title: SV18148_321 CAMP Subject


title: SV18148_317 CAMP Subject

status: Public on Jul 08 2020

type: SRA

city: Boston

first: Jiang

last: Li

state: Massachusetts

address: 181 Longwood Avenue

department: Medicine

country: USA

institute: Brigham and Women's Hospital

description:
CAMP_RAW_COUNT.txt
CAMP_NORMALIZED_COUNT.txt

library_source: transcriptomic

data_processing:
ExceRpt (http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Small_RNA-seq_Pipeline) was employed to assess the read quality and annotate miRNAs.
The read count was log transformed and normalized by quantile normalization (R package: preprocessCore).
Raw read counts less than five were filtered out and miRNAs with coverage less than 80% of all subjects were removed.
Coverage refers to the number of subjects in which a specific miRNA was detected at >=5 counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files of miRNA count for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood Serum

extract_protocol:
Total RNA was isolated from serum samples by the Qiagen miRNeasy Serum/Plasma extraction kit and QIAcube automation. All samples were quantified using the Nanodrop spectrophotometer prior to plating.
Norgen Biotek Small RNA Library Prep Kit

tag: treatment group

value: Placebo

tag: Sex

value: Male

tag: age

tag: prebronchodilator fev1% predicted baseline

tag: prebronchodilator fev1% predicted year4


title: SV18148_319 CAMP Subject


title: SV18148_318 CAMP Subject

value: Budesonide

value: Female


title: SV18148_314 CAMP Subject


title: SV18148_316 CAMP Subject


title: SV18148_313 CAMP Subject


title: SV18148_312 CAMP Subject


title: SV18148_339 CAMP Subject


title: SV18148_315 CAMP Subject


title: SV18148_311 CAMP Subject


title: SV18148_332 CAMP Subject

value: median


title: SV18148_310 CAMP Subject


title: SV18148_309 CAMP Subject

value: high


title: control rat collateral tissue replicate 1

status: Public on Aug 31 2020

type: RNA

city: Bad Nauheim

first: Kerstin

last: Troidl

address: Ludwigstr. 43

country: Germany

institute: Max-Planck-Institute for Heart and Lung Research

description:
Sample name: Psk 27 kk
Biological replicate 1 of 5. Collateral tissue Psk 27 kk (AF665) and collateral tissue Psk 28 kk (AF546)

hyb_protocol: Two differentially labelled reactions were combined into one tube and loaded onto the array

scan_protocol: Arrays were scanned using a GenePix 400B microarray scanner (Molecular Devices)

data_processing:
The annotated data were normalized using a Latin Squares algorithm by the NCode™ Profiler data analysis software
The pairwise median fold-change, P-value, tissue rank, and test statistics for the miRNAs are listed in the Analyzed Data File.  The values for each individual miRNA probe sequence printed in triplicate on the array are listed as separate rows in the analysis file. The miRNAs with p-values <0.05 for two out of the three spots on the array are considered statistically significant. A list of the statistically significant miRNAs for follow-up studies is provided on the second sheet in the Analyzed Data workbook. The replicate values for median fold-change, P-value, tissue rank, and test statistics for each of the miRNAs collapsed into one value are listed in the Collapsed Data File.
Data analysis used only the miRNA_IDs annotated in NCode Multi-Species miRNA Microarray V2.

organism: Rattus norvegicus

source_name: collateral blood vessel tissue control

label_protocol: The samples were directly labeled using Ncode Rapid labeling System (#MIRLSRPD-20) and arrayed on the multi-species miRNA Microarray V2 (#MIRA2-05)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Single femoral artery ligation and arteriovenous shunt to maximize fluid shear stress in collateral arteries. Contralateral leg was sham-operated and served as control

