeq libraries: cutadapt -a AACTGTAGGCACCATCAAT -m 15
Trimmed reads were subsampled at random to 13 million reads per library
Subsampled reads were mapped  to index with the complete YM500v3 database (PMID:27899625); by using bowtie2 with the following parameters: bowtie2 -L8 --local
Raw counts of reads were obtained from sam files, by using samtools and picard-tools
Supplementary_files_format_and_content: raw counts for all small RNAs on YM500v3 database

extract_protocol: Libraries were prepared for 1 ug of Universal miRNA Reference Kit (Agilent)  with the following protocols: TruSeq Small RNA,  NEXTFlex Small RNA, QIASeq miRNA, and RealSeq-AC

tag: amount

value: 1 ug


title: NEXTFlex_Universal miRNA Reference Kit_1 ug


title: Universal miRNA Reference Kit_100ng

description:
100ng-lib
processed data file: Raw_counts_Agilent.txt

data_processing:
Basecalling performed by Illumina RTA 1.18.54.
Reads demultiplexed by Miniseq instrument.
Reads trimmed of adapter with cutadapt with the following specifications: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 15
Reads mapped to index with the complete set of human miRNAs from miRBase 21; by using bowtie2 with the following parameters: bowtie2 -L8 --local
Raw counts of reads were obtained from sam files, by using samtools and picard-tools.
Genome_build: hg19, miRBase 21
Supplementary_files_format_and_content: Raw_counts_Agilent.txt: Raw read counts for human miRNAs from miRBase 21.

extract_protocol: RealSeq-AC libraries were prepared according to manufacturer recommendation with 100 ng, 10 ng or 1 ng of Universal miRNA Reference Kit (Agilent). Libraries were purified as recommended with AMPure beads.


title: Universal miRNA Reference Kit_10ng

description:
10ng-lib
processed data file: Raw_counts_Agilent.txt

value: 10 ng


title: QIAseq_Universal miRNA Reference Kit_1 ug


title: sox32 amplicon 2 dpf, Embryo 5

source_name: 2 dpf embryo injected with multi-guide Cas9 RNP targeting sox32


title: pair 1, diagnosis Control, replicate 1

source_name: pair 1_diagnosis Control

value: pair 1

value: Unaffected Comparison

value: Control

value: parvalbumin (PV) neurons


title: sox32 amplicon 2 dpf, Embryo 2


title: Universal miRNA Reference Kit_1ng

description:
1ng-lib
processed data file: Raw_counts_Agilent.txt

value: 1 ng


title: 13_S2_R1_001

source_name: endometrium

value: cycling progesterone at week five after calving


title: sox32 amplicon 2 dpf, Embryo 1


title: RealSeq_Universal miRNA Reference Kit_1 ug


title: pair 1, diagnosis Control, replicate 2


title: Lithospermum_officinale_Leaf

value: Leaf


title: Lithospermum_officinale_Stem

value: Stem


title: sox32 amplicon 2 dpf, Embryo 6


title: sox32 amplicon 2 dpf, Embryo 3


title: tumor C3-1 basal SOX10 low sample3 (RNA-seq)

status: Public on Jun 29 2018

city: San Diego

first: Chi-Yeh

last: Chung

address: 10770 Science Center Drive

institute: Pfizer Inc.

description:
C3_SOX10_low_S3
C3_RNAseq_RPKM.csv
sox10_neg3

data_processing:
Sequencing reads were quality checked by FastQC.
Reads were mapped to the mouse genome (mm9) with Hisat2 (version 2.0.5).
Transcripts were assembled by Stringtie (version 1.3.1c).
Transcript quantification and differential expression analysis were performed by Ballgown (version 2.10.0).
Genome_build: mm9
Supplementary_files_format_and_content: Transcriptomic RPKM value for each sample

molecule: polyA RNA

source_name: Spontaneous C3-1-TAg tumors

growth_protocol: PY230 cells were grown as described in Bao et al, 2015 (see the Methods section for transplantation details)

extract_protocol:
The normal cells were dissected and FACS isolated from primary mammary tissue. The PY230 cells were transplanted into syngeneic mice to form tumors, and the tumors were dissected and FACS isolated. The C3-1-Tag cells were dissected and FACS isolated from spontaneous tumors. See the Methods section of the manuscript for details of isolation and FACS markers.
The RNA-seq samples were prepared with the SmartSeq2 protocol. Around 2000 freshly dissected and sorted cells from each cell type were processed. Full-length cDNA were generated, and their size distribution was checked with TapeStation to ensure good RNA quality.  The cDNA were then amplified with 18 PCR cycles, tagmentated and amplified again with 10 PCR cycles using Nextera XT kit (Illumina FC-131-1096). The sequencing library was purified with AMPure XP beads. 50 bp or 75 bp single-end sequencing was performed with Illumina HiSeq 2500
SmartSeq2 (Picelli et al., 2014)

value: FVB

value: Adult

value: Spontaneous tumors


title: tumor C3-1 basal SOX10 low sample4 (RNA-seq)

description:
C3_SOX10_low_S4
C3_RNAseq_RPKM.csv
sox10_neg4


title: tumor C3-1 basal SOX10 low sample2 (RNA-seq)

description:
C3_SOX10_low_S2
C3_RNAseq_RPKM.csv
sox10_neg2


title: tumor C3-1 basal SOX10 high sample4 (RNA-seq)

description:
C3_SOX10_high_S4
C3_RNAseq_RPKM.csv
sox10_pos4


title: tumor C3-1 basal SOX10 high sample5 (RNA-seq)

description:
C3_SOX10_high_S5
C3_RNAseq_RPKM.csv
sox10_pos5


title: tumor C3-1 basal SOX10 low sample1 (RNA-seq)

description:
C3_SOX10_low_S1
C3_RNAseq_RPKM.csv
sox10_neg1


title: SALS iPSC (SALS14)-derived MN

status: Public on Jun 30 2018

city: Sinjuku-ku, Tokyo

first: Koki

last: Fujimori

address: 35 Shinanomachi

department: Physiology

institute: Keio University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Normalized data contain MAS 5.0 signal. Normalizations were performed on sample subsets.

label: biotin

source_name: Spinal motor neurons differentiated from iPSC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease status

value: Sporadic ALS (SALS)

tag: donor

value: SALS patient2

value: Spinal motor neurons

tag: drug treatment

value: untreated

tag: iPSc source

value: Lymphoblastoid B-cell line (LCL)


title: SOD1-ALS iPSC (2SOD1-4)-derived MN

value: Familial ALS (FALS)

value: FALS patient4 carrying SOD1 mutation

value: T-lymphocyte


title: tumor C3-1 basal SOX10 high sample3 (RNA-seq)

description:
C3_SOX10_high_S3
C3_RNAseq_RPKM.csv
sox10_pos3


title: SALS iPSC (SALS12)-derived MN

value: SALS patient1


title: TARDBP-ALS iPSC (A21428)-derived MN with drug-treatment

value: FALS patient2 carrying TARDBP mutation

value: treated

value: Fibroblast


title: Healthy donor iPSC (WD39)-derived MN

value: Healthy

value: Healthy donor2


title: FUS-ALS iPSC (FALS2e3)-derived MN

value: FALS patient1 carrying FUS mutation


title: Healthy donor iPSC (409B2)-derived MN

value: Healthy donor1


title: Healthy donor iPSC (LKA10)-derived MN

value: Healthy donor3


title: SOD1-ALS iPSC (1SOD1-4)-derived MN with drug-treatment

value: FALS patient3 carrying SOD1 mutation


title: TARDBP-ALS iPSC (A21412)-derived MN


title: tumor C3-1 basal SOX10 high sample2 (RNA-seq)

description:
C3_SOX10_high_S2
C3_RNAseq_RPKM.csv
sox10_pos2

value: FVB

value: Adult

value: Spontaneous tumors


title: SALS iPSC (SALS17)-derived MN with drug-treatment

value: Sporadic ALS (SALS)

value: SALS patient3

value: Spinal motor neurons

value: Lymphoblastoid B-cell line (LCL)


title: SALS iPSC (SALS30)-derived MN

value: SALS patient4

value: untreated


title: SOD1-ALS iPSC (2SOD1-4)-derived MN with drug-treatment

value: Familial ALS (FALS)