tag: gender

value: male

tag: strain

value: Spraque-Dawley

tag: tissue

value: collateral blood vessel tissue control


title: SV18148_306 CAMP Subject


title: SV18148_299 CAMP Subject


title: SV18148_302 CAMP Subject


title: SV18148_303 CAMP Subject


title: SV18148_307 CAMP Subject


title: SV18148_308 CAMP Subject


title: SV18148_298 CAMP Subject

value: low


title: SV18148_304 CAMP Subject


title: SV18148_305 CAMP Subject


title: SV18148_301 CAMP Subject


title: SV18148_297 CAMP Subject


title: SV18148_295 CAMP Subject


title: SV18148_293 CAMP Subject


title: SV18148_294 CAMP Subject


title: SV18148_292 CAMP Subject


title: SV18148_291 CAMP Subject


title: SV18148_288 CAMP Subject


title: SV18148_285 CAMP Subject


title: SV18148_287 CAMP Subject


title: SV18148_283 CAMP Subject


title: SV18148_290 CAMP Subject


title: SV18148_286 CAMP Subject


title: SV18148_284 CAMP Subject


title: SV18148_282 CAMP Subject


title: SV18148_300 CAMP Subject


title: SV18148_280 CAMP Subject


title: SV18148_275 CAMP Subject


title: SV18148_276 CAMP Subject


title: SV18148_277 CAMP Subject


title: SV18148_278 CAMP Subject


title: SV18148_271 CAMP Subject


title: SV18148_268 CAMP Subject


title: SV18148_273 CAMP Subject


title: SV18148_272 CAMP Subject


title: SV18148_266 CAMP Subject


title: SV18148_270 CAMP Subject


title: SV18148_265 CAMP Subject


title: SV18148_289 CAMP Subject


title: SV18148_274 CAMP Subject


title: SV18148_267 CAMP Subject


title: SV18148_262 CAMP Subject


title: SV18148_264 CAMP Subject


title: SV18148_261 CAMP Subject


title: SV18148_263 CAMP Subject


title: SV18148_260 CAMP Subject


title: SV18148_256 CAMP Subject


title: SV18148_259 CAMP Subject


title: SV18148_281 CAMP Subject


title: SV18148_279 CAMP Subject


title: SV18148_254 CAMP Subject


title: SV18148_255 CAMP Subject


title: SV18148_253 CAMP Subject


title: SV18148_269 CAMP Subject


title: SV18148_252 CAMP Subject


title: SV18148_247 CAMP Subject


title: SV18148_248 CAMP Subject


title: SV18148_249 CAMP Subject


title: SV18148_246 CAMP Subject


title: SV18148_244 CAMP Subject


title: SV18148_245 CAMP Subject


title: SV18148_251 CAMP Subject


title: SV18148_240 CAMP Subject


title: SV18148_241 CAMP Subject


title: SV18148_250 CAMP Subject


title: SV18148_257 CAMP Subject


title: SV18148_258 CAMP Subject


title: SV18148_242 CAMP Subject


title: SV18148_243 CAMP Subject


title: SV18148_237 CAMP Subject


title: SV18148_238 CAMP Subject


title: SV18148_235 CAMP Subject


title: SV18148_228 CAMP Subject


title: SV18148_236 CAMP Subject


title: SV18148_234 CAMP Subject


title: SV18148_227 CAMP Subject


title: SV18148_233 CAMP Subject


title: SV18148_232 CAMP Subject


title: SV18148_231 CAMP Subject


title: SV18148_229 CAMP Subject


title: SV18148_230 CAMP Subject


title: SV18148_226 CAMP Subject


title: SV18148_225 CAMP Subject


title: SV18148_224 CAMP Subject


title: SV18148_239 CAMP Subject


title: SV18148_223 CAMP Subject


title: SV18148_221 CAMP Subject


title: SV18148_220 CAMP Subject


title: SV18148_218 CAMP Subject


title: SV18148_219 CAMP Subject


title: SV18148_222 CAMP Subject


title: SV18148_216 CAMP Subject


title: SV18148_217 CAMP Subject


title: SV18148_215 CAMP Subject


title: SV18148_213 CAMP Subject


title: SV18148_214 CAMP Subject


title: SV18148_212 CAMP Subject


title: SV18148_211 CAMP Subject


title: SV18148_210 CAMP Subject


title: SV18148_209 CAMP Subject


title: SV18148_208 CAMP Subject


title: SV18148_205 CAMP Subject


title: SV18148_206 CAMP Subject


title: SV18148_203 CAMP Subject


title: SV18148_202 CAMP Subject


title: SV18148_200 CAMP Subject


title: SV18148_201 CAMP Subject


title: SV18148_199 CAMP Subject


title: SV18148_198 CAMP Subject


title: SV18148_197 CAMP Subject


title: SV18148_196 CAMP Subject


title: SV18148_190 CAMP Subject


title: SV18148_191 CAMP Subject


title: SV18148_195 CAMP Subject


title: SV18148_189 CAMP Subject


title: SV18148_185 CAMP Subject


title: SV18148_184 CAMP Subject


title: SV18148_188 CAMP Subject


title: SV18148_187 CAMP Subject


title: SV18148_182 CAMP Subject


title: SV18148_183 CAMP Subject


title: SV18148_180 CAMP Subject


title: SV18148_178 CAMP Subject


title: SV18148_175 CAMP Subject


title: SV18148_177 CAMP Subject


title: SV18148_179 CAMP Subject


title: SV18148_172 CAMP Subject


title: SV18148_204 CAMP Subject


title: SV18148_176 CAMP Subject


title: SV18148_192 CAMP Subject


title: SV18148_194 CAMP Subject


title: SV18148_193 CAMP Subject


title: SV18148_186 CAMP Subject


title: SV18148_174 CAMP Subject


title: SV18148_170 CAMP Subject


title: SV18148_207 CAMP Subject


title: SV18148_173 CAMP Subject


title: SV18148_168 CAMP Subject


title: SV18148_166 CAMP Subject


title: SV18148_171 CAMP Subject


title: SV18148_164 CAMP Subject


title: SV18148_163 CAMP Subject


title: SV18148_181 CAMP Subject


title: SV18148_162 CAMP Subject


title: SV18148_161 CAMP Subject


title: SV18148_165 CAMP Subject


title: SV18148_159 CAMP Subject


title: SV18148_158 CAMP Subject


title: SV18148_155 CAMP Subject


title: SV18148_154 CAMP Subject


title: SV18148_151 CAMP Subject


title: SV18148_153 CAMP Subject


title: SV18148_152 CAMP Subject


title: SV18148_156 CAMP Subject


title: SV18148_157 CAMP Subject


title: SV18148_169 CAMP Subject


title: SV18148_149 CAMP Subject


title: SV18148_167 CAMP Subject


title: SV18148_146 CAMP Subject


title: SV18148_147 CAMP Subject


title: SV18148_148 CAMP Subject


title: SV18148_145 CAMP Subject


title: SV18148_150 CAMP Subject


title: SV18148_142 CAMP Subject


title: SV18148_141 CAMP Subject


title: SV18148_160 CAMP Subject


title: SV18148_139 CAMP Subject


title: SV18148_144 CAMP Subject


title: SV18148_138 CAMP Subject


title: SV18148_135 CAMP Subject


title: SV18148_140 CAMP Subject


title: SV18148_143 CAMP Subject


title: SV18148_137 CAMP Subject


title: SV18148_132 CAMP Subject


title: SV18148_133 CAMP Subject


title: SV18148_136 CAMP Subject


title: SV18148_130 CAMP Subject


title: SV18148_131 CAMP Subject


title: SV18148_129 CAMP Subject


title: SV18148_128 CAMP Subject


title: SV18148_125 CAMP Subject


title: SV18148_127 CAMP Subject


title: SV18148_126 CAMP Subject


title: SV18148_124 CAMP Subject


title: SV18148_123 CAMP Subject


title: SV18148_296 CAMP Subject


title: SV18148_120 CAMP Subject


title: SV18148_119 CAMP Subject


title: SV18148_122 CAMP Subject


title: SV18148_117 CAMP Subject


title: SV18148_114 CAMP Subject


title: SV18148_121 CAMP Subject


title: SV18148_112 CAMP Subject


title: SV18148_113 CAMP Subject


title: SV18148_134 CAMP Subject


title: SV18148_109 CAMP Subject


title: SV18148_110 CAMP Subject


title: SV18148_116 CAMP Subject


title: SV18148_111 CAMP Subject


title: SV18148_104 CAMP Subject


title: SV18148_115 CAMP Subject


title: SV18148_108 CAMP Subject


title: SV18148_107 CAMP Subject


title: SV18148_105 CAMP Subject


title: SV18148_102 CAMP Subject


title: SV18148_100 CAMP Subject


title: SV18148_098 CAMP Subject


title: SV18148_095 CAMP Subject


title: SV18148_118 CAMP Subject


title: SV18148_096 CAMP Subject


title: SV18148_091 CAMP Subject


title: SV18148_092 CAMP Subject


title: SV18148_093 CAMP Subject


title: SV18148_090 CAMP Subject


title: SV18148_089 CAMP Subject


title: SV18148_106 CAMP Subject


title: SV18148_084 CAMP Subject


title: SV18148_083 CAMP Subject


title: SV18148_086 CAMP Subject


title: SV18148_087 CAMP Subject


title: SV18148_081 CAMP Subject


title: SV18148_085 CAMP Subject


title: SV18148_088 CAMP Subject


title: SV18148_077 CAMP Subject


title: SV18148_078 CAMP Subject


title: SV18148_080 CAMP Subject


title: SV18148_079 CAMP Subject


title: SV18148_103 CAMP Subject


title: SV18148_099 CAMP Subject


title: SV18148_101 CAMP Subject


title: SV18148_097 CAMP Subject


title: SV18148_073 CAMP Subject


title: SV18148_075 CAMP Subject


title: SV18148_074 CAMP Subject


title: SV18148_072 CAMP Subject


title: SV18148_070 CAMP Subject


title: SV18148_071 CAMP Subject


title: SV18148_094 CAMP Subject


title: SV18148_067 CAMP Subject


title: SV18148_069 CAMP Subject


title: SV18148_065 CAMP Subject


title: SV18148_082 CAMP Subject


title: SV18148_068 CAMP Subject


title: SV18148_064 CAMP Subject


title: SV18148_066 CAMP Subject


title: SV18148_059 CAMP Subject


title: SV18148_056 CAMP Subject


title: SV18148_060 CAMP Subject


title: SV18148_063 CAMP Subject


title: SV18148_061 CAMP Subject


title: SV18148_058 CAMP Subject


title: SV18148_055 CAMP Subject


title: SV18148_076 CAMP Subject


title: SV18148_057 CAMP Subject


title: SV18148_053 CAMP Subject


title: SV18148_054 CAMP Subject


title: SV18148_052 CAMP Subject


title: SV18148_049 CAMP Subject


title: SV18148_050 CAMP Subject


title: SV18148_051 CAMP Subject


title: SV18148_048 CAMP Subject


title: SV18148_046 CAMP Subject


title: SV18148_047 CAMP Subject


title: SV18148_045 CAMP Subject


title: SV18148_044 CAMP Subject


title: SV18148_042 CAMP Subject


title: SV18148_043 CAMP Subject


title: SV18148_036 CAMP Subject


title: SV18148_041 CAMP Subject


title: SV18148_040 CAMP Subject


title: SV18148_034 CAMP Subject


title: SV18148_035 CAMP Subject


title: SV18148_033 CAMP Subject


title: SV18148_031 CAMP Subject


title: SV18148_027 CAMP Subject


title: SV18148_016 CAMP Subject


title: SV18148_026 CAMP Subject


title: SV18148_021 CAMP Subject


title: SV18148_022 CAMP Subject


title: SV18148_013 CAMP Subject


title: SV18148_020 CAMP Subject


title: SV18148_037 CAMP Subject


title: SV18148_039 CAMP Subject


title: SV18148_062 CAMP Subject


title: SV18148_019 CAMP Subject


title: SV18148_018 CAMP Subject


title: SV18148_012 CAMP Subject


title: SV18148_010 CAMP Subject


title: SV18148_023 CAMP Subject


title: SV18148_029 CAMP Subject


title: SV18148_025 CAMP Subject


title: SV18148_008 CAMP Subject


title: SV18148_032 CAMP Subject


title: SV18148_014 CAMP Subject


title: SV18148_028 CAMP Subject


title: SV18148_009 CAMP Subject


title: SV18148_015 CAMP Subject


title: SV18148_011 CAMP Subject


title: SV18148_006 CAMP Subject


title: SV18148_024 CAMP Subject


title: SV18148_030 CAMP Subject


title: SV18148_007 CAMP Subject


title: SV18148_005 CAMP Subject


title: SV18148_004 CAMP Subject


title: SV18148_003 CAMP Subject


title: SV18148_001 CAMP Subject


title: TKO_13D_H3K27me3_rep1

status: Public on Jul 01 2020

city: Beijing

first: Wei

last: Xie

address: Haidian District

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data
Supplementary_files_format_and_content: Bisulfite-seq processed data files: methylated and unmethylated C are counted at watson and crick strand seperately
Supplementary_files_format_and_content: *mcG.txt column headers: chr, pos, mCwatson, Cwatson, mCcrick, Ccrick

molecule: genomic DNA

organism: Mus musculus

growth_protocol: ES cells were cultured in non-adhesive bacterial dishes using ES culture medium minus LIF for 4 days. Then retinoic acid (RA) (Sigma Cat. R2625) was added in to medium to the final concentration of 2ug/ml. Medium was changed every day. On the 5th day of adding RA, embryonic bodies were dissociated by 0.25% Trypsin-EDTA (Gibco Cat. 25200-056) and plated to poly-L-ornithine (Sigma Cat. P3655) and Laminin (Invitrogen Cat. 23017-015) pre-coated dish. Cells were cultured in DMEM/F-12 (Gibco Cat. 11330-032) with B27 (Life tech. Cat. 17504-044) and were incubated for two days. The medium was switched to BME (Gibco, Cat. 21010-046) with B27 for another two days. Differentiated neurons were then harvested for subsequent analyses.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

tag: genotype/variation

tag: cell type

value: mESC-derived cell

tag: chip-antibody

value: Homemade


title: WT_mES_BS_seq_rep2

data_processing:
library strategy: MethylC-seq
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data
Supplementary_files_format_and_content: Bisulfite-seq processed data files: methylated and unmethylated C are counted at watson and crick strand seperately
Supplementary_files_format_and_content: *mcG.txt column headers: chr, pos, mCwatson, Cwatson, mCcrick, Ccrick

extract_protocol:
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 6ug genomic DNA was mixed with 25ng lambda DNA and sonicated to 200-500bp.DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Bisulfite treatment is performed using commercial kit (Zymo research, Cat. D5005). DNA was amplified and 200-500bp fragments were gel selected.

value: WT

value: mESC


title: SV18148_002 CAMP Subject


title: WT_mES_BS_seq_rep1

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).


title: WT_13D_BS_seq_rep1


title: SV18148_038 CAMP Subject


title: WT_13D_BS_seq_rep2


title: TKO_mES_BS_seq_rep1


title: TKO_mES_BS_seq_rep2


title: TKO_13D_BS_seq_rep2


title: TKO_13D_BS_seq_rep1


title: PKO_Dnmt1_KO_OE_BS_seq

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt1-/- Dnmt1 oe


title: R-PKO_mES_BS_seq_rep2

value: J1 129S4/SvJae


title: PKO_Dnmt1_KO_mES_BS_seq


title: PKO_Dnmt1_KO_Dnmt3c_KO_Dnmt1_OE_BS_seq

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt1-/- Dnmt3c-/- Dnmt1 oe


title: R-PKO_Dnmt3b_OE_BS_seq_rep1

value: Dnmt3a-/- Dnmt3b-/- Tet1-/- Tet2-/- Tet3-/- Dnmt3b oe


title: R-PKO_Dnmt3b_OE_BS_seq_rep2


title: R-PKO_mES_BS_seq_rep1


title: PKO_mES_BS_seq_rep2


title: SKO_mES_BS_seq

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt3c-/-


title: PKO_mES_BS_seq_rep1


title: PKO_13D_BS_seq_rep2


title: PKO_13D_BS_seq_rep1


title: TKO_13D_H3K27ac_rep2

value: Active Motif, Cat # 39133


title: Lemna gibba fronds

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 28 nucleotides. small RNA reads were mapped to the Lemna genome.(ORG version1 genome).
Genome_build: LEMNA ORG1 Genome
Supplementary_files_format_and_content: tag count

organism: Lemna gibba

source_name: The Rutgers Duckweed Stock Cooperative

extract_protocol: sRNA library constructed from all diverse tissue types listed in the column source name" . The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by  Illumina sRNA TruSeq sample preparation kit followed by sequencing with Illumina's HiSeq 2500 instrument. The adapter sequences were removed, and the abundance of each distinct small RNA was determined."

value: fronds


title: SV18148_017 CAMP Subject

value: Placebo

value: Male


title: RF6_MT_817 [D712_D505]

status: Public on Jun 30 2020

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

country: United Kingdom

institute: WT-MRC Institute of Metabolic Science

description:
SLX-10884.D712_D505.HCMVCBBXX.s_3.r
q36-0-SLX-10884.D712_D505.cxb-raw-count

data_processing:
Cuffdiff from the Samtools suite was used to align reads
FeatureCount to count fragments overlapping annotated human genes
EdgeR package: normalization used weighted trimmed means of M-values (TMM) and a design matrix comparing affected with unaffected samples
Generalized linear modeling (glmLRT) was used for differential expression analysis
The resulting gene list was analysed using Ingenuity Pathway Analysis (IPA) software
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with fitted or raw counts for every gene and every sample.

source_name: PIK3R1(Y657X) mutant_Refed_liver

growth_protocol: Both PIK3R1(Y657X) mutant and wild-type C57Bl/6J mice were maintained on chow until 16 weeks old, at which time they were fasted for 16 hours and then refed chow for 6 hours. The tissues were harvested and snap-frozen at three time points: chow diet before overnight fast (ad libitum chow, ALC), after 16 hour fast (overnight fast, ONF), and after 6 hour refeeding (refed 6 hours, RF6).

extract_protocol:
Total RNA was extracted from the snap frozen tissues using the RNeasy kit (Qiagen) and RNA libraries were made using the Illumina TruSeq Stranded total RNA Lib Prep Kit according to manufacturer’s instructions.
Libraries were sequenced on an Illumina HiSeq 4000 (50 bp, single read sequencing). Cuffdiff from the Samtools suite was used to align reads, FeatureCount to count fragments overlapping annotated human genes, and the resulting data were analysed with the EdgeR package: normalization used weighted trimmed means of M-values (TMM) and a design matrix comparing affected with unaffected samples. Generalized linear modeling (glmLRT) was used for differential expression analysis. The resulting gene list was analysed using Ingenuity Pathway Analysis (IPA) software.

tag: strain background

tag: genotype

value: Human Pik3r1 Y657x mutation

tag: state

value: Refed

value: liver


title: ALC_MT_857 [D712_D504]

description:
SLX-10884.D712_D504.HCMVCBBXX.s_3.r
q35-0-SLX-10884.D712_D504.cxb-raw-count

source_name: PIK3R1(Y657X) mutant_Chow_liver

value: Chow


title: RF6_MT_814 [D711_D505]

description:
SLX-10884.D711_D505.HCMVCBBXX.s_3.r
q33-0-SLX-10884.D711_D505.cxb-raw-count


title: ALC_WT_850 [D711_D504]

description:
SLX-10884.D711_D504.HCMVCBBXX.s_3.r
q32-0-SLX-10884.D711_D504.cxb-raw-count

value: Wild Type


title: ONF_MT_827 [D710_D503]

description:
SLX-10884.D710_D503.HCMVCBBXX.s_3.r
q28-0-SLX-10884.D710_D503.cxb-raw-count

source_name: PIK3R1(Y657X) mutant_Fasting_liver

value: Fasting


title: RF6_WT_901 [D709_D505]

description:
SLX-10884.D709_D505.HCMVCBBXX.s_3.r
q27-0-SLX-10884.D709_D505.cxb-raw-count


title: RF6_MT_810 [D710_D505]

description:
SLX-10884.D710_D505.HCMVCBBXX.s_3.r
q30-0-SLX-10884.D710_D505.cxb-raw-count


title: ONF_MT_921 [D711_D503]

description:
SLX-10884.D711_D503.HCMVCBBXX.s_3.r
q31-0-SLX-10884.D711_D503.cxb-raw-count


title: ALC_MT_869 [D710_D504]

description:
SLX-10884.D710_D504.HCMVCBBXX.s_3.r
q29-0-SLX-10884.D710_D504.cxb-raw-count


title: ALC_MT_868 [D709_D504]

description:
SLX-10884.D709_D504.HCMVCBBXX.s_3.r
q26-0-SLX-10884.D709_D504.cxb-raw-count


title: ONF_MT_806 [D708_D503]

description:
SLX-10884.D708_D503.HCMVCBBXX.s_3.r
q22-0-SLX-10884.D708_D503.cxb-raw-count


title: ALC_MT_866 [D708_D504]

description:
SLX-10884.D708_D504.HCMVCBBXX.s_3.r
q23-0-SLX-10884.D708_D504.cxb-raw-count


title: RF6_WT_896 [D707_D505]

description:
SLX-10884.D707_D505.HCMVCBBXX.s_3.r
q21-0-SLX-10884.D707_D505.cxb-raw-count


title: ONF_WT_920 [D707_D503]

description:
SLX-10884.D707_D503.HCMVCBBXX.s_3.r
q19-0-SLX-10884.D707_D503.cxb-raw-count


title: RF6_WT_900 [D708_D505]

description:
SLX-10884.D708_D505.HCMVCBBXX.s_3.r
q24-0-SLX-10884.D708_D505.cxb-raw-count


title: ALC_MT_859 [D707_D504]

description:
SLX-10884.D707_D504.HCMVCBBXX.s_3.r
q20-0-SLX-10884.D707_D504.cxb-raw-count


title: ALC_WT_860 [D706_D504]

description:
SLX-10884.D706_D504.HCMVCBBXX.s_3.r
q17-0-SLX-10884.D706_D504.cxb-raw-count


title: RF6_WT_828 [D706_D505]

description:
SLX-10884.D706_D505.HCMVCBBXX.s_3.r
q18-0-SLX-10884.D706_D505.cxb-raw-count


title: ONF_WT_919 [D706_D503]

description:
SLX-10884.D706_D503.HCMVCBBXX.s_3.r
q16-0-SLX-10884.D706_D503.cxb-raw-count


title: RF6_MT_899 [D704_D506]

description:
SLX-10884.D704_D506.HCMVCBBXX.s_3.r
q12-0-SLX-10884.D704_D506.cxb-raw-count


title: ONF_WT_918 [D705_D503]

description:
SLX-10884.D705_D503.HCMVCBBXX.s_3.r
q13-0-SLX-10884.D705_D503.cxb-raw-count


title: ONF_WT_825 [D704_D503]

description:
SLX-10884.D704_D503.HCMVCBBXX.s_3.r
q9-0-SLX-10884.D704_D503.cxb-raw-count


title: ONF_MT_922 [D712_D503]

description:
SLX-10884.D712_D503.HCMVCBBXX.s_3.r
q34-0-SLX-10884.D712_D503.cxb-raw-count


title: ALC_MT_858 [D702_D505]

description:
SLX-10884.D702_D505.HCMVCBBXX.s_3.r
q7-0-SLX-10884.D702_D505.cxb-raw-count


title: RF6_MT_898 [D702_D506]

description:
SLX-10884.D702_D506.HCMVCBBXX.s_3.r
q8-0-SLX-10884.D702_D506.cxb-raw-count


title: ALC_WT_847 [D702_D504]

description:
SLX-10884.D702_D504.HCMVCBBXX.s_3.r
q6-0-SLX-10884.D702_D504.cxb-raw-count


title: ONF_WT_824 [D702_D503]

description:
SLX-10884.D702_D503.HCMVCBBXX.s_3.r
q5-0-SLX-10884.D702_D503.cxb-raw-count


title: ONF_MT_826 [D709_D503]

description:
SLX-10884.D709_D503.HCMVCBBXX.s_3.r
q25-0-SLX-10884.D709_D503.cxb-raw-count


title: RF6_MT_897 [D701_D506]

description:
SLX-10884.D701_D506.HCMVCBBXX.s_3.r
q4-0-SLX-10884.D701_D506.cxb-raw-count


title: ALC_WT_856 [D701_D505]

description:
SLX-10884.D701_D505.HCMVCBBXX.s_3.r
q3-0-SLX-10884.D701_D505.cxb-raw-count


title: ONF_MT_923 [D701_D504]

description:
SLX-10884.D701_D504.HCMVCBBXX.s_3.r
q2-0-SLX-10884.D701_D504.cxb-raw-count


title: ONF_WT_807 [D701_D503]

description:
SLX-10884.D701_D503.HCMVCBBXX.s_3.r
q1-0-SLX-10884.D701_D503.cxb-raw-count


title: Rpa190HTP_wt_100s_2

status: Public on Jun 24 2020

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNGTGACAN_Rpa190HTP_wt_100s_2

data_processing:
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were kept. Barcode is always first segment of each name: NNNCGCTTAGC_Rpa190HTP_wt_1.fastq NNNTAAGC_Rpa190HTP_wt_2.fastq NNNATTAGC_Rpa190HTP_wt_3.fastq NNNCGCTTAGC_Rpa190HTP_wt_4.fastq NNNGTGAGC_Rpa190HTP_wt_5.fastq NNNCACTAGC_Rpa190HTP_wt_6.fastq NNNCGCTTAGC_Rpa190HTP_wt_UVA_1.fastq NNNATTAGC_Rpa190HTP_wt_UVA_2.fastq NNNATCACGN_Rpa190HTP_wt_60s_1.fastq NNNCTAGC_Rpa190HTP_wt_80s_1.fastq NNNCACTGTN_Rpa190HTP_wt_80s_2.fastq NNNTGGAGC_Rpa190HTP_wt_100s_1.fastq NNNGTGACAN_Rpa190HTP_wt_100s_2.fastq NNNATTAGC_Rpa190HTP_wt_25rDNA_1.fastq NNNATTAGC_Rpa190HTP_wt_25rDNA_2.fastq NNNGACTTAGC_Rpa135HTP_wt_1.fastq NNNTAAGC_Rpa135HTP_wt_2.fastq NNNGTGAGC_Rpa190HTP_hmo1d_1.fastq NNNGTGAGC_Rpa190HTP_hmo1d_2.fastq
Collapsing reads: To remove PCR duplicates, reads were collapsed usinf fastx_collapser, part of FASTX Toolkit 0.0.14
Debrarcoding: The 5' barcodes were removed using pyBarcodeFilter.py v3.0 script from pyCRAC package.
Filtering reads: Reads were trimmed using flexbar v3.4.0 to remove the 3 -linker sequence (TGGAATTCTCGGGTGCCAAGGC) and were additionaly filtered and only 3'linker-containing reads were included to further analyses.
Reads alignment: Reads were aligned to the Saccharomyces cerevisiae genome sequence (Ensembl release EF4.74) by novoalign version 2.07.00.
Additional processing: novoalign SAM reads were modified using custom made script to keep only the 5' or 3' ends of reads. SAM files were converted to BAM format using samtools v1.9 and BigWig files were generated using bamCoverage v3.1.3.
Genome_build: sacCer3, EF4.74
Supplementary_files_format_and_content: Genomic coordinates of the 3' ends of mapped reads in BigWig format

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking. PAR-CRAC samples were treaded with 1 mM SU 15 min before cross-linking.


title: Rpa190HTP_wt_80s_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNCTAGC_Rpa190HTP_wt_80s_1


title: RF6_WT_815 [D704_D505]

description:
SLX-10884.D704_D505.HCMVCBBXX.s_3.r
q11-0-SLX-10884.D704_D505.cxb-raw-count


title: Rpa190HTP_wt_6

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNCACTAGC_Rpa190HTP_wt_6


title: RF6_WT_816 [D705_D505]

description:
SLX-10884.D705_D505.HCMVCBBXX.s_3.r
q15-0-SLX-10884.D705_D505.cxb-raw-count


title: Rpa135HTP_wt_2

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNTAAGC_Rpa135HTP_wt_2


title: ALC_WT_849 [D705_D504]

description:
SLX-10884.D705_D504.HCMVCBBXX.s_3.r
q14-0-SLX-10884.D705_D504.cxb-raw-count


title: Rpa190HTP_wt_100s_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNTGGAGC_Rpa190HTP_wt_100s_1


title: Rpa190HTP_wt_UVA_2

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNATTAGC_Rpa190HTP_wt_UVA_2


title: Rpa190HTP_wt_80s_2

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNCACTGTN_Rpa190HTP_wt_80s_2


title: Rpa190HTP_wt_60s_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNATCACGN_Rpa190HTP_wt_60s_1


title: Rpa190HTP_hmo1d_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNGTGAGC_Rpa190HTP_hmo1d_1

source_name: Rpa190-HTP hmo1d


title: ALC_WT_848 [D704_D504]

description:
SLX-10884.D704_D504.HCMVCBBXX.s_3.r
q10-0-SLX-10884.D704_D504.cxb-raw-count


title: Rpa135HTP_wt_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNGACTTAGC_Rpa135HTP_wt_1


title: Rpa190HTP_wt_5

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNGTGAGC_Rpa190HTP_wt_5


title: Rpa190HTP_hmo1d_2

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNGTGAGC_Rpa190HTP_hmo1d_2


title: Rpa190HTP_wt_25rDNA_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNATTAGC_Rpa190HTP_wt_25rDNA_1

source_name: Rpa190-HTP 25 rDNA


title: Rpa190HTP_wt_UVA_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNCGCTTAGC_Rpa190HTP_wt_UVA_1


title: Rpa190HTP_wt_3

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNATTAGC_Rpa190HTP_wt_3


title: Rpa190HTP_wt_2

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNTAAGC_Rpa190HTP_wt_2


title: Rpa190HTP_wt_1

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNCGCTTAGC_Rpa190HTP_wt_1


title: H3-HA_TBP-AA_T30 (rep2)

status: Public on Jun 16 2020

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

description: Paired-end 100bp

data_processing:
Sequence data was aligned to SacCer3 via bowtie2 with default settings. To visualize occupancy on the genome browser, Homer’s makeTagDirectory and makeUCSCfile codes were used to generate bigWig files, which were each normalized to 10 million. The cross correlation of Watson and Crick reads was used to infer the average fragment length, and reads were extended by this value.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig files of H3, H3-HA densities and ratios of H3-HA over H3

growth_protocol: Cells were grown overnight at 30°C  to a density at OD600 nm of 0.5–0.7 in Casamino acid medium supplemented with 2% raffinose and 0.1% glucose and lacking adenine, tryptophan and/or uracil for plasmid selection.

extract_protocol:
A detailed protocol for ChIP can be found at http://www.mimo.unige.ch/STRUBIN_LABb.htm. ChIP-Seq was performed using chromatin prepared from about 2 × 109 yeast cells (10-fold more than for conventional ChIP). Immunoprecipitation was with 20 μl anti-HA antibodies (16B12, Covance) or 10 μl anti-H3 antibodies (1791, Abcam).
After de-crosslinking and DNA purification, samples were treated with RNaseA (20 mg/mL, Sigma) for 1 hour at 37⁰C in 1x NEB buffer 2 followed by a 45 minute Calf Intestinal Phosphatase (NEB) treatment. DNA was extracted with phenol:chloroform:isoamyl alcohol and ethanol precipitated with GlycoBlue. DNA ends were polished with END-it (Epicentre) at room temperature for 1 hour. AMPure XP beads (Beckman-Coultier) were used to perform a double size selection, first adding 0.5x beads to deplete longer fragments from the supernatant which was then applied to 1.3x more beads to size select upwards of 100bp. A-tailing was performed on the beads with Klenow exo- polymerase (Epicentre). Clean-up was performed with the addition of 1.8x ABR buffer (15% PEG, 2.5 M NaCl) to the beads, which were then washed with 70% ethanol. DNA ligation (FastLink, Epicentre) to NEXTFlex (Bioo Scientific) multiplexed adapters was performed on the beads. Clean-up was performed as above with the exception of an additional ethanol wash and elution of the DNA from the beads with 39 mL water. Test 18 and 20 cycle PCR reactions were performed with 10 mL each, with a view to reduce the number of amplification cycles. The remainder of the ligated material was PCR amplified under optimum conditions. Amplified material was cleaned-up with AMPure beads as above. StrataClone was used to check the quality of the libraries. Samples were mixed in equimolar amounts (determined by KAPA Library Quantitation) and submitted to the UMass Deep Sequencing Core for HiSeq 100SR with multiplex indexing.