value: FALS patient4 carrying SOD1 mutation

value: treated

value: T-lymphocyte


title: SALS iPSC (SALS17)-derived MN


title: SOD1-ALS iPSC (1SOD1-4)-derived MN


title: SALS iPSC (SALS14)-derived MN with drug-treatment

value: SALS patient2


title: FUS-ALS iPSC (FALS2e23)-derived MN with drug-treatment

value: FALS patient1 carrying FUS mutation

value: Fibroblast


title: SALS iPSC (SALS30)-derived MN with drug-treatment


title: Healthy donor iPSC (201B7)-derived MN

value: Healthy

value: Healthy donor1


title: TARDBP-ALS iPSC (A21412)-derived MN with drug-treatment

value: FALS patient2 carrying TARDBP mutation


title: FUS-ALS iPSC (FALS2e23)-derived MN


title: tumor PY230 basal SOX10 high sample2 (RNA-seq)

description:
PY230_basal_SOX10_high_S2
PY230_RNAseq_RPKM.csv
Ba_sox10_pos2

source_name: Transplanted PY230 tumors

value: Adult

value: Transplanted tumors


title: tumor PY230 basal SOX10 high sample1 (RNA-seq)

description:
PY230_basal_SOX10_high_S1
PY230_RNAseq_RPKM.csv
Ba_sox10_pos1


title: tumor C3-1 basal SOX10 high sample1 (RNA-seq)

description:
C3_SOX10_high_S1
C3_RNAseq_RPKM.csv
sox10_pos1

value: FVB

value: Spontaneous tumors


title: FUS-ALS iPSC (FALS2e3)-derived MN with drug-treatment

value: Spinal motor neurons


title: TARDBP-ALS iPSC (A21428)-derived MN


title: SALS iPSC (SALS12)-derived MN with drug-treatment

value: Sporadic ALS (SALS)

value: SALS patient1

value: Lymphoblastoid B-cell line (LCL)


title: tumor PY230 luminal SOX10 low sample2 (RNA-seq)

description:
PY230_luminal_SOX10_low_S2
PY230_RNAseq_RPKM.csv
Lu_sox10_neg2


title: tumor PY230 luminal SOX10 low sample1 (RNA-seq)

description:
PY230_luminal_SOX10_low_S1
PY230_RNAseq_RPKM.csv
Lu_sox10_neg1


title: normal adult luminal progenitor cells sample2 (RNA-seq)

description:
Adult_LP_RNA_S2
Normal_mammary_RNAseq_RPKM.csv
LP2

source_name: WT mammary gland

value: Mammary gland


title: tumor PY230 luminal SOX10 high sample2 (RNA-seq)

description:
PY230_luminal_SOX10_high_S2
PY230_RNAseq_RPKM.csv
Lu_sox10_pos2


title: normal adult basal cells sample1 (RNA-seq)

description:
Adult_Ba_RNA_S1
Normal_mammary_RNAseq_RPKM.csv
Ba1


title: tumor PY230 luminal SOX10 high sample1 (RNA-seq)

description:
PY230_luminal_SOX10_high_S1
PY230_RNAseq_RPKM.csv
Lu_sox10_pos1


title: normal adult mature luminal cells sample2 (RNA-seq)

description:
Adult_ML_RNA_S2
Normal_mammary_RNAseq_RPKM.csv
ML2


title: PY230 SOX10 control (ChIP-seq)

description:
PY230_SOX10_control
SOX10_control-input.bigwig

data_processing:
Sequencing reads were quality checked by FastQC.
Sequence reads were then aligned to the NCBI Build 37 mouse genome (mm9) with Bowtie (version 0.12.8) using the following parameters: -m 1 --best -S -n 2 -l 40. Sam files were converted/sorted to Bam files with samtools (version 1.3.1).
MACS2 (version 2.1.1) was used to remove duplication and call peaks and generate Bedgraph signal files, with these parameters for H3K27ac: --nomodel --shift 100 --bw 150, with these parameters for SOX10: . Bedgraph files were converted into Bigwig files with BedClip and bedGraphToBigWig (version 4) and upload to UCSC Genome Browser.
H3K27ac genome wide signal was normalized with quantile normalization to ensure comparable signal-to-noise levels among samples.
Genome_build: mm9
Supplementary_files_format_and_content: For H3K27ac, Bigwig signal represents input subtracted normalized reads per million (RPM) per genomic region for each sample.
Supplementary_files_format_and_content: For SOX10, Bigwig signal represents input subtracted reads per million (RPM) per genomic region. SOX10 bed file represents SOX10 binding regions (FDR<1e-100 as determined by MACS2) that did not show enrichment in the control sample.

source_name: PY230 tumors

growth_protocol: PY230 cells were grown as described in Bao et al. 2015 (see the Methods section for transplantation details)

extract_protocol:
The normal cells were dissected and FACS isolated from primary mammary tissue. The PY230 cells were transplanted into syngeneic mice to form tumors, and the tumors were dissected and FACS isolated. See the Methods section of the manuscript for details of isolation and FACS markers.
For H3K27ac ChIP, around 20k cells were crosslinked with 1% PFA at room temperature for 10 minutes, sonicated with Covaris M220 into 200-700 bp fragments, and incubated with anti-H3K27ac antibody (Diagenode C15410174) overnight at 4¡C. Protein A beads pull down (Invitrogen 10001D), washing, on-beads tagmentation (Illumina Nextera FC-121-1030), reverse crosslinking, library amplification (13 PCR cycles) and DNA purification were performed as described. The input library was prepared by tagmentation of 1 ng of reverse crosslinked input DNA and then amplified and processed together with the ChIP DNA. Multiple input preparations were pooled together to ensure sufficient complexity of the input library.
For the SOX10 ChIP, 500k control and SOX10-AVI/BirA cells were processed as above, except that streptavidin beads (Pierce #88816) were used for pull down, and that two additional washing steps with 2% SDS in PBS were performed to significantly remove ChIP backgrounds. The input library was prepared as above.
ChIPmentation method (Schmidl et al., 2015)

value: Mammary tumors

tag: chip reagent

value: streptavidin beads (Pierce #88816)


title: normal E18 fMaSC sample2 (RNA-seq)

description:
fMaSC_RNA_S2
Normal_mammary_RNAseq_RPKM.csv
fMaSC2

value: E18 embryo


title: normal adult mature luminal cells sample1 (RNA-seq)

description:
Adult_ML_RNA_S1
Normal_mammary_RNAseq_RPKM.csv
ML1


title: PY230 input (ChIP-seq)


title: normal E18 fMaSC sample1 (RNA-seq)

description:
fMaSC_RNA_S1
Normal_mammary_RNAseq_RPKM.csv
fMaSC1


title: H3K27ac input sample 2 (ChIP-seq)


title: normal adult mature luminal cells sample1 (ChIP-seq)

description:
Adult_ML_H3K27ac_S1
ML1+2_k27ac_normalized.bigwig

value: H3K27ac (Diagenode C15410174)


title: H3K27ac input sample 1 (ChIP-seq)


title: PY230 SOX10 ChIP sample 2 (ChIP-seq)

description:
PY230_SOX10_ChIP_S2
SOX10_ChIP1+2-input.bigwig
SOX10_ChIP-ctrl_signal.bed


title: normal adult luminal progenitor cells sample1 (ChIP-seq)

description:
Adult_LP_H3K27ac_S1
LP1+2_k27ac_normalized.bigwig


title: normal adult luminal progenitor cells sample2 (ChIP-seq)

description:
Adult_LP_H3K27ac_S2
LP1+2_k27ac_normalized.bigwig


title: normal adult mature luminal cells sample2 (ChIP-seq)

description:
Adult_ML_H3K27ac_S2
ML1+2_k27ac_normalized.bigwig


title: normal adult luminal progenitor cells sample1 (RNA-seq)

description:
Adult_LP_RNA_S1
Normal_mammary_RNAseq_RPKM.csv
LP1


title: normal adult basal cells sample2 (ChIP-seq)

description:
Adult_Ba_H3K27ac_S2
Ba1+2_k27ac_normalized.bigwig


title: normal E18 fMaSC sample2 (ChIP-seq)

description:
fMaSC_H3K27ac_S2
fMaSC1+2_k27ac_normalized.bigwig


title: PY230 2D culture (ATAC-seq)

data_processing:
Sequencing reads were quality checked by FastQC.
Sequence reads were then aligned to the NCBI Build 37 mouse genome (mm9) with Bowtie (version 0.12.8) using the following parameters: -m 1 -S -n 2 -l 30. Sam files were converted/sorted to Bam files with samtools (version 1.3.1).
For paried-end sequencing samples (all normal mammary cells), each paried-end sample was mapped as single end, and the Bam files from the same sample were merged into one (this is because only the cutting sites were of interested here).
MACS2 (version 2.1.1) was used to remove duplication and call peaks and generate Bedgraph signal files, with these parameters: --nolambda --nomodel --shift -100 --extsize 200. Bedgraph files were converted into Bigwig files with BedClip and bedGraphToBigWig (version 4) and upload to UCSC Genome Browser.
Bam files were converted to bed files by bedTools (version 2.20.1) for differential peak calling by SICER-df-rb (version 1.1), using these parameters: window size: 100, gap size: 100, E-value: 0.01, FDR: 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig signal represents reads per million (RPM) per genomic region for each sample. Bed files represent called peaks, UAR/URR and differential peaks between the R1 PY230 tumor samples.

source_name: Cultured PY230 cells

extract_protocol:
The normal cells were dissected and FACS isolated from primary mammary tissue. The PY230 cells were transplanted into syngeneic mice to form tumors, and the tumors were dissected and FACS isolated. The C3-1-Tag cells were dissected and FACS isolated from spontaneous tumors. See the Methods section of the manuscript for details of isolation and FACS markers.
Around 2x10^4 nuclei from each normal and tumor cell type were used in each reaction with 20 μl of transposition mix (10 μl 2x TD, 2 μl TDE1, 8 μl H2O; Illumina Nextera FC-121-1030) and incubated at 37°C for 30 minutes. qPCR was performed to determine the cycle number for 25% library saturation. Typically, 10-14 total cycles were performed. The library was purified with AMPure XP beads (Beckman A63881), and then analyzed by Agilent TapeStation, and 50-125 bp paired-end sequencing was performed with Illumina HiSeq 2500.

value: Cultured cells


title: PY230 bulk tumor (ATAC-seq)


title: tumor PY230 luminal SOX10 low sample1 (ATAC-seq)

description:
PY230_luminal_SOX10_low_S1
PY230_ATAC_SOX10_high_closed_mm9.bed
PY230_Lu_Sox10_low.bigwig


title: tumor PY230 luminal SOX10 high sample1 (ATAC-seq)

description:
PY230_luminal_SOX10_high_S1
PY230_ATAC_SOX10_high_open_mm9.bed
PY230_Lu_Sox10_high.bigwig


title: normal adult mature luminal cells sample2 (ATAC-seq)

description:
Adult_ML_ATAC_S2
ML1+2_ATAC_macs2_q1e-3_fc_mm9.bed
Adult_ML_ATAC_S1+2.bigWig


title: normal adult basal cells sample2 (RNA-seq)

description:
Adult_Ba_RNA_S2
Normal_mammary_RNAseq_RPKM.csv
Ba2


title: normal adult luminal progenitor cells sample2 (ATAC-seq)

description:
Adult_LP_ATAC_S2
LP1+2_ATAC_macs2_q1e-3_fc_mm9.bed
Adult_LP_ATAC_S1+2.bigWig


title: normal adult luminal progenitor cells sample1 (ATAC-seq)

description:
Adult_LP_ATAC_S1
LP1+2_ATAC_macs2_q1e-3_fc_mm9.bed
Adult_LP_ATAC_S1+2.bigWig


title: normal adult basal cells sample2 (ATAC-seq)

description:
Adult_Ba_ATAC_S2
Ba1+2_ATAC_macs2_q1e-3_fc_mm9.bed
Adult_Ba_ATAC_S1+2.bigWig


title: normal adult mature luminal cells sample1 (ATAC-seq)

description:
Adult_ML_ATAC_S1
ML1+2_ATAC_macs2_q1e-3_fc_mm9.bed
Adult_ML_ATAC_S1+2.bigWig


title: normal adult basal cells sample1 (ChIP-seq)

description:
Adult_Ba_H3K27ac_S1
Ba1+2_k27ac_normalized.bigwig


title: normal adult basal cells sample1 (ATAC-seq)

description:
Adult_Ba_ATAC_S1
Ba1+2_ATAC_macs2_q1e-3_fc_mm9.bed
Adult_Ba_ATAC_S1+2.bigWig


title: PY230 SOX10 ChIP sample 1 (ChIP-seq)

description:
PY230_SOX10_ChIP_S1
SOX10_ChIP1+2-input.bigwig
SOX10_ChIP-ctrl_signal.bed


title: normal E18 fMaSC sample1 (ChIP-seq)

description:
fMaSC_H3K27ac_S1
fMaSC1+2_k27ac_normalized.bigwig


title: mHDR_control_pool2_sort1_noGFP

city: Seattle

first: Lea

middle: M

last: Starita

state: WA

department: Genome Sciences

institute: University of Washington

description: processed data file: LS927_pool2_exp.h5

data_processing:
Illumina bcl2fastq base calling and demultiplex.
FASTQ files containing either barcodes for each sample and the barcode-map for each library were used as input for the software package Enrich2.
Enrich2 was used to count the barcodes, associate each barcode with a nucleotide variant, and then translate and count both the unique-nucleotide and unique-amino acid variants.
Barcodes assigned to variants containing insertions or deletions were removed from analysis.
The counts for each protein variant were converted to frequencies by dividing by the total number of variant counts for each sample by Enrich2.
The ratio of the frequency of each variant in the GFP positive population over its frequency in the GFP negative population was calculated by Enrich2.
That ratio for each variant was then normalized to the GFP+/GFP- ratio for the wild-type sequence at ln(GFP+/GFP-) = 0 by Enrich2. That is the score.
Genome_build: genome_build.txt
Supplementary_files_format_and_content: hdf5 files with counts and scores. Columns names are descriptive, _0 denotes noGFP, _1 denotes GFP samples.
Supplementary_files_format_and_content: LS946_pool1_rerun_exp.h5: Enrich2-generated hdf5 of counts and scores for pool 1.
Supplementary_files_format_and_content: LS927_pool2_exp.h5: Enrich2-generated hdf5 of counts and scores for pool 2.
Supplementary_files_format_and_content: pool1_barcodeInsertAssignment.tsv.gz : Tab-separated file, map of barcode and variant for pool1.
Supplementary_files_format_and_content: pool2_barcodeInsertAssignment.tsv.gz: Tab-separated file, map of barcode and variant for pool2.

source_name: barcodes amplified from HeLa DR-FRT cell line

growth_protocol: DMEM supplemented with 10% fetal bovine serum and hygromycin B at 550 µg/mL.

extract_protocol:
DNeasy Blood & Tissue Kit, eluted in 200 ul H2O.
To amplify the barcode from gDNA from the GFP-positive and negative populations were spread over 8-16 reactions containing 250 ug of gDNA each (220K–440K genome equivalents by weight given HeLa triploid genome ~9 pg). Reactions also contained Kapa2G Robust Polymerase (Kapa Biosystems), a primer that annealed to the SV40 promoter 5’ of the integrated plasmid and a primer adjacent to the barcode (SV40_F and newpc5bc_nexteraR). PCR was performed using the following conditions [95˚, 5 min; {95˚, 40s, 65˚, 30s, 72˚, 3 min} x ~28 cycles; 72˚, 10 min]. The reactions produce a ~3,700 base amplicon specifically from integrated plasmids. The reactions for each sample were combined and the amplicons were purified by 0.5X Ampure and eluted with 10 mM Tris at 10% of the original reaction volume. 10% of the eluted PCR volume was re-amplified with primers containing sample indexes and Illumina cluster generating sequences (pc5bc_p5_F, nextIndex). Reactions also contained Kapa2G Robust Polymerase and 0.5X SYBR green II (ThermoFisher). PCR reactions are monitored on a Mini-opticon qPCR machine (Bio-Rad) and removed during exponential amplification using the following conditions [95˚, 3 min; {95˚, 20s, 65˚, 30s, 72˚, 20s} x 5-10 cycles]. The PCR reaction produced a 350-base amplicon that was purified using a double-Ampure protocol. First the large DNA fragments were removed by precipitation by addition of 0.6X volume Ampure beads to the reactions. Then the 350-base amplicons were purified from the supernatant using 0.9X volume Ampure beads. The samples were multiplexed and the barcodes and sample indexes were sequenced (single read, pcDNA5_barcodeSeq_F) on a Nextseq 500 High Output 75 base kit.