treatment_protocol: Cells were  arrested in G1 by treatment with 600 ng/mL alpha-factor (Primm srl, Italy) for 3 hr. Expression of H3HA was induced at T0 (min) by directly adding galactose to a final concentration of 2% . Where indicated, rapamycin (LC laboratories) was added at the same time to a final concentration of 4 ug/ml to induce nuclear depletion of TBP-FRB.  Glucose (0.5% final) was added to the control cultures (without rapamycin) to limit the induction of H3HA.

tag: genetic background

value: HHY154 genetic background

tag: time point

tag: cell cycle phase


title: H3-HA_Control_T30 (rep2)

description: Paired-end 100bp


title: H3-HA_Control_T0 (rep2)

description: Paired-end 100bp


title: Rpa190HTP_wt_25rDNA_2

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNATTAGC_Rpa190HTP_wt_25rDNA_2


title: H3_Control_T30 (rep2)

description: Paired-end 100bp


title: H3_TBP-AA_T30 (rep2)

description: Paired-end 100bp


title: H3_Control_T0 (rep2)

description: Paired-end 100bp


title: HCC8

status: Public on May 28 2020

data_processing:
Reads are mapped using STAR V2.5.1 to the human GRCh38 genome.
Gene-level counts were generated using subread (feature counts) V 1.6.1 with Ensembl Transcript GTF V74.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tab: Tab-delimited text files

source_name: Liver Tissue

extract_protocol:
Total RNA was isolated using miRNeasy kits (Qiagen) according to manufacturer instructions. Samples were stored in aliquot at – 80 °C prior to use. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Nano Kit. A RNA Integrity Number (RIN) of >7 was considered the lowest cut-off for RNA Sequencing.
Sequencing library were constructed using Illumina’s TruSeq Stranded total RNA Library Preparation Kit.

treatment_protocol: Liver tissues were snap-frozen and stored at -80*C until RNA extraction.

tag: background disease

value: Hepatocellular carcinoma

value: Liver

tag: paired tissues

value: PAIRED TO HCC-FREE8


title: HCC9

value: PAIRED TO HCC-FREE9


title: HCC7

value: PAIRED TO HCC-FREE7


title: HCC6

value: PAIRED TO HCC-FREE6


title: HCC4

value: PAIRED TO HCC-FREE4


title: HCC3

value: PAIRED TO HCC-FREE3


title: Rpa190HTP_wt_4

description:
nascent RNA
nascent RNA covalently attached to RNAPI
NNNCGCTTAGC_Rpa190HTP_wt_4


title: HCC-FREE8

value: Alcoholic liver disease (cirrhotic)

value: PAIRED TO HCC8


title: HCC-FREE6

value: PAIRED TO HCC6


title: HCC-FREE4

value: PAIRED TO HCC4


title: PH-T3-12N-WT

data_processing:
Reads are aligned using STAR V2.5.1 to the mouse GRCm38 genome.
Gene-level counts were generated using subread (feature counts) V 1.6.2 with Ensembl Transcript GTF V74.
Genome_build: GRCm38
Supplementary_files_format_and_content: *tab: Tab-delimited text files

source_name: Whole Liver Tissue

extract_protocol:
Total RNA was isolated using STAT-60 (AMS biotechnology, CS-111)/chloroform (200 uL; Sigma, Cat 650471)/isopropanol (500 uL; Sigma, cat 33539)/75% ethanol (1ml) according to previously published protocol (PMID: 26679101). Samples were stored in aliquot at – 80 °C prior to use. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Nano Kit. A RNA Integrity Number (RIN) of 8 was considered the lowest cut-off for RNA Sequencing.
Sequencing library were constructed using Illumina mRNA library prep kit.

tag: Sex

value: Male

value: Whole Liver

tag: treatment

value: Partial Hepatectomy

value: 3 days after PH


title: HCC-FREE2

value: PAIRED TO HCC2


title: PH-T3-16-WT

value: Wild Type


title: HCC-FREE3

value: Non-alcoholic fatty liver disease (cirrhotic)

value: Liver

value: PAIRED TO HCC3


title: HCC-FREE9

value: PAIRED TO HCC9


title: PH-T0-14-WT

value: Resected Liver - Baseline control

value: Day 0 (resected liver)


title: HCC-FREE7

value: PAIRED TO HCC7


title: PH-T3-13N-WT


title: PH-T3-15-WT


title: PH-T3-14N-WT


title: PH-T0-13-WT


title: PH-T0-15-WT


title: PH-T0-12N-WT


title: CCL4-27-WT

value: Control - Olive Oil IP Injection (2ul/g body weight)

value: 3 days after IP


title: CCL4-26-WT


title: CCL4-24-WT


title: CCL4-07-WT

value: CCl4 - 2ul/g body weight CCl4:olive oil [1:1 (v/v)] mix


title: HCC2

value: Hepatocellular carcinoma

value: PAIRED TO HCC-FREE2


title: CCL4-05-WT

value: Male

value: Whole Liver


title: CCL4-04-WT


title: PacBio_2

status: Public on May 27 2020

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

description: Global m6A profiling in APOBEC1-YTH expressing cells

data_processing:
Barcodes used were: CGGAAT (APOBEC1YTH 1), CTAGCT (APOBEC1YTH 2), CTATAC (APOBEC1YTH 3), CTAGCT (Low input1),  GTGATC (APOBEC1YTHmut 1),GACGAC (APOBEC1YTHmut 2), TACAGC (APOBEC1YTHmut 3), CGGAAT (APOBEC1 1), CTAGCT (APOBEC1 2). Two samples were sequenced on one SMRT cell of the PacBio Sequel instrument and processed using the Iso-Seq analysis pipeline.
Alignment to hg19 was performed using novoalign
Genome_build: hg19
Supplementary_files_format_and_content: For global m6A profiling with DART-Seq, modified sites were identified from single reads using the CIMS program (C2T transitions, p=0.1) from the CLIP ToolKit (CTK) package. Metagene profiles were performed using hg19 genomic annotations.

source_name: HEK293T cells

growth_protocol: Cells were grown in standard growth media for each cell line

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA was then subjected to DNAseI treatment to remove any contaminating DNA.
Library construction was performed using NEB low input RNA-Seq kit (Low input1 sample) or the NEBNEXT Ultra II Directional RNA-Seq kit (all other samples)
For PacBio sequencing, 1 ug of RNA was used for library preparation using the Iso-Seq system.

treatment_protocol: Cells were transfected with APOBEC1YTH-containing plasmid (APOBEC1YTH 1,2,3, low input), APOBEC1YTHmut-containing plasmid (APOBEC1YTHmut 1,2,3), or APOBEC1 alone (APOBEC1 1,2) using lipofection and RNA was isolated 24h later.

tag: cell line

value: human embryonic kidney cells


title: PacBio_1


title: nac_chr_2

status: Public on May 21 2020

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Adapter sequences were trimmed and validated read pairs were aligned to the mouse genome with TopHat2.1.1 with default parameters.
Uniquely aligned reads were used to count gene features with 'htseq-count'.
Normalization and differential expression was determined using the 'edgeR' package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text of normalized RPKM values per gene

source_name: CD8+ T cells

growth_protocol: Polyclonal T-cells were isolated from mouse spleen and inguinal lymph nodes of using the Dynabeads Untouched CD8+ T-cell kit. T-cells were activated with platebound anti-CD3 (2C11, 3 mg/mL) and anti-CD28 (19.51, 1 mg/mL) for 48 h in RPMI-1640 media containing 10% FBS, 2 mM L-glutamine, 50 mM beta-mercaptoethanol, and 10 ng/mL IL-2. For activation of OT-I transgenic CD8+ T-cells, cells were cultured at 10 million cells per mL in the presence of 1 mM SIINFEKL peptide.

extract_protocol:
RNA was isolated from cells using Trizol reagent
Libraries were prepared from poly-A+ RNA with the NEBNext Ultra RNA library prep kit.

treatment_protocol: Following 48 h of initial stimulation, T-cells were cultured at 1 million cells per mL in in RPMI-1640 media containing 10% FBS, 2 mM L-glutamine, 5 mM beta-mercaptoethanol, and 10 ng/mL IL-2. and with (chronic) or without (acute) plate-bound anti-CD3 (3 mg/mL). This was repeated every 48 h until eight days following initial stimulation, at which point cells were harvested for RNA. Where indicated, N-acetylcysteine was added at 10 mM beginning 48 h after initial stimulation. For OT-I cells, T-cells were co-cultured with B16-F10 melanoma cells that had been treated with 1 ng/mL IFN-g to induce MHC-I expression.  Cells were co-cultured at 1 million T-cells per mL with (chronic) or without (acute) the addition of 1 mM SIINFEKL.  This was repeated every 48 h until eight days following initial stimulation, at which point cells were harvested for RNA.

tag: stimulation

value: Chronic

value: 10mM N-acetylcysteine


title: nac_chr_3

tag: strain


title: nac_chr_1


title: veh_chr_2

value: vehicle


title: veh_chr_1


title: veh_chr_3


title: OTI_chr_1

value: OT-I TCR transgenic


title: OTI_chr_2


title: veh_ac_1

value: Acute


title: polyT_chr_3


title: OTI_ac_1


title: OTI_ac_3


title: polyT_chr_2


title: OTI_ac_2


title: polyT_ac_3


title: PH-T0-16-WT

value: Wild Type

tag: tissue


title: polyT_ac_2


title: polyT_ac_1


title: spik_stage4_r1_sRNA

status: Public on May 01 2020

description: small RNA

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides. small RNA reads were mapped to the maize genome (version  JGI version1 genome).
Genome_build: Setaria Genome (version JGI version1)
Supplementary_files_format_and_content: Tag count file: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Setaria viridis

source_name: sRNA  Setaria viridis spikelet, stage 4 (completely out of leaf sheath)

extract_protocol: sRNA library constructed from leaf, whole panicle, and spikelet of Setaria. The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by  Illumina TruSeq sample preparation followed by sequencing with Illumina's HiSeq 2000 instrument. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.

value: spikelet


title: spik_stage4_r2_sRNA

description: small RNA


title: veh_ac_2


title: veh_ac_3


title: OTI_chr_3


title: spik_stage3_r2_sRNA

description: small RNA

source_name: sRNA  Setaria viridis spikelet, stage 3 (coming out of leaf sheath)


title: spik_stage3_r1_sRNA

description: small RNA


title: spik_stage2_r2_sRNA

description: small RNA

source_name: sRNA  Setaria viridis spikelet, stage 2 (inside leaf sheath)


title: wp_stage5_r2_sRNA

description: small RNA

source_name: sRNA  Setaria viridis whole panicle, stage 5 (completely out of leaf sheath, after polination)

value: whole panicle


title: spik_stage2_r1_sRNA

description: small RNA


title: wp_stage5_r1_sRNA

description: small RNA


title: wp_stage4_r1_sRNA

description: small RNA

source_name: sRNA  Setaria viridis whole panicle, stage 4 (completely out of leaf sheath)


title: COL10A1 S600P and MATN3 R209P isogenic control, biological replicate 1

status: Public on May 20 2020

city: Kyoto

first: Junya

last: Toguchida

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application

description: 414C2 iPSC line

hyb_protocol: Samples were hybridized to the arrays with the GeneChip Hybridization Wash and Stain Kit. The arrays were washed and stained on the GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing:
The GeneSpring GX 14.9 software was used for analysis. Data were normalized using the RMA-16 algorithm and the baseline was adjusted to the median of all samples.
Gene expression values normalized by the RMA-16 algorithm in GeneSpring GX 14.9, with the baseline adjusted to the median of all samples.

label: biotin

source_name: COL10A1 S600P and MATN3 R209P isogenic control iPSC-derived cartilage pellet

label_protocol: Samples were fragmented and labeled with the GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: iPSCs were differentiated into hypertrophic chondrocytes in 3D culture

extract_protocol: Cartilage pellets were frozen in liquid nitrogen and powderized before RNA extraction with the QIAGEN RNeasy Micro Kit. 50-100 ng of total RNA was used for reverse transcription and amplification with the Ambion WT Expression Kit.

treatment_protocol: not applicable

value: cartilage (iPSC-derived)

value: wild type


title: wp_stage3_r2_sRNA

description: small RNA

source_name: sRNA  Setaria viridis whole panicle, stage 3 (coming out of leaf sheath)


title: COL10A1 S600P and MATN3 R209P isogenic control, biological replicate 2

description: 414C2 iPSC line


title: polyT_chr_1


title: leaf_Sv_r2_sRNA

description: small RNA

source_name: sRNA  Setaria viridis leaf

value: leaf


title: COL10A1 S600P and MATN3 R209P isogenic control, biological replicate 3

description: 414C2 iPSC line


title: wp_stage3_r1_sRNA

description: small RNA


title: wp_stage2_r1_sRNA

description: small RNA

source_name: sRNA  Setaria viridis whole panicle, stage 2 (inside leaf sheath)


title: wp_stage2_r2_sRNA

description: small RNA


title: TRAPSeq Neu RTT rep3 Lane 3

status: Public on Apr 28 2020

city: Toronto

first: Marat

last: Mufteev

address: 686 Bay St.