treatment_protocol: HDR reporter assays and FACS sorts were performed for each of the two BRCA1 variant libraries in quadruplicate. A confluent 10 cm plate of HeLa BRCA1 variant cell line was trypsinized and resuspended in 10 mL of culture media. 65 ml of the suspension was plated in each of 48 wells across two 24-well tissue culture plates. 24 hours later, each well was transfected with 30 pmol of siRNA and 1.5 ml Oligofectamine (ThermoFisher). Oligofectamine was diluted with 6 ml Opti-MEM and siRNA was diluted with 25 ml Opti-MEM for 5 minutes. The dilutions were then combined and incubated for an additional 30 minutes. The transfection mixture was then applied directly to the cells. 24 hours later, the cells were trypsinized and transferred to four 6-well tissue culture plates, then incubated for another 24 hours. Each well was then transfected with 50 pmol of siRNA, 3 mg pCBASceI (for I-SceI expression), and 3 ml Lipofectamine 2000. Plasmid and siRNA were diluted in 125 ml Opti-MEM and Lipofectamine was diluted in 125 ml Opti-MEM, then incubated for 5 minutes. The dilutions were combined and incubated for an additional 20 minutes. The transfection mixture was then applied directly to cells. Four to six hours later, the culture media was replaced with fresh media. BRCA1 3’UTR siRNA, BRCA1 coding sequence siRNA and control siRNA were used in both rounds of transfection. After 24 hours, one well of cells treated with each condition was analyzed for GFP expression using flow cytometry to confirm transfection efficiency. If cells treated with control siRNA and 3’UTR siRNA fell within 7-9% and 4-7% GFP+ cells respectively, and cells treated with BRCA1 coding sequence siRNA were 1-2% GFP+, the experiment would proceed. 72 hours post-transfection, the cells were pooled according to treatment and sorted using fluorescent activated cell sorting (FACS) using an Aria IIu instrument. Cells were resuspended and pooled in filter-sterilized sorting buffer containing 1X Phosphate Buffered Saline (Ca2+/Mg2+ free), 5 mM EDTA, 25 mM HEPES pH 7.0, and 1% heat-inactivated fetal bovine serum dialyzed against Ca2+/Mg2+ PBS. A minimum of 500,000 GFP+ cells and a maximum of 2 million GFP- cells were collected per pool.

tag: cell line

value: HeLa DR-FRT

value: HeLa with HDR reporter expressing BRCA1 variant library


title: mHDR_BRCA1_pool2_sort4_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool2_sort3_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool2_sort4_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool2_sort4_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool2_sort1_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool2_sort2_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool2_sort2_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_BRCA1_pool2_sort4_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_BRCA1_pool2_sort3_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_BRCA1_pool2_sort2_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_BRCA1_pool2_sort2_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_BRCA1_pool2_sort1_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_BRCA1_pool2_sort1_GFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool1_sort4_noGFP

description: processed data file: LS946_pool1_rerun_exp.h5


title: mHDR_control_pool1_sort4_GFP


title: mHDR_control_pool1_sort3_noGFP


title: mHDR_control_pool1_sort3_GFP


title: mHDR_control_pool1_sort2_GFP


title: mHDR_control_pool2_sort3_noGFP

description: processed data file: LS927_pool2_exp.h5


title: mHDR_control_pool1_sort2_noGFP


title: mHDR_control_pool1_sort1_GFP


title: mHDR_BRCA1_pool1_sort4_GFP


title: mHDR_BRCA1_pool1_sort3_GFP


title: mHDR_control_pool1_sort1_noGFP


title: mHDR_BRCA1_pool1_sort3_noGFP


title: mHDR_BRCA1_pool1_sort2_noGFP


title: mHDR_BRCA1_pool1_sort4_noGFP


title: mHDR_BRCA1_pool1_sort2_GFP


title: mHDR_BRCA1_pool2_sort3_GFP

description: processed data file: LS927_pool2_exp.h5


title: tumor C3-1 basal SOX10 high sample1 (ATAC-seq)

description:
C3_basal_SOX10_high_S1
C3_Ba_Sox10_high.bigwig


title: tumor C3-1 basal SOX10 high sample2 (ATAC-seq)

description:
C3_basal_SOX10_high_S2
C3_Ba_Sox10_high.bigwig


title: mHDR_BRCA1_pool1_sort1_GFP


title: tumor PY230 basal SOX10 high sample1 (ATAC-seq)

description:
PY230_basal_SOX10_high_S1
PY230_Ba_Sox10_high.bigwig


title: mHDR_BRCA1_pool1_sort1_noGFP


title: normal E18 fMaSC sample1 (ATAC-seq)

description:
fMaSC_ATAC_S1
fMaSC1+2_ATAC_macs2_q1e-3_fc_mm9.bed
fMaSC_ATAC_S1+2.bigWig


title: tumor PY230 luminal SOX10 low sample2 (ATAC-seq)

description:
PY230_luminal_SOX10_low_S2
PY230_ATAC_SOX10_high_closed_mm9.bed
PY230_Lu_Sox10_low.bigwig


title: normal E18 fMaSC sample2 (ATAC-seq)

description:
fMaSC_ATAC_S2
fMaSC1+2_ATAC_macs2_q1e-3_fc_mm9.bed
fMaSC_ATAC_S1+2.bigWig


title: tumor PY230 luminal SOX10 high sample2 (ATAC-seq)

description:
PY230_luminal_SOX10_high_S2
PY230_ATAC_SOX10_high_open_mm9.bed
PY230_Lu_Sox10_high.bigwig


title: tumor PY230 basal SOX10 high sample2 (ATAC-seq)

description:
PY230_basal_SOX10_high_S2
PY230_Ba_Sox10_high.bigwig


title: tumor PY230 luminal SOX10 low sample3 (ATAC-seq)

description:
PY230_luminal_SOX10_low_S3
PY230_ATAC_SOX10_high_closed_mm9.bed
PY230_Lu_Sox10_low.bigwig


title: tumor PY230 luminal SOX10 high sample3 (ATAC-seq)

description:
PY230_luminal_SOX10_high_S3
PY230_ATAC_SOX10_high_open_mm9.bed
PY230_Lu_Sox10_high.bigwig


title: Control 3 - Day 42_miRNA

city: London

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

country: United Kingdom

institute: King's College London

description: miRNA expression data

hyb_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions

data_processing: All samples underwent microarray analysis on Affymetrix GeneChip miRNA 4.0 arrays. Data was normalised using Expression Console software (Affymetrix) prior to generating a list of differentially expressed genes using Qlucore Omics Explorer 3.2

source_name: Skin

extract_protocol: Total RNA was isolated using RNeasy Plus Universal kit (Qiagen, Valencia, USA) and miRNAs retained according to the manufacturer’s protocol

value: skin

tag: diagnosis

value: healthy

tag: time point

value: Day 42


title: Control 6 - Day 42_miRNA

description: miRNA expression data

scan_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions


title: Control 1 - Day 42_miRNA

description: miRNA expression data

label_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions


title: Keloid 2 - Day 42_miRNA

description: miRNA expression data

value: keloid


title: Keloid 6 - Day 42_miRNA

description: miRNA expression data


title: Keloid 3 - Day 42_miRNA

description: miRNA expression data


title: Keloid 7 - Day 42_miRNA

description: miRNA expression data


title: Control 5 - Day 42_miRNA

description: miRNA expression data


title: Keloid 8 - Day 42_miRNA

description: miRNA expression data


title: Control 2 - Day 42_miRNA

description: miRNA expression data


title: Control 4 - Day 42_miRNA

description: miRNA expression data


title: Keloid 5 - Day 42_miRNA

description: miRNA expression data


title: Keloid 4 - Day 42_miRNA

description: miRNA expression data


title: Control 4 - Day 0_miRNA

description: miRNA expression data

value: Day 0


title: Keloid 1 - Day 42_miRNA

description: miRNA expression data


title: N6-2nd_S014

description:
N6-2nd_S014_R1_.fastq.gz
N6-2nd_S014_R2_.fastq.gz

data_processing:
Whole transcriptome RNA-Seq libraries were prepared on the Agilent Bravo liquid handling system using a modification of the Agilent Sureselect stranded RNA kit (Catalog 9691B). Sequencing was conducted on HiSeq2500 and HiSeq3000 (Illumina, San Diego)
Sequencing reads were aligned against the human genome sequence (hg38) using hisat2. Reads with a MAPQ (mapping quality) below 10 [-10 X log10 Pr(mapping position is wrong=0.100] and PCR duplicate reads were removed with Samtools package. The UCSC hg38 genome annotation was used to generate gene count tables for each sample using the GenomicAlignments library in R. Gene counts for the technical replicates were added together and data were normalized for library size correction using DESeq2
Principal Component Analysis (PCA) on the normalized gene counts was performed to ensure the homogeneity of the data and to exclude any potential batch effects among sequencing runs. RNA differential expression (DE) analysis was performed with the glmmADMB package in R using a mixed effect generalized linear model with a random intercept for each patient from the negative binomial family.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw or normalized counts

value: Skin

tag: Sex

value: male

value: day 42


title: Control 3 - Day 0_miRNA

description: miRNA expression data


title: Control 1 - Day 0_miRNA

description: miRNA expression data


title: Control 5 - Day 0_miRNA

description: miRNA expression data


title: Keloid 3 - Day 0_miRNA

description: miRNA expression data


title: N4-2nd_S014

description:
N4-2nd_S014_R1_.fastq.gz
N4-2nd_S014_R2_.fastq.gz


title: Keloid 5 - Day 0_miRNA

description: miRNA expression data


title: Keloid 8 - Day 0_miRNA

description: miRNA expression data


title: Keloid 4 - Day 0_miRNA

description: miRNA expression data


title: Keloid 6 - Day 0_miRNA

description: miRNA expression data


title: N5-2nd_S014

description:
N5-2nd_S014_R1_.fastq.gz
N5-2nd_S014_R2_.fastq.gz


title: Keloid 2 - Day 0_miRNA

description: miRNA expression data


title: Control 2 - Day 0_miRNA

description: miRNA expression data


title: Keloid 7 - Day 0_miRNA

description: miRNA expression data


title: Keloid 1 - Day 0_miRNA

description: miRNA expression data


title: N2-2nd_S014

description:
N2-2nd_S014_R1_.fastq.gz
N2-2nd_S014_R2_.fastq.gz


title: K7-2nd_S014

description:
K7-2nd_S014_R1_.fastq.gz
K7-2nd_S014_R2_.fastq.gz

value: female


title: K5-2nd_S014

description:
K5-2nd_S014_R1_.fastq.gz
K5-2nd_S014_R2_.fastq.gz


title: K4-2nd_S014

description:
K4-2nd_S014_R1_.fastq.gz
K4-2nd_S014_R2_.fastq.gz


title: K3-2nd_S014

description:
K3-2nd_S014_R1_.fastq.gz
K3-2nd_S014_R2_.fastq.gz


title: K6-2nd_S014

description:
K6-2nd_S014_R1_.fastq.gz
K6-2nd_S014_R2_.fastq.gz


title: K1-2nd_S014

description:
K1-2nd_S014_R1_.fastq.gz
K1-2nd_S014_R2_.fastq.gz


title: K2-2nd_S014

description:
K2-2nd_S014_R1_.fastq.gz
K2-2nd_S014_R2_.fastq.gz


title: N2-1st_S014

description:
N2-1st_S014_R1_.fastq.gz
N2-1st_S014_R2_.fastq.gz

value: day 0


title: N3-2nd_S014

description:
N3-2nd_S014_R1_.fastq.gz
N3-2nd_S014_R2_.fastq.gz


title: N1-2nd_S014

description:
N1-2nd_S014_R1_.fastq.gz
N1-2nd_S014_R2_.fastq.gz


title: K8-2nd_S014

description:
K8-2nd_S014_R1_.fastq.gz
K8-2nd_S014_R2_.fastq.gz


title: N5-1st_S014

description:
N5-1st_S014_R1_.fastq.gz
N5-1st_S014_R2_.fastq.gz


title: K8-1st_S014

description:
K8-1st_S014_R1_.fastq.gz
K8-1st_S014_R2_.fastq.gz


title: N1-1st_S014

description:
N1-1st_S014_R1_.fastq.gz
N1-1st_S014_R2_.fastq.gz


title: K6-1st_S014

description:
K6-1st_S014_R1_.fastq.gz
K6-1st_S014_R2_.fastq.gz


title: K7-1st_S014

description:
K7-1st_S014_R1_.fastq.gz
K7-1st_S014_R2_.fastq.gz


title: K4-1st_S014

description:
K4-1st_S014_R1_.fastq.gz
K4-1st_S014_R2_.fastq.gz


title: K5-1st_S014

description:
K5-1st_S014_R1_.fastq.gz
K5-1st_S014_R2_.fastq.gz


title: K3-1st_S014

description:
K3-1st_S014_R1_.fastq.gz
K3-1st_S014_R2_.fastq.gz


title: K1-1st_S014

description:
K1-1st_S014_R1_.fastq.gz
K1-1st_S014_R2_.fastq.gz


title: N6-2nd_S032

description:
N6-2nd_S032_R1_.fastq.gz
N6-2nd_S032_R2_.fastq.gz


title: N1-2nd_S032

description:
N1-2nd_S032_R1_.fastq.gz
N1-2nd_S032_R2_.fastq.gz


title: YP_ssh1_r3

city: Beijing

first: Ma

last: Xin

state: --- Select a state ---

address: 2 Yuanmingyuan West Road, Haidian District, Beijing, China, 2 Yuanmingyuan West Road, Haidian District, Beijing, China

institute: China Agricultural University

data_processing:
Raw reads were mapped to the reference genome by TopHat2 using default parameters.
Cuffdiff was used to calculate the FPKM (fragments per kilobase of exon per million mapped reads) of each gene and to identify the differentially-expressed genes (fold change ≥ 2, q-value < 0.001) between the wild type YIL100 and the ssh1 mutant.
The functional category analysis of the differentially-expressed genes was performed by the AgriGO and KEGG databases.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0, MSU7

organism: Oryza sativa Indica Group

source_name: Panicles

extract_protocol:
Total RNA was isolated using TRIzol according to the instructions.
P-aired-end libraries were constructed using a TruSeq RNA Sample Preparation Kit v2.

value: Development panicles

tag: development stage

tag: genotype


title: YP_ssh1_r2

tag: tissue


title: YP_ssh1_r1


title: K2-1st_S014

description:
K2-1st_S014_R1_.fastq.gz
K2-1st_S014_R2_.fastq.gz


title: K3-2nd_S032

description:
K3-2nd_S032_R1_.fastq.gz
K3-2nd_S032_R2_.fastq.gz


title: N4-1st_S014

description:
N4-1st_S014_R1_.fastq.gz
N4-1st_S014_R2_.fastq.gz


title: N3-1st_S014

description:
N3-1st_S014_R1_.fastq.gz
N3-1st_S014_R2_.fastq.gz


title: YP_YIL100_r3

value: wild type


title: N5-1st_S032

description:
N5-1st_S032_R1_.fastq.gz
N5-1st_S032_R2_.fastq.gz


title: YP_YIL100_r2


title: N2-1st_S032

description:
N2-1st_S032_R1_.fastq.gz
N2-1st_S032_R2_.fastq.gz


title: YP_YIL100_r1


title: K6-1st_S032

description:
K6-1st_S032_R1_.fastq.gz
K6-1st_S032_R2_.fastq.gz


title: K3-1st_S032

description:
K3-1st_S032_R1_.fastq.gz
K3-1st_S032_R2_.fastq.gz


title: N6-2nd_S021

description:
N6-2nd_S021_R1_.fastq.gz
N6-2nd_S021_R2_.fastq.gz


title: K5-1st_S032

description:
K5-1st_S032_R1_.fastq.gz
K5-1st_S032_R2_.fastq.gz


title: K2-2nd_S032

description:
K2-2nd_S032_R1_.fastq.gz
K2-2nd_S032_R2_.fastq.gz


title: N5-2nd_S021

description:
N5-2nd_S021_R1_.fastq.gz
N5-2nd_S021_R2_.fastq.gz


title: K3-2nd_S021

description:
K3-2nd_S021_R1_.fastq.gz
K3-2nd_S021_R2_.fastq.gz


title: K4-2nd_S021

description:
K4-2nd_S021_R1_.fastq.gz
K4-2nd_S021_R2_.fastq.gz


title: N2-2nd_S021

description:
N2-2nd_S021_R1_.fastq.gz
N2-2nd_S021_R2_.fastq.gz


title: K8-2nd_S021

description:
K8-2nd_S021_R1_.fastq.gz
K8-2nd_S021_R2_.fastq.gz


title: K2-2nd_S021

description:
K2-2nd_S021_R1_.fastq.gz
K2-2nd_S021_R2_.fastq.gz


title: N3-2nd_S021

description:
N3-2nd_S021_R1_.fastq.gz
N3-2nd_S021_R2_.fastq.gz


title: K1-2nd_S021

description:
K1-2nd_S021_R1_.fastq.gz
K1-2nd_S021_R2_.fastq.gz


title: N3-1st_S021

description:
N3-1st_S021_R1_.fastq.gz
N3-1st_S021_R2_.fastq.gz


title: N4-2nd_S021

description:
N4-2nd_S021_R1_.fastq.gz
N4-2nd_S021_R2_.fastq.gz


title: N1-2nd_S021

description:
N1-2nd_S021_R1_.fastq.gz
N1-2nd_S021_R2_.fastq.gz


title: K5-2nd_S021

description:
K5-2nd_S021_R1_.fastq.gz
K5-2nd_S021_R2_.fastq.gz


title: K6-2nd_S021

description:
K6-2nd_S021_R1_.fastq.gz
K6-2nd_S021_R2_.fastq.gz


title: human iPSC which is used to induce cancer stem cells

city: Okayama

first: Akimasa

last: Seno

state: Okayama

address: 1-1, Tsushima-Naka, 1-chome, Kita-Ku

department: Applied Chemistry and Biotechnology

institute: Okayama University

description: Gene expression of induced cancer stem cell induced from human iPS cell by ZR-75-1 cell culture medium