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
ribosome bound total RNA
RE_quantile_normalized_3UTR_replicates.csv
RE_quantile_normalized_gene_replicates.csv
RE_quantile_normalized_3UTR_statistics.csv
RE_quantile_normalized_gene_statistics.csv
counts_3UTR_replicates.csv
counts_gene_replicates.csv
counts_3UTR_statistics.csv
counts_gene_statistics.csv

data_processing:
Annotations of 3`UTRs were constructed from GENCODE basic gene annotations for hg19 using tool QAPA version 1.2.0
Reads from TRAPSeq and RNASeq were used for quantification of constructed 3`UTR and coding transcriptome (basic gene annotation GENCODE hg38) with alignment free quantification tool Sailfish version 0.10.0 in paired-end mode
3`UTR variants and genes with less than 150 counts were filtered out from downstream analysis
Mitochondrial and histone genes are removed from downstream analysis
Ribosomal enrichment was calculated as a ratio of TRAPSeq and RNASeq counts
Ribosomal enrichment was adjusted between replicates with quantile normalization (all quantiles)
3`UTR variants and genes with coefficient of variation larger than 0.5 are filtered out from the downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: Columns are different samples; Rows are features (3`UTR variants or genes); Value is counts or quantile normalized ribosomal enrichment (either per replicate or averaged over replicates).

source_name: Cortical neurons

growth_protocol: iPSC lines were grown on BD hESC-qualified matrigel in mTeSR medium (STEMCELL Technologies), and passaged using ReLeSR (STEMCELL Technologies) every 6-7 days. Neuronal inductions were performed as described in Brennand 2011, Nature. NPCs were grown as a monolayer in media: DMEM/F12, N2, B27, 1x NEAA, 2μg/ml Heparin, 1μg/ml laminin. Neurons were grown on poly-L-ornithine+laminin-coated plates in media: Neurobasal, N2, B27, 1μg/ml laminin, 1x penicillin-streptomycin, 10ng/ml IGF, 10ng/ml BDNF, 10ng/ml GDNF, 200μM ascorbic acid, and 10μM cAMP.

extract_protocol:
RNA extractions were performed using Absolutely RNA Nanoprep Kit (Agilent Technologies) with in-column DNase digestion according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina Total Stranded RNA kit

value: iPSC derived cortical neurons

value: MECP2 exons 3-4 deletion

value: line 20 (Cheung 2011, HMG)

tag: sequencing date yy/mm/dd


title: TRAPSeq Neu RTT rep3 Lane 2

tag: cell type


title: TRAPSeq Neu RTT rep3 Lane 1


title: RNASeq Neu RTT rep3 Lane 1

description:
rRNA depleted total RNA
RE_quantile_normalized_3UTR_replicates.csv
RE_quantile_normalized_gene_replicates.csv
RE_quantile_normalized_3UTR_statistics.csv
RE_quantile_normalized_gene_statistics.csv
counts_3UTR_replicates.csv
counts_gene_replicates.csv
counts_3UTR_statistics.csv
counts_gene_statistics.csv


title: leaf_Sv_r1_sRNA

description: small RNA


title: TRAPSeq Neu WT rep3 Lane 3

value: line 37 (Cheung 2011, HMG)


title: TRAPSeq Neu WT rep3 Lane 1


title: RNASeq Neu WT rep3 Lane 2


title: RNASeq Neu WT rep3 Lane 3


title: TRAPSeq Neu WT rep3 Lane 2


title: wp_stage4_r2_sRNA

description: small RNA


title: RNASeq Neu WT rep3 Lane 1


title: RNASeq NPC RTT rep3 Lane 1

source_name: Neural progenitor cells

value: iPSC derived neural progenitor cells


title: TRAPSeq iPSC WT rep3 Lane 3

source_name: Induced pluripotent stem cells

value: iPSC


title: wp_stage1_r2_sRNA

description: small RNA

source_name: sRNA  Setaria viridis whole panicle, stage 1 (1.5 cm, inside leaf sheath)


title: wp_stage1_r1_sRNA

description: small RNA


title: RNASeq iPSC WT rep3 Lane 3


title: TRAPSeq iPSC WT rep3 Lane 2


title: RNASeq iPSC WT rep3 Lane 1


title: RNASeq iPSC WT rep3 Lane 2


title: TRAPSeq Neu RTT rep2 Lane 2


title: TRAPSeq Neu RTT rep2 Lane 3


title: TRAPSeq iPSC WT rep3 Lane 1


title: RNASeq Neu RTT rep2 Lane 3


title: TRAPSeq Neu WT rep2 Lane 2


title: TRAPSeq Neu WT rep2 Lane 3


title: RNASeq Neu RTT rep2 Lane 1


title: RNASeq Neu RTT rep2 Lane 2


title: RNASeq Neu WT rep2 Lane 3


title: TRAPSeq NPC RTT rep2 Lane 3


title: TRAPSeq Neu RTT rep2 Lane 1


title: RNASeq Neu WT rep2 Lane 2


title: TRAPSeq NPC RTT rep2 Lane 2


title: RNASeq Neu WT rep2 Lane 1


title: TRAPSeq Neu WT rep2 Lane 1


title: TRAPSeq NPC RTT rep3 Lane 1


title: TRAPSeq NPC RTT rep2 Lane 1


title: RNASeq NPC RTT rep2 Lane 1


title: TRAPSeq NPC WT rep2 Lane 3


title: RNASeq NPC WT rep2 Lane 1


title: TRAPSeq NPC WT rep2 Lane 1


title: RNASeq NPC WT rep2 Lane 3


title: RNASeq NPC WT rep2 Lane 2


title: TRAPSeq NPC WT rep2 Lane 2


title: TRAPSeq iPSC WT rep2 Lane 3


title: TRAPSeq iPSC WT rep2 Lane 2


title: TRAPSeq iPSC WT rep2 Lane 1


title: RNASeq iPSC WT rep2 Lane 2


title: RNASeq iPSC WT rep2 Lane 3


title: TRAPSeq Neu RTT rep1 Lane 2


title: RNASeq Neu RTT rep1 Lane 1


title: RNASeq Neu RTT rep1 Lane 2


title: RNASeq Neu RTT rep1 Lane 3


title: TRAPSeq NPC RTT rep1 Lane 1


title: TRAPSeq NPC RTT rep1 Lane 2


title: TRAPSeq Neu WT rep1 Lane 2


title: RNASeq Neu WT rep1 Lane 1


title: RNASeq Neu WT rep1 Lane 3


title: TRAPSeq Neu WT rep1 Lane 3


title: TRAPSeq Neu WT rep1 Lane 1


title: TRAPSeq NPC RTT rep1 Lane 3


title: RNASeq NPC RTT rep1 Lane 3


title: RNASeq Neu WT rep1 Lane 2


title: TRAPSeq NPC WT rep1 Lane 3


title: RNASeq NPC WT rep1 Lane 3


title: RNASeq NPC RTT rep1 Lane 2


title: TRAPSeq Neu RTT rep1 Lane 3


title: TRAPSeq iPSC WT rep1 Lane 3


title: RNASeq NPC WT rep1 Lane 1


title: TRAPSeq NPC WT rep1 Lane 1


title: RNASeq NPC WT rep1 Lane 2


title: RNASeq NPC RTT rep1 Lane 1


title: TRAPSeq Neu RTT rep1 Lane 1


title: RNASeq iPSC WT rep2 Lane 1


title: TRAPSeq iPSC WT rep1 Lane 2


title: TRAPSeq iPSC WT rep1 Lane 1


title: RNASeq iPSC WT rep1 Lane 2


title: RNASeq iPSC WT rep1 Lane 1


title: Zost_veg2

status: Public on Apr 17 2020

description:
5012
small RNA

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides.
Supplementary_files_format_and_content: Text containing distinct small RNAs with their raw abundance after removing the adapter sequences

organism: Zostera marina

source_name: sRNA Zostera marina, vegetative tissue

extract_protocol: sRNA library constructed from all diverse tissue types listed in the field "source name" . The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by  Illumina sRNA TruSeq sample preparation kit followed by sequencing with Illumina's HiSeq 2500 instrument. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.

value: Vegetative tissue


title: TRAPSeq NPC WT rep1 Lane 2


title: Zost_flo_pre2

description:
5002
small RNA

source_name: sRNA Zostera marina, flower (P2, Pre-meiosis),

value: Flower


title: Zost_flo_pre1

description:
5001
small RNA

source_name: sRNA Zostera marina, flowers (P1, Pre-meiosis)


title: Trades_pistil

description:
4813
small RNA

organism: Tradescantia fluminensis

source_name: sRNA Tradescantia fluminensis, pistils from 2-5mm buds

value: Pistil


title: Zost_flo_pos2

description:
5029
small RNA

source_name: sRNA Zostera marina, M2 (Post-meiosis)


title: Trades_anther

description:
4810
small RNA

source_name: sRNA Tradescantia fluminensis, anthers from 2-5mm buds

value: Anther


title: Strep_an_4_0

description:
4995
small RNA

organism: Streptochaeta angustifolia

source_name: sRNA Streptochaeta angustifolia, 3.0-4.0 mm anthers


title: Strep_an_3_0

description:
4994
small RNA

source_name: sRNA Streptochaeta angustifolia, 1.5-3.0 mm anthers


title: Strep_an_1_5

description:
4993
small RNA

source_name: sRNA Streptochaeta angustifolia, 0.5-1.5 mm anthers


title: Sagit_leaf_r1

description:
4701
small RNA

organism: Sagittaria montevidensis

source_name: sRNA Sagittaria montevidensis, leaves

value: Leaf


title: RNASeq iPSC WT rep1 Lane 3


title: Strep_pistil

description:
4996
small RNA

source_name: sRNA Streptochaeta angustifolia, pistils from 0.5-5.0 mm anthers flowers


title: Strep_leaf

description:
4997
small RNA

source_name: sRNA Streptochaeta angustifolia, leaves


title: Sagit_pis_of_r1

description:
4704
small RNA

source_name: sRNA Sagittaria montevidensis, pistils from open flowers


title: Sagit_ant_bud_r1

description:
4702
small RNA

source_name: sRNA Sagittaria montevidensis, anthers from buds


title: Colocasia_lf

description:
3214
small RNA

organism: Colocasia esculenta

source_name: sRNA Colocasia esculenta, leaves


title: Canna_ova_of_r1

description:
4752
small RNA

organism: Canna indica

source_name: sRNA Canna indica, ovaries from open flowers

value: Ovary


title: Colocasia_ant

description:
3212
small RNA

source_name: sRNA Colocasia  esculenta, anthers


title: Sagit_ant_of_r1

description:
4703
small RNA

source_name: sRNA Sagittaria montevidensis, anthers from open flowers


title: Canna_ant_of_r1

description:
4751
small RNA

source_name: sRNA Canna indica, anthers from open flowers


title: Zost_veg1

description:
4992
small RNA

source_name: sRNA Zostera marina, vegetative tissue


title: Canna_leaf_r1

description:
4688
small RNA

source_name: sRNA Canna indica, leaves


title: Canna_sti_bud_r1

description:
4749
small RNA

source_name: sRNA Canna indica, stigmas from buds

value: Stigma


title: Canna_ova_bud_r1

description:
4750
small RNA

source_name: sRNA Canna indica, ovaries from buds


title: Bromelia_leaf

description:
4811
small RNA

organism: Goudaea ospinae

source_name: sRNA Vriesea ospinae, leaves


title: Canna_ant_bud_r1

description:
4748
small RNA

source_name: sRNA Canna indica, anthers from buds


title: Zost_flo_mid

description:
5027
small RNA

source_name: sRNA Zostera marina, F1 (Middle stage)