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized for 17 hours at 65°C with Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies) using parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: original human iPSC 201B7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Using the RNeasy column purification (QIAGEN) total RNA was prepared.

treatment_protocol: Human iPS cells obtained from Riken.

tag: gender

value: Female


title: N5-1st_S021

description:
N5-1st_S021_R1_.fastq.gz
N5-1st_S021_R2_.fastq.gz


title: N4-1st_S021

description:
N4-1st_S021_R1_.fastq.gz
N4-1st_S021_R2_.fastq.gz


title: N2-1st_S021

description:
N2-1st_S021_R1_.fastq.gz
N2-1st_S021_R2_.fastq.gz


title: N1-1st_S021

description:
N1-1st_S021_R1_.fastq.gz
N1-1st_S021_R2_.fastq.gz


title: N3-1st_S032

description:
N3-1st_S032_R1_.fastq.gz
N3-1st_S032_R2_.fastq.gz


title: K8-1st_S021

description:
K8-1st_S021_R1_.fastq.gz
K8-1st_S021_R2_.fastq.gz


title: K7-1st_S021

description:
K7-1st_S021_R1_.fastq.gz
K7-1st_S021_R2_.fastq.gz


title: K5-1st_S021

description:
K5-1st_S021_R1_.fastq.gz
K5-1st_S021_R2_.fastq.gz


title: K2-1st_S021

description:
K2-1st_S021_R1_.fastq.gz
K2-1st_S021_R2_.fastq.gz


title: K3-1st_S021

description:
K3-1st_S021_R1_.fastq.gz
K3-1st_S021_R2_.fastq.gz


title: K7-2nd_S021

description:
K7-2nd_S021_R1_.fastq.gz
K7-2nd_S021_R2_.fastq.gz


title: K6-1st_S021

description:
K6-1st_S021_R1_.fastq.gz
K6-1st_S021_R2_.fastq.gz


title: 5mM As(III) exposure

city: Tainan

first: Jiin-Shuh

last: Jean

address: 1st University Road

department: Department of Earth Science

country: Taiwan

institute: National Cheng Kung University

data_processing:
Illumina official tool, bcl2fastq2 conversion Software v2.19 can be used to convert BCL files from all Illumina sequencing systems.
In addition to removing lower base quality data, one would also remove adapters, PCR primers and other artifacts.   In practice one would combine the adapter clipping with quality trimming approaches.
In order to cope with lower quality data, quality trimming is required to remove low quality reads/bases.
Typically one would remove lower quality bases from the the 3' end using a sliding windows approach
as the per base quality gradually drops. Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters with slidewindow apporach.  Both adaptor clipping and sequence quality trimming were accomplished by Trimmomatic Ver 0.32.
Genome_build: Lysinibacillus sp. B2A1 (CP027224)
Supplementary_files_format_and_content: excel file include RPKM values for each Sample

organism: Lysinibacillus sp. B2A1

source_name: Bacteria

growth_protocol: Bacterial cells grown in chemical defined medium up to log phase.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
All RNA Sample preparation procedures were carried out according to the official Illumina protocol. Agilent's SureSelect Strand Specific RNA Library Preparation Kitwere used for library construction followed by AMPure XP Beads size selection.
The sequence was directly determined using sequencing-by-synthesis technology. Sequencing data were generated by Welgene's pinepline which based on Illumina bcl2fastq v2.1.7 and expected to generate.

treatment_protocol: log phase bacterial cells collected and washed three times with PBS and exposed to 5mM As(III), 50mM As(V) and no arsenic under the same growth medium for 3 h.

tag: strain

tag: treatment

value: 5mM NaAsO2 [As(III)] exposure

tag: treatment exposure time

value: 3 h


title: K4-1st_S021

description:
K4-1st_S021_R1_.fastq.gz
K4-1st_S021_R2_.fastq.gz

tag: age


title: 50mM As(V) exposure

value: 50mM Na2HAsO4.7H2O [As(V)] exposure


title: Testis tub dam rep1

status: Public on Jun 13 2018

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Pool of testes expressing Dam.

data_processing:
We used CASAVA v1.8.2 (Illumina, San Diego, CA) and bcl2fastq v1.8 (Illumina, San Diego, CA) for base calling, demultiplexing and BCL to FASTQ conversion.
We aligned reads using Hisat2 v2.1.0 (Kim et al. 2015. PMID: 25751142) to Drosophila genome assembly release 6 plus ISO1 MT concatenated to ERCC (SRM2374) processed as described in (Jiang et al. 2011. PMID: 21816910 and Lee et al. 2016 PMID: 27512518). We used default settings except for --max-introlen 300000, and we passed splice junctions generated using FlyBase r6.16 to --known-splicesite-infile.
We removed multi-mapping reads and low quality alignments using Samtools v1.7 (Li et al. 2009. PMID: 19505943) -q 20.
We generated strand specific (-s 2) gene level counts with featureCounts v1.6.1 (Liao et al., 2014. PMID: 24227677) using a GTF created by concatenating FlyBase r6.16 to a generated ERCC GTF. We also created unstranded (-s 0) intergenic counts by using intergenic regions from FlyBase r6.16.  Genic and intergenic GTFs can be downloaded from GSE115478.
We created strand specific browser tracks (BigWigs) using DeepTools v3.0.2 (Ramírez et al. 2016. PMID: 27079975) with --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand forward or --filterRNAstrand reverse.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GeneBank assembly accession: GCA_000001215.4)
Supplementary_files_format_and_content: *.pos.bigwig: Is a first strand bigWig file generated using DeepTools v3.0.2 using options ( --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand forward)
Supplementary_files_format_and_content: *.neg.bigwig: Is a second strand bigWig file generated using DeepTools v3.0.2 using options ( --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand reverse)
Supplementary_files_format_and_content: *.featurecounts.txt: Contains gene level + ERCC level raw counts generated using featureCounts v1.6.1 with options (-s 2)
Supplementary_files_format_and_content: *.featurecounts.intergenic.txt: Contains intergenic level raw counts generated using featureCounts v1.6.1 with options (-s 0)

organism: Drosophila melanogaster

source_name: tissue

growth_protocol: We raised parental flies at 25 ºC on molasses/yeast medium (1,212.5 mL water, 14.7 mL agar, 20.4 g yeast, 81.8 g cornmeal, 109.1 mL molasses, 10.9 mL tegosept, 3.4 mL propionic acid, 0.4 mL phosphoric acid for 100 vials) supplemented with dry yeast. Progeny generated by crossing tubP-GAL80[ts]; tubP-GAL4 (FBst0067065) females to either UAS-LT3-NDam or UAS-LT3-NDam-RpII215 (Southall, Gold et al. 2013, PMID: 23792147) males were reared in bottles (50-100 flies) in 60% relative humidity at 18 ºC, the restrictive temperature to limit Dam or Dam Pol II expression.

extract_protocol:
We collected whole males (FBbt:00007004; pool of 3-5 individuals) or whole females (FBbt:00007011; pool of 3-5 individuals) by anesthetizing flies using CO2 and placing them into a 1.5 mL eppendorf tube. Dissections to collect gonads were performed at room temperature in 1X Ringer’s solution (111 mM NaCl, 1.88 mM KCl, 64 μM NaH2PO4, 816 μM CaCl2, 2.38 mM NaHCO3). We collected ovaries (FBbt:00004865; pools 8-10 pairs) by removing reproductive tracts using forceps and separating ovaries from the common oviduct (FBbt:00004913) while keeping the lateral oviduct (FBbt:00004912). We collected testes (FBbt:00004928; pools of 8-10 pairs) by removing reproductive tract and separating from the other reproductive tissues. The testes breakpoint from other reproductive tissues varied, so some samples may include the seminal vesicle (FBbt:00004958). We stored dissected tissues in a 1.5 mL eppendorf tube without additional buffer. After collection or dissection we stored all samples at -80 ºC.    Total RNA was isolated using the Qiagen RNeasy kit (Germantown, MD, Cat # 74181 or Cat # 74182) following the spin technology section (Protocol for Isolation of Total RNA from Animal Cells using spin technology, Cat#19504) except all centrifugations were modified to ~4,000 g.
We constructed libraries using the Truseq PolyA+ stranded mRNA kit (Illumina, San Diego, CA. Cat. No. RS-122-2101 or RS-122-2102), following the manufacturer’s protocol, modified to use half reactions with 200 ng total RNA as input for all samples. For each sample we spiked in External RNA Control Consortium (ERCC) spike-ins pool 78A or 78B (SRM2374, Zook et al., 2012. PMID: 22859977). ERCCs were added to the Fragment-Prime-Finish Mix during the mRNA fragmentation step; we added pool 78A to wells A2-A5, A7-A10, and B2-B11 and pool 78B to wells A1, A6, A11, A12, B1 and B12 (20 pg / sample) (Zook et al., 2012. PMID: 22859977).  We multiplexed libraries using 24 differently barcoded adapters from TruSeq (Illumina, San Diego, CA). Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing with an Illumina HiSeq 2500 (Illumina, San Diego, CA.).