title: Zost_flo_pos1

description:
5028
small RNA

source_name: sRNA Zostera marina, M1 (Post-meiosis)


title: Acorus_spadix_r1

description:
4696
small RNA

organism: Acorus calamus

source_name: sRNA Acorus calamus, whole spadix

value: Spadix


title: Acorus_leaf_r1

description:
4595
small RNA

source_name: sRNA Acorus calamus, leaves


title: Bromelia_ant_2mm

description:
4798
small RNA

source_name: sRNA Vriesea ospinae, 2-3mm anthers


title: Trades_leaf

description:
4809
small RNA

source_name: sRNA Tradescantia fluminensis, leaves


title: Bromelia_pis_5mm

description:
4801
small RNA

source_name: sRNA Vriesea ospinae, pistils from flowers with 5mm anthers


title: Bromelia_ant_6mm

description:
4800
small RNA

source_name: sRNA Vriesea ospinae, 6mm anthers


title: Bromelia_ant_5mm

description:
4799
small RNA

source_name: sRNA Vriesea ospinae, 5-6mm anthers


title: Acorus_pis_r1

description:
4530
small RNA

source_name: sRNA Acorus calamus, pistils


title: Acorus_ant_r1

description:
4529
small RNA

source_name: sRNA Acorus calamus, anthers


title: leaf_Sb_r2

description:
5756
small RNA

organism: Sorghum bicolor

source_name: sRNA Sorghum bicolor BTx623, leaves


title: Bana_Lf

description:
3180
small RNA
Musa acuminata, cultivar Gros Michel

organism: Musa acuminata AAA Group

source_name: sRNA Musa acuminata, leaves

value: AAA

tag: cultivar

value: Gros Michel


title: Bana_mFlo

description:
3179
small RNA
Musa acuminata, cultivar Gros Michel

source_name: sRNA Musa acuminata, male flowers

value: Male flower


title: leaf_Sb_r1

description:
5755
small RNA


title: 12_ant_spik_r2

description:
5768
small RNA

source_name: sRNA Sorghum bicolor BTx623, spikelets with >1.2 mm anthers

value: Spikelet


title: 08_12_an_spik_r2

description:
5766
small RNA

source_name: sRNA Sorghum bicolor BTx623, spikelets with 0.8-1.2 mm anthers


title: 05_10_an_spik_r2

description:
5764
small RNA

source_name: sRNA Sorghum bicolor BTx623, spikelets with 0.5-1.0 mm anthers


title: 12_ant_spik_r1

description:
5767
small RNA


title: 05_ant_spik_r1

description:
5761
small RNA

source_name: sRNA Sorghum bicolor BTx623, spikelets with <0.5 mm anthers


title: 15cm_wp_r1

description:
5759
small RNA

source_name: sRNA Sorghum bicolor BTx623, 1.5 cm whole panicles

value: Whole panicle


title: 12cm_wp_r1

description:
5758
small RNA

source_name: sRNA Sorghum bicolor BTx623, 1.2 cm whole panicles


title: 05_10_an_spik_r1

description:
5763
small RNA


title: BanaL

description:
2218
small RNA
Musa acuminata, cultivar Zebrina

organism: Musa acuminata var. zebrina


title: BanaYF

description:
2213
small RNA
Musa acuminata, cultivar Zebrina

source_name: sRNA Musa acuminata, young fruits

value: Fruit


title: 2mm_wp_r1

description:
5757
small RNA

source_name: sRNA Sorghum bicolor BTx623, 2 mm whole panicles


title: 30cm_wp_r1

description:
5760
small RNA

source_name: sRNA Sorghum bicolor BTx623, 3.0 cm whole panicles


title: Bana_M_2

description:
3210
small RNA
Musa acuminata, cultivar Zebrina

source_name: sRNA Musa acuminata, anthers


title: Bana_M_0

description:
3209
small RNA
Musa acuminata, cultivar Zebrina


title: Bana_leaf

description:
2683
small RNA
Musa acuminata x balbisiana (ABB group), cultivar Silver Bluggoe

organism: Musa ABB Group

value: ABB

value: Silver Bluggoe


title: Bana_female

description:
2682
small RNA
Musa acuminata x balbisiana (ABB group), cultivar Silver Bluggoe

source_name: sRNA Musa acuminata, female flowers

value: Female flower


title: Bana_male

description:
2681
small RNA
Musa acuminata x balbisiana (ABB group), cultivar Silver Bluggoe