treatment_protocol: We induced expression of Dam or Dam Pol II 24 h before sample collection by shifting 0-3 d post eclosion (FBdv:00007075 - FBdv:00007078) flies from 18 ºC to 29 ºC.

tag: sample role

value: control

tag: cross

value: FBst0067065 x UAS-LT3-NDam

tag: dev stage

value: day 0 of adulthood - day 3 of adulthood

value: testis + seminal vesicle

tag: driver

value: tubP-GAL80[ts]; tubP-GAL4

tag: temperature regimen

value: Flies were reared at 18 oC, then shifted 0-3 d PE to 29oC for 24 h.

tag: target

tag: target source

tag: plate row id

value: B

tag: plate col id

tag: spike-in

value: ERCC (SRM2374) 78A


title: Testis tub dam rep3

description: Pool of testes expressing Dam.

tag: Sex

value: male


title: ATAC-seq_Basal Suz12-deleted 2

status: Public on Jun 28 2018

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Bowtie 2.
Two technical replicates (same library sequenced twice) for each sample were combined and reads were summarized into 150bp end-to-end windows genome-wide.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent genomic location of 150bp window and the number of reads mapping to that window.

source_name: Mammary epithelium

growth_protocol: Organoids were cultured in Advanced DMEM/F12 supplemented with growth factors excluding Wtn3a or FGF2.

extract_protocol:
Nuclei were isoluated from 50,000 cells using ATAC lysis buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL)
DNA was tagmented using Illumina Tn5, PCR-amplifed and equimolar amounts sequenced.

treatment_protocol: To induce R26creERT2-mediated deletion of Suz12, 0.1 micromolar 4-hydroxytamoxifen was added to culture medium on day 4 of culture.

tag: background strain

tag: tissue

value: Mammary epithelium organoid

tag: cell type from which organoid was derived

value: Basal

tag: genotype


title: Testis tub dam rep2

description: Pool of testes expressing Dam.


title: ATAC-seq_Basal Suz12-deleted 3


title: K1-1st_S021

description:
K1-1st_S021_R1_.fastq.gz
K1-1st_S021_R2_.fastq.gz

value: Skin

tag: diagnosis

value: keloid

tag: time point

value: day 0


title: No Arsenic exposure

tag: strain

tag: treatment

value: Without arsenic exposure

tag: treatment exposure time


title: ATAC-seq_Luminal Wt 3

value: Luminal

value: Wild-type


title: Ovary tub pol II rep3

description: Pool of ovaries expressing Dam Pol II.

tag: sample role

value: treatment

tag: cross

value: FBst0067065 x UAS-LT3-NDam-Rpll215

value: female

tag: dev stage

value: ovary + lateral oviduct

tag: driver


title: ATAC-seq_Luminal Suz12-deleted 3


title: ATAC-seq_Luminal Wt 2


title: ATAC-seq_Luminal Suz12-deleted 2


title: ATAC-seq_Basal Wt 3


title: ATAC-seq_Luminal Suz12-deleted 1


title: ATAC-seq_Basal Suz12-deleted 1


title: ATAC-seq_Basal Wt 2


title: ATAC-seq_Basal Wt 1


title: Ovary tub pol II rep1

description: Pool of ovaries expressing Dam Pol II.

value: day 0 of adulthood - day 3 of adulthood

value: tubP-GAL80[ts]; tubP-GAL4

tag: temperature regimen

tag: target

tag: target source

tag: plate row id


title: Ovary tub dam rep3

description: Pool of ovaries expressing Dam.

value: control

value: FBst0067065 x UAS-LT3-NDam

tag: Sex

value: Flies were reared at 18 oC, then shifted 0-3 d PE to 29oC for 24 h.

value: B

tag: plate col id

tag: spike-in


title: ATAC-seq_Luminal Wt 1

tag: background strain

tag: tissue

value: Mammary epithelium organoid

tag: cell type from which organoid was derived

tag: genotype


title: Ovary tub dam rep2

description: Pool of ovaries expressing Dam.

value: ERCC (SRM2374) 78A


title: Testis tub pol II rep3

description: Pool of testes expressing Dam Pol II.

value: male

value: testis + seminal vesicle

value: ERCC (SRM2374) 78B


title: Ovary tub pol II rep2

description: Pool of ovaries expressing Dam Pol II.


title: Whole female tub dam rep3

description: Pool of whole adult female expressing Dam.

source_name: whole organism

value: female organism

value: A


title: Testis tub pol II rep1

description: Pool of testes expressing Dam Pol II.

value: treatment


title: Ovary tub dam rep1

description: Pool of ovaries expressing Dam.


title: Testis tub pol II rep2

description: Pool of testes expressing Dam Pol II.

value: FBst0067065 x UAS-LT3-NDam-Rpll215


title: Whole female tub dam rep2

value: female


title: Whole female tub dam rep1


title: Whole male tub pol II rep3

description: Pool of whole adult male expressing Dam Pol II.

value: male organism


title: Whole male tub pol II rep1

value: day 0 of adulthood - day 3 of adulthood


title: Whole male tub pol II rep2

value: tubP-GAL80[ts]; tubP-GAL4


title: Whole male tub dam rep3

description: Pool of whole adult male expressing Dam.

value: control


title: Whole female tub pol II rep1

description: Pool of whole adult female expressing Dam Pol II.


title: Whole male tub dam rep2

value: FBst0067065 x UAS-LT3-NDam


title: Whole female tub pol II rep2

value: Flies were reared at 18 oC, then shifted 0-3 d PE to 29oC for 24 h.


title: Whole female tub pol II rep3


title: Whole male tub dam rep1


title: Colon Carcinoma rep376

status: Public on Jun 09 2018

city: Salt Lake City

first: Jennifer

last: Herrick

state: UT

address: 295 Chipeta Way

department: Internal Medicine

institute: University of Utah

description: miRBase database (Release 19.0)

hyb_protocol: Labeled RNA was resuspended in 18ul nuclease free water, 4.5ul 10X GE Blocking agent (Agilent) and 22.5ul of 2X Hi-RPM Hybridization buffer were added (Agilent).  The 45ul hybridization solution was placed onto Agilent Human miRNA Microarray V19.0 Arrays (Cat# G4872A-046064). The microarray contains probes for 2006 unique human miRNAs. The miRNA array contains on average 30 replicates per probe sequence for a total of 60 000 unique features. Each glass slide contains 8x60K formatted arrays.  Agilent Sure Hybridization Chambers were utilized.  Hybridization was carried out at 55C for 20 hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 5 minutes at room temperature in GE Wash Buffer 1 (Agilent) followed by a 5 minute was in GE Wash Buffer 2 at 37C.  Slides were placed in a slide holder  for scanning.

scan_protocol: Slides were scanned on an Agilent SureScan microarray scanner model G2600D with auto detect forr 8x60K array slides.

data_processing:
Data were extracted from the scanned image using Agilent Feature Extract software v.11.5.1.1. Data were required to pass stringent QC parameters established by Agilent that included tests for excessive background fluorescence, excessive variation among probe sequence replicates on the array, and measures of the total gene signal on the array to assess low signal.
Genes with fewer than 0.5 mean reads across all samples were dropped. To minimize differences that could be attributed to the array, amount of RNA, location on array, or other factors that could erroneously influence expression, total gene signal was normalized by multiplying each sample by a scaling factor which was the median of the 75th percentiles of all the samples divided by the 75th percentile of each individual sample.

source_name: Paraffin embedded colon carcinoma

label_protocol: 100 ng total RNA was labeled with Cy3 according to the manufacturer using the miRNA Complete Labeling and Hybe Kit from Agilent (p/n 5190-0456).  Labeled RNA was purified with the use of Micro Bio-Spin 6 columns (Bio-Rad) and dried.