title: Phar_leaf1

description:
5000
small RNA

organism: Pharus parvifolius

source_name: sRNAPharus parvifolius, leaves


title: Orch_fam_3bud

description:
5244
small RNA

organism: Phalaenopsis equestris

source_name: sRNA Phalaenopsis equestris, floral apical meristem with <3 mm buds

value: Bud


title: Orch_col_7bud

description:
5243
small RNA

source_name: sRNA Phalaenopsis equestris,column from 7 mm buds

value: Column


title: Phar_fem1

description:
4999
small RNA

source_name: sRNA Pharus parvifolius, female flower without bracts


title: Orch_col_5bud

description:
5241
small RNA

source_name: sRNA Phalaenopsis equestris, column from 5 mm buds


title: Phar_ant_1_0m

description:
4998
small RNA

source_name: sRNA Pharus parvifolius, 0.5-1.0 mm anthers


title: Orch_col_of

description:
5238
small RNA

source_name: sRNA Phalaenopsis equestris, column from open flower


title: 08_12_an_spik_r1

description:
5765
small RNA

source_name: sRNA Sorghum bicolor BTx623, spikelets with 0.8-1.2 mm anthers


title: 05_ant_spik_r2

description:
5762
small RNA


title: Orch_leaf

description:
5237
small RNA

source_name: sRNA Phalaenopsis equestris, leaves


title: Orch_pol_5bud

description:
5240
small RNA

source_name: sRNA Phalaenopsis equestris, pollinia with cap from 5 mm buds

value: Pollinia


title: Orch_4wbud

description:
5239
small RNA

source_name: sRNA Phalaenopsis equestris, 4 mm whole buds


title: Orch_pol_7bud

description:
5242
small RNA

source_name: sRNA Phalaenopsis equestris, pollinia with cap from 7 mm buds


title: Lirio_leaf

description:
3443
small RNA

organism: Liriope muscari

source_name: sRNA Liriope muscari, leaves


title: Nymp_pis_of_1

description:
4694
small RNA

organism: Nymphaea colorata

source_name: sRNA Nymphaea colorata, pistils from open flowers

value: Pistil


title: Nymp_ant_bud_1

description:
4689
small RNA

source_name: sRNA Nymphaea colorata, anthers from buds

value: Anther


title: Nymp_ant_yo_of_1

description:
4692
small RNA

source_name: sRNA Nymphaea colorata, young anthers from open flowers


title: Nymp_ant_ol_of_1

description:
4693
small RNA

source_name: sRNA Nymphaea colorata, anthers with pollen from open flowers


title: Nymp_leaf_1

description:
4695
small RNA

source_name: sRNA Nymphaea colorata, leaves

value: Leaf


title: Nymp_pis_bud_1

description:
4691
small RNA

source_name: sRNA Nymphaea colorata, pistils from buds


title: MzPLN_DBI

description:
317
small RNA

organism: Zea mays

source_name: sRNA Zea mays B73, pollen

value: Pollen


title: Coco_leaf

description:
2686
small RNA

organism: Cocos nucifera

source_name: sRNA Cocos nucifera, leaves


title: Lirio_imFl

description:
3445
small RNA

source_name: sRNA Liriope muscari, young flowers

value: Flower


title: Coco_female

description:
2715
small RNA

source_name: sRNA Cocos nucifera, female flowers


title: Nymp_ant_wbud_1

description:
4690
small RNA


title: Lirio_mFl

description:
3444
small RNA

source_name: sRNA Liriope muscari, mature flowers


title: Coco_male

description:
2687
small RNA

source_name: sRNA Cocos nucifera, male flowers


title: ant_0_2_3

description:
3413
small RNA

source_name: sRNA Zea mays, 0.2mm anthers


title: ROgR

description:
505
small RNA

organism: Oryza glaberrima

source_name: sRNA Oryza glabberima (accession CG14), young roots

value: Root


title: 0_3mmAnt2

description:
3170
small RNA

source_name: sRNA Zea mays, 0.3mm anthers


title: 0_3mmAnt1

description:
3169
small RNA


title: LOgL

description:
245
small RNA

source_name: sRNA Oryza glabberima (accession CG14), young leaves


title: POgP

description:
431
small RNA

source_name: sRNA Oryza glabberima (accession CG14), young panicles

value: Panicle


title: PollenFertile

description:
2145
small RNA

source_name: sRNA Zea mays, pollen


title: 5.0Fertile,r3

description:
2144
small RNA

source_name: sRNA Zea mays, 5.0mm anthers


title: 4.0Fertile,r3

description:
2143
small RNA

source_name: sRNA Zea mays, 4.0mm anthers


title: 2.5Fertile,r3

description:
2141
small RNA

source_name: sRNA Zea mays, 2.5mm anthers


title: 0.2Fertile,r1

description:
1746
small RNA


title: 3.0Fertile,r3

description:
2142
small RNA

source_name: sRNA Zea mays, 3.0mm anthers


title: 2.0Fertile,r3

description:
2140
small RNA

source_name: sRNA Zea mays, 2.0mm anthers


title: 0.2Fertile,r2

description:
1745
small RNA


title: PLNFertile,r2

description:
1744
small RNA


title: 4.0Fertile,r2

description:
1742
small RNA


title: 3.0Fertile,r2

description:
1741
small RNA


title: OP_male_mat_2

description:
5026
small RNA

organism: Elaeis guineensis

source_name: sRNA Elaeis guineensis, mature male flower

value: Male flower


title: 2.0Fertile,r2

description:
1739
small RNA


title: OP_leaf_2

description:
4989
small RNA

source_name: sRNA Elaeis guineensis, leaves


title: 1.0Fertile,r2

description:
1737
small RNA

source_name: sRNA Zea mays, 1.0mm anthers


title: 0.7Fertile,r2

description:
1736
small RNA

source_name: sRNA Zea mays, 0.7mm anthers


title: OP_male_mat_1

description:
5025
small RNA


title: 2.5Fertile,r2

description:
1740
small RNA


title: 0.4Fertile,r2

description:
1735
small RNA

source_name: sRNA Zea mays, 0.4mm anthers


title: 5.0Fertile,r2

description:
1743
small RNA


title: 1.5Fertile,r2

description:
1738
small RNA

source_name: sRNA Zea mays, 1.5mm anthers


title: OP_leaf_1

description:
4988
small RNA


title: ant_0_2_2

description:
3412
small RNA

source_name: sRNA Zea mays, 0.2mm anthers


title: OP_male_you_1

description:
4821
small RNA

source_name: sRNA Elaeis guineensis, young male flower


title: PLNFertile,r1

description:
1587
small RNA


title: 1.5Fertile,r1

description:
1586
small RNA


title: 4.0Fertile,r1

description:
1583
small RNA


title: OP_male_you_2

description:
5024
small RNA


title: 0.7Fertile,r1

description:
1585
small RNA


title: 5.0Fertile,r1

description:
1584
small RNA


title: 2.5Fertile,r1

description:
1580
small RNA


title: 2.0Fertile,r1

description:
1579
small RNA


title: ZmEar_2_0cm

description:
1576
small RNA

source_name: sRNA Zea mays, 2.0cm ears

value: Ear


title: 1.0Fertile,r1

description:
1578
small RNA


title: 0.4Fertile_r1

description:
1577
small RNA


title: Raddia_lf

description:
2429
small RNA

organism: Raddia brasiliensis

source_name: sRNA Raddia brasiliensis, leaves


title: Raddia_F

description:
2431
small RNA

source_name: sRNA Raddia brasiliensis, female flowers


title: Daylily_leaf_1

description:
4518
small RNA

organism: Hemerocallis lilioasphodelus

source_name: sRNA Hemerocallis lilioasphodelus, leaves


title: Pnapl_leaf_2

description:
4991
small RNA

organism: Ananas comosus

source_name: sRNA Ananas comosus, leaves


title: Bamboo_lf

description:
2400
small RNA

organism: Phyllostachys edulis

source_name: sRNA Phyllostachys edulis, leaves


title: Bamboo_st

description:
2401
small RNA

source_name: sRNA Phyllostachys edulis, shoots

value: Shoot


title: Bam_Leaf

description:
5151
small RNA


title: Pnapl_leaf_1

description:
4990
small RNA


title: Raddia_M

description:
2430
small RNA

source_name: sRNA Raddia brasiliensis, male flowers


title: Bam_F3

description:
5156
small RNA

source_name: sRNA Phyllostachys edulis, inflorescence

value: Inflorescence


title: Pnapl_ant_M1

description:
4819
small RNA

source_name: sRNA Ananas comosus, mature anthers


title: Pnapl_ant_M2

description:
4820
small RNA


title: Pnapl_ant_Y2

description:
4818
small RNA

source_name: sRNA Ananas comosus, young anthers


title: 3.0Fertile,r1

description:
1582
small RNA

source_name: sRNA Zea mays, 3.0mm anthers


title: Bam_F1

description:
5154
small RNA

source_name: sRNA Phyllostachys edulis, floral buds

value: Floral bud


title: Bam_F2

description:
5155
small RNA


title: Anomo_shoot

description:
2720
small RNA

organism: Anomochloa marantoidea

source_name: sRNA Anomochloa marantoidea, young shoots


title: Pnapl_flr2

description:
2684
small RNA

source_name: sRNA Ananas comosus, unopened flowers


title: Kni_leaf

description:
5479
small RNA

organism: Kniphofia uvaria

source_name: sRNA Kniphofia uvaria, leaves


title: Anomo_leaf

description:
2719
small RNA

source_name: sRNA Anomochloa marantoidea, leaves


title: Pnapl_ant_Y1

description:
4817
small RNA


title: Orch_col_of_r1

description:
4747
small RNA

organism: Prosthechea radiata

source_name: sRNA Prosthechea radiata, column from open flowers


title: Kni_05_ant_bud

description:
5480
small RNA

source_name: sRNA Kniphofia uvaria, < 0.5 mm anthers in whole buds


title: Kni_05_10_ant

description:
5481
small RNA

source_name: sRNA Kniphofia uvaria, 0.5 - 1.0 mm anthers


title: Orch_col_bud_r1

description:
4745
small RNA

source_name: sRNA Prosthechea radiata, column from buds


title: Bamboo_rt

description:
2402
small RNA

source_name: sRNA Phyllostachys edulis, roots


title: Pnapl_lf

description:
2685
small RNA

source_name: sRNA Ananas comosus, young leaves


title: Orch_leaf_r1

description:
4705
small RNA

source_name: sRNA Prosthechea radiata, leaves


title: Bam_F4

description:
5157
small RNA

source_name: sRNA Phyllostachys edulis, embryos

value: Embryo


title: Echin_pis_of_r1

description:
4687
small RNA

organism: Echinodorus uruguayensis

source_name: sRNA Echinodorus uruguayensis, pistils from open flowers

value: Pistil open flower


title: Echin_ant_of_r1

description:
4686
small RNA

source_name: sRNA Echinodorus uruguayensis, anthers from open flowers

value: Anther open flower


title: Freycin_leaf

description:
4812
small RNA

organism: Freycinetia cumingiana

source_name: sRNA Freycinetia cumingiana, leaves


title: Orch_ant_of_r1

description:
4746
small RNA

source_name: sRNA Prosthechea radiata, anthers from open flower


title: Freycin_bract

description:
4797
small RNA

source_name: sRNA Freycinetia cumingiana, bract from closed bud

value: Bract


title: Echin_leaf_r1

description:
4683
small RNA

source_name: sRNA Echinodorus uruguayensis, leaves


title: Echin_pis_bud_r1

description:
4685
small RNA

source_name: sRNA Echinodorus uruguayensis, pistils from buds

value: Pistil bud


title: Freycin_an_rec2

description:
4805
small RNA

source_name: sRNA Freycinetia cumingiana, anther receptacles from open buds


title: Echin_ant_bud_r1

description:
4684
small RNA

source_name: sRNA Echinodorus uruguayensis, anthers from buds

value: Anther bud


title: Anomo_root

description:
2721
small RNA

source_name: sRNA Anomochloa marantoidea, roots


title: Cyper_inf_old

description:
4808
small RNA

organism: Cyperus alternifolius

source_name: sRNA Cyperus alternifolius, mature inflorescence


title: Freycin_an_open

description:
4804
small RNA

source_name: sRNA Freycinetia cumingiana, anthers from open buds

value: Anther


title: Cyper_leaf

description:
4806
small RNA

source_name: sRNA Cyperus alternifolius, leaves

value: Leaf


title: Cyper_inf_you

description:
4807
small RNA

source_name: sRNA Cyperus alternifolius, young inflorescence


title: Datep_ma_bud_2

description:
4110
small RNA

organism: Phoenix dactylifera

source_name: sRNA Phoenix dactylifera, male buds

value: Male bud


title: Freycin_an_clos

description:
4802
small RNA

source_name: sRNA Freycinetia cumingiana, anthers from closed buds


title: Freycin_an_rec1

description:
4803
small RNA

source_name: sRNA Freycinetia cumingiana, anther receptacles from closed buds


title: Datep_fe_bud_1

description:
4107
small RNA

source_name: sRNA Phoenix dactylifera, female buds

value: Female bud


title: Kni_10_15_ant

description:
5482
small RNA

source_name: sRNA Kniphofia uvaria, 1.0 - 1.5 mm anthers


title: Datep_fe_bud_2

description:
4108
small RNA


title: Control_09

status: Public on Apr 14 2020

city: Austin

first: Gayatri

last: Tiwari

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description:
single nuclei RNA
Control_647C

data_processing:
A GENCODE v30 GTF file was modified to create a “pre-mRNA” GTF file so that pre-mRNAs would be included as counts in the subsequent analysis.
CellRanger-3.0.2 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq (https://support.illumina.com/) to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files.
 The FASTQ files were then aligned to the human reference genome GRCh38 with RNAseq aligner STAR.
The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell.
The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Genome_build: Human Gencode release 30(GRCh38.p12.genome.fa)
Supplementary_files_format_and_content: BAM files

organism: Homo sapiens

source_name: Human brain prefrontal cortex

extract_protocol:
Nuclei were isolated from tissue based on a modified version of Luciano Martelotto’s Customer-Developed Protocol provided on the 10XGenomics website.
Libraries were prepared using the  10X Genomics 3’ Single Cell Gene Expression protocol. Paired-end sequencing of the libraries was conducted   using a NovaSeq 6000 with an S2 chip (100 cycles).
Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, 4 rxns PN-120267, Chromium™ Single Cell A Chip Kit, 16 rxns PN-1000009, Chromium™ i7 Multiplex Kit, 96 rxns PN-120262.

treatment_protocol: Alcoholic and control donors were selected to be as close as possible in terms of age, sex,  post-mortem interval (PMI), pH of tissue, and cause of death

tag: group

value: Control

tag: age

value: Male

tag: brain ph

tag: total drinking years

tag: alcohol intake (grams/day)


title: Control_17

description:
single nuclei RNA
Control_777C


title: Control_07-1

description:
single nuclei RNA
Control_598C-1


title: Control_07-2

description:
single nuclei RNA
Control_598C-2


title: Alcohol_23

description:
single nuclei RNA
Alcohol_856A

value: Alcohol Use Disorder


title: Control_01

description:
single nuclei RNA
Control_335C


title: Alcohol_07

description:
single nuclei RNA
Alcohol_721A


title: Orch_ant_bud_r1

description:
4706
small RNA

source_name: sRNA Prosthechea radiata, anthers from buds


title: uterine tissue_PKRASWT_7680

status: Public on Apr 01 2020

city: Houston

first: Kwong-Kwok

last: Wong

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were processed with RNA-seq workflow in CLC Genomics Workbench version 11. Reads were mapped to mouse reference genome GRCm38 with default setting.
Gene expression is estimated with the EM estimation algorithm and reported as TPM (Transcripts Per Million)
Genome_build: GRCm38
Supplementary_files_format_and_content: TPMs

organism: Mus musculus

source_name: uterine tissue

extract_protocol:
Total RNA were extracted from mouse uterine tissues that have been stored in RNAlater solution using Qiagen RNeasy Mini Kit.
Sequencing libraries were prepared using KAPA Stranded mRNA seq Kit and run in a single lane using Illumina HiSeq 4000 instrument.

tag: genetic background

value: Ahmr-Cre Pten null

value: mixed C57BL/6 x 129

tag: genotype

value: WT

value: 66 weeks

value: uterine tissue


title: uterine tissue_PKRASG12V_7601

value: 36 weeks


title: uterine tissue_PKRASG12V_7686

value: 37 weeks


title: uterine tissue_PKRASG12D_7623

value: 38 weeks


title: Datep_ma_bud_1

description:
4109
small RNA


title: uterine tissue_PKRASWT_7614


title: Alcohol_14

description:
single nuclei RNA
Alcohol_780A


title: Recurrence32

status: Public on Mar 23 2020

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: Crta Can Ruti; cami de les escoles, S/N

country: Spain

institute: Germans Trias i Pujol Health Research Institute

description: RMA expression value derived from Expression Console software

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneChips were scanned by the Affymetrix Scanner 3000.

data_processing: Data were processed using Affymetrix Expression Console for quality control after summarization and Robust Multi-array Average (RMA) normalization  affymetrix-algorithm-name = sst-rma-gene-full  affymetrix-algorithm-version = 1.0  program-name = Expression Console  program-version = 1.4

label: Biotin

source_name: Recurrence

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: 20mg frozen tissue were homogenized with FASTprep and the RNA was extracted using the protocol of the Mirvana kit (Thermofisher) and we used the DNA free kit (Thermofisher).

tag: gender

value: M


title: Recurrence19


title: Tumor18

source_name: Tumor


title: Tumor21

value: F


title: Tumor26


title: Tumor23


title: Tumor30


title: Tumor20


title: Tumor17


title: Tumor11


title: Tumor25


title: Tumor24


title: Tumor5


title: Tumor16


title: Tumor22


title: Tumor31


title: Recurrence27


title: Tumor19


title: Tumor33


title: Tumor14


title: Tumor13


title: Tumor3


title: Tumor28


title: Tumor1


title: Tumor2


title: Tumor12


title: Tumor15


title: Tumor29


title: Tumor32


title: Tumor4


title: Tumor8 [CytoScanHD_Array]

type: genomic

description: Hybridized to CytoScanHD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.