extract_protocol: RNA (miRNA) was extracted from formalin-fixed paraffin embedded tissues.  Cells were dissected from 1–4 sequential sections on aniline blue stained slides using an H&E slide for reference. Total RNA containing miRNA was extracted, isolated, and purified using the RecoverAll Total Nucleic Acid isolation kit (Ambion), RNA yields were determined using a NanoDrop spectrophotometer.

tag: individual

value: Subject 385

tag: organ

value: Colon

value: Carcinoma

value: Male

tag: site

value: Proximal

tag: ajcc stage


title: Colon Carcinoma rep379

description: miRBase database (Release 19.0)

value: Subject 388

value: Distal


title: Colon Hyperplastic Polyp rep002

description: miRBase database (Release 19.0)

source_name: Paraffin embedded colon hyperplastic polyp

value: Subject 387

value: Hyperplastic Polyp


title: Colon Normal Mucosa rep347

description: miRBase database (Release 19.0)

source_name: Paraffin embedded normal colon mucosa

value: Subject 384

value: Normal Mucosa

value: Female


title: Colon Normal Mucosa rep346

description: miRBase database (Release 19.0)

value: Subject 383


title: Colon Carcinoma rep378

description: miRBase database (Release 19.0)


title: Colon Normal Mucosa rep350

description: miRBase database (Release 19.0)


title: Colon Carcinoma rep375

description: miRBase database (Release 19.0)


title: Colon Carcinoma rep374

description: miRBase database (Release 19.0)


title: Colon Normal Mucosa rep345

description: miRBase database (Release 19.0)

value: Subject 382


title: Colon Carcinoma rep373

description: miRBase database (Release 19.0)


title: Colon Normal Mucosa rep349

description: miRBase database (Release 19.0)

value: Subject 386


title: Colon Carcinoma rep380

description: miRBase database (Release 19.0)

value: Subject 389


title: Colon Normal Mucosa rep348

description: miRBase database (Release 19.0)


title: Colon Carcinoma rep377

description: miRBase database (Release 19.0)


title: Colon Normal Mucosa rep344

description: miRBase database (Release 19.0)

value: Subject 381


title: Colon Normal Mucosa rep351

description: miRBase database (Release 19.0)


title: Colon Adenoma rep048

description: miRBase database (Release 19.0)

source_name: Paraffin embedded colon adenoma

value: Adenoma


title: Colon Normal Mucosa rep352

description: miRBase database (Release 19.0)

value: Colon


title: Colon Carcinoma rep372

description: miRBase database (Release 19.0)

value: Carcinoma


title: Colon Normal Mucosa rep343

description: miRBase database (Release 19.0)

value: Subject 380


title: Colon Carcinoma rep371

description: miRBase database (Release 19.0)


title: Colon Normal Mucosa rep342

description: miRBase database (Release 19.0)

value: Subject 379

value: Male

value: Proximal


title: Colon Adenoma rep046

description: miRBase database (Release 19.0)


title: Colon Adenoma rep047

description: miRBase database (Release 19.0)

value: Distal


title: Colon Carcinoma rep370

description: miRBase database (Release 19.0)


title: Colon Carcinoma rep368

description: miRBase database (Release 19.0)

value: Subject 377


title: Colon Normal Mucosa rep341

description: miRBase database (Release 19.0)

value: Subject 378


title: Colon Carcinoma rep369

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep315

description: miRBase database (Release 19.0)

source_name: Paraffin embedded rectal carcinoma

value: Subject 741

value: Rectum

value: Rectal


title: Rectal Normal Mucosa rep249

description: miRBase database (Release 19.0)

source_name: Paraffin embedded normal rectal mucosa

value: Subject 742

value: Normal Mucosa


title: Rectal Normal Mucosa rep248

description: miRBase database (Release 19.0)

value: Female


title: Colon Adenoma rep045

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep250

description: miRBase database (Release 19.0)

value: Subject 743


title: Rectal Carcinoma rep316

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep313

description: miRBase database (Release 19.0)

value: Subject 739


title: Rectal Carcinoma rep309

description: miRBase database (Release 19.0)

value: Subject 735


title: Rectal Carcinoma rep312

description: miRBase database (Release 19.0)

value: Subject 738

value: Carcinoma


title: Rectal Carcinoma rep308

description: miRBase database (Release 19.0)

value: Subject 734


title: Rectal Normal Mucosa rep242

description: miRBase database (Release 19.0)

value: Subject 733

value: Male


title: Rectal Normal Mucosa rep243

description: miRBase database (Release 19.0)


title: Rectal High-Grade Displasia rep001

description: miRBase database (Release 19.0)

source_name: Paraffin embedded rectal high-grade displasia

value: Subject 737

value: High-Grade Displasia


title: Rectal Carcinoma rep311

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep246

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep305

description: miRBase database (Release 19.0)

value: Subject 731


title: Rectal Carcinoma rep307

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep245

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep306

description: miRBase database (Release 19.0)

value: Subject 732


title: Rectal Carcinoma rep310

description: miRBase database (Release 19.0)

value: Subject 736

value: Rectum


title: Rectal Normal Mucosa rep241

description: miRBase database (Release 19.0)

value: Rectal


title: Rectal Normal Mucosa rep247

description: miRBase database (Release 19.0)

value: Subject 740

value: Normal Mucosa


title: Rectal Carcinoma rep314

description: miRBase database (Release 19.0)

value: Female


title: Rectal Normal Mucosa rep244

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep239

description: miRBase database (Release 19.0)

value: Subject 729


title: Rectal Carcinoma rep303

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep304

description: miRBase database (Release 19.0)

value: Subject 730


title: Rectal Normal Mucosa rep240

description: miRBase database (Release 19.0)


title: Rectal Hyperplastic Polyp rep003

description: miRBase database (Release 19.0)

source_name: Paraffin embedded rectal hyperplastic polyp

value: Hyperplastic Polyp


title: Rectal Carcinoma rep302

description: miRBase database (Release 19.0)

value: Subject 728

value: Carcinoma


title: Rectal Carcinoma rep299

description: miRBase database (Release 19.0)

value: Subject 725


title: Rectal Carcinoma rep301

description: miRBase database (Release 19.0)

value: Subject 727


title: Rectal Normal Mucosa rep237

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep296

description: miRBase database (Release 19.0)

value: Subject 722

value: Male


title: Rectal Carcinoma rep295

description: miRBase database (Release 19.0)

value: Subject 721


title: Rectal Normal Mucosa rep232

description: miRBase database (Release 19.0)

value: Subject 717


title: Rectal Carcinoma rep290

description: miRBase database (Release 19.0)

value: Subject 716


title: Rectal Carcinoma rep298

description: miRBase database (Release 19.0)

value: Subject 724

value: Rectum


title: Rectal Carcinoma rep297

description: miRBase database (Release 19.0)

value: Subject 723

value: Rectal


title: Rectal Normal Mucosa rep233

description: miRBase database (Release 19.0)

value: Subject 718

value: Normal Mucosa

value: Female


title: Rectal Carcinoma rep294

description: miRBase database (Release 19.0)

value: Subject 720


title: Rectal Normal Mucosa rep235

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep293

description: miRBase database (Release 19.0)

value: Subject 719


title: Rectal Carcinoma rep292

description: miRBase database (Release 19.0)

value: Carcinoma


title: Rectal Normal Mucosa rep231

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep234

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep291

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep230

description: miRBase database (Release 19.0)

value: Subject 715


title: Rectal Carcinoma rep288

description: miRBase database (Release 19.0)

value: Subject 714


title: Rectal Carcinoma rep289

description: miRBase database (Release 19.0)


title: Rectal Normal Mucosa rep229

description: miRBase database (Release 19.0)


title: Rectal Carcinoma rep287

description: miRBase database (Release 19.0)

value: Subject 713


title: Rectal Carcinoma rep286

description: miRBase database (Release 19.0)

value: Subject 712

value: Male


title: Rectal Carcinoma rep300

description: miRBase database (Release 19.0)

value: Subject 726


title: Rectal Normal Mucosa rep238

description: miRBase database (Release 19.0)

value: Subject 728


title: Rectal Adenoma rep048

description: miRBase database (Release 19.0)

source_name: Paraffin embedded rectal adenoma

value: Adenoma


title: Rectal Normal Mucosa rep236

description: miRBase database (Release 19.0)

value: Subject 721

value: Rectum


title: Rectal Normal Mucosa rep228

description: miRBase database (Release 19.0)

value: Rectal


title: Rectal Carcinoma rep285

description: miRBase database (Release 19.0)

value: Subject 711