data_processing:
CEL files, generated by AGCC Viewer. CYCHP, generated by Chromosome Analysis Suite (all provided by Affymetrix)
CYCHP provide data for copy number and absence of heterozigosity analysis

source_name: Liver Tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: MagMAX™ DNA Multi-Sample kit was used using following manufacturer’s instructions (Thermo Fisher Scientific)


title: Recurrence32 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor18 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor11 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor23 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor22 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor20 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor21 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Nontumor9

source_name: Non tumor


title: Nontumor14


title: Nontumor4


title: Nontumor5


title: Nontumor19


title: Tumor7


title: Nontumor26


title: Nontumor18


title: Nontumor16


title: Tumor6


title: Recurrence19 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Nontumor30


title: Tumor19 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Nontumor11


title: Nontumor13


title: Nontumor2


title: Tumor17 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor9


title: Nontumor15


title: Tumor33 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Nontumor1


title: Nontumor12


title: Tumor32 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Recurrence27 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor31 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor30 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor28 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor29 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Nontumor17


title: Tumor26 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor25 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor5 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor16 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Nontumor10


title: Tumor10


title: Nontumor7


title: Tumor15 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor14 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor1 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor10 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor2 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor4 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor12 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor13 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor7 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: Tumor9 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: HT29 #83 KO Replicate 2

status: Public on Mar 20 2020

city: Freiburg

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

institute: University Hospital of Freiburg

description:
HT29_83_B
count_HT29.txt

data_processing:
Extracted RNA was paired-end sequenced on an Illumina HiSeq4000 at the Genome and Proteome Core Facility (GPCF) of the German Cancer Research Center (DKFZ, Heidelberg, Germany)
Paired-end reads were filtered to remove bad quality reads and adapter sequences using Trimmomatic (Reference: AM Bolger, M Lohse, B Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics 30 (2014) 2114–2120)
The selected reads were aligned to the human reference genome GRCh37 and read count per gene was quantified with STAR aligner (Reference: A Dobin, CA Davis, F Schlesinger, J Drenkow, C Zaleski, S Jha, P Batut, M Chaisson, TR Gingeras, STAR: ultrafast universal RNA-seq aligner, Bioinformatics 29 (2013) 5-21)
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include raw count values for each sample.

source_name: colorectal adenocarcinoma cell line HT29

growth_protocol: HCT116 and HT29 CRC cells were cultivated in DMEM supplemented with 10% (v/v) FCS, 10 mM HEPES, 1% (v/v) MEM non-essential amino acids solution, and 1% (v/v) penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using the PeqGOLD total RNA kit (#732-2871, Peqlab/VWR Life Science, Bruchsal, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina HiSeq4000 at the Genome and Proteome Core Facility (GPCF) of the German Cancer Research Center (DKFZ, Heidelberg, Germany))

treatment_protocol: no treatment

value: TCF7L2 KO


title: Tumor24 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: HT29 #62 Het Replicate 2

description:
HT29_62_B
count_HT29.txt

value: TCF7L2 Het


title: HT29 #57 KO Replicate 2

description:
HT29_57_B
count_HT29.txt


title: HT29 #57 KO Replicate 1

description:
HT29_57_A
count_HT29.txt


title: HT29 #86 KO Replicate 2

description:
HT29_86_B
count_HT29.txt


title: HT29 #62 Het Replicate 1

description:
HT29_62_A
count_HT29.txt


title: HT29 #83 KO Replicate 1

description:
HT29_83_A
count_HT29.txt


title: HT29 #56 WT Replicate 2

description:
HT29_56_B
count_HT29.txt

value: TCF7L2 WT


title: HT29 #56 WT Replicate 1

description:
HT29_56_A
count_HT29.txt


title: HCT116 #18 KO Replicate 1

description:
HCT_18_A
count_HCT116.txt

source_name: colorectal carcinoma cell line HCT116


title: HCT116 #18 KO Replicate 2

description:
HCT_18_B
count_HCT116.txt


title: HCT116 #3 WT Replicate 2

description:
HCT_3_B
count_HCT116.txt


title: P60 brain pre-myelinating oligodendrocytes_RNASeq_n3 [plp2mn3]

status: Public on Mar 14 2020

first: Sarah

last: Moyon

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

data_processing:
85 ng of total RNA per sample were used for library construction with the Ultra-Low-RNA-Seq Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument for the FACS samples according to the manufacturer's instructions for 100 bp paired end read runs.
High-quality reads were aligned to the mouse reference genome (mm10), RefSeq exons, splicing junctions, and contamination databases (ribosome and mitochondria sequences) using the Burrows-Wheeler Aligner (BWA) algorithm. The read count for each RefSeq transcript was extracted using uniquely aligned reads to exon and splice-junction regions for each transcript.
The raw read counts were inputted into DESeq2 v1.2.5 (Anders and Huber, 2010) for calculation of normalized signal for each transcript and to ascertain differential gene expression with associated  p-values.
Differentially expressed genes were selected at a q-value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized signal for each transcript, for each sample.

source_name: Brain

extract_protocol:
Total RNAs were obtained from FAC-sorted P60 oligodendrocyte progenitor cells and from P60 myelinating oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: Post-natal day 60

value: Primary FAC-sorted PLP::GFP+ cells


title: P60 brain oligodendrocyte progenitor cells_RNASeq_n3 [pdgfra2mn3]

value: Primary FAC-sorted PDGFRa::GFP+ cells


title: P60 brain pre-myelinating oligodendrocytes_RNASeq_n1 [plp2mn1]


title: P60 brain pre-myelinating oligodendrocytes_RNASeq_n2 [plp2mn2]


title: Tumor6 [CytoScanHD_Array]

description: Hybridized to CytoScanHD


title: HT29 #86 KO Replicate 1

description:
HT29_86_A
count_HT29.txt


title: P60 brain oligodendrocyte progenitor cells_RNASeq_n2 [pdgfra2mn2]


title: P60 brain oligodendrocyte progenitor cells_RNASeq_n1 [pdgfra2mn1]


title: KO_mRPM_4

status: Public on Mar 11 2020

data_processing:
RNAseq: Reads were trimmed with cutadapt v.2.8  and aligned using STAR V2.5.1 to the human GRCh38 genome
Gene-level counts where generated using subread (feature counts) V 1.6.2
ATACseq: Reads were trimmed with Trim Galore! V. 0.50 and alogned to the reference genome (GRCh38) with Bowtie2 V. 2.3.5
Genome_build: GRCh38

source_name: IL1RL1-/- RPM mouse 4

growth_protocol: Splenocytes were freshly sorted using an LSRII Fortessa (BD) flow cytometer

extract_protocol:
RNA-seq: Cell lysates were frozen in RLT plus buffer at -80oC prior to processing. ATAC-seq: cells were processed immediately
For RNA-Seq: total RNA was extracted using the RNEasy plus micro kit (Qiagen).  Cells were reuspended in RLT plus buffer and stored briefly at – 80 °C prior to extraction. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Nano Kit. A RNA Integrity Number (RIN) of 6.3 was the lowest cut-off for RNA Sequencing.  For ATAC-seq, cells were processed immediately as described (Corces et al (2017), Nat. Methods, 14, 959)
RNA-seq libraries were constructed using the Stranded total RNA-seq v2-pico kit (Takara) and ATAC-seq libraries were constructed as described (Corces et al (2017), Nat. Methods, 14, 959)

value: red pulp macrophage

value: Balb/c

tag: sorting

value: Ly6Glo CD11blo/- F4/80hi cells


title: WT_mRPM_4

source_name: wild type RPM mouse 4

value: Wild Type


title: KO_pRPM_4

source_name: IL1RL1-/- pre-RPM mouse 4

value: pre-RPM

value: Ly6Glo CD11bhi F4/80lo cells


title: WT_pRPM_4

source_name: wild type pre-RPM mouse 4


title: KO_MONO_4

source_name: IL1RL1-/- splenic monocytes mouse 4

value: Monocyte

value: Ly6Glo CD11bhi F4/80- cells


title: WT_MONO_4

source_name: wild type splenic monocytes mouse 4


title: WT_mRPM_3

source_name: wild type RPM mouse 3


title: WT_pRPM_3

source_name: wild type pre-RPM mouse 3


title: KO_mRPM_3

source_name: IL1RL1-/- RPM mouse 3


title: HCT116 #3 WT Replicate 1

description:
HCT_3_A
count_HCT116.txt


title: WT_pRPM_2

source_name: wild type pre-RPM mouse 2


title: WT_MONO_2

source_name: wild type splenic monocytes mouse 2


title: WT_mRPM_2

source_name: wild type RPM mouse 2


title: KO_mRPM_2

source_name: IL1RL1-/- RPM mouse 2


title: KO_MONO_3

source_name: IL1RL1-/- splenic monocytes mouse 3


title: KO_pRPM_2

source_name: IL1RL1-/- pre-RPM mouse 2


title: KO_mRPM_1

source_name: IL1RL1-/- RPM mouse 1


title: KO_MONO_1

source_name: IL1RL1-/- splenic monocytes mouse 1


title: KO_MONO_2

source_name: IL1RL1-/- splenic monocytes mouse 2


title: KO_pRPM_1

source_name: IL1RL1-/- pre-RPM mouse 1


title: Splenocytes - Kor_4

source_name: IL1RL1-/- RPM mouse 4


title: Splenocytes - Kor_2


title: Splenocytes - Kor_3


title: Splenocytes - Kor_1


title: Splenocytes - Kop_1


title: Splenocytes - Kop_2


title: KO_pRPM_3

source_name: IL1RL1-/- pre-RPM mouse 3


title: Splenocytes - Kop_4

source_name: IL1RL1-/- pre-RPM mouse 4


title: WT_MONO_3

source_name: wild type splenic monocytes mouse 3


title: WT_MONO_1

source_name: wild type splenic monocytes mouse 1


title: Splenocytes - Kom_1


title: Splenocytes - Kom_2


title: Splenocytes - Wtr_2


title: Splenocytes - Wtr_1

source_name: wild type RPM mouse 1


title: Splenocytes - Wtr_3

source_name: wild type RPM mouse 3


title: Splenocytes - Wtp_3

source_name: wild type pre-RPM mouse 3


title: Splenocytes - Wtp_2

source_name: wild type pre-RPM mouse 2


title: Splenocytes - Wtr_4

source_name: wild type RPM mouse 4


title: Splenocytes - Kom_4

source_name: IL1RL1-/- splenic monocytes mouse 4


title: Splenocytes - Wtp_4

source_name: wild type pre-RPM mouse 4


title: Splenocytes - Wtm_4

source_name: wild type splenic monocytes mouse 4


title: Splenocytes - Wtp_1

source_name: wild type pre-RPM mouse 1


title: Splenocytes - Wtm_2

source_name: wild type splenic monocytes mouse 2


title: Splenocytes - Wtm_3


title: Splenocytes - WTm_1


title: WT_mRPM_1


title: blood_T_728_day14

status: Public on Mar 07 2020

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene count matrix

source_name: T cells

growth_protocol: freshly isolated cells from human tissue

extract_protocol:
cells were isolated from heparinized blood using ficoll gradient and from skin biopsies using collagenase IV + mesh filtering
Illumina
SMART-seq

value: blood

value: T cells

tag: time

value: Day 14 (after transplantation)


title: WT_pRPM_1


title: Splenocytes - Kom_3

source_name: IL1RL1-/- splenic monocytes mouse 3


title: Splenocytes - Kop_3


title: blood_T_718_day14


title: blood_T_717_day14


title: blood_T_719_day14


title: blood_T_721_day14


title: blood_T_722_day14


title: blood_T_723_day14


title: blood_T_713_day14


title: blood_T_728_day100

value: Day 100 (after transplantation)


title: blood_T_712_day14


title: blood_T_727_day100


title: blood_T_718_day100


title: blood_T_717_day100


title: blood_T_719_day100


title: blood_T_722_day100


title: blood_T_723_day100


title: blood_T_721_day100


title: blood_T_712_day100


title: blood_T_710_day100


title: blood_T_723_day0

value: Day 0 (day of transplantation)


title: blood_T_728_day0


title: blood_T_727_day0


title: blood_T_722_day0


title: blood_T_719_day0


title: blood_T_727_day14


title: blood_T_718_day0


title: blood_T_717_day0


title: blood_T_712_day0


title: blood_T_713_day0


title: blood_T_713_day100


title: blood_T_723_day-7

value: Baseline


title: blood_T_719_day-7


title: blood_T_717_day-7


title: blood_T_722_day-7


title: blood_T_718_day-7


title: blood_T_721_day0


title: blood_T_721_day-7


title: blood_T_728_day-7


title: blood_T_710_day0


title: blood_T_727_day-7


title: blood_T_713_day-7


title: blood_T_712_day-7


title: blood_T_710_day-7